|
| Status |
Public on Apr 12, 2017 |
| Title |
ChIP-seq for FOXO3 [SL16038] |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
antibody (clone id#) used: R5.2.1B7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Exponentially growing cells from ENCODE Tier 1 and Tier 2 cell lines were crosslinked in 1% formaldehyde and harvested in batches of 20 million cells per replicate. Prepared nuclei were resuspended in RIPA buffer and chromatin shearing was performed on a Bioruptor Twin instrument (Diagenode). Antibody (5 µg/rxn) was coupled to M-280 Dynabeads (ThermoFisher Scientific; 11201) overnight prior to addition of sheared chromatin. A small aliquot of the sheared chromatin was reserved as an input control. Following incubation and wash steps, captured chromatin and input control were reverse crosslinked overnight at 65°C and recovered using the QIAquick PCR Purification System (Qiagen; 28104).
ChIP-seq libraries (illumina) were prepared and run on an Illumina HiSeq 2500 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
CHIP-seq reads were aligned to hg19-female using Bowtie2 with default parameters
Peaks were called using MACS2 with default parameters
Genome_build: hg19-female
Supplementary_files_format_and_content: bed (narrowPeak) files were generated using macs2
|
| |
|
| Submission date |
Apr 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anand Venkataraman |
| E-mail(s) |
avenka11@jhu.edu
|
| Phone |
4105021871
|
| Organization name |
Johns Hopkins University
|
| Department |
Neuroscience
|
| Lab |
Seth Blackshaw
|
| Street address |
733 N Broadway, MRB 322
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE97661 |
Testing mAbs generated by the PCRP pipeline in ChIP-seq application |
|
| Relations |
| BioSample |
SAMN06710669 |
| SRA |
SRX2733452 |
