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Sample GSM4911595 Query DataSets for GSM4911595
Status Public on Dec 31, 2022
Title H9_WT
Sample type SRA
 
Source name Embryonic stem cells
Organism Homo sapiens
Characteristics cell line: H9-WT
cell type: embryonic stem cells
Treatment protocol iCas9 or idCas9 hESC lines were generated by transfecting with PB-TRE-CAS9-PGK-puro-T2A-rtTA (50 ng) or PB-TRE-dCAS9-PGK-puro-T2A-rtTA plasmids (50 ng) plus transposase mPB.Cas9 (dCas9) was inducible by doxycycline (Dox) in these cells.
Growth protocol hESCs were cultured in matrigel-coated plates in the Essential 8TM hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. hESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from hESCs using the Trizol kit (Thermo Fisher Scientific, catalog. no. 15596018) following the manufacturer’s instructions. PolyA(+) RNA was isolated for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC. whose results were parsed using MultiQC. Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore.
Trimmed read pairs were aligned to genome with STAR.
We computed the number of mapping reads unambiguously attributed to each gene and repeat locus using the featureCounts package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Nov 17, 2020
Last update date Dec 31, 2022
Contact name Denghui Chen
E-mail(s) chendh39@mail.sysu.edu.cn
Organization name Sun Yat-sen University
Department Zhongshan School of Medicine
Street address No. 74 Zhongshan 2nd Road
City Guangzhou City
ZIP/Postal code 510080
Country China
 
Platform ID GPL20795
Series (2)
GSE161634 Cas9 interactions with host RNAs and transposable elements impair neurodevelopment (RNA-seq)
GSE161635 Cas9 interactions with host RNAs and transposable elements impair neurodevelopment
Relations
BioSample SAMN16817760
SRA SRX9521159

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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