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Sample GSM3175502 Query DataSets for GSM3175502
Status Public on Feb 18, 2019
Title Adult Duodenal cells human patient 1
Sample type SRA
 
Source name human Adult Duodenal cells
Organism Homo sapiens
Characteristics cell type: human Adult Duodenal cells
genotype: Wild-Type
treatment: NO
Extracted molecule genomic DNA
Extraction protocol Patient Duodenal biopsy tissue was dissected, epithelial cells were scrapped and fixed for subsequent chromatin pull down
Whole cell lysates were sonicated and incubated with 6 uL CDX2 antibody overnight for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
 
Description Hbiopsy_Cdx2_rep1_NK69
human Adult Duodenal cells
Data processing Alignment: ChIP-seq:bowtie2 version 2.2.6. RNA-seq: Tophat, version 2.1.0
peak calling: macs 1.4.1
RNA-seq cxb files: cuffquant v2.2.1
Bigwig: bamCoverage 2.4.2
Genome_build: mm9, hg19
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: cxb file for expression profile and cuffnorm table with normalized gene expression values
 
Submission date Jun 04, 2018
Last update date Feb 18, 2019
Contact name Michael P Verzi
Organization name Rutgers, the State University of New Jersey
Department Genetics
Lab Verzi
Street address 145 Bevier Road
City Piscataway
State/province NJ
ZIP/Postal code 08854
Country USA
 
Platform ID GPL21697
Series (1)
GSE115314 The lineage-specific transcriptional regulator, CDX2, navigates a dynamic chromatin landscape to control distinct stages of intestinal development
Relations
BioSample SAMN09345338
SRA SRX4161612

Supplementary file Size Download File type/resource
GSM3175502_Hbiopsy_Cdx2_rep1_NK69.bw 94.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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