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Status |
Public on Mar 24, 2023 |
Title |
S.islandicus.REY15A.E234.ChIP-seq.CreN7.replicate2 |
Sample type |
SRA |
|
|
Source name |
microbial cells
|
Organism |
Sulfolobus islandicus REY15A |
Characteristics |
genotype: E234 (pyrEF, lacS) chip antibody: CreN7 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
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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|
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
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Submission date |
Feb 19, 2023 |
Last update date |
Mar 24, 2023 |
Contact name |
Finn Werner |
E-mail(s) |
f.werner@ucl.ac.uk
|
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 |
GPL33142 |
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 |
SAMN33356250 |
SRA |
SRX19417398 |