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| Status |
Public on Jul 25, 2023 |
| Title |
Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 2 (RNA-seq) |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: CD8+ T cell
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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.
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| Submission date |
Jul 20, 2023 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Kathleen Abadie |
| E-mail(s) |
abadiek@uw.edu
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| Organization name |
University of Washington
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| Department |
Bioengineering
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| Lab |
Kueh Lab
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN36656101 |
| SRA |
SRX21106741 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7655058_M3_low_low_abundance.h5 |
43.6 Mb |
(ftp)(http) |
H5 |
| GSM7655058_M3_low_low_abundance.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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