title: SEC EVs from untreated THP-1 macrophages rep 3

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

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 left untreated.
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: UT

value: THP-1 macrophages

tag: ev fraction

value: SEC EVs

tag: replicate


title: yFR930-chd1D_Rpb3vsInput_20190519_repl1

status: Public on Jul 26 2021

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 1 of 2. 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_yFR930-chd1D_Rpb3vsInput_20190519_rep1-2_S.cerevisiaeApr11_438378.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 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)

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: genotype

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: DCcells_G2_wk25_rep1 [S533]

type: RNA

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

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

molecule: total RNA

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


title: DCcells_G2_wk25_rep5 [S529]


title: yFR930_chd1D_Spt16vsInput_20150711_repl2

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_yFR930_chd1D_Spt16vsInput_20150711_rep1-2_S.cerevisiaeApr11_442878.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in chd1Δcells.
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: Tcells_G2_wk25_rep1 [S530]

value: Tcells


title: yFR930_chd1D_Spt16vsInput_20150711_repl1

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_yFR930_chd1D_Spt16vsInput_20150711_rep1-2_S.cerevisiaeApr11_442878.bed


title: SEC EVs from untreated THP-1 macrophages rep 5

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

organism: Homo sapiens

tag: cell type

tag: batch


title: Bcells_G2_wk25_rep1 [S531]

value: Bcells


title: Bcells_G2_wk25_rep5 [S527]


title: 2204_UC uninflamed sigmoid colon

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

country: USA

institute: Genentech, Inc.

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.

source_name: UC uninflamed sigmoid colon

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Quick Amp Labeling Kit (Agilent). For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).

extract_protocol: RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.

tag: Sex

value: not determined

tag: diagnosis

value: Ulcerative colitis

tag: inflammation

value: Uninflamed

tag: tissue

value: Colon

source_name: Universal human reference (UHR) from Stratagene

tag: sample type

value: pooled human reference RNA


title: yFR928_isw2D_Spt16vsInput_20190211_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in isw2Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR928_isw2D_Spt16vsInput_20190211_rep1-2_S.cerevisiaeApr11_405141.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in isw2Δ 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: yFR928_isw2D_Spt16vsInput_20190211_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in isw2Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR928_isw2D_Spt16vsInput_20190211_rep1-2_S.cerevisiaeApr11_405141.bed


title: 10K EVs from untreated THP-1 macrophages rep 3

tag: treatment

tag: ev fraction

value: 10K EVs


title: S_72a01_6mo_b1_2

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

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

value: iPSC-derived cerebral organoid

tag: cell line

tag: age

tag: technical replicate


title: yFR930-chd1D_Rpb3vsInput_20190519_repl2

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_yFR930-chd1D_Rpb3vsInput_20190519_rep1-2_S.cerevisiaeApr11_438378.bed

tag: strain

tag: genotype

tag: chip antibody


title: yFR928_isw2D_Rpb3vsInput_20190211_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in isw2Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR928_isw2D_Rpb3vsInput_20190211_rep1-2_S.cerevisiaeApr11_532683.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in isw2Δ 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: S_72a01_6mo_b1_1


title: 10K EVs from untreated THP-1 macrophages rep 5

tag: replicate


title: SEC EVs from untreated THP-1 macrophages rep 2


title: yFR930_chd1D_Rpb3vsInput_20150711_repl1

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_yFR930_chd1D_Rpb3vsInput_20150711_rep1-2_S.cerevisiaeApr11_732197.bed

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (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: 10K EVs from untreated THP-1 macrophages rep 4


title: S_72a01_4mo_b3_3


title: S_72a01_4mo_b3_2


title: S_72a01_4mo_b3_4

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


title: S_72a01_4mo_b3_1


title: S_72a01_4mo_b2_4


title: 10K EVs from untreated THP-1 macrophages rep 2


title: S_72a01_4mo_b2_3


title: DCcells_G2_wk25_rep3 [S525]

tag: subject

tag: timepoint

tag: subset

tag: group

tag: immunogen


title: yFR928_isw2D_Rpb3vsInput_20190211_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in isw2Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR928_isw2D_Rpb3vsInput_20190211_rep1-2_S.cerevisiaeApr11_532683.bed


title: Tcells_G2_wk25_rep5 [S526]


title: Tcells_G2_wk25_rep3 [S522]


title: yFR912-kin28asbur2D_Rpb3vsInput_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in kin28asbur2Δ cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR912-kin28asbur2D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_977321.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in kin28asbur2Δ cells treated with 6 μM NAPP1 for 15 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 for the WT cells and in yeast nitrogen base (YNB) medium lacking uracil for kin28as strains) and allowed to grow to an OD600 of 0.8. Cells were then treated with 6 μM of 1-Naphthyl PP1 (NAPP1; Tocris Bioscience) for 15 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.

value: MAT{alpha}, ade2::hisG, his3{delta}200, leu2{delta}0, lys2{delta}0, met15{delta}0, trp1{delta}63, ura3{delta}0, bur2{delta}::LEU2, kin28::kin28as(L83G) [pSH579, CEN, URA3, kin28as(L83G)]


title: yFR912-2_kin28asbur2D_Spt16_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in kin28asbur2Δ cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR912_kin28asbur2D_Spt16_Rep1-2_S.cerevisiaeApr11_815293.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in kin28asbur2Δ cells treated with 6 μM NAPP1 for 15 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)

treatment_protocol: 6 μM of 1-Naphthyl PP1 (NAPP1; Tocris Bioscience) for 15 min


title: DCcells_G2_wk25_rep4 [S521]


title: Bcells_G2_wk25_rep3 [S523]


title: SEC EVs from R848-treated THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 20 µg/ml R848 (24 h; Invivogen).
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: cell type

tag: batch


title: S_72a01_4mo_b2_2

tag: tissue


title: yFR912-kin28asbur2D_Rpb3vsInput_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in kin28asbur2Δ cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR912-kin28asbur2D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_977321.bed


title: 10K EVs from untreated THP-1 macrophages rep 1

tag: treatment

value: UT


title: SEC EVs from untreated THP-1 macrophages rep 1

value: THP-1 macrophages

tag: ev fraction


title: S_72a01_4mo_b2_1

tag: cell line


title: S_72a01_4mo_b1_4

tag: age


title: 10K EVs from R848-treated THP-1 macrophages rep 5


title: S_72a01_4mo_b1_3

tag: technical replicate


title: SEC EVs from R848-treated THP-1 macrophages rep 4

value: SEC EVs


title: yFR762-2_WT_Spt16vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR762_WT_Spt16vsInput_Rep3-4_S.cerevisiaeApr11_601466.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in WT cells treated with 6 μM NAPP1 for 15 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: MAT{alpha}, ade2::hisG, his3{delta}200, leu2{delta}0, lys2{delta}0, met15{delta}0, trp1{delta}63, ura3{delta}0


title: DCcells_G2_wk25_rep2 [S517]

value: DCcells


title: Bcells_G2_wk25_rep4 [S519]


title: yFR912-1_kin28asbur2D_Spt16_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in kin28asbur2Δ cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR912_kin28asbur2D_Spt16_Rep1-2_S.cerevisiaeApr11_815293.bed

tag: genotype

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


title: S_72a01_4mo_b1_2


title: Tcells_G2_wk25_rep4 [S518]

value: Tcells


title: DCcells_G1_wk25_rep1 [S493]


title: yFR763-1_kin28as_Spt16vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in kin28as cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR763_kin28as_Spt16vsInput_Rep3-4_S.cerevisiaeApr11_464778.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in kin28as cells treated with 6 μM NAPP1 for 15 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: MAT{alpha}, ade2::hisG, his3{delta}200, leu2{delta}0, lys2{delta}0, met15{delta}0, trp1{delta}63, ura3{delta}0, kin28::kin28as(L83G) [pSH579, CEN, URA3, kin28as(L83G)]

tag: chip antibody


title: Bcells_G2_wk25_rep2 [S515]

value: Bcells


title: yFR763-2_kin28as_Spt16vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in kin28as cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR763_kin28as_Spt16vsInput_Rep3-4_S.cerevisiaeApr11_464778.bed


title: yFR762-1_WT_Spt16vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells treated with 6 μM of 1-Naphthyl PP1 (NAPP1) for 15 min. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR762_WT_Spt16vsInput_Rep3-4_S.cerevisiaeApr11_601466.bed


title: S_72a01_4mo_b1_1


title: S_72a01_2mo_b3_4


title: 10K EVs from R848-treated THP-1 macrophages rep 4

tag: replicate


title: SEC EVs from R848-treated THP-1 macrophages rep 3


title: 10K EVs from R848-treated THP-1 macrophages rep 2


title: Bcells_G1_wk25_rep1 [S491]

tag: subject


title: 10K EVs from R848-treated THP-1 macrophages rep 3


title: yFR729_isw1D_Rpb3vsInput_20190211_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in isw1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR729_isw1D_Rpb3vsInput_20190211_rep1-2_S.cerevisiaeApr11_874005.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in isw1Δ 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_72a01_2mo_b3_3


title: yFR729_isw1D_Spt16vsInput_20190211_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in isw1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR729_isw1D_Spt16vsInput_20190211_rep1-2_S.cerevisiaeApr11_50442.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in isw1Δ 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: yFR729_isw1D_Spt16vsInput_20190211_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in isw1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR729_isw1D_Spt16vsInput_20190211_rep1-2_S.cerevisiaeApr11_50442.bed


title: DCcells_G1_wk25_rep5 [S489]

tag: timepoint


title: SEC EVs from R848-treated THP-1 macrophages rep 1


title: SEC EVs from R848-treated THP-1 macrophages rep 2


title: yFR729_isw1D_Rpb3vsInput_20190211_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in isw1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR729_isw1D_Rpb3vsInput_20190211_rep1-2_S.cerevisiaeApr11_874005.bed


title: 10K EVs from R848-treated THP-1 macrophages rep 1


title: SEC EVs from P3CSK4-treated THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 1.25 ng/ml Pam3CSK4 (24 h; Invivogen).
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.


title: S_72a01_2mo_b3_1


title: S_72a01_2mo_b3_2


title: Tcells_G1_wk25_rep1 [S490]

tag: subset


title: yFR721_spt4D_Spt16vsInput_repl2_20130731

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in spt4Δ cells (S288C background). Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR721_spt4D_Spt16vsInput_Rep1-2_20130731_S.cerevisiaeApr11_541787.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in spt4Δ cells (S288C background).
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, spt4∆::KanMX4


title: Tcells_G2_wk25_rep2 [S514]

tag: group


title: 10K EVs from P3CSK4-treated THP-1 macrophages rep 5


title: S_72a01_2mo_b2_4


title: Bcells_G1_wk25_rep5 [S487]

tag: immunogen


title: Tcells_G1_wk25_rep5 [S486]


title: yFR721_spt4D_Spt16vsInput_repl1_20130731

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in spt4Δ cells (S288C background). Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR721_spt4D_Spt16vsInput_Rep1-2_20130731_S.cerevisiaeApr11_541787.bed


title: Bcells_G1_wk25_rep4 [S483]


title: S_72a01_2mo_b2_2


title: DCcells_G1_wk25_rep4 [S485]


title: yFR721_spt4D_Rpb3vsInput_repl2_20130731

description:
Biological replicate 1 of 1. RNAPII (Rpb3) occupancy by ChIP-chip in spt4Δ cells (S288C background). Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR721_spt4D_Rpb3vsInput_Rep2_20130731_S.cerevisiaeApr11_673948.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in spt4Δ cells (S288C background).
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: yFR705_spt4D_Spt16vsInput_20190502_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in spt4Δ cells (W303 background). Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR705_spt4D_Spt16vsInput_20190502_rep1-2_S.cerevisiaeApr11_176269.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in spt4Δ 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 P3CSK4-treated THP-1 macrophages rep 4

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


title: S_72a01_2mo_b2_1

tag: batch


title: 10K EVs from P3CSK4-treated THP-1 macrophages rep 3


title: S_72a01_2mo_b2_3

tag: tissue


title: SEC EVs from P3CSK4-treated THP-1 macrophages rep 3

tag: treatment


title: yFR705_spt4D_Spt16vsInput_20190502_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in spt4Δ cells (W303 background). Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR705_spt4D_Spt16vsInput_20190502_rep1-2_S.cerevisiaeApr11_176269.bed


title: S_72a01_2mo_b1_3


title: S_72a01_2mo_b1_4


title: yFR705_spt4D_Rpb3vsInput_20190502_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in spt4Δ cells (W303 background). Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR705_spt4D_Rpb3vsInput_20190502_rep1-2_S.cerevisiaeApr11_750444.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in spt4Δ 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: DCcells_G1_wk25_rep3 [S481]

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: yFR705_spt4D_Rpb3vsInput_20190502_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in spt4Δ cells (W303 background). Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR705_spt4D_Rpb3vsInput_20190502_rep1-2_S.cerevisiaeApr11_750444.bed


title: S_72a01_2mo_b1_2


title: yFR682-bur2D_Rpb3vsInput_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in bur2Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR682-bur2D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_610621.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in bur2Δ 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, bur2{delta}::kanMX4


title: 10K EVs from P3CSK4-treated THP-1 macrophages rep 2

tag: ev fraction


title: Tcells_G1_wk25_rep3 [S478]


title: S_72a01_2mo_b1_1

tag: cell line


title: SEC EVs from P3CSK4-treated THP-1 macrophages rep 2


title: Bcells_G1_wk25_rep3 [S479]


title: yFR682-bur2D_Rpb3vsInput_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in bur2Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR682-bur2D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_610621.bed


title: DCcells_G2_wk2_rep5 [S461]

value: ALVAC


title: DCcells_G1_wk25_rep2 [S477]


title: Bcells_G1_wk25_rep2 [S475]


title: Tcells_G1_wk25_rep2 [S474]


title: yFR682_bur2D_Spt16vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in bur2Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR682_bur2D_Spt16vsInput_rep1-2_S.cerevisiaeApr11_803618.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in bur2Δ 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: yFR682_bur2D_Spt16vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in bur2Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR682_bur2D_Spt16vsInput_rep1-2_S.cerevisiaeApr11_803618.bed


title: 10K EVs from P3CSK4-treated THP-1 macrophages rep 1

value: 10K EVs


title: 10K EVs from LPS90-treated THP-1 macrophages rep 4

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by media (90 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.


title: S_6e11_6mo_b3_4

value: iPSC-derived cerebral organoid

tag: age


title: SEC EVs from LPS90-treated THP-1 macrophages rep 2


title: SEC EVs from LPS120-treated THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by media (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.


title: Bcells_G2_wk2_rep5 [S459]


title: yFR682_bur2D_Pob3vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Pob3) occupancy by ChIP-chip in bur2Δ cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR682_bur2D_Pob3vsInput_rep1-2_S.cerevisiaeApr11_326702.bed

data_processing:
BED description:  A genome browser-ready file for Pob3 occupancy by ChIP-chip (IP/Input) in bur2Δ cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Pob3 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

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


title: S_6e11_6mo_b3_3

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: technical replicate


title: yFR682_bur2D_Pob3vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Pob3) occupancy by ChIP-chip in bur2Δ cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR682_bur2D_Pob3vsInput_rep1-2_S.cerevisiaeApr11_326702.bed

tag: strain


title: SEC EVs from P3CSK4-treated THP-1 macrophages rep 1


title: S_6e11_6mo_b3_2

tag: genotype


title: S_6e11_6mo_b3_1


title: Tcells_G2_wk2_rep5 [S458]


title: S_6e11_6mo_b2_4


title: S_6e11_6mo_b2_3


title: Bcells_G2_wk2_rep1 [S455]


title: yFR551-ctk1D_Rpb3vsInput_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ctk1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR551-ctk1D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_880052.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in ctk1Δ 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, ctk1{delta}::kanMX4

tag: chip antibody

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


title: 10K EVs from LPS120-treated THP-1 macrophages rep 4

value: THP-1 macrophages

tag: replicate


title: DCcells_G2_wk2_rep1 [S457]

tag: subject


title: yFR551_ctk1D_Spt16vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in ctk1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR551_ctk1D_Spt16vsInput_rep1-2_S.cerevisiaeApr11_447630.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ctk1Δ 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 LPS120-treated THP-1 macrophages rep 3

value: SEC EVs


title: DCcells_G2_wk2_rep4 [S453]

tag: timepoint


title: Tcells_G2_wk2_rep1 [S454]

tag: subset


title: S_6e11_6mo_b2_2


title: SEC EVs from LPS120-treated THP-1 macrophages rep 4


title: yFR551_ctk1D_Spt16vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in ctk1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR551_ctk1D_Spt16vsInput_rep1-2_S.cerevisiaeApr11_447630.bed


title: Bcells_G2_wk2_rep4 [S451]

tag: group


title: SEC EVs from LPS120-treated THP-1 macrophages rep 2


title: S_6e11_6mo_b1_4


title: Tcells_G2_wk2_rep4 [S450]

tag: immunogen


title: SEC EVs from LPS+R848-treated THP-1 macrophages rep 4

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 20 µg/ml R848 (120 min; Invivogen).
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: cell type


title: 10K EVs from LPS120-treated THP-1 macrophages rep 2

tag: batch


title: yFR348_set2D_Spt16vsInput_20160924_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in set2Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR348_set2D_Spt16vsInput_20160924_rep1-2_S.cerevisiaeApr11_462654.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in set2Δ 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: DCcells_G2_wk2_rep3 [S449]


title: yFR551-ctk1D_Rpb3vsInput_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ctk1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR551-ctk1D_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_880052.bed


title: 10K EVs from LPS120-treated THP-1 macrophages rep 1


title: S_6e11_6mo_b1_3

tag: tissue


title: yFR348_set2D_Spt16vsInput_20160924_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in set2Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR348_set2D_Spt16vsInput_20160924_rep1-2_S.cerevisiaeApr11_462654.bed


title: yFR551_ctk1D_Pob3vsInput_repl1

description:
Biological replicate 1 of 2. FACT (Pob3) occupancy by ChIP-chip in ctk1Δ cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR551_ctk1D_Pob3vsInput_rep1-2_S.cerevisiaeApr11_914943.bed

data_processing:
BED description:  A genome browser-ready file for Pob3 occupancy by ChIP-chip (IP/Input) in ctk1Δ 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 LPS120-treated THP-1 macrophages rep 1

tag: treatment


title: yFR348_set2D_Rpb3vsInput_20160924_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in set2Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR348_set2D_Rpb3vsInput_20160924_rep1-2_S.cerevisiaeApr11_728226.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in set2Δ 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_G2_wk2_rep3 [S447]


title: SEC EVs from LPS+R848-treated THP-1 macrophages rep 5

tag: ev fraction


title: yFR551_ctk1D_Pob3vsInput_repl2

description:
Biological replicate 2 of 2. FACT (Pob3) occupancy by ChIP-chip in ctk1Δ cells. Pob3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Pob3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR551_ctk1D_Pob3vsInput_rep1-2_S.cerevisiaeApr11_914943.bed


title: 10K EVs from LPS+R848-treated THP-1 macrophages rep 4


title: S_6e11_6mo_b1_2

tag: cell line


title: Tcells_G2_wk2_rep3 [S446]


title: S_6e11_6mo_b1_1

tag: age


title: S_6e11_4mo_b3_4

tag: technical replicate


title: S_6e11_4mo_b3_3


title: yFR348_set2D_Rpb3vsInput_20160924_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in set2Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR348_set2D_Rpb3vsInput_20160924_rep1-2_S.cerevisiaeApr11_728226.bed

tag: strain


title: 10K EVs from LPS+R848-treated THP-1 macrophages rep 3


title: S_6e11_4mo_b3_2

tag: genotype


title: S_6e11_4mo_b3_1


title: SEC EVs from LPS+R848-treated THP-1 macrophages rep 2


title: Tcells_G2_wk2_rep2 [S442]


title: Bcells_G1_wk2_rep4 [S439]

value: ALVACempty


title: DCcells_G1_wk2_rep4 [S441]

value: DCcells


title: yFR3216_cet1_Pro_205-549_Spt16vsInput_20190708_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in cet1Pro205-549 cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3216_cet1_Pro_205-549_Spt16vsInput_20190708_rep1-2_S.cerevisiaeApr11_409755.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in cet1Pro205-549 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, ura3-52, leu2{delta}1, trp1{delta}63, his3{delta}200, lys2{delta}202, cet1{delta}1::TRP1 [pRS315-CET1(Pro+205-549)]

tag: chip antibody

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


title: yFR3216_cet1_Pro_205-549_Rpb3vsInput_20190708_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in cet1Pro205-549 cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3216_cet1_Pro_205-549_Rpb3vsInput_20190708_rep1-2_S.cerevisiaeApr11_488993.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in cet1Pro205-549 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: yFR3216_cet1_Pro_205-549_Spt16vsInput_20190708_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in cet1Pro205-549 cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3216_cet1_Pro_205-549_Spt16vsInput_20190708_rep1-2_S.cerevisiaeApr11_409755.bed


title: 10K EVs from LPS+R848-treated THP-1 macrophages rep 2

tag: replicate


title: SEC EVs from LPS+R848-treated THP-1 macrophages rep 1


title: S_6e11_4mo_b1_3


title: Bcells_G1_wk2_rep1 [S435]

tag: subject


title: DCcells_G1_wk2_rep1 [S437]

tag: timepoint


title: S_6e11_4mo_b1_4


title: yFR3215_WT_CET1_Rpb3vsInput_20190708_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3215_WT_CET1_Rpb3vsInput_20190708_rep1-2_S.cerevisiaeApr11_76233.bed

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

value: MATa, ura3-52, leu2{delta}1, trp1{delta}63, his3{delta}200, lys2{delta}202, cet1{delta}1::TRP1 [pRS315-CET1]


title: Tcells_G1_wk2_rep4 [S438]

tag: subset

value: Tcells


title: yFR3216_cet1_Pro_205-549_Rpb3vsInput_20190708_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in cet1Pro205-549 cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3216_cet1_Pro_205-549_Rpb3vsInput_20190708_rep1-2_S.cerevisiaeApr11_488993.bed

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


title: 10K EVs from LPS+R848-treated THP-1 macrophages rep 1


title: yFR3215_WT_CET1_Spt16vsInput_20190708_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_yFR3215_WT_CET1_Spt16vsInput_20190708_rep1-2_S.cerevisiaeApr11_970263.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)


title: Tcells_G1_wk2_rep1 [S434]

tag: group


title: S_6e11_4mo_b1_2


title: Tcells_G1_wk25_rep4 [S482]

tag: immunogen


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 20 µg/ml R837 (120 min; Invivogen).
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: cell type


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 4

tag: batch


title: Bcells_G2_wk2_rep2 [S443]

value: Bcells


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 4


title: S_6e11_6mo_b2_1

tag: tissue


title: yFR3215_WT_CET1_Spt16vsInput_20190708_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in WT cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3215_WT_CET1_Spt16vsInput_20190708_rep1-2_S.cerevisiaeApr11_970263.bed


title: S_6e11_2mo_b3_4


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 5

tag: treatment


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 3

tag: ev fraction


title: S_6e11_2mo_b3_2

tag: cell line


title: S_6e11_2mo_b3_1

tag: age


title: S_6e11_4mo_b1_1

tag: technical replicate


title: yFR3215_WT_CET1_Rpb3vsInput_20190708_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3215_WT_CET1_Rpb3vsInput_20190708_rep1-2_S.cerevisiaeApr11_76233.bed

tag: strain


title: DCcells_G1_wk2_rep3 [S429]


title: DCcells_G1_wk2_rep5 [S433]


title: S_6e11_2mo_b3_3

tag: genotype


title: yFR3209_rtf1D_Spt16vsInput_20190529_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in rtf1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3209_rtf1D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_803421.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in rtf1Δ 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, rtf1{delta}::URA3

tag: chip antibody


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 3

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: replicate


title: yFR3208_cdc73D_Spt16vsInput_20190529_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in cdc73Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3208_cdc73D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_329535.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in cdc73Δ 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, cdc73{delta}::URA3


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 2


title: yFR3209_rtf1D_Spt16vsInput_20190529_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in rtf1Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3209_rtf1D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_803421.bed


title: yFR3209_rtf1D_Rpb3vsInput_20190530_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in rtf1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3209_rtf1D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_63510.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in rtf1Δ 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: S_6e11_2mo_b2_2


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 1


title: S_6e11_2mo_b2_4


title: S_6e11_2mo_b2_3


title: S_6e11_2mo_b2_1


title: Tcells_G1_wk2_rep5 [S430]

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


title: S_6e11_2mo_b1_4


title: S_6e11_2mo_b1_3


title: Bcells_G1_wk2_rep3 [S427]

tag: timepoint


title: Bcells_G1_wk2_rep5 [S431]

tag: subset


title: Bcells_G1_wk2_rep2 [S423]

tag: group


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 2

value: 10K EVs


title: DCcells_G2_wk0_rep5 [S421]

tag: immunogen

value: ALVAC


title: DCcells_G1_wk2_rep2 [S425]


title: S_6e11_2mo_b1_2

value: iPSC-derived cerebral organoid


title: Tcells_G1_wk2_rep2 [S422]


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

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 0.15 ng/ml PrgI (M. Geyer, University of Bonn) with 1 µg/ml PA (90 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+PrgI

tag: cell type


title: yFR3209_rtf1D_Rpb3vsInput_20190530_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in rtf1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3209_rtf1D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_63510.bed


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

tag: batch


title: yFR3208_cdc73D_Rpb3vsInput_20190530_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in cdc73Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3208_cdc73D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_121127.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in cdc73Δ 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: yFR3208_cdc73D_Spt16vsInput_20190529_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in cdc73Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3208_cdc73D_Spt16vsInput_20190529_rep1-2_S.cerevisiaeApr11_329535.bed


title: Tcells_G2_wk0_rep5 [S418]


title: S_6a02_6mo_b3_4

tag: tissue


title: yFR3198_ubp10D_Spt16vsInput_20190502_repl1

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in ubp10Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3198_ubp10D_Spt16vsInput_20190502_rep1-2_S.cerevisiaeApr11_686822.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in ubp10Δ 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_wk2_rep3 [S426]


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

tag: treatment


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

tag: ev fraction


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


title: S_6e11_2mo_b1_1

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: cell line


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


title: yFR3208_cdc73D_Rpb3vsInput_20190530_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in cdc73Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3208_cdc73D_Rpb3vsInput_20190530_rep1-2_S.cerevisiaeApr11_121127.bed


title: Bcells_G2_wk0_rep5 [S419]


title: yFR3198_ubp10D_Rpb3vsInput_20190502_repl2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp10Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3198_ubp10D_Rpb3vsInput_20190502_rep1-2_S.cerevisiaeApr11_902414.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp10Δ 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: yFR3198_ubp10D_Spt16vsInput_20190502_repl2

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in ubp10Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3198_ubp10D_Spt16vsInput_20190502_rep1-2_S.cerevisiaeApr11_686822.bed


title: DCcells_G2_wk0_rep1 [S417]


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


title: yFR3198_ubp10D_Rpb3vsInput_20190502_repl1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp10Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR3198_ubp10D_Rpb3vsInput_20190502_rep1-2_S.cerevisiaeApr11_902414.bed


title: yFR3075vs3084_3HA-chd1K407RvsNoTag_20190519_repl2

description:
Biological replicate 2 of 2. Chd1 K407R occupancy by ChIP-chip in 3HA-tagged chd1K407R cells. Chd1 K407R 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_yFR3075vs3084_3HA-chd1K407RvsNoTag_20190519_rep1-2_S.cerevisiaeApr11_688418.bed

data_processing:
BED description:  A genome browser-ready file for Chd1 K407R occupancy by ChIP-chip (IP tag/IP No tag) 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)

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: S_6a02_6mo_b3_3

tag: age


title: S_6a02_6mo_b3_2

tag: technical replicate


title: yFR3075vs3084_3HA-chd1K407RvsNoTag_20190519_repl1

description:
Biological replicate 1 of 2. Chd1 K407R occupancy by ChIP-chip in 3HA-tagged chd1K407R cells. Chd1 K407R 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_yFR3075vs3084_3HA-chd1K407RvsNoTag_20190519_rep1-2_S.cerevisiaeApr11_688418.bed

tag: strain


title: S_6a02_6mo_b3_1

tag: genotype


title: Bcells_G2_wk0_rep1 [S415]


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

value: THP-1 macrophages


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

value: SEC EVs


title: S_6a02_6mo_b2_3_P3_F9


title: Tcells_G2_wk0_rep1 [S414]


title: yFR3075_3HA-chd1K407R_Rpb3vsInput_20190519_repl2

description:
Biological replicate 2 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

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)

tag: chip antibody


title: S_6a02_6mo_b2_3_P3_E9


title: DCcells_G2_wk0_rep4 [S413]


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

tag: replicate


title: S_6a02_6mo_b2_2


title: Bcells_G2_wk0_rep4 [S411]

tag: subject


title: yFR3075_3HA-chd1K407R_Spt16vsInput_20190519_repl2

description:
Biological replicate 2 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

data_processing:
BED description:  A genome browser-ready file for Spt16 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)


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

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.

value: LPS+Nig


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