|
| Status |
Public on Nov 21, 2022 |
| Title |
RNA-seq in XY E13.5 Fgf9 Δ306 gonads rep3 |
| Sample type |
SRA |
| |
|
| Source name |
E13.5 XY Gonads
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Fgf9 <delta>306
developmental stage: E13.5
tissue: gonads
|
| Growth protocol |
E13.5 gonads were microdissected in 1XPBS and separated from mesonephros using syringes and snapped frozen in liquid N.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using RNase Micro kit (Qiagen).
RNA-seq libraries were performed using the NEBNext Ultra II Directional RNA library prep kit for Illumina including the Poly(A) magnetic isolation module.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
XY_13.5_Fgf9_306_rep3
|
| Data processing |
Base calling with standard Illumina Software.
Fastq files were mapped to mm10 genome using STAR version 2.7.10a with parameters (-- outFilterMultimapNmax 1).
Gene expression was quantified using featureCounts from subREAD package with default parameters.
Sample scaling and differential gene expression analysis were performed using the R package DESeq2.
Assembly: mm10
Supplementary files format and content: Counts.csv = Merged matrix containing counts from all samples in the different columns.
Supplementary files format and content: DEseq2.csv = Differential gene expression analysis, direct output from DESeq2.
|
| |
|
| Submission date |
Nov 09, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Irene Mota-Gomez |
| E-mail(s) |
irene211092@gmail.com
|
| Organization name |
Max Delbruck Center
|
| Lab |
Dario Lupianez
|
| Street address |
Hannoversche strasse 28
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE217617 |
Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis [RNA-seq] |
| GSE217618 |
Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis |
|
| Relations |
| BioSample |
SAMN31670039 |
| SRA |
SRX18222250 |
