|
| Status |
Public on Oct 26, 2018 |
| Title |
WT Villus CDX2 ChIP-seq replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse intestinal villus epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129 mixed background
cell type: Adult differentiated jejunal epithelial cells; middle 1/3 of intestine
genotype: Cdx2f/f
developmental stage: adult
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Villi from middle 1/3rd of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were cross-linked and immediately snap-frozen in liquid nitrogen for subsequent ChIP analysis.
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with beads pre-bound to CDX2 antibody (#12306, Cell Signaling) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Adult_CDX2_ChIP rep1
supplementary file: WT_AdultVillus_CDX2.bw
|
| Data processing |
Alignment: ATAC-seq and ChIP-seq: Bowtie2. RNA-seq: STAR aligner, version 2.5.3a.
ATAC-seq differential region identification: diffReps; Peak calling: MACS2; RNA-seq raw read counts: HTSeq
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: ATAC-Seq & ChIP-seq: bigwig file for visualizing aligned sequence tags (available in tar archives on the series record).
Supplementary_files_format_and_content: RNA-seq: text file with raw read counts
|
| |
|
| Submission date |
Jun 08, 2018 |
| Last update date |
Oct 26, 2018 |
| Contact name |
Ramesh Shivdasani |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Shivdasani
|
| Street address |
450 Brookline Ave. Dana 720D
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE115541 |
Chromatin and tissue plasticity precede commitment to intestinal differentiation during endoderm development |
|
| Relations |
| BioSample |
SAMN09385760 |
| SRA |
SRX4187763 |
