|
Status |
Public on Jan 01, 2021 |
Title |
KOArrest.2 |
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) |
1710944@tongji.edu.cn
|
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 |
SAMN12058427 |
SRA |
SRX6071681 |