description:
Biological replicate 1 of 2. Rpb3 occupancy in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Thio-Rapa30min_Rpb3vsInput_20171031_rep1-2__S.cerevisiaeApr11_737165.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


title: yFR1480_Spt6-AA_DMSO_H4vsInput_20171102_rep2

status: Public on Jul 30 2019

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 2 of 2. H4 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_H4vsInput_20171031_rep1-2__S.cerevisiaeApr11_523077.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.

hyb_protocol: Hybridization: Resuspend colored pellet in 110 uL of hybridization mix (100 uL DIG Easy Hyb buffer, 5 uL 10mg/mL Salmon Sperm DNA, 5 uL 8mg/mL yeast tRNA). Put at 95°C for 5 min. Put at 42°C for 10 min (keep samples at 42°C while waiting for hybridization). Follow standard Agilent chamber hybridization protocol. Incubate overnight (16-24h) at 42°C in Agilent hybridization oven at 20 rpm rotation speed.  Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 min at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in Wash buffer #2 pre-warmed at 31°C for 5 min on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Stripping: Stripping is done in 1 L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 20 to 25 min. Do not overboil it. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. 1M Potassium phosphate buffer pH 6.6: mix 3.81 mL of 1M K2HPO4 + 6.19 mL of 1M KH2PO4. Dilute 5 mL of this 1M solution in 1 L Milli-Q water to obtain 5 mM Potassium phosphate buffer pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180K. Set the scan as follow: pixel size = 2µm; speed = 20; Scan Mode = Normal; Acquisition Mode = Simultaneous; Focus = Auto. Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing:
The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = median normalized

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Standard Yeast aa-dUTP Labeling. Blunting: Do everything on ice. Add 70 uL of the blunting solution (11 uL NEB Buffer #2, 0.5 uL BSA 10mg/mL, 0.5 uL 20mM dNTPs, 0.2 uL T4 DNA Polymerase 3U/uL, 57.8 uL ddH2O) to 40 uL of the resuspended DNA obtained at the end of the cleanup step. For Inputs, use 4uL + 36uL ddH2O. Incubate 20 min at 12°C. Precipitation: Add 11.5 uL 3M NaOAc pH 5.2 and 0.5 uL Glycogen 20mg/mL and vortex briefly. Extract with 120 uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110 uL to a new tube and add 230 uL of cold 100% EtOH (-20°C). Spin 20 min at 4°C. Wash the pellet with 700 uL of cold 70% EtOH (-20°C) and spin 5 min at 4°C. Resuspend the pellet in 25 uL ddH2O and place on ice. Ligation: Thaw everything and do all manipulations on ice. Add 25 uL of ligase mix (10 uL 5x T4 Ligase Buffer, 6.7 uL 15uM unidirectional linkers, 0.5 uL T4 DNA Ligase (5U/uL), 8 uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16°C. Precipitation: Add 6 uL 3M NaOAc pH 5.2 and vortex. Add 130 uL of cold 100% EtOH (-20°C) and incubate at least 30 min at -20°C. Centrifuge 20 min at 4°C at maximum speed. Wash the pellet (should be a smear on the side of the tube) with 500 uL cold 70% EtOH (-20°C). Spin 5 min at 4°C. Dry the pellet and resuspend in 25 uL ddH2O. Leave on ice for about 20 min, vortex, centrifuge briefly and put on ice. Labeling: Add 15 uL of PCR labeling mix (4 uL 10x ThermoPol Buffer, 2 uL 5mM aa-dUTP mix, 1.25 uL 40uM Oligo FR1, 7.75 uL ddH2O) to the pellet from the ligation step. Start the PCR program and during the first step (4 min at 55°C), add 10 uL of the polymerase mix (1 uL 10x ThermoPol buffer, 1 uL Taq Polymerase 5U/uL, 0.01 uL Pfu Polymerase Turbo 2.5U/uL, 8 uL ddH2O). PCR cycling conditions: 1) 4 min at 55°C; 2) 5 min at 72°C; 3) 2 min at 95°C; 4) 30 sec at 95°C; 5) 30 sec at 55°C; 6) 1 min at 72°C; 7) Repeat steps 4-6 31 more times; 8) 4 min at 72°C; 9) Forever at 4°C. Purify PCR reactions with QIAquick PCR purification kit (Qiagen), following manufacturer's protocol but use a Phosphate Wash buffer and a Phosphate Elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns twice and elute with 50 uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5 uL 0.1M Sodium Carbonate buffer pH 9.0. Add 4.5 uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dyes should be resuspended in 73 uL DMSO. Mix well and incubate at room temperature in the dark for one hour. Add 35 uL 0.1M NaOAc pH 5.2. Purify using the QIAquick PCR purification kit (Qiagen), wash twice and elute in 50 uL. Mix both samples of a pair (Cy5 and Cy3) in the same tube. Speed-vac until 10-20uL are left. Phosphate Wash buffer (100 mL): 0.5 mL 1M KPO4 pH 8.5, 15.25 mL ddH2O, 84.25 mL 95% EtOH. Solution will be cloudy upon mixing. Phosphate Elution buffer (10 mL): 0.04 mL 1M KPO4 pH 8.5, 9.96 mL ddH2O. 1M KPO4 pH 8.5 (10 mL): 9.5 mL 1M K2HPO4, 0.5 mL 1M KH2PO4. 1M Sodium Carbonate buffer pH 9.0 (100 mL): 10.8g Na2CO3, 80 mL ddH2O and pH to 9.0 with concentrated HCl. Adjust volume to 100 mL with ddH2O. Dilute 1:10 when using. Solution will change composition over time. Use only if less than a month old.

growth_protocol: 200 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium. Cells are grown to an OD600 of ~0.5-0.6. Then 50 mL of cell culture is poured in a flask and treated with DMSO (50µL) for 30 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol:
Cells are thawed on ice and resuspended in 700 uL Lysis buffer with protease inhibitors. 500 uL of acid-washed glass beads (Sigma) are added and the cells are lysed using a bead-beater (4 x 5 min cycles, with 5 min breaks on ice). The tubes are pierced with an 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2 mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x20sec at output 7 Watts, with a 1 min break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4°C max speed and the supernatant used immediately for ChIP (or saved and frozen at -80°C). Lysis buffer: 50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM PMSF, 1mM Benzamidine, 10ug/mL Aprotinin, 1ug/mL Leupeptin, 1ug/mL Pepstatin.
Beads are spun down and supernatant is transferred to a new 1.5 mL tube. 350 uL of a mix of (345 uL TE, 3 uL RNAse A 10mg/mL, 2 uL Glycogen 20mg/mL) is added to the supernatant. Samples are vortexed and incubated at 37°C for 2 hr. 15 uL 10% SDS and 7.5 uL Proteinase K are then added, vortexed and incubated for another 2 hr at 37°C. The samples are then extracted twice with 400 uL phenol/chloroform/isoamyl alcohol (25:24:1). 14 uL of 5M NaCl is added to the final extract of about 350 uL. 1 mL of cold 100% EtOH (-20°C) is added and the samples are centrifuged at maximum speed for 20 min at 4°C. The supernatant is discarded and the pellet is washed with 700 uL of cold 70% EtOH (-20°C) and centrifuged 5 min at 4°C. The supernatant is discarded and the pellet resuspended in 50 uL TE and stored at -20°C.

treatment_protocol:
DMSO for 30 min
H4 ChIP. Antibody from A. Verreault (ryH4). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

tag: strain

tag: genotype

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, SPT6-FRB::kanMX6

tag: antibody

value: ryH4 (A.Verreault)

treatment_protocol:
DMSO for 30 min
none


title: yFR1480_Spt6-AA_DMSO_H3K4me3vsInput_20171102_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_H3K4me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_245913.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.

treatment_protocol:
DMSO for 30 min
H3K4me3 ChIP. Antibody from Abcam (ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5ug/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K4me3 (Abcam ab8580)


title: EAC-T9_INPUT

type: SRA

city: Los Angeles

first: Li

last: Chen

state: CA

address: 8700 Beverly Blvd

department: Medicine

country: USA

institute: Cedars-Sinai Medical Center

library_source: genomic

data_processing:
Single end 49 bp or pair end 150 bp reads were aligned to the hg19 reference genome using Bowtie1
PCR duplicate reads were removed using Picard MarkDuplicates
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

organism: Homo sapiens

source_name: Esophageal Adenocarcinoma tissue

growth_protocol: Eso26, OACM5.1, OACp4C and OE19 cell lines are cultured in RPMI-1640 medium; Flo-1, SKGT4, JH-EsoAd1, and OE33 cell lines are maintained in Dulbecco’s modiﬁed Eagle medium (DMEM). KYAE-1 is cultured in RPMI-1640:Hams F12 1:1 medium. ChTRT and GihTRT cell lines were cultured in Epithelial Cell Medium-2 medium with supplements. All media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol

tag: cell line


title: EAC-T10_H3K27Ac


title: yFR1480_Spt6-AA_DMSO_Rpb3vsInput_20171102_rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_Rpb3vsInput_20171031_rep1-2__S.cerevisiaeApr11_412782.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.

treatment_protocol:
DMSO for 30 min
Rpb3 ChIP. Antibody from BioLegend (665004). Pan Mouse IgG Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (1.5 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: Rpb3 (BioLegend 665004)


title: EAC-T8_INPUT


title: MBJ_iMGL_GFP_1

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road, Room 3200

department: Neurobiology and Behavior

institute: University of California, Irvine

library_source: transcriptomic

data_processing:
FASTQ files generated using bcl2fastq
FASTQ files were preprocessed using BBDuk to remove rRNA and Phix reads, trim Illumina adapters, and trim base pairs with a PHRED score less than 10
Kallisto (v0.45.0) was used to pseudoalign samples to the GRCh38.p12 human transcriptome without bootstraps.
Kallisto count tables were read into DESeq2 via TxImport, genes with less than 10 counts across all samples were removed, and differential gene expression analysis was performed between cell types.
Genome_build: GRCh38.p12 release 94
Supplementary_files_format_and_content: tab-delimited text file containing Kallisto gene count matrix for all samples

molecule: polyA RNA

source_name: iMGL

extract_protocol:
Trizol LS was added directly to cultured or FACS-isolated cells, immediately frozen on dry ice, and stored at -80C until isolation. ClonTech SMART-Seq v4 Ultra Low Input kit (#634891) was used with 2-10ng of total RNA.
Libraries were prepared according to standard Illumina protocols

value: AICS-0036 (Coriell)

tag: cell type

value: InVitro

tag: cell sex

value: Male

tag: host organism

tag: host sex

tag: host age (months)

tag: treatment

tag: cdna fragment length

tag: cdna fragment sd


title: MBJ_iMGL_GFP_2


description:
Biological replicate 1 of 2. H4 occupancy in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Rapa30min_H4vsInput_20171031_rep1-2__S.cerevisiaeApr11_121003.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.

growth_protocol: 200 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium. Cells are grown to an OD600 of ~0.5-0.6. Then 50 mL of cell culture is poured in a flask and treated with 1 μg/mL of rapamycin (Bio Basic Inc.) for 30 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
1 μg/mL of rapamycin for 30 min
H4 ChIP. Antibody from A. Verreault (ryH4). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

treatment_protocol:
1 μg/mL of rapamycin for 30 min
none


description:
Biological replicate 1 of 2. Rpb3 occupancy in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Rapa30min_Rpb3vsInput_20171031_rep1-2__S.cerevisiaeApr11_395386.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.

treatment_protocol:
1 μg/mL of rapamycin for 30 min
Rpb3 ChIP. Antibody from BioLegend (665004). Pan Mouse IgG Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (1.5 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


title: EAC-T8_H3K27Ac


title: EAC-T9_H3K27Ac


description:
Biological replicate 1 of 2. H3K36me3 occupancy in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Thio-Rapa30min_H3K36me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_685567.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.

growth_protocol: 200 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium. Cells are grown to an OD600 of ~0.5-0.6. Then 50 mL of cell culture is poured in a flask and treated with both 1 μg/mL of rapamycin (Bio Basic Inc.) and 3 μg/mL of thiolutin (Tocris Bioscience) for 30 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
1 μg/mL of rapamycin + 3 μg/mL of thiolutin  for 30 min
H3K36me3 ChIP. Antibody from Abcam (ab9050). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K36me3 (Abcam Ab9050)

treatment_protocol:
1 μg/mL of rapamycin + 3 μg/mL of thiolutin  for 30 min
none


title: yFR1480_Spt6-AA_DMSO_H3K36me3vsInput_20171102_rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_H3K36me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_488797.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.

treatment_protocol:
DMSO for 30 min
H3K36me3 ChIP. Antibody from Abcam (ab9050). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


title: EAC-T7_INPUT


description:
Biological replicate 1 of 2. H4 occupancy in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Thio-Rapa30min_H4vsInput_20171031_rep1-2__S.cerevisiaeApr11_983073.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.

treatment_protocol:
1 μg/mL of rapamycin + 3 μg/mL of thiolutin  for 30 min
H4 ChIP. Antibody from A. Verreault (ryH4). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Thio-Rapa30min_H3K4me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_204637.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.

treatment_protocol:
1 μg/mL of rapamycin + 3 μg/mL of thiolutin  for 30 min
H3K4me3 ChIP. Antibody from Abcam (ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5ug/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


title: EAC-T6_H3K27Ac


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Rapa30min_H3K4me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_740872.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.

treatment_protocol:
1 μg/mL of rapamycin for 30 min
H3K4me3 ChIP. Antibody from Abcam (ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5ug/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


title: EAC-T7_H3K27Ac


title: EAC-T5_H3K27Ac


title: EAC-T4_H3K27Ac


title: EAC-T4_INPUT


title: EAC-T6_INPUT


description:
Biological replicate 1 of 2. Rpb3 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_Rpb3vsInput_20171031_rep1-2__S.cerevisiaeApr11_412782.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.


title: EAC-T3_INPUT


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_H3K4me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_245913.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.


title: EAC-T5_INPUT


description:
Biological replicate 1 of 2. H4 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_H4vsInput_20171031_rep1-2__S.cerevisiaeApr11_523077.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.


title: EAC-T2_H3K27Ac


title: EAC-T2_INPUT


description:
Biological replicate 1 of 2. H3K36me3 occupancy in Spt6-AA (anchor-away) cells treated with DMSO for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_DMSO_H3K36me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_488797.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with DMSO for 30 min.


title: yFR1478_Spt16-AA_Thio-Rapa30min_Rpb3vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_Rpb3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_950859.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.

treatment_protocol:
1 μg/mL of rapamycin + 3 μg/mL of thiolutin  for 30 min
Rpb3 ChIP. Antibody from BioLegend (665004). Pan Mouse IgG Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (1.5 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, SPT16-FRB::kanMX6


title: EAC-T1_INPUT


title: yFR1478_Spt16-AA_Rapa30min_H4vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H4 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Rapa30min_H4vsInput_20170712_Rep1-2__S.cerevisiaeApr11_994637.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.


title: GihTRT_INPUT

source_name: Barrett's esophagus cell line

value: GihTRT


title: GihTRT_H3K27Ac


title: EAC-T1_H3K27Ac


title: ChTRT_INPUT

value: ChTRT


title: yFR1478_Spt16-AA_DMSO_H3K4me3vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with DMSO for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_DMSO_H3K4me3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_652015.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with DMSO for 30 min.


title: yFR1478_Spt16-AA_Thio-Rapa30min_H3K36me3vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_H3K36me3vsInput_20170712_Rep1-2__S.cerevisiaeApr11_279110.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


title: ChTRT_H3K27Ac


title: yFR1478_Spt16-AA_Thio-Rapa30min_H4vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H4 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_H4vsInput_20170712_Rep1-2__S.cerevisiaeApr11_406766.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


title: yFR1478_Spt16-AA_Rapa30min_H3K4me3vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Rapa30min_H3K4me3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_230872.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.


description:
Biological replicate 1 of 2. H4 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_H4vsInput_20170712_Rep1-2__S.cerevisiaeApr11_406766.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


title: yFR1478_Spt16-AA_DMSO_H4vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H4 occupancy in Spt16-AA (anchor-away) cells treated with DMSO for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_DMSO_H4vsInput_20170712_Rep1-2__S.cerevisiaeApr11_453288.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with DMSO for 30 min.


description:
Biological replicate 1 of 2. H4 occupancy in Spt16-AA (anchor-away) cells treated with DMSO for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_DMSO_H4vsInput_20170712_Rep1-2__S.cerevisiaeApr11_453288.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with DMSO for 30 min.


title: yFR1478_Spt16-AA_Thio-Rapa30min_H3K4me3vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_H3K4me3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_442855.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


title: yFR1478_Spt16-AA_Rapa30min_H3K36me3vsInput_20170718_Rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Rapa30min_H3K36me3vsInput_20170712_Rep1-2__S.cerevisiaeApr11_554337.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.

treatment_protocol:
1 μg/mL of rapamycin for 30 min
H3K36me3 ChIP. Antibody from Abcam (ab9050). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


title: SKGT4_H3K27Ac

source_name: Esophageal Adenocarcinoma cell line


title: OE33_INPUT


title: SKGT4_INPUT


description:
Biological replicate 1 of 2. H3K36me3 occupancy in Spt16-AA (anchor-away) cells treated with DMSO for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_DMSO_H3K36me3vsInput_20170712_Rep1-2__S.cerevisiaeApr11_228628.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with DMSO for 30 min.


title: OE19_INPUT


title: OE33_H3K27Ac


title: OE19_H3K27Ac


description:
Biological replicate 1 of 2. H4 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Rapa30min_H4vsInput_20170712_Rep1-2__S.cerevisiaeApr11_994637.bed
A genome browser-ready file for H4 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.


title: OACp4C_INPUT


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_H3K4me3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_442855.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


description:
Biological replicate 1 of 2. H3K36me3 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Rapa30min_H3K36me3vsInput_20170712_Rep1-2__S.cerevisiaeApr11_554337.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.


description:
Biological replicate 1 of 2. Rpb3 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Rapa30min_Rpb3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_806958.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.


description:
Biological replicate 1 of 2. Rpb3 occupancy in Spt16-AA (anchor-away) cells treated with DMSO for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_DMSO_Rpb3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_406219.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with DMSO for 30 min.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Rapa30min_H3K4me3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_230872.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.


title: OACp4C_H3K27Ac


description:
Biological replicate 1 of 2. H3K36me3 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_H3K36me3vsInput_20170712_Rep1-2__S.cerevisiaeApr11_279110.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


title: yFR2114_WT_6hrs-YPD_H3K79me3vsInput_20161201_rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K79me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_594932.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

growth_protocol: For the histone H4 depletion experiments, strains are grown as previously described (Wyrick et al. 1999) with minor modifications. In brief, strains are streaked from glycerol stocks onto 2% agar yeast extract-peptone (YEP)-2% galactose plates and grown at 30°C for 3-4 days. An isolated colony is then grown for 24h at 30°C in 10 mL of YEP-2% galactose. This pre-culture is used to inoculate 100 mL of YEP-2% galactose at an OD600 of 0.075 which is grown overnight until OD600 value reached ~0.7. Then, 20 and 40 OD units of wild-type and mutant cells respectively are centrifuged 3 min at 3500 rpm at room temperature and resuspended in 200 mL of YPD (yeast extract-peptone-2% glucose) to generate cultures starting at 0.1 OD600 and 0.2 OD600 respectively. Cultures are incubated at 30°C for 6h, at which point they both reached ~0.7 OD600. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
switch to YPD medium for 6 h
H3K79me3 ChIP. Antibody from Abcam (ab2621). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K79me3 (Abcam ab2621)

treatment_protocol:
switch to YPD medium for 6 h
none


title: OACM5.1_INPUT


title: OACM5.1_H3K27Ac


description:
Biological replicate 1 of 2. H3K4me3 occupancy in Spt16-AA (anchor-away) cells treated with DMSO for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_DMSO_H3K4me3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_652015.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with DMSO for 30 min.


title: KYAE1_INPUT


title: KYAE1_H3K27Ac


title: JH-EsoAd1_INPUT


title: OACp4C_GATA6


title: JH-EsoAd1_H3K27Ac


title: Flo-1_INPUT


title: Flo-1_H3K27Ac


title: Eso26_INPUT


title: Eso26_H3K4me3


title: yFR2114_WT_6hrs-YPD_H3K4me1vsInput_20161130_rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K4me1vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_767758.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
H3K4me1 ChIP. Antibody from Abcam (ab8895). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K4me1 (Abcam ab8895)


description:
Biological replicate 1 of 2. H3K4me2 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K4me2vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_569757.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
H3K4me2 ChIP. Antibody from Abcam (ab7766). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K4me2 (Abcam ab7766)


title: yFR2114_WT_6hrs-YPD_H3K4me2vsInput_20161130_rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K4me2vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_569757.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


description:
Biological replicate 1 of 2. Rpb3 occupancy in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1478_Spt16-AA_Thio-Rapa30min_Rpb3vsInput_20170630_Rep1-2__S.cerevisiaeApr11_950859.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in Spt16-AA (anchor-away) cells treated with both 1 μg/mL of rapamycin and 3 μg/mL of thiolutin for 30 min.


description:
Biological replicate 1 of 2. H3K79me3 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K79me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_594932.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


title: Eso26_ELF3-Flag


title: Eso26_KLF5


title: Eso26_H3K27Ac


title: Eso26_GATA6


title: yFR2114_WT_6hrs-YPD_H3K18acvsInput_20161201_rep2

description:
Biological replicate 2 of 2. H3K18ac occupancy in WT cells switched to medium containing glucose for 6 hr. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K18acvsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_947320.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
H3K18ac ChIP. Antibody from Abcam (ab1191). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K18ac (Abcam ab1191)


title: EAC-T3_H3K27Ac


description:
Biological replicate 1 of 2. H3K79me3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K79me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_34841.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: yFR2113_pGAL1-H4_6hrs-YPD_H3K79me3vsInput_20161201_rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K79me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_34841.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: yFR2114_WT_6hrs-YPD_H3K36me3vsInput_20161201_rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K36me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_335447.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
H3K36me3 ChIP. Antibody from Abcam (ab9050). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


title: yFR2113_pGAL1-H4_6hrs-YPD_H3K4me2vsInput_20161130_rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K4me2vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_266135.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: yFR2114_WT_6hrs-YPD_H2BubvsInput_20161130_rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in WT cells switched to medium containing glucose for 6 hr. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H2BubvsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_885856.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
H2Bub ChIP. Antibody from Cell Signaling Technology (#5546). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H2Bub (Cell Signaling Technology 5546)


title: KO4

city: San Francisco

first: Eric

middle: Joseph

last: Wigton

address: 500 Parnassus Ave.

department: Immunology

institute: UCSF

data_processing:
Illumina HiSeq2400
STAR 2.4.2a alignment
normalized read counts
DeSeq2 differential
Genome_build: Ensembl Mouse GRCh38.78
Supplementary_files_format_and_content: counts.text is raw counts for Ensembl alignment.  All_genes.xlx Normalized read/DESeq2 analysis with meta-info.

molecule: total RNA

organism: Mus musculus

source_name: NP binding Germinal Center B cells

extract_protocol:
LNs were harvested and 10e3 NP binding GC B cells were sorted directly into lysis buffer (Dynabead direct mRNA extraction kit Thermofisher) mRNA was isolated followind manufacturerers directions.
Ovation RNA-seq System V2 for HISeq 4000 SE read

treatment_protocol: Mice were immunized in the scruff and flanks with the T-dependent antigen (NP-CGG) bound to CpG oligo ODN1826

value: Germinal Center B cell

tag: timing

value: Day 14 post Subcutaneous immunization


description:
Biological replicate 1 of 2. H2Bub occupancy in WT cells switched to medium containing glucose for 6 hr. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H2BubvsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_885856.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


title: KO3


description:
Biological replicate 1 of 2. H3K18ac occupancy in WT cells switched to medium containing glucose for 6 hr. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K18acvsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_947320.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


description:
Biological replicate 1 of 2. H3K36me3 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K36me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_335447.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


description:
Biological replicate 1 of 2. H3K4me1 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YPD_H3K4me1vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_767758.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


title: yFR2113_pGAL1-H4_6hrs-YPD_H3K36me3vsInput_20161201_rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K36me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_911918.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: KO2


title: KO1


title: WT4

value: Wild type


title: WT3


title: yFR2113_pGAL1-H4_6hrs-YPD_H3K18acvsInput_20161201_rep2

description:
Biological replicate 2 of 2. H3K18ac occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K18acvsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_731439.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


description:
Biological replicate 1 of 2. H3K36me3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K36me3vsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_911918.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: yFR2113_pGAL1-H4_6hrs-YPD_H3K4me1vsInput_20161130_rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K4me1vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_948688.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


description:
Biological replicate 1 of 2. H3K4me1 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K4me1vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_948688.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


description:
Biological replicate 1 of 2. H3K4me2 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K4me2vsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_266135.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: yFR2113_pGAL1-H4_6hrs-YPD_H2BubvsInput_20161130_rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H2BubvsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_350238.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: Case 14

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

hyb_protocol: Cases were hybridized according to the manufacturer’s protocol.  Array slides were scanned with the DNA Microarray Scanner with extraction software (Agilent, Santa Clara, USA).

scan_protocol: Array slides were scanned with the DNA Microarray Scanner G2505C with extraction software  (Agilent, Santa Clara, USA).

data_processing:
The CytoSure Interpret software 020022 (OGT) and Nexus Biodiscovery were used for data analysis.
The data were segmented using a modified Circular Binary Segmentation (CBS) algorithm. Genomic aberrations were identified by applying log2 intensity ratios of sample to reference (Cy3/Cy5: log2-ratios). Threshold factor for deletions was set as a log2 ratio of -0.6 that is less stringent than the theoretical log2 score of -1 (heterozygous deletion log2(1/2)=-1; No change in allele number log2(2/2)=0; heterozygous duplication log2(3/2)=0.59). The software uses the Derivative Log Ratio (DLR) Spread, which is used as a quality control check. This metric calculates probe-to-probe log ratio noise of an array and hence of the minimum log ratio difference required to make reliable amplification or deletion calls. A DLR of 0.08-0.19 is accepted, 0.20-0.29 is borderline, and -0.30 is rejected. The DLR for all arrays shown was scored by this scale.

source_name: TUMOR, Burkitt-lymphoma

extract_protocol: Genomic DNA was extracted from 9 Burkitt-like with 11q samples and 2 BL was extracted using standard protocols.

tag: gender

value: male

tag: tissue

value: TUMOR, Burkitt-lymphoma

source_name: pool 4 normal male dna


title: Case 10

source_name: TUMOR, Burkitt-like with 11q

value: TUMOR, Burkitt-like with 11q


title: Case 4


title: Case 11


description:
Biological replicate 1 of 2. H4 occupancy in WT cells switched to medium containing glucose for 6 hr. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YEP-Glucose_H4vsInput_20161121_rep1-2_MN__S.cerevisiaeApr11_714650.bed
A genome browser-ready file for H4 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
H4 ChIP. Antibody from A. Verreault (ryH4). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: ryH4 (A.Verreault)


title: Case 12


title: Case 1


description:
Biological replicate 1 of 2. Spt16 occupancy in WT cells switched to medium containing glucose for 6 hr. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_Spt16vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_200941.bed
A genome browser-ready file for Spt16 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
Spt16 ChIP. Antibody from T. Formosa. Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: Spt16 (T. Formosa)


title: yFR2114_WT_6hrs-YEP-Glucose_H4vsInput_20161121_rep2

description:
Biological replicate 2 of 2. H4 occupancy in WT cells switched to medium containing glucose for 6 hr. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_6hrs-YEP-Glucose_H4vsInput_20161121_rep1-2_MN__S.cerevisiaeApr11_714650.bed
A genome browser-ready file for H4 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


title: yFR2113_pGAL1-H4_6hrs-YEP-Glucose_H4vsInput_20161121_rep2

description:
Biological replicate 2 of 2. H4 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YEP-Glucose_H4vsInput_20161121_rep1-2_MN__S.cerevisiaeApr11_323220.bed
A genome browser-ready file for H4 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: Case 9


title: Case 6


title: Case 8


description:
Biological replicate 1 of 2. H4 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H4 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YEP-Glucose_H4vsInput_20161121_rep1-2_MN__S.cerevisiaeApr11_323220.bed
A genome browser-ready file for H4 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


description:
Biological replicate 1 of 2. Rpb3 occupancy in WT cells switched to medium containing glucose for 6 hr. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_Rpb3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_556636.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
Rpb3 ChIP. Antibody from Neoclone (W0012). Pan Mouse IgG Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: Rpb3 (Neoclone W0012)


title: Case 3

value: female

source_name: pool 5 normal female dna


title: yFR2114_WT_Spt16vsInput_6hrsYPD_20160703_rep2

description:
Biological replicate 2 of 2. Spt16 occupancy in WT cells switched to medium containing glucose for 6 hr. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_Spt16vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_200941.bed
A genome browser-ready file for Spt16 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


title: yFR2114_WT_H3K4me3vsInput_6hrsYPD_20160703_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_H3K4me3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_100233.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.

treatment_protocol:
switch to YPD medium for 6 h
H3K4me3 ChIP. Antibody from Abcam (ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5ug/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K4me3 (Abcam ab8580)


title: yFR2113_pGAL1-H4_Spt16vsInput_6hrsYPD_20160703_rep2

description:
Biological replicate 2 of 2. Spt16 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_Spt16vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_468341.bed
A genome browser-ready file for Spt16 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: yFR2114_WT_Rpb3vsInput_6hrsYPD_20160703_rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in WT cells switched to medium containing glucose for 6 hr. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_Rpb3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_556636.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.


title: yFR2113_pGAL1-H4_Rpb3vsInput_6hrsYPD_20160703_rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_Rpb3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_921419.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


title: Case 2


title: KO+poly I:C: ZNF598 KO short poly I:C stimulation

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Total RNA was extracted from HeLa cells, and subjected to the microarray analysis.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Human immortalized cells

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: WT and ZNF598 knockout HeLa cells were cultured in MEM with heat-inactivated 10% FCS in a 24-well plate.

extract_protocol: Total RNA was extracted using TRIZOL reagents according to the manufacture's protocol.

treatment_protocol: short poly I:C (LMW poly I:C) was purchased from Invivogen. 100 ng/ml of short polyI:C was trasnfected into cells using Lipofectaimin 2000 according to manufacture's protocol. 9 hr after trasnfection, total RNA was extracted.

value: HeLa

tag: genotype/variation

value: ZNF598 KO


title: yFR2113_pGAL1-H4_H3K4me3vsInput_6hrsYPD_20160703_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_H3K4me3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_287568.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells switched to medium containing glucose for 6 hr. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2114_WT_H3K4me3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_100233.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells switched to medium containing glucose for 6 hr.