|
| Status |
Public on Jan 01, 2021 |
| Title |
KOArrest.1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryos
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Dcaf11 knock out
tissue: Embryo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs in embryos lysis with a polyadenylated tail were captured, reverse transcripted and preamplified following the protocol for Smart-seq2 sequence library generation
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq raw reads were processed by BBDuk(version 38.34) to removed adapters and trim low-quality reads. Reads( >35bp) were aligned to the mouse genome (mm9) using STAR(version 0.6.0).
Refseq genes were quantified to FPKM using Stringtie.
Deseq2 was used to perform differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 14, 2019 |
| Last update date |
Jan 02, 2021 |
| Contact name |
Yixin Huang |
| E-mail(s) |
[email protected]
|
| Organization name |
Tongji University
|
| Street address |
Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE132745 |
Single cell RNA-seq Analysis of Wild Type(WT), Dcaf11 knockout(KO) and Dcaf11 knockdown(KD) embryos |
| GSE132746 |
Dcaf11 facilitates telomere elongation in early embryos and embryonic stem cells (ESCs) through activating the Zscan4-mediated alternative lengthening telomere (ALT) mechanism |
|
| Relations |
| BioSample |
SAMN12058428 |
| SRA |
SRX6071680 |
