|
| Status |
Public on Mar 24, 2023 |
| Title |
S.islandicus.REY15A.cbp1.ChIP-seq.TFB1.replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
microbial cells
|
| Organism |
Sulfolobus islandicus REY15A |
| Characteristics |
genotype: cbp1, pyrEF, lacS
chip antibody: TFB1
cell type: microbial cells
|
| Growth protocol |
Strains were grown in Brock medium supplemented with 0.2% sucrose, 0.2% tryptone, and 20 µg/ml uracil at 75 °C in Erlenmeyer shake flasks at 150 rpm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen QIAquick PCR purification
NEBNext Ultra II DNA library prep kit for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired-end reads were mapped using Bowtie v1.1.2 [30] with parameters -v 2 -m 1 --fr over the first 50 nt allowing only for uniquely mapped read pairs to be included
We sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 120 bp, sd 18 bp) using a custom R script (https://github.com/fblombach/ChIP-seq/blob/master/read_sampling.R)
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width)
Assembly: NC_017276.1
Supplementary files format and content: bigwig files with occupancy normalised against the chromatin input samples, scaled by the Signal Extraction Scaling method
|
| |
|
| Submission date |
Feb 19, 2023 |
| Last update date |
Mar 24, 2023 |
| Contact name |
Finn Werner |
| E-mail(s) |
[email protected]
|
| Organization name |
University College London
|
| Department |
Institute of Structural and Molecular Biology
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23498 |
| Series (2) |
| GSE225598 |
ChIP-seq data for chromatin proteins Cbp1 and CreN7 |
| GSE226026 |
Cbp1-Cren7 chromatinization of CRISPR arrays favours transcription from CRISPR leaders over cryptic promoters. |
|
| Relations |
| BioSample |
SAMN33356244 |
| SRA |
SRX19417404 |
