|
Status |
Public on Feb 28, 2019 |
Title |
B2_12 |
Sample type |
SRA |
|
|
Source name |
Healthy control iPSCs-derived d12 neural progenitor cells
|
Organism |
Homo sapiens |
Characteristics |
genotype: WT cell type: Neural progenitor cells protocol: Neural 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.
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|
|
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
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|
|
Submission date |
Oct 17, 2018 |
Last update date |
Feb 28, 2019 |
Contact name |
Jose Ichisima |
E-mail(s) |
ichisima.jose@cira.kyoto-u.ac.jp
|
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 |
|
Relations |
BioSample |
SAMN10251201 |
SRA |
SRX4897967 |