|
| Status |
Public on Nov 07, 2014 |
| Title |
IVF2C_2_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
2-cell IVF embryos
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 2-cell IVF embryos
cell/embryos number: 25 embryos
strain: C57BL/6J oocyte x CAST/EiJ sperm
|
| Growth protocol |
Cumulus cells were collected from adult BDF1 females through superovulation by injecting 7.5 IU of pregnant mare serum gonadotropin (PMSG; Harbor) and 7.5 IU of human chroinic gonadotropin (hCG; Millipore). Fifteen hours after the hCG injection, cumulus-oocyte complexes (COCs) were collected from the oviducts and briefly treated with Hepes-buffered potassium simplex-optimized medium (KSOM) medium containing 300 U/ml bovine testicular hyaluronidase (Calbiochem # 385931) to obtain dissociated cumulus cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The embryos were directly lysed and used for cDNA synthesis using SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech). After amplification, the cDNA samples were fragmented using Covaris sonicator (Covaris). Sequencing libraries were made with the fragmented DNA using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer’s instruction (New England Biolabs). Single end 50 bp sequencing was done on Hiseq 2500 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were mapped against the mouse genome (mm9) with Novoalign. All programs were performed with default setting (unless otherwise specified). The unique mapped reads (about 70% of total reads) were subsequently assembled into transcripts guided by reference annotation (UCSC gene models) with Cufflinks v2.0.2. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuting Liu |
| E-mail(s) |
ytliu1985@gmail.com
|
| Organization name |
Harvard Medical School
|
| Department |
Department of Genetics
|
| Lab |
Yi Zhang lab
|
| Street address |
82 Walnut St. Unit 3
|
| City |
Brookline |
| State/province |
MA |
| ZIP/Postal code |
02445 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE59073 |
Identification of epigenetic barrier that prevents reprogramming in somatic cell nuclear transfer |
|
| Relations |
| BioSample |
SAMN02902423 |
| SRA |
SRX645370 |
