|
| Status |
Public on Nov 10, 2020 |
| Title |
FLB_E9_20somites_delCS3840_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
forelimb buds
|
| Organism |
Mus musculus |
| Characteristics |
genotype: del(CS38-40)
strain: B6CBAF1
embryonic day: E9.5
|
| Treatment protocol |
Micro-dissected forelimb buds from either E9.5 wild type or del(CS38-40) embryos. Tissues were dissected and placed in RNAlater (invitrogen) and kept at -80ªC until further use. The rest of the embryo was stained with DAPI and somites were counted to classify the embryonic timing.
|
| Extracted molecule |
polyA 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 |
Forelimb buds mouse E9.5 del(CS38-40) 20 somites RNA-seq
|
| Data processing |
Analysis was performed on our local galaxy server.
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 using using awk.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized bedgraph of the forward or reverse strand unique read coverage.
|
| |
|
| Submission date |
Jul 10, 2020 |
| Last update date |
Nov 11, 2020 |
| 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) |
| GSE154188 |
Chromatin topology and the timing of enhancer function at the HoxD locus [RNA-seq] |
| GSE154189 |
Chromatin topology and the timing of enhancer function at the HoxD locus |
|
| Relations |
| BioSample |
SAMN15502797 |
| SRA |
SRX8706942 |
