|
| Status |
Public on Nov 21, 2014 |
| Title |
E12.5 Digits RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA from E12.5 mouse digits
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6CBAF1/J
Stage: E12.5
genotype: Digits
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from a genital tubercle at E15.5 or from a pair of E12.5 forelimb presumptive digits using QIAGEN RNeasy Plus Micro Kit after disruption and homogenization
After ribodepletion, total RNA was prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) by the Genomics Platform of the University of Geneva
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Mapping and RNA-seq analyses were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly with bowtie version 2.1.0 with the parameters --end-to-end --sensitive -k 20
Genome_build: mm9
Supplementary_files_format_and_content: Density file (bigWig)
|
| |
|
| Submission date |
Oct 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolas Lonfat |
| Organization name |
EPFL - Ecole Polytechnique Fédérale de Lausanne
|
| Department |
School of Life Sciences
|
| Lab |
Laboratory of developmental genomics
|
| Street address |
EPFL-SV-ISREC-UPDUB- Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE62268 |
Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci (RNA-seq) |
| GSE62269 |
Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci |
|
| Relations |
| BioSample |
SAMN03104582 |
| SRA |
SRX731077 |
