title: H3K56ac/H3_Input_spt6-1004_rep2

description:
Adapter 16 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. Input signal of spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C.This Input DNA was obtained from the same yeast extract used to perform H3K56ac and H3 ChIP-seq.

data_processing:
Reads for each biological replicate were independently aligned to the S. cerevisiae (UCSC sacCer3) and S. pombe (Downloaded from https://www.pombase.org/ on March 10th 2018) reference genomes using the short read aligner Bowtie 2 (version 2.2.4) (Langmead and Salzberg, 2012).  Coverage for each base pair of the S. cerevisiae genome was computed using genomeCoverageBed from BEDTools (version 2.19.1) (Quinlan and Hall, 2010) and normalized using S. pombe reads as follow. The read density at each position of the S. cerevisiae genome was multiplied by a normalisation factor N defined as:  N = 1,000,000 * P / R * C  where: 1,000,000 is an arbitrary chosen number used for convenience.  R is the total number of reads in the ChIP sample that mapped to the S. pombe genome.   C is the total number of reads in the Input sample that mapped to the S. cerevisiae genome.   P is the total number of reads in the Input sample that mapped to the S. pombe genome.  Simpler normalisation schemes without the use of the Input sample (hence, leaving out C and P) were used before (Bonhoure et al., 2014; Chen et al., 2015b; Hu et al., 2015) and should, in theory, allow for direct comparisons between samples. Such simple scheme, however, assumes that the same number of cells is used as starting material for all ChIP samples. As routinely done when working with yeast, we evaluated cell number using the OD600 of our cultures. In the course of analysing our ChIP-seq data, we noticed that the ratio of the reads mapping to the S. cerevisiae versus the S. pombe genome was systematically lower in the Input material from spt16-197 and spt6-1004 samples compared to the WT sample, suggesting that the number of spt16-197 and spt6-1004 cells used in our experiments was overestimated. We then confirmed that at identical OD600, spt16-197 and spt6-1004 cultures contain fewer cells than their wild type counterparts using dilutions/plating assays (not shown). For FACT, this observation is most likely due to the known fact that spt16-197 cells elicit a delay in G1 (Morillo-Huesca et al., 2010), hence skewing the population for larger cells. Despite this has never been reported before for Spt6, similar reasons may explain the observed spt6-1004 result. To correct for that defect, we used the sequencing of the Input samples and introduced the variables C and P in our scaling factor. Note that the conclusions reached in our analyses were the same, whether we used C and P or not.  Replicate samples showed high correlation and were combined using MergeSamFiles from Picard Tools (version 1.56.0) (http://broadinstitute.github.io/picard/) prior to the calculation of the coverage and the normalization.
Genome_build: S. cerevisiae (UCSC sacCer3) and S. pombe (Downloaded from https://www.pombase.org/ on March 10th 2018)
Supplementary_files_format_and_content: Normalized BigWig files (ending in “norm.bigwig”) represent individual replicate ChIP fragment coverage normalized using reads mapped to the S. pombe genome.  Combined normalized BigWig files (ending in “comb.bigwig”) represent combined replicates ChIP fragment coverage normalized using reads mapped to the S. pombe genome.

source_name: Yeast cell extract (MATα, his3Δ200, leu2Δ1, lys2-128δ, ura3-52, spt6-1004-FLAG)

growth_protocol: Cells were grown at 30°C and 200 rpm in YPD (yeast extract-peptone-2% glucose) medium as follow. 50 mL of YPD medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reached OD600 ~0.5. Cell cultures were then switched to 37°C and allowed to grow for additional 80 min before crosslinking, at which point they had reached ~0.9 OD600. The S. pombe strain (yFR2050) used as spike-in control was grown in similar conditions as the S. cerevisiae strains but omitting the switch to 37°C.

extract_protocol: Crosslinked cells were collected by centrifugation and washed twice with 1 X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cells were then resuspended in 700 uL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin). The same number of OD600 units was used for all samples. A fixed amount of crosslinked S. pombe cells (representing 10% of the S. cerevisiae cells) was added to the S. cerevisiae cells prior to cell lysis. This spike-in control was used to normalise samples. Cells were lysed by bead beating and the lysate was 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. Soluble fragmented chromatin was recovered by centrifugation. 20 uL of the chromatin sample were saved for control of the average chromatin fragment size. For H3K4me3 and H4 immunoprecipitations, 25% (150 uL) of the chromatin sample, completed to 600 uL with Lysis buffer, was used. For H3K56ac and H3 immunoprecipitations, 50% (300 uL) of the chromatin sample, completed to 600 uL with Lysis buffer, was used. 6 uL (1%) of the diluted chromatin samples were saved as Input sample. 12.5 uL of Protein G Dynabeads (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated rabbit polyclonal antibody were added to the 600 uL of diluted chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Immunoprecipitated chromatin was eluted and reverse-crosslinked with 50 uL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Input and fragment size control samples were also added with 50 uL TE/SDS and incubated overnight at 65°C to reverse crosslinking. Eluted chromatin as well as Input and fragment size control samples were treated with RNase A (345 uL TE, 3 uL RNAse A 10 mg/mL, 2 uL Glycogen 20 mg/mL) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 uL 10% SDS, 7.5 uL Proteinase K 20 mg/mL) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 uL of TE and subjected to a 1.7X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 40 uL of elution buffer (10 mM Tris pH 8.0).   The sample used for determining the average chromatin fragment size was analysed on an Agilent 2100 Bioanalyzer instrument using Agilent High Sensitivity DNA Kit.  DNA concentration of the ChIP and Input samples was determined by qPCR using a standard curve made with the fragment size control sample. 3-10 ng of ChIP and Input DNA were used for ChIP-seq library preparation as follow. The ends of DNA were repaired using T4 DNA polymerase (NEB, M0203L) and T4 polynucleotide kinase (NEB, M0201S) at 12˚C for 30 min. Repaired DNA was then subjected to a 1.7X cleanup using KAPA Pure Beads before dA tailing using Klenow Fragment (3'→5' exo-) (NEB, M0212M) at 37˚C for 30 min. After a 1.8X cleanup with KAPA Pure Beads, the A-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A, 12 adapters (07141530001) and SeqCap Adapter kit B, 12 adapters (07141548001)) using T4 DNA ligase (ThermoFisher, 15224041) at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads, followed by a double size selection (0.52X-1X) leading to fragments in the 200-600 bp range. Libraries were PCR amplified with 12-13 cycles using KOD Hot Start DNA polymerase (Millipore, 71086-3) and cleaned up using 1X KAPA Pure Beads. Libraries were qualified on Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit and quantified by qPCR using NEBNext Library Quant Kit for Illumina. Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on an Illumina HiSeq 2500 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp single-end reads.

treatment_protocol: For both S. cerevisiae and S. pombe strains, cultures were crosslinked with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min. Crosslinking was quenched with 125 mM glycine.

tag: spike-in

value: Schizosaccharomyces pombe (yFR2050 strain)

tag: strain name

value: MAT{alpha}, his3{delta}200, leu2{delta}1, lys2-128{delta}, ura3-52, spt6-1004-FLAG

tag: chip antibody


status: Public on Jul 30 2019

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 1 of 2. H3K18ac occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H3K18acvsInput_20161201_rep1-2_MN__S.cerevisiaeApr11_731439.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.

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

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

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

molecule: genomic DNA

organism: Saccharomyces cerevisiae

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

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

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

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

tag: strain

tag: genotype

tag: antibody

value: H3K18ac (Abcam ab1191)

treatment_protocol:
switch to YPD medium for 6 h
none


title: H3K56ac/H3_Input_spt6-1004_rep1

type: SRA

description:
Adapter 7 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. Input signal of spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C.This Input DNA was obtained from the same yeast extract used to perform H3K56ac and H3 ChIP-seq.

library_source: genomic


title: H3K56ac/H3_Input_spt16-197_rep1

description:
Adapter 2 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. Input signal of spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K56ac and H3 ChIP-seq.

source_name: Yeast cell extract (MATα, leu2Δ1, spt16-197)

value: MAT{alpha}, leu2{delta}1, spt16-197


description:
Biological replicate 1 of 2. H2Bub occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_6hrs-YPD_H2BubvsInput_20161130_rep1-2_MN__S.cerevisiaeApr11_350238.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.

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

value: H2Bub (Cell Signaling Technology 5546)


description:
Biological replicate 1 of 2. Spt16 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_Spt16vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_468341.bed
A genome browser-ready file for Spt16 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.

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

value: Spt16 (T. Formosa)


title: H3K56ac/H3_Input_WT_rep2

description:
Adapter 11 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. Input signal of WT cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K56ac and H3 ChIP-seq.

source_name: Yeast cell extract (MATα, leu2Δ1)

value: MAT{alpha}, leu2{delta}1


title: H3K4me3/H4_Input_spt16-197_rep2

description:
Adapter 19 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. Input signal of spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K4me3 and H4 ChIP-seq.


title: H3K4me3/H4_Input_spt6-1004_rep1

description:
Adapter 1 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. Input signal of spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K4me3 and H4 ChIP-seq.


title: H3K56ac/H3_Input_WT_rep1

description:
Adapter 10 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. Input signal of WT cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K56ac and H3 ChIP-seq.


title: H3K4me3/H4_Input_spt6-1004_rep2

description:
Adapter 8 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. Input signal of spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K4me3 and H4 ChIP-seq.


title: H3K56ac_ChIP-seq_spt16-197_rep1

description:
Adapter 2 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3K56ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K56ac ChIP sample was performed using a rabbit polyclonal antibody against H3K56ac.
H3K56ac_yFR973spt16-197_CJ17-CJ19_comb.bigwig

value: H3K56ac (Millipore 07-677-I); 0.2 μL/ChIP


title: H3K4me3/H4_Input_WT_rep1

description:
Adapter 5 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. Input signal of WT cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K4me3 and H4 ChIP-seq.


title: H3K56ac_ChIP-seq_spt16-197_rep2

description:
Adapter 7 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3K56ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K56ac ChIP sample was performed using a rabbit polyclonal antibody against H3K56ac.


title: H3K56ac_ChIP-seq_spt6-1004_rep2

description:
Adapter 9 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3K56ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K56ac ChIP sample was performed using a rabbit polyclonal antibody against H3K56ac.


title: H3K56ac_ChIP-seq_spt6-1004_rep1

description:
Adapter 15 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3K56ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K56ac ChIP sample was performed using a rabbit polyclonal antibody against H3K56ac.
H3K56ac_yFR974spt6-1004_CJ21-CJ23_comb.bigwig


title: H3K4me3/H4_Input_WT_rep2

description:
Adapter 6 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. Input signal of WT cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K4me3 and H4 ChIP-seq.


title: H3K56ac_ChIP-seq_WT_rep1

description:
Adapter 5 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3K56ac occupancy in WT cells treated 80 minutes at 37°C. H3K56ac ChIP sample was performed using a rabbit polyclonal antibody against H3K56ac.
H3K56ac_yFR971WT_CJ13-CJ15_comb.bigwig


title: H3K4me3/H4_Input_spt16-197_rep1

description:
Adapter 12 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. Input signal of spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K4me3 and H4 ChIP-seq.


title: WT+poly I:C: Wild type short poly I:C stimulation

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

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

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

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

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

molecule: total RNA

organism: Homo sapiens

source_name: Human immortalized cells

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

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

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

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

tag: cell line

value: HeLa

tag: genotype/variation

value: Wild Type


title: β-manno-oligosaccharides 2 LP WCFS1

city: Mysuru

first: Mukesh

last: Kapoor

state: Karnataka

address: CFTRI

department: Protein Chemistry and Technology

country: India

institute: CSIR-Central Food Technological Research Institute

description: Gene expression in presence of β-manno-oligosaccharides

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Custom L.plantarum GXP_8X15k Array designed by Genotypic Technology Private Limited. (AMADID: 067475). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

organism: Lactiplantibacillus plantarum WCFS1

source_name: MRS broth, mid log phase

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Lactobacillus plantarum WCFS1 was passaged microaerophilically 5 times in MRS containing LBG derived galacto-manno-oligosaccharides, mannose, glucose or galactose (1% w/v, 370C, static,  overnight) as the sole carbon source to reduce carryover between indivual sugars. The cells from 5th passage were innoculated ( OD600 ~0.2, 10 µl ) in the MRS medium (30 ml) containing respective substrates in duplicates, and were grown till the mid log phase (OD600 ~0.5, 10 h, 370C, static conditions). The cells were then harvested by centrifugation (3000 rpm, 10 min, 40C), supernatant was discarded, and the pellet was washed  with phosphate buffer saline (10 ml) to remove any residual medium. Lactobacillus plantarum WCFS1  grown using different substrates were incubated in RNA later (Sigma) overnight at 40C and then stored at -800C till RNA was extracted.

extract_protocol: RNA extraction was carried out using Rneasy Mini Kit from Quiagen (cat. #/ID: 74106) according to manufacturer's recommendation

treatment_protocol: Locust bean gum derived galacto-manno-oligosaccharides, mannose, glucose and galactose (1% w/v)  were used as the sole carbon source in  MRS medium for the growth of Lactobacillus plantarum WCFS1.

tag: tissue

value: whole organism

tag: Stage

value: Mid log phase


title: WT: Wild type not stimulation


title: β-manno-oligosaccharides 1 LP WCFS1


title: H3K56ac_ChIP-seq_WT_rep2

description:
Adapter 12 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3K56ac occupancy in WT cells treated 80 minutes at 37°C. H3K56ac ChIP sample was performed using a rabbit polyclonal antibody against H3K56ac.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_H3K4me3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_287568.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.

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

value: H3K4me3 (Abcam ab8580)


description:
Biological replicate 1 of 2. Rpb3 occupancy in WT cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1221_WT_80min37C_Rpb3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_621451.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium. Cells are grown to an OD600 of ~0.7 and an equal volume of YPD pre-warmed to 49°C is added to the flask, which is immediately transferred to a 37°C incubator for 80 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
heat-shock at 37°C, switch to 37°C for 80 min
Rpb3 ChIP. Antibody from BioLegend (665004). Pan Mouse IgG Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (1.5 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, ura3-52, SUC2+

value: Rpb3 (BioLegend 665004)

treatment_protocol:
heat-shock at 37°C, switch to 37°C for 80 min
none


description:
Biological replicate 1 of 2. Rpb3 occupancy in cells where the sole source of histone H4 is under the control of a galactose-responsive promoter switched to medium containing glucose for 6 hr. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2113_pGAL1-H4_Rpb3vsInput_6hrsYPD_20160703_rep1-2_MN__S.cerevisiaeApr11_921419.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in cells switched to medium containing glucose for 6 hr which induce H4 depletion.

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

value: Rpb3 (Neoclone W0012)


title: yFR1221_WT_80min37C_Rpb3vsInput_20170621_Rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in WT cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1221_WT_80min37C_Rpb3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_621451.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: KO: ZNF598 KO no stimulation

value: ZNF598 KO


title: yFR971-2_WT_Rpb3_Rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in WT cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_WT_Rpb3_Rep1-2_MN__S.cerevisiaeApr11_30665.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

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

treatment_protocol:
switch to 37°C for 80 min
Rpb3 ChIP. Antibody from Neoclone (W0012). Pan Mouse IgG Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, leu2Δ1

treatment_protocol:
switch to 37°C for 80 min
none


description:
Biological replicate 1 of 2. H3K36me3 occupancy in WT cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K36me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_101668.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K36me3 ChIP. Antibody from Abcam (ab9050). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K36me3 (Abcam Ab9050)


title: yFR973-1_spt16ts_Rpb3_Rep1

description:
Biological replicate 1 of 2. Rpb3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16ts_Rpb3_Rep1-2_MN__S.cerevisiaeApr11_452825.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: yFR971-1_WT_Rpb3_Rep1

description:
Biological replicate 1 of 2. Rpb3 occupancy in WT cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_WT_Rpb3_Rep1-2_MN__S.cerevisiaeApr11_30665.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: H3_ChIP-seq_spt6-1004_rep1

description:
Adapter 3 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample was performed using a rabbit polyclonal antibody against H3.
H3_yFR974spt6-1004_CJ22-CJ24_comb.bigwig

value: Schizosaccharomyces pombe (yFR2050 strain)

value: MAT{alpha}, his3{delta}200, leu2{delta}1, lys2-128{delta}, ura3-52, spt6-1004-FLAG

value: H3 (Abcam ab1791); 0.5 ug/ChIP


title: H3_ChIP-seq_spt6-1004_rep2

description:
Adapter 25 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample was performed using a rabbit polyclonal antibody against H3.


title: yFR1214_rpb1-1_80min37C_Rpb3vsInput_20170621_Rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in rpb1-1 temperature-sensitive cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1214_rpb1-1_80min37C_Rpb3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_849357.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in rpb1-1 temperature-sensitive cells treated 80 min at 37°C.

value: MATa, ura3-52, rpb1-1


title: H3_ChIP-seq_spt16-197_rep1

description:
Adapter 4 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample was performed using a rabbit polyclonal antibody against H3.
H3_yFR973spt16-197_CJ18-CJ20_comb.bigwig

value: MAT{alpha}, leu2{delta}1, spt16-197


title: H3_ChIP-seq_spt16-197_rep2

description:
Adapter 16 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample was performed using a rabbit polyclonal antibody against H3.


title: H3_ChIP-seq_WT_rep1

description:
Adapter 6 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3 occupancy in WT cells treated 80 minutes at 37°C. H3 ChIP sample was performed using a rabbit polyclonal antibody against H3.
H3_yFR971WT_CJ14-CJ16_comb.bigwig

value: MAT{alpha}, leu2{delta}1


title: H4_ChIP-seq_spt6-1004_rep2

description:
Adapter 6 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H4 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample was performed using a rabbit polyclonal antibody against H4.

value: ryH4 (A.Verreault); 0.5 μL/ChIP


title: yFR973-2_spt16ts_Rpb3_Rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16ts_Rpb3_Rep1-2_MN__S.cerevisiaeApr11_452825.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: Mannose 2 LP WCFS1

description: Gene expression in presence of mannose

value: whole organism


title: H4_ChIP-seq_spt6-1004_rep1

description:
Adapter 5 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H4 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample was performed using a rabbit polyclonal antibody against H4.
H4_yFR974spt6-1004_80min37C_CJ134-CJ136_comb.bigwig


title: yFR974-2_spt6ts_Rpb3_Rep2

description:
Biological replicate 2 of 2. Rpb3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6ts_Rpb3_Rep1-2_MN__S.cerevisiaeApr11_961223.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: H3_ChIP-seq_WT_rep2

description:
Adapter 19 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3 occupancy in WT cells treated 80 minutes at 37°C. H3 ChIP sample was performed using a rabbit polyclonal antibody against H3.


title: yFR974_spt6-1004_80min37C_H3K79me3vsInput_20170621_Rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K79me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_53208.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K79me3 ChIP. Antibody from Abcam (ab2621). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K79me3 (Abcam ab2621)


title: H4_ChIP-seq_spt16-197_rep2

description:
Adapter 1 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H4 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample was performed using a rabbit polyclonal antibody against H4.


title: H4_ChIP-seq_WT_rep1

description:
Adapter 2 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H4 occupancy in WT cells treated 80 minutes at 37°C. H4 ChIP sample was performed using a rabbit polyclonal antibody against H4.
H4_yFR971WT_80min37C_CJ31-CJ33_comb.bigwig


title: H3K4me3_ChIP-seq_spt6-1004_rep2

description:
Adapter 20 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample was performed using a rabbit polyclonal antibody against H3K4me3.

value: H3K4me3 (Abcam ab8580); 0.625 ug/ChIP


title: yFR974-1_spt6ts_Rpb3_Rep1

description:
Biological replicate 1 of 2. Rpb3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6ts_Rpb3_Rep1-2_MN__S.cerevisiaeApr11_961223.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: H4_ChIP-seq_spt16-197_rep1

description:
Adapter 19 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H4 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample was performed using a rabbit polyclonal antibody against H4.
H4_yFR973spt16-197_80min37C_CJ34-CJ35_comb.bigwig


title: H3K4me3_ChIP-seq_spt6-1004_rep1

description:
Adapter 10 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample was performed using a rabbit polyclonal antibody against H3K4me3.
H3K4me3_yFR974spt6-1004_80min37C_CJ104-CJ106_comb.bigwig


title: Galactose 2 LP WCFS1

description: Gene expression in presence of glalactose

value: Mid log phase


description:
Biological replicate 1 of 2. Rpb3 occupancy in rpb1-1 temperature-sensitive cells treated 80 minutes at 37°C. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1214_rpb1-1_80min37C_Rpb3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_849357.bed
A genome browser-ready file for Rpb3 occupancy (IP/Input) in rpb1-1 temperature-sensitive cells treated 80 min at 37°C.

value: Rpb3 (BioLegend 665004)


title: H3K4me3_ChIP-seq_spt16-197_rep2

description:
Adapter 27 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample was performed using a rabbit polyclonal antibody against H3K4me3.


title: Mannose 1 LP WCFS1

description: Gene expression in presence of mannose


title: Galactose 1 LP WCFS1


title: H3K4me3_ChIP-seq_WT_rep2

description:
Adapter 9 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample was performed using a rabbit polyclonal antibody against H3K4me3.


title: H4_ChIP-seq_WT_rep2

description:
Adapter 7 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. H4 occupancy in WT cells treated 80 minutes at 37°C. H4 ChIP sample was performed using a rabbit polyclonal antibody against H4.


title: Glucose 2 LP WCFS1

description: Gene expression in presence of glucose


title: H3K4me3_ChIP-seq_WT_rep1

description:
Adapter 3 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample was performed using a rabbit polyclonal antibody against H3K4me3.
H3K4me3_yFR971WT_80min37C_CJ1-CJ3_comb.bigwig


title: p35S_PPV_12wk_4

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

country: USA

institute: University of Maryland, College Park

description: polysomal RNA from PPV infected 12-week-old leaf tissue

library_source: transcriptomic

data_processing:
Reads were mapped to the Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1) using the CLC Genomics Workbench v10.0.1 RNA-seq analysis tool and default parameters (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10 - CLC Bio, Aarhus, Denmark)
Genome_build: Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1)
Supplementary_files_format_and_content: tab-delimited text files include Gene ID, Chromosome, Region, TPM, RPKM, Unique gene reads, Total gene reads, Unique exon reads and Total exon reads.

organism: Prunus domestica

growth_protocol: Transgenic plum trees expressing promoter:His6FLAG-RPL18 were maintained in the plant biosafety level 3 containment facility at the USDA facility at Fort Detrick, Frederick, MD, USA. Plants in the quarantine greenhouse were subjected to a cycle of 60 days of cold dormancy (4°C) followed by 84-90 days of growth at normal greenhouse temperatures (27°C). Leaf samples were collected at two, four, six, and twelve weeks post cold induced dormancy over two consecutive vegatative growth periods

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothereitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue. Samples were centrifuged at 16,000 g for 15 min at 4°C. The supernatant was loaded onto an 8 mL 1.6 M sucrose cushion. The polysome fraction was pelleted by centrifuging the samples at 170,000 g for 18 h at 4 °C. The pellet was resuspended in 1 mL of PEB. 50 μl of Anti-FLAG magnetic beads (Sigma Chemical Company, St. Louis, MO, USA) was added to the resuspended pellet and incubated at 4°C overnight with gentle rocking. The beads were recovered using their magnetic property and were washed four times in wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). Polysome-RNA complexes were eluted by treatment of the magnetic beads with 100 μl of Elution Buffer (100 μl wash buffer, 10 μl of 5 mg/mL FLAG3 peptide—Sigma Chemical Company, St. Louis, MO USA, 0.5 μl of 2 U/ml RNAse OUT—Thermo Fisher Scientific Cleveland, OH, USA). RLT buffer plus β-mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA, USA) was added to the eluted complexes. A 0.5 × volume of 100% ethanol was then added, and the sample transferred to Qiagen RNeasy columns. Washes and RNA elutions were performed according to the manufacturer’s instructions. Isolated RNA was measured on a NanoDrop 2000 and with the Qubit RNA Assay Kit (Thermo Fisher Scientific, Cleveland, OH, USA). Quality of the RNA was analyzed using an RNA ScreenTape assay (Agilent Technologies, Palo Alto, CA, USA).
Library preparation and paired-end sequencing on the Illumina HiSeq system was done by Genewiz (South Plainfield, NJ, USA).

treatment_protocol: PPV_D isolate Penn7 (EF640935) was used in this study. A Myzus persicae aphid colony was maintained inside containment and transmissions were conducted using symptomatic P. persica cv. GF 305 peach leaves as the inoculum source for aphid transmission to P. domestica L. transgenic plant lines.

tag: cultivar

value: P. domestica L 'President'

tag: developmental stage

value: 12 weeks

tag: infection status

value: PPV infected


title: H3K4me3_ChIP-seq_spt16-197_rep1

description:
Adapter 22 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample was performed using a rabbit polyclonal antibody against H3K4me3.
H3K4me3_yFR973spt16-197_80min37C_CJ4-CJ5_comb.bigwig


title: Glucose 1 LP WCFS1

description: Gene expression in presence of glucose


title: H3K56ac/H3_Input_spt16-197_rep2

description:
Adapter 4 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. Input signal of spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. This Input DNA was obtained from the same yeast extract used to perform H3K56ac and H3 ChIP-seq.


title: p35S_PPV_12wk_3


title: p35S_PPV_12wk_2


description:
Biological replicate 1 of 2. H3K79me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K79me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_693338.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: yFR973_spt16-197_80min37C_H3K36me3vsInput_20170621_Rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K36me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_74391.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: H3K36me3 (Abcam Ab9050)


description:
Biological replicate 1 of 2. H3K36me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K36me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_74391.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


description:
Biological replicate 1 of 2. H3K79me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K79me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_53208.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: yFR971_SPT16-WT_80min37C_H3K79me3vsInput_20170621_Rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in WT cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K79me3vsInput_20170621_Rep1-2MN__S.cerevisiaeApr11_971448.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1


title: yFR971_SPT16-WT_80min37C_H3K36me3vsInput_20170621_Rep2

description:
Biological replicate 2 of 2. H3K36me3 occupancy in WT cells treated 80 minutes at 37°C. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K36me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_101668.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

value: H3K36me3 (Abcam ab9050)


title: SedMYC siAHR-5-1

city: Dallas

first: Spencer

middle: Dann

last: Barnes

state: Texas

address: 5323 Harry Hines Blvd

department: Bioinformatics

institute: University of Texas Southwestern

description:
SedMYC.siAHR5.1
Poly-A RNA
processed data file: logcpm_counts.txt

data_processing:
RNA-seq assessment of the raw sequencing reads was done using NGS QC Toolkit (Patel and Jain 2012).
The reads were aligned to the genome RGSC 6.0/rn6 using HISAT2 (version 2.1.0) aligner. A minimum read count filter of 10 total reads was applied to remove low-expressed genes. Filtered reads were then normalized using DESeq2 (Love et al. 2014).
DESeq2 uses a negative binomial distribution to estimate data variability and uses an error model for a more robust statistical test for significance. A false discovery rate cutoff of < 5% was used to select significantly altered genes between experiment conditions.
Genome_build: RGSC 6.0/rn6
Supplementary_files_format_and_content: logcpm_counts.txt: Tab-delimited text file including logCPM values for all samples.

organism: Rattus norvegicus

source_name: myc -/- rat fibroblasts (HO15.19)

growth_protocol: Cells were cultured in DMEM with 10% FBS and 100 U/mL penicillin/streptomycin.

extract_protocol:
Harvested cells were sent to Genewiz. Total RNA was extracted using Qiagen RNeasy Plus Mini Kit (Qiagen, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina by following manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, mRNA were first enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA).

treatment_protocol: Stable cell lines were generated via retroviral or lentiviral infection. For knockdowns, 5 × 10e4 cells were seeded in six-well plates and, the next day, transfected with 40 nM siRNA. 48 h after transfection cells were harvested.

tag: human myc overexpression

value: Yes

tag: transfection

value: siRNA AHR-5

tag: time post transfection (hours)


description:
Biological replicate 1 of 2. H3K79me3 occupancy in WT cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K79me3vsInput_20170621_Rep1-2MN__S.cerevisiaeApr11_971448.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: SedMYC siAHR-2-3

description:
SedMYC.siAHR2.3
Poly-A RNA
processed data file: logcpm_counts.txt

value: siRNA AHR-2


title: SedMYC siAHR-5-2

description:
SedMYC.siAHR5.2
Poly-A RNA
processed data file: logcpm_counts.txt


title: yFR974_spt6-1004_80min37C_H3K4me2vsInput_20170607_Rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K4me2vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_422765.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K4me2 ChIP. Antibody from Abcam (ab7766). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K4me2 (Abcam ab7766)


title: SedMYC siAHR-5-3

description:
SedMYC.siAHR5.3
Poly-A RNA
processed data file: logcpm_counts.txt


title: SedMYC siAHR-2-2

description:
SedMYC.siAHR2.2
Poly-A RNA
processed data file: logcpm_counts.txt


title: SedMYC siAHR-2-1

description:
SedMYC.siAHR2.1
Poly-A RNA
processed data file: logcpm_counts.txt


title: SedMYC siCtrl-2

description:
SedMYC.siCtrl.2
Poly-A RNA
processed data file: logcpm_counts.txt

value: siRNA Control


title: p35S_PPV_6wk_6

description: polysomal RNA from PPV infected 6-week-old leaf tissue

value: 6 weeks


title: p35S_PPV_6wk_5


title: SedMYC siCtrl-1

description:
SedMYC.siCtrl.1
Poly-A RNA
processed data file: logcpm_counts.txt


title: p35S_PPV_12wk_1

description: polysomal RNA from PPV infected 12-week-old leaf tissue


title: SedMYC siCtrl-3

description:
SedMYC.siCtrl.3
Poly-A RNA
processed data file: logcpm_counts.txt


title: p35S_PPV_6wk_4


title: Sed siCtrl-3

description:
control.3
Poly-A RNA
processed data file: logcpm_counts.txt

value: No


title: Sed siCtrl-2

description:
control.2
Poly-A RNA
processed data file: logcpm_counts.txt


title: p35S_PPV_6wk_3


title: Sed siCtrl-1

description:
control.1
Poly-A RNA
processed data file: logcpm_counts.txt


description:
Biological replicate 1 of 2. H3K4me2 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K4me2vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_422765.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: yFR974_spt6-1004_80min37C_H3K4me1vsInput_20170607_Rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K4me1vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_967072.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K4me1 ChIP. Antibody from Abcam (ab8895). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K4me1 (Abcam ab8895)


description:
Biological replicate 1 of 2. H3K4me1 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K4me1vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_967072.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: SedMYC-3

description:
Myc3
Poly-A RNA
processed data file: logcpm_counts.txt


title: Sed-3

description:
Sed.3
Poly-A RNA
processed data file: logcpm_counts.txt


title: p35S_PPV_6wk_1


title: CONTROL-Rep2

city: Columbus

first: Pooja

last: Gangras

state: OH

address: 191 W. 9th Ave, apt A3

department: Molecular Genetics

institute: The Ohio State University

description:
polyA RNA
After second strand synthesis, end repair, and 3' end adenylation per the TruSeq protocol (Illumina, Inc.), libraries were constructed using an Apollo 324 automated library system

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing
Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters -m 20 --discard-untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters -p 12
Multi-mapped reads were removed based on tophat alignment score (< 50) and PCR duplicates were removed only for the RIP-seq data based on random barcodes
RIP-Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters -s -c -F 0.51 -sorted
Genome_build: GRCz10
Supplementary_files_format_and_content: RNA-Seq: FPKM as caculated by DESeq2 for each gene in the samples
Supplementary_files_format_and_content: RIP-seq: RPKM each transcript in the samples

organism: Danio rerio

source_name: Whole embryo

growth_protocol: All embryos were raised at 28.5C upto the required developmental timepoint.

extract_protocol:
RIP-Seq samples were extracted from the IP eluate by Phenol-Chloroform-Isoamyl alcohol extraction. RNA-seq samples were obatined by harvesting whole embryos in TRIZOL.
Libraries were prepared using a custom protocol described in detail in Gangras et al., Methods Mol Biol. 2018;1680:1-28. Briefly, a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription (RT) product, which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.

treatment_protocol:
mRNA was purified from 1 µg total RNA using Dynabeads oligo(dT)25 magnetic beads (Thermo Fisher Scientific) followed by clean-up with AMPure XP SPRI beads (Beckman Coulter). mRNA was then fragmented for 5 minutes at 70°C using Ambion's RNA Fragmentation Reagent (AM8740) followed by an additional clean-up step using AMPure XP SPRI beads. Fragmented RNA was reverse transcribed using random primers and SuperScript III (Thermo Fisher Scientific). After second strand synthesis, end repair, and 3' end adenylation per the TruSeq protocol (Illumina, Inc.), libraries were constructed using an Apollo 324 automated library system.
NA

value: 12 hpf

tag: rip-antibody

value: CONTROL


title: SedMYC-2

description:
Myc2
Poly-A RNA
processed data file: logcpm_counts.txt


title: SedMYC-1

description:
Myc1
Poly-A RNA
processed data file: logcpm_counts.txt


title: Sed-1

description:
Sed.1
Poly-A RNA
processed data file: logcpm_counts.txt


title: p35S_PPV_4wk_6

description: polysomal RNA from PPV infected 4-week-old leaf tissue

value: P. domestica L 'President'

value: 4 weeks


title: p35S_PPV_4wk_5

value: PPV infected


title: UPF1-MO-Rep2


title: Sed-2

description:
Sed.2
Poly-A RNA
processed data file: logcpm_counts.txt


title: p35S_PPV_4wk_4


title: CONTROL-Rep1


title: UPF1-MO-Rep1


title: p35S_PPV_4wk_3


description:
Biological replicate 1 of 2. H3K4me2 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me2vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_574294.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: p35S_PPV_6wk_2

description: polysomal RNA from PPV infected 6-week-old leaf tissue


title: p35S_PPV_4wk_2


title: p35S_PPV_4wk_1


title: p35S_PPV_2wk_5

description: polysomal RNA from PPV infected 2-week-old leaf tissue

value: 2 weeks


title: p35S_PPV_2wk_4


title: yFR973_spt16-197_80min37C_H3K4me1vsInput_20170607_Rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me1vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_758499.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: yFR973_spt16-197_80min37C_H3K4me2vsInput_20170607_Rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me2vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_574294.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me1vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_758499.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: p35S_PPV_2wk_3


title: yFR973_spt16-197_80min37C_H3K79me3vsInput_20170621_Rep2

description:
Biological replicate 2 of 2. H3K79me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K79me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K79me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K79me3vsInput_20170621_Rep1-2_MN__S.cerevisiaeApr11_693338.bed
A genome browser-ready file for H3K79me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: H3K79me3 (Abcam ab2621)


title: PL 13,5#60 vs Q 13,5 #43 [2]

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

description: TNBC PDX model sensitive (IDB-02S) and resistant (IDB-02R) to docetaxel

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

extract_protocol: Total RNA was isolated by standard procedures using TriPure (Roche, #11667165001)

value: tumor

tag: pdx model

value: IDB-02S model

tag: sensitivity to docetaxel

value: Sensitive

value: IDB-02R model

value: Resistant


title: yFR971_SPT16-WT_80min37C_H3K4me2vsInput_20170607_Rep2

description:
Biological replicate 2 of 2. H3K4me2 occupancy in WT cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me2vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_337301.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1

value: H3K4me2 (Abcam ab7766)


title: PL 13,5#27 vs Q 13,5#32 [2]


title: Q 24,11#37 vs PL 24,11 #40 [2]

description: TNBC PDX model sensitive (IDB-01S) and resistant (IDB-01R) to docetaxel

value: IDB-01R model

value: IDB-01S model


title: yFR971_SPT16-WT_80min37C_H3K4me1vsInput_20170607_Rep2

description:
Biological replicate 2 of 2. H3K4me1 occupancy in WT cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me1vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_101001.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

value: H3K4me1 (Abcam ab8895)


title: PL 13,5#60 vs Q 13,5 #43


title: Q 24,11#46 vs PL 24,11 #52 [2]


title: Q 13,5#37 vs PL 13,5#31


description:
Biological replicate 1 of 2. H3K4me2 occupancy in WT cells treated 80 minutes at 37°C. H3K4me2 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me2 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me2vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_337301.bed
A genome browser-ready file for H3K4me2 occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: p35S_PPV_2wk_2


description:
Biological replicate 1 of 2. H3K4me1 occupancy in WT cells treated 80 minutes at 37°C. H3K4me1 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me1 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me1vsInput_20170607_Rep1-2_MN__S.cerevisiaeApr11_101001.bed
A genome browser-ready file for H3K4me1 occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: Q 13,5#37 vs PL 13,5#31 [2]


title: p35S_PPV_2wk_1


title: yFR974_spt6-1004_80min37C_H2BvsInput_20170608_Rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_329608.bed
A genome browser-ready file for H2B occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H2B ChIP. Antibody from Abcam (ab1790). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H2B (Abcam ab1790)


title: MAGOH-WTsib-21hpf-Rep3

description:
Ribosomal RNA depleted total RNA
ribosomal RNA removed with Ribo-Zero kit (Illumina, Cat# MRZH116) prior to base hydrolysis of RNA. RNA fragments were then used to generate strand-specific libraries using a custom library preparationprotocol described in detail in Gangras et al., Methods Mol Biol. 2018;1680:1-28.

treatment_protocol:
None
NA

value: 21 hpf

value: MAGOH-WTsib


title: 3AB4

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip primeview human gene expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 7G system.

data_processing: The data were analyzed using the Gene Spring GX 13.1.1 software program (Agilent Technologies). We used RMA as summarization algorithm and performed quantile normalizaion. Baseline transformation was not performed.

label: biotin

source_name: iPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng of total RNA

growth_protocol: iPSCs were cultured in StemFit medium on plates coated with laminin-511 E8 fragments.

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

tag: gender

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: method

value: Episomal plasmid


title: p35S_Control_12wk_5

description: polysomal RNA from PPV infected 12-week-old leaf tissue

value: P. domestica L 'President'

value: 12 weeks

value: healthy control


description:
Biological replicate 1 of 2. H2Bub occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_ubH2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_841929.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H2Bub ChIP. Antibody from Cell Signaling Technology (#5546). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

tag: strain

tag: genotype

tag: antibody

value: H2Bub (Cell Signaling Technology 5546)


title: yFR973_spt16-197_80min37C_ubH2BvsInput_20170608_Rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in WT cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_ubH2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_33826.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: yFR974_spt6-1004_80min37C_ubH2BvsInput_20170608_Rep2

description:
Biological replicate 2 of 2. H2Bub occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_ubH2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_841929.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: MAGOH-WTsib-21hpf-Rep2

tag: genotype/variation


title: p35S_Control_12wk_4


title: MA9-CD97_WT_biological_replicate2

city: New York

first: Christopher

middle: Y.

last: Park

state: New York

address: 550 First Avenue

department: Pathology

institute: New York University

description: The Illumina Adapter sequence: 'AGATCGGAAGAGC' was trimmed from the raw fastq file using cutadapt version 1.2.1. and the following parameters:    Maximum trimming error rate: 0.1 (default)  Minimum required adapter overlap (stringency): 3 bp  Minimum required sequence length for both reads before a sequence pair gets removed: 25 bp

data_processing:
For RNA-Seq data generated from HL60 cells and MA9 transformed mouse cells, raw fastq files were aligned to the hg19 and mm10 reference genomes, respectively. Read counts were extracted using R with Rsamtools package (v1.24.0) and differentially expressed genes analyzed using the DESeq2 package (v 1.12.3).
Genome_build: hg19 for HL60 RNA-seq
Genome_build: mm10 for MA9 RNA-seq
Supplementary_files_format_and_content: Read count files for i) HL60 RNA-seq data ii) MA9 RNA-seq data

organism: Mus musculus

source_name: Purified HSPCs from wild type (WT) mice transduced with the leukemogenic oncogene MA9.

extract_protocol:
Samples were FACS-sorted into Trizol LS (Thermo Fisher, Rockford, Illinois).
Poly-A selected cDNA libraries were prepared using a SMARTer mRNA amplification kit (Clontech, Mountain View, California).

tag: tissue


description:
Biological replicate 1 of 2. H2Bub occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_329608.bed
A genome browser-ready file for H2B occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: MAGOH-Mutant-21hpf-Rep2

value: MAGOH-Mutant


title: PL 13,5#27 vs Q 13,5#32

value: tumor

value: IDB-02S model

value: Sensitive

value: IDB-02R model

value: Resistant


title: p35S_Control_12wk_3

tag: cultivar


title: p35S_Control_12wk_2

tag: developmental stage


title: MA9-CD97_KO_biological_replicate2

source_name: Purified HSPCs from CD97 deficient (CD97-/-) mice transduced with the leukemogenic oncogene MA9.


title: Q 24,11#46 vs PL 24,11 #52

value: IDB-01R model

value: IDB-01S model


title: MAGOH-Mutant-21hpf-Rep1

value: 21 hpf


title: p35S_Control_12wk_1

tag: infection status


title: p35S_Control_6wk_4

description: polysomal RNA from PPV infected 6-week-old leaf tissue

value: 6 weeks


description:
Biological replicate 1 of 2. H3K36me3 occupancy in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min. H3K36me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K36me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1480_Spt6-AA_Rapa30min_H3K36me3vsInput_20171031_rep1-2__S.cerevisiaeApr11_507349.bed
A genome browser-ready file for H3K36me3 occupancy (IP/Input) in Spt6-AA (anchor-away) cells treated with 1 μg/mL of rapamycin for 30 min.

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

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

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

value: H3K36me3 (Abcam Ab9050)

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


title: PL 24,11#32 vs Q 24,11#41