|
| Status |
Public on Jun 01, 2019 |
| Title |
D14 MODY1-1A |
| Sample type |
SRA |
| |
|
| Source name |
HiPSC-derived hepato-pancreatic progenitors
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: HNF4A p.Ile271fs
family identifier: iN904-1
gender: female
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested from cells using the PrepEase RNA Spin Kit (Affymetrix)
mRNA was first isolated with poly dT beads from 1-10µg of total RNA. RNA-seq libraries were prepared using the NEXTflex Rapid Directional RNA-SEQ Kit (dUTP-Based) v2 as per manufacturer's direction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.33, and then mapped to hg19 whole genome using tophat-2.0.14
Raw counts were calculated using HtSeq-count
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, raw htseq counts for each sample, edgeR output
|
| |
|
| Submission date |
Oct 30, 2017 |
| Last update date |
Jun 01, 2019 |
| Contact name |
Adrian Kee Keong Teo |
| E-mail(s) |
ateo@imcb.a-star.edu.sg
|
| Organization name |
IMCB, A*STAR
|
| Department |
Stem Cells and Diabetes Laboratory
|
| Street address |
61 Biopolis Drive, Proteos
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE106335 |
Loss-of-function due to MODY1/HNF4A mutation abrogates liver and pancreas differentiation from MODY1-hiPSCs |
|
| Relations |
| BioSample |
SAMN07947985 |
| SRA |
SRX3343317 |
