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Sample GSM7763379 Query DataSets for GSM7763379
Status Public on Sep 06, 2023
Title mouse CD8, CsA, 30hr, rep 2
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: CD8+ T cells
genotype: WT
time: 30 hr
treatment: CsA
Extracted molecule total RNA
Extraction protocol Cells were washed 1x in ice-cold PBS, resuspended in 350 ul Trizol (Invitrogen Cat # 15596018) and vortexed for 30 sec to lyse the cells and frozen at -80°C. RNA was then isolated with the RNeasy Micro kit (Qiagen Cat # 74004) starting from step 2.
RNA was eluted in RNase free water and shipped on dry ice to Novogene Corporation Inc. (Sacramento, CA) for library preparation and sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description B4
Data processing Raw fastq files from paired-end sequencing were aligned to the GRCm38/mm10 reference genome using Kallisto (v0.46.1) using the following code: kallisto quant -i transcriptome.idx -o kallisto -b 100 A4_1.fq.gz A4_2.fq.gz
Bootstrapped transcript-level abundance estimates generated by Kallisto were imported into R using sleuth (v0.30.0) for downstream analysis. Transcripts with low counts (<5) were removed.
Differentially expressed genes were identified with sleuth (v0.30.0) in R.
Assembly: GRCm38/mm10
Supplementary files format and content: The bootstrapped abundance.h5 file for each sample is a HDF5 binary file containing columns including Ensembl transcript ID and abundance estimates.
Supplementary files format and content: The abundance.tsv file for each sample is a plain text file containing columns including Ensembl transcript ID and abundance estimates.
 
Submission date Sep 06, 2023
Last update date Sep 06, 2023
Contact name Hao Yuan Kueh
E-mail(s) kueh@uw.edu
Organization name University of Washington
Department Bioengineering
Lab Kueh Lab
Street address 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platform ID GPL24247
Series (2)
GSE242418 Antigen perception in T cells by long-term Erk and NFAT signaling dynamics [RNAseq]
GSE242495 Antigen perception in T cells by long-term Erk and NFAT signaling dynamics
Relations
BioSample SAMN37298453
SRA SRX21645159

Supplementary file Size Download File type/resource
GSM7763379_B4_abundance.h5 43.5 Mb (ftp)(http) H5
GSM7763379_B4_abundance.tsv.gz 1.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA

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