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Sample GSM1530537 Query DataSets for GSM1530537
Status Public on Dec 08, 2014
Title Hnf4a-/-;Cdx2-/- biological rep2
Sample type SRA
Source name Hnf4a;Cdx2 double-knockout mouse jejunum epithelium
Organism Mus musculus
Characteristics strain/background: 129xC57/Bl6xSvJ mixed background
genotype/variation: Hnf4a;Cdx2 double-knockout
cell type: adult jejunal epithelium
Treatment protocol All mice were injected with 1mg tamoxifen for 5 consecutive days to activate Cre recombinase 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 Hnf4a;Cdx2 KO_2
Data processing Alignment: Tophat, version 2.0.9, default options.
Normalized and differential expression: Cufflinks, version 2.1.1; settings: -b, -u, and default; Cuffmerge was used with reference gtf and default settings; Cuffquant was used with default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals. There are two processed data matrices that apply to all of the samples. First is the normalized expression table, prepared using Cuffnorm, which contains the normalized FPKM expression values for all 4 RNA-seq samples. The second is the differential expression table, prepared using Cuffdiff with an FDR of 5%, which contains average normalized FPKM values for Control and Hnf4a;Cdx2_KO samples, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
Submission date Oct 22, 2014
Last update date May 15, 2019
Contact name Adrianna Katrina San Roman
Organization name Dana Farber Cancer Institute and Harvard Medical School
Department Medical Oncology
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL19057
Series (1)
GSE62633 Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction With the Transcription Factor CDX2
BioSample SAMN03135787
SRA SRX878122

Supplementary file Size Download File type/resource
GSM1530537_773CH4_genes.fpkm_tracking.txt.gz 771.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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