title: yFR1630_endoCTDWT-MYC_DMSO_2h_MYCvsInput_20170707_rep2

description:
Anti-Flag M2 (Sigma F3165). Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. Anti-Flag M2 (Sigma F3165) is added (5ug/ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody is added to 500 uL of lysate, and incubated overnight at 4'C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4'C, and 50uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65'C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 2 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with DMSO for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1630_endoCTDWT-MYC_DMSO_2h_MYCvsInput_20170707_rep1-2__S.cerevisiaeApr11_676412.bed
A genome browser-ready file for CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with DMSO for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


status: Public on Jan 21 2019

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 1 of 2. rpb1-CTDY1F-3xFLAG occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min. CTDY1F ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against FLAG and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1630_exo-CTDY1F-FLAG_6-AU_2h_FLAGvsInput_20170712_rep3-4__S.cerevisiaeApr11_89260.bed
A genome browser-ready file for CTDY1F occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.

hyb_protocol: Combined samples were resuspended in 110 µL of a hybridization mix (5 µL of 10 mg/mL ssDNA, 5 µL of 8 mg/mL tRNA and 100 µL DIG EASY (Roche, 11603558001)) and incubated 5 min at 95˚C followed by 5 min at 42˚C. Samples were incubated overnight on Agilent microarrays in SureHyb chambers with rotation. Microarrays were washed 5 min at room temperature with Wash I buffer (6X SSPE, 0.005% N-lauroylsarcosine) and washed a second time with a pre-warmed (42˚C) Wash II buffer (0.06X SSPE) during 5 min at room temperature.

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2µm resolution. Scanner was set as follow: pixel size = 2µm; speed = 20; Scan Mode = Normal; Acquisition Mode = Simultaneous; Focus = Auto. Detection gain for 635 and 532 wavelengths were manually adjusted in order to have less than 5% spot saturation.

data_processing: Correction = Foreground-Background; Normalisation = limma loess (subgrid)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: DNA blunting was done starting from 40 µL of ChIP DNA or about 400 ng of Input DNA. Samples were added to 11 µL 10X NEB2 buffer, 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA pol (New England Biolabs, M0203L) in a final volume of 70 µL and incubated 20 min at 12˚C. Then, 11.5 µL of 3 M NaOAc pH 5.2 and 2 µL of 20 mg/mL glycogen were added, followed by a phenol/chloroform/isoamyl alcool extraction ethanol precipitation. DNA pellets were resuspended in 25 µL H2O and DNA linkers were ligated using 10 µL 5x ligase buffer, 6.7 µL annealed linkers (made of the annealing of the following oligos: oligo 1, GCGGTGACCCGGGAGATCTGAATTC and oligo 2, GAATTCAGATC) and 0.5 µL (2.5 units) of T4 DNA ligase (ThermoFisher, 15224041), overnight at 16˚C. Samples were precipitated with 6 µL of 3M NaOAc pH 5.2 and ethanol, and resuspended in 25 µL H2O. 15 µL of labeling mix (4 µL 10X ThermoPol buffer, 2 µL of 5 mM a.a.-dUTP/dNTP mix (5mM each dATP, dGTP and dCTP, 3mM dTTP and 2mM aminoallyl-dUTP) and 1.25 µL of oligo 1 (from 40 µM stock) was add to each sample. Samples were placed in a thermocycler and temperature was raised to 55˚C.  10 µL of enzyme mix (8 µL H2O, 1 µL 10X ThermoPoll buffer, 1 µL (5 units) Taq polymerase (ThermoFisher, 18038240) and 0.01 µL (0.025 units) Pfu (Fermentas, EP0502)) was added and the following program was run. 1) 72˚C, 5 min, 2) 95˚C, 2 min, 3) 31 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1min, 4) 72˚C, 4min, 5) 4˚C, forever. PCR products were purified using QIAgen PCR purification kit with few modifications: PE buffer was replaced by a Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Supernatants were dried in a speed-vac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 (ChIP samples) or Cy3 (control samples)-ester dye (GE Healthcare, CA95017-373L and CA95017-379L) were added. Samples were incubated 1 hr at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 was added and samples were purified on QIAgen PCR purification kit (28106) using the manufacturer’s protocol. ChIP and control samples were combined and dried in a speed-vac.

growth_protocol:
YNB-HIS-URA + 2%Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reaches OD600=0.5-0.6. Cell cultures are treated with 50 microg/ml of 6-AU and allowed to grow for additional 120 min. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.
YNB-HIS-URA + 2%Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reaches OD600=0.5-0.6. Cell cultures are treated with 50 microg/ml of 6-AU and allowed to grow for additional 120 min. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.

extract_protocol: Frozen cell pellets were resuspended in 700 µL of Lysis buffer (50 mM HEPES-KOH 1 M pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) supplemented with protease inhibitors (1 mM PMSF, 1 mM benzamidine, 10 µg/mL aprotinin, 1 µg/mL leupeptin and 1 µg/mL pepstatin) and lysed by bead beating. The extracts were sonicated with a Model 100 Sonic dismembrator equipped with a micro probe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles to obtain fragments averaging 500 bp. Samples were centrifuged at 20,000 g for 5 min at 4˚C to remove cell debris and 500 µL of soluble chromatin were used per ChIP experiment. 5 µL (1% of the amount used for IP) was also kept as an Input sample.

treatment_protocol:
50 microg/ml 6-AU for 120 min
50 microg/ml 6-AU for 120 min

tag: strain

tag: genotype

value: MATa, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, GAL+, psi+, RPB1-3xMYC::URA3, [pFR511 (CEN, HIS3, rpb1-CTDY1F-3xFLAG)]

tag: antibody

value: Flag M2 R (Sigma)


title: genomic DNA from BFC23

city: Houston

first: Oxana

middle: Yu.

last: Naumova

state: TX

address: 4849 Calhoun Rd, TIMES, Rm 373

department: Psychology

country: USA

institute: University of Houston

description: Family-reared kid

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: Illumina GenomeStudio Methylation Module v1.8

label: Cy5 and Cy3

organism: Homo sapiens

source_name: whole blood BFC23

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: whole blood

tag: disease state

value: normal


title: genomic DNA from BFC20

description: Family-reared kid

source_name: whole blood BFC20

value: Male


description:
Anti-Flag M2 (Sigma F3165). Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. Anti-Flag M2 (Sigma F3165) is added (5ug/ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody is added to 500 uL of lysate, and incubated overnight at 4'C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4'C, and 50uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65'C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 1 of 2. rpb1-CTDY1F-3xFLAG occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with DMSO for 120 min. CTDY1F ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against FLAG and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1630_exo-CTDY1F-FLAG_DMSO_2h_FLAGvsInput_20170712_rep3-4__S.cerevisiaeApr11_397458.bed
A genome browser-ready file for CTDY1F occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with DMSO for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.

growth_protocol:
YNB-HIS-URA + 2%Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reaches OD600=0.5-0.6. Cell cultures are treated with DMSO (same amount as 6-AU (50ug/ml) treatment) and allowed to grow for additional 120 min. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.
YNB-HIS-URA + 2%Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reaches OD600=0.5-0.6. Cell cultures are treated with DMSO (same amount as 6-AU (50ug/ml) treatment) and allowed to grow for additional 120 min. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.

treatment_protocol:
DMSO for 120 min
DMSO for 120 min


description:
Anti-Flag M2 (Sigma F3165). Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. Anti-Flag M2 (Sigma F3165) is added (5ug/ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody is added to 500 uL of lysate, and incubated overnight at 4'C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4'C, and 50uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65'C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 1 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with DMSO for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1630_endoCTDWT-MYC_DMSO_2h_MYCvsInput_20170707_rep1-2__S.cerevisiaeApr11_676412.bed
A genome browser-ready file for CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with DMSO for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.

value: 9E10 (lab stock by AF)


title: yFR1630_endoCTDWT-MYC_6-AU_2h_MYCvsInput_20170707_rep2

description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 2 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1630_endoCTDWT-MYC_6-AU_2h_MYCvsInput_20170707_rep1-2__S.cerevisiaeApr11_113998.bed
A genome browser-ready file for CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


title: genomic DNA from BFC21

description: Family-reared kid

source_name: whole blood BFC21


title: yFR1630_exo-CTDY1F-FLAG_6-AU_2h_FLAGvsInput_20170712_rep4

description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 2 of 2. rpb1-CTDY1F-3xFLAG occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min. CTDY1F ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against FLAG and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1630_exo-CTDY1F-FLAG_6-AU_2h_FLAGvsInput_20170712_rep3-4__S.cerevisiaeApr11_89260.bed
A genome browser-ready file for CTDY1F occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 1 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1630_endoCTDWT-MYC_6-AU_2h_MYCvsInput_20170707_rep1-2__S.cerevisiaeApr11_113998.bed
A genome browser-ready file for CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1F-3xFLAG cells treated with 6-AU for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


title: yFR1506_exo-CTDWT-FLAG_DMSO_2h_FLAGvsInput_20170712_rep4

description:
Anti-Flag M2 (Sigma F3165). Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. Anti-Flag M2 (Sigma F3165) is added (5ug/ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody is added to 500 uL of lysate, and incubated overnight at 4'C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4'C, and 50uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65'C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 2 of 2. Rpb1-3xFLAG occupancy in endo-Rpb1-3xMYC and exo-Rpb1-3xFLAG cells treated with DMSO for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against FLAG and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1506_exo-CTDWT-FLAG_DMSO_2h_FLAGvsInput_20170712_rep3-4__S.cerevisiaeApr11_397136.bed
A genome browser-ready file for exo-CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and endo-RPB1-3xFLAG cells treated with DMSO for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.

value: MATa, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, GAL+, psi+, RPB1-3xMYC::URA3, [pFR482 (CEN, HIS3, RPB1-CTDWT-3xFLAG)]


title: genomic DNA from BFC24

description: Family-reared kid

source_name: whole blood BFC24


title: genomic DNA from BFC19

description: Family-reared kid

source_name: whole blood BFC19


description:
Anti-Flag M2 (Sigma F3165). Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. Anti-Flag M2 (Sigma F3165) is added (5ug/ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody is added to 500 uL of lysate, and incubated overnight at 4'C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4'C, and 50uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65'C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 1 of 2. Rpb1-3xFLAG occupancy in endo-Rpb1-3xMYC and exo-Rpb1-3xFLAG cells treated with DMSO for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against FLAG and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1506_exo-CTDWT-FLAG_DMSO_2h_FLAGvsInput_20170712_rep3-4__S.cerevisiaeApr11_397136.bed
A genome browser-ready file for exo-CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and endo-RPB1-3xFLAG cells treated with DMSO for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


title: yFR1506_endoCTDWT-MYC_DMSO_2h_MYCvsInput_20170707_rep2

description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 2 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-Rpb1-3xFLAG cells  treated with DMSO for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1506_endoCTDWT-MYC_DMSO_2h_MYCvsInput_20170707_rep1-2__S.cerevisiaeApr11_279274.bed
A genome browser-ready file for endo-CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and endo-RPB1-3xFLAG cells treated with DMSO for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


title: An-control_time-120_rep-C

type: SRA

city: Madison

first: Daniel

last: Amador-Noguez

state: WI

address: 1550 Linden Dr

department: Bacteriology

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
Reads were quality checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). According to FastQC reports, quality scores remained high throughout the reads and adapter content was below 0.5 percent. Therefore, reads were not trimmed before alignment.
Raw reads in fastq format were aligned to the Z. mobilis ZM4 ATCC 31821 genome (GenBank accession no. CP023715) using bowtie-2 via RSEM (https://deweylab.github.io/RSEM/) Alignment parameters were set to the default value.
Estimated read counts were obtained for each gene using the RSEM method “rsem-calculate-expression” using the “bowtie2” option. (http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html)
Differential expression analysis was conducted using edgeR (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/). Log2 fold-change values were calculated using edgeR for each gene at each time-point compared to time zero. O2 samples were all compared to the O2 zero time-point, whereas An samples were compared to the An time zero.
mRNA seq data were subjected to a repeated measures analysis of variance (ANOVA) test for statistical analysis. Transcripts per million were used as input for this analysis. The repeated measures ANOVA was used to identify genes whose abundance or expression level changed in response to oxygen. Statistical significance indicates that at least one time-point during the oxygen exposure time-course had a mean value that was different from the means at the other time-points. This allowed us to obtain a single p-value for each gene rather than a unique p-value for every time-point compared to time zero or an anaerobic control. Anaerobic controls were not included in statistical analysis because, due to limiting costs, anaerobic control samples were not collected at every time-point and are therefore not statistically comparable. Time was considered as a categorical rather than continuous variable to avoid choosing a specific relationship (e.g. linear, quadratic) of gene expression with respect to time. P-values were corrected for multiple hypothesis testing using the Benjamini-Hochberg method to calculate false discovery rate (FDR) (http://www.jstor.org/stable/2346101)
Genome_build: Z. mobilis ZM4 ATCC 31821 genome (GenBank accession no. CP023715)
Supplementary_files_format_and_content: Tab-delimited text files containing log2-fold-change values for each gene/locus tag (rows) and each sample (column) and p-values/FDR for each gene (final two columns)

molecule: total RNA

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: anaerobic control

growth_protocol: Zymomonas mobilis strain ZM4 (ATCC 31821) was struck onto rich media-glucose plates (20g/L glucose, 2g/L KH2PO4, 10g/L yeast extract, 18g/L Agar) from a frozen glycerol stock and incubated at 30°C anaerobically for 3-6 days. A single colony was used to inoculate liquid rich media (20g/L glucose, 2g/L KH2PO4, 10g/L yeast extract). The rich media over-night was then sub-cultured through two passages of Zymomonas minimal media (20g/L glucose, 1g/L KH2PO4, 1g/L K2HPO4, 0.5g/L NaCl, 1g/L (NH4)2SO4, 0.2g/L MgSO4 • 7 H2O, 0.025 g/L Na2MoO4 • 2 H20, 0.025g/L FeSO4 • 7 H2O, 0.01 g/L CaCl2 • 2 H2O, 1mg/L Calcium Pantothenate). The second minimal media overnight culture was then used to inoculate all experimental cultures with a starting OD600nm of 0.04 to 0.07 under anaerobic conditions. All experimental cultures were grown in Zymomonas minimal media with a 80 mL starting culture volume in 500 mL Erlenmeyer flasks. Experimental cultures that were exposed to oxygen were grown in baffled flasks to ensure full aeration. Experimental cultures left anaerobic as controls were stirred with a stir bar at 120 rpm. All media was kept anaerobic for at least 16 hours prior to inoculation. The atmosphere in the anaerobic glove bag was composed of 1% H2, 5% CO2, and remaining percentage N2. Oxygen levels were kept below 50 ppm.

extract_protocol:
At the time of extraction, 6mL of culture was collected from the culture flask and immediately combined with 6mL of methanol that had been kept on dry ice in a 15mL centrifuge tube. The mixture was then centrifuged at 5,000 × g for 15 min at -10°C. Supernatant was discarded and pellets were frozen at -80°C until RNA extraction. Total RNA was extracted at 4°C using the RNeasy® Mini Kit (Qiagen, cat. no. 74106) and submitted to the University of Wisconsin-Madison Biotech center for further analysis. RNA purity and quality was assessed by NanoDrop and AgilentQC. Samples with A260/280 below 1.8 were re-run through the RNeasy® column to remove contaminants.
Samples were processed to remove rRNA using the Illumina EpiCentre Ribo-Zero Magnetic Kit for Bacteria. The cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Cultures were grown until they reached an OD600 of  0.3-0.45, at which point the time zero time-point extractions were taken. Immediately following the time-zero time-point, aerobic (O2) cultures were removed from the anaerobic glove bag and placed in a 30°C water bath under atmospheric conditions where they were shaken at 250 rpm for the duration of the two-hour time-course. Anaerobic (An) cultures remained in the glove bag. Extractions were taken for mRNA sequencing at t = 0, 5, 15, 30, 45, 60, and 120 minutes after O2 cultures were transferred and t = 0, 60, and 120 minutes for anaerobic control

tag: condition

value: anaerobic

tag: time

tag: replicate

value: C


title: An-control_time-120_rep-A

value: A


description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 1 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-Rpb1-3xFLAG cells  treated with DMSO for 120 min. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1506_endoCTDWT-MYC_DMSO_2h_MYCvsInput_20170707_rep1-2__S.cerevisiaeApr11_279274.bed
A genome browser-ready file for endo-CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and endo-RPB1-3xFLAG cells treated with DMSO for 120 min.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


title: An-control_time-120_rep-B

value: B


title: An-control_time-60_rep-C


title: An-control_time-60_rep-A


title: genomic DNA from BFC16

description: Family-reared kid

source_name: whole blood BFC16


title: An-control_time-60_rep-B


title: yFR2227_CTDY1E-3xFLAG-Exo_FLAGvsInput_20151125_rep2

description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 2 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1E-3xFLAG cells. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2227_CTDWT-3xWT-endo_MYCvsInput_20151125_rep1-2__S.cerevisiaeApr11_365457.bed
A genome browser-ready file for CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1E-3xFLAG cells.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.

growth_protocol:
YNB-HIS + 2%Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reaches OD600=0.8. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.
YNB-HIS + 2%Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reaches OD600=0.8. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.

value: MATa, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, GAL+, psi+, RPB1-3xMYC::URA3, [pFR576 (CEN, HIS3, rpb1-CTDY1E-3xFLAG)]


title: An-control_time-0_rep-B


title: An-control_time-0_rep-C


title: KIL_gill_3

type: RNA

city: Sopot

first: Magdalena

last: Malachowicz

address: Powstańców Warszawy

country: Poland

institute: Institute of Oceanology Polish Academy of Sciences

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned in an Agilent Technologies Scanner G2505C US10353831, according to the manufacturer’s protocol GE2_1010_Sep10

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.10.1.1) following the Agilent protocol GE2_1010_Sep10. Arrays normalization was performed using the Limma package in R. The raw mean signal (gMeanSignal) was background corrected (normexp method). Next lowess and quantile normalization were performed.

organism: Gadus morhua

source_name: Gills of cod from Kiel Bight

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: RNA was isolated using the ISOLATE II RNA Mini Kit (Bioline). Concentration of extracted RNA was determined at 260 nm on microplate using the Epoch Microplate Spectrophotometer (BioTek Instruments). The RNA integrity was verified using an Agilent Bioanalyser (Agilent Technologies)

tag: tissue

value: gill

source_name: mix of all samples


title: yFR2227_CTDY1E-3xFLAG-Exo_FLAGvsInput_20151125_rep1

description:
9E10 anti-Myc antibody. Anti-mouse Dynabeads (PanMouse) (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM 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.
Biological replicate 1 of 2. Rpb1-3xMYC occupancy in endo-Rpb1-3xMYC and exo-rpb1-CTDY1E-3xFLAG cells. CTDWT ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against MYC and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2227_CTDWT-3xWT-endo_MYCvsInput_20151125_rep1-2__S.cerevisiaeApr11_365457.bed
A genome browser-ready file for CTDWT occupancy (IP/Input) in endo-RPB1-3xMYC and exo-rpb1-CTDY1E-3xFLAG cells.
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).
Supernatants were recovered and treated with RNase A (345 μL TE (10 mM Tris-HCl pH 8, 1 mM EDTA), 3 μL RNAse A 10 mg/mL, 2 μL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. DNA was extracted twice with phenol/chloroform/isoamyl alcool, ethanol-precipitated and resuspended in 50 µL TE.


title: An-control_time-0_rep-A


title: KIL_gill_1


title: genomic DNA from BFC13

description: Family-reared kid

source_name: whole blood BFC13


title: O2_time-120_rep-C

source_name: oxygen exposure

value: oxygen


title: genomic DNA from BFC17

description: Family-reared kid

source_name: whole blood BFC17


title: O2_time-120_rep-B


title: genomic DNA from BFC14

description: Family-reared kid

source_name: whole blood BFC14


title: O2_time-120_rep-D

value: D


title: KIL_gill_2


title: GDA_gill_5

source_name: Gills of cod from Gdansk Bay


title: genomic DNA from BFC12

description: Family-reared kid

source_name: whole blood BFC12


title: GDA_gill_4


title: O2_time-60_rep-D


title: GDA_gill_3


title: O2_time-120_rep-A


title: GDA_gill_2


title: GDA_gill_1


title: Normal donor 4, technical rep 2

city: São Paulo

first: Rodrigo

last: Fernando

state: SP

address: 824 Doutor Diogo de Faria, 5th floor

country: Brazil

institute: Federal University of São Paulo

description:
G5 II
LARSII_(HuEx-1_0-st-v2).CEL

hyb_protocol: Following labeling, cDNA were hybridized for 17h on Affymetrix GeneChip® Human Exon 1.0 ST Array. Then, the GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450 according to the Affymetrix protocol.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix), and raw data was extracted from the scanned images and quantified using the Affymetrix GeneChip Command Console® Software (Affymetrix), producing raw probe intensity data in the Affyemetrix CEL files.

data_processing: Microarray raw data preprocessing and identification of differentially expressed genes were performed using the AltAnalyze software. Once the analysis parameters were set, the raw data, in CEL format, was preprocessed by the Robust Multi-array Analysis (RMA) method, which includes background correction, quantile normalization and summarization of the  probes into specific probe sets.

label: Biotin

source_name: bone-marrow mesenchymal stem cells isolated from normal donor

label_protocol: Biotinylated cDNA were prepared according to the manufacturer's instruction (Affymetrix).

growth_protocol: Bone marrow was harvested from the iliac crest of individuals after informed consent. Mononuclear cells were isolated by density gradient using Ficoll-Paque PLUS (GE Healthcare, Little Chalfont, Bucks, GBR), according to the manufacturer's instructions. Finally, MSC were sorted by Magnetic-Activated Cell Sorting (MACS) methodology, using CD105+ as a positive marker (Miltenyi Biotec, Bergisch Gladbach, DEU). MSC were incubated at 37°C, 5% CO2 and high humidity. After 48 hours, nonadherent cells were removed by washing. MSC expansion was performed on αMEM with GlutaMAX and nucleoside medium, supplemented with penicillin (100 U/mL) / streptomycin (100 μg/mL), fungizone (2.5 μg / mL) (All Gibco, Carlsbad, CA, USA) and 10% fetal bovine serum (FBS) (Vitrocell, Campinas, SP, BRA). MSC were incubated at 37°C, 5% CO2 and high humidity. During passage zero, the cells were fed twice a week, replacing only 50% of culture medium volume, until the cells reached 80% confluence or up to 21 days. Then, MSC were detached from the culture plastic with the aid of 0.25% trypsin-EDTA reagent (Gibco, Carlsbad, CA, USA), counted by tripan blue exclusion method and seeded again. From the first passage onwards, 80% of the culture medium volume was replaced at the same conditions.

extract_protocol: Total RNA from each cell culture was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA), according to the manufacturer's instruction.

treatment_protocol: Not applicable

tag: subject status

value: normal donor

tag: subject id

value: donor 4

tag: age

value: 1 year

tag: cell type

value: bone-marrow mesenchymal stem cells


title: genomic DNA from BFC08

description: Family-reared kid

source_name: whole blood BFC08

value: Female

value: whole blood


title: O2_time-60_rep-B


title: genomic DNA from BFC11

description: Family-reared kid

source_name: whole blood BFC11

value: Male

value: normal


title: Normal donor 4, technical rep 1

description:
G5 I
LARSI_(HuEx-1_0-st-v2).CEL


title: H3.1

city: Durham

first: Devjanee

last: Swain Lenz

state: NC

address: 130 Bioscience Drive

institute: Duke University

description: chromatin accessibile DNA

library_source: genomic

data_processing:
map reads to native genome using bowtie2 default settings for 150 paired end reads
reciprocal liftover to hg19
macs2 for peak calling using paired-end reads algorithm
take union peaks for three species
create dataframe of read counts for each peak, peaks where at least one sample has zero counts are removed
Genome_build: hg19
Supplementary_files_format_and_content: count table

source_name: Adipose from NICHD Brain and Tissue Bank for Developmental Disorders Donor 602

growth_protocol: frozen postmortem samples

extract_protocol:
We homogenized 20 mg of frozen pulverized adipose tissue in nuclei isolation buffer (20 nM Tris-HCl, 50 mM EDTA, 5mM spermidine, 0.15 mM spermine, 0.1% beta meracptoethanol, 40% glycerol, 1% NP40, pH 7.5) with a dounce homogenizer. The homogenate was centrifuged at 1,100 g for 10 minutes at 4C and the pellets resuspended in resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH 7.4).
We ran tagmentation reactions at 37C for 30 minutes, purified samples with Qiagen MinElute kits, and amplified libraries with NEB NextPCR

treatment_protocol: ground in frozen nitrogen with cell crusher

value: adipose

tag: Sex

value: male

value: adult


title: O2_time-60_rep-A

value: A


title: genomic DNA from BFC18

description: Family-reared kid

source_name: whole blood BFC18


title: Normal donor 4, technical rep 3

description:
G5 III
LARSIII_(HuEx-1_0-st-v2).CEL


title: genomic DNA from BFC15

description: Family-reared kid

source_name: whole blood BFC15


title: O2_time-45_rep-D


title: H2.1

description: chromatin accessibile DNA

source_name: Adipose from NICHD Brain and Tissue Bank for Developmental Disorders Donor 1442


title: genomic DNA from BFC10

description: Family-reared kid

source_name: whole blood BFC10


title: genomic DNA from BFC09

description: Family-reared kid

source_name: whole blood BFC09


title: O2_time-45_rep-C

value: C


title: Normal donor 3, technical rep 3

description:
G4 III
G5III_(HuEx-1_0-st-v2).CEL

value: donor 3

value: 46 years


title: Normal donor 3, technical rep 2

description:
G4 II
G5II_(HuEx-1_0-st-v2).CEL


title: H1.3

description: chromatin accessibile DNA

source_name: Adipose from NICHD Brain and Tissue Bank for Developmental Disorders Donor 1104


title: genomic DNA from BFC06

description: Family-reared kid

source_name: whole blood BFC06


title: O2_time-45_rep-B

value: oxygen

value: B


title: H1.2

description: chromatin accessibile DNA


title: genomic DNA from BFC02

description: Family-reared kid

source_name: whole blood BFC02


title: O2_time-45_rep-A

source_name: oxygen exposure


title: H2.2

description: chromatin accessibile DNA


title: genomic DNA from BFC04

description: Family-reared kid

source_name: whole blood BFC04


title: Normal donor 2, technical rep 3

description:
G3 III
G4III_(HuEx-1_0-st-v2).CEL

value: normal donor

value: donor 2

value: 31 years


title: Normal donor 2, technical rep 2

description:
G3 II
G4II_(HuEx-1_0-st-v2).CEL

value: bone-marrow mesenchymal stem cells


title: H1.1

description: chromatin accessibile DNA


title: O2_time-30_rep-E

value: E


title: Normal donor 2, technical rep 1

description:
G3 I
G4I_(HuEx-1_0-st-v2).CEL

value: Female


title: abc.del.E2.HiC [Hi-C]

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

data_processing:
Reads were trimmed by Trim Galore! (https://github.com/FelixKrueger/TrimGalore).
Mapped to mm10 using HiCUP v0.5.9 (Wingett et al., 2015).
Allele parsed using SNPsplit v0.3.0 (Krueger and Andrews, 2016).
Hi-C eigenvector was calculated using Juicer (Durand et al., 2016) at 200Kb resolution.
Genome_build: mm10
Supplementary_files_format_and_content: *_HiC_chr16.juicebox.200Kb.eigen.txt
Supplementary_files_format_and_content: *_HiC_chr16.juicebox.200Kb.cor.txt

organism: Mus musculus

growth_protocol: Mouse ESCs were maintained on 1% gelatin coated dishes. Hybrid cells (Cas/129) were grown in DMEM supplemented with 2i plus LIF.

extract_protocol: Hi-C was performed as previously described (Dryden et al., 2014). Hi-C libraries from 25 million cells were constructed with 4 base cutter MboI, and were then sequenced on Illumina NextSeq 550 with 150bp pair end.

value: mESC

tag: hybrid cells


title: O2_time-60_rep-C


title: O2_time-30_rep-D

value: D


title: genomic DNA from IC29

description: Institution-reared kid

source_name: whole blood IC29

value: Male

value: whole blood

value: normal


title: Normal donor 3, technical rep 1

description:
G4 I
G5I_(HuEx-1_0-st-v2).CEL


title: genomic DNA from BFC05

description: Family-reared kid

source_name: whole blood BFC05


title: genomic DNA from BFC07

description: Family-reared kid

source_name: whole blood BFC07


title: abc.del.A6.HiC [Hi-C]


title: O2_time-30_rep-C


title: NPC [Capture Hi-C]

data_processing:
Reads were trimmed by Trim Galore! (https://github.com/FelixKrueger/TrimGalore).
Mapped to mm10 using HiCUP v0.5.9 (Wingett et al., 2015).
Allele parsed using SNPsplit v0.3.0 (Krueger and Andrews, 2016).
Capture Hi-C heatmaps were plotted in R using interaction matrix for 10kb windows.
Genome_build: mm10
Supplementary_files_format_and_content: *mat: Tab-delimited text

source_name: NPC

growth_protocol: Mouse ESCs were maintained on 1% gelatin coated dishes. Hybrid cells (Cas/129) were grown in DMEM supplemented with 2i plus LIF. ESC to NPC differentiation was carried out as previously described (Abranches et al., 2009). mESCs were plated on 0.1% gelatin-coated dishes in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.) at high density. After 24 hours, cells were passaged to RHB-A media (Stem Cell Science Inc.) at the density of 1x10^4cells/cm2 and maintained for 12 days with media changed every other day.

extract_protocol: Capture Hi-C enriching 45488946-50879849 on chromosome 16 was performed as previously described (Dryden et al., 2014). Hi-C libraries from 25 million cells were constructed with 4 base cutter MboI, and target enrichment was performed using Agilent SureSelect RNA oligo system with custom designed capture probes (50bp RNA targeting Mbo1 fragments containing at least 1 SNP). Capture Hi-C libraries were then sequenced on Illumina NextSeq 550 with 150bp pair end.

value: NPC


title: O2_time-30_rep-B


title: Normal donor 1, technical rep 3

description:
G2 III
G3III_(HuEx-1_0-st-v2).CEL

source_name: bone-marrow mesenchymal stem cells isolated from normal donor

value: donor 1

value: 22 years


title: mESC [Capture Hi-C]

source_name: mESC


title: genomic DNA from IC24

description: Institution-reared kid

source_name: whole blood IC24


title: genomic DNA from IC28

description: Institution-reared kid

source_name: whole blood IC28


title: O2_time-30_rep-A

value: A


title: Normal donor 1, technical rep 2

description:
G2 II
G3II_(HuEx-1_0-st-v2).CEL


title: genomic DNA from IC26

description: Institution-reared kid

source_name: whole blood IC26


title: genomic DNA from IC27

description: Institution-reared kid

source_name: whole blood IC27


title: DNA methylation analysis of HBx transgenic mouse liver

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

description: Note from submitter: We only have processed data file due to hard drive crash.

data_processing:
Library strategy: MIRA-Seq
We extended the 34-bp reads toward the 3' end to cover DNA fragments bound by the MBD proteins. The readout was converted to browser extensible data (BED) files for visualization in the UCSC genome browser (http://genome.ucsc.edu).
Genome_build: mm9
Supplementary_files_format_and_content: BED

source_name: Liver

extract_protocol:
Genomic DNA from 25 mg liver tissue was purified by using DNeasyR Blood & Tissue Kit (Qiagen, Valencia, CA). Genomic DNA samples from 3 mice were pooled at the same concentration. MIRA was carried out as previously described (Rauch et al. 2006). GSTtagged MBD2b and His-tagged MBD3L1 proteins were prepared as described (Rauch et al. 2007). 15 ug of genomic DNA was fragmented to 100 ~ 500 bp by sonication and incubated with 28 ug of purified GST-MBD2b protein, 28 ug of His-MBD3L1 protein, and 7 ug of JM110 Bacterial DNA for 6 hours. 30 ul of MagneGST beads (Promega, Madison, WI) preblocked with 7 ug of JM110 bacterial RNA, were added and incubated at 4°C with rotating for 45 minutes in final 600 uL of MIRA binding buffer (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 1 mM EDTA, 1 mM DTT, 3mM MgCl2, 0.1 % Triton X-100, 5 % glycerol, 25 ug/ml BSA). Beads were washed three times with 1 ml of washing buffer (10 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 mM EDTA, 3 mM MgCl2, 0.1 % Triton X-100), and methylated fragments were eluted by incubation at room temperature for 5 minutes and 56 o C for 30 minutes with 30 ul of TE containing RNase A (100 ug, Qiagen) and Proteinase K (15 ug, Qiagen). Eluted DNA fragments were further purified by using Qiaquick PCR purification kits (Qiagen).
We used 10 ng of eluted DNA for Illumina Genome Analyzer sequencing. Following ligation of a pair of Solexa adaptors, ligation products with the maximum insert size of 200 bp were gel purified on 2 % agarose and subjected to PCR amplification. Cluster generation and 36 cycles of sequencing were performed following the manufacturer’s instructions. We sequenced 120 ul of adaptor-ligated, size-fractionated DNA (2 ~ 4 pM) on the Illumina Genome Analyzer. Sequence tags were mapped to the mouse genome (UCSC mm9 database based on NCBI Build 37 assembly) using the Solexa Analysis Pipeline (version 0.3.0). Sequenced reads of 34 bp (excluding the first and last nucleotide) that passed quality control filters were used.

tag: phenotype

value: HBx transgenic

value: liver


title: O2_time-15_rep-D

value: oxygen


title: O2_time-15_rep-C

value: C


title: Multiple myeloma patient 4, technical rep3

description:
BTS III
G2III_(HuEx-1_0-st-v2).CEL

source_name: bone-marrow mesenchymal stem cells isolated from multiple myeloma patient

value: Multiple myeloma patient

value: patient 4

value: 62 years


title: genomic DNA from IC23

description: Institution-reared kid

source_name: whole blood IC23


title: O2_time-15_rep-B

value: B


title: OCI-P5X miR-181a low-n3

city: Ann Arbor

first: Analisa

last: DiFeo

state: MI

address: 1600 Huron Parkway

department: Pathology

institute: The University of Michigan

description: dif-a18006.dif-a1-10.rma-gene-full-Signal

hyb_protocol: Labeled samples were hybridized to the arrays overnight in a rotating Hybridization Oven.

scan_protocol: Arrays were stained and washed in Affymetrix FS45U Fluidics Stations according to Affymetrix automated procedures.

data_processing: Data is collected using the GC3000 scanner with autoloader. The Clariom S Assays for the microarray data were downloaded. The data was pre-processed with RMA (Robust multichip average algorithm) using the R/Bioconductor package Oligo (42) where background subtraction, quantile normalization, and summarization (via median-polish) was accomplished.

label: biotin

source_name: OCI-P5X miR-181a low

label_protocol: In brief, for the WT Plus assay, 150ng of total RNA was labeled using a reverse transcription priming method to prime the entire length of each RNA transcript, including both polyA and non-polyA mRNA to provide complete and unbiased transcriptome coverage. This protocol efficiently generated amplified and biotinylated sense-stranded DNA targets, avoiding loss of specificity due to antisense strand interference.  Data was check for quality before being assessed on the Affymetrix Clariom S Human MicroArray. Changes in mRNA expression were then identified using the Clariom S Human MicroArray. On this array expression for each gene was assessed by approximately 11 probes, which were tiled throughout the transcript. The array provides basic gene level coverage of known genes.

extract_protocol: Total RNA was extracted from cell lysates of OCI-P5X miR-181a high and OCI-P5X miR-181a low cells in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry.

tag: cell line

value: high-grade serous ovarian carcinoma (HGSOC) cell line

value: OCI-P5X miR-181a low


title: Multiple myeloma patient 3, technical rep3

description:
LARS III
BTSIII_(HuEx-1_0-st-v2).CEL

value: patient 3

value: Female

value: 63 years

value: bone-marrow mesenchymal stem cells


title: genomic DNA from IC20

description: Institution-reared kid

source_name: whole blood IC20

value: whole blood

value: normal


title: O2_time-15_rep-A

source_name: oxygen exposure

value: A


title: genomic DNA from BFC03

description: Family-reared kid

source_name: whole blood BFC03

value: Male


title: genomic DNA from IC22

description: Institution-reared kid

source_name: whole blood IC22


title: genomic DNA from BFC01

description: Family-reared kid

source_name: whole blood BFC01


title: Multiple myeloma patient 3, technical rep2

description:
LARS II
BTSII_(HuEx-1_0-st-v2).CEL


title: OCI-P5X miR-181a low-n2

description: dif-a18005.dif-a1-10.rma-gene-full-Signal


title: O2_time-5_rep-D

value: D


title: O2_time-5_rep-C

value: oxygen


title: genomic DNA from IC19

description: Institution-reared kid

source_name: whole blood IC19


title: Multiple myeloma patient 3, technical rep1

description:
LARS I
BTSI_(HuEx-1_0-st-v2).CEL


title: O2_time-5_rep-B


title: genomic DNA from IC18

description: Institution-reared kid

source_name: whole blood IC18


title: Multiple myeloma patient 2, technical rep3

description:
31V III
31VIII_(HuEx-1_0-st-v2).CEL

value: patient 2

value: 70 years


title: OCI-P5X miR-181a high-n2

description: dif-a18002.dif-a1-10.rma-gene-full-Signal

source_name: OCI-P5X miR-181a high

value: OCI-P5X miR-181a high


title: Multiple myeloma patient 4, technical rep1

description:
BTS I
G2I_(HuEx-1_0-st-v2).CEL

value: Multiple myeloma patient

value: patient 4

value: 62 years


title: Normal donor 1, technical rep 1

description:
G2 I
G3I_(HuEx-1_0-st-v2).CEL

source_name: bone-marrow mesenchymal stem cells isolated from normal donor

value: normal donor

value: donor 1

value: 22 years


title: Multiple myeloma patient 2, technical rep2

description:
31V II
31VII_(HuEx-1_0-st-v2).CEL


title: DNA methylation analysis of normal mouse liver

value: Normal

value: liver

tag: strain


title: OCI-P5X miR-181a low-n1

description: dif-a18004.dif-a1-10.rma-gene-full-Signal

value: high-grade serous ovarian carcinoma (HGSOC) cell line

value: OCI-P5X miR-181a low


title: OCI-P5X miR-181a high-n3

description: dif-a18003.dif-a1-10.rma-gene-full-Signal


title: Multiple myeloma patient 2, technical rep1

description:
31V I
31VI_(HuEx-1_0-st-v2).CEL

value: bone-marrow mesenchymal stem cells


title: O2_time-5_rep-A

value: A


title: C1.3

description: chromatin accessibile DNA

organism: Pan troglodytes

source_name: Adipose from Southwest National Primate Research Center donor 4 x 521

value: adipose

value: male

value: adult


title: O2_time-0_rep-D

value: oxygen

value: D


title: genomic DNA from IC13

description: Institution-reared kid

source_name: whole blood IC13

value: Male

value: whole blood

value: normal


title: C1.2

description: chromatin accessibile DNA

source_name: Adipose from Southwest National Primate Research Center donor 4 x 520


title: O2_time-0_rep-C

value: C


title: C1.1

description: chromatin accessibile DNA

source_name: Adipose from Southwest National Primate Research Center donor 4 x 519


title: Multiple myeloma patient 4, technical rep2

description:
BTS II
G2II_(HuEx-1_0-st-v2).CEL

value: Multiple myeloma patient

value: patient 4

value: Female

value: 62 years


title: Multiple myeloma patient 1, technical rep3

description:
27V III
27VIII_(HuEx-1_0-st-v2).CEL

value: patient 1

value: 80 years


title: O2_time-0_rep-B

value: B


title: Multiple myeloma patient 1, technical rep2

description:
27V II
27VII_(HuEx-1_0-st-v2).CEL

value: bone-marrow mesenchymal stem cells


title: C2.2

description: chromatin accessibile DNA

source_name: Adipose from Southwest National Primate Research Center donor 4 x 327

value: adipose


title: SraL

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to Salmonella Typhimurium SL1344 genome (chromosome and plasmids) using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010
Genome_build: Salmonella enterica subsp. enterica serovar Typhimurium SL1344
Supplementary_files_format_and_content: tab-delimited text file including normalized reads for each sample and MS2-SraL/SraL ratio

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Bacterium

growth_protocol: Salmonella Typhimurium SL1344 strains were grown in LB medium at 37°C (100 mL). Cells were harvested in (A) exponential phase after anaerobic shock (with agitation until an OD600nm=0.3, and then transferred in a filled 50 ml tube, incubated without agitation at 37ºC for 30 min) and in (B) late stationary phase (with agitation until an OD600nm=2 + 6h).

extract_protocol:
Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT). Cells were then transferred to screw cap tubes containing 200 μL of glass beads (0.1 mm bead diameter; BioSpec). Cells were disrupted using Precellys®24 Homogenizer (three cycles: 6500 rpm for 20 s, followed by 1 min in ice; Bertin). The lysate was centrifuged at 17,000g for 30 min at 4 °C and the supernatant was applied to the column for affinity purification. MS2-affinity purification was performed as previously described (Lalaouna et al., 2017). Both lysates were applied on the same column (200 pmol of the MS2-MBP protein immobilized on an amylose resin). Afterward, RNA samples (output) were treated with TURBO™DNase (Ambion).
cDNA libraries were prepared with ScriptSeq™ v3 RNA-Seq Library Preparation Kit (Illumina) ScriptSeq™

treatment_protocol: The expression of MS2-sraL (or sraL control) was induced by addition of 1mM IPTG for 10 min. Then, harvested cells were chilled for 20 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT).

value: SL1344 sraL-

tag: growth conditions

value: anaerobic shock and late stationary phase of growth


title: O2_time-0_rep-A

value: oxygen

value: A


title: Multiple myeloma patient 1, technical rep1

description:
27V I
27VI_(HuEx-1_0-st-v2).CEL

source_name: bone-marrow mesenchymal stem cells isolated from multiple myeloma patient

tag: gender

value: Male


title: M1.1

description: chromatin accessibile DNA

organism: Macaca mulatta

source_name: Adipose from Oregon Health & Science University

value: male

value: adult


title: genomic DNA from IC11

description: Institution-reared kid

source_name: whole blood IC11

tag: sample type

value: whole blood

value: normal


title: C2.1

description: chromatin accessibile DNA


title: MS2-SraL


title: genomic DNA from IC16

description: Institution-reared kid

source_name: whole blood IC16

tag: disease state


title: Id1_Lung1

status: Public on Jan 20 2019

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw fastq files were imported into Strand software (v9.5, Agilent) for trimming, alignment and statistical analysis.  Sequence with a Q score of <30 were discarded, 1 base from the 3’ and 5’, and adaptors sequences were removed.
Reads were aligned to mm10  and duplicate reads were removed. Raw counts  were computed for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes  ENSEMBL id  and raw counts for each gene, in each sample

source_name: ILC2 cells from the lung

extract_protocol:
trizol was used to extract RNA using standard protocol from the vendor.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: lung

value: ILC2 cells


title: Id1_Lung2


title: Id1_Lung3


title: dKO_Lung1

value: plck-Cre; E2Af/fHEBf/f


title: genomic DNA from IC15

description: Institution-reared kid

source_name: whole blood IC15


title: dKO_T3

source_name: ILC2 cells from the thymus

value: thymus


title: dKO_Lung3


title: dKO_T1


title: DN3d_D7

source_name: DN3 thymocytes cultured on OP9-DL1 in ILC2 condition for 7 days and 4-OHT was added on Day4

value: DN3 thymocytes


title: genomic DNA from IC10

description: Institution-reared kid

source_name: whole blood IC10


title: DN3c_D7


title: DN3b_D7


title: genomic DNA from IC08

description: Institution-reared kid

source_name: whole blood IC08

value: Female


title: OCI-P5X miR-181a high-n1

description: dif-a18001.dif-a1-10.rma-gene-full-Signal

source_name: OCI-P5X miR-181a high

value: high-grade serous ovarian carcinoma (HGSOC) cell line

value: OCI-P5X miR-181a high


title: genomic DNA from IC07

description: Institution-reared kid

source_name: whole blood IC07


title: DN3d_D5

source_name: DN3 thymocytes cultured on OP9-DL1 in ILC2 condition for 5 days and 4-OHT was added on Day4


title: DN3a_D7


title: DN3c_D5


title: DN3b_D5


title: genomic DNA from IC17

description: Institution-reared kid

source_name: whole blood IC17


title: genomic DNA from IC21

description: Institution-reared kid

source_name: whole blood IC21


title: DN3d_D4

source_name: DN3 thymocytes cultured on OP9-DL1 in ILC2 condition for 4 days


title: DN3c_D4


title: M1.2

description: chromatin accessibile DNA

value: adipose


title: DN3b_D4


title: DN1c_D7

source_name: DN1 thymocytes cultured on OP9-DL1 in ILC2 condition for 7 days and 4-OHT was added on Day7

value: DN1 thymocytes


title: DN3a_D4


title: DN1b_D7


title: DN1d_D5

source_name: DN1 thymocytes cultured on OP9-DL1 in ILC2 condition for 5 days and 4-OHT was added on Day4


title: DN1c_D5


title: DN1a_D7


title: DN1b_D4

source_name: DN1 thymocytes cultured on OP9-DL1 in ILC2 condition for 4 days


title: Actinomycin D 150 ng/mL rep 2

city: Cambridge

first: Tanaz

last: Sharifnia

state: MA

address: 415 Main Street

department: Chemical Biology and Therapeutics Science Program

institute: Broad Institute

description:
processed data file: all_counts.txt
actinomycin150_b

data_processing:
Base calls performed with Illumina RTA
Reads were trimmed for adapter sequences with TrimGalore (version 0.4.1)
Reads were aligned to the genome (GRCh38) and quantified with STAR (version 2.4.2) using the Gencode annotation (version 23)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file contains read counts per gene for all samples

source_name: UM-Chor1 chordoma cells

growth_protocol: UM-Chor1 cells were maintained in IMDM/RPMI (4:1) media + 10% fetal bovine serum (FBS) and 1X non-essential amino acids.

extract_protocol:
Cell pellets were used for RNA extraction using an RNeasy Kit (Qiagen).
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), and libraries were sequenced using the Illumina NextSeq 500 instrument with single-end, 75 bp reads.

treatment_protocol: UM-Chor1 cells were seeded overnight in 6 cm collagen I-coated dishes at a density of 750,000 cells per dish. The following day, media was replaced with standard growth media containing compound at the final concentration or DMSO. Compound- and DMSO-treated cells were harvested 4 h after compound or DMSO addition. Two biological replicates were generated for each condition.

value: chordoma

value: UM-Chor1 chordoma cells

tag: agent

value: Actinomycin D

tag: dose

value: 150 ng/mL


title: Actinomycin D 150 ng/mL rep 1

description:
processed data file: all_counts.txt
actinomycin150_a


title: DN1b_D5

tag: tissue


title: DN1a_D5


title: Actinomycin D 10 ng/mL rep 2

description:
processed data file: all_counts.txt
actinomycin10_b

value: 10 ng/mL


title: genomic DNA from IC04

description: Institution-reared kid

source_name: whole blood IC04

value: whole blood


title: DN1d_D4


title: Actinomycin D 10 ng/mL rep 1

description:
processed data file: all_counts.txt
actinomycin10_a


title: genomic DNA from IC25

description: Institution-reared kid

source_name: whole blood IC25

value: normal


title: genomic DNA from IC06

description: Institution-reared kid

source_name: whole blood IC06


title: DN1d_D7


title: THZ1 500 nM rep 2

description:
processed data file: all_counts.txt
thz500_b


title: genomic DNA from IC05

description: Institution-reared kid

source_name: whole blood IC05

value: Male


title: THZ1 100 nM rep 1

description:
processed data file: all_counts.txt
thz100_a


title: THZ1 100 nM rep 2

description:
processed data file: all_counts.txt
thz100_b


title: THZ1 500 nM rep 1

description:
processed data file: all_counts.txt
thz500_a


title: UM-Chor1_WCE

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
All datasets were aligned using Bowtie2 (version 2.2.1) to build version NCBI37/HG19 (Langmead et al., 2009). Alignments were performed using all default parameters except for –N 1.
wiggles were made using MACS 1.4.2 pileups
Genome_build: hg19
Supplementary_files_format_and_content: .wig wiggles of read pileups across the whole genome

source_name: UM-Chor1 cell line

growth_protocol: UM-Chor1, MUG-Chor1, U-CH1, U-CH2, and JHC7 chordoma cell lines were obtained from the Chordoma Foundation. UM-Chor1 cells were maintained in IMDM/RPMI (4:1) media + 10% FBS and 1X non-essential amino acids. MUG-Chor1, U-CH1, and U-CH2 cell lines were maintained in IMDM/RPMI (4:1) media + 10% FBS. JHC7 cells were maintained in DMEM/F12 (1:1) + 10% FBS. All chordoma cell lines were maintained on collagen I-coated plates.

extract_protocol:
For H3K27ac ChIP of patient-derived tissue: approximately 100 mg of flash-frozen tissue was minced into 1-2 mm pieces and incubated in 1% formaldehyde for 15 minutes, followed by quenching with glycine (125 mM final concentration). Fixed tissue pieces were homogenized with a Tissue Tearor rotor stator homogenizer (Biospec) set to 30,000 RPM for 60 seconds. Homogenate was washed with ice-cold PBS containing 1X HALT protease inhibitor. Homogenized pellets were then resuspended in cytosolic lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL, 0.25% Triton X-100, 1X HALT protease inhibitor) and the protocol was continued as described below. For H3K27ac ChIP of chordoma cell lines: Chordoma cell lines were grown in 175 cm collagen I-coated plates (3 plates per cell line) and cross-linked by adding 1/10 of the cell culture volume of 11% formaldehyde solution (1M HEPES-KOH pH 7.5, 0.5 M EDTA pH 8.0, 0.5 M EGTA pH 8.0, 5 M NaCl, 37% formaldehyde) for 10 minutes, followed by quenching (125 mM glycine). Cells were washed in PBS and harvested by cell scraper in PBS. Cells were centrifuged at 1,350 X g for 5 min at 4°C, washed with PBS, and centrifuged again at 1,350 X g for 5 min at 4°C. Cell pellets were flash frozen and stored at -80°C until further processing.
For both cell line and tissue ChIP-seq: samples were subsequently rotated end-over-end for 10 minutes at 4º C in cytosolic lysis buffer and then collected by spinning at 1,350 x g for 5 minutes. Samples were resuspended in nuclear lysis buffer (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 1X HALT protease inhibitor) and rotated end-over-end for 10 minutes at 4º C and spun at 1,350 x g for 5 minutes. Samples were resuspended in 1 mL sonication buffer ( 0.1% Na-Deoxycholate, 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 1X HALT protease inhibitor) with SDS added to a final concentration of 0.5%. Chromatin was sheared by sonication using a Bioruptor water bath sonicator (Diagenode) for 25 cycles. Samples were clarified by centrifuging 10 minutes at 20,000 x g at 4º C. A 50 uL aliquot of supernatant was set aside as non-IP input control. The remaining sheared chromatin was diluted 1:5 in sonication buffer and each sample was incubated overnight at 4º C with 100 uL of Protein G Dynabeads (Life Technologies) bound with 10 µg of anti-H3K27ac antibody (abcam, #ab4729). Beads were washed while rotating end-over-end at 4º C with the following buffers: twice in sonication buffer, once in sonication buffer with NaCl added to a final concentration of 500 mM, once in LiCl wash buffer (20 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% IGEPAL, 0.5% Na-Deoxycholate), and once in TE-NaCl buffer (50 mM Tris-HCl pH 8, 50 mM NaCl). Chromatin was eluted by resuspending beads in 200 uL elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) and heating for 15 minutes at 65º C. Beads were pelleted by centrifuging at 20,000 G for 30 seconds and supernatant was collected. Elution buffer (150 uL) was also added to input chromatin samples. Samples were incubated at 65º C overnight to reverse crosslinks. Samples were then incubated with RNAse A (Thermo Scientific) for 2 hours at 37º C, followed by incubation with Proteinase K (Ambion) for 30 minutes at 55º C. DNA isolation was performed via phenol-chloroform extraction and concentrated by ethanol precipitation. Sequencing libraries were generated with the Thruplex DNAseq Single Index Kit (Rubicon) and sequenced on an Illumina NextSeq 500 with single-end, 75 bp reads. ChIP-seq was performed once for each sample.

tag: antibody

tag: barcode

value: GGCTACAG

tag: antibody maker

value: abcam

tag: antibody catalog number


title: DMSO rep 1

description:
processed data file: all_counts.txt
dmso_a

value: DMSO

value: control


title: UM-Chor1_H3K27AC

value: CTTGTACT


title: U-CH2_H3K27AC

source_name: U-CH2 cell line

value: CGATGT


title: U-CH1_WCE

source_name: U-CH1 cell line

value: TGGTTGTT


title: genomic DNA from IC02

description: Institution-reared kid

source_name: whole blood IC02

value: Female


title: DMSO rep 2

description:
processed data file: all_counts.txt
dmso_b


title: U-CH1_H3K27AC

value: TCTCGGTT


title: PRIMARY_CHOR_4616_WCE (MGH_3)

source_name: patient-derived chordoma MGH_3

tag: cell type

value: patient-derived chordoma MGH_3

value: GGCACAAC


title: U-CH2_WCE

value: ATCACG


title: PRIMARY_CHOR_194A1_WCE (CF_194)

source_name: patient-derived chordoma CF_194

value: patient-derived chordoma CF_194

value: TACTAGTC


title: PRIMARY_CHOR_4616_H3K27AC (MGH_3)

value: TCTCACGG


title: PRIMARY_CHOR_194A1_H3K27AC (CF_194)

value: ATCACGTT


title: PRIMARY_CHOR_243A2_WCE (CF_243)

source_name: patient-derived chordoma CF_243

value: patient-derived chordoma CF_243

value: TCCAGTCG


title: PRIMARY_CHOR_142A2_WCE (CF_142)

source_name: patient-derived chordoma CF_142

value: patient-derived chordoma CF_142

value: TTAGGCAT

value: abcam


title: PRIMARY_CHOR_A269A1_WCE (CF_269)

source_name: patient-derived chordoma CF_269

value: patient-derived chordoma CF_269

value: TAGTGACT


title: PRIMARY_CHOR_01192016_WCE (MGH_2)

source_name: patient-derived chordoma MGH_2

value: patient-derived chordoma MGH_2

value: TATGCCAG


title: PRIMARY_CHOR_142A2_H3K27AC (CF_142)

value: TGACCACT


title: PRIMARY_CHOR_12132013_H3K27AC (MGH_1)

source_name: patient-derived chordoma MGH_1

value: patient-derived chordoma MGH_1

value: TAGCTTGT


title: genomic DNA from IC01

description: Institution-reared kid

source_name: whole blood IC01

value: Male

value: whole blood

value: normal


title: PRIMARY_CHOR_01192016_H3K27AC (MGH_2)

value: TCAGATTC


title: MUG-Chor1_WCE

source_name: MUG-Chor1 cell line

value: TAAGCGTT


title: PRIMARY_CHOR_243A2_H3K27AC (CF_243)

value: patient-derived chordoma CF_243

value: TGTATGCG


title: MUG-Chor1_H3K27AC

value: TCCGTCTT


title: genomic DNA from IC14

description: Institution-reared kid

source_name: whole blood IC14


title: genomic DNA from IC03

description: Institution-reared kid

source_name: whole blood IC03


title: genomic DNA from IC12

description: Institution-reared kid

source_name: whole blood IC12


title: PRIMARY_CHOR_12132013_WCE (MGH_1)

value: GATCAGCG


title: 160831_CHOR_input (MGH_4)

source_name: patient-derived chordoma MGH_4

value: patient-derived chordoma MGH_4

value: TCGAGCGT

value: abcam


title: JHC7_H3K27AC

source_name: JHC7 cell line

value: ACTTGATG


title: 160831_CHOR_H3K27Ac (MGH_4)

value: TGATACGT


title: 160831_NAT_H3K27Ac (MGH_4_NAT)

source_name: matched normal adjacent to MGH_4 chordoma

value: TTGGAGGT


title: genomic DNA from IC09

description: Institution-reared kid

source_name: whole blood IC09

value: Female


title: U-CH2_2

description: ATAC-Seq

data_processing:
All paired-end datasets were aligned using Bowtie2 (version 2.2.1) to build version NCBI37/HG19 with the following parameters: -k 1. Aligned bams were filtered and sorted using samtools (0.1.19) by removing chrM and duplicate reads, and filtering against the ENCODE blacklist (https://sites.google.com/site/anshulkundaje/projects/blacklists). Peaks were called using MACS version 1.4.2 with a p-value cutoff of 1e-9.
wiggles were made using MACS 1.4.2 pileups
Genome_build: hg19
Supplementary_files_format_and_content: .wig wiggles of read pileups across the whole genome

source_name: U-CH2 rep2

growth_protocol: For U-CH2 cells: IMDM:RPMI 1640 mixed 4 parts IMDM:1 part RPMI; 10% FBS not heat inactivated, + Pen-strep. Cells are grown on 0.1% gelatin coated plates and are split 1:2 when nearing confluence, about every 5 days.

extract_protocol: For each cell line (MUG-Chor1 and U-CH2), 50,000 cells were lysed for 10 minutes at 4°C in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360). After lysis, the pellets were subject to a transposition reaction (37°C, 60 minutes) using the 2X TD buffer and transposase enzyme (Illumina Nextera DNA preparation kit, FC-121-1030). The transposition mixture was purified using a Qiagen MinElute PCR purification kit. Library amplification was performed using custom Nextera primers and the number of total cycles determined by running a SYBR-dye based qPCR reaction and calculating the cycle number that corresponds to ¼ the maximum. Amplified libraries were purified using a Qiagen PCR purification kit and sequenced with paired-end 100 bp reads on an Illumina HiSeq 2000.


title: MUG-Chor1

description: ATAC-Seq

growth_protocol: For MUG-Chor1 cells: IMDM:RPMI 1640 mixed 4 parts IMDM:1 part RPMI; 10% FBS not heat inactivated, 1X ITS, 1X glutamine (2mm), + Pen-strep. Cells are grown on regular plastic and are split 1:2, when nearing confluence, about every 4-5 days.


title: DN3a_D5

source_name: DN3 thymocytes cultured on OP9-DL1 in ILC2 condition for 5 days and 4-OHT was added on Day4

value: thymus

value: DN3 thymocytes


title: clone_47

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Bisulfite sequencing
processed data file: HKG_methylation.tab

data_processing:
Basecalls performed using MiSeq and HiSeq control software.
For reporter assay libraries, fastq files were trimmed to the promoter sequence and aligned to mm9 using bowtie for libraries where the design allowed efficient alignment (See table 2). For mutant promoter libraries, reads were matched to the reference sequences using the "stringdistmatrix" function in R (van der Loo, 2014). The frequency of each barcode sequence was calculated to get counts for each sample. Genomic DNA and RNA samples were scaled to each other by normalizing to the smaller total number of counts. Only barcodes that were sufficiently represented on genomic DNA (more than 20 reads after scaling) were used for further analysis. Enrichments of barcodes in the RNA sample were then calculated as nr/nd + alpha, where nr are the RNA counts and nd the DNA counts for a particular barcode and alpha represents a pseudo-count, set to 0.05.
ChIP-seq samples were mapped to the mm9 assembly of the mouse genome using the R package QuasR (Gaidatzis et al, 2015), which internally uses bowtie (Langmead et al, 2009). ChIP-seq peaks were called using Peakzilla with default parameters (Bardet et al, 2013)
For amplicon Bis-seq, sequences were aligned to the mutant promoter libraries using QuasR (Gaidatzis et al, 2015), using default settings for Bis-converted samples. DNA methylation was quantified using qMeth and the average methylation across each promoter was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Activities (Act_*), number of barcodes (nBCs_*), activities relative to the wt sequence (relAct_*), percentage of C+Gs (GC), percentage of dinucleotides that are CpGs (CpG), CpG observed/expected (OE), number of CpGs (nCGs), coordinates (chr, start, end, strand), percentage of CpGs mutated (CpGmut), qPCR values (qPCR), fraction methylated (methylation).

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured on cell culture plates coated with 0.2% gelatine in DMEM medium with 15% fetal calf serum, 2mM L-glutamine, 1 x non-essential amino acids, LIF and 0.001% b-mercaptoethanol. Cells were incubated at 37 °C with 7% CO2.

extract_protocol:
RNA was isolated from cell lines containing the expression libraries with Quiagen RNeasy Mini Kit with on-column DNase digestion and reverse transcribed using Takara PrimeScript RT Reagent Kit (#RR047A). For DNA isolation cell pellet was resuspended in Bradleys-Buffer, 6 ul RNaseA (10mg/ml) was added and samples were incubated for 1h at 37 degree C. Subsequently 30 ul protease K was added and samples were incubated at 50 degree C over night. Then DNA was extracted using Phenol and Chloroform. Bio-ChIP was performed as previously described (Baubec et al, 2013). For amplicon Bis-seq, cells containing integrated mutant CGI promoter libraries were thawed, plated at low density and 96 clones picked and expanded to a minimum cell number of 20,000 cells. Cells were lysed with Baradley Buffer (10mM Tris-HCl (pH 7.5), 10mM EDTA (pH 8.0), 0.5% SDS, 10mM NaCl) and DNA extracted with beads (Homemade). DNA was Bisulfite converted using Zymo lightning conversion kit (D5046) and cleaned up using MagBeads (Zymno). Bis-converted DNA was amplified with primers RSG353 and RSG354 (Table 1). Amplified DNA was purified with Ampure beads and sequencing libraries were prepared using the Illumina NEBNext ChIP-seq library prep kit with 96 dual indexing.
DNA and cDNA barcodes were amplified with KAPA HIFI Hotstart using Primer DH.P6 and indexing primer (Table 1). PCR products were purified using AmPure XP beads (Beckman Coulter, #A63880) and sequenced using 50 cycle Kit on HiSeq 2500.

treatment_protocol: Mouse embryonic stem cells with a RMCE site in the beta-globin locus were used for integration of expression libraries for the transcriptional reporter assay (Lienert et al, 2011). Dnmt1, Dnmt3a and Dnmt3b was deleted in these cells using CRISPR-Cas9 gene editing as previously described (Domcke et al, 2015). Mouse HA36 ES cells (mixed 129-C57Bl/6 strain) were used for Bio-ChIP (Baubec et al, 2013).

value: embryonic stem cells

value: Wild Type

tag: library type

value: amplicon Bis-seq


title: clone_46


title: clone_44


title: clone_40


title: clone_37


title: JHC7_WCE

value: CAGATCTG


title: 160831_NAT_input (MGH_4_NAT)

value: matched normal adjacent to MGH_4 chordoma

value: TCTGCTGT


title: clone_36


title: clone_35


title: clone_34


title: clone_32


title: clone_31


title: clone_30


title: U-CH2_1

description: ATAC-Seq

source_name: U-CH2  rep1


title: clone_45


title: clone_29


title: clone_27


title: clone_26


title: clone_25


title: clone_28


title: clone_43


title: clone_24


title: clone_23


title: clone_42


title: clone_41


title: clone_39


title: clone_21


title: clone_22


title: clone_20


title: clone_19


title: clone_18


title: clone_17


title: clone_33


title: clone_38


title: clone_15


title: clone_13


title: clone_11


title: clone_10


title: clone_12


title: clone_14


title: clone_9


title: clone_7


title: clone_8


title: clone_6


title: clone_5


title: clone_1


title: clone_3


title: clone_4