|
| Status |
Public on Sep 14, 2020 |
| Title |
input.expon.chip-seq.r1 |
| Sample type |
SRA |
| |
|
| Source name |
input.expon.chip-seq.r1
|
| Organism |
Saccharolobus solfataricus |
| Characteristics |
strain: P2
growth: exponential phase, 0.1% tryptone, 0.2% glucose
chip antibody: none (input)
|
| Treatment protocol |
Cells were crosslinked with 0.4% formaldehyde for 1 min before quenching by addition of 100 mM TRIS/Cl pH 8.0, cells were washed in PBS buffer 3x
|
| Growth protocol |
Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% glucose, 0.1% tryptone to mid-exponential growth phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in lysis buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100) and DNA was sheared by sonication. Lysates were cleared by centrifugation. Chromatin-immunoprecipitation was carried out with protein-A-purified polyclonal antibodies. Immunoprecipitated DNA was recovered by QIAquick PCR purification
NEBnext Ultra II DNA library preparation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
paired-end reads were trimmed to 50 bp and aligned with bowtie to the Saccharolobus solfataricus P2 genome using the following settings: -v 2 -m 1 --fr
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(www.github.com/fblombach)
Coverage was calculated using bamCoverage from the deeptools package
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width)
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with score representing either raw coverage after sampling ("Coverage") or coverage normalised to input after sampling ("normRatio")
|
| |
|
| Submission date |
Dec 02, 2019 |
| Last update date |
Sep 15, 2020 |
| Contact name |
Finn Werner |
| 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 |
GPL27815 |
| Series (2) |
| GSE141286 |
Pervasive promoter-proximal regulation in archaea: ChIP-seq exponential growth |
| GSE141290 |
Pervasive promoter-proximal regulation in archaea |
|
| Relations |
| BioSample |
SAMN13446985 |
| SRA |
SRX7255750 |
