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Status |
Public on May 16, 2022 |
Title |
H9_t24h |
Sample type |
SRA |
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Source name |
Differentiating embryonic stem cell line
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Organism |
Homo sapiens |
Characteristics |
Stage: treated with BMP4/IWP2 for 24h cell type: intermediate differentiating stage
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Treatment protocol |
For TE differentiation, H9 hESC were treated with 10 ng/mL BMP4 and 2µM IWP2 in minimal media containing DMEM/F12, 1x ITS, 64μg/ml L-ascorbic acid, 543μg/ml NaHCO3, and 2% BSA. Media was changed every day and conversion into TE-like cells was confirmed based on surface EGFR expression of over 90% by flow cytometry at day 4. For Conversion into TSC, TE cells at day 4 were detached with TrypLE Express, re-plated onto collagen IV-coated plates and grown in TSC media.
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Growth protocol |
Primed H9 hESC were cultured in StemFlex media on Geltrex-coated plates. Primed H9 hESC-derived TSC were cultured onto collagen IV-coated plates in TSC media containing: Advanced DMEM/F12, 1x N2, 1x B27, 1x Glutmax, 150μM 1-thioglycerol, 0.05% BSA, 1% Knockout serum replacement, 2µM CHIR99021, 0.5µM A83-01, 1µM SB431542, 5µM Y27632, 130µg/mL Valproic Acid sodium salt, 100ng/mL recombinant human FGF2, 50ng/mL recombinant human EGF, 50ng/mL recombinant human HGF, and 20ng/mL Noggin.
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Extracted molecule |
total RNA |
Extraction protocol |
Chromium Next GEM Single Cell 3' reagent kit v3.3 from 10X Genomics was used to extract RNA from single cells. Chromium Next GEM Single Cell 3' reagent kit v3.3 from 10X Genomics was used to rpepare the libraries from single cells
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Alignment and quantification with CellRanger v 6.0.1 count function with default parameters to human reference genome (GRCh38-2020-A) Genome_build: human reference genome (GRCh38-2020-A) Supplementary_files_format_and_content: Comma separated values text file containing the counts for all genes and all demultiplexed samples (one matrix per sample)
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Submission date |
Aug 25, 2021 |
Last update date |
May 17, 2022 |
Contact name |
Robert E Morey |
E-mail(s) |
robmoreyucsd@gmail.com, remorey@health.ucsd.edu
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Organization name |
UCSD
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Department |
Pathology
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Lab |
Parast
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Street address |
2880 Torrey Pines Scenic Dr
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
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Platform ID |
GPL24676 |
Series (2) |
GSE182790 |
Derivation of functional trophoblast stem cells from human primed pluripotent stem cells [scRNA-seq] |
GSE182791 |
Derivation of functional trophoblast stem cells from human primed pluripotent stem cells |
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Relations |
BioSample |
SAMN20981545 |
SRA |
SRX11911262 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5537052_H9_t24h_matrix.csv.gz |
15.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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