|
Status |
Public on Jun 16, 2015 |
Title |
SUPeR-seq_zygote3 |
Sample type |
SRA |
|
|
Source name |
mouse zygote
|
Organism |
Mus musculus |
Characteristics |
cell type: zygote strain: CD-1 gender: female
|
Treatment protocol |
To validate the zygotic genes in mouse embryonic development, we treated the mouse zygotes with 0.1mg/ml a-Amanitine and then collected the 2-cell embryos to build libraries with SUPeR-seq
|
Growth protocol |
Mouse embryonic stem cells were maintained without feeders on gelatinlized dishes in the presence of 1,000U/ml leukemia inhibitory factor (LIF, Millipore) in Dulbecco's Modification of Eagle's Medium (DMEM/F-12, Gibco) containing 20% fetal calf serum (FCS, Gibco) for routine passage while the HKE293T cells were cultured in DMEM/High glucose. Metaphse II oocytes ,zygotes and 2-cell embryos (after mating with CD-1 male mice) were recovered from the oviduct ampulla of super-ovulated mice of CD-1 strain.
|
Extracted molecule |
total RNA |
Extraction protocol |
Single cells were picked into the lysis buffer which contained Rnase inhibitor to prevent RNA degration Cells were picked into the lysis buffer to release all RNAs; then the released RNAs were reverse transcribed with SuperScript III(Invitrogen), then digested the unreacted primers with ExoSAP-IT(USB) and tailed the first strand cDNA with a poly(A) sequence with terminal deoxynucleotidyl transferase (TdT, Invitrogen) , then used poly(T) primers to synthesize the sencond strand cDNA.the cDNAs were then enriched by two rounds of PCR amplifications each with size-selection by 2% agarose gel recovery.then the library construction waa conducted following the illumina library preparing protocol. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
extracted from female mouse single cell RNA-seq
|
Data processing |
Illumina CASAVA version 1.8 were used to the basecalling. Reads were trimmed to remove the adapter sequences and low quality bases. RNA-seq reads were aligned to the mouse refference genome (mm10) using BWA software gene expression level was estimated using comstomized Perl scripts. Genome_build: mm10 and hg19 Supplementary_files_format_and_content: txt files reflect FPKM of each gene in Refseq.
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|
|
Submission date |
Sep 03, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Xiaoying Fan |
E-mail(s) |
sharryfan100@gmail.com
|
Organization name |
Peking University
|
Department |
College of Life Sciences
|
Lab |
Biodynamic Optical Imaging Center
|
Street address |
5 Yiheyuan Road
|
City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100871 |
Country |
China |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE53386 |
Single-cell RNA-Seq transcriptome analysis of circular RNAs in mouse embryos |
|
Relations |
BioSample |
SAMN03018597 |
SRA |
SRX694862 |