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| Status |
Public on Dec 22, 2021 |
| Title |
Smad4KO_2 |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
strain: C57BL/6
cells: Early effector CD8 T cells
time: 6 days post infection
genotype: Smad4 deficient
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy Plus Kit (Qiagen)
Standard Illumina library construction protocols
RNA samples were sent to Otogenetics Corporation for RNA-Sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The data sets were analyzed with Tophat2 mapping (DNAnexus).
Expression levels were measured with Cuffilinks software (DNAnexus)
Differential expression analysis was done with Cuffdiff software (DNAnexus).
Genes with transcriptional changes over two folds (Log2 fold change >1 or <-1,p<0.05, false discovery rate<0.05) were selected for Ingenuity pathway analysis (Qiagen) and Gene set enrichment analysis
Supplementary_files_format_and_content: gtf file with FPKM values for each sample
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| Submission date |
Jun 02, 2020 |
| Last update date |
Dec 22, 2021 |
| Contact name |
Linda S Cauley |
| E-mail(s) |
lcauley@uchc.edu
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| Organization name |
UConn Health
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| Department |
Immunology
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| Lab |
Cauley Lab
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| Street address |
263 Farmington Ave
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE151637 |
Transcriptional profile of Smad4-deficient CTLs is similar to TRM |
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| Relations |
| BioSample |
SAMN15082263 |
| SRA |
SRX8453892 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4587195_S4KO2.gtf.gz |
4.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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