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Sample GSM3433673 Query DataSets for GSM3433673
Status Public on Feb 28, 2019
Title S2-2_5
Sample type SRA
Source name Disease iPSCs-derived definitive endodermal cells
Organism Homo sapiens
Characteristics genotype: MT (Clone 2)
cell type: Definitive endodermal cells
protocol: Definitive endodermal cell differentiation protocol
Growth protocol iPSC clones were cultured on Laminin511-E8 fragment iMatrix-511-coated tissue culture plates with StemFit AK02N medium at 37 °C.
neural differentiation protocol: iPSCs were dissociated into single cells and quickly re-aggregated in DFK 5% medium (DMEM/F-12 Ham medium (SIGMA) containing KnockOut™ Serum Replacement (Thermo Fisher Scientific), NEAA (Gibco™), 2-mercaptoethanol (Nacalai), GlutaMAX (Gibco™), SB-431542, Dorsomorphin (Tocris), and Y-27632 (Tocris)) (9,000 cells/well) using a Nunclon Sphera Microplates 96U-Well Plate (Thermo Fisher Scientific).
definitive endodermal cell differentiation protocol: iPSCs were dissociated, resuspended with RPMI1640 (Sigma) medium containing 1× B27 supplement (Invitrogen), 100 ng/mL rhActivin A (R&D SYSTEMS), 1 μM CHIR99021 (Calbiochem), and 10 μM Y-27632 (Tocris) and seeded on culture dishes coated with Matrigel (Corning) at a density of 1 × 105 cells/cm2. On the next day, Y27632 was removed from the medium, and 0.5 mM NaB (Wako) was added in the culture medium.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using the RNeasy kit, and the quality was tested with a Bioanalyzer.
RNA-seq libraries were prepared by using a SureSelect Strand Specific RNA Library Preparation Kit (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 1500 (Illumina) in 100-base pair-end mode.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Bulk RNA-Seq data
Data processing All sequence reads were extracted in FASTQ format as described in "library construction protocol" section
base-calling: CASAVA ver 1.8.2    
raw read quality filtering: FASTX-Toolkit 0.0.13 
alignment: Tophat ver 2.1.0
normalization: Cufflinks ver 2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Submission date Oct 17, 2018
Last update date Feb 28, 2019
Contact name Jose Ichisima
Organization name Center for iPS cell research and application (CiRA), Kyoto University
Department Clinical Application Research
Street address 53, Shogoin-Kawahara cho, Sakyo
City Kyoto
State/province Kyoto
ZIP/Postal code 606-8507
Country Japan
Platform ID GPL18460
Series (1)
GSE121384 Verification and rectification of cell type-specific splicing of a Seckel syndrome-associated ATR mutation using iPS cell model
BioSample SAMN10251187
SRA SRX4897977

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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