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Sample GSM922149 Query DataSets for GSM922149
Status Public on Aug 10, 2013
Title 4-cell embryo#1 -Cell#4
Sample type SRA
 
Source name 4-cell embryo#1
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 19
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_C7.expression.txt: hg19
 
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 SRX144343
BioSample SAMN00989118

Supplementary file Size Download File type/resource
GSM922149_Sample_C7.bed.gz 218.5 Mb (ftp)(http) BED
GSM922149_Sample_C7.expression.txt.gz 207.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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