|
| Status |
Public on Feb 12, 2016 |
| Title |
"default" NC, biological rep 2 of 3 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
differentiation day: day 12
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol and cleaned up using a Qiagen RNEasy column
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat v1.3.3 with these parameters: -p8 -r 180 --library-type fr-unstranded --no-coverage-search --no-novel-juncs
Analysis with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with DESeq output with fold change compared to CNS samples are provided.
|
| |
|
| Submission date |
Mar 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lorenz Studer |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Developmental Biology
|
| Street address |
430 E. 67th St. RRL 945
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE66148 |
RNA Sequencing of default, melanocyte biased and enteric human neural crest populations (NC) and neuroectoderm (CNS) |
|
| Relations |
| BioSample |
SAMN03430675 |
| SRA |
SRX958156 |
