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Series GSE255980 Query DataSets for GSE255980
Status Public on Feb 20, 2024
Title Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi
Organisms Macaca fascicularis; Gorilla gorilla; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution and single-cell RNA-seq CRISPR interference screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct in the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPR interference screen. Hence, we provide valuable resources for performing and further extending CRISPRi screens in human and non-human primates.
 
Overall design Three human, three gorilla, and two cynolmolgus inducible KRAB-dCas9 iPS cell lines with an integrated SOX2-targeting gRNA were culture in +dox or -dox conditions for 4 days to compare between SOX2-knockdown (+dox) and normal condition (-dox).
Web link https://www.cell.com/iscience/fulltext/S2589-0042(24)01315-4
 
Contributor(s) Edenhofer FC, Térmeg A, Ohnuki M, Jocher J, Briem E, Kliesmete Z, Hellmann I, Enard W
Citation(s) 38947524
Submission date Feb 16, 2024
Last update date Jul 24, 2024
Contact name Wolfgang Enard
E-mail(s) enard@bio.lmu.de
Organization name Ludwig-Maximilians-Universität München
Street address Großhadernerstr. 2
City Planegg
ZIP/Postal code 82152
Country Germany
 
Platforms (3)
GPL30882 NextSeq 1000 (Homo sapiens)
GPL34203 NextSeq 1000 (Gorilla gorilla)
GPL34204 NextSeq 1000 (Macaca fascicularis)
Samples (68)
GSM8083692 SOX2 knockdown bulk RNA-seq H.i1_clone1 +Dox biol_rep1
GSM8083693 SOX2 knockdown bulk RNA-seq H.i1_clone1 +Dox biol_rep2
GSM8083694 SOX2 knockdown bulk RNA-seq H.i1_clone1 +Dox biol_rep3
Relations
BioProject PRJNA1077348

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE255980_Sox2_gorilla.dgecounts.rds.gz 14.3 Mb (ftp)(http) RDS
GSE255980_Sox2_human.dgecounts.rds.gz 19.1 Mb (ftp)(http) RDS
GSE255980_Sox2_macaque.dgecounts.rds.gz 9.5 Mb (ftp)(http) RDS
GSE255980_sample_annotation_data_submission.xlsx 11.6 Kb (ftp)(http) XLSX
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Raw data are available in SRA

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