|
| Status |
Public on Nov 14, 2012 |
| Title |
mRNA_JQ1treated_Tcell_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+ T cells
treatment: JQ1 treated
|
| Treatment protocol |
Freshly isolated human CD4+ T-cells treated with or without 500nM JQ1 for 24hr
|
| Growth protocol |
CD4+ T-cells were purified from normal human peripheral blood using the human CD4+ T-cell Isolation Kit II (Miltenyl Biotech).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen) and purified by RNeasy mini-kit (Qiagen, Valencia, USA). Poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The cDNA fragments were then subjected to an end repair process of addition of a single 'A' base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final cDNA library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Alignment (bed files): Sequence reads were obtained and mapped to the human (hg18) genomes using Bowtie using default parameters and m 1, k 2, best and strata. All reads mapping with two or fewer mismatches were retained.
Sequence reads were obtained and mapped to the human (hg18) genomes using ELAND of the Illumina Genome Analyzer pipeline. All reads with at most two ambiguous base calls and mapping with two or fewer mismatches were retained. Refseq transcript level expression [RPKM data not submitted] estimation was performed using the Partek Genomics SuiteTM RNA-seq workflow (Partek(r) software, version 6.5 build 6.11.0121 Copyright (c) 2010).
|
| |
|
| Submission date |
Oct 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Keh-chuang Chin |
| E-mail(s) |
kehchuang_chin@immunol.a-star.edu.sg
|
| Organization name |
Singapore Immunology Network
|
| Department |
Laboratory of Gene Regulation
|
| Street address |
Biopolis, 8A Biomedical Grove, #03-06 Immunos
|
| City |
Singapore |
| ZIP/Postal code |
138648 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE33281 |
Bromodomain-Containing-Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells |
|
| Relations |
| SRA |
SRX198032 |
| BioSample |
SAMN01773251 |
