title: yFR3075_3HA-chd1K407R_Spt16vsInput_20190519_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in 3HA-tagged chd1K407R cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3075_3HA-chd1K407R_Spt16vsInput_20190519_rep1-2_S.cerevisiaeApr11_873946.bed


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 5

status: Public on Jul 26 2021

type: RNA

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

hyb_protocol: Was performed as a service in the Thermo Fisher laboratories in San Diego according to the manufacturer’s protocol.

data_processing: Raw intensity values, CHP files containing signal space transformation-robust multi-array average (SST-RMA) normalized data, as well as transcript annotation, were provided by ThermoFisher. Additional probe annotation was obtained using the Bioconductor clariomdhumantranscriptcluster.db package v8.7.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Extracellular vesicles from THP-1 macrophages

label_protocol: Was performed as a service in the Thermo Fisher laboratories in San Diego according to the Clariom manufacturer’s protocol.

growth_protocol: THP-1 monocytes were maintained in RPMI 10% FCS 1% PenStrep

extract_protocol: RNA was extracted using the miRCURY RNA Isolation Kit – Cell and Plant (Exiqon) according to the manufacturer’s instructions. Subsequently, DNase digest was performed using the Turbo DNA-free kit (Invitrogen).

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 10 µM nigericin (90 min; Invitrogen).
THP-1 monocytes were differentiated with 100 nM PMA for 12 to 16 h, after which the cells were washed once with PBS and rested for 24 h before stimulation. Per condition, 30 million PMA-differentiated WT THP-1 macrophages were primed with LPS and subsequently treated with an inflammasome activator, primed only, TLR-stimulated or left untreated. Tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. 2K and 10K pellets were washed in PBS prior to analysis. Supernatant was filtered using a 0.2 µm filter (Millipore) and then concentrated to a total volume of 0.5 ml using a 10K NMWL filter (Amicon Ultra, Sigma-Aldrich). The sample was then transferred onto a size exclusion chromatography column (qEV original, Izon). Fractions of 0.5 ml were collected, the SEC EVs referred to within this study comprise fraction 7, 8 and 9.

tag: treatment

value: LPS+Nig

tag: cell type

value: THP-1 macrophages

tag: ev fraction

value: 10K EVs

tag: replicate

tag: batch


title: S_6a02_6mo_b2_1

type: SRA

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

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.2b).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts

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:
Total RNA was extracted from individual organoids in a single batch using the KingFisher Flex (ThermoFisher Scientific) automated system and MagMAX mirVana Total RNA isolation kit (ThermoFisher Scientific).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina, and sequenced as paired-end 150bp reads on the Illumina HiSeq 4000.

treatment_protocol: No treatment

tag: tissue

value: iPSC-derived cerebral organoid

tag: cell line

tag: age

tag: technical replicate

tag: genotype


title: DCcells_G2_wk0_rep3 [S409]

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

organism: Macaca mulatta

label_protocol: Isolated mRNA was amplified and biotynlated using the TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 for microarray studies

growth_protocol: Not applicable. Cells were isolated directly from PBMCs

extract_protocol: RNA was extracted from sorted DCs, CD4+ T cells and B cells using TRIzol and phenol-chloroform extraction

treatment_protocol: Sorting of CD4 T cells was performed in a resting state without any prior treatment or experimental manipulation

tag: subject

tag: timepoint

tag: subset

value: DCcells

tag: group

tag: immunogen

value: ALVAC


title: Bcells_G2_wk0_rep3 [S407]

value: Bcells


title: S_6a02_6mo_b1_3


title: S_6a02_6mo_b1_4


title: S_6a02_6mo_b1_2


title: DCcells_G2_wk0_rep2 [S405]


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 4

scan_protocol: Was performed as a service in the Thermo Fisher laboratories in San Diego according to the manufacturer’s protocol.


title: yFR3075_3HA-chd1K407R_Rpb3vsInput_20190519_repl1

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in 3HA-tagged chd1K407R cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3075_3HA-chd1K407R_Rpb3vsInput_20190519_rep1-2_S.cerevisiaeApr11_745893.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 Rpb3 occupancy by ChIP-chip (IP/Input) in 3HA-tagged chd1K407R 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)

molecule: genomic DNA

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-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.

tag: strain

tag: chip antibody

value: anti-Rpb3 (BioLegend 665004, 1.5 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: S_6a02_6mo_b1_1


title: yFR3061vs116_WT_3HA-Chd1vsNoTag_20190519_repl1

description:
Biological replicate 1 of 2. Chd1 occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Chd1 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3061vs116_WT_3HA-Chd1vsNoTag_20190519_rep1-2_S.cerevisiaeApr11_616012.bed

data_processing:
BED description:  A genome browser-ready file for Chd1 occupancy by ChIP-chip (IP tag/IP No tag) in WT (3HA-tagged Chd1) 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-HA (Santa Cruz Biotechnology sc-7392, 15 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-HA (Santa Cruz Biotechnology sc-7392, 15 uL)


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 3

tag: treatment


title: yFR3061_WT_3HA-Chd1_Spt16vsInput_20190519_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_3HA-Chd1_Spt16vsInput_20190519_rep1-2_S.cerevisiaeApr11_387747.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT (3HA-tagged Chd1) 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-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.

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


title: yFR3061vs116_WT_3HA-Chd1vsNoTag_20190519_repl2

description:
Biological replicate 2 of 2. Chd1 occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Chd1 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against a similar ChIP sample performed from an isogenic strain where the CHD1 gene is not tagged (Cy3-labeled).
SmthBED_yFR3061vs116_WT_3HA-Chd1vsNoTag_20190519_rep1-2_S.cerevisiaeApr11_616012.bed


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 2

tag: cell type

value: SEC EVs


title: Bcells_G2_wk0_rep2 [S403]


title: Tcells_G2_wk0_rep3 [S406]

value: Tcells


title: Tcells_G2_wk0_rep4 [S410]


title: DCcells_G1_wk0_rep4 [S401]

value: ALVACempty


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 3

tag: ev fraction


title: yFR3061_WT_3HA-Chd1_Spt16vsInput_20190519_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_3HA-Chd1_Spt16vsInput_20190519_rep1-2_S.cerevisiaeApr11_387747.bed


title: Tcells_G2_wk0_rep2 [S402]


title: S_6a02_4mo_b3_3

description: outlier in 3D PCA, thereby removed in the downstream analyses


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 2

tag: replicate


title: yFR3061_WT_3HA-Chd1_Rpb3vsInput_20190519_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_3HA-Chd1_Rpb3vsInput_20190519_rep1-2_S.cerevisiaeApr11_560001.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT (3HA-tagged Chd1) 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)


title: Bcells_G1_wk0_rep4 [S399]


title: yFR297_chd1delta_Spt16vsinput_repl1_20131119

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR297_chd1delta_Spt16vsinput_rep1-2_20131119_S.cerevisiaeApr11_442249.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in chd1Δ 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)

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0, chd1{delta}::KanMX4


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 1

tag: batch


title: yFR3061_WT_3HA-Chd1_Rpb3vsInput_20190519_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT (3HA-tagged Chd1) cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3061_WT_3HA-Chd1_Rpb3vsInput_20190519_rep1-2_S.cerevisiaeApr11_560001.bed


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 1


title: S_6a02_4mo_b3_2

tag: tissue


title: 10K EVs from LPS+MSU-treated THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 500 µg/ml MSU crystals (120 min).
THP-1 monocytes were differentiated with 100 nM PMA for 12 to 16 h, after which the cells were washed once with PBS and rested for 24 h before stimulation. Per condition, 30 million PMA-differentiated WT THP-1 macrophages were primed with LPS and subsequently treated with an inflammasome activator, primed only, TLR-stimulated or left untreated. Tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. 2K and 10K pellets were washed in PBS prior to analysis. Supernatant was filtered using a 0.2 µm filter (Millipore) and then concentrated to a total volume of 0.5 ml using a 10K NMWL filter (Amicon Ultra, Sigma-Aldrich). The sample was then transferred onto a size exclusion chromatography column (qEV original, Izon). Fractions of 0.5 ml were collected, the SEC EVs referred to within this study comprise fraction 7, 8 and 9.

value: LPS+MSU


title: yFR297_chd1delta_Spt16vsinput_repl2_20131119

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in chd1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR297_chd1delta_Spt16vsinput_rep1-2_20131119_S.cerevisiaeApr11_442249.bed


title: DCcells_G1_wk0_rep1 [S397]


title: S_6a02_4mo_b3_4

tag: cell line


title: S_6a02_4mo_b2_3

tag: age


title: S_6a02_4mo_b3_1

tag: technical replicate


title: Tcells_G1_wk0_rep4 [S398]


title: S_6a02_4mo_b2_2

tag: genotype


title: S_6a02_4mo_b2_4


title: SEC EVs from LPS+MSU-treated THP-1 macrophages rep 4


title: Bcells_G1_wk0_rep1 [S395]

tag: subject


title: DCcells_G1_wk0_rep5 [S393]

tag: timepoint


title: yFR297_chd1delta_Rpb3vsinput_repl2_20131119

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR297_chd1delta_Rpb3vsinput_rep1-2_20131119_S.cerevisiaeApr11_958327.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in chd1Δ 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: Tcells_G1_wk0_rep1 [S394]

tag: subset


title: S_6a02_4mo_b2_1


title: SEC EVs from LPS+MSU-treated THP-1 macrophages rep 2


title: yFR297_chd1delta_Rpb3vsinput_repl1_20131119

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in chd1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR297_chd1delta_Rpb3vsinput_rep1-2_20131119_S.cerevisiaeApr11_958327.bed


title: 10K EVs from LPS+MSU-treated THP-1 macrophages rep 4


title: Bcells_G1_wk0_rep5 [S391]

tag: group


title: Tcells_G1_wk0_rep5 [S390]

tag: immunogen


title: yFR265_gcn5D_Rpb3vsInput_20150723_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in gcn5Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR265_gcn5D_Rpb3vsInput_20150723_rep1-2_S.cerevisiaeApr11_874545.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in gcn5Δ 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)

tag: strain

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0, gcn5{delta}kanMX4


title: S_6a02_4mo_b1_3


title: S_6a02_4mo_b1_4


title: yFR265_gcn5D_Rpb3vsInput_20150723_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in gcn5Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR265_gcn5D_Rpb3vsInput_20150723_rep1-2_S.cerevisiaeApr11_874545.bed

tag: chip antibody


title: 10K EVs from LPS+MSU-treated THP-1 macrophages rep 2

tag: treatment


title: SEC EVs from LPS+MSU-treated THP-1 macrophages rep 1

tag: cell type


title: yFR265_gcn5D_Spt16vsInput_20150723_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in gcn5Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR265_gcn5D_Spt16vsInput_20150723_rep1-2_S.cerevisiaeApr11_844430.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in gcn5Δ 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)


title: yFR2035_ubp8D_Spt16vsInput_20150711_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in ubp8Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2035_ubp8D_Spt16vsInput_20150711_rep1-2_S.cerevisiaeApr11_916848.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in ubp8Δ 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)


title: SEC EVs from LPS+MSU-treated THP-1 macrophages rep 3

tag: ev fraction


title: yFR265_gcn5D_Spt16vsInput_20150723_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in gcn5Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR265_gcn5D_Spt16vsInput_20150723_rep1-2_S.cerevisiaeApr11_844430.bed


title: yFR2035_ubp8D_Spt16vsInput_20150711_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in ubp8Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2035_ubp8D_Spt16vsInput_20150711_rep1-2_S.cerevisiaeApr11_916848.bed


title: S_6a02_4mo_b1_2


title: SEC EVs from LPS+IFM-treated THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 2.5 µM IFM (90 min; IFM Therapeutics).
THP-1 monocytes were differentiated with 100 nM PMA for 12 to 16 h, after which the cells were washed once with PBS and rested for 24 h before stimulation. Per condition, 30 million PMA-differentiated WT THP-1 macrophages were primed with LPS and subsequently treated with an inflammasome activator, primed only, TLR-stimulated or left untreated. Tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. 2K and 10K pellets were washed in PBS prior to analysis. Supernatant was filtered using a 0.2 µm filter (Millipore) and then concentrated to a total volume of 0.5 ml using a 10K NMWL filter (Amicon Ultra, Sigma-Aldrich). The sample was then transferred onto a size exclusion chromatography column (qEV original, Izon). Fractions of 0.5 ml were collected, the SEC EVs referred to within this study comprise fraction 7, 8 and 9.

value: LPS+IFM

tag: replicate


title: Bcells_G1_wk0_rep3 [S387]


title: yFR2035_ubp8D_Rpb3vsInput_20150711_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp8Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2035_ubp8D_Rpb3vsInput_20150711_rep1-2_S.cerevisiaeApr11_867998.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp8Δ 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)


title: Tcells_G1_wk0_rep3 [S386]


title: S_6a02_4mo_b1_1

tag: batch


title: S_6a02_2mo_b3_4

tag: tissue


title: DCcells_G1_wk0_rep3 [S389]


title: 10K EVs from LPS+IFM-treated THP-1 macrophages rep 4

value: THP-1 macrophages


title: 10K EVs from LPS+IFM-treated THP-1 macrophages rep 5

value: 10K EVs


title: S_6a02_2mo_b3_3

value: iPSC-derived cerebral organoid

tag: cell line


title: S_6a02_2mo_b3_2

tag: age


title: SEC EVs from LPS+IFM-treated THP-1 macrophages rep 4


title: Bcells_G1_wk0_rep2 [S383]


title: DCcells_G1_wk0_rep2 [S385]

value: DCcells


title: S_6a02_2mo_b3_1

tag: technical replicate


title: yFR2024_bre1D_Spt16vsInput_20150711_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in bre1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2024_bre1D_Spt16vsInput_20150711_rep1-2_S.cerevisiaeApr11_613871.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in bre1Δ 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)

tag: genotype


title: yFR2024_bre1D_Spt16vsInput_20150711_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in bre1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2024_bre1D_Spt16vsInput_20150711_rep1-2_S.cerevisiaeApr11_613871.bed


title: DCcells_G2_pre_rep4 [S345]

tag: subject

value: pre


title: SEC EVs from LPS+IFM-treated THP-1 macrophages rep 3


title: S_6a02_2mo_b2_4


title: Tcells_G1_wk0_rep2 [S382]

tag: timepoint


title: 10K EVs from LPS+MSU-treated THP-1 macrophages rep 3


title: yFR2035_ubp8D_Rpb3vsInput_20150711_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp8Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2035_ubp8D_Rpb3vsInput_20150711_rep1-2_S.cerevisiaeApr11_867998.bed


title: 10K EVs from LPS+IFM-treated THP-1 macrophages rep 2


title: S_6a02_2mo_b2_3


title: yFR2024_bre1D_Rpb3vsInput_20150711_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in bre1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2024_bre1D_Rpb3vsInput_20150711_rep1-2_S.cerevisiaeApr11_943210.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in bre1Δ 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)


title: 10K EVs from LPS+IFM-treated THP-1 macrophages rep 3


title: Bcells_G2_pre_rep4 [S343]

tag: subset

value: Bcells


title: DCcells_G1_pre_rep2 [S341]

tag: group


title: Tcells_G2_pre_rep4 [S342]

tag: immunogen


title: TRE-EM

first: Yingjie

last: Zhu

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: not provided

scan_protocol: One hundred nanograms of RNA was loaded for hybridization with nCounter® PanCancer Progression Panel, according to the manufacturer’s instructions (NanoString, Seattle, WA, USA). The hybridization signals were analyzed by nCounter® FLEX Analysis System (NanoString).

data_processing: Raw count data, which include 740 endogenous genes, 6 positive controls, 8 negative controls, and 30 housekeeping genes, were preprocessed using R package NanoStringNorm 67. Raw counts were merged by patients by taking average of samples. Speciﬁcally, geometric mean-based normalization was used to normalize for technical assay variation, followed by background adjustment based on negative controls, where “mean.2sd” is used. RNA content normalization was performed by all 30 housekeeping genes with parameter “housekeeping.geo.mean”.

label: NOT PROVIDED

source_name: breast

label_protocol: not provided

extract_protocol: RNA was isolated from FFPE samples of post-NAT residual tumors using High Pure FFPET RNA Isolation Kit (Roche Diagnostics, Meylan, France), according to the manufacturer’s instructions.

tag: Stage

value: IIB

tag: tissue type

value: frozen tumor tissue


title: SEC EVs from LPS+IFM-treated THP-1 macrophages rep 1

tag: treatment


title: S_6a02_2mo_b2_2


title: yFR1552_leo1D_Spt16vsInput_20190529_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in leo1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1552_leo1D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_922229.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in leo1Δ 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)

tag: strain

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0, leo1{delta}::KanMX4

tag: chip antibody

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


title: 10K EVs from LPS+IFM-treated THP-1 macrophages rep 1

data_processing: Raw intensity values, CHP files containing signal space transformation-robust multi-array average (SST-RMA) normalized data, as well as transcript annotation, were provided by ThermoFisher. Additional probe annotation was obtained using the Bioconductor clariomdhumantranscriptcluster.db package v8.7.

tag: cell type

tag: ev fraction

tag: replicate


title: yFR2024_bre1D_Rpb3vsInput_20150711_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in bre1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR2024_bre1D_Rpb3vsInput_20150711_rep1-2_S.cerevisiaeApr11_943210.bed


title: yFR1552_leo1D_Spt16vsInput_20190529_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in leo1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1552_leo1D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_922229.bed


title: yFR1552_leo1D_Rpb3vsInput_20190530_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in leo1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1552_leo1D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_852521.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in leo1Δ 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)

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


title: S_6a02_2mo_b1_4

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.2b).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts

tag: tissue

tag: cell line

tag: batch


title: yFR1552_leo1D_Rpb3vsInput_20190530_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in leo1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1552_leo1D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_852521.bed

tag: genotype


title: SAV-MI

tag: age

value: IIA


title: PIC-CO

value: IIIA


title: LOU-AN


title: S_6a02_2mo_b2_1

tag: technical replicate


title: Tcells_G1_pre_rep2 [S338]

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

tag: subject

tag: timepoint

tag: subset

value: Tcells


title: S_6a02_2mo_b1_3


title: yFR1526_exoCTD-S7A-FLAG_Spt16vsInput_Rapamycin_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD S7A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1526_exoCTD-S7A-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_349935.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in cells expressing RPB1 CTD S7A-FLAG plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein.
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 yeast nitrogen base (YNB) medium lacking histidine was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.5. Cells were then treated with 1 μg/mL of rapamycin (Bio Basic) for 90 min to anchor-away the endogenous Rpb1 protein 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.

value: MAT{alpha}, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, tor1-1, fpr1{delta}::NAT, RPL13A-2xFKBP12::TRP1, RPB1-FRB::KanMX6, [pFR494 (CEN, HIS3, rpb1-CTDS7A-3xFLAG)]


title: Bcells_G1_pre_rep2 [S339]

tag: group

tag: immunogen


title: SEC EVs from LPS+IFM-treated THP-1 macrophages rep 2

tag: treatment

value: SEC EVs


title: LAS-MA

tag: Stage

tag: tissue type


title: S_6a02_2mo_b1_2


title: LAL-BE


title: Bcells_G1_pre_rep4 [S335]


title: Tcells_G1_pre_rep4 [S334]


title: Day 13 single cell suspension derived from HNF1B+/- hiPSCs (10X)

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

data_processing:
[Bulk RNAseq Processing Pipeline]  RNA sequencing analyses were carried out following standard procedures (Conesa et al., 2016).
[Bulk RNAseq Processing Pipeline]  Reads were aligned to the reference human genome assembly GRCh38 with TopHat v2.0.13.
[Bulk RNAseq Processing Pipeline]  Reads with Mapping Quality Value <10 were filtered out with SAMtools.
[Bulk RNAseq Processing Pipeline]  FeatureCounts was used on paired-end reads to count fragments in annotated gene features, and genes with no counts were filtered out.
[Bulk RNAseq Processing Pipeline]  Read counts were normalised into fragments per kilobase of transcript per million mapped reads (FPKM).
[10X scRNA-seq Processing Pipeline]  cellranger V2.01
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression in fragments per kilobase of transcript per million mapped reads (FPKM) for bulk RNA-seq samples.
Supplementary_files_format_and_content: cellranger filtered gene-barcode matrices for 10X scRNA-seq samples.

growth_protocol:
[Bulk RNAseq Protocol]  For the bulk RNA-seq experiments, one HNF1B+/+, one HNF1B+/- and one HNF1B-/- (targeted wild-type) clone from the FSPS13.B hiPSC line were differentiated along the pancreatic lineage.
[10X scRNA-seq Protocol]  Single cell libraries were generated from HNF1B+/+ and HNF1B+/- clones from the FSPS13.B hiPSC line, which were differentiated along the pancreatic lineage.

extract_protocol:
[Bulk RNAseq Protocol]  RNA was extracted using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to manufacturer’s protocol.
[Bulk RNAseq Protocol]  RNA-seq library construction and sequencing was carried out by the DNA pipelines core facility at the Wellcome Sanger Institute.
[Bulk RNAseq Protocol]  Standard Illumina unstranded poly-A enriched libraries were prepared and sequenced using Illumina HiSeq 2500 v4 (Illumina, San Diego, CA, USA), with 75bp paired-end reads per sample and a library fragment size of 100-1000 bp.
[10X scRNA-seq Protocol]  For the preparation of cells for single-cell sequencing we used the Chromium Single Cell 3′ library and gel bead kit v2 protocol.
[10X scRNA-seq Protocol]  Single cell libraries were generated using the Chromium Single Cell 3′ library and gel bead kit v2 (PN #120237) from 10x Genomics. Briefly, to reach a target cell number of 2000 cells per sample, 3500 cells per sample were loaded onto a channel of the 10x chip to produce Gel Bead-in-Emulsions (GEMs). This underwent reverse transcription to barcode RNA before cleanup and cDNA amplification followed by enzymatic fragmentation and 5′adaptor and sample index attachment. Libraries were sequenced on the HiSeq4000 (Illumina).
[10X scRNA-seq Protocol]  RNA-seq. Illumina-C HiSeq V4 Paired end sequencing

treatment_protocol:
[Bulk RNAseq Protocol]  Human iPSCs were passaged and seeded onto 12-well plates using E8 supplemented with Y27632 (Rho-associated, coiled-coil containing protein kinase, ROCK Inhibitor; 10μM). Cells were plated as single cells and the plating density was optimised for each hiPSC line (approximately 80,000 to 100,000 cells per well of a 12-well plate). After 24 hours, the media was replaced with fresh E8 media without ROCK Inhibitor. To induce definitive-endoderm differentiation (days 1-3), cells were cultured in CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml), Ly294002 (10μM) and CHIR99021 (3μM) on day 1, CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml) and Ly294002 (10μM) on day 2 then RPMI/B27 media containing Activin (100ng/ml), FGF2 (80ng/ml) on day 3. For primitive gut tube differentiation (days 4-6), cells were cultured in Adv-BSA media supplemented with SB-431542 (10μM), FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml) and L-Ascorbic acid (250μM) for 3 days. For posterior foregut differentiation (days 7-8), cells were cultured in Adv-BSA with FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml), KAAD-cyclopamine (0.238μM), PdBU (50nM) and L-Ascorbic acid (250μM). Pancreatic progenitor specification (days 9- 13) was induced by culturing cells in RA (1μM), Noggin (150μg/ml), KAAD-cyclopamine (200ng/ml), EGF (100ng/ml), Nicotinamide (10mM), and L-Ascorbic acid (250μM) for 5 days. Cells were then grown in Adv-BSA containing glucose (final concentration 25mM), B27 (1%), RA (100nM), DAPT (1μM), Alk5i (10μM) and the small molecule BNZ (0.1mM) for 3 days to induce maturation of pancreatic progenitors to endocrine progenitor cells (fifth stage; days 14-16). For maturation of endocrine cells and further differentiation into C-peptide-producing beta cells, cells were cultured for 3 additional days in Adv-BSA containing B27 (1%), RA (100nM) and Alk5i (10μM) followed by 11 days in Adv-BSA containing B27 (1%), RA (100nM) (sixth stage; days 17-27).
[10X scRNA-seq Protocol]  Human iPSCs were passaged and seeded onto 12-well plates using E8 supplemented with Y27632 (Rho-associated, coiled-coil containing protein kinase, ROCK Inhibitor; 10μM). Cells were plated as single cells and the plating density was optimised for each hiPSC line (approximately 80,000 to 100,000 cells per well of a 12-well plate). After 24 hours, the media was replaced with fresh E8 media without ROCK Inhibitor. To induce definitive-endoderm differentiation (days 1-3), cells were cultured in CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml), Ly294002 (10μM) and CHIR99021 (3μM) on day 1, CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml) and Ly294002 (10μM) on day 2 then RPMI/B27 media containing Activin (100ng/ml), FGF2 (80ng/ml) on day 3. For primitive gut tube differentiation (days 4-6), cells were cultured in Adv-BSA media supplemented with SB-431542 (10μM), FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml) and L-Ascorbic acid (250μM) for 3 days. For posterior foregut differentiation (days 7-8), cells were cultured in Adv-BSA with FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml), KAAD-cyclopamine (0.238μM), PdBU (50nM) and L-Ascorbic acid (250μM). Pancreatic progenitor specification (days 9- 13) was induced by culturing cells in RA (1μM), Noggin (150μg/ml), KAAD-cyclopamine (200ng/ml), EGF (100ng/ml), Nicotinamide (10mM), and L-Ascorbic acid (250μM) for 5 days. Cells were then grown in Adv-BSA containing glucose (final concentration 25mM), B27 (1%), RA (100nM), DAPT (1μM), Alk5i (10μM) and the small molecule BNZ (0.1mM) for 3 days to induce maturation of pancreatic progenitors to endocrine progenitor cells (fifth stage; days 14-16). For maturation of endocrine cells and further differentiation into C-peptide-producing beta cells, cells were cultured for 3 additional days in Adv-BSA containing B27 (1%), RA (100nM) and Alk5i (10μM) followed by 11 days in Adv-BSA containing B27 (1%), RA (100nM) (sixth stage; days 17-27).

tag: day

tag: hnf1b genotype

value: Het


title: DCcells_G1_pre_rep4 [S337]


title: JA-A


title: GUT-NA


title: yFR1503_exoCTD-S5A-FLAG_Spt16vsInput_Rapamycin_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD S5A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1503_exoCTD-S5A-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_471417.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in cells expressing RPB1 CTD S5A-FLAG plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein.
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)

treatment_protocol: 1 μg/mL of rapamycin (Bio Basic) for 90 min

tag: strain

value: MAT{alpha}, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, tor1-1, fpr1{delta}::NAT, RPL13A-2xFKBP12::TRP1, RPB1-FRB::KanMX6, [pFR490 (CEN, HIS3, rpb1-CTDS5A-3xFLAG)]

tag: chip antibody


title: yFR1526_exoCTD-S7A-FLAG_Spt16vsInput_Rapamycin_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD S7A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1526_exoCTD-S7A-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_349935.bed


title: yFR1503_exoCTD-S5A-FLAG_Spt16vsInput_Rapamycin_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD S5A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1503_exoCTD-S5A-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_471417.bed


title: yFR1501_exoCTD-S2A-FLAG_Spt16vsInput_Rapamycin_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD S2A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1501_exoCTD-S2A-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_243332.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in cells expressing RPB1 CTD S2A-FLAG plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein.
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)

value: MAT{alpha}, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, tor1-1, fpr1{delta}::NAT, RPL13A-2xFKBP12::TRP1, RPB1-FRB::KanMX6, [pFR486 (CEN, HIS3, rpb1-CTDS2A-3xFLAG)]


title: GIL-CH


title: Day 13 single cell suspension derived from HNF1B+/+ hiPSCs (10X)

value: WT


title: S_6a02_2mo_b1_1

tag: tissue

value: iPSC-derived cerebral organoid

tag: cell line


title: Bcells_G1_pre_rep1 [S327]

value: pre


title: DCcells_G1_pre_rep1 [S329]

value: DCcells


title: E48D44C2

city: Wuhan

first: cao

last: lu

state: Hubei

address: 7 Donghu South Road

department: Chinese Academy   of Sciences

country: China

institute: Institute of Hydrobiology

data_processing:
HISAT2 2.1.0 £»bowtie 2.2.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell, C., Williams, B.A., Pertea, G., et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology, 2010
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Danio rerio

source_name: CD44a mutants  zebrafish

growth_protocol: Wild-type AB/TU and  CD44a mutant zebrafish larave were raised and maintained  at 28¡ãC in fish water

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the hatched larvae (4 dpf) from wild-type and CD44a mutants (CD44a-/--14del) infected with E. piscicida for  specific points in time

value: zebrafish larave

value: infected with E. piscicida for 48h

tag: genotype

value: CD44a mutants


title: CON-BE

tag: age

value: IIB

value: frozen tumor tissue


title: yFR1501_exoCTD-S2A-FLAG_FLAGvsInput_Rapamycin_repl2

description:
Biological replicate 2 of 2. RNAPII (CTD S2A-Flag) occupancy by ChIP-chip in cells expressing the RPB1 CTD S2A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. CTD S2A-Flag ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Flag and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1501_exoCTD-S2A-FLAG_FLAGvsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_874697.bed

data_processing:
BED description:  A genome browser-ready file for RNAPII CTD S2A-Flag occupancy by ChIP-chip (IP/Input) in cells expressing RPB1 CTD S2A-FLAG plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein.
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-Flag (Sigma-Aldrich F3165, 5 μg). 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-Flag (Sigma-Aldrich F3165, 5 μg)


title: BEC-FR


title: VEY-CL

value: IIA


title: Tcells_G1_pre_rep1 [S326]

value: Tcells


title: Tcells_G2_pre_rep5 [S322]


title: Bcells_G2_pre_rep5 [S323]

value: Bcells


title: yFR1501_exoCTD-S2A-FLAG_FLAGvsInput_Rapamycin_repl1

description:
Biological replicate 1 of 2. RNAPII (CTD S2A-Flag) occupancy by ChIP-chip in cells expressing the RPB1 CTD S2A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. CTD S2A-Flag ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Flag and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1501_exoCTD-S2A-FLAG_FLAGvsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_874697.bed


title: DCcells_G2_pre_rep5 [S325]


title: E48WT3

source_name: wild-type zebrafish

value: wild type


title: yFR1501_exoCTD-S2A-FLAG_Spt16vsInput_Rapamycin_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD S2A-FLAG mutant plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1501_exoCTD-S2A-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_243332.bed

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


title: E48WT2


title: RA-M


title: E48D44C1


title: E24D44C3

value: infected with E. piscicida for 24h


title: DCcells_G2_pre_rep3 [S316]


title: E48WT1


title: yFR1368_ctr9D_Spt16vsInput_20190529_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in ctr9Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1368_ctr9D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_561535.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in ctr9Δ 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)

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0, ctr9{delta}::KanMX4


title: yFR1499_exoCTDwt-FLAG_Spt16vsInput_Rapamycin_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD WT-FLAG plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1499_exoCTDwt-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_497213.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in cells expressing RPB1 CTD WT-FLAG plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein.
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)

value: MAT{alpha}, ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, ura3, tor1-1, fpr1{delta}::NAT, RPL13A-2xFKBP12::TRP1, RPB1-FRB::KanMX6, [pFR482 (CEN, HIS3, RPB1-CTDWT-3xFLAG)]


title: PF-A


title: yFR1499_exoCTDwt-FLAG_Spt16vsInput_Rapamycin_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in cells expressing the RPB1 CTD WT-FLAG plasmid treated with rapamycin for 90 min to anchor-away the endogenous FRB-tagged Rpb1 protein. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1499_exoCTDwt-FLAG_Spt16vsInput_Rapamycin_rep1-2_S.cerevisiaeApr11_497213.bed


title: ME-F

value: IIIA


title: yFR1368_ctr9D_Spt16vsInput_20190529_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in ctr9Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1368_ctr9D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_561535.bed


title: Tcells_G2_pre_rep3 [S313]

value: pre


title: Bcells_G2_pre_rep3 [S314]


title: E48D44C3


title: E24D44C1


title: yFR1368_ctr9D_Rpb3vsInput_20190530_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ctr9Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1368_ctr9D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_99085.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ctr9Δ 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)

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


title: E24D44C2

value: zebrafish larave


title: FAS-MA


title: FER-JA


title: DIO-MI


title: yFR1368_ctr9D_Rpb3vsInput_20190530_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ctr9Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1368_ctr9D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_99085.bed


title: DI-N


title: E24WT3


title: E24WT2


title: DCcells_G2_pre_rep2 [S312]

value: DCcells


title: Tcells_G2_pre_rep2 [S309]


title: DE-C


title: E24WT1


title: yFR1350_paf1D_Spt16vsInput_20190529_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in paf1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1350_paf1D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_892372.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in paf1Δ 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)

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0, paf1{delta}::KanMX4


title: DCcells_G2_pre_rep1 [S308]


title: yFR1350_paf1D_Spt16vsInput_20190529_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in paf1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1350_paf1D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_892372.bed


title: Bcells_G2_pre_rep2 [S310]


title: MOI-OD

value: IIB


title: SUE-NA

value: frozen tumor tissue


title: CH-Y


title: CH-B


title: yFR1350_paf1D_Rpb3vsInput_20190530_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in paf1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1350_paf1D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_493475.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in paf1Δ 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)


title: GFP Rep 2

city: Durham

first: Anne

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

data_processing:
 RNA was sent to Novogene (CA, USA) for quality control and sequencing. 150bp paired-end sequencing was performed on a NovoSeq 6000 instrument with a minimum depth of 20M reads per sample.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mRatBN7.2 using STAR v2.7.2b with parameters --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMunmapped Within
Raw gene reads were counted with HTSeq v0.10.0 using the parameters --type=gene --format=bam --stranded=yes --idattr=gene_id --mode=union.
Genome_build: mRatBN7.2
Supplementary_files_format_and_content: Tab-deliminated text files with the number of reads mapping to each gene.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: GFP

extract_protocol:
DIV7 hippocampal neurons exogenously expressing WT or mutant H1.4 CFT were lysed directly in Trizol Reagent (Invitrogen cat# 15596026). RNA was purified using Direct-zol mini-prep kit (Zymo Research cat#R2050) with on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Corporation Inc.

tag: strain background

value: CD (Sprague Dawley) IGS Rats from Charles River Laboratories

tag: genotype/variation

value: GFP control

value: Primary hippocampal neurons


title: GFP Rep 3


title: yFR1350_paf1D_Rpb3vsInput_20190530_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in paf1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1350_paf1D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_493475.bed


title: Tcells_G2_pre_rep1 [S305]

tag: subject

tag: timepoint

value: Tcells


title: DCcells_G1_pre_rep5 [S304]

tag: subset

tag: group


title: Bcells_G1_pre_rep5 [S302]

value: Bcells

tag: immunogen


title: H1.4 CFT Rep 4

source_name: H1.4 CFT

value: H1.4 CFT


title: yFR1221_WT_Rpb3vsInput_20120516_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells after heat-shock at 37°C for 80 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1221_WT_Rpb3vsInput_20120516_Rep1-2_S.cerevisiaeApr11_494711.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT 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: MAT{alpha}, ura3-52, SUC2+

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


title: GE-C

data_processing: Raw count data, which include 740 endogenous genes, 6 positive controls, 8 negative controls, and 30 housekeeping genes, were preprocessed using R package NanoStringNorm 67. Raw counts were merged by patients by taking average of samples. Speciﬁcally, geometric mean-based normalization was used to normalize for technical assay variation, followed by background adjustment based on negative controls, where “mean.2sd” is used. RNA content normalization was performed by all 30 housekeeping genes with parameter “housekeeping.geo.mean”.

tag: Stage

value: IIA


title: yFR1221_WT_Spt16vsInput_20120516_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT 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_yFR1221_WT_Spt16vsInput_20120516_Rep1-2_S.cerevisiaeApr11_245858.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT 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)

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


title: yFR1221_WT_Spt16vsInput_20120516_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT 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_yFR1221_WT_Spt16vsInput_20120516_Rep1-2_S.cerevisiaeApr11_245858.bed


title: H1.4 CFT Rep 3


title: Bcells_G2_pre_rep1 [S306]

value: pre


title: DR-D

value: IIIA

tag: tissue type


title: GFP Rep 4


title: H1.4 CFT Rep 2


title: Tcells_G1_pre_rep5 [S301]


title: DCcells_G1_pre_rep3 [S300]


title: BE-C


title: yFR1221_WT_Rpb3vsInput_20120516_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells after heat-shock at 37°C for 80 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1221_WT_Rpb3vsInput_20120516_Rep1-2_S.cerevisiaeApr11_494711.bed


title: CAOV4cis H3K27ac input DNA

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

source_name: CAOV4cis cell line

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 type

value: human epithelial ovarian cancer

tag: treatment

value: Cisplatin treated

value: none (input)


title: CAOV4cis H3K27ac

value: H3K27ac (Abcam, ab4729)


title: Bcells_G1_pre_rep3 [S298]

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.


title: yFR1214_rpb1-1ts_Spt16vsInput_20120516_repl2

description:
Biological replicate 2 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)

tag: strain

value: MATa, ura3-52, rpb1-1


title: WT H1.4 Rep 4

source_name: WT H1.4

value: CD (Sprague Dawley) IGS Rats from Charles River Laboratories

value: Exogenous wildtype H1.4


title: DCcells_G1_pre_rep4 [S296]

value: DCcells


title: WT H1.4 Rep 3

value: Primary hippocampal neurons


title: CAOV4 H3K27ac input DNA

source_name: CAOV4 cell line

tag: chip antibody


title: H1.4 CFT Rep 1

tag: tissue


title: WT H1.4 Rep 2


title: WT H1.4 Rep 1


title: Tcells_G1_pre_rep3 [S297]

value: Tcells


title: yFR1214_rpb1-1ts_Rpb3vsInput_20120516_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in rpb1-1 temperature sensitive cells after heat-shock at 37°C for 80 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1214_rpb1-1ts_Rpb3vsInput_20120516_Rep1-2_S.cerevisiaeApr11_40713.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 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)


title: A2780 H3K27ac shMBD3.232 input DNA

source_name: A2780 cells line

tag: cell line

value: 1 week MBD3 knockdown by shRNA


title: CAOV4 H3K27ac


title: Tcells_G1_pre_rep4 [S293]


title: A2780 H3K27ac shMBD3.232


title: Bcells_G1_pre_rep4 [S294]

value: Bcells


title: yFR1214_rpb1-1ts_Rpb3vsInput_20120516_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in rpb1-1 temperature sensitive cells after heat-shock at 37°C for 80 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR1214_rpb1-1ts_Rpb3vsInput_20120516_Rep1-2_S.cerevisiaeApr11_40713.bed

tag: genotype

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


title: DCcells_G1_pre_rep1 [S288]


title: yFR117_WT_Spt16vsinput_repl1_20131119

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_20131119_S.cerevisiaeApr11_801467.bed

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)

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


title: Bcells_G1_pre_rep1 [S286]


title: A2780 H3K27ac shMBD3.26 input DNA


title: yFR117_WT_Spt16vsinput_repl2_20131119

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_20131119_S.cerevisiaeApr11_801467.bed

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


title: 2Month_SC-3_20191017_nuclei

city: Beijing

first: Zeyuan

last: Liu

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

institute: Institute of Biophysics,Chinese Academy of Sciences

description:
BC-1 (in barcodes.tsv)
matrix.mtx, barcodes.tsv, features.tsv

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: 2 months

value: brain

tag: region

value: superior colliculus

tag: sequencing stragery

value: 10X Genomic single-cell sequencing


title: 2Month_SC-4_20191219_nuclei

description:
BC-2 (in barcodes.tsv)
matrix.mtx, barcodes.tsv, features.tsv


title: Tcells_G1_pre_rep1 [S285]

tag: subject

value: pre


title: mir85_HS_3

city: La Jolla

first: Delaney

last: Pagliuso

state: CA

address: 9500 Gilman Dr

department: Biological Sciences

institute: University of California, San Diego

description: HS sample replicate 6

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

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

value: HS


title: yFR117_WT_Spt16vsInput_repl2_20130731

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_20130731_S.cerevisiaeApr11_665835.bed


title: mir85_HS_2

description: HS sample replicate 5


title: yFR117_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_yFR117_WT_Spt16vsInput_rep1-2_S.cerevisiaeApr11_927936.bed


title: A2780 H3K27ac shMBD3.26

value: human epithelial ovarian cancer

value: H3K27ac (Abcam, ab4729)


title: cell60

description:
rep7-OP_lp38
smart-seq-raw-counts-for-geo.txt

value: 3 months


title: cell59

description:
rep7-InG_ZI50
smart-seq-raw-counts-for-geo.txt


title: mir85_HS_1

description: HS sample replicate 4


title: N2_HS_3

description: HS sample replicate 3


title: A2780 H3K27ac shRen

value: 1 week control knockdown by shRNA


title: cell58

description:
rep7-InG_ZI49
smart-seq-raw-counts-for-geo.txt