|
| Status |
Public on Feb 18, 2019 |
| Title |
ChIP-seq control library human |
| Sample type |
SRA |
| |
|
| Source name |
human Wnt+Fgf-specified intestinal culture cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human Wnt+Fgf-specified intestinal culture cells
genotype: Wild-Type
treatment: NO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Intestinal Specified Endoderm culture cells were fixed and frozen for subsequent chromatin pulldown
Whole cell lysates were sonicated and incubated without any antibody overnight for determining background chromatin pulldown.
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 |
H_Day4-Input_NK09
Human embryonic stem cells (line H9, WiCell Research Institute, NIH registration number 0062) were maintained and differentiated into endoderm, hindgut and intestinal organoids as published previously
human Wnt+Fgf-specified intestinal culture 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 |
SAMN09345333 |
| SRA |
SRX4161614 |
