|
| Status |
Public on Dec 08, 2014 |
| Title |
Control biological rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Control mouse jejunum epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: 129xC57/Bl6xSvJ mixed background
genotype/variation: Cre- control
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 |
Control_1
Control_755
|
| 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 |
|
| Relations |
| BioSample |
SAMN03135788 |
| SRA |
SRX878119 |
