|
| Status |
Public on Jul 18, 2024 |
| Title |
RNA-seq of E10.5 headless embryo HoxB Del(i9-13) homozygous replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
headless embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: headless embryo
genotype: HoxB Del(i9-13) homozygous
library: Ribo-depleted
|
| Growth protocol |
Murine E9.5 and E10.5 mutant or wild-type littermate embryos were dissected to remove the head.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy plus micro kit (Qiagen) following the manufacturer recommendation.
The E9.5 samples libraries are poly(A)-enriched and E10.5 are ribo-depleted. Both were prepared with stranded RNA TruSeq kits (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
For data analysis, adapter and bad quality bases were removed from fastq files using cutadapt version 1.18 (Martin, 2011) (-q 30 -m 15 and sequences for -a and -A were adapted to the library).
Filtered reads were aligned on mm10 using STAR version 2.7.10a (Dobin et al, 2013) with the ENCODE parameters and a custom gtf (https://doi.org/10.5281/zenodo.7510406). Coverages were generated by STAR.
FPKM were computed with cufflinks version 2.2.1 (Roberts et al, 2011; Trapnell et al, 2010) using --max-bundle-length 10000000 --multi-read-correct --library-type "fr-firststrand" -b mm10.fa --no-effective-length-correction -M mm10_chrM.gtf.
Assembly: mm10
Supplementary files format and content: bw: normalized coverage on uniquely mapped reads
Supplementary files format and content: AllCufflinks_Simplified_E.txt.gz: table with all FPKM values (one row per ensembl id, one column per sample)
Supplementary files format and content: AllHTSeqCounts_E.txt.gz: table with all count values obtained with STAR (one row per ensembl id, one column per sample)
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| |
|
| Submission date |
Jul 16, 2024 |
| Last update date |
Jul 18, 2024 |
| Contact name |
Lucille Lopez-Delisle |
| E-mail(s) |
lucille.delisle@epfl.ch
|
| Organization name |
EPFL
|
| Street address |
Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE272384 |
CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length [RNA-seq embryo] |
| GSE272483 |
CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length |
|
| Relations |
| BioSample |
SAMN42535841 |
| SRA |
SRX25346516 |
