|
| Status |
Public on Dec 06, 2016 |
| Title |
RNA-HL-E105-Wt-Mm-Rep1-L6497 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Limb Bud
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Hindlimb
developmental stages: E10.5
genotype: wild type
|
| Growth protocol |
Limb bud and midbrain were micro-dissected from mouse embryos
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from the different tissues using a RNeasy kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were mapped to the mouse reference genome (mm9) using the STAR mapper (Dobin et al., 2013) (splice junctions based on RefSeq ;options: ‐‐alignIntronMin 20 ‐‐alignIntronMax 500000 --outFilterMultimapNmax 5 ‐‐outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.1).
To create bigwig files coverage profiles were generated by creating a bedgraph file using bedtools genomecov (-ibam —bg split -scale (normalized per million reads)) (bedtools v2.17.0) and then transformed to bigwig files using the bedgraphtobigwig tool from UCSC (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v287/bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for normalized RNA-seq profiles
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Guillaume Andrey |
| E-mail(s) |
guillaume.andrey@unige.ch
|
| Phone |
+41223795703
|
| Organization name |
University of Geneva
|
| Department |
Department of Genetic Medicine and Development
|
| Street address |
Rue Michel-Servet 1
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE84794 |
Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [RNA-seq] |
| GSE84795 |
Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding |
|
| Relations |
| BioSample |
SAMN05438876 |
| SRA |
SRX1975220 |
