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Sample GSM7473136 Query DataSets for GSM7473136
Status Public on Apr 16, 2024
Title KK-4: RPMI-grown for 2 h; Replicate-2
Sample type SRA
 
Source name wild-type cells
Organism Nakaseomyces glabratus
Characteristics growth phase: 2 h grown
treatment: RPMI grown
genotype: wild-type
Growth protocol Cell samples were collected in two biological replicates.THP-1 monocytes were treated with phorbol 12-myristate 13-acetate (PMA; 16 nM) for 12 h for their differentiation into macrophages, followed by 12 h recovery in the fresh RPMI medium containing 10% FBS. PMA-activated THP-1 (2.2 x 107) cells were infected with YPD medium-grown C. glabrata wild-type at a MoI (multiplicity of infection) of 1.0. After 2 h and 10 h of infection, macrophage-internalized C. glabrata cells were collected, by lysing infected macrophages in ice-cold water. To separate C. glabrata cells from macrophage debris, macrophage lysates were gently vortexed, and centrifuged at 6000 rpm for 5 min at 4°C. The C. glabrata cell pellet was collected and suspended in ice-cold water. As a control, overnight YPD medium-grown C. glabrata cells were grown in 10% FBS-containing RPMI medium for 2 h and 10 h, and cell pellets were collected.
Extracted molecule genomic DNA
Extraction protocol Cell pellets were dissolved in MNase-digestion buffer [10 mM Tris-Cl (pH 8.0) and 1 mM CaCl2], and lysed using glass beads. Cell lysates (1 mg) were incubated with MNase (10 units/1 mg lysate) at 37°C for 60 min. The digestion was stopped by adding the Stop Buffer (8.6% SDS and 0.007 M EDTA), followed by proteinase K (20 mg/ml) digestion in two steps, first incubation at room temperature for 30 min, and later at 65°C for overnight. DNA was isolated with PCI (Phenol:Chloroform:Isoamyl alcohol) extraction, precipitated with sodium acetate and ethanol, and was suspended in nuclease-free water, followed by RNase A digestion for 30 min at 37°C. DNA was run on 2% agarose gel, and bands of ~ 150 bp, corresponding to mononucleosomal DNA fragments, were excised, and purified using the QIAquick extraction kit.
The prepared libraries were sequenced (2x100 bp paired-end sequencing) on the HiSeq 2500 (Illumina) platform.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2500
 
Description RPMI-grown for 2 h; Replicate-2
Data processing Processed sequence reads were aligned to the C. glabrata genome version s04-m01-r06 (www.candidagenome.org) using bowtie2, version 2.5.0.
Nucleosome position and dynamics were analysed using the DANPOS3 software.
Dynamic nucleosomes were identified using the following criteria: Position shift: ≥ 50 bp shift; Occupancy change: ≥ 2-fold change (FDR ≤ 0.05); or Fuzziness change: ≥ 1.5-fold change (FDR ≤ 0.05).
Assembly: Candida glabrata CBS138 genome version s04-m01-r06
Supplementary files format and content: text files; File contain: chr, start, end, smt_pos, smt_value, fuzziness_score, txStart, txEnd, CAGL ID, strand and distance
 
Submission date Jun 12, 2023
Last update date Apr 16, 2024
Contact name Rupinder Kaur
Organization name Centre for DNA Fingerprinting and Diagnostics
Lab Laboratory of Fungal Pathogenesis
Street address Inner ring road, Uppal
City Hyderabad
State/province Telangana
ZIP/Postal code 500039
Country India
 
Platform ID GPL33483
Series (2)
GSE234671 MNase-Seq analysis of wild-type Candida glabrata strain in RPMI-growth and macrophage-internalized conditions at 2 h and 10 h post-infection.
GSE234809 SWI/SNF complex-mediated chromatin remodelling in Candida glabrata is vital for immune evasion
Relations
BioSample SAMN35714009
SRA SRX20657812

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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