|
| Status |
Public on Sep 01, 2012 |
| Title |
H3K36me3_minusRA |
| Sample type |
SRA |
| |
|
| Source name |
Ntera2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Ntera2
antibody: H3K36me3
vendor: Abcam (Cat. # ab9050)
treatment: no retinoic acid
|
| Treatment protocol |
The H3K36me3 antibody was provided by Abcam (Cat. # ab9050). The cells were treated with 10 uM all-trans RA for 48 hours, and then lysed and subject to standard ChIP preparation procedure. 2 ug of antibodies were used to precipitate the samples.
|
| Growth protocol |
Ntera2 cells were cultured in MEMalpha medium with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The libraries were constructed following Illumina's Chip-Seq sample preparation kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ChIP on H3K36me3
|
| Data processing |
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie and the read counts on each gene were computed by using BedTools.
|
| |
|
| Submission date |
Jul 22, 2011 |
| 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 |
GPL9115 |
| Series (2) |
| GSE30876 |
Retinoic Acid-Induced DR2 Alu Transcripts in Stem Cells Generate Functional Small RNAs that Mediate Target mRNA Degradation |
| GSE42602 |
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation |
|
| Relations |
| SRA |
SRX084800 |
| BioSample |
SAMN00672676 |
