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Status |
Public on Mar 09, 2018 |
Title |
DLL4- HE cells with 2ug/ml Dox treatment at Day5 of Differentiation |
Sample type |
SRA |
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Source name |
inducible ETS1 H1 human embryonic stem cells (iETS1-hESCs)
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Organism |
Homo sapiens |
Characteristics |
cell type: inducible ETS1 H1 human embryonic stem cells (iETS1-hESCs)
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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.
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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
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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.
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Submission date |
Aug 22, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Oleg Moskvin |
Organization name |
University of Wisconsin-Madison
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Street address |
1220 Capitol Court
|
City |
Madison |
State/province |
WI |
ZIP/Postal code |
53715 |
Country |
USA |
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Platform ID |
GPL16791 |
Series (1) |
GSE96815 |
Enhancement of Arterial Specification in Human Pluripotent Stem Cell Cultures Promotes Definitive Hematoendothelial Program with Broad Myelolymphoid Potential |
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Relations |
BioSample |
SAMN07532252 |
SRA |
SRX3113428 |