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Sample GSM1817695 Query DataSets for GSM1817695
Status Public on Sep 15, 2015
Title Control Villus biological rep 3
Sample type SRA
Source name Control mouse villus cells
Organism Mus musculus
Characteristics strain: B6;129 mixed background
cell type: Adult jejunum villus
genotype: Cdx2F/F; Cre-
Treatment protocol Mice were injected with 1-2mg Tamoxifen for 4-5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.
Growth protocol Epithelium from mouse jejunum was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Epithelium was 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) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.
The TruSeq RNA Sample Preparation Kit (Illumina) 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 Control_VC_3
Data processing Alignment: ChIP-seq:bowtie. RNA-seq: Tophat, version 2.0.9
ChIP-Seq - peak calling: MACS, version 1.4.2, considering input and local background, p<0.0001 cutoff.
RNA-Seq - normalized and differential expression: Cufflinks, version 2.1.1; settings: -b, -u, and default; Cuffmerge was used with custom 3' 1000 bp reference gtf and default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: Bed file for significant peaks, bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: There are two processed data matrices that apply to all the samples. First, is the normalized expression table, prepared using Cuffnorm, which contains the normalized Log2(FPKM+1) expression values for all 9 RNA-seq samples. The second is the differential expression table, prepared using Cuffdiff with an FDR of 5%, which contains average FPKM values for villus, control ISC and Cdx2-del ISC, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing. The third is the custom gtf used in cuffdiff for correction of 3' bias in the RNA-seq samples.
Submission date Jul 10, 2015
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)
GSE70766 Distinct processes and transcriptional targets underlie CDX2 requirements in intestinal stem cells and differentiated villus cells
BioSample SAMN03854479
SRA SRX1091854

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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