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Sample GSM2337683 Query DataSets for GSM2337683
Status Public on Feb 28, 2017
Title Input_for_p300_FG_DMSO
Sample type SRA
 
Source name Foregut explants
Organism Xenopus laevis
Characteristics Stage: NF20
genotype/variation: Wild Type
tissue: Foregut 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: p300_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 SAMN05864204
SRA SRX2213227

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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