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Sample GSM5537053 Query DataSets for GSM5537053
Status Public on May 16, 2022
Title H9_d4
Sample type SRA
 
Source name Differentiating embryonic stem cell line
Organism Homo sapiens
Characteristics Stage: treated with BMP4/IWP2 for 4 days (96h)
cell type: primed-TE
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.
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.
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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)
 
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
Organization name UCSD
Department Pathology
Lab Parast
Street address 2880 Torrey Pines Scenic Dr
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
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
Relations
BioSample SAMN20981546
SRA SRX11911263

Supplementary file Size Download File type/resource
GSM5537053_H9_d4_matrix.csv.gz 2.9 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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