{"text_format":"3","workbook":"xlsx","n_sheets":7,"sheets":["Supplemental Table 2A. ","Supplemental Table 2B. ","Supplemental Table 2C. ","Supplemental Table 2D. ","Supplemental Table 2E. ","Supplemental Table 2F. ","Supplemental Table 2G. "],"read":"whole","date_system":"1900"}

{"sheet":"Supplemental Table 2A. ","index":0,"n_rows":21,"n_cols":7,"rows_kept":21}
["Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis."]
[" A. Whole-lung (WL) tissue - SQuIRE"]
["Repeats ","baseMean","log2FoldChange","lfcSE","stat","pvalue","padj"]
["MLT1E2-int:ERVL-MaLR:LTR",36.3482524358036,1.1566167458458,0.329904376303166,3.50591513458108,4.5504028194202E-4,0.0123970334534414]
["LTR33C:ERVL:LTR",37.298415247688,1.02171088900551,0.321691708538906,3.17605602471392,0.00149292116087389,0.0284682985348421]
["LTR45B:ERV1:LTR",40.1018564649463,0.79561054272664,0.231270096516885,3.44017905777349,0.000581329447856271,0.0144737363635695]
["HERV4_I-int:ERV1:LTR",77.3544787443071,0.984897471485792,0.317966093871513,3.09749212406207,1.95165582240313E-3,0.0344428984892929]
["MER61C:ERV1:LTR",90.8117952155677,0.854628008602805,0.288239983588177,2.96498770907459,3.02695022790383E-3,0.0468582013553528]
["HERVK14-int:ERVK:LTR",115.586278497716,0.696862874264309,0.19849780051706,3.51068310303226,0.000446956873688223,0.0122509301872765]
["LTR47A2:ERVL:LTR",172.614178367161,0.554932696270109,0.175100317373561,3.16922724409579,1.52844841753465E-3,0.028961684172675]
["LTR108a_Mam:ERVL:LTR",186.718047839897,1.08646490374664,0.366384372244465,2.96536912066137,0.00302319951379485,0.0468582013553528]
["LTR22A:ERVK:LTR",195.87746151894,-1.05786207331065,0.306137368609617,-3.45551435982852,0.00054924393422489,0.0140240284538755]
["LTR39:ERV1:LTR",200.596946315899,-0.94266371064044,0.259753998813099,-3.62906332509906,0.000284451463385824,0.00882829446966935]
["LTR2B:ERV1:LTR",304.374989773795,0.793412969684832,0.207041646445296,3.83214190626361,0.000127032425708453,4.79394275718631E-3]
["HUERS-P1-int:ERV1:LTR",355.723275218949,0.767959621222505,0.191363792799182,4.01308737660946,{"v":5.99297168972824e-05,"d":"5.99E-05"},0.0027242293784545]
["MER49:ERV1:LTR",390.438403128663,0.51662642277699,0.126427634018893,4.08634098696957,{"v":4.3822958702702e-05,"d":"4.38E-05"},2.14676351774942E-3]
["SVA_B:SVA:Retroposon",411.608291563871,0.53721238393489,0.169873666753958,3.16242295936885,1.56462129384063E-3,0.0293995280902142]
["MER113A:hAT-Charlie:DNA",440.770874491999,0.490914493735045,0.159183243995606,3.08395834519239,2.04266193332622E-3,0.0356298037420593]
["MER117:hAT-Charlie:DNA",623.878476487821,0.364361626726623,0.0994099681052171,3.66524236624819,0.000247104457478066,0.00792996813339366]
["MST-int:ERVL-MaLR:LTR",1212.52479015114,-0.632374156201744,0.208551704464155,-3.03221763555729,0.00242764103621715,0.0402922011110813]
["LTR18B:ERVL:LTR",2286.28671249136,-1.23869667386165,0.203503144671196,-6.08686748238233,{"v":1.15141193706687e-09,"d":"1.15E-09"},{"v":3.23852598111574e-07,"d":"3.24E-07"}]

{"sheet":"Supplemental Table 2B. ","index":1,"n_rows":77,"n_cols":7,"rows_kept":77}
["Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis."]
["B. Alveolar type II (AT2) cells - SQuIRE "]
["Repeats ","baseMean","log2FoldChange","lfcSE","stat","pvalue","padj"]
["MER34B-int:ERV1:LTR",521.864186560711,0.308908860140107,0.117981755833719,2.61827651196747,0.00883751600815125,0.0419642915763536]
["AmnSINE1:5S-Deu-L2:SINE",312.530669899854,0.309456764084719,0.11702639734018,2.64433299766692,8.18520865912435E-3,0.0395962903580359]
["SVA_F:SVA:Retroposon",559.895393633574,0.356323917315854,0.134017846916856,2.65877959923438,0.00784242477676159,0.0384395013232692]
["Charlie16a:hAT-Charlie:DNA",272.837188798816,0.382488718779142,0.125469278407002,3.04846511939291,0.00230013613467267,0.0151273280972712]
["Charlie1b:hAT-Charlie:DNA",463.155437478504,0.398016786468939,0.123477862632475,3.22338577930858,0.0012668481094484,0.00959344897661007]
["MER104:TcMar-Tc2:DNA",240.171426621038,0.405106454572495,0.158612065283026,2.55407086371158,0.0106471584914809,0.0482023578668341]
["MER4-int:ERV1:LTR",839.944266399861,0.416716467715687,0.153977777373292,2.70634162165773,6.80290234126765E-3,0.0345662965634446]
["MER63C:hAT-Blackjack:DNA",132.128250965999,0.416817439745327,0.152004113901412,2.74214578176264,0.00610392446207296,0.0320881474759209]
["MER117:hAT-Charlie:DNA",392.253455959789,0.422680704589738,0.155066124899629,2.72580942396884,0.00641440223627254,0.0331915391238076]
["SVA_B:SVA:Retroposon",279.697622527467,0.428311114614877,0.157403069763642,2.72111030145749,0.0065063047893776,0.0335657682923404]
["L5:RTE-X:LINE",46.6354123025759,0.42935347286691,0.156759153671569,2.73893717088102,0.00616381514946268,0.0323206058004083]
["OldhAT1:hAT-Ac:DNA",1326.7185915147,0.4354931036785,0.12310948278744,3.53744564446281,0.000404017336422494,3.89078186699823E-3]
["L1MDa:L1:LINE",1047.26857660178,0.436641541799405,0.165751307065922,2.63431733679026,0.00843066525897715,0.0405118817847281]
["MER45B:hAT-Tip100:DNA",103.790278243548,0.476134210523866,0.186822056474103,2.54859741676095,0.0108157074781076,0.0487226634678843]
["L2:L2:LINE",6693.77124176505,0.477500024828327,0.177463173674778,2.69069923038457,0.007130244618963,0.0358881710271921]
["MER20B:hAT-Charlie:DNA",518.317709566283,0.480461969318693,0.127469602160113,3.76922780942857,0.000163753377652478,0.00186570011420853]
["MSTB1:ERVL-MaLR:LTR",635.988854752858,0.480790737986502,0.176099489262891,2.73022221699207,0.00632916470690514,0.0329359726294285]
["L1PA2:L1:LINE",1155.22433448554,0.494288075795996,0.171496798132658,2.8822000245955,0.00394908955299653,0.0230324876620175]
["MST-int:ERVL-MaLR:LTR",831.333157761562,0.504155016139116,0.190591158430647,2.6452172298568,0.00816384885534161,0.039552295482097]
["L1MC5a:L1:LINE",3259.79724366809,0.5115693830834,0.136088583501768,3.75909110022263,0.000170531739892309,1.92778566391449E-3]
["MLT1O:ERVL-MaLR:LTR",367.670462901765,0.517569633292867,0.188509694062872,2.74558629923958,0.00604028787255908,0.031894285142317]
["MER85:PiggyBac:DNA",86.0786963150521,0.527370611805145,0.176611277921286,2.98605286147236,2.82603787180181E-3,0.0177448451917066]
["MER39:ERV1:LTR",313.305379256708,0.547421727868603,0.149658314540457,3.65781032313188,0.000254379180184743,0.00266624448113592]
["LTR48:ERV1:LTR",109.325589747154,0.548717103567949,0.147838763145085,3.71159154672753,2.05960150921517E-4,2.23580000332534E-3]
["THE1C-int:ERVL-MaLR:LTR",176.463679823219,0.552406192863412,0.205062151011587,2.69384764637623,0.00706324426917453,0.0356108379517526]
["LTR19A:ERV1:LTR",66.3880496447279,0.560707175510593,0.216711190152949,2.58734758973388,0.00967179721602327,0.0448524690138585]
["LTR16B2:ERVL:LTR",108.365807239586,0.600515565051033,0.218995550694384,2.74213591621811,6.10410780238333E-3,0.0320881474759209]
["LTR14B:ERVK:LTR",108.413624160115,0.601078515991185,0.19079615943905,3.15037010052186,0.00163063751787767,0.0115852679114926]
["MER63B:hAT-Blackjack:DNA",197.8248805008,0.604163866845083,0.18325252062941,3.29689253261011,0.000977609000451781,0.0078441682180931]
["Kanga1:TcMar-Tc2:DNA",76.6485601543513,0.605383962868549,0.172002163133778,3.51962993859386,0.000432149296523666,0.0041133806841243]
["L1PA10:L1:LINE",1235.27008636003,0.608485554995669,0.239359333629454,2.54214258441097,0.0110175218390823,0.0494084973301642]
["PRIMA4-int:ERV1:LTR",73.4022445337956,0.626891231325277,0.191369619954007,3.27581374450104,0.0010535801838617,0.00834718821298159]
["L1M3de:L1:LINE",70.168390043617,0.646142484235097,0.19803636052058,3.26274671245511,0.00110338086519977,0.00864368491657951]
["LTR104_Mam:Gypsy:LTR",65.5371058780794,0.646243134523152,0.205462856115117,3.14530395781646,0.00165914350651596,0.0117303374423941]
["MamGypsy2-I:Gypsy:LTR",58.102056652532,0.657407373455679,0.238096139061978,2.76110052034297,0.00576069429197539,0.0308394265278732]
["MamGypsy2-LTR:Gypsy:LTR",34.0655882072683,0.676956151339983,0.201243908170666,3.36385909761744,0.000768607729692072,0.00648450440763924]
["LTR37A:ERV1:LTR",105.415635107071,0.693138356183842,0.228745381779249,3.03017420851257,0.0024441271644525,0.0158318316086968]
["HERVKC4-int:ERVK:LTR",97.9692064565237,0.695204558906878,0.263166773176937,2.64168819837854,0.00824939614959608,0.0398071599221265]
["MER57B1:ERV1:LTR",55.4132284578742,0.723892242092941,0.219236376366131,3.3018801628249,0.000960390921603594,0.00773527658774428]
["MSTD-int:ERVL-MaLR:LTR",64.6965172291409,0.728813237780265,0.251603508664181,2.896673586349,0.00377141932139848,0.0222955940770823]
["L1M3b:L1:LINE",48.168988124787,0.731216189949765,0.268778162431754,2.72051934329088,0.00651794583563034,0.0335982467678091]
["MER34A:ERV1:LTR",70.1166770862572,0.754885103948148,0.251271423831251,3.0042616563319,0.00266226259093405,0.0169421611254312]
["L4_C_Mam:RTE-X:LINE",390.513370731384,0.755908930348369,0.206929975317984,3.65296970236807,0.000259224827747226,2.70800185706465E-3]
["LTR85b:Gypsy?:LTR",57.6377128737208,0.790368448792345,0.263984919544887,2.99399090734027,0.00275354150326589,0.0174199319380896]
["L1PA13:L1:LINE",1734.67471431764,0.796096759787953,0.194493205173275,4.09318546156255,{"v":4.25487126079217E-5,"d":"4.25E-05"},0.00062777662357979]
["HERVIP10B3-int:ERV1:LTR",347.953457729695,0.801642406578645,0.269463070776076,2.97496203939875,0.00293024806265274,0.0182533060685101]
["HERV35I-int:ERV1:LTR",46.2321565472876,0.823595515168466,0.296296579043567,2.77963221116827,0.00544204955012345,0.0295210835204625]
["L1M2b:L1:LINE",20.9063659802896,0.834853700569992,0.289012802466469,2.88863916561915,0.00386912778567244,0.0226735932150864]
["LTR10B1:ERV1:LTR",51.5602163800946,0.838979853857381,0.317895657724022,2.63916739179159,0.00831099326006511,0.0400593274314386]
["MamGypLTR1d:Gypsy:LTR",34.6582202214339,0.842353998504784,0.256702891918313,3.28143556237316,1.03280120108869E-3,0.0082170883745689]
["HERV4_I-int:ERV1:LTR",44.3165966882774,0.848046601036524,0.228815134372627,3.70625222567436,2.10348823471271E-4,0.0022677743941534]
["L1M4c:L1:LINE",7815.64370197613,0.879274418204665,0.323895207434701,2.71468795468958,0.00663382446341517,0.0340003789296429]
["LTR86B1:ERVL:LTR",26.0724273691843,0.879768259122962,0.327584889118036,2.6856191733739,0.00723955519565834,0.0362862979184832]
["LTR26:ERV1:LTR",38.2572108561393,0.891380652473247,0.326251343215884,2.73218998483452,0.00629148500979877,0.0328439206380857]
["MLT1A0-int:ERVL-MaLR:LTR",105.709536067688,0.922882134647777,0.258130102683132,3.57525962704421,0.000349880511173786,0.00346317423553433]
["LTR57:ERVL:LTR",89.0867318015625,0.954488228558906,0.194881797371318,4.89778030289958,{"v":9.69253149251403e-07,"d":"9.69E-07"},{"v":2.64873005540354e-05,"d":"2.65E-05"}]
["X7C_LINE:CR1:LINE",45.5768212801613,0.997914724502478,0.26565353695811,3.75645186557345,1.72339400351283E-4,1.94472276063662E-3]
["L1PBb:L1:LINE",19.9457176814218,1.01141918462494,0.326647889669941,3.0963591580124,1.95912906650837E-3,0.0134137028605962]
["L1M3c:L1:LINE",71.3866069690694,1.01523250717317,0.269186719415826,3.77148066359428,0.000162281735162576,0.00185566064173774]
["HERVK14-int:ERVK:LTR",103.45259805011,1.03091425841641,0.298043139713761,3.45894308926721,0.000542299476923021,0.00496147449629329]
["LTR89:ERVL?:LTR",229.297829860085,1.07682020758741,0.265382667705905,4.05761317005351,{"v":4.95767952012705e-05,"d":"4.96E-05"},0.00071197262019433]
["MER136:DNA:DNA",8.75225207760074,1.08370537054135,0.377364521041698,2.87177333881265,0.00408175614671361,0.0236308240412748]
["MER110-int:ERV1:LTR",12.4986460051133,1.0890696519341,0.39834165215267,2.73400897457919,0.00625683390197561,0.0327173766099978]
["MER41G:ERV1:LTR",29.5844830123014,1.09532305246187,0.38257216903787,2.86304948741175,0.00419585024557611,0.0241283782343956]
["MER65C:ERV1:LTR",106.925030404844,1.1123066509193,0.214799546063848,5.1783473070687,{"v":2.23860189215385e-07,"d":"2.24E-07"},{"v":7.73096653451519e-06,"d":"7.73E-06"}]
["L1PA12:L1:LINE",222.946649199087,1.16881179355707,0.341052790288769,3.42707002211427,0.000610131717153733,5.41394995701214E-3]
["LTR14C:ERVK:LTR",13.9422461485878,1.1983967556568,0.385464573691096,3.10896730192689,1.87742494465269E-3,0.012972050112265]
["MER65-int:ERV1:LTR",3450.57539884975,1.23600214338624,0.485621806160557,2.54519489797703,0.0109216760470725,0.0491032721849308]
["MER65B:ERV1:LTR",14.4377078341582,1.33499617645726,0.354928170052122,3.76131366597702,0.000169023312081529,0.00191532666623155]
["MER57F:ERV1:LTR",81.3571673505947,1.35629295966749,0.357898045752932,3.78960705642909,1.50885774103055E-4,0.00174653293829786]
["FordPrefect_a:hAT-Tip100:DNA",10.4377294511425,1.45640395716237,0.565170688521002,2.57692761981985,0.00996828215154572,0.0459227774858407]
["UCON49:L2:LINE",6.21007594026802,1.55068091850337,0.549470582595457,2.82213637567025,0.00477048863614824,0.0267396949236656]
["Ricksha_a:MULE-MuDR:DNA",10.8105193753862,1.58959428100025,0.507375395464056,3.13297470711281,0.00173044353140605,0.0121660116436214]
["LTR91:ERVL:LTR",2.9218967548673,2.05276823317149,0.639512111221271,3.20989735323595,0.00132782380108421,0.00988450280033317]

{"sheet":"Supplemental Table 2C. ","index":2,"n_rows":13,"n_cols":7,"rows_kept":13}
["Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis."]
["C. Alveolar macrophages (AM) - SQuIRE"]
["Repeats ","baseMean","log2FoldChange","lfcSE","stat","pvalue","padj"]
["MLT1G:ERVL-MaLR:LTR",375.321447072182,0.319127054733574,0.0950537291093742,3.35733334950351,0.000786981687073164,0.0199035513172796]
["MER61E:ERV1:LTR",43.437935826415,0.631827147720823,0.199279450629129,3.17055845811564,1.52146215606417E-3,0.0299926330539418]
["LTR45B:ERV1:LTR",53.6307499439831,0.729226506025558,0.223735989676196,3.25931696139248,0.00111680819288539,0.024333115903435]
["MER84:ERV1:LTR",277.689142976616,0.765802433693217,0.195100553072464,3.92516792819538,{"v":8.66692552013872e-05,"d":"8.67E-05"},4.19789772797365E-3]
["AmnSINE2:tRNA-Deu:SINE",353.708427135415,0.780381691609393,0.172225148873406,4.53117153165018,{"v":5.86574854696314e-06,"d":"5.87E-06"},0.00059531671220824]
["Kanga1a:TcMar-Tc2:DNA",92.9853966465363,0.847932031457439,0.213135086241053,3.97837843788159,{"v":6.93868711526521e-05,"d":"6.94E-05"},3.62384874060735E-3]
["Charlie18a:hAT-Charlie:DNA",790.841926512027,0.920980818089789,0.248265452048441,3.70966161618851,2.07536442689972E-4,0.008117984671303]
["MER61F:ERV1:LTR",54.1464099160831,0.93523450751205,0.310590030955514,3.01115430084749,0.00260256563422897,0.0419477049098934]
["MER65-int:ERV1:LTR",112.296684577882,1.10149986507025,0.346934295312105,3.17495237557686,0.00149861094900138,0.0296163930134933]
["hAT-N1_Mam:hAT-Tip100?:DNA",91.524518146392,1.22364298982046,0.249738750677016,4.89969212428303,{"v":9.59869480099489e-07,"d":"9.60E-07"},0.000139812099920788]

{"sheet":"Supplemental Table 2D. ","index":3,"n_rows":22,"n_cols":8,"rows_kept":22}
["Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis."]
["D. Whole-lung (WL) tissue - REdiscoverTE"]
["baseMean","log2FoldChange","lfcSE","stat","pvalue","padj","repName","repClass"]
[34.6544311001459,1.03255969720433,0.231527081543014,4.45977934988352,{"v":8.20440742011124E-6,"d":"8.20E-06"},3.76373290964419E-4,"LTR45B","LTR"]
[109.495759837606,0.752006629663476,0.196650665508097,3.82407365731754,1.31264671798587E-4,0.00323031430129903,"HERVK14-int","LTR"]
[34.3880097384865,1.12825016906154,0.302062867207739,3.73515016754972,0.000187603206947472,0.00426660262360273,"MLT1E2-int","LTR"]
[266.937699141863,0.50629906235924,0.141406221690346,3.58045817437894,0.00034299224585145,0.00680065973080976,"MER49","LTR"]
[37.5078853235008,1.30557408006774,0.368173913086161,3.54607981082628,0.000391007765126745,0.00751195650677417,"AluYi6_4d","SINE"]
[51.7809138709868,0.601086924271092,0.189261404261304,3.17596145192498,1.49340794364492E-3,0.0208071023341836,"MER68-int","LTR"]
[54.8716754584108,0.894798897770132,0.281805969998115,3.17523045298195,0.00149717546016659,0.0208442400335617,"U4","snRNA"]
[168.793688425749,0.661165644414731,0.20979930565651,3.15141960239474,1.62478886826922E-3,0.0220879748683584,"HUERS-P1-int","LTR"]
[180.894418902724,1.04030255485706,0.330320418866789,3.14937404846473,0.00163620621711039,0.02214338531625,"LTR108a_Mam","LTR"]
[27.0550143078052,0.998176310055646,0.321746781638786,3.10236610595305,0.00191980371873853,0.0248257576276316,"LTR33C","LTR"]
[24.735885410628,0.914953955254358,0.296343494666691,3.08747778075385,0.00201862861894172,0.0257722267592929,"MER87B","LTR"]
[131.929773804134,1.65546842840872,0.555262238231857,2.9814172735396,0.002869175538935,0.0332851950742796,"U8","snRNA"]
[69.1334556093083,0.746684181985579,0.251366758475685,2.97049692056957,0.00297318386294802,0.0343267591449453,"MLT-int","LTR"]
[137.763422075424,0.52651414490991,0.180198914482492,2.92184970382309,0.00347959406210507,0.0383916802554163,"LTR47A2","LTR"]
[209.734985206047,0.498532512119729,0.172047466983275,2.89764517235346,0.00375975689219314,0.0406282730893956,"MER2B","DNA"]
[229.652709650664,0.686231807515108,0.238028005923454,2.88298767555861,0.00393922852684305,0.0421911298712713,"LTR2B","LTR"]
[58.7357703526774,0.919738947011029,0.322031330941451,2.85605423646884,4.28941854231188E-3,0.0448067833012925,"HERV4_I-int","LTR"]
[20.3383089009834,0.891870775746446,0.313087460471217,2.84863141565658,0.0043907715610852,0.0454718102012815,"MER9a1","LTR"]
[136.86570528054,0.457225325952616,0.1624845612818,2.81396166100755,0.00489350642030755,0.0493234377284967,"SVA_B","Retroposon"]

{"sheet":"Supplemental Table 2E. ","index":4,"n_rows":90,"n_cols":8,"rows_kept":90}
["Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis."]
["E. Alveolar type II (AT2) cells - REdiscoverTE"]
["baseMean","log2FoldChange","lfcSE","stat","pvalue","padj","repName","repClass"]
[66.8820335077836,1.02111986109805,0.211900274086855,4.81886994010921,{"v":1.44373626037451E-6,"d":"1.44E-06"},{"v":3.97743116732056e-05,"d":"3.98E-05"},"MER65C","LTR"]
[186.770749790508,1.61804996675426,0.345547018561363,4.68257539448838,{"v":2.83292938167561e-06,"d":"2.83E-06"},{"v":7.16386474499691e-05,"d":"7.16E-05"},"ALR/Alpha","Satellite"]
[55.8113822057885,0.95662318681798,0.210600923246775,4.5423503946231,{"v":5.56304742921415e-06,"d":"5.56E-06"},0.000124431207852396,"LTR57","LTR"]
[52.7753062852549,1.45554693922662,0.327892571223343,4.43909703045752,{"v":9.03370852646257e-06,"d":"9.03E-06"},0.000186104586774812,"MER57F","LTR"]
[4.57679949343964,4.20212758467699,0.953484331206769,4.40712809549645,{"v":1.04750244903222e-05,"d":"1.05E-05"},0.000209418805252422,"(GGAAT)n","Simple_repeat"]
[99.8170602824291,1.21078370039605,0.27527572424015,4.39843979609247,{"v":1.09031862281945E-5,"d":"1.09E-05"},0.00021608593729459,"LTR89","LTR"]
[8.24275102080152,2.10204008892705,0.503469305688366,4.17511070720199,{"v":2.97841175404462e-05,"d":"2.98E-05"},0.000501453491231101,"(TGCGGC)n","Simple_repeat"]
[670.241818284679,1.10616154388562,0.267614814431497,4.13340922936376,{"v":3.57421493716848e-05,"d":"3.57E-05"},0.000584634543081569,"(TCT)n","Simple_repeat"]
[48.1027058254472,1.14293110293277,0.281472941882692,4.06053631758718,{"v":4.89601204215781e-05,"d":"4.90E-05"},0.000762775404447328,"L1M3c","LINE"]
[1.43212393049457,3.77910922011123,0.936138438528882,4.03691277333939,{"v":5.41591939092852e-05,"d":"5.42E-05"},0.000826647135214798,"(TGTGTC)n","Simple_repeat"]
[3.05589765577611,2.84384292514285,0.712180531979752,3.99314892424454,{"v":6.52015886440536E-5,"d":"6.52E-05"},0.000959116119259996,"(TCCAT)n","Simple_repeat"]
[14.7216892897389,1.76726271377552,0.471294128171554,3.74980847020488,1.76969684074386E-4,0.00215859109878137,"(GATG)n","Simple_repeat"]
[159.252826649725,1.28049530482769,0.342195637099856,3.74199775216313,0.00018256314873671,0.00221519196041896,"L1PA12","LINE"]
[81.5961712192142,0.653911920042996,0.175991671377728,3.71558446444614,2.02734525994978E-4,0.00240627246591811,"(TC)n","Simple_repeat"]
[211.70688036119,0.774089543335394,0.209450384376751,3.69581342922243,2.19183892118265E-4,0.00256695161974144,"L4_C_Mam","LINE"]
[1349.78120499898,0.371210679209582,0.103441669957595,3.58859905647071,0.000332459674519376,3.58484354228695E-3,"GA-rich","Low_complexity"]
[10.1743101277689,1.1599919622928,0.326892967880781,3.54853752227504,0.000387376801534983,0.0040406672003441,"MER65B","LTR"]
[16.4295359582396,1.21671255147137,0.34533816970913,3.52324955129107,0.000426289773285281,0.00436464731430176,"U4","snRNA"]
[71.1792881338876,1.00336251284582,0.285513652480359,3.51423654921316,0.000441019892635344,0.00448850102512548,"HERVK14-int","LTR"]
[167.280683993067,0.607397121704846,0.172846391288303,3.51408621943239,4.41269560186804E-4,0.00448925490478943,"MER39","LTR"]
[9.78862191085659,1.6430268957512,0.498432813494624,3.29638589448309,0.00097937389456501,0.00842769201900001,"Ricksha_a","DNA"]
[31.1271531589736,0.651592330898105,0.198793630440444,3.27773243767644,0.001046445351245,0.00887933018583796,"MER85","DNA"]
[8.91831576887884,2.31666530879338,0.710102174011045,3.26243939756949,1.10457787291496E-3,0.00927757268998116,"(GATTC)n","Simple_repeat"]
[273.573266717502,0.696714424741736,0.213894895737898,3.25727466444769,0.00112487529983167,0.00940436949493014,"Harlequin-int","LTR"]
[76.9402020872138,0.470955831453933,0.146086344522112,3.22381830413073,0.0012649363129485,0.0102690598517782,"LTR48","LTR"]
[42.7938361039869,0.783072223919839,0.243655747635592,3.21384671413946,1.30969570925879E-3,0.0105460411032788,"LTR14B","LTR"]
[20.8024826910261,1.09874248442361,0.344440502285584,3.18993404414624,1.42305267076377E-3,0.0112532522674749,"LTR86B1","LTR"]
[18.5535057063797,0.747101089347286,0.234421699123284,3.18699630683241,0.00143758610491592,0.0113306215870829,"L5","LINE"]
[25.8857810665311,0.83165946213106,0.265905954236806,3.12764512745892,0.00176212800033378,0.013237904231856,"HERV9-int","LTR"]
[1.9374285428583,2.28858939718131,0.732566761377203,3.12406939249992,1.78368385659942E-3,0.0133752941064403,"(GCGCC)n","Simple_repeat"]
[3.33204983447951,2.17948090693306,0.704769455352032,3.09247356051265,0.00198495914865228,0.0145616830974015,"UCON46","Unknown"]
[2.03987084543355,1.98437634589824,0.644991012088345,3.07659534583784,2.09379328006581E-3,0.0152354151102163,"MER75B","DNA"]
[1.23466688305545,3.77205722471578,1.22819621519473,3.07121710525522,0.00213188076157618,0.0154270205350853,"(TGCTGCTG)n","Simple_repeat"]
[10.4301741962647,1.08097314694002,0.353769868630989,3.05558285990591,0.0022462352660654,0.0160815600146256,"(TGAGA)n","Simple_repeat"]
[1.09735028728886,3.0363471753951,0.994811359908521,3.05218385893212,0.00227182900388573,0.0162300020728207,"(TTCTGA)n","Simple_repeat"]
[56.4534513692636,0.556369916090131,0.182826754012043,3.04315371728079,0.00234112711296111,0.0166139997040105,"PRIMA4-int","LTR"]
[6.04534386966694,1.2795662320714,0.421160629978205,3.0381905168525,2.38003432792762E-3,0.0168134726796899,"(ATGG)n","Simple_repeat"]
[14.4497459521195,1.13175442825194,0.372579022287598,3.03762251911845,0.00238452448723368,0.0168358887159945,"L1PBb","LINE"]
[24.1039105927112,0.86194525086109,0.284555438288402,3.02909428140148,2.45288121089273E-3,0.0172044886248789,"(TTCT)n","Simple_repeat"]
[100.642636249868,0.586315711355703,0.193752921665198,3.02609997473405,0.00247730377589814,0.0173460553597107,"MER63B","DNA"]
[14.2482839161018,0.836386019925239,0.283882884405374,2.94623616241305,0.00321666704721287,0.0211445902372444,"MamGypsy2-LTR","LTR"]
[2.90627693698094,1.41459593279011,0.480145923151454,2.94617920215872,0.00321725948614882,0.0211445902372444,"(GCAGCG)n","Simple_repeat"]
[7.5842186709977,1.6056665372534,0.545997423336182,2.94079508185657,0.0032737102511541,0.0214110197700194,"LTR14C","LTR"]
[20.0002523829761,0.895579763670981,0.306584439411833,2.92115204995108,0.00348739581319907,0.0224977949432873,"X7C_LINE","LINE"]
[4.93737628951718,1.79438508918706,0.617085147830904,2.90784034503901,0.0036393408617301,0.0232376095082397,"(GAATG)n","Simple_repeat"]
[4.93737628951718,1.79438508918706,0.617085147830904,2.90784034503901,0.0036393408617301,0.0232376095082397,"(GAATG)n","Satellite"]
[137.818245947622,0.39975434182894,0.137720010038949,2.90265983654723,0.00370008292435989,0.0235607272837323,"Charlie16a","DNA"]
[1.92883370465814,3.42835501981178,1.19344890942718,2.8726449810552,0.00407051259014544,0.0254753304478968,"(TGGAA)n","Simple_repeat"]
[1.7510021580649,1.91364561383637,0.66872105813707,2.86164999673769,0.00421442029165169,0.0261646112618667,"LSAU","Satellite"]
[40.0395815788585,0.47509471587469,0.16663847712774,2.85105051404483,0.00435750463129087,0.026837861576387,"UCON80_AMi","Unknown"]
[70.6302883031526,0.581084268665444,0.204400730865311,2.8428678616044,0.00447096025694691,0.0273848993601114,"L1HS","LINE"]
[301.614783767183,0.531223698894881,0.188073251628159,2.82455742268533,0.00473459636909664,0.0285887318782061,"L1PA2","LINE"]
[36.0931440719513,0.666800981096165,0.237157439318281,2.81163847532218,4.92898690268068E-3,0.0294701775383382,"MER57B1","LTR"]
[125.552200249105,0.500419676356848,0.178544506514241,2.80277274348362,0.00506653563661081,0.0301445310881061,"MER51A","LTR"]
[1705.53322648179,0.406795197145008,0.145960219492713,2.78702785292343,0.00531939067328938,0.0312379347365512,"L1MC5a","LINE"]
[6.20313180261292,1.39532507043091,0.501423707183158,2.78272656526237,0.00539042143403085,0.0315715368340157,"(AATGG)n","Simple_repeat"]
[138.681394975068,0.530683196098908,0.192153618829995,2.76176529659024,5.74897890118959E-3,0.0331704794826931,"SVA_B","Retroposon"]
[38.0880889340388,0.682336893889432,0.248493950829487,2.74588935308788,0.00603471126250685,0.0344382652092076,"MSTD-int","LTR"]
[13.4243802695758,1.76235000737373,0.643943651760518,2.73680779763187,0.00620385278782569,0.0351446267169403,"(CATT)n","Simple_repeat"]
[79.2996098600296,0.579745706283833,0.212744202469742,2.72508345493593,6.42852357447139E-3,0.0361065823439483,"MER45B","DNA"]
[67.0894801137648,0.551377508074363,0.20293035921021,2.71707747534812,6.58611886458385E-3,0.0367804095438949,"BLACKJACK","DNA"]
[70.1312851463855,0.453183354594776,0.166810493212401,2.71675567805998,0.00659252536163611,0.0367920767071794,"AmnSINE1","SINE"]
[297.68265207908,0.354610915767766,0.13083105329394,2.7104491390974,0.00671921527601512,0.0372944211091766,"MER20B","DNA"]
[77.2557224430622,0.590290762719499,0.217863840496619,2.70944807258485,0.00673952539862116,0.0373453780182952,"MLT1J-int","LTR"]
[210.039266878793,0.434597176103327,0.161476073286513,2.69140292588243,0.00711522020381033,0.038952402511909,"MER117","DNA"]
[4.76328234089224,1.09848222805432,0.408251115964938,2.69070232780126,0.00713017842448653,0.0390229861713523,"(CCGCCGC)n","Simple_repeat"]
[771.760792297985,0.481623927643898,0.179371141010352,2.68506920863096,0.00725147887383592,0.0394869667494119,"L1MA9","LINE"]
[3.1378774157678,1.54430769790209,0.576523308815918,2.67865613460424,0.00739182610386902,0.0400974806220062,"LTR38-int","LTR"]
[5.17258704215702,1.07862368231967,0.404945305721424,2.66362806798827,0.00773029803035443,0.0414411405837789,"(TCTTCT)n","Simple_repeat"]
[15.0759290327347,1.52480935317207,0.573853642233645,2.65713980177413,0.00788067549950849,0.0420269816062649,"U14","snRNA"]
[20.981531894068,0.59417650049054,0.223723318239706,2.65585413789508,0.00791078231247229,0.0421551941549367,"PABL_B-int","LTR"]
[11.8434454935508,0.902558181260198,0.341326691561473,2.64426487460224,0.00818685633553744,0.0433164671097579,"(CGGCTC)n","Simple_repeat"]
[1340.46266332134,1.25907320741985,0.476445474611546,2.64263861136764,0.00822627860677159,0.0434710704548827,"MER65-int","LTR"]
[120.721656330564,0.439914809879428,0.166486071419029,2.64235203659895,0.00823324304796998,0.0434898949926447,"MER104","DNA"]
[8.36986203817874,0.995507928109723,0.378095554467355,2.63295327423818,0.0084645991531494,0.0443727582426527,"(GAAA)n","Simple_repeat"]
[373.468337938238,0.554241356419407,0.210643746313497,2.63117878465066,8.50892605409782E-3,0.0445685727308062,"MST-int","LTR"]
[78.1321426899825,0.441417337003101,0.168228658510059,2.62391283930204,0.00869260269566362,0.0452525107956294,"(GAAGAT)n","Simple_repeat"]
[37.7660661005827,0.661689930573668,0.252731048058013,2.61815845602706,0.00884057423668386,0.0458454606359147,"L1M3b","LINE"]
[3.08717914730985,1.39158694738286,0.531832888684667,2.61658685837302,0.00888137649501342,0.0460103893559297,"(CAT)n","Simple_repeat"]
[208.72153012756,0.430286357407769,0.164668788454637,2.61304137502842,0.00897404373828801,0.0463589416474179,"MLT1O","LTR"]
[1.34012424298408,1.85441313836472,0.712677617622701,2.60203645029648,0.00926720020280616,0.0474800080931748,"LTR108e_Mam","LTR"]
[1291.75207180211,0.519109143421983,0.199543596286126,2.60148234813625,0.00928218418549675,0.0475377245365405,"L1MEc","LINE"]
[72.6428000743248,0.599043925836926,0.230588085605709,2.59789626278112,0.00937968258345127,0.0478763518331148,"LTR37A","LTR"]
[9.29999535837984,1.0699504506663,0.412433322685427,2.59423861219472,0.00948006680919231,0.0481747938866648,"MER110-int","LTR"]
[5311.58474941522,0.865652351622102,0.33490313530543,2.58478425659596,0.00974399471626813,0.0492419389041532,"L1M4c","LINE"]
[3.47771488422155,1.18714647382179,0.459629057110765,2.58283599667135,0.00979918925799501,0.0494467800378288,"(ATAT)n","Simple_repeat"]
[58.8495567759271,0.755565786467289,0.292612980843257,2.58213352083659,0.00981915875582752,0.0495043606293604,"MLT1A0-int","LTR"]

{"sheet":"Supplemental Table 2F. ","index":5,"n_rows":12,"n_cols":8,"rows_kept":12}
["Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis."]
["F. Alveolar macrophages (AM) - REdiscoverTE"]
["baseMean","log2FoldChange","lfcSE","stat","pvalue","padj","repName","repClass"]
[48.5168838518975,1.17532454006717,0.239839807493265,4.90045648531539,{"v":9.56142342187784e-07,"d":"9.56E-07"},0.000146828956367243,"hAT-N1_Mam","DNA"]
[39.7049395587324,1.05020728583924,0.240073506177513,4.3745238804598,{"v":1.21697801008967E-5,"d":"1.22E-05"},0.000982529055244643,"Kanga1a","DNA"]
[8.02036882302594,1.53470654649264,0.396869109985245,3.86703451561071,1.10166840509677E-4,0.00499166177101706,"UCON14","DNA?"]
[509.684060463027,0.926221043541526,0.264039479363211,3.50788846340444,0.000451678377806733,0.0141287742570219,"Charlie18a","DNA"]
[37.1008904371901,0.710408567859466,0.203988797985229,3.48258617569239,0.000496595360692911,0.0149373544135376,"MER61E","LTR"]
[306.716113093803,0.383360927606462,0.112691094051776,3.40187421936225,0.000669254321394658,0.0182251336802193,"(CCG)n","Simple_repeat"]
[80.4288363832248,0.57667825756343,0.184147164146962,3.13161628219918,1.73846926395119E-3,0.0343389712252796,"MER9a3","LTR"]
[12.4599081690954,1.00463150564132,0.324595890252387,3.09502225940131,0.00196798127119968,0.0375645322270862,"(CGCCC)n","Simple_repeat"]
[36.646986325989,0.547824115916534,0.183132104038843,2.99141496130214,0.00277687867772763,0.0468331710271752,"Penelope1_Vert","LINE"]

{"sheet":"Supplemental Table 2G. ","index":6,"n_rows":9,"n_cols":4,"rows_kept":9}
["Supplemental Table 2. Summary of the differential analysis of the TE families between the IPF patients and the donors in different cells based on SQuIRE and REdiscoverTE analysis."]
["G. Summary of all changes in REdiscoverTE analysis"]
[null,"WL","AT2","AM"]
["TE Family","UP/DOWN","UP/DOWN","UP/DOWN"]
["SINE","1/0","1/0","0/0"]
["LINE","0/0","13/2","1/0"]
["LTR","14/6","28/10","2/4"]
["Other","4/16","45/13","6/3"]
["Genes","1379/984","3085/1905","697/550"]