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Sample GSM2491753 Query DataSets for GSM2491753
Status Public on Jun 01, 2017
Title Control CD274+69+ RNA-seq biological rep2
Sample type SRA
Source name CD 274,69 labeled mouse intestinal cells
Organism Mus musculus
Characteristics strain background: B6;129 mixed background
genotype/variation: wild type
tissue/cell type: Adult Epitheial cells; proximal 1/3 of intestine
Treatment protocol No treatment
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 total RNA
Extraction protocol Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description processed data file: Read_Counts_All_Cells.txt
Data processing 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; read density
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types
Submission date Feb 15, 2017
Last update date May 15, 2019
Contact name Ramesh Shivdasani
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
BioSample SAMN06335542
SRA SRX2564006

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

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