|
| Status |
Public on Feb 18, 2019 |
| Title |
Naïve endoderm + induced CDX2 human culture rep2 |
| Sample type |
SRA |
| |
|
| Source name |
human Naïve endoderm + induced CDX2 culture cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human Naive endoderm + induced CDX2 culture cells
genotype: Wild-Type
treatment: Doxycycline
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Naïve endoderm + induced CDX2 culture cells were fixed and frozen for subsequent chromatin pulldown
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 |
TetON_Cdx2_rep2_NK76
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 Naïve endoderm + induced CDX2 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 19, 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 |
SAMN09345339 |
| SRA |
SRX4161611 |
