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Sample GSM2238614 Query DataSets for GSM2238614
Status Public on Apr 09, 2017
Title Control B (CSES7, Cas9 No guide)
Sample type SRA
Source name Human embryonic stem cells
Organism Homo sapiens
Characteristics group: Control
Extracted molecule total RNA
Extraction protocol RNA was isolated using NucleoSpin RNA Plus kit (Macherey-Nageland). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (200 ng–1 µg per sample, RIN > 9)
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description hESC_RB1.txt
Data processing Reads were mapped to the human reference genome (GRCh38/hg38) using Tophat (version 2.0.4)
Human embryonic stem cell expression values were obtained and normalized using HTSeq (Anders et al., 2015) and DESeq2 (Love et al., 2014). Batch-effect removal was performed using SVseq2.
In the teratoma-derived data, fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks (version 2.0.2)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: hESC data: Tab-delimited text file includes FPKM values for each sample; Teratoma data: Tab-delimited text file includes relative expression values for each sample
Submission date Jul 18, 2016
Last update date May 15, 2019
Contact name Yishai Avior
Phone +972-2-6584803
Organization name Hebrew University of Jeursalem
Department Genetics
Lab Nissim Benvenisty
Street address Edmond J. Safra Campus, Givat Ram
City Jerusalem
State/province Israel
ZIP/Postal code 91904
Country Israel
Platform ID GPL18573
Series (1)
GSE84504 Modeling Trilateral Retinoblastoma using Human Embryonic Stem Cells
BioSample SAMN05413960
SRA SRX1958691

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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