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Sample GSM5597711 Query DataSets for GSM5597711
Status Public on Feb 11, 2022
Title EBdCas9-dox_2
Sample type SRA
 
Source name EBdCAS9-WTC-11
Organism Homo sapiens
Characteristics tissue: hiPSCS
treatment: no dox
Growth protocol cells were grown in mTeSR1 stem cell media
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol (Life Technologies) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing Reads were aligned using Hisat2(Kim et al., 2019) version 2.1.0, to version hg38 of the human genome with EBdCas9 sequence added.
Differentially expressed genes were identified with DESeq2
RNA-seq read counts were generated with featureCounts using Ensembl GRCH38 gene annotations
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited file of gene-level transcript per million (TPM) for each sample.
 
Submission date Sep 27, 2021
Last update date Feb 11, 2022
Contact name Hannele Ruohola-Baker
E-mail(s) hannele@u.washington.edu
Organization name Institute for Stem Cell and Regenerative Medicine
Street address 850 Republican Street
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL30173
Series (2)
GSE155022 dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [bulk RNA-seq]
GSE195555 dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region
Relations
BioSample SAMN21854786
SRA SRX12369240

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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