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Status |
Public on Feb 20, 2024 |
Title |
SOX2 knockdown bulk RNA-seq G.i1_clone1 -Dox biol_rep1 |
Sample type |
SRA |
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Source name |
KRAB-dCas9 iPSCs
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Organism |
Gorilla gorilla |
Characteristics |
cell line: KRAB-dCas9 iPSCs cell type: iPSCs treatment: -Dox
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Growth protocol |
Cell were grown in SF03 +Dox (1 µg/mL) or -Dox for 4 days.
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 1000 |
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Description |
sample_annotation_data_submission.xlsx Sox2_gorilla.dgecounts.rds SOX2_KD_bulkRNA-seq_G.i1_clone1_5 BC: CGATTCCTTCAA
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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.
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Submission date |
Feb 16, 2024 |
Last update date |
Feb 20, 2024 |
Contact name |
Wolfgang Enard |
E-mail(s) |
enard@bio.lmu.de
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Organization name |
Ludwig-Maximilians-Universität München
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Street address |
Großhadernerstr. 2
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City |
Planegg |
ZIP/Postal code |
82152 |
Country |
Germany |
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Platform ID |
GPL34203 |
Series (1) |
GSE255980 |
Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi |
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Relations |
BioSample |
SAMN39968309 |
SRA |
SRX23645627 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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