NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2220226 Query DataSets for GSM2220226
Status Public on Sep 10, 2016
Title Scr 1
Sample type SRA
 
Source name Control oocytes
Organism Mus musculus
Characteristics strain: (C57BL x CBA) F1
developmental stage: Metaphase II
Treatment protocol injections with siRNAs
Growth protocol Ovaries were dissected from two to five 10-12 day old (C57BL x CBA) F1 females. To obtain individual follicles, the ovaries were incubated in modified MEM-alpha medium optimized for in vitro culture of follicles (MEM-alpha (Gibco 12000-014) supplemented with 0.026M NaHCO3 (Sigma), 5678U/100 ml Penicillin G (Sigma) and 8265U/100ml Streptomycin (Sigma), 1x ITS (Insulin/Transferrin/Selenium Solution; Sigma; Stock is 100x), 5% FBS (Fetal Bovine Serum; Gibco 16000044) and 0.01 µg/ml FSH (Follicle Stimulating Hormone; National Hormone and Peptide Program, NDDK-oFSH-20) that was supplemented with 2 mg/ml collagenase (Roche) for about 30-40 minutes total. During incubation with collagenase, the ovaries were pipetted up and down every 10 minutes to facilitate dissociation and then washed through several droplets of follicle culture medium without collagenase and were cultured at 37°C in 5% CO2 on membrane inserts in 6 well or 12 well culture dishes filled with follicle culture medium (see above). After 8-10 days of culture the oocytes were isolated in M2 medium supplemented with 10% FBS and matured until reached metaphase of the second meiotic division (MII).
Extracted molecule total RNA
Extraction protocol NucleoSpin RNA XS (Macherey-Nagel)
A cDNA library was prepared using SMARTer® Ultra™Low Input RNA for Sequencing (Clonetech Laboratories) and the samples were processed by BGI Tech Solutions. The cDNA product was synthesized and amplified using SMARTer PCR cDNA Synthesis Kit (Clontech) from the total RNA (10 ng) of sample. The cDNA was fragment by Covaris E210 (Covaris) and the median insert length was about 200bp.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Illumina OLB(off-line Basecaller) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bwa with parameters GenomeBwaOptions_PE = -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
The mapped read counts for each gene were normalized for RNA length and for the total read number in each lane using the fragments per kilobase per million (FPKM) method.We used a strict algorithm to identify differentially expressed genes (DEGs) based on comparing the exposed with unexposed group to generate the DEGs.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample
 
Submission date Jun 29, 2016
Last update date May 15, 2019
Contact name Michał Pasternak
E-mail(s) mpasternak.student@gmail.com
Phone +447895431334
Organization name MRC Laboratory of Molecular Biology
Street address Francis Crick Avenue
City Cambridge
State/province - None -
ZIP/Postal code CB2 0QH
Country United Kingdom
 
Platform ID GPL21103
Series (1)
GSE83876 Transcriptome comparison of oocytes treated with RNAi against Btg4 or with control siRNAs
Relations
BioSample SAMN05326601
SRA SRX1885921

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap