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ChIPseq mapping of chromatin proteins Cren7 and Sso7D in the Sulfolobus solfataricus genome

ABSTRACT: ChIPseq mapping of chromatin proteins Cren7 and Sso7D in the Sulfolobus solfataricus genome

PROVIDER: PRJNA576889 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10258006.fastq.gz	Fastqsanger.gz
	SRR10258007.fastq.gz	Fastqsanger.gz
	SRR10258008.fastq.gz	Fastqsanger.gz
	SRR10258009.fastq.gz	Fastqsanger.gz
	SRR10258010.fastq.gz	Fastqsanger.gz

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ChIPseq mapping of chromatin proteins Cren7 and Sso7D in the Sulfolobus solfataricus genome

Project description:Purpose: To identify the genome binding sites of Cren7 and Sso7D, and to determine whether binding patterns differ between wild type and an epigenetically evolved strain in which they are heritably hypomethylated. Because methylated residues were solvent facing, it was predicted that binding patterns would not change between the strains. Methods: Chromosomal fragments 300-500bp long were immunoprecipitated in triplicate using polyclonal antibody serum for Cren7 or Sso7D and sequenced using Illumina Hiseq. Results: Cren7 and Sso7D had distinct binding patterns. ChIPseq peak patterns had slight variation between wild type and the evolved strain, but not at genes whose expression was thought to be epigentically dependent. Conclusions: As predicted, neither binding location or binding affinity correlated with epigenetic expression patterns in the evolved strain.

2019-10-11 | GSE138713 | GEO

Transcription profiling of hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius to UV irradiation

Project description:Analysis of transcriptional response to UV irradiation in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius.

2007-11-21 | E-MEXP-1252 | biostudies-arrayexpress

Sulfolobus solfataricus P2 growth curve, tiling arrays

2011-06-27 | GSE26779 | GEO

Sulfolobus solfataricus P2 growth curve, tiling arrays

Project description:Experimentally mapped transcriptome structure of Sulfolobus solfataricus P2 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 25 nt). Sulfolobus solfataricus P2 growth curve experiments were conducted in batch culture. Reference samples were cultured at mid-log phase (OD600 = 0.312). Eight samples were collected that spanned the key phases of the growth curve. Total RNA from samples of growth curve and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. Dye-flip experiments were done for each sample. Log ratios were calculated for each probe (growth curve sample/reference). Transcriptome browser is available at http://baliga.systemsbiology.net/enigma/.

2011-06-27 | E-GEOD-26779 | biostudies-arrayexpress

Transcriptome analysis of infection of the archaeon Sulfolobus solfataricus with STIV

Project description:Time series of infection of Sulfolobus solfataricus strain 2-2-12 cells infected with STIV are compared with uninfected cells over 32 h.

2008-07-25 | GSE12235 | GEO

Adaptation of Sulfolobus solfataricus P2 to fluctuating O2 concentrations

2009-06-01 | GSE16043 | GEO

Adaptation of Sulfolobus solfataricus P2 to fluctuating O2 concentrations

Project description:Sulfolobus solfataricus P2 was grown aerobically, with O2 concentrations ranging from 1.5 to 26 % (v/v; gas phase). To gain some insight in control of the respiratory system, transcriptomes of the strain cultivated in different O2 concentrations (1.5 % vs 21 %, 1.5 % vs 26 %) were compared using a DNA microarray approach. Two-condition experiments: 1.5% O2 vs two other O2 concentrations (21 or 26% O2). Biological replicates independently grown. One replicate per array. Dye swaps.

2010-05-18 | E-GEOD-16043 | biostudies-arrayexpress

Transcriptome analysis of infection of the archaeon Sulfolobus solfataricus with STIV

Project description:Time series of infection of Sulfolobus solfataricus strain 2-2-12 cells infected with STIV are compared with uninfected cells over 32 h. Two-condition experiment, Control vs. Infected cells sampled at 5 time points (0, 8, 16, 24, 32 h post infection). Biological replicates: 3 control, 3 infected, paired samples independently grown. One replicate per array. Dye swaps.

2008-07-25 | E-GEOD-12235 | biostudies-arrayexpress

Sulfolobus solfataricus P1 genome assembly

Project description:Hyperthermophilic Sulfolobus solfataricus P1, a model crenarchaeal organism.

| PRJEB13308 | ENA

HU treatment of Sulfolobus solfataricus P2

Project description:Hydroxyurea (HU) is toxic to Sulfolobus cells. To address the basis of the HU toxicity, we performed transcriptome analyses on untreated cells and cells following exposure to 5 mM HU for 4 hours.

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