|
| Status |
Public on Oct 09, 2016 |
| Title |
ALS iPSCs patient M rep3 |
| Sample type |
SRA |
| |
|
| Source name |
human iPS cells - C9/ALS patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Induced Pluripotent Stem Cells (iPSCs)
genotype/variation: C9/ALS patient
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRI Reagent (Sigma). Depletion of rRNA was performed using the Ribominus kit (Invitrogen).
cDNA libraries were generated using the TruSeq RNA sample preparation kit and protocol (Illumina), and stranded, ligation-based libraries were sequenced as previously described (Engreitz et al., 2013) .
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ALS C9-iPSCs M10
|
| Data processing |
RNA-seq reads were aligned to the genome (hg19) using STAR.
Coverage of C9orf72 second exon (chr9:27566674-27567162) and first intron (chr9:27567163-27573426) were calculated using samtools depth tool.
Genome_build: hg19
Supplementary_files_format_and_content: Comparison of intron retention values in C9orf72 gene in ALS and normal cells. Coverage of C9orf72 second exon and first intron were calculated and normalized to the exon\intron lengths to get average coverage per base. The file includes average coverage valuse for each sample.
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sebastian Kadener |
| E-mail(s) |
[email protected]
|
| Organization name |
Brandeis University
|
| Street address |
415 South Street
|
| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
9190401 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE87273 |
C9/ALS Human Embryonic Stem Cells and C9/ALS Induced Pluripotent Stem Cells |
|
| Relations |
| BioSample |
SAMN05806431 |
| SRA |
SRX2186364 |
