|
| Status |
Public on Jul 22, 2016 |
| Title |
LNCaP shTET1, hMe-Seal-seq |
| Sample type |
SRA |
| |
|
| Source name |
prostate cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
genotype/variation: shTET1
chemical labeling: 5hmC
|
| Treatment protocol |
Cells were subjected to lentiviral infection by scramble or shFOXA1/shTET1.
|
| Growth protocol |
Cell lines were maintained in RPMI supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using a probe sonicator, immunoprecipitated using the indicated antibody or chemically labeled, purified and sequenced using Illumina Genome Analyzers following protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Enrichment of 5hmC by chemical pulldown
|
| Data processing |
library strategy: hMe-Seal-seq
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file
|
| |
|
| Submission date |
Sep 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan.yu@emory.edu
|
| Organization name |
Emory University
|
| Department |
Urology
|
| Lab |
Jindan Yu's lab
|
| Street address |
E330, 1760 Haygood Dr NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE73363 |
FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function |
|
| Relations |
| BioSample |
SAMN04103940 |
| SRA |
SRX1280796 |
