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Sample GSM7976448 Query DataSets for GSM7976448
Status Public on Apr 17, 2024
Title RNA-seq in E18.5 wild type female urogenital sinus replicate 3
Sample type SRA
 
Source name urogenital sinus
Organism Mus musculus
Characteristics tissue: urogenital sinus
Sex: female
Stage: E18.5
genotype: wild type
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNAseq_mm_E185_wt_FUGS_rep3
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)
 
Submission date Dec 15, 2023
Last update date Apr 17, 2024
Contact name Aurelie Hintermann
E-mail(s) aur.hin@gmail.com
Organization name University of Geneva
Department Genetics and Evolution
Street address 30 quai Ernest-Ansermet
City Geneva
ZIP/Postal code 1205
Country Switzerland
 
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
Relations
BioSample SAMN38851312
SRA SRX22897301

Supplementary file Size Download File type/resource
GSM7976448_RNAseq_mm_E18_wt_FUGS_rep3_Uniq_fwd_norm.bw 61.8 Mb (ftp)(http) BW
GSM7976448_RNAseq_mm_E18_wt_FUGS_rep3_Uniq_norm.bw 122.0 Mb (ftp)(http) BW
GSM7976448_RNAseq_mm_E18_wt_FUGS_rep3_Uniq_rev_norm.bw 62.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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