|
| Status |
Public on Jul 29, 2013 |
| Title |
human oocyte 3 |
| Sample type |
SRA |
| |
|
| Source name |
oocyte
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: oocyte
ethnicity: Han Chinese
supplementary file: Human_expression_mat.txt
|
| Treatment protocol |
Single cells were washed twice with 1x PBS containing 0.1% BSA before placing in lysis buffer.
|
| Growth protocol |
Single blastomeres were isolated by removing the zona pellucida using acidic tyrode solution (Sigma, cat. no. T1788), then separated by gentle mouth pipetting in a calcium-free medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from single cells or single morula embryos and amplified as previously described (Tang et al., 2010, Nat Protoc)
Library construction was performed following Illumina manufacturer suggestions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads from the Illumina HiSeq2000 were mapped to the hg19 genome using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression in all stages (average RPKM<0.5) were filtered out, followed by quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: human_expression_mat.txt: matrix listing normalized RPKM
|
| |
|
| Submission date |
Jun 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Huang |
| Phone |
310-267-0438
|
| Organization name |
UCLA
|
| Department |
Human Genetics
|
| Lab |
Guoping Fan
|
| Street address |
Gonda BLDG Rm. 6554, P.O.Box 957088
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44183 |
Genetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-Sequencing |
|
| Relations |
| BioSample |
SAMN02195142 |
| SRA |
SRX300874 |
