|
| Status |
Public on Feb 28, 2019 |
| Title |
cS2-1-6_12 |
| Sample type |
SRA |
| |
|
| Source name |
Corrected iPSCs-derived d12 neural progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: WT (Corrected)
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.
|
| |
|
| 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 |
| 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 |
SAMN10251184 |
| SRA |
SRX4897979 |
