|
| Status |
Public on Dec 25, 2020 |
| Title |
T4OC.3 |
| Sample type |
SRA |
| |
|
| Source name |
oocyte in secondary follicle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: oocyte in secondary follicle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvested oocytes were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. cDNA were synthesized using primers with 24-nt poly(dT),then a universal tail was added to the second strand cDNAs. After 18-20 cyclesof PCR, the PCR product is purified by QIAquick PCR purification kit(28104).
The prepared cDNA are sheared using Covaris S220. Fragment ends are repaired using NEBNext End Repair Module(E6050), then a NEBNext dA-Tailing Module(E6053) was used to yield a protruding 3- 'A' base for ligation of Illumina's adapters.After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles. library fragments of 200-500bp were band isolated from an agarose gel.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.0.13 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.3.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
Dec 26, 2020 |
| Contact name |
Xiaolong Chen |
| E-mail(s) |
xiaolong.chen@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE111685 |
DNA methylation dynamics of oocyte in follicular maturation (RNA-Seq data set) |
| GSE111687 |
DNA methylation dynamics of oocyte in follicular maturation |
|
| Relations |
| BioSample |
SAMN08687003 |
| SRA |
SRX3781771 |
