| Series | GSE65481 |
| Title | Human Embryo Single Cell Transcriptome Analysis |
|---|
| Year | 2015 |
|---|
| Country | USA |
|---|
| Article | Camarillo DB,Reijo Pera RA,Behr BB,Han J,Yanez LZ.Human oocyte developmental potential is predicted by mechanical properties within hours after fertilization.Nature communications.2016 Feb 24 |
|---|
| PMID | 26904963 |
|---|
| Bio Project | BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA274140 |
|---|
| Sra | SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP053004 |
|---|
| Overall Desgin | We sequenced the transcriptomes of 22 human zygotes (2PN stage) embryos, of which 11 were predicted nonviable and 11 were predicted viable. We excluded 5 which had no siblings in this data set. From the remaining 17 embryos, we analyzed the set of genes that was differentially expressed between those predicted viable and those predicted nonviable. |
|---|
| Summary | We sorted 2PN stage human embryos by predicted viability using a noninvasive measurement we previously developed. We then performed RNA-seq on each embryo (which was a single cell) and looked for differences in expression between viable and nonviable embryos. |
|---|
| Experimental Protocol | SMARTer® Ultra™ Low RNA kit (Clontech); NEBNext® DNA Sample Prep Master Mix Set (New England Biolabs)
|
|---|
| Data processing | Adapter clipping and trimming using fastq_quality_trimmer and fastx_clipper; Align reads to hg18 using STAR aligner; Convert files from sam to bam format and sort reads by name; Output read counts using HTSeq-count; Obtain adjusted expression values using edgeR and ComBat packages in R; Genome_build: hg18; Supplementary_files_format_and_content: Processed files contain read counts for each gene ([sample name]_paired_count.txt). There is also a file adjusted_expression_data.txt which contains all the data values used to generate figures along with adjusted_expression_qvals.txt which contains the q-values for all genes.
|
|---|
| Platform | GPL11154 |
|---|
| Public On | Public on Nov 30 2015 |
|---|
