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Sample GSM4150567 Query DataSets for GSM4150567
Status Public on Feb 20, 2020
Title RNA-seq_G1E-ER4_dCas9-cBIO_sgAct_24hr_rep1
Sample type SRA
 
Source name Mouse G1E-ER4
Organism Mus musculus
Characteristics tissue: G1E-ER4 cells
Treatment protocol G1E-ER4 cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.
Growth protocol Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS). G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).
Extracted molecule total RNA
Extraction protocol For RNA-seq analysis using the illumina NextSeq500, 200ng of total RNA was processed for library generation using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RNA-seq_RPKM.txt
Data processing Sequencing reads were aligned to human genome assembly hg19 or mm10 by STAR.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Genome_build: hg19, mm10
Supplementary_files_format_and_content: text file of gene FPKM values
 
Submission date Nov 05, 2019
Last update date Feb 20, 2020
Contact name Jian Xu
E-mail(s) Jian.Xu@stjude.org
Phone 9015955208
Organization name St. Jude Children's Research Hospital
Department Pathology
Street address 262 Danny Thomas Place, MS 345
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL19057
Series (2)
GSE139116 RNA-seq transcriptonal profiling in human K562 cells and G1E-ER4 cells with or without dCas9 and sgRNAs
GSE139117 Analysis of CRE-mediated chromatin interactions by CAPTURE2.0
Relations
BioSample SAMN13207871
SRA SRX7101457

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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