|
| Status |
Public on Jun 16, 2015 |
| Title |
rRNA-mRNA-depleted-1 |
| Sample type |
SRA |
| |
|
| Source name |
human HEK293T cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human HEK293T cell
passage: diluted from HEK293T cell total RNA
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rRNA-mRNA-depleted 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 RPKM of each gene in Refseq.
|
| |
|
| Submission date |
Jun 02, 2015 |
| 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 |
GPL16791 |
| Series (1) |
| GSE53386 |
Single-cell RNA-Seq transcriptome analysis of circular RNAs in mouse embryos |
|
| Relations |
| BioSample |
SAMN03757450 |
| SRA |
SRX1046505 |
