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Sample GSM2201116 Query DataSets for GSM2201116
Status Public on Jun 01, 2017
Title CD274+69+ DT-Treated ATAC Biological rep2
Sample type SRA
 
Source name CD 274,69 labeled mouse intestinal cells after DT treatment
Organism Mus musculus
Characteristics strain: B6;129 mixed background
cell type: Adult Epitheial cells; proximal 1/3 of intestine
genotype: Wild-Type
Treatment protocol Mice were injected with diphtheria toxin (50 µg/kg mouse weight) four times on alternate days, and sacrificed 1 day after the last injection.
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 0.5U/ml Dispase in DMEM for 30 minutes at 37°C. Cell were stained with antibodies against CD69 (BV421 conjugate, BD Biosciences 562920 ) and CD274 (APC conjugate, BD Biosciences 564715) at 4°C for 30 minutes. CD 69+ 274+ cells were sorted by flow cytometry and 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 CD274+69+ DT-Treated ATAC Biological rep2
CD274+69+_DT-Treated_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 SAMN05254247
SRA SRX1847653

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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