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| Status |
Public on Apr 07, 2023 |
| Title |
D5, WT, 3 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Mus musculus |
| Characteristics |
tissue: Blood
cell line: OTII
cell type: OTII TCR-transgenic CD4+ T cells
genotype: WT
treatment: sensitized with HDM extract and LPS-free EndoFit ovalbumin
time: day 5
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the Single Cell RNA Purification kit (Norgen)
RNA libraries were prepared for sequencing using standard Illumina protocols. All libraries were prepared at Genewiz.
Ultra-Low Input RNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
D5B63
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| Data processing |
Quality Control: fastQC, multiQC
Adapter Trimming: TrimGalore 0.4.4, phred 33, paired, nextera adapters
Alignment: STAR 2.5.2a, default settings
Read Count: HTseq-count 0.6.1p1, unstranded, GCF_000001635.27_GRCm39_genomic.gtf
Downstream Analysis: edgeR to find differentially expressed genes among pairs of sample groups
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files of counts per gene for each sample
Supplementary files format and content: tab-delimited text file of counts per million for all samples
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| Submission date |
Aug 26, 2022 |
| Last update date |
Apr 07, 2023 |
| Contact name |
Dave Durell Hill |
| E-mail(s) |
[email protected]
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| Organization name |
University of Alabama at Birmingham
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| Department |
Microbiology
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| Street address |
1720 Second Avenue South
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE212158 |
IL-6 prevents Th2 cell polarization by promoting SOCS3-dependent suppression of IL-2 signaling |
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| Relations |
| BioSample |
SAMN30526253 |
| SRA |
SRX17242652 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6510402_D5B63.count.txt.gz |
143.8 Kb |
(ftp)(http) |
TXT |
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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