|
Status |
Public on Aug 10, 2013 |
Title |
Late blastocyst #2 -Cell#7 |
Sample type |
SRA |
|
|
Source name |
Late blastocyst #2
|
Organism |
Homo sapiens |
Characteristics |
cell type: human preimplantation blastomere developmental stage: early blastomere tissue: human preimplantation embryos
|
Growth protocol |
Donated human preplantation embryos were dissociated into individual blastmeres and were separately amplied to set up single cell cDNA libraries.
|
Extracted molecule |
total RNA |
Extraction protocol |
Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Sample 82 cDNAs of individual cells of preimplantation embryos
|
Data processing |
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60] Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842] Merge the *.bed files from samples in the same stage [available on Series records] Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records] Genome_build: hg19 Sample_H7.expression.txt: hg19
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|
|
Submission date |
Apr 25, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Mingyu Yang |
E-mail(s) |
yangmingyucherry@gmail.com
|
Organization name |
Peking University
|
Street address |
5 Yiheyuan Road
|
City |
Beijing |
ZIP/Postal code |
100871 |
Country |
China |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE36552 |
Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq |
|
Relations |
SRA |
SRX144406 |
BioSample |
SAMN00989181 |