|
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.
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|
|
Submission date |
Jul 10, 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 |
GPL19057 |
Series (1) |
GSE70766 |
Distinct processes and transcriptional targets underlie CDX2 requirements in intestinal stem cells and differentiated villus cells |
|
Relations |
BioSample |
SAMN03854479 |
SRA |
SRX1091854 |