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Sample GSM4147343 Query DataSets for GSM4147343
Status Public on Feb 14, 2022
Title IWP2
Sample type SRA
 
Source name mesoderm
Organism Homo sapiens
Characteristics cell type: ES-derived mesoderm
treatment: IWP2 + ACTIVIN A
Growth protocol The H1 hESC lines were maintained on irradiated mouse embryonic fibroblasts in hESC media. For differentiation, hPSC were cultured on matrigel-coated plasticware for 24 hours, followed by embryoid body generation. hPSCs were dissociated with brief trypsin-EDTA (0.05%) treatment, followed by scraping. Aggregates were resuspended in serum-free media (SFD) supplemented with L-glutamine (2 mM), ascorbic acid (1 mM), monothioglycerol (MTG, 4x10-4 M), transferrin (150 ug/mL), and BMP-4 (10 ng/mL). On day one, bFGF (5 ng/mL) was added. On day two, Activin A, SB-431542 (6 uM), CHIR99021 (3 uM), and/or IWP2 (3 uM) were added.
Extracted molecule total RNA
Extraction protocol Unsorted cells from CHIR+SB or IWP2 day 3 differentiation cultures were methanol-fixed as described in doi: 10.1186/s12915-017-0383-5.
Libraries were prepared following the manufacturer's instruction using the 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236), and Chromium i7 Multiplex Kit (PN-120262).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description allcells_matrix.txt
metadata.txt
Data processing Sequencing reads were processed using the Cell Ranger software pipeline (version 3.1.0) using default arguments.
Using Seurat (version 3.2.2) implemented in R (version 3.6.2), the dataset was filtered by removing genes expressed in fewer than 3 cells and cells where greater than 10% of the UMIs are mitochondrial genes.
Dataset was filtered to retain cells with unique gene counts between 200 and 6000.
Remaining UMI counts were log-normalized with a scale factor of 10,000 and variable features were calculated using the vst selection method.
Data were then scaled by regressing out mitochondrial gene percentage and UMI count.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: Gene counts in tab-delimited text
Supplementary_files_format_and_content: Metadata in tab-delimited text
 
Submission date Nov 01, 2019
Last update date Feb 14, 2022
Contact name Stephanie Luff
E-mail(s) stephanie.luff@mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Cell, Developmental, & Regenerative Biology
Lab Sturgeon
Street address 1425 Madison Ave
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL21290
Series (2)
GSE139850 Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells [scRNA-seq]
GSE139853 Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells
Relations
BioSample SAMN13181526
SRA SRX7087555

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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