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| Status |
Public on Mar 06, 2014 |
| Title |
WTLOHI |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
time: 8 days post-infection
genotype: WT
cell type: CD4+CD44+Ly6cLO PSGL-1HI
genetic background: C57/BL6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens were removed at 8 days post-LCMV infection. Cells were sorted based on CD4+CD44+ Ly6c and PSGL-1 expression (LO LO ,LO HI, and HI HI, respectively). RNA was isolated using Qiazol reagent and miRNeasy kit. Sample preparation and Illumina HiSeq 2000 sequencing was conducted at the Yale Center for Genomic Analysis.
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 2000 |
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| Description |
alldiff_nonovel.txt
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| Data processing |
Bustard was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.8 with parameters -q -n 2 -m 1 -p 8 -t
Gerald was used for sequence analysis, and ELAND was used to sequence alignment
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Mar 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Joe Craft |
| E-mail(s) |
joseph.craft@yale.edu
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| Organization name |
Yale University
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| Department |
Immunobiology
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| Street address |
300 Cedar St.
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE55596 |
Transcriptome Analysis of Follicular Helper T cells, Central Memory Precursors, and Terminal Effector Th1 Cells from Wild Type and Stat3fl/fl Cd4cre mice |
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| Relations |
| BioSample |
SAMN02673342 |
| SRA |
SRX481212 |
| 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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