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Sample GSM1843527 Query DataSets for GSM1843527
Status Public on May 20, 2016
Title Eed-null Villus RNA-seq biological rep 1
Sample type SRA
 
Source name Eed-del Villus cells
Organism Mus musculus
Characteristics strain background: B6;129 mixed
genotype/variation: EedF/F; Villin-CRE
cell type: Adult Epitheial cells; proximal 1/3 of intestine
Treatment protocol Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.
Extracted molecule total RNA
Extraction protocol Epithelium from proximal 1/3 of mouse intestine 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.
Total RNA was extracted with TRIzol reagent (Invitrogen) followed by DNase treatment with the RNeasy kit (Qiagen).
The TruSeq RNA Sample Preparation Kit V2 (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 HiSeq 2000
 
Description Eed-del_Villus_1
343_EED_KO_Villus_RNAseq
Data processing Alignment: ChIP-seq:bowtie. RNA-seq: Tophat, version 2.0.6
ChIP-Seq - peak calling: SICER, version 1.1
RNA-Seq - normalized and differential expression: Cufflinks, version 2.0.1; default setting; Cuffdiff was used with default settings and FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq Tag Density bigwig file for visualizing aligned sequence tags
RNA-Seq: Differential expression table, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Control ISC, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
RNA-Seq: Differential expression tables, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Eed-del Villus, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
 
Submission date Aug 04, 2015
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 GPL13112
Series (1)
GSE71713 Acquired tissue-specific promoter bivalency is a basis for PRC2 necessity in adult somatic cells
Relations
BioSample SAMN03956391
SRA SRX1132745

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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