|
| Status |
Public on Jan 01, 2013 |
| Title |
LK2(GS/GS)-iPSC |
| Sample type |
SRA |
| |
|
| Source name |
iPSCs bearing homozygous LRRK2(G2019S) mutation
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSCs
ChIP: H3K4me3
|
| Treatment protocol |
iPSCs were obtained by reprogramming of patient fibroblasts, and NSCs were differentiated from iPSCs
|
| Growth protocol |
iPSCs were cultured in mTeSR medium, and NSCs were maintained in NSMM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline. Reads were mapped to human hg18 with Bowtie. Unique monoclonal reads were selected and reported as bed files. Read densities across the genome were obtained using BEDtools and bigWig were created for genome browser display.
|
| |
|
| Submission date |
Nov 30, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulrich Wagner |
| Organization name |
Uiversity Hospital Zurich
|
| Street address |
Schmelzbergstrasse 12
|
| City |
Zurich |
| ZIP/Postal code |
8091 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE34061 |
Progressive degeneration of human neural stem cells caused by pathogenic LRRK2 |
|
| Relations |
| SRA |
SRX110016 |
| BioSample |
SAMN00761078 |
