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Sample GSM2201144 Query DataSets for GSM2201144
Status Public on Jun 01, 2017
Title Enteroendocrine Cells RNA-seq biological rep2
Sample type SRA
 
Source name mouse Enteroendocrine cells
Organism Mus musculus
Characteristics strain: B6;129 mixed background
cell type: Adult Epitheial cells; proximal 1/3 of intestine
genotype: Wild-Type
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 CD24 (Alexa Fluor 647 conjugate) and Lectin (Lectin from Ulex europaeus - Atto 488 conjugate) at 4°C for 30 minutes. CD 24Hi, UEA-lectin- cells were sorted by flow cytometry and frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
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 Enteroendocrine Cells RNA-seq biological rep2
EntEndo_Rep2
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
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 SAMN05254228
SRA SRX1847681

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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