title: EV_miRNA

hyb_protocol: Flashtag Biotin HSR kit (Thermo Fisher Scientific) was used with a prolonged ~40 hour hybridization step

scan_protocol: not provided

data_processing: Microarray data were obtained using GeneChip Command Console software, analyzed with Affymetrix Expression Console software (Thermo Fisher Scientific), and normalized using the Robust Multichip Analysis (RMA) method

source_name: EVs from MPCs

label_protocol: not provided

growth_protocol: MPCs cultured in 15% Normal Horse Serum, Ham's F10, 1% Pen/Strep, and bFGF

extract_protocol: EVs were exrtacted from media using ExoQuick TC, and RNA was extracted using the ExoRNeasy Serum/Plasma kit (Qiagen)

value: myogenic progenitor cells (MPCs)

tag: cell fraction

value: Extracellular vesicles (EVs)

tag: rna fraction

value: miRNA


title: TAZ4SA_FLAG_IP_Rep2 (chipseq)

status: Public on Dec 01 2020

type: SRA

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

country: USA

institute: University of Iowa

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads from the SW872 line was aligned against the ensembl reference ‘hg38’
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: SW872 liposarcoma cells ATCC

growth_protocol: SW872 cells were stably transduced and grown to 90% confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)

extract_protocol:
Cells were cross-linked and prepared using the SimpleChIP Enzymatic Chromatin IP KIt according to manufacturer's instructions. Flag tagged proteins were immunoprecipated with the anti-DYKDDDDK rabbit monoclonal antibody (Cell Signaling)
The SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina was used to prepare the DNA library according to manufacturer's instructions

tag: cell line

value: SW872 liposarcoma cells


title: naive5_216000_OT-I_cell

type: RNA

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 130ng of each fluorescently labelled cRNA population was used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20). Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.
Text files resulting from the first data processing step were first imported into R (version 3.4.0) using the read.maimages() function from the R package Limma (version 3.32.10). Preprocessing steps included background correction and quantile normalization and were performed with the Limma functions backgroundCorrect() and normalizeBetweenArrays(), respectively. Afterwards, control probes and lowly variable genes were filtered out using the rowSds() function from the genefilter package (version 1.58.1). The microarray data then was condensed using the avereps() function from Limma so that values for within-array replicate probes are replaced with their average.

label: Alexa Fluor 555 Reactive Dye

molecule: total RNA

organism: Mus musculus

source_name: naive5, 216000 OT-I cell

label_protocol: 3.5ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one-round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to each processed sample. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

extract_protocol: Isolation of total RNA from samples obtained by flow cytometry sorting using >99% purified specific CD8 T cells (OT-I) was performed according to the manufacturer´s protocol (RNeasy Plus Micro Kit, Qiagen, Hilden, Germany) at the Research Core Unit Genomics (RCUG) of the Hannover Medical School (MHH).

treatment_protocol: C57BL/6 wild-type (CD90.2+) mice either received HDI for the generation of OVA+ liver tumors or were left untreated. Tumors were allowed to grow for 2 weeks and 5×10^3 naive, CD90.1+ OT-I cells were adoptively transferred into both mice groups. One day after T cell transfer all mice received PLGA-SIINFEKL+ PolyI:C priming, followed by LM-OVA infection 7 days later. OT-I cells were isolated on day 12 after LM-OVA from each group. Naive OT-I cells were isolated from uninfected mice as reference. Technical procedure for the isolation of OT-I cells for subsequent RNA-Isolation: livers of OVA+ tumor-bearing mice or livers from control mice, respectively, were cardially perfused, prior to harvesting using 37°C pre-warmed PBS, in order to remove in blood circulating lymphocytes. Livers/liver tumors were sliced to small pieces, treated with digestion medium (collagenase IV (0,2mg/ml), DNaseI (0,01mg/ml), penicillin (50 U/ml), streptomycin (50 μg/ml) in RPMI-1640 + GlutaMAX-I medium) for 30 minutes at 220 rpm at 37°C. Tissue digestion was stopped by adding RPMI-1640 medium with 10% fetal calve serum. Cells were pelleted by centrifugation (300 g for 10 minutes at 4°C) and subsequently resuspended in MACS buffer (PBS with added 1% FCS, penicillin (50 U/ml), streptomycin (50 μg/ml)). Fc receptors were blocked by treatment with anti-mouse CD16/32 antibody (TruStain FcX, Biolegend, San Diego, CA, USA). The specific CD8 T cells (the adoptively transferred CD90.1+ OT-I cells) were enriched by MACS technology (Miltenyi Biotec, Germany) using CD90.1 MicroBeads and LS Columns according to the manufacturer´s instructions. Afterwards, flow cytometry sorting using FACSAria IIu (Becton Dickinson, San Jose, CA, USA) was performed to receive specific CD8 T cells (OT-I) of >99% purity. The OT-I cells were isolated from OVA+ tumor-bearing livers (exhausted T cells) or livers of tumor-free control mice  (effector T cells), respectively. As additional reference data, naive OT-I cells (naive T cells) were isolated from spleens of naive mice, that have previously received adoptive transfer of naive OT-I cells.

tag: tissue

value: spleen

tag: cell type

value: CD8 T cells

tag: phenotype

value: naive


title: TAZ4SA_FLAG_IP_Rep1 (chipseq)


title: 18b, brain, male

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: microRNA

library_source: transcriptomic

data_processing:
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences: UEA sRNA WorkbenchV3.2
filtering: UEA sRNA WorkbenchV4.6; parameters: 17-25 nt in length, minimum abundance of at least 6 supporting reads, tRNA and rRNA sequences excluded.
mapping: the filtered reads were mapped to Sscrofa10.2 genome and miRBase 22.1, using miRCat tool embeded in UEA sRNA WorkbenchV4.6. The following parameters were applied - default animal parameters, except for: minimum abundance (6), minimum length (17 nt) and maximum length (25 nt).
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: FASTA files after filtering and adaptor trimming, generated with the use of UEA sRNA Workbench V4.6. They include the number of reads of detected sequences.
miRNA mapping.xlsx

organism: Sus scrofa

source_name: 990 synthetic line brain tissue

extract_protocol:
The quantity and quality of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland).
microRNA libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C at 10nM concentration until further use.

treatment_protocol: Immediately after slaughter, tissue samples were frozen in liquid nitrogen and stored at -80°C

tag: breed

value: Polish 990 synthetic line

value: brain

tag: gender

value: male


title: 19b, brain, female

description: microRNA

value: female


title: 17b, brain, female

description: microRNA


title: Empty Vector_Input_2 (chipseq)


title: Empty Vector_IgG_Rep 2 (chipseq)


title: 16b, brain, female

description: microRNA


title: Empty Vector_Input_1 (chipseq)


title: naive1_142000_OT-I_cell

source_name: naive1, 142000 OT-I cell


title: 24M.WT.M_13N: WT-male-liver-normal-animal13

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

description: Gene expression data from a mouse, age 24 months, wild type, male, normal liver tissue, animal 13

hyb_protocol: 500 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 2.0 ST Arrays according to the manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labeled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized and quantile-normalized using RMA algorithm from oligo package.
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

label: biotin

source_name: Mouse, age 24 months, wild type, male, normal liver tissue, animal 13

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA samples were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: The generation of homozygous hepatocyte-specific Cyp51 knock-out (HCyp51-/-, written as KO) and wild type (HCyp51+/+  written as WT) on a mixed genetic background (129/Pas (10%) × C57BL/6J (90%)) was established by crossbreeding between transgenic mouse strains with floxed exons 3 and 4 of the Cyp51 and transgenic mice expressing Cre recombinase under albumin-reporter (Cre-Alb) as has been reported previously [Lorbek G et al. Lessons from hepatocyte-specific Cyp51 knockout mice: impaired cholesterol synthesis leads to oval cell-driven liver injury. Scientific reports. 2015; 5: 8777; Urlep Z et al. Disrupting Hepatocyte Cyp51 from Cholesterol Synthesis Leads to Progressive Liver Injury in the Developing Mouse and Decreases RORC Signalling. Scientific reports. 2017; 7: 40775]. Animals were bred under controlled conditions: a 12 h light and dark cycle (7:00 am till 7:00 pm light), temperature of 22±1 ºC, humidity 55±10%, maintained on standard rodent chow (diet 1324, Altromin, Germany) and acidified tap water (pH = 3) ad libitum. The experiment was performed at the Medical Experimental Center, Faculty of Medicine, University of Ljubljana. During the experiment the routine health microbiological monitoring was done. Genotypes were confirmed by polymerase chain reaction (PCR) of ear or tail gDNA as was descripted previous [Lorbek G et al. Lessons from hepatocyte-specific Cyp51 knockout mice: impaired cholesterol synthesis leads to oval cell-driven liver injury. Scientific reports. 2015; 5: 8777].

extract_protocol: We sacrificed KO and WT mice of both sexes after a 5 h fast with cervical dislocation at age 24 months. Mice were weighed, organs (liver, kidney, spleen, heart, gonads) were removed and patho-morphologically examined. Livers were cut into thin slices and snap frozen in liquid nitrogen. The material was fresh frozen and stored at – 80 °C for subsequent analysis. Livers were pulverized and the RNA was isolated using TRI Reagent according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop-1000 and Agilent 2100 Bioanalyzer instruments, respectively. All samples were of sufficient purity and integrity for microarray hybridization.

treatment_protocol: not applicable

tag: strain

value: liver

tag: age

value: 24 months

tag: genotype

value: WT

tag: Sex

value: M

tag: tissue type

value: normal

tag: animal


title: Empty Vector_IgG_Rep 1 (chipseq)


title: 14b, brain, male

description: microRNA


title: 24M.WT.M_14N: WT-male-liver-normal-animal14

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression data from a mouse, age 24 months, wild type, male, normal liver tissue, animal 14

source_name: Mouse, age 24 months, wild type, male, normal liver tissue, animal 14


title: camta1_input_rep2 (chipseq)


title: 13b, brain, female

description: microRNA


title: 12b, brain, female

description: microRNA


title: anti-Ang2 treated replicate 1

city: Heidelberg

first: Nicolas

last: Gengenbacher

address: Im Neuenheimer Feld 280

department: Vascular Oncology and Metastasis

institute: German Cancer Research Center

description: Ret #13

hyb_protocol: 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays.

scan_protocol: Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: All intensity data were quantile normalized with R using the normalize.quantiles function from the Bioconductor package preprocessCore

label: Biotin

source_name: MT-ret tumor tissue

label_protocol: Biotin-labeled ss-cDNA samples were prepared from 250ng total RNA according to Affymetrix's recommended sample labeling procedure as described in the Gene Chip WT Plus Reagent Kit guide

growth_protocol: MT-ret tumor fragments were implanted on the ventral flank of C57BL/6N mice.

extract_protocol: Total tumor RNA was isolated by smashing tissue pieces in TRIzol (Thermo Fisher Scientific) followed by Chloroform extraction. Afterwards, RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Neo-adjuvant antibody treatment was initiated 7 days post fragment implantation and discontinued after primary tumor resection. Total tumor RNA was analyzed

tag: treatment

value: MT-ret tumor


title: 24M.WT.F_10N: WT-female-liver-normal-animal10

description: Gene expression data from a mouse, age 24 months, wild type, female, normal liver tissue, animal 10

source_name: Mouse, age 24 months, wild type, female, normal liver tissue, animal 10

value: F


title: 24M.WT.M_11N: WT-male-liver-normal-animal11

description: Gene expression data from a mouse, age 24 months, wild type, male, normal liver tissue, animal 11

source_name: Mouse, age 24 months, wild type, male, normal liver tissue, animal 11


title: naive4_234000_OT-I_cell

source_name: naive4, 234000 OT-I cell


title: 24M.WT.F_07N: WT-female-liver-normal-animal07

description: Gene expression data from a mouse, age 24 months, wild type, female, normal liver tissue, animal 07

source_name: Mouse, age 24 months, wild type, female, normal liver tissue, animal 07


title: CAMTA1_input_rep1 (chipseq)


title: 11b, brain, male

description: microRNA


title: 15b, brain, male

description: microRNA


title: 24M.WT.M_12N: WT-male-liver-normal-animal12

description: Gene expression data from a mouse, age 24 months, wild type, male, normal liver tissue, animal 12

source_name: Mouse, age 24 months, wild type, male, normal liver tissue, animal 12


title: 24M.WT.F_08N: WT-female-liver-normal-animal08

description: Gene expression data from a mouse, age 24 months, wild type, female, normal liver tissue, animal 08

source_name: Mouse, age 24 months, wild type, female, normal liver tissue, animal 08


title: CAMTA1_FLAG_IP Rep 1 (chipseq)


title: 24M.KO.M_06S: KO-male-liver-tumorSurrounding-animal06

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, tumor surrounding liver tissue, animal 06

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, tumor surrounding liver tissue, animal 06

value: Cyp51 KO

value: surrounding tumor


title: 9b, brain, female

description: microRNA


title: 8b, brain, female

description: microRNA


title: 24M.WT.F_09N: WT-female-liver-normal-animal09

description: Gene expression data from a mouse, age 24 months, wild type, female, normal liver tissue, animal 09

source_name: Mouse, age 24 months, wild type, female, normal liver tissue, animal 09


title: CAMTA1_FLAG_IP_Rep 3 (chipseq)

value: SW872 liposarcoma cells


title: 24M.KO.M_06T: KO-male-liver-tumor-animal06

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, liver tumor tissue, animal 06

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, liver tumor tissue, animal 06

value: tumor


title: 24M.KO.F_04S: KO-female-liver-tumorSurrounding-animal04

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 04

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 04


title: 24M.KO.M_05S: KO-male-liver-tumorSurrounding-animal05

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, tumor surrounding liver tissue, animal 05

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, tumor surrounding liver tissue, animal 05


title: 7b, brain, male

description: microRNA


title: CAMTA1_FLAG_IP_Rep 2 (chipseq)

source_name: SW872 liposarcoma cells ATCC


title: YAP-TFE3 rep 1 (rnaseq_sw872)

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads from the SW872 line was aligned against the ensembl reference ‘hg38’
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample ...

molecule: polyA RNA

growth_protocol: SW872 cells were stably transduced and grown to confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)

extract_protocol:
Total RNA was isolated using the PureLink™ RNA mini kit (Invitrogen-ThermoFisher Scientific).  On-column DNase (Invitrogen) treatment was performed according to manufacturer’s instructions
Illumina TruSeq stranded mRNA sample preparation kit


title: YAP-TFE3 rep 3 (rnaseq_sw872)


title: 6b, brain, female

description: microRNA

source_name: 990 synthetic line brain tissue


title: 24M.KO.F_03S: KO-female-liver-tumorSurrounding-animal03

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 03

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 03


title: 10b, brain, female

description: microRNA


title: YAP5SA rep 3 (rnaseq_sw872)


title: 4b, brain, female

description: microRNA


title: YAP5SA rep 2 (rnaseq_sw872)


title: 24M.KO.F_03T: KO-female-liver-tumor-animal03

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 03

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 03


title: 2b, brain, female

description: microRNA


title: TFE3 rep 3 (rnaseq_sw872)


title: YAP5SA rep 1 (rnaseq_sw872)


title: TFE3 rep 2 (rnaseq_sw872)


title: 5b, brain, female

description: microRNA


title: 24M.KO.F_01T: KO-female-liver-tumor-animal01

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 01

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 01


title: 24M.KO.F_02S: KO-female-liver-tumorSurrounding-animal02

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 02

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 02


title: MG1655 sulfite no treatment 2

city: Leioa

first: Ander

middle: Hernández

last: Plágaro

state: Bizkaia

address: Barrio Sarriena S/N

department: Immunology, Microbiology and Parasitology

country: Spain

institute: University of the Basque Country

description:
used for signal normalization
Sample 8

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 40 uL. Temperature (ºC): 65. Duration: 17 hours at 10 rpm in the hybridization oven. Wash procedure with Stabilization and Drying solution (Agilent Technologies) and ozone-barrier slide covers (Agilent) to prevent ozone related Cy-5 degradation.

scan_protocol: Scanned on a G2565CA DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies).

data_processing:
Raw data from Feature Extraction software was subsequently processed on GeneSpring GX 11.5.1 (Agilent Technologies). Feature Extraction protocol for data extraction was GE2_107_Sep09, this algorithm adjusts for the dye bias by multiplying the background-subtracted signals with the appropriate dye normalization factors. Dye Biases Normalization correction was based on Linear and Lowess.
The two color data was analyzed as single color experiment, where each sample file was split in two files, one for each channel, in order to apply the present/absent (P/A) filter in each channel. Otherwise, despite the P/A call for each channel, all the samples where there is an Absent call in any channel (Cy5 P/Cy3 A; Cy5 A/Cy3 P and Cy5 A/Cy3 A) are considered as Absent. But we want to retain Cy5 P/Cy3 P; Cy5 P/Cy3 A; and Cy5 A/Cy3 P, and remove Cy5 A/Cy3 A.   The statistical analysis was performed using MultiExperiment Viewer (MeV) vs. 4.7.1 (http://www.tm4.org/mev/) application. For the significance analysis LIMMA package was used, with an adjusted p-value <0.05 as lower threshold to identify differentially expressed genes with statistical significance.
log2 ratio (control/treatment)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell extract

label_protocol: Amount of nucleic acid labeled: 5 ug. Agilent Protocol "Two-Color Microarray-Based Prokaryote Analysis. FairPlay III Labeling” Ver. 1.3 August 2010. Samples are retrotranscribed (first strand synthesis) and labeled using FairPlay III labeling kit (Stratagene) following manufacturer instructions. First, total RNA is retrotranscribed with AffinityScript HC (high concentration) Reverse Transcriptase (AffinityScript HC RT), an engineered thermostable mutant derived from Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, using random primers. After preparing amino allyl modified cDNA, mono-reactive Cy-5 and Cy-3 dyes (GE Healthcare) are chemically coupled to the modified cDNA. Labeled samples are purified with silica-based fiber matrix columns included in the labeling kit.

growth_protocol: Escherichia coli MG1655 overnight cultures were diluted in 40 mL fresh M9 minimal medium supplemented with 0.4% glucose and futher incubated in 250 mL flasks, at 37 ºC, darkness and with shaking (90 rpm) until OD600 reached 0.5-0.6. RNA was isolated before and after sulfite treatment.

extract_protocol: Aliquots of cell cultures were mixed with cold stop solution (5% phenol in ethanol) at an 8:1 ratio. The cells were collected by centrifugation (15 min, 4 ◦ C, 4000 g), suspended in 250 μl of 1× TE (pH 8.0) supplemented with lysozyme (0.5 mg ml −1 ; Sigma), mixed with an equal volume of lysis buffer [200 mM NaCl, 20 mM Tris–HCl (pH 7.5), 40 mM EDTA, 0.5% SDS] and incubated at 95 ◦ C for 30 s. RNA was extracted from the cell lysates by phenol, phenol/chloroform/isoamyl alcohol (25:24:1) and chloroform/isoamyl alcohol (24:1), precipitated with isopropanol, washed with 80% ethanol, air-dried for 5 min and dissolved in RNase-free water (Accugene). To remove genomic DNA, RNA was further treated with the RNase-free DNase I (Thermo Scientific) for 30 min at 37 ◦ C, extracted with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with ethanol. The resulting RNA pellets were washed with 80% ethanol, air-dried and suspended in RNase-free water (Accugene).

treatment_protocol: When cultures reached OD600 0.5-0.6 sidum metabisulfite was added to a final concentration of 2 mM Na2S2O5 (equivalent to 4 mM sodium bisulfite).

value: no treatment control


title: MG1655 sulfite treatment 6

description:
-
Sample 6

value: Escherichia coli str. K-12 substr. MG1655

value: sulfite treatment


title: 24M.KO.F_02T: KO-female-liver-tumor-animal02

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 02

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 02


title: MG1655 sulfite no treatment 1

description:
used for signal normalization
Sample 7


title: TAZ-CAMTA1 rep 3 (rnaseq_sw872)


title: TAZ-CAMTA1 rep 2 (rnaseq_sw872)


title: TFE3 rep 1 (rnaseq_sw872)


title: TAZ-CAMTA1 rep 1 (rnaseq_sw872)


title: YAP-TFE3 rep 2 (rnaseq_sw872)


title: MG1655 sulfite treatment 5

description:
-
Sample 5


title: 3b, brain, female

description: microRNA

value: Polish 990 synthetic line

value: brain


title: 24M.KO.F_04T: KO-female-liver-tumor-animal04

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 04

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, liver tumor tissue, animal 04


title: 24M.KO.F_01S: KO-female-liver-tumorSurrounding-animal01

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 01

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, female, tumor surrounding liver tissue, animal 01


title: Treated with Th2 interleukins, rep 2

city: Isnes Gembloux

first: Roland

last: Hubaux

state: Namur

address: rue Jean Sonet 10

department: R&D

country: Belgium

institute: StratiCELL

description:
Th2_2
Gene expression data from reconstructed human epidermis (StratiCELL) treated with Th2 interleukins (IL-4, IL-13) and IL-25

hyb_protocol: Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip® Expression Amplification Reagent Hybridization Controls (Cat# 900454) and the Hybridization Module for GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720) and mixed with amplified cDNA samples. GeneChip® Human Gene 2.0 ST Arrays (Cat# 902112) were treated according to the manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix).

data_processing: The data were analyzed after RMA normalization with Affymetrix GeneChip™ Command Console Software for QC. Statistical analyses were performed with “Moderated t” method implemented in  R package Limma 3.26.8 (Smyth, 2004).

source_name: Reconstructed human epidermis treated with Th2 interleukins

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Reconstruction of the human epidermis by the manufacturer (StratiCELL) for 14 days at the air-liquid interface

extract_protocol: Qiagen RNeasy kit, protocol following the manufacturer's instructions.

treatment_protocol: Tissue samples were treated with interleukins IL-4, IL-13, and IL-25, for 48h

value: epidermis

value: exposure to interleukins 4, 13, and 25


title: TAZ4SA rep 3 (rnaseq_sw872)


title: Treated with Th2 interleukins, rep 3

description:
Th2_3
Gene expression data from reconstructed human epidermis (StratiCELL) treated with Th2 interleukins (IL-4, IL-13) and IL-25


title: Treated with Th2 interleukins, rep 1

description:
Th2_1
Gene expression data from reconstructed human epidermis (StratiCELL) treated with Th2 interleukins (IL-4, IL-13) and IL-25


title: control, replicate 2

description:
Control_2
Gene expression data from reconstructed human epidermis (StratiCELL) untreated

source_name: Reconstructed human epidermis untreated

value: control


title: MG1655 sulfite treatment 3

description:
-
Sample 3


title: MG1655 sulfite treatment 2

description:
-
Sample 2


title: TAZ4SA rep 1 (rnaseq_sw872)


title: MG1655 sulfite treatment 1

description:
-
Sample 1


title: Empty Vector Sub-Confluent Rep 3 (rnaseq_sw872)


title: Empty Vector Sub-Confluent Rep 2 (rnaseq_sw872)


title: control, replicate 3

description:
Control_3
Gene expression data from reconstructed human epidermis (StratiCELL) untreated


title: MG1655 sulfite treatment 4

description:
-
Sample 4


title: Empyt Vector Sub Confluent Rep 1 (rnaseq_sw872)


title: Empty Vector Rep 3 (rnaseq_sw872)


title: B67_1034

city: Cardiff

first: Matthew

middle: John

last: Smalley

state: Cardiff

address: Hadyn Ellis Building, Maindy Road

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description:
MS1155 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx

data_processing:
Library strategy: Exome sequencing
Raw FASTQ sequence files were quality control checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read pairs were mapped against the mouse genome (build 38) using BWA “mem” algorithm with default parameters.
Resulting bam files were used for mutation calling or copy number variation analysis comparing tumor sequencing with spleen from the same animal.
Genome_build: Mouse genome build 38 (GRCm38)
Supplementary_files_format_and_content: Mutation_calling.xlsx
Supplementary_files_format_and_content: CNV_by_exome.xlsx

source_name: Spleen

extract_protocol:
DNA harvested from snap frozen tumor material and matched spleen from a euthanised genetically modified mouse.
Genomic DNA was extracted from snap-frozen tumor material using the Gentra Puregene Tissue Kit (QIAGEN).
Genomic DNA (200-600ng) was fragmented to 200bp using a Covaris E Series and the resultant libraries were subjected to DNA Capture using SureSelect XT Mouse All Exon kit (Agilent, Stockport, Cheshire) following manufacturer’s instructions. Final libraries were quantified using qPCR and clustered at a molarity of 14.5 pM, sequencing was performed on an Illumina HiSeq 2500 using 2x76 cycles of version 3 SBS chemistry.

value: Spleen

tag: reproductive history

value: Parous

tag: tumor diagnosis

tag: amplification status of erbb2/neu locus


title: B67_0035

description:
MS1210 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: B67_0025

description:
MS1156 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: B67_0023

description:
MS1213 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx

value: Virgin


title: TAZ4SA rep 2 (rnaseq_sw872)


title: B67_0033

description:
MS1218 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: B67_0027

description:
MS1166 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: Empty Vector Rep 1 (rnaseq_sw872)


title: B67_0026

description:
MS1349 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: Empty Vector Rep 2 (rnaseq_sw872)


title: B67_0021

description:
MS1163 spleen
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: B67_0032

description:
MS1210.1
Mutation_calling.xlsx
CNV_by_exome.xlsx

source_name: Mammary tumor

value: Mammary tumor

value: Metaplastic Adenosquamous Carcinoma

value: Non / low amplification


title: control, replicate 1

description:
Control_1
Gene expression data from reconstructed human epidermis (StratiCELL) untreated


title: CAMTA1 Rep 1 (rnaseq_sw872)


title: B67_0018

description:
MS1166.1
Mutation_calling.xlsx
CNV_by_exome.xlsx

value: Adenocarcinoma (No Special Type)


title: CGHNK2-shCtrl-serum starvation-rep1

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: replicate 1

hyb_protocol: cDNA was hybridized to Affymetrix GeneChip Human Gene 2.0 ST array according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Expression values were processed with Signal Space Transformation (SST) and Robust Multichip Average method, which included log2 transformation and quantile normalization.

source_name: LDOC1 expressing

label_protocol: RNA was amplified (in vitro transcription) and generate biotin labeled Single-stranded cDNA according to manufacturer's instructions.

growth_protocol: Cells were cultured in normal growth medium and serum starvation for 16 hours before RNA extraction.

extract_protocol: RNA was extracted by TriZol reagent according to manufacturer's instructions. One microgram of RNA from each sample was processed with the QIAGEN miRNeasy mini kit (QIAGEN, Hilden, Germany).

value: male

value: Oral  keratinocyte

tag: tumor stage

value: untransformed


title: B67_0017

description:
MS1349.1
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: Bacteroides ovatus NLAE-zl-H59 mucin O-linked glycans 3

city: Ann Arbor

first: Eric

last: Martens

state: MI

address: 1150 W. Medical Center Dr.

institute: University of Michigan

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in mucin O-linked glycans was compared to gene expression in glucose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and normalized expression level >1%
Genome_build: NZ_ADCK00000000.1, NZ_ACRS00000000.1, NZ_ACGA00000000.2, Ga0011936
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample

organism: Bacteroides ovatus

source_name: Bacterial Total RNA

growth_protocol: Strains were grown to mid-log on 5 mg/ml mucin O-linked glycans or glucose as a sole carbon source in vitro.

extract_protocol:
Qiagen RNeasy kit and rRNA depleted with Bacteria Ribo-Zero Kit (Epicentre/Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with two volumes of RNA Protect (Qiagen) of the original culture volume then frozen at -80C until RNA was extracted

tag: carbon source

value: mucin O-linked glycans


title: MYC3-bHLH-PBM.GenomeDesign

type: protein

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

description: bHLH-PBM GenomeDesign

hyb_protocol: The binding mixture containing the protein extract in binding buffer was adjusted to 175 µl and contained 2% milk and 0.89 µg of denatured salmon sperm DNA (ssDNA). This mixture was added to an array and incubated for 2.5 hours at room temperature and later on was washed 3 times with PBS-1% Tween 20 (5 min), 3x  in PBS-0.01% Triton X-100 (5 min) and spun dry by centrifugation (1000 g).

scan_protocol: PBMs were scanned in a DNA Microarray Scanner at 5 µm resolution and quantified with Feature Extraction 9.0 software (Agilent Technologies)

data_processing: Raw intensities were adjusted to account for spatial non-uniformities across the microarray using the script ‘normalize_agilent_array.pl’ included in the PBM Analysis Suite (http://thebrain.bwh.harvard.edu/PBMAnalysisSuite/indexSep2017.html)

molecule: protein

organism: Arabidopsis thaliana

source_name: Protein expressed in E.coli

label_protocol: DNA-protein complexes were incubated with 16 ug of rabbit polyclonal to MBP (Abcam, http://www.abcam.com/) in PBS–2% milk for 16 h at room temperature. Slides were washed 3x in PBS0.05% Tween 20, 3x in PBS-0.01% Triton X-100 (5 min each wash) and dried. Labeling of DNA-protein complexes was performed by incubating the microarrays with 0.4 ug of goat anti-rabbit IgG DyLight 549 conjugated (Pierce, http://www.piercenet.com/) in PBS–2% milk for 3 h at room temperature, followed by the same washes as before and the slides were then dried for scanning.

growth_protocol: E.coli (BL21 strain) was induced with 1 mM IPTG at OD600=0.6, and incubated for 4 hours at 28 ºC. After induction, cultures were centrifuged and cell pellets frozen at -80 ºC

extract_protocol: Cell pellet from 25 ml cultures were resuspended in 1ml in 1 mL 1x binding buffer, sonicated (2x30 s) and centrifuged twice to obtain cleared extracts of soluble proteins.

tag: protein expressed

value: Recombinant fusion protein MBP-MYC3


title: Bacteroides ovatus NLAE-zl-H59 mucin O-linked glycans 2


title: MYC4-bHLH-PBM.GenomeDesign

description: bHLH-PBM GenomeDesign

value: Recombinant fusion protein MBP-MYC4


title: CGHNK2-shLDOC1-serum starvation-rep1

description: replicate 1

source_name: LDOC1 deficient

tag: cell line

tag: cell type

value: transformed


title: SW872 Yap5SA-TFE3 replicate 2 (atacseq)

description:
accessible DNA
SW872_YT_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: narrowPeak

source_name: SW872 liposarcoma cells ATCC

growth_protocol: SW872 cells were stably transduced and plated

extract_protocol:
50,000 cells were trypsinized, pelleted, and subjected to tranposition via Tn5 Transposae (Nextera) according to the manufacturer's instructions
Transposed DNA fragments were PCR amplified using the Nextera XT Index Kit per the manufacturer's instruction of generate indexed libraries

value: SW872 liposarcoma cells


title: SW872 Yap5SA-TFE3 replicate 3 (atacseq)

description:
accessible DNA
SW872_YT_3


title: B67_0015

description:
MS1155.3
Mutation_calling.xlsx
CNV_by_exome.xlsx

tag: tissue

value: High Amplification


title: Bacteroides ovatus NLAE-zl-H59 mucin O-linked glycans 1


title: SW872 Yap5SA-TFE3 replicate 1 (atacseq)

description:
accessible DNA
SW872_YT_1


title: bHLH17-bHLH-PBM.GenomeDesign

description: bHLH-PBM GenomeDesign

value: Recombinant fusion protein MBP-b17


title: CAMTA1 Rep 3 (rnaseq_sw872)


title: MYC2-bHLH-PBM.GenomeDesign

description: bHLH-PBM GenomeDesign

value: Recombinant fusion protein MBP-MYC2


title: MYC3-bHLH-PBM.PromDesign

description: bHLH-PBM PromDesign

hyb_protocol: The binding mixture containing the protein extract in binding buffer was adjusted to 175 µl and contained 2% milk and 0.89 µg of denatured salmon sperm DNA (ssDNA). This mixture was added to an array and incubated for 2.5 hours at room temperature and later on was washed 3 times with PBS-1% Tween 20 (5 min), 3x in PBS-0.01% Triton X-100 (5 min) and spun dry by centrifugation (1000 g).


title: MYC4-bHLH-PBM.PromDesign

description: bHLH-PBM PromDesign


title: CAMTA1 Rep 2 (rnaseq_sw872)


title: B67_0014

description:
MS1213.1
Mutation_calling.xlsx
CNV_by_exome.xlsx


title: MYC2-bHLH-PBM.PromDesign

description: bHLH-PBM PromDesign


title: SW872 YAP5SA replicate 3 (atacseq)

description:
accessible DNA
SW872_YAP5SA_3


title: Bacteroides ovatus NLAE-zl-H59 glucose 3

value: glucose


title: bHLH17-bHLH-PBM.PromDesign

description: bHLH-PBM PromDesign


title: B67_0016

description:
MS1156.1
Mutation_calling.xlsx
CNV_by_exome.xlsx

value: Parous

value: Mammary Sarcoma


title: B67_0013

description:
MS1218.2
Mutation_calling.xlsx
CNV_by_exome.xlsx

value: Mammary tumor


title: Bacteroides ovatus NLAE-zl-H59 glucose 2


title: SW872 YAP5SA replicate 2 (atacseq)

description:
accessible DNA
SW872_YAP5SA_2


title: SW872 YAP5SA replicate 1 (atacseq)

description:
accessible DNA
SW872_YAP5SA_1


title: B67_0031

description:
MS1163.2
Mutation_calling.xlsx
CNV_by_exome.xlsx

value: Virgin


title: SW872 TFE3 replicate 3 (atacseq)

description:
accessible DNA
SW872_TFE3_3


title: Bacteroides ovatus NLAE-zl-H59 glucose 1


title: B67_0011

description:
MS1163.1
Mutation_calling.xlsx
CNV_by_exome.xlsx

value: Adenocarcinoma (No Special Type)


title: Bacteroides ovatus D2 glucose 3


title: SW872 Taz-Camta1 replicate 3 (atacseq)

description:
accessible DNA
SW872_TC_3


title: Bacteroides ovatus D2 mucin O-linked glycans 3


title: Sorafenib treated liver tumors 1

city: Tübingen

first: Omelyan

last: Trompak

state: BW

address: Otfried-Müller-Straße 14

department: Internal Medicine VIII

institute: University Hospital of Tübingen

data_processing:
Basecalling was assessed using ngs-bits to identify and trimm sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification
Reads were aligned using STAR v2.6.1c (Dobin et al.,2013) to the grcm38
Normalized read counts for all genes were obtained using Subread (v1.6.3) and edgeR (v3.22.5)
Genome_build: grcm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver tumors

growth_protocol: To generate murine liver tumors, we co-delivered transposable elements encoding for Myc and oncogenic NrasG12V via hydrodynamic injection into the hepatocytes of C57BL/6 wildtype mice.

extract_protocol:
RNA was isolated from tumor samples via TRIZOL (Invitrogen) and the RNeasy Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina TruSeq stranded protocol. mRNA fraction was enriched using polyA capture from 100ng of total RNA using the TruSeq stranded protocol (Illumina). The libraries were denaturated according to the manufacturer’s instructions and sequenced as single-end using the 75 cycle chemistry on an Illumina HiSeq2500 (Illumina).

treatment_protocol: Treatment of mice with Carrier or Sorafenib for 3 weeks every second day

value: Sorafenib


title: Sorafenib treated liver tumors 2


title: Bacteroides ovatus D2 glucose 2


title: Bacteroides ovatus D2 mucin O-linked glycans 2


title: Bacteroides ovatus D2 mucin O-linked glycans 1


title: SW872 TFE3 replicate 2 (atacseq)

description:
accessible DNA
SW872_TFE3_2


title: Bacteroides ovatus D2 glucose 1


title: SW872 Taz4sa replicate 3 (atacseq)

description:
accessible DNA
SW872_TAZ4SA_3


title: SW872 Taz-Camta1 replicate 2 (atacseq)

description:
accessible DNA
SW872_TC_2


title: Carrier treated liver tumors 2

value: Carrier


title: Bacteroides ovatus 3_1_23 mucin O-linked glycans 3


title: SW872 Taz4sa replicate 2 (atacseq)

description:
accessible DNA
SW872_TAZ4SA_2


title: Carrier treated liver tumors 1


title: SW872 Taz-Camta1 replicate 1 (atacseq)

description:
accessible DNA
SW872_TC_1


title: Exosome2_1

city: Suwon-si

first: Paulami

last: Mandal

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu, Room 6317, School of Medicine

department: Molecular Cell Biology

country: South Korea

institute: Sungkyunkwan University

description: small RNA

data_processing:
After sequencing, the raw sequence reads are filtered based on quality.The quality of produced data is determined by the phred quality score at each cycle. The adapter sequences are also trimmed off the raw sequence reads.
Both the trimmed reads and non-adapter reads as processed reads are used, to do analyzing long  target (>= 50bp). Adapter trimming process is done using Cutadapt
The processed reads are gathered forming a unique cluster. This cluster contains reads that are 100%  match to the sequence identity as well as read length. The cluster is given its temporary cluster ID  and the number of reads it holds.
Most of the RNA composition is usually known as rRNA. In order to eliminate the effect of large  amounts of rRNA from this study, reads were aligned to the 45S pre-rRNA and mitochondrial rRNA  of Mus musculus and have them removed.
For each sample, final processed reads are sequentially aligned to reference genome, miRBase v21 and non-coding RNA database (RNAcentral release 10.0) to  classify known  miRNAs and other types of RNA such as piRNA, tRNA, snRNA, snoRNA etc. Genome mapping is processed by Bowtie and STAR using RSEM. Bowtie was subsequently used for miRDeep2 analysis using a genomic sequence. If it's necessary, the RSEM program can be used to align readings to transcript sequences using STAR. Known/novel miRNA predicted by miRDeep2 and other small RNAs (smRNAs) matching RNAcentral were aligned using Bowtie (target smRNA, <50 nt) and Bowtie2 (target smRNA, >=50nt). Quantification step is divided into three procedures. At First, mature miRNA sequences of relevant species are aligned to precursor miRNA sequences from miRBase v21 (bowtie option : -f -v 0 -a--best --strata --norc). In the second step, unique clustered reads are aligned to precursor sequence (bowtie option : -f -v 1 -a --best --strata --norc). Bowtie aligner is used in the mapping steps. In the third step, we determine overlapping mature miRNA regions between two mapping results. Afterwards, the read count of mature miRNAs are extracted from the overlapping regions in the miRDeep2 Quantifier module. If a read is mapped to multiple mature miRNAs, the read counts are assigned equally to the abundance level of each mature miRNA. Differentially expressed smRNAs are determined through comparing across conditions each smRNA using statistical methods like fold Change, exactTest using edgeR, Hierarchical Clustering.
Genome_build: mm10
Supplementary_files_format_and_content: processed fastq files

source_name: MIN6-derived exosomes

growth_protocol: The MIN6 cells were maintained in Dulbecco's modified Eagle medium (DMEM) (Welgene Inc., Gyeongsan, South Korea) supplemented with exosome-depleted  15% fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific, Inc., MA, USA), 1X penicillin-streptomycin (P/S, Welgene Inc., Gyeongsan, South Korea), and 55 µM freshly added β-mercaptoethanol (β-ME) (Sigma Aldrich, MO, USA) in T75 tissue culture flasks.

extract_protocol:
The small RNA from the MIN6 cells and the MIN6-derived exosomes were isolated using Qiagen's miRNeasy Serum/Plasma Kit
1) Input RNA is first polyadenylated in order to provide a priming sequence for an oligo(dT) primer.
2) cDNA synthesis is primed by the 3' smRNA dT Primer, which incorporates an adapter sequence (green) at the 5' end of each first-strand cDNA molecule.
3) When the MMLV-derived PrimeScript Reverse Transcriptase (RT) reaches the 5' end of each RNA template, it adds non-templated nucleotides which are bound by the SMART smRNA Oligo-enhanced with locked nucleic acid (LNA) technology for greater sensitivity.
4) PrimeScript RT uses the SMART smRNA Oligo as a template for the addition of a second adapter sequence (purple) to the 3' end of each first-strand cDNA molecule.
5) Full-length Illumina adapters are added during PCR amplification.
6) cDNA fragments are sequenced by the read length using sequence by synthesis method on the illumina platform.
SMARTer smRNA-Seq Kit for Illumina

tag: source

value: Pancreatic beta cell-derived exosomes

tag: tumor

value: Insulinoma cell-derived exosomes


title: Cell2_1

description: small RNA

value: Pancreatic beta cells

value: Insulinoma cells


title: Bacteroides ovatus 3_1_23 glucose 3

tag: strain


title: Exosome1_1

description: small RNA


title: Bacteroides ovatus 3_1_23 mucin O-linked glycans 2

value: mucin O-linked glycans


title: 1b, brain, female

description: microRNA

source_name: 990 synthetic line brain tissue

tag: breed

value: Polish 990 synthetic line

value: brain

tag: gender

value: female


title: SW872 Taz4sa replicate 1 (atacseq)

description:
accessible DNA
SW872_TAZ4SA_1

value: SW872 liposarcoma cells


title: Cell1_1

description: small RNA


title: SW872 Empty Vector replicate 1 (atacseq)

description:
accessible DNA
SW872_EV_1


title: 24M.KO.M_05T: KO-male-liver-tumor-animal05

description: Gene expression data from a mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, liver tumor tissue, animal 05

source_name: Mouse, age 24 months, hepatocyte specific deletion of Cyp51, male, liver tumor tissue, animal 05

value: liver

tag: age

value: 24 months

tag: genotype

value: Cyp51 KO

tag: Sex

value: M

tag: tissue type

value: tumor


title: 7294_P4_LG

type: genomic

city: nottingham

first: Rachel

last: Clifford

address: Biodiscovery Institute 3

institute: University of Nottingham

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: fun2norm normalized average beta

label: Cy3, Cy5

source_name: Parenchymal Fibroblast

label_protocol: Not provided

growth_protocol: Grown to confluence, serum starved for 24 hours and then collected

extract_protocol: Qiagen AllPrep kit

treatment_protocol: Basal

value: Parenchymal Fibroblast

tag: disease

value: Asthmatic

tag: smoking status

value: Non

tag: passage

value: F


title: Bacteroides ovatus 3_1_23 mucin O-linked glycans 1

tag: carbon source


title: SW872 Empty Vector replicate 3 redo (atacseq)

description:
accessible DNA
SW872_EV_3redo


title: 7229_P4_LG


title: 7240_LG_P4


title: 7218_lg_p4


title: SW872 CAMTA1 replicate 3 (atacseq)

description:
accessible DNA
SW872_CAMTA1_3


title: 7298_br_p5

source_name: Airway Fibroblast

value: Airway Fibroblast


title: 2019_CSF

city: Madison

first: Ziyue

last: Wang

state: WI

address: 425 Henry Mall

institute: UW Madison

data_processing:
bcl2fastq-1.8.4 software was used for basecalling
Sequencing reads were mapped to the mm10 genome using the short-read aligner Bowtie v1.0.0 (Langmead et al., 2009)
The transcript expected countx were estimated using RSEM v1.2.7 (Li et al., 2011) with parameters -p 5 and then normalized by the size of the library using EBSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expected count values for each sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: cd11b+ cells enriched from half brain hemispheres

extract_protocol:
Mice (ages p14 or p15) were perfused with PBS following a fatal dose of pentobarbital sodium. Brains were isolated and bisected sagittally. Left brain hemispheres were formalin fixed for other studies and microglia were enriched from the right hemisphere by pull down utilizing CD11b-conjugated magnetic beads (Miltenyi Biotech) using published methods with the Percoll method for myelin removal (Nikodemova et al; PMCID: 4297717). Cell pellets were suspended in TRIzol (Thermo Fisher) and RNA was purified using the TRIzol Plus Purification kit including an on-column DNAse digestion step (Thermo Fisher).
RNA quality and quantity was assayed with the RNA 6000 Pico Kit (Agilent) and Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher). Libraries for RNAseq were generated using the TruSeq RNA Library Prep Kit v2 (Illumina).

value: CSF1 over-expression (C57Bl/6 X CD1 F1)

value: p14 or p15


title: 1936_CSF


title: SW872 Empty Vector replicate 2 (atacseq)

description:
accessible DNA
SW872_EV_2


title: 7291_lg_p4


title: 7294_BR_P4


title: Bacteroides ovatus 3_1_23 glucose 2

value: glucose


title: 7298_LG_P5


title: 7232_lg_p4

value: Current


title: 1932_CSF

value: brain


title: SW872 CAMTA1 replicate 2 (atacseq)

description:
accessible DNA
SW872_CAMTA1_2


title: 7232_BR_P4


title: SCoV_XL1_Exp2

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Sequencing reads were trimmed using a custom python script to identify a 10 bp UMI in R2
Trimmed reads were aligned with bwa. UMI-aware PCR duplicates were removed using picard tools.
Per-base coverages were determined using bedtools
Genome_build: NC_045512.2
Supplementary_files_format_and_content: Read count abundances per position in the virus reference genome

source_name: SARS-CoV-2 infected HUH-7 cell line

growth_protocol: We maintained HuH-7 cells in DMEM media (Thermo Fisher Scientific) supplemented with 10% heat-inactivated FBS (Thermo Fisher Scientific), and 100 units/ml streptomycin and 100 mg/ml penicillin. Cells were grown at 37°C and 5% CO2 atmosphere.

extract_protocol:
Following UV crosslinking, cells were then lysed on the tissue culture plate by adding 1 ml of RAP lysis buffer (10 mM Tris pH 7.5, 500 mM LiCl, 0.5% dodecyl maltoside (DDM), 0.2% sodium dodecyl sulphate (SDS), 0.1% sodium deoxycholate, EDTA-free Protease Inhibitor Cocktail (Thermo Fisher Scientific) and Murine RNase Inhibitor (New England Biolabs)). Lysates were then collected and flash-frozen in liquid nitrogen for storage at -80°C. RAP-MS was carried out as described in Munschauer et al., Nature (2018). eCLIP and sequencing of crosslinked RNA fragments of RAP-MS purified proteins were carried out as described in the methods section of our manuscript "A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells".
eCLIP-seq (Nostrand et al. Nature Methods (2016)).

treatment_protocol: SARS-CoV-2 infection of HuH-7 cells was carried out with an MOI of 10 for 24 hours. Cells were washed once with PBS and then crosslinked on ice using 0.8 J/cm2 of 254 nm UV light in a GS Gene Linker (Bio-Rad).

tag: antibody

tag: target

value: SARS-CoV-2 genome

tag: agent


title: Bacteroides ovatus 3_1_23 glucose 1


title: 7240_br_p4

tag: tissue


title: 1874_CO

value: Control for CSF1 over-expression (C57Bl/6 X CD1 F1)


title: 1931_CSF


title: SCoV_XL2_Exp2

tag: cell line


title: 1934_CO


title: RMRP_XL1_Exp2

value: RMRP


title: H3K4me3_ChIP

city: Detroit

first: Allison

middle: V

last: Mitchell

address: 4100 John R Rd

department: Oncology

institute: Wayne State University

data_processing:
Read aligment using Bowtie2 (Galaxy Version 2.3.2.2).
Enriched ChIP peaks were called using MACS2 (Galaxy Version 2.1.1.20160309.0)vwith the mapped input DNA reads as the background control. FDR (q-value) was set to 0.001. Peaks that were detected in both the replicate ChIP samples were utilized for downstream analysis.
RNA seq: The count abundance was estimated using RSEM and the differential expression analysis was done using EdgeR v3.12.1 in the Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files include all differentially expressed genes identfied by RNA-seq of HMLE/FOXQ1 and HMLE/LACZ cells. Alignment of the differentially expressed gene promoter regions (+/- 10kb of TSS) as bed files with the FOXQ1 and RbBP5 ChIP-seq binidng peaks (bed) revealed gene targets under direct transcriptional regulation. Direct gene targets with FOXQ1 bound within the promoter are included (FOXQ1_DEGtargets.csv) with the differential expression p-value and fold change from EdgeR.  Direct gene targets that were bound by both FOXQ1 and RbBP5 within the promoter are included (FOXQ1_RbBP5_DEGtargets.csv) with the differential expression p-value and fold change from EdgeR.

source_name: HMLE/FOXQ1 cells

growth_protocol: Human mammary epithelial (HMLE) cells were obtain from Dr. Robert Weinbergs lab at MIT and cultured in 50:50 DMEM/F12 media (HyClone) containing 10% FBS, 1% pen/strep, EGF (10µg/L), insulin (10µg/L) and hydrocotrisol (500ng/L). HMLE cells were subject to lentiviral transduction of human FOXQ1 gene or LACZ vector control and maintained under 10µg/mL blasticidin.

extract_protocol:
Cells were harvested, fixed in 1% formaldhyde and sonicated to shear chromatin. DNA-protein complexes were harvested by antibodies.
DNA ends were repaired by the Epicentre End-IT DNA End-Repair Kit (Lucigen, ER0720) followed by addition of poly A tail and ligation of custom Illumina adapters. PCR was performed using Phusion High Fidelity PCR master mix. Libraries were sequenced on Illumina HiSeq4000, single-end 50 bp platform according to manufacture's protocol.

value: human mammary luminal epithelial cells

tag: stable expression

tag: chip antibody

value: H3K4me3( EMD Millipore, 17-614)


title: 7188_lg_p4_R


title: SCoV_XL3_Exp1


title: 1872_CO

tag: strain


title: 7229_BR_P4


title: SW872 CAMTA1 replicate 1 (atacseq)

city: Iowa City

first: Michael

last: Chimenti

address: 431 Newton Road

institute: University of Iowa

description:
accessible DNA
SW872_CAMTA1_1

value: SW872 liposarcoma cells


title: primary mesangial cells, KO379_B_IP_rnaseq

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

data_processing:
Illumina Casava1.18.64 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using TopHat run (v2.0.14) with Bowtie version 2.1.0.1 with default parameter settings
Gene-levels count for each mm10 RefSeq genes are summarized  using HTseq-count  version 0.6.0 with settings -s reverse (strand-specific) and -a 10 (filteration of poor alignment reads).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file containing raw reads count for each gene

source_name: kidney glomerular mesngial cells

growth_protocol: Roswell Park Memorial Institute medium (RPMI) 1640 medium supplemented with 10% foetal bovine serum

extract_protocol:
Qiagen Rneasy spin columns  and/or phenol/chloroform extraction and ethanol precipitation, Immunoprecipitated with Ago2 antibody (Wako, Japan)
Nature communications 7, 12864, (2016). Cell 153, 654-665, (2013). Nature Methods 13, 508, (2016).
Nature communications 7, 12864, (2016). Cell 153, 654-665, (2013). Nature Methods 13, 508, (2016).

treatment_protocol: No treatment

value: miR-379 knockout (KO)

value: C57BL/6J (Jackson lab)

tag: cell type

value: kidney glomerular mesngial cells

tag: rip antibody

value: Ago2 antibody (Wako, Japan)


title: RMRP_XL2_Exp2


title: input_DNA

extract_protocol:
Cells were harvested, fixed in 1% formaldhyde and sonicated to shear chromatin. DNA was purified.
DNA ends were repaired by the Epicentre End-IT DNA End-Repair Kit (Lucigen, ER0720) followed by addition of poly A tail and ligation of custom Illumina adapters. PCR was performed using Phusion High Fidelity PCR master mix. Libraries were sequenced on Illumina HiSeq4000, single-end 50 bp platform according to manufacture's protocol.


title: primary mesangial cells, KO379_A_IP_rnaseq

tag: genotype


title: 1827_CO

tag: age


title: K562_CRISPR_IGF1KO_rep2_RNAseq

city: Singapore

first: Melissa

last: Fullwood

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description:
K562 cells with CRISPR/Cas9 vector targeting a distal interacting regions of IGF2 with high H3K27me3 signal (MRR2-A1).
RHK151

data_processing:
ChIP-seq reads of H3K27me3, H3K27ac and H3K4me3 from HAP1 WT and EZH2  KO cells were mapped by BOWTIE2(v2.2.5) using default parameters in  paired-end mode. We filtered out alignments with mapq scores smaller than 30. The  two replicates were combined and peaks and bigWig files were generated  by MACS2(2.1.0.20150731) using option '-q 0.01' for H3K27ac and  H3K4me3 and '--broad --broad-cutoff 0.1 -q 0.05' for H3K27me3.
For the RNA-seq reads of HAP1 EZH2KO/WT and K562 GSK343/DMSO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For 4C reads, we trimmed off the HINDIII digestion site using tagdust(2.33). The remaining read 1s were mapped by BOWTIE2(v2.2.5) with option '--end-to-end' in single-end mode. r3Cseq(1.24.0) was used to call interactions against the HINDIII digested genome background in hg19.
Genome_build: hg19
Supplementary_files_format_and_content:
*.narrowPeak: ENCODE narrowPeak format generated by MACS2.
*.broadPeak: ENCODE broadPeak format generated by MACS2.
*_abundance.tsv: *_abundances.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
*interaction.txt: *.interaction.txt is the output generated by R3Cseq package. Field contained: 1. chromosome. Chromosome name; 2. start. Start of the fragment; 3. end. End of the fragment; 4. nReads. Number of reads mapped to this fragment; 5. RPMs. Reads per million per restriction fragment (RPM) as normalized interaction frequency values; 6. p.value. P value of this fragment interact with the 4C bait; 7. q.value. Q value of this fragment interact with the 4C bait.

source_name: K562 cells with CRISPR/Cas9 vector targeting MRR2-A1 region

growth_protocol: Cell cultures were maintained at 37 °C, 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen), with on-column DNase I treatment (Qiagen). The quality of the RNA extracted was checked using Agilent RNA 6000 Nano Kit (Agilent), and quantitated using Nanodrop ND1000 (Thermo Scientific).
850ng of RNA was used for the construction of cDNA library for Illumina HiSeq 2500 High Output v4 NGS sequencing using TruSeq Stranded Total RNA LT (w/ Ribo- Zero Gold) Set A (Illumina) as per protocol.

treatment_protocol: The plasmid construct was then electroporated into the K562 cell line using the Amaxa Nucleofector Kit V (Lonza). After 48 hours, transfected cells emitting GFP fluorescence due to uptake of construct were FACS sorted into 96-well plates as single cell colonies and cultured in 5% CO2 incubator.

tag: cell line background

tag: treatment


title: 7218_BR_P5

tag: disease

value: Asthmatic

tag: smoking status

value: Non

tag: Sex

value: M


title: primary mesangial cells, WT_B_IP_rnaseq

value: Wild type


title: SCoV_XL2_Exp1

tag: antibody


title: primary mesangial cells, WT_A_IP_rnaseq


title: FOXQ1_ChIP

value: V5 (invitrogen, 46-0705)


title: RbBP5_ChIP

value: RbBP5 (Bethyl Labs, A300-109A)


title: primary mesangial cells, KO379_A_rnaseq


title: K562_CRISPR_IGF1KO_rep1_RNAseq

description:
K562 cells with CRISPR/Cas9 vector targeting a distal interacting regions of IGF2 with high H3K27me3 signal (MRR2-A1).
RHK150

value: CRISPR/Cas9 vector targeting MRR2-A1 region


title: 7188_br_p4

value: Airway Fibroblast

value: Current

tag: passage

value: F


title: K562_CRISPR_EV_rep2_RNAseq

description:
K562 transfected with empty vector.
RHK141

source_name: K562 cells with empty vector

value: empty vector


title: K562_CRISPR_FGF1KO_rep2_RNAseq

description:
K562 cells with CRISPR/Cas9 vector targeting a distal interacting regions of FGF18 with high H3K27me3 signal (MRR1-A1).
RHK155

source_name: K562 cells with CRISPR/Cas9 vector targeting MRR1-A1 region


title: primary mesangial cells, KO379_B_rnaseq


title: HAF147

value: Healthy

value: Ex


title: 7291_br_p4


title: Lung_403_Low_Day180_rep5

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, Low, Day 180, replicate 5

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing:
Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)
Data were normalized by shift to 75.0 percentile and filtered by flags and by expression based on the signal intensity values (to remove very low signal values and those that have reached saturation)

organism: Rattus norvegicus

source_name: Rat, Lung, NM-403, Low, Day 180

label_protocol: For each of the 72 samples (6 control, 6 exposed rats to low dose and 6 exposed rats to high dose per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation  6 hours/day, 5 days/week for 4 weeks to two doses of NM-403 carbon nanotube.

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

value: female

value: 13 weeks-old (at the onset of inhalation)

tag: dose

value: Low

tag: time

value: Day 180


title: K562_CRISPR_FGF1KO_rep1_RNAseq

description:
K562 cells with CRISPR/Cas9 vector targeting a distal interacting regions of FGF18 with high H3K27me3 signal (MRR1-A1).
RHK154

value: CRISPR/Cas9 vector targeting MRR1-A1 region


title: Lung_403_Low_Day180_rep4

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, Low, Day 180, replicate 4

tag: tissue


title: Lung_403_Low_Day180_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, Low, Day 180, replicate 6


title: 7016_BR_P4

value: Asthmatic

value: Non


title: HAF146


title: HAF091

value: M


title: 1μMGSK343treatment_K562_GSK343_rep2_techRep3_RNASeq

description:
Biological replicate 2, technical replicate 3.
RHO1302_GTGAAA_S6_L007

source_name: K562 cells treated with 1μM GSK343

treatment_protocol: Small molecular inhibitor GSK343 (Sigma-Aldrich) targeting EZH2 were solubilized in DMSO (Sigma-Aldrich) according to manufacturer’s instructions and used at a final concentration of 1μM. K562 cells with GSK343 were incubated at 37 °C, 5% CO2 humidified incubator for 48 hours before harvesting for various experiments.

value: 1uM GSK343


title: Lung_403_Low_Day180_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, Low, Day 180, replicate 3


title: primary mesangial cells, KO379_B_CLASH_seq

data_processing:
Illumina Casava1.18.64 software used for basecalling.
Paired-end raw sequenced reads were merged using pear v0.9.5 with parameter setting -n 30 -p 1.0, then removed any merged reads which could be alilgned  to mouse whole genome (GRCm38.p5) or RNA transcripts (GENCODE vM13) using Bowtie2 (v2.1.0) on paired-end readswith  parameter settings --very-sensitive --no-unal -p 16 .
Searched mature miRNA  location on merged reads using blanstn program in blastallv2.2.26 against mature miRNA database (miRbase release 21) with parameters -e 10 -S 3 -W 7 -m 8
Searched for mRNA sequences location on merged reads using blastn program in blastall v2.2.16 against mRNA sequences (GENCODE vM13) with parameter -e 0.1 -S 3 -W 7 -m 8
Identified chimeric reads  from the merged reads which satisfy 1) partially aligned to mature miRNA and mRNA; and 2) the aligned regions are not overlapped.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file for each identified chimeric reads, each with the location of miRNA and mRNA.

extract_protocol:
Qiagen Rneasy spin columns  and/or phenol/chloroform extraction and ethanol precipitation, Immunoprecipitated with Ago2 antibody (Wako, Japan), ligated by T4 RNA ligase (NEB),
Nature communications 7, 12864, (2016). Cell 153, 654-665, (2013). Nature Methods 13, 508, (2016).
Nature communications 7, 12864, (2016). Cell 153, 654-665, (2013). Nature Methods 13, 508, (2016).

value: miR-379 knockout (KO)

value: C57BL/6J (Jackson lab)

value: Ago2 (Wako, Japan)

tag: ligation

value: T4 RNA ligase (NEB)

value: kidney glomerular mesangial cells


title: K562_CRISPR_EV_rep1_RNAseq

description:
K562 transfected with empty vector.
RHK140

value: empty vector


title: Lung_403_High_Day180_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, High, Day 180, replicate 6

source_name: Rat, Lung, NM-403, High, Day 180

tag: strain

value: Sprague Dawley

value: High


title: primary mesangial cells, WT_A_rnaseq

value: Wild type

tag: cell type

value: kidney glomerular mesngial cells


title: Lung_403_Low_Day180_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, Low, Day 180, replicate 1

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Low


title: HAF073

value: Airway Fibroblast

value: Healthy

value: Ex

value: F


title: 1μMGSK343treatment_K562_GSK343_rep1_techRep3_RNASeq

description:
Biological replicate 1, technical replicate 3.
RHO1301_CTTGTA_S4_L007

value: 1uM GSK343


title: primary mesangial cells, KO379_A_CLASH_seq

value: miR-379 knockout (KO)

value: C57BL/6J (Jackson lab)

tag: rip antibody

value: Ago2 (Wako, Japan)


title: 1μMGSK343treatment_K562_GSK343_rep3_techRep3_RNASeq

description:
Biological replicate 3, technical replicate 3.
RHO1303_AGTCAA_S5_L007


title: HAF082

value: Non


title: HAF090


title: HAF074


title: Lung_403_High_Day180_rep4

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, High, Day 180, replicate 4

value: Sprague Dawley

value: Day 180


title: HAF071

value: M


title: primary mesangial cells, WT_B_CLASH_seq

tag: genotype

value: Wild type

value: T4 RNA ligase (NEB)

value: kidney glomerular mesangial cells


title: 1μMGSK343treatment_K562_GSK343_rep3_techRep2_RNASeq

description:
Biological replicate 3, technical replicate 2.
RHO1297_AGTCAA_S5_L006


title: primary mesangial cells, WT_A_CLASH_seq


title: Hepatocytes, M1_24h_uninf_Dual

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated Fastq files were mapped against the mm9 mouse reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition

source_name: hepatocytes

extract_protocol:
Total RNA from cells was extracted using a NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: sirna treatment

value: Cd302 & Cr1l

tag: infection

value: Uninfected

tag: mouse strain

value: hOChep

tag: mouse id

value: hepatocytes


title: T05_12043_P4

value: Parenchymal Fibroblast

tag: disease

value: Healthy

tag: smoking status

value: Ex

tag: age


title: T032423_P4

tag: passage

tag: Sex


title: Lung_403_Low_Day180_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, Low, Day 180, replicate 2

value: accessory lobe of lung

tag: gender

value: female

value: 13 weeks-old (at the onset of inhalation)

tag: treatment

tag: dose

value: Low


title: t05_3278_p4

tag: tissue

value: F


title: Hepatocytes, M1_24h_HCV_Dual

value: HCV MOI 1


title: 1μMGSK343treatment_K562_GSK343_rep2_techRep2_RNASeq

description:
Biological replicate 2, technical replicate 2.
RHO1296_GTGAAA_S6_L006

tag: cell line background

value: 1uM GSK343


title: 1μMGSK343treatment_K562_GSK343_rep1_techRep2_RNASeq

description:
Biological replicate 1, technical replicate 2.
RHO1295_CTTGTA_S4_L006


title: Hepatocytes, M1_24h_uninf_control

value: control

tag: cell type


title: Hepatocytes, M1_24h_HCV_control


title: 1μMGSK343treatment_K562_GSK343_rep3_techRep1_RNASeq

description:
Biological replicate 3, technical replicate 1.
RHO1291_AGTCAA_S5_L005


title: Lung_403_High_Day180_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, High, Day 180, replicate 3

tag: strain

value: Sprague Dawley

value: High

tag: time

value: Day 180


title: 1μMGSK343treatment_K562_GSK343_rep1_techRep1_RNASeq

description:
Biological replicate 1, technical replicate 1.
RHO1289_CTTGTA_S4_L005


title: Lung_403_High_Day180_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, High, Day 180, replicate 2


title: 1μMGSK343treatment_K562_GSK343_rep2_techRep1_RNASeq

description:
Biological replicate 2, technical replicate 1.
RHO1290_GTGAAA_S6_L005


title: Hepatocytes, M3_78_S5_L001_R1_001

tag: sirna treatment

value: Cd302 & Cr1l

value: WT


title: L6


title: Lung_403_Control_Day180_rep4

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-403, Control, Day 180, replicate 4

source_name: Rat, Lung, NM-403, Control, Day 180

value: Control


title: Lung_403_High_Day180_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, High, Day 180, replicate 1


title: Lung_403_Control_Day180_rep5

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-403, Control, Day 180, replicate 5


title: 1μMGSK343treatment_K562_DMSO_rep2_techRep3_RNASeq

description:
Biological replicate 2, technical replicate 3.
RHO1299_ACAGTG_S2_L007

source_name: K562 cells treated with DMSO

treatment_protocol: K562 cells with DMSO vehicle control were incubated at 37 °C, 5% CO2 humidified incubator for 48 hours before harvesting for various experiments.

value: DMSO


title: Lung_403_Control_Day180_rep6

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-403, Control, Day 180, replicate 6


title: Hepatocytes, M3_34_S4_L001_R1_001

tag: infection

value: hepatocytes


title: 1μMGSK343treatment_K562_DMSO_rep1_techRep3_RNASeq

description:
Biological replicate 1, technical replicate 3.
RHO1298_CGATGT_S1_L007


title: L8

value: Parenchymal Fibroblast

value: Healthy

value: Ex

value: M


title: T03_3445_P4


title: Lung_403_Control_Day180_rep3

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-403, Control, Day 180, replicate 3

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)


title: Lung_403_Control_Day180_rep2

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-403, Control, Day 180, replicate 2


title: Lung_403_Control_Day180_rep1

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-403, Control, Day 180, replicate 1


title: L23L

value: Non

value: F


title: Hepatocytes, M3_12_S3_L001_R1_001

value: control

value: Uninfected

tag: mouse strain


title: 1μMGSK343treatment_K562_DMSO_rep3_techRep3_RNASeq

description:
Biological replicate 3, technical replicate 3.
RHO1300_CAGATC_S3_L007


title: Hepatocytes, M3_56_S5_L001_R1_001

tag: mouse id


title: 1μMGSK343treatment_K562_DMSO_rep3_techRep2_RNASeq

description:
Biological replicate 3, technical replicate 2.
RHO1294_CAGATC_S3_L006


title: Hepatocytes, M2_56_S1_L001_R1_001

value: hOChep


title: primary mesangial cells, WT_B_rnaseq

tag: genotype

value: Wild type

value: C57BL/6J (Jackson lab)

value: kidney glomerular mesngial cells


title: 1μMGSK343treatment_K562_DMSO_rep2_techRep2_RNASeq

description:
Biological replicate 2, technical replicate 2.
RHO1293_ACAGTG_S2_L006

value: DMSO


title: Hepatocytes, M2_12_S44_L002_R1_001

value: hepatocytes


title: Hepatocytes, M2_34_S15_L002_R1_001

value: HCV MOI 1


title: Hepatocytes, M2_78_S2_L001_R1_001

value: Cd302 & Cr1l


title: 1μMGSK343treatment_K562_DMSO_rep1_techRep2_RNASeq

description:
Biological replicate 1, technical replicate 2.
RHO1292_CGATGT_S1_L006


title: 1μMGSK343treatment_K562_DMSO_rep3_techRep1_RNASeq

description:
Biological replicate 3, technical replicate 1.
RHO1288_CAGATC_S3_L005


title: CU037N

city: Cheras

first: Elena

middle: AB

last: Azizan

state: Wilayah Persekutuan Kuala Lumpur

address: PPUKM, Jalan Yaacob Latif, Bandar Tun Razak

department: Department of Medicine

country: Malaysia

institute: The National University of Malaysia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were visualized and extracted with the GenomeStudio data analysis software (version 2009.2; Illumina) with Illumina’s default analysis settings.

source_name: Cushing

label_protocol: Each RNA sample (total RNA, 1  g) was converted to cDNAby reverse transcription and subjected to labeling and hybridization using the whole-genome cDNA mediated annealing, selection, extension, and ligation (DASL) assay (Illumina HumanRef-8 version 3 Expression BeadChip; Illumina, San Diego, CA).

extract_protocol: Approximately 0.125 cm3 of tissue was used for RNA extraction.  Total RNA was isolated from AAG and APA using  Trizol with a PureLink kit (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. On-column deoxyribonuclease treatment was performed on all RNA samples.

value: Adrenal

tag: sentrix position

value: H

tag: chip no


title: L2

value: Parenchymal Fibroblast

tag: disease

value: Healthy

tag: smoking status

tag: passage

tag: age


title: L14

value: Ex

tag: Sex

value: M


title: Lung_403_Low_Day90_rep4

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, Low, Day 90, replicate 4

source_name: Rat, Lung, NM-403, Low, Day 90

value: Sprague Dawley

tag: tissue

value: accessory lobe of lung

tag: gender

value: female

value: 13 weeks-old (at the onset of inhalation)

tag: treatment

tag: dose

value: Low

value: Day 90


title: Lung_403_Low_Day90_rep5

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, Low, Day 90, replicate 5

tag: strain

tag: time


title: CN059N

source_name: AAG

value: F


title: CN059C

source_name: APA

value: E


title: Hepatocytes, M1_78_S43_L002_R1_001

tag: sirna treatment

tag: infection

value: hOChep

tag: cell type

value: hepatocytes


title: CH040N

value: D


title: CH040C

value: Adrenal

value: C


title: 1μMGSK343treatment_K562_DMSO_rep1_techRep1_RNASeq

description:
Biological replicate 1, technical replicate 1.
RHO1286_CGATGT_S1_L005

tag: cell line background

value: DMSO


title: Lung_403_Low_Day90_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, Low, Day 90, replicate 2


title: L12

source_name: Parenchymal Fibroblast

value: Parenchymal Fibroblast

value: Healthy


title: Hepatocytes, M1_56_S42_L002_R1_001

value: Cd302 & Cr1l

value: Uninfected

tag: mouse strain

tag: mouse id


title: CU024N

tag: sentrix position

value: G

tag: chip no


title: ham007_p4

tag: disease

tag: smoking status

value: Current

tag: passage


title: HAM011

tag: tissue

tag: Sex

value: M

tag: age


title: Hepatocytes, M1_34_S41_L002_R1_001

value: control

value: HCV MOI 1


title: 1μMGSK343treatment_K562_DMSO_rep2_techRep1_RNASeq

description:
Biological replicate 2, technical replicate 1.
RHO1287_ACAGTG_S2_L005

tag: treatment


title: HAM020_lg


title: HAP1_EZH2KO_rep2_RNASeq

source_name: HAP1 EZH2 KO cells

value: HAP1 EZH2 knock-out cells purchased from Horizon

tag: genotype/variation

value: EZH2 knock-out


title: HAP1_EZH2KO_rep1_RNASeq


title: Lung_403_High_Day90_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, High, Day 90, replicate 6

source_name: Rat, Lung, NM-403, High, Day 90

tag: strain

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

value: female

value: 13 weeks-old (at the onset of inhalation)

tag: dose

value: High

tag: time

value: Day 90


title: Lung_403_High_Day180_rep5

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-403, High, Day 180, replicate 5

value: Day 180


title: CH018C

value: Adrenal

value: A


title: Lung_403_Low_Day90_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, Low, Day 90, replicate 3

value: Low


title: ham006_p4

value: Parenchymal Fibroblast

value: Healthy

value: Ex

value: F


title: Liver, TL3

source_name: total liver

extract_protocol:
Total RNA from total liver was extracted using a NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: donor mouse

value: BALB/c

value: liver


title: HAP1_WT_rep2_RNASeq

source_name: HAP1 wildtype cells

tag: cell line background

tag: cell type

value: haploid human cell line that was derived from KBM7 cells (purchased from Horizon)


title: Hepatocytes, M1_12_S40_L002_R1_001

tag: sirna treatment

value: control

tag: infection

value: Uninfected

tag: mouse strain

value: hOChep

tag: mouse id

value: hepatocytes


title: Lung_403_Low_Day90_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, Low, Day 90, replicate 1

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)


title: CH018N

value: Adrenal

tag: sentrix position

value: B

tag: chip no


title: PH073N

source_name: Phaeochromocytoma

tag: tissue

value: H


title: HAP1_WT_rep1_RNASeq


title: ham001_p4

value: Parenchymal Fibroblast

tag: disease

value: Healthy

tag: smoking status

value: Current

tag: passage

tag: Sex

tag: age


title: Liver, TL2


title: Liver, TL1

value: FVB/NJ


title: HAP1_EZH2KO_rep2_IgG_ChIPSeq

extract_protocol:
5 million cells per ChIP was harvested, washed twice and resuspended in PBS. The cells were crosslinked with 1% methanol-free formaldehyde (Thermo Scientific) at room temperature for 10 minutes, followed by quenching with glycine for 5 minutes at room temperature. The cell pellet was washed with twice with PBS supplemented with 1mM PMSF (Sigma). The fixed cell pellet was lysed in 1% SDS lysis buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 1% SDS) supplemented with protease inhibitor cocktail tablet (Roche), and sonicated using Bioruptor (Diagenode) and 200-500bp DNA fragments were achieved. The cell lysate was cleared through centrifugation at 13,200rpm for 35 minutes at 4°C. 9 volumes of dilution buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate) was added to the lysate to achieve 0.1% SDS lysis buffer, and the precleared through incubation with Protein G Dynabeads (Invitrogen) overnight at 4°C, with rotation. Antibody-conjugated beads were prepared by incubating 3.5ug antibody in 15uL Protein G Dynabeads in 50uL wash buffer (PBS, 0.1% Triton X-100) overnight at 4°C, with rotation. The precleared lysate was added into the prepared antibody-conjugated beads, and was incubated overnight at 4°C, with rotation. The beads were washed thrice in 0.1% SDS lysis buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS), once in high salt wash buffer (50 mM HEPES pH 7.5, 350 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS), once in lithium chloride wash buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Igepal- CA-630, 0.5% Sodium Deoxycholate), and once in TE buffer. The beads were then eluted in elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS), treated with RNase A (Qiagen) with 55°C for 30 minutes, and decrosslinked with Proteinase K (Ambion) at 37°C overnight. ChIP DNA was cleaned up with QIAquick PCR purification kit (Qiagen), and quantitated using Qubit High Sensitivity dsDNA Assay (Invitrogen).
1ng of ChIP DNA was used for the construction of DNA library for Illumina HiSeq 4000 NGS sequencing using ThruPLEX DNA-seq 48D Kit (Rubicon) as per protocol. Final libraries were quantitated and pooled at the same molarity using Agilent High Sensitivity DNA Kit (Agilent).

value: HAP1 EZH2 knock-out cells purchased from Horizon

tag: genotype/variation

value: EZH2 knock-out

tag: chip antibody

value: mouse IgG (#sc-2025, Santa Cruz)


title: HAP1_EZH2KO_rep1_IgG_ChIPSeq


title: Hepatocytes, PMH3

tag: donor mouse

value: BALB/c


title: HAP1_EZH2KO_H3K4me3_rep2_ChIPSeq

description:
CHH48014
processed data file: HAP1_EZH2KO_H3K4me3_peaks.narrowPeak

tag: cell line background

value: H3K4em3  (#ab8580, Abcam)


title: PH068N

value: G


title: Hepatocytes, PMH2

tag: cell type

value: hepatocytes


title: Lung_403_High_Day90_rep5

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, High, Day 90, replicate 5

tag: strain

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

tag: treatment

tag: dose

value: High

tag: time

value: Day 90


title: Lung_403_High_Day90_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, High, Day 90, replicate 2

value: female

value: 13 weeks-old (at the onset of inhalation)


title: HAP1_EZH2KO_H3K27me3_rep1_ChIPSeq

description:
CHH48012
processed data file: HAP1_EZH2KO_H3K27me3_peaks.broadPeak

value: H3K27me3  (C36B11, Cell Signaling Technologies)


title: Lung_403_High_Day90_rep4

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, High, Day 90, replicate 4


title: HAP1_EZH2KO_H3K4me3_rep1_ChIPSeq

description:
CHH48010
processed data file: HAP1_EZH2KO_H3K4me3_peaks.narrowPeak


title: FM2

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: Microglia was treated with 100 uM Formaldehyde (FM) for 2 hours

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
We trimmed the adapter sequences (TruSeq™ index adapter with option “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC”, and the reverse complementary sequence of TruSeq™ universal adapter with the option “-a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT”) by applying the cutadapter software
The remained reads were then aligned to the Mus musclus genome (GRCm38.89) with STAR (2.5.3a) by with default option. The aligned reads were assembled into genes by calculating read count with HTSeq (0.6.1). Then, TMM normalization method was conducted using EdgeR (3.12.1).
Genome_build: Mus musclus genome (GRCm38.89)
Supplementary_files_format_and_content: tab-delimited text files including TMM normalized count for each sample.

source_name: Primary microglia cell

growth_protocol: Streptococcus pneumoniae were cultured in sterilized Todd-Hewitt media containing 30 g of Todd Hewitt Broth, 0.5% Yeast extract, and 1.5% Agar per liter. Subsequently, the pneumococcus grown on THY agar plate was transferred into THY broth. The transferred pneumococci were cultured at 37°C incubator for 24~48 hours until OD550 = 0.3 to a concentration of 108 CFU/ml and used to infect cells at MOI=100 for 2 hours. Seperation of the pellets and supernatants is done by centrifugation at 4,000 ×  g at 4°C for 10 min.

extract_protocol:
Total RNA was extracted from primary microglia with Trizol reagent (Invitrogen) and contaminating DNA was depleted with clearance procedure according to the manufacturer's protocol with Riboclear™  plus (GeneAll).
Full length cDNA was generated following manufacturers recommended protocols of the SMARTer-Seq v4 Ultra Low input RNA Kit for sequencing (Clontech, 634888). First-strand cDNA synthesis was initiated by adding 1 μl of 3’ SMART CDS primer II A at 72℃ for 3 min from 10 ng of total RNA. The second strands were synthesis by adding SMARTer-seq v4 oligo and SMARTScribe reverse transcriptase, and the reaction was incubated at 42℃ for 90 min, followed by inactivation at 70℃ for 10 min. Double-strand cDNA was amplified by PCR for 8 cycles and purified using Agencourt AMPure beads(Beckman, A63881).   mRNA-seq library is was generated following manufacturers recommended protocols of the Nextera XT DNA library preparation kit (illumina, FC-131-1024). The cDNA was subjected to tagmentation (simultaneous fragmentation and tagging with sequencing adapters) and amplified by PCR using Index Primers from the Nextera XT DNA Index Kit (Illumina, FC-131-1001). After PCR, the DNA library was purified using AMPure beads and the quality was assessed using an Agilent 2100 Bioanalyzer.  The DNA libraries from individual samples were quantified using KAPA Library Quantification kit (KAPA biosystems, KK4854) followed by pooling. All libraries were sequenced on an illumina Hiseq2500 instrument to generate dual indexed 100 bp paired reads, generating an average 58 million reads for each sample.

treatment_protocol: In each sample condition, microglia was treated with condition specific molecules for 2 hours.

tag: developmental stage

value: Mouse cortex

value: Primary microglia cell

value: Formaldehyde (FM)


title: HYP063N

source_name: Hyperplastic Adrenal

tag: tissue

value: Adrenal

tag: sentrix position

value: E

tag: chip no


title: PH066N

value: F


title: Lung_403_Control_Day90_rep6

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-403, Control, Day 90, replicate 6

source_name: Rat, Lung, NM-403, Control, Day 90

value: control

value: Control


title: Lung_403_Control_Day90_rep5

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-403, Control, Day 90, replicate 5


title: CN067N

value: D


title: 2-PF2

description: Microglia was treated with 100 uM 2-pentylfuran (2-PF) for 2 hours

value: 2-pentylfuran (2-PF)


title: HAP1_WT_rep2_IgG_ChIPSeq

value: haploid human cell line that was derived from KBM7 cells (purchased from Horizon)

value: mouse IgG (#sc-2025, Santa Cruz)


title: CN067C

value: C


title: CN032N

value: H


title: CN062C

value: A


title: Lung_403_High_Day90_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, High, Day 90, replicate 1

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)

value: High

value: Day 90


title: CN062N

value: Adrenal

value: B


title: HAP1_WT_rep1_IgG_ChIPSeq


title: HAP1_EZH2KO_H3K27me3_rep2_ChIPSeq

description:
CHH48016
processed data file: HAP1_EZH2KO_H3K27me3_peaks.broadPeak

value: HAP1 EZH2 knock-out cells purchased from Horizon

value: EZH2 knock-out

value: H3K27me3  (C36B11, Cell Signaling Technologies)


title: Hepatocytes, PMH1

tag: mouse strain

value: FVB/NJ

value: hepatocytes


title: Lung_403_Control_Day90_rep4

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-403, Control, Day 90, replicate 4

value: control

value: Control


title: CN032C

value: G


title: HAP1_WT_H3K27ac_rep2_ChIPSeq

description:
CHH48007
processed data file: HAP1_WT_H3K27ac_peaks.narrowPeak

value: haploid human cell line that was derived from KBM7 cells (purchased from Horizon)

value: H3K27ac  (#ab4729, Abcam)


title: FM1

value: Mouse cortex

value: Primary microglia cell

value: Formaldehyde (FM)


title: S.pneu3

description: Microglia was treated with MOI 100 S.pneumoniae (S.pneu) culture supernatant for 2 hours


title: 2-PF1

value: 2-pentylfuran (2-PF)


title: CH069C

value: F


title: Lung_403_Control_Day90_rep3

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-403, Control, Day 90, replicate 3

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Day 90


title: Lung_403_Control_Day90_rep1

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-403, Control, Day 90, replicate 1


title: Lung_403_Low_Day30_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, Low, Day 30, replicate 6

source_name: Rat, Lung, NM-403, Low, Day 30

value: Low

value: Day 30


title: S.pneu2

value: S.pneumoniae (S.pneu) culture supernatant


title: Lung_403_Control_Day90_rep2

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-403, Control, Day 90, replicate 2

value: control

value: Control


title: HAP1_WT_H3K27ac_rep1_ChIPSeq

description:
CHH48003
processed data file: HAP1_WT_H3K27ac_peaks.narrowPeak

value: haploid human cell line that was derived from KBM7 cells (purchased from Horizon)


title: HAP1_WT_H3K4me3_rep2_ChIPSeq

description:
CHH48006
processed data file: HAP1_WT_H3K4me3_peaks.narrowPeak

value: H3K4em3  (#ab8580, Abcam)


title: CH049N

value: Adrenal

value: E


title: HAP1_WT_H3K4me3_rep1_ChIPSeq

description:
CHH48002
processed data file: HAP1_WT_H3K4me3_peaks.narrowPeak


title: Vehicle2

description: Controls that did not treat anything on microglia

value: Mouse cortex

value: Primary microglia cell

value: no treatment


title: Vehicle3


title: Lung_403_Low_Day30_rep5

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, Low, Day 30, replicate 5

value: Sprague Dawley