|
| Status |
Public on Feb 07, 2019 |
| Title |
S125.G11 |
| Sample type |
SRA |
| |
|
| Source name |
Primary
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Primary
donorid: M.Sample1
age (weeks): 9.29
captureplate: 1771043089
capturechamber: 1771043089-G11
|
| Growth protocol |
Cerebral organoids using Kadoshima et al., 2013 from Sasai lab
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fluidigm C1 small IFC (100-5759; 100-6201); SMARTer® Ultra™ Low RNA Kit (634832)
Nextera XT tagmentation kit (FC-131-096)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PrimaryOrganoidAndPublishedCPM.txt
|
| Data processing |
Trim Galore 3.7
HISAT2
subread-1.5.0 function featureCounts
Human GRCh38.79.gtf
The listed genes in the processed data file are human genes mapped to each respective species using the comparative annotation toolkit (PMID: 29884752). Reads are mapped to each species' native genome and quantified based transcript models from comparative annotation toolkit.
The file GSE124299-metadata on processed samples.xlsx includes the metadata for all samples in this study-- both the new samples listed in this Series and the re-analyzed samples, including accession IDs, when available.
Genome_build: Human: GRCh38.p2; NCBI:GCA_000001405.17
Genome_build: Chimpanzee: Clint_PTRv2 / UCSC: panTro6
Genome_build: Macaque: RheMac8
Supplementary_files_format_and_content: log(CPM+1)
|
| |
|
| Submission date |
Jan 18, 2019 |
| Last update date |
Feb 07, 2019 |
| Contact name |
Christopher Villarreal |
| Organization name |
444015
|
| Department |
Genomics Institute
|
| Lab |
Kent
|
| Street address |
1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL19129 |
| Series (1) |
| GSE124299 |
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution |
|
| Relations |
| BioSample |
SAMN10775526 |
| SRA |
SRX5265821 |
