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Sample GSM8083724 Query DataSets for GSM8083724
Status Public on Feb 20, 2024
Title SOX2 knockdown bulk RNA-seq G.i1_clone1 -Dox biol_rep1
Sample type SRA
 
Source name KRAB-dCas9 iPSCs
Organism Gorilla gorilla
Characteristics cell line: KRAB-dCas9 iPSCs
cell type: iPSCs
treatment: -Dox
Growth protocol Cell were grown in SF03 +Dox (1 µg/mL) or -Dox for 4 days.
Extracted molecule polyA RNA
Extraction protocol Cells that were cultured in 24-wells, were lysed in 200 µL Buffer RLT Plus supplemented with 1 % 2-Mercaptoethanol and then stored at -80 °C until processing.
Libraries were constructed following the published prime-seq protocol. (Janjic, A., Wange, L.E., Bagnoli, J.W. et al. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 23, 88 (2022). https://doi.org/10.1186/s13059-022-02660-8); https://www.protocols.io/view/prime-seqs9veh66
polyA-capture bulk RNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 1000
 
Description sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_5
BC: CGATTCCTTCAA
Data processing Fastq data file quality assessment was conducted using fastqc (Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
polyA trimming was performed with cutadapt (Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.).
Quality filtering, mapping and counting was done using the zUMIs pipeline (Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018). zUMIs—A fast and flexible pipeline to process RNA sequencing data with UMIs. GigaScience, 7(6), giy059).
Assembly: hg38, gorGor6, macFas6, all extended by the KRAB-dCas9 encoding sequence that was integrated in the genomes of the cell lines
Supplementary files format and content: We provide a separate count table per species as rds files
Supplementary files format and content: The sample conditions are noted in the additional sample_annotation_data_submission file.
 
Submission date Feb 16, 2024
Last update date Feb 20, 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
 
Platform ID GPL34203
Series (1)
GSE255980 Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi
Relations
BioSample SAMN39968309
SRA SRX23645627

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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