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Sample GSM6935310

Query DataSets for GSM6935310

Status

Public on Feb 24, 2023

Title

DMSO_Input_5_Rep2

Sample type

SRA

Source name

Saccharomyces cerevisiae cells

Organism

Saccharomyces cerevisiae

Characteristics

strain: KY4306
genotype: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX
chip antibody: none
spike in species: Schizosaccharomyces pombe
spike in type: DNA
spike in to sample ratio: 1:10

Treatment protocol

DMSO (same volume as IAA+DMSO to achive 500mM IAA) was added to the culture before incubation at 30 °C for 60 minutes proir to crosslinking and cell harvest.
For auxin-induced degradation experiments, indole-3-acetic acid (IAA; Sigma-Aldrich, I3750), dissolved in DMSO, was added to the culture at a final concentration of 500 mM and incubated at 30 °C for one hour. All chromatin was crosslinked with formaldehyde and prior to chromatin immunoprecipitation (ChIP).

Growth protocol

cells were grown to mid log phase in YPD
Cells were grown to log phase at 30 °C in YPD medium (48) supplemented with 400 µM tryptophan (W).

Extracted molecule

genomic DNA

Extraction protocol

ChIP was performed essentially as described previously (70,71). Briefly, 200 or 250 mL of cell cultures were grown to log phase (OD600 = 0.8 - 1.0). Cells were crosslinked for 20 min at room temperature by addition of formaldehyde to 1% (v/v). Lysates were prepared in FA lysis buffer (72). Chromatin was sheared in Bioruptor® Pico 15 mL tubes with 300 µL beads (Diagenode C30010017) by 25 cycles of 30 sec on and 30 sec off using a Bioruptor® (Diagenode B01060010). Sonicated chromatin was brought up to a volume of 6 mL in FA lysis buffer and centrifuged at 50,000 rpm for 20 min at 4˚C. Chromatin in the supernatant was aliquoted, flash-frozen, and stored at -80˚C.
S. cerevisiae chromatin was mixed with Schizosaccharomyces pombe chromatin (KP07 or KP08) at a 1:10 ratio (S. pombe : S. cerevisiae) based on protein concentration (Pierce BCA protein assay kit; Thermo Fisher Scientific 23227), and IP reactions were conducted with anti-V5 (Invitrogen R960-25, 1 µL/225 µg or 10 µL/1800 µg), anti-Rpb1-CTD (8WG16; BioLegend 664906, 1 µL/225 µg or 8 µL/1800 µg), anti-HSV (Sigma-Aldrich H6030, 1.75 µL/450 µg or 7 µL/1800 µg), anti-HA (Santa Cruz sc-7392 AC, 15 µL/225 µg), anti-Spt5 (gift from Grant Hartzog, 4 µL/1800 µg), anti-H2BK123ub (Cell Signaling 5546, 5 µL/1000 µg), anti-total H3 (Abcam ab1791, 2 µL/1000 µg), anti-H3K4me2 (Millipore 07-030, 5 µL/1000 µg), anti-H3K4me3 (Active motif 39159, 5 µL/1000 µg), or anti-Myc (gift from John Woolford, used as a non-specific IgG control, 5 µL/1000 µg) primary antibodies. While S. pombe chromatin was included for the ChIP assays in Fig. S4, it was not used for normalization of the S. cerevisiae data as it increased variance in the qPCR measurements. IP reactions were incubated overnight at 4˚C on an end-over-end roller. Protein A or G beads (Cytiva 17-5280-01 or 17-0618-01) were washed with FA lysis buffer with 275 mM NaCl and added to the chromatin-antibody mixture and placed on the roller for 1 hr at room temperature. Beads were washed and DNA recovered as previously described (71). DNA was purified using the QIAquick PCR Purification Kit (Qiagen, 28106).
ChIP-sequencing (ChIP-seq) libraries were prepared using a NEBNext Ultra II kit and indices (E7645, E7335, E7500, E7710, E7730). Libraries were quantified by Qubit and fragment length distribution was assessed by agarose gel electrophoresis. DNA sequencing was conducted by the University of Pittsburgh Health Sciences Sequencing Core at UPMC Children’s Hospital of Pittsburgh on an Illumina NextSeq2000.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

NextSeq 2000

Data processing

ChIP-seq reads were aligned to the S. pombe genome (Ensembl EF2) and then unaligned reads were aligned to the S. cerevisiae genome (Ensembl R64-1-1), using Bowtie2 (75) before SAM to BAM conversion, and PCR duplicate removal with the SAMtools suite (76). Spike-in normalization factors were calculated via a custom bash script using established methods (77). BAM to BigWig conversion was conducted while simultaneously applying the normalization factors (74). This was done by multiplying each base pair of the genome by the normalization factor using deepTools3 bamCoverage.
Assembly: S. cerevisiae genome (Ensembl R64-1-1)
Supplementary files format and content: bigwig files containing ChIP-seq occupancy data after spike-in normalization

Submission date

Jan 15, 2023

Last update date

Feb 24, 2023

Contact name

Mitchell A Ellison

E-mail(s)

[email protected], [email protected], [email protected], [email protected]

Phone

8024519507

Organization name

University of Pittsburgh