Transposable elements in a myxozoan–fish system: their role in the lateral transfer of host Siglec genes


Amr G. A. Ibrahim, Fábio S. R. Amaral, Edson A. Adriano


Supplementary File S2. Data Source List for TE Analysis.

This text file provides a comprehensive list of genomic and transcriptomic datasets used for transposable element (TE) detection, comparative analysis, and expression profiling. It includes:
●	Fish genomes:

○	Oncorhynchus mykiss (GCA_013265735.3)


●	Fish RNA-seq and DNA-seq datasets: Listed comprehensively in Supplementary File S3 – O_mykiss_SraAccList.table, including uninfected and infected host samples.

●	Infected Oncorhynchus mykiss RNA-seq data: Accession numbers SRX9928040 to SRX9928099, representing host transcriptomes under C. shasta infection conditions.

●	Whole Genome Amplification (WGA) data for fish: SRX26028961.

●	Ceratonova shasta datasets:

○	Genome assembly: GCA_918559645.1 (same as in Supplementary File S1).

○	RNA-seq: SRX49911, SRX501670, SRX698178, SRX700962, SRX3741971.

○	WGS DNA methylation data: SRX8144395, SRX8144396.

This file serves as the primary index of data sources employed in TE annotation, expression quantification, and comparative evolutionary analyses between C. shasta and fish hosts.


Data Source List For TE Analysis

####Fish:
##Gennome
GCA_013265735.3
GCA_029834435.1
GCA_025558465.1

##List of SRR data of Fish RNA-seq && DNA-seq
*Supplementary File 3=="O_mykiss_SraAccList.table"*

##Infecte RNA-seq
SRX9928099
SRX9928098
SRX9928097
SRX9928096
SRX9928095
SRX9928094
SRX9928093
SRX9928092
SRX9928091
SRX9928090
SRX9928089
SRX9928088
SRX9928087
SRX9928086
SRX9928085
SRX9928084
SRX9928083
SRX9928082
SRX9928081
SRX9928080
SRX9928079
SRX9928078
SRX9928077
SRX9928076
SRX9928075
SRX9928074
SRX9928073
SRX9928072
SRX9928071
SRX9928070
SRX9928069
SRX9928068
SRX9928067
SRX9928066
SRX9928065
SRX9928064
SRX9928063
SRX9928062
SRX9928061
SRX9928060
SRX9928059
SRX9928058
SRX9928057
SRX9928056
SRX9928055
SRX9928054
SRX9928053
SRX9928052
SRX9928051
SRX9928050
SRX9928049
SRX9928048
SRX9928047
SRX9928046
SRX9928045
SRX9928044
SRX9928043
SRX9928042
SRX9928041
SRX9928040

##WGA
SRX26028961

####Ceratonova 
##Genome
GCA_918559645.1

##RNA-seq
SRX49911
SRX501670
SRX698178
SRX700962
SRX3741971

##WGS DNA-methylation
SRX8144395
SRX8144396