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| Status |
Public on Oct 24, 2017 |
| Title |
WT1 CD4+YFP+ |
| Sample type |
SRA |
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| Source name |
Treg cells
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| Organism |
Mus musculus |
| Characteristics |
genotype: Foxp3 YFP-Cre Wildtype
infection: LCMV Armstrong
cell type: Treg cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen AllPrep DNA/RNA kit with an additional on-column Dnase 1 treatment.
Each sample was processed using Truseq Stranded mRNA Sample Preparation, October 2013, Rev. E., with one modification at the end of the protocol on pg.41; post-amplification the libraries were purified with Ampure XP beads twice. The libraries were individually barcoded and multiplexed into a single sample. This multiplexed sample was clustered on a Paired-end, RAPID, 2-lane flowcell and sequenced on a Hiseq 2500 DNA sequencer for 100 cycles in each read direction, for a total of 200 cycles, plus an additional 7 cycles to sequence the barcodes.
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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 |
Illumina Casava1.8.2 software used for basecalling.
Reads were processed using fastx toolkit to trim for adapter and quality and filter for low quality.
Processed reads were mapped to the Mus musculus genome using Hisat2.
Reads mapping to genes were counted using htseq-count.
Gene normalization and differential expression analysis was performed using Deseq2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.
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| Submission date |
Oct 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig Martens |
| E-mail(s) |
[email protected]
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| Phone |
406-363-9415
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| Organization name |
NIAID
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| Department |
DIR
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| Lab |
RTB
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| Street address |
903 S. 4th St
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| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE104507 |
Type I interferon signaling attenuates regulatory T cell function in viral infection and in the tumor microenvironment |
| GSE104517 |
Type I interferon signaling attenuates Regulatory T cells function in viral infection and in the tumor microenvironment |
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| Relations |
| BioSample |
SAMN07731012 |
| SRA |
SRX3238212 |
| 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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