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| Status |
Public on Aug 08, 2019 |
| Title |
13-MP2 |
| Sample type |
SRA |
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| Source name |
SP tetramer+ CD8+ T cels
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| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cells
mouse strain: C57BL6/J
treatment: MOG+SP
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| Treatment protocol |
Tetramer postive cells, Ly49+, Ly49- cells were obtained from 10 days post MOG, MOG+SP immunized mice
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were bulk sorted and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
count_matrix.txt.gz
tpm_matrix.txt.gz
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| Data processing |
Read quality was determined with FastQC 0.11.4
Using TopHat v2.0.13, we aligned the reads to the mouse reference genome (NCBI/ assembly GRCm38).
One MOG + PPT sample was removed from downstream analysis as an identified outlier. (not shown)
TPM values were calculated with RSEM v1.3.0
Genome_build: GRCm38
Supplementary_files_format_and_content: count_matrix and tpm_matrix are matrices with expression values for each gene in each cell. count_matrix is the raw counts for reads aligning to each gene. tpm_matrix is identically structured, but values are transcripts per million (TPM).
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| Submission date |
May 09, 2019 |
| Last update date |
Aug 08, 2019 |
| Contact name |
Michael Sikora |
| E-mail(s) |
[email protected]
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| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Steinmetz
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| Street address |
450 Serra Mall
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE130975 |
RNA seq on SP specific CD8+ T cells, Ly49+ and Ly49-CD8+ T cells from MOG and MOG + SP immunized mice [RNA-Seq] |
| GSE133364 |
RNA seq on SP specific CD8+ T cells, Ly49+ and Ly49-CD8+ T cells from MOG and MOG + SP immunized mice and DNA sequencing for multiple rounds of the pMHC-yeast display selection for TCR6, TCR7 and FluTCR |
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| Relations |
| BioSample |
SAMN11613270 |
| SRA |
SRX5813633 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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