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Sample GSM5627422 Query DataSets for GSM5627422
Status Public on May 23, 2022
Title Pcgf4-/-Pcgf2fl_Input_UNT_rep2
Sample type SRA
 
Source name Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control,Pcgf4-/-Pcgf2 fl/fl, Input
Organisms Homo sapiens; Mus musculus
Characteristics cell line: Pcgf4-/-Pcgf2 flfl
strain: Rosa26::ERT2-Cre
treatment: untreated
treatment time: 0h
additional treatment: none
additional treatment time: none
replicate: 2
spike-in reference organism: Homo sapiens
spike-in cell line: HEK293T
type of chip: cross-linked
ChIP: CDK8
antibody: rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories)
Treatment protocol Med13/13lfl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 96 hours. Pcgf4-/-/Pcgf2fl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 72 hours. For RA differentiation, ESCs were treated with 1µM retinoic acid (Sigma-Aldrich) for 48h.
Growth protocol Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. HEK293T celles were grown in EC-10 medium (DMEM supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.4 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).
Extracted molecule genomic DNA
Extraction protocol For cross-linked ChIP, 50x10^6 ES cells were fixed for 45min with with 2mM DSG (ThermoFisher scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, ThermoFisher scientific). Reactions were quenched by the addition of glycine to a final concentration of 125 µM and the fixed cells were washed in ice-cold 1xPBS and snap frozen in liquid nitrogen. 50x10^6 HEK293T cells were fixed as above, snap frozen in 2x106 aliquots, and stored at -80°C until further use. For calibrated ChIPseq, 2x10^6 HEK293T cells were resuspended in 1ml ice-cold lysis buffer (50mM HEPES pH 7.9, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and added to 50x10^6 fixed ESCs, resuspended in 9ml lysis buffer. The cell suspension was incubated for 10 min at 4°C. The released nuclei were then washed (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C. The chromatin pellet was resuspended in 1mL of ice-cold sonication buffer (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 25 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to produce fragments between 300bp and 1kb. Following sonication, Triton X-100 was added to a final concentration of 1%. Two hundred and fifty µg chromatin diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Three reactions were set up per condition to allow for maximal DNA recovery suitable for library preparation. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described in Farcas et al 2012. ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20 μg/ml Proteinase K and purified using ChIP DNA Clean and Concentrator kit (Zymo research). The three reactions per condition were pooled at this stage. For each sample, corresponding Input DNA was also reverse cross-linked and purified. The efficiency of the ChIP experiments was confirmed by quantitative PCR. Prior to library preparation, 5-10ng ChIP material was diluted to 50ul in TLE buffer (10mM Tris-HCl pH8.0, 0.1mM EDTA) and sonicated with Bioruptor Pico sonicator for 17 min (30 sec on/off). The antibodies used for ChIPseq experiments were rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories, 2.5μl), rabbit monoclonal anti-RING1B (5694, Cell signaling, 3 μl), rabbit polyclonal anti-PCGF2 (sc-10744, Santa Cruz, 3ul), rabbit monoclonal anti-T7-Tag (D9E1X) (13246, Cell signaling, 3ul). The antibodies used for ChIP-qPCR for TetO targeting experiments were rabbit polyclonal anti-FS2 (produced in house, 59, 3ul), polyclonal anti-MED12 (A300-774A, Bethyl laboratories, 3ul), polyclonal anti-MED1 (A300-793A, Bethyl laboratories, 3ul), polyclonal anti-CCNC (A301-989A, Bethyl laboratories, 3ul). For native ChIP, 50x10^6 ESCs were mixed with 20x10^6 SG4 Drosophila cells and washed with 1x PBS prior to chromatin isolation. Nuclei were released in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40), washed and resuspended in 1ml ice cold digestion buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 1x cOmplete protease inhibitor cocktail (Roche)). Chromatin was digested with 200mM MNase (ThermoFisher scientific) for 5 min at 37°C and the reaction was stopped by the addition of 4mM EDTA pH 8.0. The samples were centrifuged at 1500g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300μl of nucleosome release buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 0.2mM EDTA, 1x protease inhibitor cocktail (Roche)) at 4°C for 1 h, passed five times through a 27G needle using a 1mL syringe, and spun at 1500g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. Digestion to mostly mononucleosomes was confirmed on a 1.5% agarose gel. The prepared native chromatin was aliquot, snap frozen in liquid nitrogen and stored at -80°C until further use. ChIPs were performed as described in Fursova et al 2019, using 5ul of H3K27me3 antibody prepared in-house.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description input for CDK8 ChIPs in Pcgf4-/-Pcgf2 flfl
Data processing For cChIP-seq, Bowtie2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.
 
Submission date Oct 14, 2021
Last update date May 23, 2022
Contact name Emilia Dimitrova
E-mail(s) emilia.dimitrova@bioch.ox.ac.uk
Organization name University of Oxford
Department Biochemistry
Lab Rob Klose
Street address South Parks Road
City Oxford
ZIP/Postal code OX1 3QU
Country United Kingdom
 
Platform ID GPL19415
Series (2)
GSE185927 Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction (ChIP-Seq)
GSE185930 Distinct roles of CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction
Relations
BioSample SAMN22307004
SRA SRX12622693

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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