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| Status |
Public on Aug 11, 2018 |
| Title |
Invivo_22 |
| Sample type |
SRA |
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| Source name |
Invivo 2-cell embryo
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| Organism |
Mus musculus |
| Characteristics |
strain: BDF1
sample group: in vivo fertilized embryos
developemental stage: Invivo 2-cell embryo
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| Extracted molecule |
total RNA |
| Extraction protocol |
The in vivo embryos were produced by superovulating C57BL/6 female mice and mating with DBA2 male mouse. The NTC embryos were manufactured by cumulus cell nuclear transfer and sequential embryos in an in vitro culture. The NTM embryos were manufactured by MEF cell nuclear transfer and sequential embryos in an in vitro culture. Each type of embryo was collected at 6 pronuclear stages, i.e., the 2-cell, 4-cell, 8-cell, morula and blastocyst stages. Each embryo was transferred to lysate buffer in a PCR tube and immediately stored in a -80℃ refrigerator. Embryos were collected from each stage in at least three independent experiments
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8 whole genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
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| Submission date |
Apr 16, 2018 |
| Last update date |
Aug 11, 2018 |
| Contact name |
Yong Liu |
| E-mail(s) |
liuyong@fync.edu.cn
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| Organization name |
Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province
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| Street address |
Qinghe West Road
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| City |
Fuyang |
| ZIP/Postal code |
236037 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE113164 |
Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing |
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| Relations |
| BioSample |
SAMN08935288 |
| SRA |
SRX3940263 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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