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Sample GSM2297864 Query DataSets for GSM2297864
Status Public on Nov 04, 2016
Title G1B_cOrg2PR55d
Sample type SRA
 
Source name iPSC PR818-5
Organism Pan troglodytes
Characteristics Stage: 55 days
tissue: Dissociated whole cerebral organoid
Treatment protocol Whole cerebral organoids and microdisseccted ventricles were dissociated in 2 ml of Accutase (StemPro) containing 2.0 U/µl Dnase I (Roche) for approximately 45 minutes. Dissociated cells were filtered through 30, and 20 μm diameter strainers to create a single cell suspension.
Extracted molecule total RNA
Extraction protocol Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file: data_chimpOrg_344cells_log2FPKM_annotated.txt
Data processing "freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38, panTro4
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.
 
Submission date Aug 29, 2016
Last update date May 15, 2019
Contact name Gray Camp
E-mail(s) graycamp@gmail.com
Organization name Max Planck Institute for Evolutionary Anthropology
Department Evolutionary Genetics
Street address Deutscher Pl. 6
City Leipzig
ZIP/Postal code 04103
Country Germany
 
Platform ID GPL19148
Series (1)
GSE86207 Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
Relations
Reanalyzed by GSE124299
BioSample SAMN05714950
SRA SRX2065596

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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