|
| Status |
Public on Oct 06, 2016 |
| Title |
E12.5 RNA-seq Dup-L∆Bor Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
E12.5 limb buds
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Dup-LdeltaBor
age: E12.5
tissue: limb buds
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from snap-frozen tissue by lysis in Trizol and subsequent purification using the Qiagen RNAeasy Mini Kit
polyA enriched RNA-seq libraries were constructed using the Illumina TruSeq RNA V2 Kit according to manufacturer's instructions
|
| |
|
| 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).
The uniquely mapped read counts per gene (annotation based on RefSeq genes) were subsequently transformed to FPKM.
Differential Expression was calculated based on the raw read counts per gene via the DEseq2 package (Love et al 2014; default settings).
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 |
Feb 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Murad Ibrahim |
| E-mail(s) |
ibrahim@molgen.mpg.de, daniel.ibrahim@bih-charite.de
|
| Phone |
030 84131516
|
| Organization name |
Berlin Institute of Health
|
| Department |
Center for Regenerative Therapies
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE78105 |
Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (RNA-seq) |
| GSE78109 |
Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) |
|
| Relations |
| BioSample |
SAMN04504862 |
| SRA |
SRX1594182 |
