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| Status |
Public on Aug 05, 2016 |
| Title |
Entinostat_2 |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HACAT
treatment: Entinostat
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| Extracted molecule |
total RNA |
| Extraction protocol |
See methods section in the associated manuscript
See methods section in the associated manuscript
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Entinostat_2
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| 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
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| Submission date |
Jan 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dario Beraldi |
| E-mail(s) |
dario.beraldi@cruk.cam.ac.uk
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| Organization name |
Cambridge Research Institute
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| Street address |
Robinson Way
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE76688 |
G-quadruplex structures mark human regulatory chromatin |
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| Relations |
| BioSample |
SAMN04393144 |
| SRA |
SRX1525712 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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