|
| Status |
Public on Jun 12, 2019 |
| Title |
PFL_E12_aR5_delattP-Rel5_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Proximal forelimb mouse E12.5_delattp-Rel5_RNA-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6CBAF1
genotype/variation: delHoxd(attP-Rel5)d9lac
embryonic day: E12.5
tissue: Proximal Forelimbs
|
| Treatment protocol |
Micro-dissected proximal and distal segments of E12.5 forelimbs either from wild type or mutant embryos (invHoxD(attP-Itga6) and del(HoxD(attP-Rel5)d9lac). Tissues were dissected and placed in RNAlater (invitrogen) and kept at -80ªC until further use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the it RNAeasy (Microkit, QIAGEN).
Truseq Stranded mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Proximal forelimb mouse E12.5_delattp-Rel5_RNA-seq
|
| Data processing |
Analysis was performed using the facilities of the Scientific IT and Application Support Center of EPFL. The gtf used for STAR and cufflinks, based on the version 94 of ensembl annotations, is available on figshare (doi:10.6084/m9.figshare.7775837). Adapters were removed using cutadapt (v1.16) and aligned onto mm10 using STAR with ENCODE parameters.
Strand specific coverage was performed on uniquely mapped reads (tag NH:i:1) with bedtools version 2.27.1
Bedgraphs were normalized to the number of million uniquely mapped reads and replicates were merged using the tool unionbedg (bedtools v2.27).
Genome_build: mm10
Supplementary_files_format_and_content: Mean of normalized bedgraph of the forward or reverse strand unique read coverage.
|
| |
|
| Submission date |
Apr 05, 2019 |
| Last update date |
Jun 14, 2019 |
| Contact name |
Eddie Rodríguez-Carballo |
| E-mail(s) |
edgardo.rodriguez@unige.ch
|
| Organization name |
Université de Genève
|
| Department |
Department of Genetics and Evolution
|
| Street address |
4, Boulevard d'Yvoy
|
| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE129424 |
Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes [RNA-seq] |
| GSE129427 |
Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes |
|
| Relations |
| BioSample |
SAMN11352853 |
| SRA |
SRX5649315 |
