|
| Status |
Public on Jun 01, 2017 |
| Title |
Bmi1-GFP-Irradiated ATAC 24hr biological rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bmi1-GFP+ mouse intestinal cells after irradiation
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129 mixed background
cell type: Adult Epitheial cells; proximal 1/3 of intestine
genotype: Bmi-1GFP/+
|
| Treatment protocol |
Mice were given whole body radiation dose of 10Gy and intestinal tissue was harvested after 24 hours.
|
| Growth protocol |
Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Bmi1-GFP+ve cells were sorted by flow cytometry. Cell were immediately used for chromatin transposition.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Bmi1-GFP-Irradiated ATAC 24hr biological rep2
Bmi1_Rad_24hr_ATAC.bw
|
| Data processing |
Library strategy: ATAC-seq
Alignment: ATAC-seq and ChIP-seq:bowtie2. RNA-seq: Tophat, version 2.0.6
ATAC-seq peak calling: MACS, version 1.4
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types
|
| |
|
| Submission date |
Jun 15, 2016 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE83394 |
Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells |
|
| Relations |
| BioSample |
SAMN05254241 |
| SRA |
SRX1847647 |
