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Sample GSM3569627 Query DataSets for GSM3569627
Status Public on Feb 07, 2019
Title S101.F7
Sample type SRA
 
Source name iPS-derived cerebral organoid
Organism Homo sapiens
Characteristics tissue: iPS-derived cerebral organoid
donorid: H3
cloneid: WTC
age (weeks): 10.7
datecaptured: 2016-01-07
Sex: Male
organoidid: H3.3
protocol: Kadoshima
captureplate: 1771049161
capturechamber: 1771049161.F7
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 GPL16791
Series (1)
GSE124299 Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Relations
BioSample SAMN10775410
SRA SRX5265346

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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