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Sample GSM5071362 Query DataSets for GSM5071362
Status Public on May 04, 2021
Title IC_6h_3
Sample type SRA
Source name A6 Kidney Cells
Organism Xenopus laevis
Characteristics treatment: 6 hours poly(I:C)
cell type: A6
Treatment protocol Cells on a subconfluent 6-well dish were transfected with 2μg poly(I:C) (or mock) using lipofectamine 3000
Growth protocol 28°C at 5% CO2 in NCTC 109 media supplemented with 1x L-Glutamine, 15% ddH2O, and 10% FBS
Extracted molecule total RNA
Extraction protocol Cells were washed once with PBS and RNA was extracted using trizol and Zymo direct-zol columns
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description readcount_genename.csv
Data processing fastp was used to clean reads
HISAT2 was used to map reads
Stringtie was used to predict novel transcripts
Featurecounts was used to quantify mapped reads and convert to RPKM
DEseq2 was used to perform differential expression analysis
Genome_build: xenLae2
Supplementary_files_format_and_content: BAM containing mapped reads
Supplementary_files_format_and_content: BAI containing index for BAM files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Submission date Feb 09, 2021
Last update date May 04, 2021
Contact name Ian Boys
Organization name UT Southwestern Medical Center
Department Microbiology
Lab Schoggins
Street address 6000 Harry Hines Blvd
City Dallas
State/province Texas
ZIP/Postal code 75390
Country USA
Platform ID GPL28901
Series (1)
GSE166455 Poly(I:C) transfection time course in Xenopus laevis A6 cells
BioSample SAMN17841791
SRA SRX10059508

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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