NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4200371 Query DataSets for GSM4200371
Status Public on Sep 14, 2020
Title Spt45.expon.chip-seq.r1
Sample type SRA
 
Source name Spt45.expon.chip-seq.r1
Organism Saccharolobus solfataricus
Characteristics strain: P2
growth: exponential phase, 0.1% tryptone, 0.2% glucose
chip antibody: polyclonal antibodies against Spt4/5
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 SAMN13446982
SRA SRX7255738

Supplementary file Size Download File type/resource
GSM4200371_Spt45.expon_r1.Coverage.bw 10.5 Mb (ftp)(http) BW
GSM4200371_Spt45_expon_r1.normRatio.bw 19.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap