|
| Status |
Public on Feb 28, 2017 |
| Title |
Input_for_bcat_HG_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Hindgut explants
|
| Organism |
Xenopus laevis |
| Characteristics |
Stage: NF20
genotype/variation: Wild Type
tissue: Hindgut explants
treated with: DMSO
chip antibody: none
|
| Treatment protocol |
Small molecule inhibitors were dissolved in DMSO and embryos were cultured from stages NF12-20 with either DMSO vehicle in 0.1XMBS or 40 μM DMH1 (TOCRIS) or BIO (60 μM; TOCRIS). To activate the hsp:Dkk1GFP transgene, we gave a pulse of 30min in 37C followed by incubation at 13C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPed DNA fragments were purified with phenol:chloroform:isoamylalcohol and precipitated in ethanol.
Libraries were constructed with ThruPLEX® DNA-seq kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: bcat_FGHG_IDR_peaks.bed
|
| Data processing |
Quality check and quality trimming of raw reads was performed using FastQC and Trimmomatic respectively at default parameters. Quality trimmed reads were mapped to the X. laevis genome assembly 9.1 using Bowtie2 at default parameters. Duplicate mapped reads and multi-mapped were removed using picard and samtools respectively. Uniquely mapped reads were used for peak calling. MACS2 was used for peak calling and differential peak analysis at default parameters. IDR ananlysis was performed using MACS2 peaks.
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Peak Files in BED format; direct output of IDR pipeline that is .regionPeak Format [UCSC Compatible]
|
| |
|
| Submission date |
Oct 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron M Zorn |
| E-mail(s) |
aaron.zorn@cchmc.org
|
| Phone |
636 3770
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Develpomental Biology
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45236 |
| Country |
USA |
| |
|
| Platform ID |
GPL18936 |
| Series (2) |
| GSE87652 |
Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors [ChIP-seq] |
| GSE87654 |
Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors |
|
| Relations |
| BioSample |
SAMN05864212 |
| SRA |
SRX2213223 |
