TitleHuman cerebral organoids recapitulate gene expression programs of fetal neocortex development.
Data descriptionscRNA-seq of 774 cells of fetal neocortex development
Doi10.1073/pnas.1520760112
Web-link of the paperhttp://www.pnas.org/content/112/51/15672.short
Data typescRNA-seq
DatabaseGEO
Accession numberGSE75140
URL of the datahttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75140
SpeciesHuman
TissueHuman cerebral organoids and fetal neocortex
Cell typeFetal neocortex
organoids
cortical regions
Number of cells#226
#333
#175
Cell capture platformFluidigm C1
Library preparation protocolSMARTer
Unique molecular identifier (Y/N)N
Spike-in (Y/N)Y
Full-length (Y/N)N
Brief summary of the scientific questionOrganoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue to organize into cerebral cortex-like regions.
Comparison of in vivo and in vitro cortical single-cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures.
Brief summary of the bioinformatics processingRaw reads were processed using a custom script and aligned to a Bowtie2 indexed human genome (grch38 sourced from ENSEMBL) using TopHat \with default settings. Transcript levels were quantified as fragments per kilobase of mapped reads (FPKM) generated by Cufflinks using gencode protein coding genes (grch38 v22 Havana).
CitationCamp, J. G., Badsha, F., Florio, M., Kanton, S., Gerber, T., Wilsch-Bräuninger, M., . . . Treutlein, B. (2015). Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proceedings of the National Academy of Sciences of the United States of America, 112(51), 15672.
Web-link of the paperhttp://www.pnas.org/content/112/51/15672.short