|
| Status |
Public on Aug 05, 2016 |
| Title |
rhh074_Input1_N701_N501_HEKnp_FAIRE_BG4DIPseq_09112014 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NHEK
treatment: NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See methods section in the associated manuscript
See methods section in the associated manuscript
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
rhh_hek_09112014_FAIRE
processed data file: rhh_hek_09112014_FAIRE.narrowPeak.gz
|
| Data processing |
bcl files were converted to fastq using bcl2fastq v2.15.0.4 with default options.
See https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/. The text format files are differential binding and differential expression tables with columns: logFC: the log-abundance ratio, i.e. fold change, for each tag in the two groups being compared, logCPM: the log-average concentration/abundance for each tag in the two groups being compared, PValue exact p-value for differential expression using the NB model, FDR the p-value adjusted for multiple testing
|
| |
|
| Submission date |
Jan 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dario Beraldi |
| E-mail(s) |
dario.beraldi@cruk.cam.ac.uk
|
| Organization name |
Cambridge Research Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE76688 |
G-quadruplex structures mark human regulatory chromatin |
|
| Relations |
| BioSample |
SAMN04393169 |
| SRA |
SRX1525737 |
