|
| Status |
Public on Aug 26, 2011 |
| Title |
Th17-Gata3-KO [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
T-helper 17 cells w/ Gata3 knockout
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Gata3 knockout
cell type: T-helper 17 cells
|
| Treatment protocol |
n/a
|
| Growth protocol |
DP cells are separated from WT and GATA3-knockout mice respectively. Naïve CD4 cells are separated from Gata3fl/fl mice and then are infected with Retroviruses containing hCre-GFP-RV when the cells are diffentiated under Th1, Th2, Th17 and iTreg conditions, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard RNA-seq protocol. Cells were lysed in the buffer containing PCR buffer, NP-40, DTT and Rnase Inhibiter and mRNAs were reverse-transcribed into cDNA using a poly(T) primer with anchor sequence (UP1) and unused primers are digested. Poly(A) tails are added to the first-strand cDNAs at the 3' end, and second-strand cDNAs are synthesized using poly(T) primers with another anchor sequence (UP2). Then cDNAs are evenly amplified by PCR using UP1 and UP2 primers, fragmented, and Illumina adaptors are ligated to the ends. After PCR amplification with Illumina primers, 200-300bp DNA fragments are purified for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RNA-seq of mRNA fraction
|
| Data processing |
Reads were aligned using the ELAND algorithm from Solexa. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
|
| |
|
| Submission date |
Mar 16, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian J Abraham |
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Computational Biology
|
| Street address |
262 Danny Thomas Blvd
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38112 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE20898 |
Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types |
|
| Relations |
| SRA |
SRX018096 |
| BioSample |
SAMN00010526 |
