 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 11, 2019 |
| Title |
Fmn 7 c |
| Sample type |
SRA |
| |
|
| Source name |
fully grown competent oocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: Fmn2 +/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Oocytes were freshly collected as described in Verlhac et al, Development 120, 1017-1025 (1994). Total RNA was extracted from oocytes using the RNAqueous®-Micro Total RNA Isolation Kit (Thermofisher, Ref. AM1931). Oocytes were washed 3 times in PBS, resuspended in lysis buffer, freezed in liquid nitrogen and conserved at -80°C overnight. After unfreezing, RNA extraction was carried out following the manufacturer’s instructions.
Library preparation and Illumina sequencing were performed at the Ecole normale superieure Genomic Platform (Paris, France). 1 ng of total RNA were amplified and converted to cDNA using NuGEN’s Ovation RNA-Seq kit V2. Following amplification, 1 µg of cDNA was fragmented to ∼200 bps using Covaris S200.
The remainder of the library preparation was done using 200 ng of cDNA following TruSeq RNA Sample Prep v2 kit from the End Repair step.
Three runs were performed following the same design: libraries were multiplexed by 4 on 1 flow cell lane. A 50 bp read sequencing was performed on a HiSeq 1500 device (Illumina). A mean of 17,3 ± 3,9 million passing Illumina quality filter reads was obtained for each of the 4 samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina bcl2fastq 1.8.4 software used for basecalling.
Raw reads passing Illumina quality filters were cleaned of adapters, and mapped with STAR.
For each sample, between 4 and 15 millions reads were mapped at a unique location on the Mus musculus genome (mm10 GRCm38, with Ensembl83 annotation).
Read counts per gene were also generated by STAR, and the DESeq2 package was used for differential expression analysis.
Differentially expressed genes with an adjusted p-value threshold of 0.05 were selected for further analysis.
Genome_build: mm10 GRCm38, with Ensembl83 annotation
Supplementary_files_format_and_content: STAR raw read count files
|
| |
|
| Submission date |
Sep 11, 2017 |
| Last update date |
Sep 12, 2019 |
| Contact name |
Stephane Le Crom |
| Organization name |
IBENS
|
| Department |
Genomic Core Facility
|
| Street address |
46 rue Ulm
|
| City |
PARIS |
| ZIP/Postal code |
75230 |
| Country |
France |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE103718 |
Active fluctuations of the nuclear envelope shape the transcriptional dynamics in oocytes |
|
| Relations |
| BioSample |
SAMN07629892 |
| SRA |
SRX3177144 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2779643_fmn7c.ReadsPerGene.out.tab.gz |
187.8 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
