|
| Status |
Public on Jan 06, 2014 |
| Title |
Ent-Pro_DHS |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal crypt enterocyte progenitors
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh intestinal crypt epithelial cells were collected by removing villi manually and incubating crypts in 5 mM EDTA for 50 min at 4°C. Lgr5+ intestinal stem cells were purified from Lgr5-eGFP-Cre mice using flow cytometry for GFP. Crypt secretory progenitors (Sec-Pro) were enriched by treating mice with the Notch inhibitor Dibenzazepine or by deleting Rbpj, and mature goblet cells (GOB) were isolated from Rbpj-/- mouse villi. Enterocyte progenitors (Ent-Pro) and mature enterocytes (ENT) were isolated from Atoh1-/- mouse (which lacks all secretory cells) crypts and villi, respectively. Cells were fixed in 1% formaldehyde for 25 min at room temperature and lysed. Chromatin was sheared by sonication. DNA was amplified using ThruPLEX-FD kit (Rubicon Genomics).
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DNase-seq
|
| Data processing |
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with default settings. Only uniquely aligned tags were retained
Peaks were called using MACS2 with the following settings: Q value <= 0.01, shiftsize = 146 for histone marks and shiftsize = 100 forATOH1 ChIP and DNaseI hypersensitive fragments
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were converted from wig files generated using unique reads from MACS2
|
| |
|
| Submission date |
Oct 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Fugen Li |
| E-mail(s) |
fugen_li@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE51458 |
Analyses of the chromatin and transcriptional basis for lateral inhibition in isolated intestinal epithelial cells. |
| GSE51464 |
An epigenetic basis for lateral inhibition and lineage plasticity in intestinal differentiation |
|
| Relations |
| BioSample |
SAMN02378569 |
| SRA |
SRX365691 |
