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| Status |
Public on Mar 09, 2018 |
| Title |
D4 HEP |
| Sample type |
SRA |
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| Source name |
differentiated WA01 human embryonic stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: differentiated WA01 human embryonic stem cells
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| Treatment protocol |
Where indicated, the D4 hemogenic endothelial progenitors were plated onto collagen IV- and IgG-Fc fragment-coated plates (IgG Control) and treated with either DAPT (NOTCH inhibition condition), DMSO (control condition), or were plated ontol collagen IV- and DLL1-Fc-coated plates and treated with DMSO (NOTCH activation condition). Where indicated, 24 hours later the CD144+ endothelial subsets were FACSorted for HE:DLL4-, HE:DLL4+, AHP, and nonAHPs and plated the HE:DLL4- and HE:DLL4+ were plated either onto OP9 (no NOTCH activation), or OP9-DLL4 (NOTCH activation).
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| Growth protocol |
WA01 human embryonic stem cells were differentiated into hematoendothelial lineages in serum- and feeder-free conditions, using a modified version of a protocl previously described (Uenishi et al, 2015). After 4 days of differentiation (D4), EMHlin-CD31+CD144+ hemogenic endothelial progenitors were magnetically purified and plated onto collagen-coated plates with either DAPT or DMSO (vehicle control), or plated onto collagen- and DLL1-coated plates with DMSO. Additional growth factors of EGF, IGF-I, and IGFII (all 50ng/ml) were added on top of the original cytokines to improve endothelial growth. Where indicated, the cells were collected 24 hours later and plated onto either OP9 or OP9-DLL4 in a-MEM with 10% FBS containing IL-6, TPO (50ng/ml), IL3 (10ng/ml), and SCF (20ng/ml).
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| Extracted molecule |
total RNA |
| Extraction protocol |
MicroRNeasy Plus RNA Extraction kit (Qiagen)
One hundred nanograms of total RNA was used to prepare sequencing libraries using the TruSeq RNA Sample Preparation kit (Illumina, San Diego, CA). Final cDNA libraries were quantitated with the Qubit Fluorometer (Life Technologies, Carlsbad, CA) and multiplexed with eighteen total indexed libraries per lane. Sequencing was performed using the HiSeq 3000 (Illumina, San Diego, CA) with a single read of 64 bp and index read of 7 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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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 1.3.0, with Bowtie 1.1.2 for alignment
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing "Expected Counts" (posterior mean estimate) and "Transcripts Per Million" expression estimates calculated by RSEM.
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| Submission date |
Sep 12, 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
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE95028 |
NOTCH Signaling Specifies a Transient Arterial-Type Hemogenic Endothelium that Gives Rise to Definitive-Type Hematopoiesis from Human Pluripotent Stem Cells |
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| Relations |
| BioSample |
SAMN07633886 |
| SRA |
SRX3178545 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2780327_Counts_add.txt.gz |
62.3 Kb |
(ftp)(http) |
TXT |
| GSM2780327_TPM_add.txt.gz |
88.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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