|
| Status |
Public on Jul 12, 2017 |
| Title |
invDFL |
| Sample type |
SRA |
| |
|
| Source name |
distal limb
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6CBAF1
tissue: distal limb
developmental stage: E12.5
genotype: invDFL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from E12.5 embryonnic forelimb tissues was extracted shortly after dissection in cold PBS and isolated using Trizol.
Library preparation using the Illumina TruSeq protocol is applied with a Poly A selection
|
| |
|
| 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) with bowtie2 with parameters --end-to-end --sensitive -k 20
Reads Per Kilobase per Million reads (RPKM) for each transcript were calculated from the raw counts with program rnacounter 1.5.2 (https://pypi.python.org/pypi/rnacounter)
Genome_build: mm9
Supplementary_files_format_and_content: One density file per strand (bigWig) and one tab-delimited text file with raw counts and RPKM per transcript.
|
| |
|
| Submission date |
Apr 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Pierre J Fabre |
| E-mail(s) |
fabre.pierre@gmail.com
|
| Organization name |
EPFL
|
| Department |
ISREC
|
| Lab |
Laboratory of Developmental Genomics
|
| Street address |
Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE98232 |
Analysis of gene expression in the distal forelimbs in 2.4Mb inversion adjacent to the HoxD cluster |
| GSE98233 |
Large-scale genomic reorganizations of topological domains (TADs) at the HoxD locus |
|
| Relations |
| BioSample |
SAMN06835121 |
| SRA |
SRX2765872 |
