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Sample GSM7655059 Query DataSets for GSM7655059
Status Public on Jul 25, 2023
Title Splenocyte antigen-experienced, 1 (RNA-seq)
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics tissue: spleen
cell type: CD8+ T cell
Extracted molecule total RNA
Extraction protocol Sorted cells were centrifuged at 500g for 5 minutes, resuspended in 350 µL of Trizol (Ambion), mixed well, and frozen at -80°C for processing, starting from step 2 of the RNeasy micro kit (Qiagen, #74004) following the manufacturer’s instructions.
After processing, RNA was resuspended in RNase free water, quantified using a NanoDrop 2000c (Thermo Scientific), 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
 
Data processing Raw FASTQ files from RNA-seq paired-end sequencing were aligned to the GRCm38/mm10 reference genome using Kallisto (v0.46.1)
Transcript-level abundance estimates generated by Kallisto (HDF5 files) were imported to genes by cells matrices in R using tximport (v1.18.0) for downstream analysis. Transcripts with low counts (<10) were removed.
Differentially expressed genes were identified with DESeq2 (v1.30.1).
Assembly: GRCm38/mm10
Supplementary files format and content: The 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 Jul 20, 2023
Last update date Jul 25, 2023
Contact name Kathleen Abadie
E-mail(s) abadiek@uw.edu
Organization name University of Washington
Department Bioengineering
Lab Kueh Lab
Street address 3720 15th Ave NE
City Seattle
State/province Washington
ZIP/Postal code 98195
Country USA
 
Platform ID GPL24247
Series (2)
GSE237828 Flexible and scalable control of T cell memory by a reversible epigenetic switch (RNA-seq)
GSE237830 Flexible and scalable control of T cell memory by a reversible epigenetic switch
Relations
BioSample SAMN36656100
SRA SRX21106742

Supplementary file Size Download File type/resource
GSM7655059_M4_Ag_abundance.h5 44.9 Mb (ftp)(http) H5
GSM7655059_M4_Ag_abundance.tsv.gz 1.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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