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Sample GSM2748259 Query DataSets for GSM2748259
Status Public on Mar 09, 2018
Title DLL4- HE cells with 2ug/ml Dox treatment at Day5 of Differentiation
Sample type SRA
 
Source name inducible ETS1 H1 human embryonic stem cells (iETS1-hESCs)
Organism Homo sapiens
Characteristics cell type: inducible ETS1 H1 human embryonic stem cells (iETS1-hESCs)
Treatment protocol iETS1-hESCs were differentiated in defined conditions for 5 days with Day 2-5 of Dox treatment (No, 1, 1.5 and 2ug/ml) and DLL-/+ HE cells were sorted using a FACSAria cell sorter.
Growth protocol Single cells were plated at 10,000 cells/cm2 onto six-well plates coated with 0.5μg/cm2 of ColIV (Sigma-Aldrich) in E8 medium supplemented with 10 μM Rho kinase inhibitor (Tocris Y-27632). After 24 hr (day 0), the medium was changed to IF9S medium supplemented with 50ng/ml FGF2 (Miltenyi Biotech), 50ng/ml BMP4 (Peprotech), 15ng/ml Activin A (Peprotech) and 2 mM LiCl (Sigma). On day 2, the medium was changed to IF9S medium supplemented with 50ng/ml FGF2 and VEGF with or without Doxycycline (1, 1.5 and 2ug/ml). On day 4, the medium was changed to IF9S medium supplemented with 50ng/ml FGF2, VEGF, TPO, SCF and IL-6 and 10ng/ml IL3 with or without Doxycycline (1, 1.5 and 2ug/ml). On day5, DLL-/+ HE cells were sorted from differentiation cultures
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy Plus Micro Kit (Qiagen)
DNA libraries were prepped using the LM-Seq protocol described in Hou et al 2015 (PMID 25831155)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 1 --seed-length 25 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.
 
Submission date Aug 22, 2017
Last update date May 15, 2019
Contact name Oleg Moskvin
Organization name University of Wisconsin-Madison
Street address 1220 Capitol Court
City Madison
State/province WI
ZIP/Postal code 53715
Country USA
 
Platform ID GPL16791
Series (1)
GSE96815 Enhancement of Arterial Specification in Human Pluripotent Stem Cell Cultures Promotes Definitive Hematoendothelial Program with Broad Myelolymphoid Potential
Relations
BioSample SAMN07532252
SRA SRX3113428

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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