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Sample GSM1817697 Query DataSets for GSM1817697
Status Public on Sep 15, 2015
Title Control ISC biological rep 2
Sample type SRA
Source name Control mouse intestinal stem cells
Organism Mus musculus
Characteristics strain: B6;129 mixed background
cell type: Adult intestinal stem cell; proximal 2/3 of intestine
genotype: Cdx2+/+; Lgr5-EGFP-IRES-CREERT2
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 Crypts from the proximal 2/3 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 Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry.
Extracted molecule polyA RNA
Extraction protocol poly-A RNA was extracted with oligo dT magnetic beads (New England Biolabs) followed by DNase treatment with the RNeasy kit (Qiagen).
The Encore Complete RNA-Seq Library System (Nugen) was used, modified for 1/2 volume reactions. 200-450 bp fragments were submitted for sequencing 50 bp single-end reads on an Illumina Hi-Seq 2000 instrument.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Control_ISC_2
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 GPL13112
Series (1)
GSE70766 Distinct processes and transcriptional targets underlie CDX2 requirements in intestinal stem cells and differentiated villus cells
BioSample SAMN03854481
SRA SRX1091856

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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