|
| Status |
Public on Aug 14, 2019 |
| Title |
129_I_RFVCT |
| Sample type |
SRA |
| |
|
| Source name |
RNA in water
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Rfx6f/f Vilin-CreERT2
time: 8_days
|
| Treatment protocol |
Adult mice were given tamoxifen (10mg) (Sigma) by gavage twice per day, every second day during 5 days.
|
| Growth protocol |
Mutant (Rfx6f/f; Vilin-CreERT2) and control mice (Rfx6f/+, or Rfx6f/f) were generated starting from Rfx6f/+ (Piccand et al, 2014) and Vilin-CreERT2 mice (El Marjou et al 2004)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Ileon was harvested at 8 days and 3 months after tamoxifen gavage. Total RNA was extracred using TRI-reagent or RNeasy® Midi Kit (Qiagen).
Library prep for total RNA-seq Ribozero/standard quantity
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
rawdata_8days.txt
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads mapping to rRNA and ERCC spikes were identified using Bowtie version 1.0.0 and removed from the analysis.
Remaining reads were mapped onto the mm9 assembly of mouse genome using Tophat version 2.0.10 and the Bowtie2 version 2.1.0 aligner.
Quantification of gene expression was performed using HTSeq version 0.6.1 (parameter “--intersection_nonempty”) and gene annotations from Ensembl release 67
Genome_build: mm9
Supplementary_files_format_and_content: The two tab-delimited text file include raw read counts for the two experiments (at 8 days and 3 months)
|
| |
|
| Submission date |
Jun 19, 2019 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Gérard Gradwohl |
| E-mail(s) |
gradwohl@igbmc.fr
|
| Organization name |
IGBMC
|
| Street address |
1 rue Laurent Fries
|
| City |
Illkirch-Graffenstaden |
| State/province |
- |
| ZIP/Postal code |
67400 |
| Country |
France |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE132997 |
Identification of Rfx6-dependent genes in the adult mouse ileon by RNAseq |
| GSE133038 |
Rfx6-regulated genes in the mouse intestine |
|
| Relations |
| BioSample |
SAMN12095370 |
| SRA |
SRX6094157 |
