|
| Status |
Public on Jan 20, 2015 |
| Title |
5009_CD4_Naive_48 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Primary Naïve CD4 T Cell
|
| Organism |
Homo sapiens |
| Characteristics |
activation: anti-CD3/CD28 beads, 48 hours
|
| Treatment protocol |
Purified naïve and memory CD4 T cells were cultured in RPMI supplemented with 10% FBS, 100 U/ml penicillin and 100mg/ml streptomycin at 37C and 5% CO2 with anti-CD3/CD28 activator beads (Invitrogen) for 0 or 48 hours.
|
| Growth protocol |
Naïve and memooy CD4 cells were negatively selected using magnetic beads (Stem Cell Technologies). CD8 T cells and CD19 B cells were positively selected on magnetic beads (Miltenyi Biotec).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from cell pellets with TriZol following standard protocols
Total RNA was converted to cDNA with the Ovation RNA-seq system (NuGEN) following standard protocols. cDNA was S1 endonuclease digested. cDNA libraries were end-repaired, A-tailed, and ligated to indexed adapters. Purified library was amplified with 15 cylces of PCR followed by size selection. Cluster generation and sequencing was conducted on an Illumina GAIIx following manufacturer's intructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNAseq
|
| Data processing |
Basecalls performed using CASAVA version 1.5
RNAseq reads were mapped to hg18 with Tophat v1.4 using default parameters. No junctions file (-j) or GTF file (-G) was specified. Gene-level FPKM values were calculated with Cufflinks v2.0.2 in quantitation-only mode (-G) with the GENCODE gene models downloaded from the Human Genome Browser at UCSC in GTF format.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include RPKM for individual files.
|
| |
|
| Submission date |
Jul 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Salomon |
| E-mail(s) |
[email protected]
|
| Organization name |
The Scripps Research Institute
|
| Department |
Molecular & Experimental Medicine
|
| Lab |
Salomon
|
| Street address |
10550 N Torrey Pines Rd, MEM-241
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE59846 |
Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation [RNA-Seq] |
| GSE59860 |
Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation |
|
| Relations |
| BioSample |
SAMN02943970 |
| SRA |
SRX665109 |
