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Sample GSM1579293 Query DataSets for GSM1579293
Status Public on Feb 15, 2015
Title FSB_culture3_RNAseq
Sample type SRA
 
Source name Neural crest-like progeny
Organism Homo sapiens
Characteristics cell type: ES-derived CD271+CD73+ neural crest-like progeny
passages: 6 to 7
treatment: Nodal/Activin/TGFb inhibitor and FGF2
cell line: H9
Treatment protocol The neural crest cells expanded under FSB for 4 passages were divided in half. Then one was continuously manintained in FSB, and the other was culrured under F for 3 more passages.
Growth protocol H9 hESCs were treated with collagenase to generate clumps, which were plated onto gelatin-coated dishes. The clumps were cultured for 6 days in Differentiation medium: CDM supplemented with 10 µM SB431542 at 37oC under 5% CO2/5% O2. The CDM (chemically defined medium) is Iscove modified Dulbecco’s Medium: Ham’s F12 (1:1), 5 mg/ml fatty acid-free bovine serum albumin, 2% (v/v) chemically defined lipid concentrate, 2 mM GlutaMax, 100 μg/ml holo-transferrin, 20 μg/ml insulin, 0.17 mM ascorbic acid-2-phosphate, and 0.4 mM monothioglycerol. On the day of harvest, a suspension of single cells was prepared by treatment of the culture with TrypLE Select diluted 2.5 fold with 0.5% (w/v) EDTA in PBS, and the CD271hiCD73- neural crest-like progeny were isolated by FACS, which were then plated onto fibronectin-coated dishes and cultured in CDM supplemented with FGF2 at 5-10 ng/ml and/or SB431542 at 3-5 µM (FSB or F) at 37oC under 5% CO2/5% O2. Generated cells were passaged every 3-4 days by the diluted TrypLE Select.
Extracted molecule total RNA
Extraction protocol AT passage 6-7, cultures were havested and RNAs were extracted using RNAeasy mini kit from Qiagen.
RNA-sequencing libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent technologies, Santa Clara, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Sequenced reads were mapped against the human reference genome (GRCh37), using TopHat v2.0.12
Expression levels were calculated as fragments per kilobase of exon per million mapped fragments (FPKMs) using Cufflinks v2.1.1
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM
 
Submission date Jan 07, 2015
Last update date May 15, 2019
Contact name Naoki Nakayama
E-mail(s) naoki.nakayama@uth.tmc.edu
Organization name the University of Texas Health Science Center at Houston
Department Institute of Molecular Medicine
Street address 7000 Fannin, Suite 1200
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL18460
Series (1)
GSE64752 Long-term expandable SOX9+ chondrogenic ectomesenchymal cells from human pluripotent stem cells
Relations
BioSample SAMN03277109
SRA SRX832785

Supplementary file Size Download File type/resource
GSM1579293_FSB3.cuff.txt.gz 829.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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