|
| Status |
Public on Oct 06, 2016 |
| Title |
S17-4_TH17 OX40L treated |
| Sample type |
SRA |
| |
|
| Source name |
OX40L treated_In vitro Th17
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD4+ T cell
age: 6-8 weeks
genotype: wild type
culture protocol: in the presence of OX40L-TG APCs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA preparation, 5 million CD4+ T cells cultured under Th17-polarizing conditions were collected for RNA extraction using the miRNAeasy Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software 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 Tophat2
Transcripts FPKM were calculated by Cufflink using Reference Annotation: mm9.gtf from UCSC
Differential gene expression were called by CuffDiff using Reference Annotation: mm9.gtf from UCSC
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
xiang xiao |
| E-mail(s) |
xxiao@houstonmethodist.org
|
| Phone |
7134418828
|
| Organization name |
Houston Methodist Hospital and Houston Methodist Research Institute
|
| Street address |
6670 Bertner Avenue, R7-217
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE80010 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type APC and OX40L-TG APC induced T helper 17 cell Transcriptomes [RNA-seq] |
|
| Relations |
| BioSample |
SAMN04622896 |
| SRA |
SRX1686323 |
