description:
Biological replicate 1 of 2. H3K14ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K14ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_499915.bed
A genome browser-ready file for H3K14ac occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: yFR973_spt16-197_80min37C_H3K18ac-H4_20161102_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. H3K18ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K18ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_401897.bed
A genome browser-ready file for H3K18ac occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

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: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 0.5. Cell cultures are then switched to 37°C and allowed to grow for additional 80 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:
switch to 37°C for 80 min
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.

tag: strain

tag: genotype

value: MATα, leu2Δ1, spt16-197

tag: antibody

value: H3K18ac (Abcam ab1191)

treatment_protocol:
switch to 37°C for 80 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.

value: ryH4 (A.Verreault)


title: yFR1321_WT_90minRap_H3K4me3vsInput_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated with 1 μg/mL of rapamycin for 90 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1321_WT_90minRap_H3K4me3vsInput_rep1-2_MN__S.cerevisiaeApr11_965735.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated with 1 μg/mL of rapamycin for 90 min.

growth_protocol: 50 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 and then treated with 1 μg/mL of rapamycin (Bio Basic Inc.) for 90 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 90 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)

treatment_protocol:
1 μg/mL of rapamycin for 90 min
none


description:
Biological replicate 1 of 2. H2Bub occupancy in WT cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit monoclonal antibody against H2Bub and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H2B.
SmthBED_yFR971_SPT16-WT_80min37C_H2BubvsH2B_20161107_Rep1-2_MN__S.cerevisiaeApr11_57600.bed
A genome browser-ready file for H2Bub occupancy (IP/H2B) in WT cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
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: MATα, leu2Δ1

value: H2Bub (Cell Signaling Technology 5546)

treatment_protocol:
switch to 37°C for 80 min
H2B ChIP. Antibody from Abcam (ab1790). 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 (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: H2B (Abcam ab1790)


description:
Biological replicate 1 of 2. H3K14ac occupancy in WT cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K14ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_914550.bed
A genome browser-ready file for H3K14ac occupancy (IP/H4) in WT cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K14ac ChIP. Antibody from Millipore (07-353). 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: H3K14ac (Millipore 07-353)


description:
Biological replicate 1 of 2. H3K18ac occupancy in WT cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K18ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_239781.bed
A genome browser-ready file for H3K18ac occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: yFR974_spt6-1004_80min37C_H3K4me2vsH4_20161024_Rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K4me2vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_953374.bed
A genome browser-ready file for H3K4me2 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
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: yFR971_SPT16-WT_80min37C_H3K18ac-H4_20161102_Rep2

description:
Biological replicate 2 of 2. H3K18ac occupancy in WT cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K18ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_239781.bed
A genome browser-ready file for H3K18ac occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: yFR971_SPT16-WT_80min37C_H3K14ac-H4_20161102_Rep2

description:
Biological replicate 2 of 2. H3K14ac occupancy in WT cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K14ac-H4_20161102_Rep1-2_MN__S.cerevisiaeApr11_914550.bed
A genome browser-ready file for H3K14ac occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: WT

type: SRA

city: Wuhan

first: cheng

last: qingyun

address: Bayi Street

department: Chemistry

country: China

institute: Wuhan Universiy

library_source: transcriptomic

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: The xlsx file contains FPKM values.

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: Cells are cultured using DMEM basic medium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
mRNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: cell line

value: wild type


description:
Biological replicate 1 of 2. H3K4me2 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K4me2vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_953374.bed
A genome browser-ready file for H3K4me2 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: yFR974_spt6-1004_80min37C_H3K4me1vsH4_20161024_Rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K4me1vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_899330.bed
A genome browser-ready file for H3K4me1 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
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)


title: LCH_S11_4 [ATAC-seq]

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: ATAC-seq of sorted LCH-S11 cells

library_source: genomic

data_processing:
Trimming using Skewer v0.1.126, alignment with Bowtie 2 v2.2.4 (parameters: --very-sensitive --no-discordant). Keep deduplicated, uniquely mapped reads with MQ ≥30.
Peak calling with MACS2 v2.1.0 (parameters: -q 0.1 -g hs).
Peaks not overlapping blacklisted regions were merged and reads overlapping the merged coordinates counted.
Raw read counts were loaded into DESeq2 v1.22.2 for normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: MACS .narrowPeak file (peak coordinates), bigWig file (coverage tracks), Comma-separated text file (summary of normalized read counts per peak)

source_name: LCH cells from a lymph node biopsy, enriched for LCH-S11 cell subset using FACS, replicate 2

growth_protocol: None. Primary cells isolated from biopsy.

extract_protocol:
Cells were pelleted and lysed in a buffer containing Digitonin and transposase enzyme. After transposition the DNA was purified.
The purified samples were enriched using index primers and purified librareies were quality checked and sequenced on Illumina HiSeq 4000 instruments.

treatment_protocol: Subsets were isolated from biopsy LCH_E, from frozen/thawed cells. LCH cells were enriched for subset-specific markers using FACS.

value: lymph node

tag: Sex

value: female

tag: age

value: child

value: multi-system

tag: disease

value: Langerhans cell histiocytosis

tag: frozen

value: thawed


title: LCH_S11_3 [ATAC-seq]

description: ATAC-seq of sorted LCH-S11 cells

source_name: LCH cells from a lymph node biopsy, enriched for LCH-S11 cell subset using FACS, replicate 1


title: LCH_S12_4 [ATAC-seq]

description: ATAC-seq of sorted LCH-S12 cells

source_name: LCH cells from a lymph node biopsy, enriched for LCH-S12 cell subset using FACS, replicate 2


title: LCH_S12_3 [ATAC-seq]

description: ATAC-seq of sorted LCH-S12 cells

source_name: LCH cells from a lymph node biopsy, enriched for LCH-S12 cell subset using FACS, replicate 1


title: LCH_S1_4 [ATAC-seq]

description: ATAC-seq of sorted LCH-S1 cells

source_name: LCH cells from a lymph node biopsy, enriched for LCH-S1 cell subset using FACS, replicate 2


description:
Biological replicate 1 of 2. H3K4me1 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K4me1vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_899330.bed
A genome browser-ready file for H3K4me1 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: yFR973_spt16-197_80min37C_H3K4me2vsH4_20161024_Rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K4me2vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_202708.bed
A genome browser-ready file for H3K4me2 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


description:
Biological replicate 1 of 2. H3K4me2 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K4me2vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_202708.bed
A genome browser-ready file for H3K4me2 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: LCH_K

description: scRNA-seq analysis of an LCH biopsy

data_processing:
Reads were demultiplexed, converted to FASTQs, and aligned using 10X CellRanger (v1.3.0).
Pre-processed data were loaded into R and analyzed using Seurat (v2.3.4).
Genome_build: GRCh38
Supplementary_files_format_and_content: CellRanger sparse matrix HDF5 file with UMI counts per barcode and gene.

source_name: bone biopsy from patient LCH_K, male child, single-system LCH

extract_protocol:
Cells were loaded onto a 10X Genomics Chromium Controller following manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.
Per manufacturer instructions, droplet emulsions were broken, cDNA was amplified, and libraries were generated using enzymatic fragmentation followed by enrichment PCR and sequencing on Illumina HiSeq 4000 platform.

treatment_protocol: Biopsies LCH_E, LCH_N, and LCH_O were from frozen/thawed cells, the rest was fresh. LCH cells were enriched for CD1a and Cd207 expressing cells prior to scRNA-seq in biopsies LCH_E and LCH_N using FACS.

value: bone

value: male

value: single-system

value: fresh

value: no


title: LCH_O

description: scRNA-seq analysis of an LCH biopsy

source_name: bone biopsy from patient LCH_O, male child, single-system LCH


title: LCH_N

description: scRNA-seq analysis of an LCH biopsy

source_name: skin biopsy from patient LCH_N, male adult, multi-system LCH

value: skin

value: adult

value: enriched for CD1A+CD207+ cells


title: yFR973_spt16-197_80min37C_H3K4me1vsH4_20161024_Rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K4me1vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_404809.bed
A genome browser-ready file for H3K4me1 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: ryH4 (A.Verreault)


title: yFR971_SPT16-WT_80min37C_H3K4me1vsH4_20161024_Rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in WT cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me1vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_937479.bed
A genome browser-ready file for H3K4me1 occupancy (IP/H4) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1

value: H3K4me1 (Abcam ab8895)


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H3 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H3.
SmthBED_yFR974_spt6-1004_80min37C_H3k4me3vsH3_20150718_Rep1-2_MN__S.cerevisiaeApr11_570936.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H3) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 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)

treatment_protocol:
switch to 37°C for 80 min
H3 ChIP. Antibody from Abcam (ab1791). 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 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: H3 (Abcam ab1791)


title: LCH_S1_3 [ATAC-seq]

description: ATAC-seq of sorted LCH-S1 cells

source_name: LCH cells from a lymph node biopsy, enriched for LCH-S1 cell subset using FACS, replicate 1

value: lymph node

value: female

value: child

value: multi-system


title: LCH_J

description: scRNA-seq analysis of an LCH biopsy

source_name: skin biopsy from patient LCH_J, female elderly, multi-system LCH

value: aged

value: Langerhans cell histiocytosis


title: yFR971_SPT16-WT_80min37C_H3K4me2vsH4_20161024_Rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in WT cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me2vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_731901.bed
A genome browser-ready file for H3K4me2 occupancy (IP/H4) in WT cells treated 80 min at 37°C.

value: H3K4me2 (Abcam ab7766)


title: yFR974_spt6-1004_80min37C_H3k4me3vsH3_20150718_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H3 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H3.
SmthBED_yFR974_spt6-1004_80min37C_H3k4me3vsH3_20150718_Rep1-2_MN__S.cerevisiaeApr11_570936.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H3) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: yFR971_WT_80min37C_H3k4me3vsH3_20150718_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H3 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H3.
SmthBED_yFR971_WT_80min37C_H3k4me3vsH3_20150718_Rep1-2_MN__S.cerevisiaeApr11_961606.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H3) in WT cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K4me1vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_404809.bed
A genome browser-ready file for H3K4me1 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.
SmthBED_yFR973_spt16-197_H3K4me3vsMock_20150409_rep1-2_MN__S.cerevisiaeApr11_732941.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Mock) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
Mock ChIP. Rabbit IgG from Millipore (12-370). 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: rabbit IgG


description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H3 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H3.
SmthBED_yFR971_WT_80min37C_H3k4me3vsH3_20150718_Rep1-2_MN__S.cerevisiaeApr11_961606.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H3) in WT cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.
SmthBED_yFR974_spt6-1004_H3K4me3vsMock_20150409_rep1-2_MN__S.cerevisiaeApr11_412362.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Mock) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me1 occupancy in WT cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me1vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_937479.bed
A genome browser-ready file for H3K4me1 occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: LCH_H

description: scRNA-seq analysis of an LCH biopsy

source_name: skin biopsy from patient LCH_H, female infant, multi-system LCH

value: skin

value: infant

value: fresh

value: no


title: LCH_E

description: scRNA-seq analysis of an LCH biopsy

source_name: lymph node biopsy from patient LCH_E, female child, multi-system LCH

value: thawed

value: enriched for CD1A+CD207+ cells


description:
Biological replicate 1 of 2. H3K4me2 occupancy in WT cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me2vsH4_20161024_Rep1-2_MN__S.cerevisiaeApr11_731901.bed
A genome browser-ready file for H3K4me2 occupancy (IP/H4) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1

value: ryH4 (A.Verreault)


title: yFR973_spt16-197_80min37C_H3k4me3vsH3_20150718_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H3 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H3.
SmthBED_yFR973_spt16-197_80min37C_H3k4me3vsH3_20150718_Rep1-2_MN__S.cerevisiaeApr11_907267.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H3) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: H3K4me3 (Abcam ab8580)

value: H3 (Abcam ab1791)


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H3 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H3.
SmthBED_yFR973_spt16-197_80min37C_H3k4me3vsH3_20150718_Rep1-2_MN__S.cerevisiaeApr11_907267.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H3) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: yFR971_WT-SPT16_H3K4me3vsMock_20150409_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.
SmthBED_yFR971_WT-SPT16_H3K4me3vsMock_20150409_rep1-2_MN__S.cerevisiaeApr11_832620.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Mock) in WT cells treated 80 min at 37°C.


title: LCH_I

description: scRNA-seq analysis of an LCH biopsy

source_name: bone biopsy from patient LCH_I, male child, single-system LCH

value: bone

value: male

value: child

value: single-system


title: Sample 3: 5X_Male

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road, Room 3200

department: Neurobiology and Behavior

country: USA

institute: University of California, Irvine

data_processing:
All FASTQ files for a given sample were aligned via CellRanger v2 using default settings.
Human gene count tables were read into the R package Seurat (v2.3.4). Cells were log normalized, scaled, and centered and then PCA was performed on all genes in the dataset. PCs 1:10 were then used for clustering with a resolution parameter of 0.3. Clusters identified as doublets, dividing, or damaged were removed in addition to any cells that were identified as murine in origin.
QC cutoffs were then applied to the remaining cells to keep cells with less then 2 times the median genes and UMI
Samples were then log normalized, scaled, and centered using the negbinom general linear model and PCA was performed on the list of highly variable genes and subsequently used for clustering, TSNE plotting, and differential gene expression analysis
Genome_build: GRCh38.p12 release 94
Supplementary_files_format_and_content: R1 FASTQ: 26bp read (16bp barcode + 10bp UMI); R2 FASTQ: 98bp mRNA read; *_barcodes.tsv: tab-delimited file containing aligned human cellular barcodes; *_genes.tsv: tab-delimited file containing the list of human genes; *_matrix.mtx: matrix file containing the counts for each gene/barcode pair; *_Mousebarcodes.tsv: tab-delimited file containing aligned mouse cellular barcodes.

source_name: Microglia

extract_protocol:
Half brains were enzymatically digested using the Miltenyi Tumor Dissociation Kit and the gentleMACS octodissociator with heaters. 5ug/mL actinomycin D, 10uM triptolide, and 27.1 ug/mL anisomycin were added to the enzymatic mixture to limit transcriptional and translational changes induced by the digestion. Isolated cells were then centrifuged in 23% Percoll to remove myelin and debris and human cells were negatively sorted using the Miltenyi Mouse Cell Depletion kit. Cells were then resuspended at a concentration of 1000 cells/uL in preparation for single-cell sequencing.
Libraries were prepared according to standard 10X genomics 3' v2 protocols

value: AICS-0036 (Coriell)

tag: cell type

value: xMG

tag: cell sex

value: Male

tag: host organism

value: Mus Musculus

tag: host genotype

tag: host sex

tag: host age (months)


title: Sample 4: 5X_Female

value: Female


description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.
SmthBED_yFR971_WT-SPT16_H3K4me3vsMock_20150409_rep1-2_MN__S.cerevisiaeApr11_832620.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Mock) in WT cells treated 80 min at 37°C.

value: rabbit IgG


title: yFR973_spt16-197_80min37C_H3K79me3vsH4_20150323_Rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K79me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_881807.bed
A genome browser-ready file for H3K79me3 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
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: MATα, leu2Δ1, spt16-197

value: H3K79me3 (Abcam ab2621)


title: Sample 2: WT_Female

value: MITRG


title: yFR974_spt6-1004_H3K4me3vsMock_20150409_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.
SmthBED_yFR974_spt6-1004_H3K4me3vsMock_20150409_rep1-2_MN__S.cerevisiaeApr11_412362.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Mock) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: MBJ_iMGL_GFP_6

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

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: InVitro

tag: treatment

tag: cdna fragment length

tag: cdna fragment sd


title: yFR973_spt16-197_H3K4me3vsMock_20150409_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.
SmthBED_yFR973_spt16-197_H3K4me3vsMock_20150409_rep1-2_MN__S.cerevisiaeApr11_732941.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Mock) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

tag: strain


description:
Biological replicate 1 of 2. H3K79me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K79me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_421990.bed
A genome browser-ready file for H3K79me3 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

tag: genotype

value: ryH4 (A.Verreault)


title: MBJ_iMGL_GFP_4


description:
Biological replicate 1 of 2. H3K79me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K79me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_881807.bed
A genome browser-ready file for H3K79me3 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

tag: antibody


title: MBJ_iMGL_GFP_5

tag: cell line


title: MBJ_iMGL_GFP_3


title: Sample 1: WT_Male


title: yFR974_spt6-1004_80min37C_H3K79me3vsH4_20150323_Rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_80min37C_H3K79me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_421990.bed
A genome browser-ready file for H3K79me3 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: MBJ_ExVivo_2

value: ExVivo

value: Homo Sapiens


title: MBJ_xMG_10C_4

value: BIONi010-C (EBiSC)


description:
Biological replicate 1 of 2. H3K36me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K36me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_268761.bed
A genome browser-ready file for H3K36me3 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 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)


title: MBJ_ExVivo_1


title: MBJ_xMG_10C_3


description:
Biological replicate 1 of 2. H3K79me3 occupancy in WT cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K79me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_125646.bed
A genome browser-ready file for H3K79me3 occupancy (IP/H4) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1


title: yFR973_spt16-197_80min37C_H3K36me3vsH4_20150323_Rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_80min37C_H3K36me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_268761.bed
A genome browser-ready file for H3K36me3 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: yFR971_SPT16-WT_80min37C_H3K79me3vsH4_20150323_Rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in WT cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K79me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_125646.bed
A genome browser-ready file for H3K79me3 occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: MBJ_xMG_10C_2


title: yFR971_SPT16-WT_80min37C_H3K36me3vsH4_20150323_Rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in WT cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K36me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_723783.bed
A genome browser-ready file for H3K36me3 occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: MBJ_xMG_10C_1


title: MBJ_xMG_CDI_6

value: iCell Hematopoietic Progenitor Cells (CDI)


title: MBJ_xMG_CDI_5


title: MBJ_xMG_CDI_4


description:
Biological replicate 1 of 2. H3K36me3 occupancy in WT cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_SPT16-WT_80min37C_H3K36me3vsH4_20150323_Rep1-2_MN__S.cerevisiaeApr11_723783.bed
A genome browser-ready file for H3K36me3 occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: MBJ_xMG_CDI_3


title: yFR974_spt6-1004_H3K4me3vsH4_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_H3K4me3vsH4_Rep1-2_MN__S.cerevisiaeApr11_130755.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

value: H3K4me3 (Abcam ab8580)


title: MBJ_xMG_CDI_2

value: xMG


title: MBJ_xMG_CDI_1

value: Male


title: yFR971_WT_H3K4me3vsH4_SPIKE-IN_Rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_WT_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_765232.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: yFR974_spt6-1004_H3K4me3vsH4_Rep1

description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR974_spt6-1004_H3K4me3vsH4_Rep1-2_MN__S.cerevisiaeApr11_130755.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_775521.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: MBJ_xMG_GFP_LPS_5

value: AICS-0036 (Coriell)

value: Mus Musculus

value: Intraperitoneal 2mg/kg LPS (3X)


title: MBJ_xMG_GFP_LPS_4


title: MBJ_xMG_GFP_LPS_3


title: MBJ_xMG_GFP_LPS_2


title: yFR971_WT_H3K4me3vsH4_SPIKE-IN_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR971_WT_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_765232.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in WT cells treated 80 min at 37°C.


title: yFR2995vs971_Asf1-3FLAGvsNoTag_WT_80min-37C_20180222_Rep1

description:
Biological replicate 1 of 2. Asf1 occupancy in WT cells treated 80 minutes at 37°C. Asf1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Asf1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the ASF1 gene is not tagged (Cy3-labeled).
SmthBED_yFR2995vs971_Asf1-3FLAGvsNoTag_WT_20171203_Rep1-2_MN__S.cerevisiaeApr11_971324.bed
A genome browser-ready file for Asf1 occupancy (IP/no tag) in WT cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
Flag ChIP. Antibody from Sigma-Aldrich (F3165). 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 (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: MATα, leu2Δ1, ASF1::3xFLAG-KanMX

value: Flag (Sigma-Aldrich F3165)


title: yFR973_spt16-197_H3K4me3vsH4_SPIKE-IN_Rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Spike PhiX174 DNA was added to the extract prior to immunoprecipitation (Jeronimo et al. 2015). H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against H4 ChIP sample (Cy3-labeled), also performed on the some extract using a rabbit polyclonal antibody anti-H4.
SmthBED_yFR973_spt16-197_H3K4me3vsH4_SPIKE-IN_Rep1-2_MN__S.cerevisiaeApr11_775521.bed
A genome browser-ready file for H3K4me3 occupancy (IP/H4) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: yFR2995vs971_Asf1-3FLAGvsNoTag_WT_80min-37C_20180222_Rep2

description:
Biological replicate 2 of 2. Asf1 occupancy in WT cells treated 80 minutes at 37°C. Asf1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Asf1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the ASF1 gene is not tagged (Cy3-labeled).
SmthBED_yFR2995vs971_Asf1-3FLAGvsNoTag_WT_20171203_Rep1-2_MN__S.cerevisiaeApr11_971324.bed
A genome browser-ready file for Asf1 occupancy (IP/no tag) in WT cells treated 80 min at 37°C.


title: yFR3000vs971_Hir1-3FLAGvsNoTag_WT_80min-37C_20180222_Rep2

description:
Biological replicate 2 of 2. Hir1 occupancy in WT cells treated 80 minutes at 37°C. Hir1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Hir1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the HIR1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3000vs971_Hir1-3FLAGvsNoTag_WT_20171203_Rep1-2_MN__S.cerevisiaeApr11_729188.bed
A genome browser-ready file for Hir1 occupancy (IP/no tag) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1,HIR1::3xFLAG-KanMX


title: MBJ_xMG_GFP_LPS_1


title: yFR2997vs973_Asf1-3FLAGvsNoTag_spt16-197_80min-37C_20180222_Rep2

description:
Biological replicate 2 of 2. Asf1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Asf1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Asf1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the ASF1 gene is not tagged (Cy3-labeled).
SmthBED_yFR2997vs973_Asf1-3FLAGvsNoTag_spt16-197_20171203_Rep1-2_MN__S.cerevisiaeApr11_556058.bed
A genome browser-ready file for Asf1 occupancy (IP/no tag) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197, ASF1::3xFLAG-KanMX


title: yFR3002vs973_Hir1-3FLAGvsNoTag_spt16-197_80min-37C_20180222_Rep2

description:
Biological replicate 2 of 2. Hir1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Hir1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Hir1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the HIR1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3002vs973_Hir1-3FLAGvsNoTag_spt16-197_20171203_Rep1-2_MN__S.cerevisiaeApr11_167062.bed
A genome browser-ready file for Hir1 occupancy (IP/no tag) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197, HIR1::3xFLAG-KanMX


title: yFR2997vs973_Asf1-3FLAGvsNoTag_spt16-197_80min-37C_20180222_Rep1

description:
Biological replicate 1 of 2. Asf1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Asf1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Asf1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the ASF1 gene is not tagged (Cy3-labeled).
SmthBED_yFR2997vs973_Asf1-3FLAGvsNoTag_spt16-197_20171203_Rep1-2_MN__S.cerevisiaeApr11_556058.bed
A genome browser-ready file for Asf1 occupancy (IP/no tag) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: yFR3000vs971_Hir1-3FLAGvsNoTag_WT_80min-37C_20180222_Rep1

description:
Biological replicate 1 of 2. Hir1 occupancy in WT cells treated 80 minutes at 37°C. Hir1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Hir1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the HIR1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3000vs971_Hir1-3FLAGvsNoTag_WT_20171203_Rep1-2_MN__S.cerevisiaeApr11_729188.bed
A genome browser-ready file for Hir1 occupancy (IP/no tag) in WT cells treated 80 min at 37°C.


title: MBJ_xMG_GFP_3

value: Intraperitoneal DPBS


title: yFR3002vs973_Hir1-3FLAGvsNoTag_spt16-197_80min-37C_20180222_Rep1

description:
Biological replicate 1 of 2. Hir1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Hir1 ChIP sample (Cy5-labeled) was performed from a 3xFlag-tagged Hir1 strain using a mouse monoclonal anti-Flag antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the HIR1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3002vs973_Hir1-3FLAGvsNoTag_spt16-197_20171203_Rep1-2_MN__S.cerevisiaeApr11_167062.bed
A genome browser-ready file for Hir1 occupancy (IP/no tag) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: MBJ_xMG_GFP_2


title: yFR1478_Spt16-AA_Rapa30min_Rpb3vsInput_20170718_Rep2

description:
Biological replicate 2 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.

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
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

value: Rpb3 (BioLegend 665004)

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


title: MBJ_xMG_GFP_1


title: yFR1478_Spt16-AA_DMSO_H3K36me3vsInput_20170718_Rep2

description:
Biological replicate 2 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.

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.

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.

value: H3K36me3 (Abcam Ab9050)

treatment_protocol:
DMSO for 30 min
none


title: MBJ_iMGL_LPS_3

value: iMGL

value: 24hrs, 100ng/mL LPS


title: yFR1480_Spt6-AA_Thio-Rapa30min_H3K4me3vsInput_20171102_rep2

description:
Biological replicate 2 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.

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
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: 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

value: H3K4me3 (Abcam ab8580)

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


title: yFR1480_Spt6-AA_Thio-Rapa30min_H4vsInput_20171102_rep2

description:
Biological replicate 2 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.

value: ryH4 (A.Verreault)


title: MBJ_iMGL_LPS_2

value: AICS-0036 (Coriell)

value: Male


title: MBJ_iMGL_LPS_1


title: MBJ_iMGL_SAL_2

value: DPBS


title: MBJ_iMGL_SAL_3


title: yFR1480_Spt6-AA_Thio-Rapa30min_Rpb3vsInput_20171102_rep2

description:
Biological replicate 2 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.

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.


title: yFR1480_Spt6-AA_Thio-Rapa30min_H3K36me3vsInput_20171102_rep2

description:
Biological replicate 2 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.

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.


title: yFR1478_Spt16-AA_DMSO_Rpb3vsInput_20170718_Rep2

description:
Biological replicate 2 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.

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.


title: MBJ_iMGL_SAL_1


title: NGEJ-4_H3K27Ac

city: Los Angeles

first: Li

last: Chen

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

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

source_name: Gastroesophageal junction 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

value: NGEJ


title: NGEJ-5_H3K27Ac


title: NGEJ-3_H3K27Ac


title: yFR1480_Spt6-AA_Rapa30min_Rpb3vsInput_20171102_rep2

description:
Biological replicate 2 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.


title: yFR1480_Spt6-AA_Rapa30min_H4vsInput_20171102_rep2

description:
Biological replicate 2 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.

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.


title: yFR1480_Spt6-AA_Rapa30min_H3K4me3vsInput_20171102_rep2

description:
Biological replicate 2 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: NGEJ-2_H3K27Ac


title: NGEJ-1_H3K27Ac


title: EAC-T11_H3K27Ac

source_name: Esophageal Adenocarcinoma tissue


title: EAC-T10_INPUT


title: yFR1480_Spt6-AA_Rapa30min_H3K36me3vsInput_20171102_rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in Spt6-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_yFR1480_Spt6-AA_Rapa30min_H3K36me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_507349.bed
A genome browser-ready file for H3K36me3 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
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.