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Sample GSM4147213 Query DataSets for GSM4147213
Status Public on Feb 14, 2022
Title KDR+CXCR4+ replicate #1
Sample type SRA
 
Source name mesoderm
Organism Homo sapiens
Characteristics cell type: ES-derived mesoderm
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 KDR+CXCR4+ and KDR+CXCR4- cells were sorted using an BD Aria II. RNA was isolated with the miRNeasy Mini kit (Qiagen).
Libraries were prepared using the Clontech SMARTer kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description counts.txt
FPKM.txt
Data processing Basecalling with Illumina RTA 1.9.
Demultiplexing with custom demultipler written in python.
Fastq files were aligned to using STAR (version 2.7.1a).
Gene counts were obtained using Subread (version 1.6.5).
Expression values were filtered to only include protein coding genes using Ensembl BioMart.
FPKM calculation was performed using DESeq2 (version 1.24.0).
Genome_build: GENCODE GRCh38 version 23
Supplementary_files_format_and_content: Gene counts in tab-delimited text format.
 
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 GPL11154
Series (2)
GSE139838 Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells [CXCR4]
GSE139853 Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells
Relations
BioSample SAMN13181008
SRA SRX7087246

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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