|
| Status |
Public on Jun 06, 2023 |
| Title |
HNF4A,HALO,hBJ,rep2,input |
| Sample type |
SRA |
| |
|
| Source name |
BJ fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BJ fibroblasts
cell type: Human foreskin fibroblasts
chip antibody: HALO(Promega G9281)
time: ChIP-seq after 48 hours ectopic expression
|
| Growth protocol |
DMEM, 4.5g/L D-Glucose, L-Glutamine, 110 mg/L Sodium Pyruvate, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a COVARIS.
ChIP-seq libraries were prepared using the NEBNect Ultra II for DNA Library Prep, following manufacturers protocols, with an input of 5-10 ng of immunoprecipitated DNA. The size distribution of amplified fragments was assessed by TapeStation, and the concentration of libraries was determined by Qubit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Basecalling and Fastq generation was automated through BaseSpace.
Single-end reads were aligned to the human genome build hg19 using bowtie2 v2.3.4.1 with run parameters --local -X 1000.
Optical and PCR duplicate reads were marked and removed using PICARD MarkDuplicates REMOVE_DUPLICATES=TRUE ASSUME_SORT_ORDER=queryname (GATK 4.2.6.0).
BED files were generated from BAMs using the bedtools command bamToBed (bedtools v2.27.1).
Peaks were called from BED files using MACS2 callpeak against a matched input control with a FDR of 0.1% (MACS2 v2.2.7.1), with final peak sets selected by taking the union of biological replicates.
Bigwig files for visualization of signal over specific genomic regions was generated with deeptools (version 3.5.0).
Assembly: hg19
Supplementary files format and content: bigWig, bed (except for input samples)
|
| |
|
| Submission date |
Dec 08, 2022 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Kenneth S. Zaret |
| E-mail(s) |
zaret@pennmedicine.upenn.edu
|
| Phone |
2155735813
|
| Organization name |
University of Pennsylvania School of Medicine
|
| Department |
Cell and Developmental Biology
|
| Lab |
Zaret lab
|
| Street address |
9-132, SCTR, 3400 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104-5157 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE220567 |
Distinct Chromatin Scanning Modes Lead to Targeting of Compacted Chromatin by Pioneer Factors FOXA1 and SOX2 [ChIP-seq] |
| GSE220570 |
Different chromatin scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2 |
|
| Relations |
| BioSample |
SAMN32117480 |
| SRA |
SRX18543063 |
