|
| Status |
Public on Dec 29, 2012 |
| Title |
plusRA_GRO-seq |
| Sample type |
SRA |
| |
|
| Source name |
NTera2/D1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NTera2/D1
treatment: RA
|
| Treatment protocol |
For induction, the cells were treated with 1 μM atRA (Sigma) for 2 days.
|
| Growth protocol |
Ntera2/D1 cells (American Type Culture Collection) were kept in minimum essential medium α (Invitrogen) plus 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads. Run-on RNA was then polyadenylated to generate primer sites for first strand cDNA synthesis. Complementary poly-T primers contain two adaptor sequences separated by an Ape1 restriction site, which after circularization and Ape1 digestion, will terminate both ends, thus permitting cDNA generation, PCR-amplification, and library generation for deep sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to hg18 using BFAST, and we kept only 1 aligned read/ genome position for downstream analyses.
An equal number of reads (4.4 million) was randomly extracted from each sample, and the sequencing reads were counted over the entire gene body on the sense strand with respect to the gene orientation using BedTools.
Genome_build: hg18
Supplementary_files_format_and_content: BED aligned files and BEDGRAPH files
|
| |
|
| Submission date |
Nov 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
MICHAEL G ROSENFELD |
| E-mail(s) |
mrosenfeld@ucsd.edu
|
| Organization name |
HHMI/UCSD
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE42563 |
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation (RNA-seq) |
| GSE42602 |
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation |
|
| Relations |
| SRA |
SRX206684 |
| BioSample |
SAMN01820059 |
