|
| Status |
Public on Nov 01, 2018 |
| Title |
RNAseq-iPSC-KCNQ2-1 |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cells (iPSCs)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: induced pluripotent stem cells (iPSCs)
genotype/variation: KCNQ2
passages: P30-40
days of differentiation: n/a
|
| Growth protocol |
All iPSC lines were maintained on matrigel coating, with complete media change every day in mTeSR (StemCellTechnologies). Neurons were generated by 7-day overexpression of NEUROG2 followed by 21-day maturation in Neurobasal media (Gibco), 1x B27 (Gibco), 1x glutamax (Gibco), 1x pen/strep (Gibco), laminin (10 μg/ml, Sigma), BDNF (10 ng/μl, Peprotech) and GDNF (10 ng/μl, Peprotech)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared using NEBNext Ultra RNA Library Preparation kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
251106
|
| Data processing |
Data quality was assessed using FastQC v.0.11.2
Trimmed reads were screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.4.3
RSeQC package v.2.3.7 was used to assess read distribution, positional read duplication and confirm strandedness of alignments
Raw trimmed reads were aligned to the reference genome hg19 using Tophat v.2.0.11
Tophat alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Raw gene counts were loaded and sample-normalized using DESeq v.1.18.0
Two-condition differential expression was done with the edgeR R package, v.3.8.6
The method used for normalizing the data was TMM, implemented by the calcNormFactors(y) function
The test for differential expression was done using the quasi-likelihood F-test functionality in edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample
|
| |
|
| Submission date |
Dec 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen W Scherer |
| E-mail(s) |
[email protected]
|
| Organization name |
The Hospital for Sick Children
|
| Department |
Genetics and Genomic Biology
|
| Street address |
686 Bay Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE107878 |
Disruption of Autism Spectrum Disorder-Susceptibility Genes Predominantly Reduces Functional Connectivity of Isogenic Human Neurons |
|
| Relations |
| BioSample |
SAMN08164313 |
| SRA |
SRX3463942 |
