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Status |
Public on Apr 17, 2024 |
Title |
RNA-seq in E18.5 wild type female urogenital sinus replicate 3 |
Sample type |
SRA |
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Source name |
urogenital sinus
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Organism |
Mus musculus |
Characteristics |
tissue: urogenital sinus Sex: female Stage: E18.5 genotype: wild type
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Extracted molecule |
total RNA |
Extraction protocol |
E18.5 male and female UGS were collected with a dissection separating the bladder from the urogenital sinus but including the proximal urethra (and vagina in females). Tissues were stored in RNALater (ThermFisher AM7020) and processed in parallel with Qiagen RNeasy extraction kits (Qiagen 74034). RNA quality was assessed on an Agilent Bioanalyzer 2100, with RIN scores > 9.5. RNA sequencing libraries were prepared at the University of Geneva genomics platform using Illumina TruSeq stranded total RNA with Ribo-Zero TM Gold Ribo-deleted RNA kits to produce strand-specific single-end reads.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
RNAseq_mm_E185_wt_FUGS_rep3
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Data processing |
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024. Raw RNA-seq reads were processed with CutAdapt version 4.1 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 30 -m 15) to remove TruSeq adapters and bad quality bases. Filtered reads were mapped on the mouse genome mm39 with STAR version 2.7.10a with ENCODE parameters with a custom gtf file based on Ensembl version 108 (10.5281/ZENODO.7510796). This custom gtf file was obtained by removing readthrough transcripts and all noncoding transcripts from a protein-coding gene. FPKM values were evaluated by Cufflinks version 2.2.1 with options --max-bundle-length 10000000 --multiread-correct --library-type “fr-firststrand” -b mm10.fa --no-effective-length-correction -M MTmouse.gtf -G Uniquely mapped reads were filtered using the "NH:i:1" tag. Coverage (strand specific or not) were computed with bedtools version 2.30.0 using the ‘-scale’ argument to normalize to the million uniquely mapped reads. Assembly: mm39 Supplementary files format and content: _Uniq_norm.bw: Normalized coverage strand unspecific Supplementary files format and content: _Uniq_fwd_norm.bw: Normalized coverage on the forward strand Supplementary files format and content: _Uniq_rev_norm.bw: Normalized coverage on the reverse strand Supplementary files format and content: AllCufflinks_Simplified.txt.gz: All FPKM values into a single table (multiple lines for the same gene id were summed)
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Submission date |
Dec 15, 2023 |
Last update date |
Apr 17, 2024 |
Contact name |
Aurelie Hintermann |
E-mail(s) |
aur.hin@gmail.com
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Organization name |
University of Geneva
|
Department |
Genetics and Evolution
|
Street address |
30 quai Ernest-Ansermet
|
City |
Geneva |
ZIP/Postal code |
1205 |
Country |
Switzerland |
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Platform ID |
GPL13112 |
Series (2) |
GSE250266 |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [RNA-seq] |
GSE250267 |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS |
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Relations |
BioSample |
SAMN38851312 |
SRA |
SRX22897301 |