|
| Status |
Public on Nov 30, 2015 |
| Title |
S4 |
| Sample type |
SRA |
| |
|
| Source name |
Human zygote (2PN)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: embryo
developmental stage: 2PN zygote
predicted viability: bad
|
| Treatment protocol |
micropipette aspiration to measure mechanical parameters
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SMARTer® Ultra™ Low RNA kit (Clontech)
NEBNext® DNA Sample Prep Master Mix Set (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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.
|
| |
|
| Submission date |
Jan 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Livia Zarnescu Yanez |
| E-mail(s) |
livia.z.yanez@gmail.com
|
| Organization name |
Stanford University
|
| Department |
Bioengineering
|
| Lab |
Camarillo Lab
|
| Street address |
443 Via Ortega
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE65481 |
Human Embryo Single Cell Transcriptome Analysis |
|
| Relations |
| BioSample |
SAMN03322770 |
| SRA |
SRX861641 |
