|
| Status |
Public on Jan 02, 2024 |
| Title |
C9P5 Rex |
| Sample type |
SRA |
| |
|
| Source name |
iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: iPSCs
cell line: C9orf72 patient derived iPSC line
cell type: iPSC
genotype: C9orf72 repeat expansion carrier
treatment: None
|
| Treatment protocol |
None
|
| Growth protocol |
iPSC culture
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic tip
No-Amp (PacBio)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Sequel II |
| |
|
| Description |
Single molecule sequencing 5mC methylation around C9orf72 gene locus
|
| Data processing |
SMRT Link v13.0 generated HiFi reads with 5mC methylation tags using CCS (BAM)
pb-CpG-tools v2.3.2 generated combined methylation proportions using "--pileup-mode count" (BED and BW)
Assembly: hg38
Supplementary files format and content: BED containing combined methylation proportions
Supplementary files format and content: BW containing combined methylation proportions
Library strategy: single molecule sequencing of C9orf72
|
| |
|
| Submission date |
Dec 28, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Claire Clelland |
| E-mail(s) |
claire.clelland@ucsf.edu
|
| Organization name |
UCSF
|
| Street address |
1651 4th St
|
| City |
San Francisco |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL28352 |
| Series (1) |
| GSE252200 |
Reversal of C9orf72 mutation-induced transcriptional dysregulation and pathology in cultured human neurons by allele-specific excision |
|
| Relations |
| BioSample |
SAMN39182474 |
| SRA |
SRX23233153 |
