title: A2780cis H3K9ac input DNA

source_name: A2780cis cell ine

value: Cisplatin treated

value: none (input)


title: N2_HS_2

status: Public on Jul 26 2021

type: SRA

city: La Jolla

first: Delaney

last: Pagliuso

state: CA

address: 9500 Gilman Dr

department: Biological Sciences

country: USA

institute: University of California, San Diego

description: HS sample replicate 2

library_source: transcriptomic

data_processing:
Default base-calling software for the Illumina HiSeq 4000 platform was used
Sequenced reads were aligned using STAR with default parameters to WS235
Genome_build: ce11 for C. elegans
Supplementary_files_format_and_content: tab-deliminted text files with raw gene counts for each sample

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole L4 stage worm

growth_protocol: WT (Bristol N2) and mir-85(m4117) animals were grown under standard growth conditions (20°C) until HS was performed

extract_protocol:
L4 staged animals were washed 3 times with M9 buffer and collected before being snap-frozen in dry ice ethanol. RNA was isolated using Trizol.
Illumina TruSeq Standard Total RNA Library Preparation was performed using 1ug of total RNA (SR75)

treatment_protocol: CTL animals maintained at 20°C for 47hrs and HS animals were grown at 20°C for 44hrs before being HS-treated for 3hrs at 35°C

tag: strain

tag: treatment

value: HS


title: cell57

city: Beijing

first: Zeyuan

last: Liu

address: 15 Datun Road, Chaoyang District, Beijing, 100101, China

country: China

institute: Institute of Biophysics,Chinese Academy of Sciences

description:
rep7-InG_ZI48
smart-seq-raw-counts-for-geo.txt

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to GRCm38 mouse genome and mm10 mouse genome by STAR(v2.5.3a) and Cellranger(v3.0.2)
Filtered count matrix was merged by Seurat Package
Genome_build: GRCm38, mm10
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx and txt file, and barcode and gene information was with tsv format

organism: Mus musculus

source_name: mouse brain

extract_protocol:
Mouse brain samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single nuclei were extracted by lysis buffer
Chromium™ Single Cell 3’ Reagent Kits v3

tag: age

value: 3 months

tag: tissue

value: brain

tag: region

value: superior colliculus

tag: sequencing stragery


title: A2780cis H3K9ac

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

library_source: genomic

data_processing:
Sequencing was performed on an Illumina HiSeq 3000 deep sequencer acquiring 2 x 150 bp paired end reads.
Reads were mapped to the human reference genome GRCh37 (hg19) using Bowtie2.
The ChIP-seq data was quantile normalized and peaks were identified using the MACS2 peak calling algorithm.
For peak calling, noise reduction was performed by comparing the input (control) samples to the IP samples using MACS2 bdgcmp.
Broad peaks were then called from the bedGraph datasets using MACS2 bdgbroadcall.
For all A2780 and A2780cis ChIP-seq data 1500 was used as a cutoff for peaks and 750 as a cutoff for linking regions.
For CAOV4 andCAOV4cis ChIP-seq data 1000 was used as a cutoff for peaks and 500 as a cutoff for linking regions.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files and bed files containing called peaks

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Mononucleosomes were prepared from lysates by Mnase digest and supplemented with spike-in control (5% of total, mononucleosomes, D. melanogaster). Histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared and sequenced by the Max Planck Genome center Cologne.

tag: cell line

tag: cell type

value: human epithelial ovarian cancer

tag: chip antibody

value: H3K9ac (Abcam, ab12179)


title: A2780 H3K27ac shRen input DNA

source_name: A2780 cells line

value: 1 week control knockdown by shRNA


title: cell56

description:
rep7-InG_ZI47
smart-seq-raw-counts-for-geo.txt


title: yFR117_WT_Spt16vsInput_20190529_repl2

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_711046.bed

hyb_protocol: ChIP and control samples were combined and dried by SpeedVac. Combined samples were resuspended in 110 µL of fresh hybridization mix (5 µL 10 mg/mL Salmon Sperm DNA (Thermo Fisher Scientific, 15632011), 5 µL 8 mg/mL Yeast tRNA (Thermo Fisher Scientific, 15401011) and 100 µL DIG Easy Hyb (Roche, 11603558001)) and incubated 5 min at 95˚C followed by 5 min at 45˚C. Samples were hybridized to Agilent microarrays in SureHyb enabled chambers (Agilent, G2534A) with rotation at 42˚C for at least 18 hr. Microarrays were washed on an orbital shaker for 5 min at room temperature with Wash I buffer (6X SSPE, 0.005% N-Lauroylsarcosine), followed by a second wash with pre-warmed (31˚C) Wash II buffer (0.06X SSPE) for 5 min at room temperature. The microarrays used were described before (Jeronimo and Robert, 2014) and were custom designed by Agilent Technologies and contain a total of about 180,000 Tm-adjusted 60-mer probes covering the entire yeast genome with virtually no gaps between probes.

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2 µm resolution.

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

organism: Saccharomyces cerevisiae

label_protocol: The ChIP and Input samples were blunted as follow. 40 µL of ChIP DNA or about 400 ng of Input DNA were added to 70 µL of blunting¬¬ mix (11 µL 10X NEBuffer 2 (NEB, B7002S), 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA polymerase (NEB, M0203L)) and incubated at 12˚C for 20 min. Then, the blunted DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) in the presence of 280 mM of NaOAc pH 5.2 and 10 μg of glycogen, precipitated with ethanol and resuspended in 25 µL ddH2O. Blunted DNA was ligated to 100 pmol of annealed linkers (see Table S2) with 2.5 units of T4 DNA ligase (Thermo Fisher Scientific, 15224041) in the supplied buffer, in a final volume of 50 µL, overnight at 16˚C. Samples were precipitated with 6 µL of 3 M NaOAc pH 5.2 and 130 µL ethanol, and resuspended in 25 µL ddH2O. 15 µL of labeling mix (4 µL 10X ThermoPol Reaction buffer (NEB, B9004S), 2 µL of 5 mM aa-dUTP/dNTP mix (5 mM each dATP, dGTP and dCTP, 3 mM dTTP and 2 mM 5-(3-aminoallyl)-dUTP (Thermo Fisher Scientific, AM8439)) and 1.25 µL of 40 µM oligo 1) were added to each sample. Samples were placed in a thermocycler and when temperature reached 55˚C, 10 µL of enzyme mix (1 µL 10X ThermoPol Reaction buffer, 1 µL (5 units) Taq DNA polymerase (Thermo Fisher Scientific, 18038240) and 0.01 µL (0.025 units) Pfu DNA polymerase (Thermo Fisher Scientific, EP0502)) were added and the following program was run. 1) 72˚C, 5 min; 2) 95˚C, 2 min; 3) 32 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1 min; 4) 72˚C, 4 min; 5) 4˚C, forever. PCR products were purified using QIAquick PCR Purification kit (QIAGEN, 28106) with few modifications: PE buffer was replaced by Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Eluates were dried by SpeedVac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 Mono-Reactive NHS Ester Fluorescent Dye (ChIP samples) or Cy3 Mono-Reactive NHS Ester Fluorescent Dye (control samples Input DNA or no-tag ChIP) (GE Healthcare, PA25001 and PA23001) were added. Samples were incubated 1 hr in the dark at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 were added and samples were purified using QIAquick PCR Purification kit according to the manufacturers’ instructions.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Spt16 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the 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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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.
Cleanup protocol:  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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

tag: genotype

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0

value: anti-Spt16 (a gift from T. Formosa, 1 uL)

extract_protocol:
IP protocol:  none
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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.
Cleanup protocol:  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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.


title: yFR117_WT_Spt16vsInput_20150723_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Spt16vsInput_20150723_rep1-2_S.cerevisiaeApr11_275686.bed


title: yFR117_WT_Spt16vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Spt16vsInput_rep1-2_S.cerevisiaeApr11_927936.bed


title: yFR117_WT_Spt16vsInput_20190529_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_711046.bed


title: mir85_CTL_3

description: Control sample replicate 6

value: CTL


title: cell55

description:
rep7-InG_ZI46
smart-seq-raw-counts-for-geo.txt


title: A2780 H3K9ac input DNA


title: yFR117_WT_Spt16vsInput_20150723_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Spt16vsInput_20150723_rep1-2_S.cerevisiaeApr11_275686.bed


title: yFR117_WT_Spt16vsInput_repl1_20130731

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Spt16vsInput_Rep1-2_20130731_S.cerevisiaeApr11_665835.bed


title: cell54

description:
rep7-InG_ZI45
smart-seq-raw-counts-for-geo.txt


title: A2780 H3K9ac


title: cell52

description:
rep7-InG_ZI43
smart-seq-raw-counts-for-geo.txt


title: N2_CTL_3

description: Control sample replicate 3


title: cell53

description:
rep7-InG_ZI44
smart-seq-raw-counts-for-geo.txt


title: mir85_CTL_1

description: Control sample replicate 4


title: A2780cis H3K27ac input DNA


title: mir85_CTL_2

description: Control sample replicate 5


title: N2_CTL_2

description: Control sample replicate 2


title: A2780cis H3K27ac

value: H3K27ac (Abcam, ab4729)


title: N2_HS_1

description: HS sample replicate 1


title: cell51

description:
rep7-InG_ZI42
smart-seq-raw-counts-for-geo.txt


title: A2780 H3K27ac input DNA


title: N2_CTL_1

description: Control sample replicate 1


title: cell50

description:
rep7-InG_ZI41
smart-seq-raw-counts-for-geo.txt


title: A2780 H3K27ac


title: cell49

description:
rep7-InG_ZI40
smart-seq-raw-counts-for-geo.txt


title: yFR117_WT_Rpb3vsinput_repl2_20131119

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Rpb3vsinput_rep1-2_20131119_S.cerevisiaeApr11_655316.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (Neoclone W0012, 3 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the 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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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.
Cleanup protocol:  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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: anti-Rpb3 (Neoclone W0012, 3 uL)


title: yFR117_WT_Rpb3vsinput_repl1_20131119


title: MNaseInput_Rpb3_yFR116WT_R2

description:
Barcode ID: Adapter 21 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. Input signal of WT cells. This Input DNA was obtained from the same yeast extract used to perform Rpb3 MNase-ChIP-seq.

data_processing:
Paired-end reads from MNase-ChIP-seq data where aligned on the S. cerevisiae genome version sacCer3 using Bowtie2 version 2.3.4.3 (Langmead and Salzberg, 2012) with the parameter “-X 1000” to include longer fragments. Unmapped and low-quality fragments were removed using SAMtools version 1.9 using the following parameters “view -f 2 -F 2048”. Duplicates were removed using SAMtools with the following parameter “fixmate -m” and then “markdup -r”. The aligned files were converted to BED using BEDTools version 2.27.1 using a custom software called seqtools version 1.0 available at https://github.com/francoisrobertlab/seqtools with the command “seqtools bam2bed” resulting in BED files containing the DNA fragments. The BED files of replicates were merged using seqtools with command “seqtools merge”. Genome coverage files were generated using customs scripts “seqtools” with commands “mnasetools prepgenomecov” and “seqtools genomecov” that require BEDTools version 2.27.1 and KentUtils (downloaded on July 16th 2018). The genome coverage files were converted to the bigWig format using the utilities from UCSC Genome Browser (Casper et al., 2018).
Genome_build: S. cerevisiae (UCSC sacCer3)
Supplementary_files_format_and_content: bigWig files for both individual replicates (beginning with "CJ") and the combined biological replicates (beginning with "MNase").

source_name: Yeast cell extract

growth_protocol: Cells were grown at 30°C and 200 rpm in YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium as follow. Strains were streaked from glycerol stocks onto 2% agar YPD plates and grown at 30°C for 2-3 days. An isolated colony was then grown overnight in 20 mL of YPD. This preculture was used to inoculate 500 mL of YPD at an OD600 of 0.1 which was grown to an OD600 of 0.7-0.9.

extract_protocol: MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.

treatment_protocol: Cultures were crosslinked with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min. Crosslinking was quenched with 125 mM glycine.

tag: strain name


title: MNaseInput_Rpb3_yFR116WT_R1

description:
Barcode ID: Adapter 20 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. Input signal of WT cells. This Input DNA was obtained from the same yeast extract used to perform Rpb3 MNase-ChIP-seq.
processed data file (two biological replicates combined): MNaseInput_Rpb3_yFR116WT_CJ13-CJ14_20191218.bw


title: cell48

description:
rep7-InG_ZI39
smart-seq-raw-counts-for-geo.txt


title: yFR117_WT_Rpb3vsInput_20190530_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_606483.bed

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (BioLegend 665004, 1.5 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the 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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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.
Cleanup protocol:  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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: anti-Rpb3 (BioLegend 665004, 1.5 uL)


title: cell47

description:
rep7-InG_ZI38
smart-seq-raw-counts-for-geo.txt


title: cell46

description:
rep7-InG_ZI37
smart-seq-raw-counts-for-geo.txt


title: yFR117_WT_Rpb3vsInput_repl1_20130731

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Rpb3vsInput_Rep1-2_20130731_S.cerevisiaeApr11_292139.bed


title: MNaseChIP_Rpb3_yFR116WT_R1

description:
Barcode ID: Adapter 13 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by MNase-ChIP-seq in WT cells. Rpb3 MNase-ChIP-seq was performed using a mouse monoclonal antibody against Rpb3.
processed data file (two biological replicates combined): MNaseChIP_Rpb3_yFR116WT_CJ9-CJ10_20191218.bw


title: MNaseChIP_Rpb3_yFR116WT_R2

description:
Barcode ID: Adapter 14 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by MNase-ChIP-seq in WT cells. Rpb3 MNase-ChIP-seq was performed using a mouse monoclonal antibody against Rpb3.


title: cell45

description:
rep7-InG_ZI36
smart-seq-raw-counts-for-geo.txt


title: MNaseInput_Spt16_yFR930chd1D_R2

description:
Biological replicate 2 of 2. Input signal of chd1D cells. This Input DNA was obtained from the same yeast extract used to perform Spt16 MNase-ChIP-seq.
processed data file (two biological replicates combined):  MNaseInput_Spt16_yFR930chd1D_CJ7-CJ8_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 25 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: cell44

description:
rep7-InG_ZI35
smart-seq-raw-counts-for-geo.txt


title: cells_siFSCN1

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

data_processing: Hisat2, samtools, htseq-count packages were used to align 150 bp paired-end reads with hg19 (UCSC). The expression of genes and transcripts were quantified by using cufflinks tools.

source_name: colorectal cancer cells

growth_protocol: The HCT15 human colon cancer cell lines were purchased from the Typical Culture Preservation Commission Cell Bank, Chinese Academy of Sciences. HCT15 was maintained on gelatinized 10cm-plate in RPMI-1640 Medium (Gibco) supplemented with 10% FBS (fetal bovin serum) (Gibco), 100 U penicillin/100 mg streptomycin (Gibco) at 37℃ and 5% CO2.

extract_protocol:
Then total RNA was isolated by the RNA pure Tissue and Cell Kit and the RNA was sequencing by the 150 bp paired method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The siRNA sequences against human FSCN1 and non-silencing were designed and chemically synthesized by Genepharma (Shanghai, China). HCT15 cells were transfected with 100 ~ 200 pmol siRNA using 5 ~ 10 μL INTERFERin® transfection reagent (Polyplus) in a 6-well plate.

value: colorectal cancer cells

value: FSCN1 siRNA transfected cells


title: MNaseInput_Spt16_yFR930chd1D_R1

description:
Biological replicate 1 of 2. Input signal of chd1D cells. This Input DNA was obtained from the same yeast extract used to perform Spt16 MNase-ChIP-seq.
processed data file (two biological replicates combined):  MNaseInput_Spt16_yFR930chd1D_CJ7-CJ8_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 23 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: cells_P

value: NC siRNA transfected cells


title: yFR117_WT_Rpb3vsInput_20150723_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Rpb3vsInput_20150723_rep1-2_S.cerevisiaeApr11_584271.bed


title: cell43

description:
rep7-InG_ZI34
smart-seq-raw-counts-for-geo.txt


title: MNaseInput_Spt16_yFR116WT_R2

description:
Biological replicate 2 of 2. Input signal of WT cells. This Input DNA was obtained from the same yeast extract used to perform Spt16 MNase-ChIP-seq.
processed data file (two biological replicates combined):  MNaseInput_Spt16_yFR116WT_CJ5-CJ6_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 21 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: yFR116_WT_Spt16vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_rep1-2_S.cerevisiaeApr11_941877.bed


title: yFR1214_rpb1-1ts_Spt16vsInput_20120516_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in rpb1-1 temperature sensitive cells after heat-shock at 37°C for 80 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1214_rpb1-1ts_Spt16vsInput_20120516_Rep1-2_S.cerevisiaeApr11_672966.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in rpb1-1 cells after heat-shock at 37°C for 80 min.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.7. Then, an equal volume of YPD pre-warmed to 49°C was added to the flask, which was immediately transferred to 37°C for additional 80 min before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol: heat-shock at 37°C for 80 min

value: MATa, ura3-52, rpb1-1


title: MNaseInput_Spt16_yFR116WT_R1

description:
Biological replicate 1 of 2. Input signal of WT cells. This Input DNA was obtained from the same yeast extract used to perform Spt16 MNase-ChIP-seq.
processed data file (two biological replicates combined):  MNaseInput_Spt16_yFR116WT_CJ5-CJ6_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 20 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: BAT_control diet_rep3

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: maternal control diet

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

source_name: MeDIP DNA from control diet

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from fat samples using Dneasy Blood & Tissue Kit.

value: brown adipose tissue

value: 16 week

tag: sample type

value: MeDIP DNA

source_name: input DNA from maternal control diet

value: input DNA


title: G7A01_b3_6mo_G6E11_b3_6mo

city: New York

first: Alison

last: Goate

state: NY

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Digital expression was carried out using Drop-Seq tools
STAR v2.5.2a was used for read alignments
HTO antibodies were counted using CITE-Seq Count (v1.4.2) and demultiplexed using Seurat v3.0
Cells with <200 detectable genes, <500 reads and >20% mitochondrial rate were removed using Seurat v3.0(dev)
Data were integrated using SCTransform (Seurat v3.0 (dev)) and annotated using SingleR with custom reference libraries built from Polioudakis et al. Neuron, 2019 and Zhang et al. Neuron, 2016
Genome_build: Hg19
Supplementary_files_format_and_content: Gene read counts per cell

molecule: polyA RNA

source_name: iPSC-derived cerebral organoid

growth_protocol: Cerebral organoids were generated as per previously published protocol - see Yoon et al. Nature Methods, 2019.

extract_protocol:
Organoids were dissociated into single cell suspensions using Papain (Worthington). Resulting cells were labelled with hash-tag oligonucleotide antibodies as described in Stoeckius et al. Genome Biology, 2018.
Libraries were prepared and sequenced using either the 10x Genomics Single Cell v2 or v3 platforms. Libraries were sequenced with either a 26x90bp or 28x90bp read length
Single-cell RNA sequencing

treatment_protocol: No treatment

value: 6 months

tag: batch


title: yFR117_WT_Rpb3vsInput_20150723_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Rpb3vsInput_20150723_rep1-2_S.cerevisiaeApr11_584271.bed


title: yFR116_WT_Spt16vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_rep1-2_S.cerevisiaeApr11_941877.bed


title: cell41

description:
rep7-InG_ZI32
smart-seq-raw-counts-for-geo.txt

value: 3 months

value: brain

value: superior colliculus


title: BAT_control diet_rep2

description: maternal control diet


title: yFR116_WT_Spt16vsInput_20190502_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_20190502_rep1-2_S.cerevisiaeApr11_98167.bed

value: anti-Spt16 (a gift from T. Formosa, 1 uL)


title: MNaseChIP_Spt16_yFR930chd1D_R2

description:
Biological replicate 2 of 2. Spt16 occupancy by MNase-ChIP-seq in chd1D cells. Spt16 MNase-ChIP-seq was performed using a rabbit polyclonal antibody against Spt16.
processed data file (two biological replicates combined):  MNaseChIP_Spt16_yFR930chd1D_CJ3-CJ4_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 18 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq

value: anti-Spt16 (a gift from T. Formosa, 1 μL)


title: yFR117_WT_Pob3vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Pob3) occupancy by ChIP-chip in WT cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Pob3vsInput_rep1-2_S.cerevisiaeApr11_450517.bed

data_processing:
BED description:  A genome browser-ready file for Pob3 occupancy by ChIP-chip (IP/Input) in WT cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Pob3 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the 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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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.
Cleanup protocol:  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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0

value: anti-Pob3 (a gift from T. Formosa, 1 uL)


title: G6A02_b3_6mo_NDB09_b3_6mo


title: cell40

description:
rep7-InG_ZI31
smart-seq-raw-counts-for-geo.txt


title: yFR117_WT_Pob3vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Pob3) occupancy by ChIP-chip in WT cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Pob3vsInput_rep1-2_S.cerevisiaeApr11_450517.bed


title: yFR116_WT_Spt16vsInput_20190502_repl2

description:
Biological replicate 2 of 2. FACT (Spt16)occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_20190502_rep1-2_S.cerevisiaeApr11_98167.bed


title: BAT_maternal high fat diet_rep1

description: maternal high fat diet

source_name: MeDIP DNA from maternal high fat diet

source_name: input DNA from maternal high fat diet


title: G7A01_b2_6mo_G6E11_b2_6mo


title: yFR116_WT_Spt16vsInput_20190211_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_20190211_rep1-2_S.cerevisiaeApr11_643401.bed


title: cell42

description:
rep7-InG_ZI33
smart-seq-raw-counts-for-geo.txt


title: MNaseChIP_Spt16_yFR116WT_R2

description:
Biological replicate 2 of 2. Spt16 occupancy by MNase-ChIP-seq in WT cells. Spt16 MNase-ChIP-seq was performed using a rabbit polyclonal antibody against Spt16.
processed data file (two biological replicates combined):  MNaseChIP_Spt16_yFR116WT_CJ1-CJ2_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 14 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: MNaseChIP_Spt16_yFR930chd1D_R1

description:
Biological replicate 1 of 2. Spt16 occupancy by MNase-ChIP-seq in chd1D cells. Spt16 MNase-ChIP-seq was performed using a rabbit polyclonal antibody against Spt16.
processed data file (two biological replicates combined):  MNaseChIP_Spt16_yFR930chd1D_CJ3-CJ4_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 15 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: yFR117_WT_Rpb3vsInput_20190530_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_606483.bed

value: anti-Rpb3 (BioLegend 665004, 1.5 uL)


title: MNaseChIP_Spt16_yFR116WT_R1

description:
Biological replicate 1 of 2. Spt16 occupancy by MNase-ChIP-seq in WT cells. Spt16 MNase-ChIP-seq was performed using a rabbit polyclonal antibody against Spt16.
processed data file (two biological replicates combined):  MNaseChIP_Spt16_yFR116WT_CJ1-CJ2_20191021.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 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 High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 13 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: BAT_maternal high fat diet_rep2

description: maternal high fat diet


title: BAT_control diet_rep1

description: maternal control diet


title: NDB06_b3_6mo_G7F02_b2_6mo


title: BAT_maternal high fat diet_rep3

description: maternal high fat diet


title: yFR116_WT_Spt16vsInput_20160924_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_20160924_rep1-2_S.cerevisiaeApr11_496811.bed

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Spt16 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the 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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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.
Cleanup protocol:  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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.


title: yFR116_WT_Spt16vsInput_20190211_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_20190211_rep1-2_S.cerevisiaeApr11_643401.bed

extract_protocol:
IP protocol:  none
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (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.
Cleanup protocol:  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). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) 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 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.


title: cell37

description:
rep7-InG_ZI28
smart-seq-raw-counts-for-geo.txt

extract_protocol:
Mouse brain samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single nuclei were extracted by lysis buffer
Chromium™ Single Cell 3’ Reagent Kits v3


title: cell38

description:
rep7-InG_ZI29
smart-seq-raw-counts-for-geo.txt


title: G6A02_b2_6mo_G7B12_b2_6mo


title: yFR116_WT_Spt16vsInput_20160924_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR116_WT_Spt16vsInput_20160924_rep1-2_S.cerevisiaeApr11_496811.bed


title: G7F02_b3_6mo_G7B12_b3_6mo