|
| Status |
Public on Aug 24, 2017 |
| Title |
WT-1 DNase-seq |
| Sample type |
SRA |
| |
|
| Source name |
Myelinating Schwann Cell
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: Schwann cell line S16
genotype/variation: WT
passage: 6
|
| Growth protocol |
S16 cells were cultured using standard growth media supplemented with L-glutamine. The cells were cultured in a T-75 flask and passaged every 2-3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 20 million cells per sample were used to extract genomic DNA. Extraction and preparation were performed according to Song and Crawford, DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells, 2010.
Libraries were prepared for sequencing according to Song and Crawford, DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells, 2010.
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
barcode2
|
| Data processing |
Read Trimming: Adapter or linker DNA sequences were removed from each read, resulting 18~26nt left at the 5’ end of each read. The trimmed reads which are shorter than 18nt were discarded.
Read quality assessment by FastQC
Alignment: The raw reads were aligned uniquely to Rn5 assembly by Bowtie. Up to two mismatches were allowed.
Peak Calling: Peaks were called using F-seq with default parameters.
Peak annotation: Peaks annotated by Homer.
BigWig File Generation: Wig files generated from F-seq were convereted into BigWig files.
Genome_build: rn5
Supplementary_files_format_and_content: BigWig files of DNase HSS peaks.
|
| |
|
| Submission date |
May 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Anthony Antonellis |
| E-mail(s) |
antonell@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Human Genetics
|
| Street address |
1241 E Catherine St.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48104 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE81669 |
DNase Hypersensitivity Peaks from Rat Schwann Cells |
|
| Relations |
| BioSample |
SAMN05150134 |
| SRA |
SRX1776226 |
