|
| Status |
Public on May 27, 2021 |
| Title |
Mix-2/4cell-Blasto |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
mixed blastomere stage: 2 and 4 cell
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell capture were performed according to the manufacturer’s instructions of Fluidigm C1. RNA from each sample was uniquely barcoded and libraries were constructed using the CELSeq2 protocol as described in Hashimshony et al (Genome Biology 2016).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Blasto_umi_counts.txt
|
| Data processing |
The reads were aligned to the reference genome GRCm38 with the software HISAT2 (ver. 2.2.6).
Per gene unique molecular identifier (UMI) counts were produced by HTSeq (ver.0.6.1) where a consensus read was counted for each group of duplicate reads sharing the same UMI tag.
The UMI counts were normalized as described and were input to DESeq2 (ver. 1.10.1) to determine differentially expressed genes.
Genome_build: GRCm38
|
| |
|
| Submission date |
Dec 17, 2020 |
| Last update date |
May 27, 2021 |
| Contact name |
Yu-ichi Tsukada |
| E-mail(s) |
ytsukada@ifrc.kyushu-u.ac.jp
|
| Organization name |
Kyushu University
|
| Department |
INAMORI Frontier Research Center Advanced Biological Information Research Division
|
| Street address |
744 Motooka, Fukuoka Nishi-ku
|
| City |
Fukuoka |
| ZIP/Postal code |
819-0395 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE163427 |
Totipotency of mouse zygotes extends to single blastomeres of 4-cell stage embryos |
|
| Relations |
| BioSample |
SAMN17105209 |
| SRA |
SRX9698561 |
