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Sample GSM7039811

Query DataSets for GSM7039811

Status

Public on Feb 28, 2024

Title

hop1loop2_Hop1_ChIP_Rep1

Sample type

SRA

Source name

Nucleus

Organism

Saccharomyces cerevisiae

Characteristics

tissue: Nucleus
cell line: SK1
cell type: Meiosis Hour 3
genotype: hop1-loop2

Growth protocol

Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606 which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

Extracted molecule

genomic DNA

Extraction protocol

For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles.
libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads or 100 bp single-end reads.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NextSeq 500

Description

MidOutput 2x150-300
11644-NHantiHop1-20220331-20220125-20221004-Reps-SK1Yue-PM-PE_B4_W3_MACS2_FE.bdg.gz

Data processing

Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

Submission date

Feb 12, 2023

Last update date

Feb 28, 2024

Contact name

Carolyn R Milano

E-mail(s)

crmilano@gmail.com, cm5497@nyu.edu

Organization name

New York University

Street address

15 Washington Place, Apartment 3M