|
| Status |
Public on Aug 10, 2013 |
| Title |
Zygote #2 |
| Sample type |
SRA |
| |
|
| Source name |
cDNAs of individual cells of preimplantation embryos
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human preimplantation blastomere (zygote)
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 manufacturer suggestion protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8". [1]. 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_C2.expression.txt: hg19
|
| |
|
| Submission date |
Mar 16, 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 |
SRX130001 |
| BioSample |
SAMN00828834 |
