title: Cx12-Plasma EV Healthy control

city: Mexico City

first: Diana

middle: Emilce

last: Alvarez Suarez

state: Mexico

address: Av cuautemoc 330

department: Unidad de Investigacion Medica Enf. Infecciosas

country: Mexico

institute: hospital de pediatria CMNSXXI

description: microRNA expression in human extraceular vesicules of healty controls.

hyb_protocol: Hybridization mix was added to labeled samples containing 2X hybridization mix, 27% formamide, DMSO and 20X hybridization control probes in nuclease free water. Each sample was introduced in to a GeneChip miRNA 4 array (Affymetrix 902411), hybridized at 48°C for 18 h. Each sample was washed in the GenChip Fluidics Station 450 following FS450-0002 protocol

scan_protocol: Array fluorescence was measured by the GeneChip Scanner 3000 7 G.

data_processing: Raw data from .cel files with fluorescence signals were analyzed using Affymetrix Expression Console software to normalize them and obtain quality control data. We used Robust Multichip Analysis (RMA) to adjust signal to noise ratio and to generate .chp files for further analysis. In .chp files two types of data were obtained for each probe or miRNA in the array: 1) detection call data, categorizing each miRNA as ‘present’ or ‘absent’ and 2) log2 intensity signal data.

label: Biotin

source_name: Human EV

label_protocol: RNA 150 ng was poly-A tailed and biotin incorporated in to tails with Flash Tag  biotin for miRNA microarrays (Affymetrix  901911), including an Enzyme Linked Oligosorbent Assay (ELOSA) to confirm biotin labeling according to manufacturer instructions

growth_protocol: without growth protocol

extract_protocol: Total RNA was isolated from 0.5 ml of each plasma sample and 100 microliters purified EVs using TRIzol reagent (Invitrogen 15596026), solubilized in nuclease free water and quantified using a Nanodrop

treatment_protocol: without treatment

tag: disease state

value: Healthy controls

value: EV


title: Cx10-Plasma EV Healthy control

status: Public on Mar 31 2020

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Ctrl_C1_LSD1i_24hr

city: Otsu

first: Goichi

last: Tatsumi

address: Seta Tsukinowa-cho

country: Japan

institute: Shiga University of Medical Science

description: Gene expression data from human erythroid leukemia (HEL) cell lines.

hyb_protocol: Following fragmentation, 5.5 ug of single stranded DNA was hybridized for 17 hr at 45C on GeneChip Human Gene 2.0 ST Arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Hybridized microarrays were scanned using an Affymetrix GeneChip Scanner.

data_processing: Images from scanned chips were processed by using the default settings of Affymetrix GeneChip Command Console (AGCC) software. The CEL files created by AGCC were imported into Affymetrix Expression Console software. Expression signals of all genes (probe sets) were calculated using the RMA algorithm (default settings), and obtained the CHP files.

label: biotin

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

growth_protocol: Human erythroid leukemia (HEL) cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin in 37C at 5% CO2.

extract_protocol: Total RNA was extracted by using an RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: HEL cells were cultured in the RPMI 1640 medium supplemented with a LSD1 inhibitor (NCD38) (2 microM) or vehicle (DMSO) for 24 hours.

tag: cell line

value: HEL

tag: cell type

value: Erythroleukemia cell line

tag: genotype/variation

value: Control

tag: treatment

value: LSD1i 24hr


title: PDX160403

type: SRA

city: New York

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Alignment was performed using STAR with default settings
The reference genome was hg19.
The gene counts were aligned by STAR 2.4.2.8 using HTSeq-counter
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: PDX primary culture

growth_protocol: Primary cultures for human GBM primary or PDX  tissues were established in SFM with EGF, FGF, PDGF-AA and NRG1 (10 ng/ml each).

extract_protocol:
Qiagen Rneasy Extraction kit
Manufactory Protocol

value: Glioblastoma PDX cell culture


title: Ctrl_C2_DMSO_24hr

value: DMSO 24hr


title: Cx9-Plasma EV Healthy control


title: Cx2-Plasma EV Healthy control


title: Ctrl_C5_DMSO_24hr


title: Cx3-Plasma EV Healthy control


title: Cx6-Plasma EV Healthy control


title: Cx4-Plasma EV Healthy control


title: Cx8-Plasma EV Healthy control


title: Ctrl_C5_LSD1i_24hr


title: Px12-Plasma EV Rb case

description: microRNA expression in human extraceular vesicules of patients with retinoblastoma.

value: Retinoblastoma


title: PDX160929


title: Cx1-Plasma EV Healthy control


title: Px11-Plasma EV Rb case


title: PDX160324


title: PDX160225


title: Ctrl_C1_DMSO_24hr


title: PDC1156

source_name: Patient derived primary cell

value: Glioblastoma cell culture


title: PDC12-224


title: Cx5-Plasma EV Healthy control


title: Junbfl/flCd4-Cre2

city: Tokyo

first: Takaharu

last: Katagiri

address: 5-21-16 Omori-Nishi,Ota-ku

department: Biochemistry

institute: Toho University School of Medicine

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent SureScan G4900DA Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Colon on the fifth day after drinking DSS

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Not applicable

extract_protocol: Total RNAs were extracted from the colon of mice of the indicated genotype using Trizol according to the manufacturer’s instructions

treatment_protocol: Not applicable

tag: strain

value: Whole colon

tag: genotype


title: PDC13-050


title: PDC12-178


title: Junbfl/flCd4-Cre1


title: Control1

value: Junbfl/fl


title: PDC12-095


title: Px9-Plasma EV Rb case


title: Control2


title: PDC12-111


title: DA_rep3

city: Braunschweig

first: Jasper

last: Schierstaedt

address: Messeweg 11-12

department: EP

country: Germany

institute: Julius kühn-Institute

data_processing:
To reveal transcriptional differences in S. Typhimurium 14028s exposed to the different media Illumina HiSeq sequencing were performed at the ZIEL - Institute for Food & Health, Core Facility Microbiome/NGS, Technische Universität München, Freising, Germany.
The sequence analyses were mapped to NC_003197.2 whole genome using Bowtie2 v0.6 with parameters -s -p -x -U -s -o
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1 with cufflinks parameters -I 1 -F 0.0 -j 0.0 -G, cuffmerge parameters -g cuffdiff parameters -FDR 0.05 -c 10 -library-norm-method geometric -dispersion-method pooled
Genome_build: NC_003197.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each treatment, fold change and significance levels

organism: Salmonella enterica

source_name: RNA from Salmonella grown in suspension of autoclaved DS soil

growth_protocol: Salmonella was grown overnight at 37°C in LB broth . The cells were pelleted at  (1500 x g, 10 min), washed twice in 10 mM MgCl2 and OD600 = 1 was prepared. Two mL of this suspension were pipetted into dialysis tubes which were placed into 50 mL conical tubes containing 30 mL of  minimal medium (MM). 2x 0.5 mL from each dialysis tube were mixed with RNAprotect then pelleted and the pelletes used for RNA extraction.

extract_protocol:
The total RNA from the bacterial samples was extracted, the rRNA was removed and  then the RNA was fragmented using the ultrasonicator.
The library preparation was done with the TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: The minimal medium (MM) consisted of 20% M9 salts, 2 mM MgSO4 and 1.23 mM glucose in sterile deionized water. Tomato Medium (TM) and Lettuce medium (LM) contained 25% (v/v) plant extract and 20% M9 salts and 55% sterile deionized water. Plant root exudate media (LX, TX) consisted of lyophilized exudates (from about 25 plants, 4 h) resuspended in MgCl2. Soil suspensions consisted of 33% (v/v) soil in MgCl2.

tag: serovar

value: Typhimurium

tag: medium

value: suspension of autoclaved DS soil


title: DA_rep2


title: Px6-Plasma EV Rb case


title: Px7-Plasma EV Rb case


title: DA_rep1


title: Px2-Plasma EV Rb case


title: Px5-Plasma EV Rb case


title: Px3-Plasma EV Rb case


title: TM_rep3

source_name: RNA from Salmonella grown in tomato medium

value: tomato medium


title: Px4-Plasma EV Rb case


title: C10-Plasma healthy control

description: microRNA expression in human plasma of healty controls.

source_name: Human Plasma

value: Plasma


title: VISUAL-V5

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

description: VISUAL-V5 96h

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

scan_protocol: Scanning procedure ws conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = AraGene-1_0-st
program-name = Expression Console
program-version = 1.3.1.187

organism: Arabidopsis thaliana

source_name: VISUAL: does not induce CC differentiation

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Arabidopsis seeds were sterilized with sodium hypochlorite for 5 min, and then washed with sterile water. These seeds were grown with MS liquid medium at 22ºC under the continuous light conditions for 6 days.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with Rneasy Micro Kit (QIAGEN).

treatment_protocol: WT cotyledons were cultured with the VISUAL induction medium containing 2,4-D (1.25 mg/L), kinetin (0.25 mg/L), and bikinin (10 uM) for 48 hours and then transferred to VISUAL-CC induction medium. Samples were collected at 96 hours after CC-induction.

tag: ecotype background

value: 6-day-old cotyledons

tag: time point

value: 96 hours after CC-induction


title: TM_rep2


title: VISUAL-V4

description: VISUAL-V4 96h


title: VISUAL-V3

description: VISUAL-V3 96h


title: TM_rep1


title: Px1-Plasma EV Rb case

value: EV


title: TX_rep3

source_name: RNA from Salmonella grown in tomato root exudates

value: tomato root exudates


title: C7-Plasma healthy control

value: Healthy controls


title: C8-Plasma healthy control


title: C9-Plasma healthy control


title: VISUALCC-M4

description: VISUALCC-M4 96h

source_name: CC-M: moderately induces CC differentiation


title: C11-Plasma healthy control


title: VISUALCC-S5

description: VISUALCC-S5 96h

source_name: CC-S: strongly induces CC differentiation


title: TX_rep2


title: VISUALCC-M3

description: VISUALCC-M3 96h


title: C6-Plasma healthy control


title: DS_rep3

source_name: RNA from Salmonella grown in DS soil suspension

value: DS soil suspension


title: DS_rep2


title: TX_rep1


title: VISUALCC-M5

description: VISUALCC-M5 96h


title: DS_rep1


title: C4-Plasma healthy control


title: C1-Plasma healthy control


title: P11-Plasma Rb case

description: microRNA expression in human plasma of patients with retinoblastoma.


title: C3-Plasma healthy control


title: C5-Plasma healthy control


title: P10-Plasma Rb case


title: patient 1 [T4]

city: Kamakura

first: Satoshi

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

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

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

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

source_name: primary uterine cervix

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

extract_protocol: Cells were collected and preserved at -80 C in the form of pellet. These pellet then underwent extract procedure with QIAGEN miRNeasy Mini Kit, according to the manufacturer's protocol.

value: primary uterine cervix


title: C2-Plasma healthy control


title: VISUALCC-S4

description: VISUALCC-S4 96h


title: P12-Plasma Rb case


title: patient 2 [T5]


title: P8-Plasma Rb case


title: P9-Plasma Rb case


title: patinet 3 [T6]


title: cell line 3 [NIKS]

source_name: human cell line

value: Normal immortal human keratinocytes (NIKS)


title: P7-Plasma Rb case


title: D7_MSC_MOB: MSC non-immobilized at Day 7 post-injury

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

library_source: genomic

data_processing:
QC: We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample. We use TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) to trim low-quality bases (quality score lower than 20), adapter sequences (nextera adapter, required overlap of 6bp), and end-repair bases from the 3’ end of reads. Reads shorter than 20bp after trimming are discarded.
Aligment: We align trimmed reads to mm10 with Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4.1) with the ATAC specific parameters -X 2000 --no-mixed --no-discordant, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads are marked with Picard (Picard) (v2.20.2). Alignments to autosomes are kept (i.e. sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard are removed, and alignments below a MAPQ threshold are removed (< 10). These filtering steps are performed with samtools (Li et al., 2009) (v1.2). Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) are removed with bedtools (Quinlan and Hall, 2010) (v2.28.0).
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: Sample-wise peaks are called with macs2 (Zhang et al., 2008) (v2.1.2) with the ATAC specific flags -f BAM --nomodel --shift -100 --extsize 200. Peaks over all samples are then merged with bedops (Neph et al., 2012) (v2.4.36).
Differential Methylation: For each model and contrast, we use the edgeR R Bioconductor package (McCarthy et al., 2012) (v3.26.5) to identify differential open chromatin regions (DOCRs). For each sample, the read count falling in the merged peaks is determined, and a library size normalization factor is determined. With no replicates, we manually tune the BCV (biological coefficient of variance) parameter. We then fit each model using the glmFit function, and test each contrast with a likelihood ratio test. With replicates, the common, trended, and tagwise negative binomial dispersions are calculated. We then fit each model using the glmQLFit function, and test each contrast with an empirical Bayes quasi-likelihood F-test. The DOCRs are then annotated to CpG island and genic annotations using the annotatr R Bioconductor package (v1.10.0)
Genome_build: mm10
Supplementary_files_format_and_content: Tab dellimited .txt file of basic alignment statistics and methylation statistics for each sample
Supplementary_files_format_and_content: BED files (*summits.bed)

molecule: genomic DNA

extract_protocol: ATAC-Seq libraries were prepared at the UM Epigenomics Core by using the Omni-ATAC protocol for cells as described in Corces et al., 2017 without modifications.

value: Mesenchymal Stem Cells (MSC)


title: cell line 1 [Ect]


title: cell line 2 [End]


title: VISUALCC-S3

description: VISUALCC-S3 96h


title: P6-Plasma Rb case

value: Retinoblastoma


title: P3-Plasma Rb case


title: P5-Plasma Rb case


title: FeSO4 37C replicate 2 VS control - Condition 4

city: ORSAY

first: Thomas

last: Denecker

address: Bâtiments 400 - UFR des Sciences - Université Paris-Sud - 15, rue Georges Clémenceau

department: Genome Biology

country: France

description: Biological replicate 2/3.

hyb_protocol: Probe hybridization with Quick Amp Kit (Agilent) was performed with Agilent Technologies according to the manufacturer’s instructions.

scan_protocol: Data acquisition was performed with Agilent Technologies according to the manufacturer’s instructions.

data_processing: Inter-channel (Cy5 and Cy3) fluorochrome normalization was done with ManGo R package, duplicate spots were averaged. To identify the genes whose expression was significantly modified in response to BPS addition (iron depleted condition) or to FeSO4 addition (iron excess condition), Linear Models for MicroArray data (LIMMA R package) was applied. This algorithm was chosen because it is the recommended algorithm for differential analysis of microarrays. Default parameters were used during algorithm runs. Differentially expressed genes were selected based on an adjusted p-values lower than 1% and an absolute Z-score value higher than 1.5.

molecule: polyA RNA

organism: Nakaseomyces glabratus

source_name: FeS04 37°

label_protocol: Probe labelling with Quick Amp Kit (Agilent) was performed with Agilent Technologies according to the manufacturer’s instructions.

growth_protocol: The WT C. glabrata ATCC 2001 (CBS 138) used for gene expression analysis under iron depleted and excess conditions was frozen in 40% glycerol at -80°C and used thereafter. Yeasts were first cultured on yeast extract-peptone-glucose (YPD) agar plates and then sub-cultured in YPD liquid medium at 30°C at 150 rpm for 24h by inoculating 107 yeasts to 10 ml of medium.

extract_protocol: RNAs were isolated using RNeasy Mini Kit for purification of total RNA (QUIAGEN, GmbH, Germany) according to the manufacturer’s instructions. Concentration was determined using a Nanodrop 2000 instrument. RNAs quality was checked using Agilent 2 bioanalyser Nanochip system according to the manufacturer's instructions.

treatment_protocol: Control condition being culture in YPD, for each strain, a sample of 2.106 cells was inoculated to 10 mL of YPD medium and respectively the medium corresponding to the tested condition then cultured under gentle shaking (150 rpm) at 37°C or 30°C for 4 hours (log phase, determined from growth curves). YPD medium supplemented with 100 µM bathophenanthrolinedisulfonic acid (4,7-diphenyl-1,10-phenanthrolinedisulfonic acid disodium salt hydrate (BPS) (SIGMA-ALDRICH®, France) was used as iron depleted condition (determinate in preliminary experiments as affecting but not stopping the yeast growth). YPD medium supplemented with 100 µM BPS then 500 µM of FeSO4 heptahydrate (SIGMA-ALDRICH®, France) used as iron excess condition (determined in preliminary experiments as the higher concentration that affect but do not stop the yeast growth). It is to note that the concentration of 500 µM of FeSO4  heptahydrate is as a gentle excess, close to the iron concentrations in the human gut and urine. W0 minimum medium used only for the reference RNA mix. After culture, an aliquot of 1 ml with 2 x107 was frozen at -80°C for RNA purification.

tag: addition

tag: culture temperature

source_name: control


title: P4-Plasma Rb case


title: FeSO4 37C replicate 1 VS control - Condition 4

description: Biological replicate 1/3.


title: FeSO4 37C replicate 3 VS control - Condition 4

description: Biological replicate 3/3.


title: APB_Treg_Pre_VDJ

city: Gainesville

first: Todd

last: Brusko

state: FL

address: 1275 Center Drive

institute: University of Florida

description: adult peripheral blood Tregs, pre-expansion

data_processing:
fastq files were generated from bcl files using cellranger mkfastq
unfiltered gene-barcode matrices were generated using cellranger count
T-cell receptor annotations were generated using cellranger vdj
Genome_build: Homo sapiens genome assembly GRCh37 (hg19)
Supplementary_files_format_and_content: unfiltered gene-barcode matrix (mtx), tsv with barcode for each column of mtx file, tsv with gene annotation for each row of mtx file (cellranger count default outputs)

extract_protocol: Gene expression and V(D)J libraries were prepared from 5,000 pre- and post-expansion CB and APB Treg cells using the Chromium Single Cell 50 Bead and Library Kit v1 and the Chromium Single Cell V(D)J Human TCR Analysis Kit (10X Genomics). Libraries were sequenced on an Illumina HiSeq instrument at a target read depth of 50,000 reads per cell.

tag: expansion state

value: pre

tag: source

value: adult peripheral blood

value: Tregs


title: APB_Treg_Post_GEX

description: adult peripheral blood Tregs, post-expansion

value: post


title: APB_Treg_Post_VDJ

source_name: adult peripheral blood Tregs, post-expansion


title: CB_Treg_Pre_VDJ

description: umbilical cord blood Tregs, pre-expansion

value: umbilical cord blood


title: CB_Treg_Post_VDJ

description: umbilical cord blood Tregs, post-expansion


title: P2-Plasma Rb case


title: APB_Treg_Pre_GEX

source_name: adult peripheral blood Tregs, pre-expansion


title: FeS04 30C replicate 3 VS control - Condition 3

description: Biological replicate 3/3.

source_name: FeS04 30°


title: CB_Treg_Post_GEX

source_name: umbilical cord blood Tregs, post-expansion


title: FeS04 30C replicate 1 VS control - Condition 3

description: Biological replicate 1/3.


title: YPGlu 37C replicate 3 VS control - Condition 5

description: Biological replicate 3/3.

source_name: YPGlu 37°


title: FeS04 30C replicate 2 VS control - Condition 3

description: Biological replicate 2/3.


title: Capsella orientalis 10 day old seedlings 3

city: Uppsala

first: Adrien

last: Sicard

address: Almas Allé 5

department: Uppsala BioCenter

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
RNA545 Seq data were processed using Trimmomatic (Bolger et al., 2014) to remove adapter sequences.
Reads for all samples were mapped against the C. rubella reference genome (Cru_183 from phytozome.org).
Quantification for C. rubella predicted genes was done using HTSeq-count (Anders et al., 2015).
Genome_build: Cru_183 (phytozome.org).
Supplementary_files_format_and_content: Raw read counts.

organism: Capsella orientalis

source_name: 10 day old seedlings

extract_protocol:
Total RNA was extractedusing RNeasy Plant Mini Kit (Qiagen).
TruSeq RNA libraries were generated according to the manufacturer’s instructions (Illumina) and sequenced using the Illumina HiSeq2000 instrument (1 × 50 cycles).

tag: developmental stage

value: 10 day old seedlings


title: YPGlu 37C replicate 2 VS control - Condition 5

description: Biological replicate 2/3.


title: P1-Plasma Rb case

tag: disease state

value: Plasma


title: BPS 37C replicate 1 VS control - Condition 2

description: Biological replicate 1/3.

source_name: BPS 37°

value: BPS


title: Williams82-8hpi-rep2

city: Blacksburg

last: Saghai Maroof

state: VA

address: 220 Ag Quad Ln

department: School of Plant and Environmental Sciences

institute: Virginia Tech

data_processing:
Base-calling was performed by the service company Novogene (Sacramento, CA).
Sequenced reads were trimmed for adaptor sequences and low quality bases and removed of low quality reads using Trimmomatic (version 0.30) with the following parameters, java -jar <path to trimmomatic jar> PE -threads <threads> -phred33 -trimlog <logFileR1> <logFileR2> <inputR1> <inputR2> <outputR1> <outputR2> ILLUMINACLIP:<fastaWithAdapters>:2:30:10 LEADING:30 TRAILING:30 MINLEN:50
Sequenced reads were mapped to ‘Williams82’ soybean reference genome (Wm82.a2.v1, downloaded from Phytozome) using STAR (version 2.5.3a) with the following parameters, --runThreadN <threads> --genomeDir <path to genome directory> --runMode alignReads --alignIntronMax 15000 --readFilesIn <path to R1> <path to R2> --readFilesCommand bzcat --outFileNamePrefix <path to output file directory and prefix> --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Mapped reads were counted using featureCounts (version 1.5.3) with the following parameters, -T 6 -p -B -a <annotation.gtf> -t exon -g gene_id -o < counts_ouput.txt> <mapping_results_PE.bam>
Read count expression data was normalized using DESeq2 (version 1.22.2) in R (version 3.5.1). Genes with less than one count were removed. Data were then normalized using the variance stabilizing transformation function, vst(). Significantly differentially expressed genes were identified between L29 and Williams82 at each of the five time points. Significantly differentially expressed genes were defined as those with a FDR adjusted p-value  < 0.05, log2 fold change >|1.0|, and base mean >10.
Significantly differentially expressed genes were clustered into co-expression modules using the R package 'mclust' (version 5.4.2).
Regulatory interactions were inferred between significantly differentially expressed transcription factor genes and co-expression modules using five distinct network inference algorirthms - ARACNE, context likelihood (CLR), LARS, partial correlation, and Random Forest. These algorithms represent the top performing inference methods according to the DREAM5 benchmark challenge (Marbach et al. 2012). ARACNE and CLR inference methods were implemented with the R package minet (version 3.40.0). For both, the “estimator” parameter was set as “pearson”. For ARACNE, the “eps” parameter was set at 0.1. The LARS inference method was implemented with the R package tigress (version 0.1.0) with “nstepsLARS” set at 4. The partial correlation inference method was implemented with the R package GeneNet (1.2.13) using the “dynamic” shrinkage method. Lastly, the Random Forest inference method was implemented with the R package GENIE3 (version 1.4.3) with all default parameters. Only putative interactions detected by four out of five inference methods were used in further downstream analyses.
Genome_build: Soybean reference genome, 'Williams82' (Wm82.a2.v1, downloaded from Phytozome) was built using STAR (version 2.5.3a) using the following parameters, --runMode genomeGenerate --runThreadN <threads> --genomeDir <path to genome directory> --genomeFastaFiles <path to genome fasta> --sjdbGTFfile <path to annotations_gene_exons.gtf> --sjdbOverhang 100
Supplementary_files_format_and_content: Read count, normalized expression data, differential expression, co-expression clustering modules of significantly differentially expressed genes, and putative regulatory interactions predicted by network inference  in xlsx files.
Rsv3_featureCounts_ReadCounts.xlsx: Mapped read count gene expression generated by featureCounts
Rsv3_DESeq2_VSTnormalized_Expression.xlsx: Normalized gene expression generated by DESeq2 vst() function
Rsv3_DifferentialExpression_ContrastResults.xlsx: Differential expression analysis output of between L29 and Williams82 at each time point; generated by DESeq2
Rsv3_DEG_Co-expressionModules.xlsx: Clustering results of significantly differentially expressed genes generated by mclust
Rsv3_Network_Inference_Interactions.xlsx: Putative regulatory interactions between differentially expressed transcription factor genes and co-expression modules predicted by network inference methods

organism: Glycine max

source_name: SMV-G7 inoculated leaf

growth_protocol: L29 (Rsv3-genotype ‘resistant’) and Williams82 (rsv3-genotype ‘susceptible’) plants were grown in controlled greenhouse conditions.

extract_protocol:
Inoculated unifoliolate leaves were collected at 0, 2, 4, 6, and 8 hours post inoculation (hpi) with three biological replications and stored at -80°C until RNA extraction. High-quality total RNA (RIN 7-9) was extracted with RNAeasy Plant Mini Kit (Qiagen) with on-column Dnase digestion.
20 mRNA libraries of biological duplicates were prepared for sequencing by the service company Novogene (Sacramento, CA) using NEB Next Ultra RNA Library Kit.

treatment_protocol: Soybean mosaic virus (SMV) strain G7 (SMV-G7) was maintained on greenhouse-grown soybean cultivar “York” (rsv3-genotype ‘susceptible’). At first trifoliolate stage, carborundum powder was dusted over unifoliolate leaves of plants, and the SMV-G7 inoculum (prepared by crushing systemically-infected, trifoliolate leaves with mosaic symptoms in 0.01M sodium phosphate buffer – pH 7.0 (1:10 w/v)) was gently rubbed onto unifoliolate leaves.

tag: hours post inoculation (hpi) sampled

value: 8 hpi

tag: tissue

value: leaf


title: Williams82-6hpi-rep2

value: 6 hpi


title: Williams82-4hpi-rep2

value: 4 hpi


title: Williams82-4hpi-rep1


title: Williams82-8hpi-rep1


title: YPGlu 30C replicate 1 VS control - Condition 5

description: Biological replicate 1/3.

source_name: YPGlu 30°


title: YPGlu 37C replicate 1 VS control - Condition 5

description: Biological replicate 1/3.


title: Williams82-2hpi-rep2

value: 2 hpi


title: YPGlu 30C replicate 3 VS control - Condition 5

description: Biological replicate 3/3.


title: BPS 37C replicate 2 VS control - Condition 2

description: Biological replicate 2/3.


title: YPGlu 30C replicate 2 VS control - Condition 5

description: Biological replicate 2/3.


title: BPS 30C replicate 1 VS control - Condition 1

description: Biological replicate 1/3.

source_name: BPS 30°


title: CB_Treg_Pre_GEX

source_name: umbilical cord blood Tregs, pre-expansion

tag: cell type


title: P.aeruginosa PA14, Ribo-off (Vazyme), exponential phase, biol. Repl. 2, tech. Repl. 1

first: Florian

last: Engelhardt

address: Inhoffenstraße 7

department: Molecular Bacteriology

institute: Helmholtz Centre for Infection Research

data_processing:
A first evaluation of the sequencing data quality of the demultiplexed raw fastq files was performed by using FastQC (version 0.11.4). For removal of potentially remaining adapter reads and clipping of the reads, Fastq-Mcf (version 1.04.803, -q 20 -l 30) was used. Mapping was carried out by bowtie2 (version 2.2.6, -p 8 --rf -X 1200) based on genome data retrieved from NCBI (CP000438.1) and featureCounts (version 1.6.4, -s 2 -T 10 -p -M -O) was used to determine the number of sequencing reads that can be assigned to each genomic feature.
Genome_build: CP000438.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

organism: Pseudomonas aeruginosa PA14

source_name: P.aeruginosa cultivated in LB medium

extract_protocol:
For cell lysis, thawed samples were centrifuged for 5 minutes at 8000 rpm and the supernatant was removed. 100 µL of TE buffer containing 800 µg/mL lysozyme was added to the cells and mixed thoroughly by vortexing for 30 s. After an incubation for 10 minutes at RT, intermitted by occasional short vortexing, 350 µL of RLT buffer (from RNeasy Mini Kit, Qiagen) containing 1% mercaptoethanol were added to the sample. The mixture was inverted several times and incubated for 1 h at -80 °C. Samples were then thawed on ice and loaded into a QIAshredder column (Qiagen), followed by centrifugation for 2 minutes at 14000 rpm. RNA was extracted from the supernatant with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Subsequently, remaining DNA was removed from the extracted RNA samples by treatment with the DNA-free™ DNA Removal kit (Invitrogen) according to the manufacturer’s protocol.
Sequencing libraries of the depleted RNA samples were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit accordingly to the manufacturer’s instructions

treatment_protocol: 1 mL of the main culture was mixed with 1 mL RNAprotect® Cell Reagent (Qiagen) and incubated at room temperature (RT) for 10 minutes. After a centrifugation at 8000 rpm at RT for 15 minutes, the supernatant was discarded and samples were stored at -80 °C until use.

tag: depletion method

value: Ribo-off kit (Vazyme)

tag: growth phase

value: exponential phase

tag: biological replicate

tag: technical replicate


title: P.aeruginosa PA14, Ribo-off (Vazyme), exponential phase, biol. Repl. 2, tech. Repl. 2


title: P.aeruginosa PA14, Ribo-off (Vazyme), exponential phase, biol. Repl. 1, tech. Repl. 1


title: Williams82-6hpi-rep1

tag: genotype


title: BPS 30C replicate 3 VS control - Condition 1

description: Biological replicate 3/3.

tag: strain


title: Capsella orientalis 10 day old seedlings 2


title: P.aeruginosa PA14, Ribo-off (Vazyme), exponential phase, biol. Repl. 1, tech. Repl. 2


title: BPS 30C replicate 2 VS control - Condition 1

description: Biological replicate 2/3.


title: Px8-Plasma EV Rb case

source_name: Human EV

value: EV


title: Williams82-2hpi-rep1


title: Capsella orientalis 10 day old seedlings 1


title: P.aeruginosa PA14, Ribo-off (Vazyme), stationary phase, biol. Repl. 2, tech. Repl. 1

value: stationary phase


title: Williams82-0hpi-rep2

value: 0 hpi


title: Williams82-0hpi-rep1


title: H019-NO differentiated

city: Hong Kong

first: Suet Yi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

country: Hong Kong

institute: The University of Hong Kong

description: H019-NO differentiated

data_processing:
Sequence data was mapped to the human genome (GRCh38) using CellRanger (version 2.2.0). Unique molecular identifier (UMI) count matrices were imported into R (version 3.5.1) and were processed with R package Seurat (version 2.3.4).
We excluded cells with very low (< 500) and very high UMI counts (> 8000), as well as cells with a high percentage of counts assigned to mitochondrial (> 20%) or ribosomal genes (> 40%). Genes that had less than 5 total counts across a dataset, or were expressed in less than 3 individual cells, were also removed.
Log-normalized expression was obtained by NormalizeData function of the Seurat package.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI count data as well as Log-normalized expression data for each cell in a tab-delimited text format.

source_name: Human colon normal organoid

growth_protocol: Organoids were cultured in a standard colon organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and SB202190.

extract_protocol: Organoids with or without differentiation were dissociated into single cells using TrypLE and single cells were FACS-sorted based on standard parameters for forward scatter area versus forward scatter peak liner. Dead cells were removed based on DAPI staining. Single cells were encapsulated into Gel Beads. Libraries were constructed using a Chromium Single Cell 5' Library & Gel Bead Kit (10x genomics) according to the manufacturer's instructions.

treatment_protocol: Normal and colorectal cancer organoid were cultured in a standard colon organoid medium, while APC mutant tumor organoids were cultured in a standard colon organoid medium without Wnt-3A and R-spondin1. Differentiated normal organoids have been cultured in a standard colon organoid medium without Wnt-3A for 4 days. Differentiated RSPO fusion tumor organoids have been cultured in a standard colon organoid medium with 5% Wnt-3A for 4 days.

tag: culture condition

value: Standard colon organoid medium without Wnt-3A for 4 days

value: colon normal organoid


title: H016-TO

source_name: Human colon tumor organoid

value: Mutation:APC mutant

value: Standard colon organoid medium without Wnt-3A and R-spondin1

value: colon tumor organoid


title: Capsella orientalis dividing flower buds 2

source_name: dividing flower buds

value: dividing flower buds


title: L29-8hpi-rep2

value: L29 (Rsv3-genotype 'resistant')


title: L29-8hpi-rep1

value: 8 hpi


title: P.aeruginosa PA14, Ribo-off (Vazyme), stationary phase, biol. Repl. 2, tech. Repl. 2


title: H019-TO

value: Mutation:RSPO fusion

value: Standard colon organoid medium


title: P.aeruginosa PA14, Ribo-off (Vazyme), stationary phase, biol. Repl. 1, tech. Repl. 1


title: Capsella orientalis dividing flower buds 1


title: Capsella orientalis dividing flower buds 3


title: L29-6hpi-rep2

value: 6 hpi

value: leaf


title: H019-TO differentiated

description: H019-TO differentiated

value: Standard colon organoid medium with 5% Wnt-3A for 4 days


title: H019-NO


title: Capsella orientalis expanding/maturing flower buds 3

source_name: expanding/maturing flower buds

value: expanding/maturing flower buds


title: P.aeruginosa PA14, custom-made protocol, exponential phase, biol. Repl. 2, tech. Repl. 1

value: custom-made protocol

value: exponential phase


title: Capsella orientalis expanding/maturing flower buds 2


title: H011-TO differentiated

description: H011-TO differentiated


title: L29-6hpi-rep1


title: IEC_Na2S3_60min

city: Okinawa

first: Sayomi

last: Higa-Nakamine

address: 207 Uehara, Nishihara

department: Department of Biochemistry

institute: Graduate School of Medicine, University of the Ryukyus

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

organism: Rattus norvegicus

source_name: IEC6 cell, Na2S3 60min

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: IEC6 cells were grown on 60-mm Petri dishes in a culture medimum consisting DMEM and 10% FCS.

extract_protocol: Total RNA was extracted using an Rneasy Mini Kit (Qiagen, MD) .

treatment_protocol: IEC6 cells were treated with 100 mM Na2S3 for 60 min in DMEM containing 0.1% FCS.

tag: cell line

value: culltured small intestine/epithelium cells

tag: treament

value: 100 uM Na2S3 for 60min


title: Capsella orientalis expanding/maturing flower buds 1


title: L29-4hpi-rep2

value: 4 hpi


title: H011-TO


title: Ctrl_C2_LSD1i_24hr

value: HEL

value: Erythroleukemia cell line

tag: genotype/variation

value: Control

tag: treatment

value: LSD1i 24hr


title: P.aeruginosa PA14, custom-made protocol, exponential phase, biol. Repl. 1, tech. Repl. 1


title: P.aeruginosa PA14, Ribo-off (Vazyme), stationary phase, biol. Repl. 1, tech. Repl. 2

value: Ribo-off kit (Vazyme)

value: stationary phase


title: IEC6_cont

source_name: IEC6 cell, H2O 60min

value: H2O 60min


title: H011-NO differentiated

description: H011-NO differentiated

value: Standard colon organoid medium without Wnt-3A for 4 days

value: colon normal organoid


title: P.aeruginosa PA14, custom-made protocol, stationary phase, biol. Repl. 2, tech. Repl. 1


title: P.aeruginosa PA14, custom-made protocol, stationary phase, biol. Repl. 2, tech. Repl. 2


title: H009-TO

value: Mutation:APC mutant

value: Standard colon organoid medium without Wnt-3A and R-spondin1

value: colon tumor organoid


title: H011-NO

value: Standard colon organoid medium


title: L29-0hpi-rep2

value: L29 (Rsv3-genotype 'resistant')

value: 0 hpi

value: leaf


title: P.aeruginosa PA14, custom-made protocol, exponential phase, biol. Repl. 1, tech. Repl. 2

value: custom-made protocol

value: exponential phase


title: L29-0hpi-rep1


title: L29-2hpi-rep2

value: 2 hpi


title: SUM159_BRD7_KO_clone_4_H3K4me3

status: Public on Mar 30 2020

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Adapter sequences of ChIP-seq raw reads are removed by using cutadapt (DOI:10.14806/ej.17.1.200).
Trimmed reads are aligned by bowtie2 using default parameters to version hg19 of human genome. The samtools {Li, 2009 #8524} and picard (http://broadinstitute.github.io/picard) are used to sort and remove duplicated reads to avoid PCR bias from the sequencing process.
Peak calling (identification of regions of ChIP-seq enrichment over background) is performed by using MACS2 {Zhang, 2008 #6025} with parameters of “--extsize=146 –nomodel”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of signals & bed files of called peaks are generated using MACS2

source_name: breast cancer cells

growth_protocol: SUM149, SUM159, SUM149R, SUM159R cells were grown in SUM Medium

extract_protocol:
Cells were grown in SUM Medium. The media were then removed and replaced with media containing 1% formaldehyde (EM grade; tebu-bio) and crosslinked for 8 min. Crosslinking was quenched by adding glycine to a final concentration of 0.2 M. The cells were washed with ice-cold PBS, harvested in PBS, and the cell pellet was washed with PBS. The nuclear fraction was extracted by first resuspending the pellet in 10 ml of LB1 buffer (50mM HEPES-KOH [pH 7.5], 140mMNaCl, 1mMEDTA, 10% glycerol, 0.5% NP-40 or Igepal CA-630, and 0.25% Triton X-100) for 10 min at 4C. Cells were pelleted, resuspended in 10 ml of LB2 buffer (10 mM Tris-HCL [pH 8.0], 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and mixed for 5 min. Cells were pelleted and resuspended in 1ml  LB3 buffer (10 mM Tris-HCl [pH 7.4], 1 mM EDTA, 0.1%SDS, 1%Triton X-100, 0.1% Na-deoxycholate, 1Mm DTT, 0.25% N-lauroylsarcosine, protease inhibitors and phosphatase inhibitors) and sonicated in a covaris sonicator for 10 min. A total of 30 l of 5M Nacl was added, and lysate was centrifuged for 10 min at 20,000 rcf to purify the debris. The supernatant was then incubated with 50 l of magnetic beads (Life Technologies) prebound with 20 g BRD4 antibody (Bethyl, A301-985A), and immunoprecipitation (IP) was conducted overnight in the cold room. The beads were washed ten times in 1 ml of RIPA buffer and twice in 100mM ammonium hydrogen carbonate (AMBIC) solution. DNA was eluted in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS). Cross-links were reversed overnight at 65C. RNA and protein were digested with 0.2 mg/mL RNase A for 2 hr followed by 0.2 mg/mL Proteinase K for 1 hr. DNA was purified with phenol chloroform extraction and ethanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: SUM149, SUM159, SUM149R, SUM159R cells were incubated for 12 hr with JQ1 or DMSO treatment.

tag: antibody

value: histone H3K4me3 (Abcam, ab1012)

tag: brd7 status

value: Knockout

tag: number of cells

value: 10 million cells


title: H002-TO


title: P.aeruginosa PA14, custom-made protocol, exponential phase, biol. Repl. 2, tech. Repl. 2


title: L29-2hpi-rep1

tag: hours post inoculation (hpi) sampled


title: P.aeruginosa PA14, custom-made protocol, stationary phase, biol. Repl. 1, tech. Repl. 1

value: stationary phase


title: SUM159_BRD7_KO_clone_4_H3K27me3

value: histone H3K27me3 (Cell Signaling, 9733)


title: P.aeruginosa PA14, custom-made protocol, stationary phase, biol. Repl. 1, tech. Repl. 2


title: SUM159_BRD7_KO_clone_4_40MC_INPUT

value: 40 million cells


title: SUM159_BRD7_KO_clone_4_BRD4

value: BRD4 (Bethyl, A301-985A)


title: SUM159_BRD7_KO_clone_4_H3K27ac

value: histone H3K27ac (Abcam, ab4729)


title: SUM159_BRD7_KO_clone_4_10MC_INPUT


title: SUM159_BRD7_scramble_H3K4me3

value: Wild type


title: SUM159_BRD7_scramble_H3K27me3


title: SUM159_BRD7_scramble_BRD4


title: SUM159_BRD7_scramble_H3K27ac


title: SUM159_BRD7_scramble_10MC_INPUT


title: L29-4hpi-rep1

value: 4 hpi

tag: tissue


title: BRD7_KO_JQ1_Clone2_Rep2

data_processing:
Raw RNA-seq reads are aligned to version hg19 of human genome by using Tophat2 {Kim, 2013 #8525} with the default parameters.
Gene counts are quantified by using HT-seq {Anders, 2015 #7390} with REFSEQ annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts

extract_protocol:
Total RNA was extracted using the standard QIAGEN RNeasy kit
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

treatment_protocol: SUM149, SUM159, SUM149R, SUM159R cells were incubated in biological duplicates for 12 hr with JQ1 or DMSO treatment.

tag: time

tag: replication


title: SUM159_BRD7_scramble_40MC_INPUT


title: BRD7_KO_JQ1_Clone2_Rep1


title: H007-TO

value: Mutation:APC mutant

value: Standard colon organoid medium without Wnt-3A and R-spondin1

value: colon tumor organoid


title: BRD7_KO_JQ1_Clone1_Rep2


title: BRD7_KO_JQ1_Clone1_Rep1


title: BRD7_KO_DMSO_Clone2_Rep2

value: DMSO


title: BRD7_KO_DMSO_Clone2_Rep1


title: BRD7_KO_DMSO_Clone1_Rep2


title: BRD7_KO_DMSO_Clone1_Rep1


title: BRD7_WT_JQ1_Clone2_Rep2


title: BRD7_WT_JQ1_Clone2_Rep1


title: BRD7_WT_JQ1_Clone1_Rep1


title: BRD7_WT_DMSO_Clone1_Rep1


title: BRD7_WT_DMSO_Clone2_Rep2


title: SUM159_JQ1R_starvation_JQ1_3h_R1


title: SUM159_JQ1R_starvation_JQ1_3h_R2


title: BRD7_WT_DMSO_Clone2_Rep1


title: BRD7_WT_JQ1_Clone1_Rep2


title: BRD7_WT_DMSO_Clone1_Rep2


title: SUM159_JQ1R_starvation_JQ1_12h_R1


title: SUM159_JQ1R_starvation_JQ1_12h_R2


title: SUM159_JQ1R_starvation_DMSO_12h_R1

description: JQ1 starvation


title: SUM159_JQ1R_JQ1_3h_R2


title: SUM159_JQ1R_JQ1_3h_R1


title: SUM159_JQ1R_JQ1_24h_R1


title: SUM159_JQ1R_starvation_DMSO_12h_R2

description: JQ1 starvation


title: SUM159_JQ1R_starvation_DMSO_3h_R1

description: JQ1 starvation


title: SUM159_JQ1R_JQ1_24h_R2


title: SUM159_JQ1R_DMSO_3h_R1


title: SUM159_JQ1R_DMSO_3h_R2


title: SUM159_JQ1R_DMSO_24h_R1


title: SUM159_JQ1R_DMSO_24h_R2


title: SUM159_JQ1_12h_R2


title: SUM159_JQ1_24h_R1


title: SUM159_DMSO_3h_R2


title: SUM159_DMSO_24h_R2


title: SUM159_DMSO_3h_R1


title: SUM149R_JQ1_2uM_12h_R3


title: SUM159_DMSO_12h_R2


title: SUM159_JQ1R_starvation_DMSO_3h_R2

description: JQ1 starvation


title: SUM159_JQ1_3h_R1


title: SUM159_DMSO_24h_R1


title: SUM149R_JQ1_2uM_12h_R2


title: SUM159_JQ1_24h_R2


title: SUM149R_JQ1_10uM_12h_R3


title: SUM159_DMSO_12h_R1


title: SUM149R_JQ1_2uM_12h_R1


title: SUM149R_JQ1_10uM_12h_R1


title: SUM149R_JQ1_10uM_12h_R2


title: SUM149R_DMSO_12h_Replicate1

description: JQ1 starvation


title: SUM149_JQ1_2uM_12h_R1


title: SUM149R_DMSO_12h_Replicate2

description: JQ1 starvation


title: SUM149_JQ1_2uM_12h_R3


title: SUM149_JQ1_10uM_12h_R2


title: SUM149_JQ1_2uM_12h_R2


title: SUM159_JQ1_3h_R2


title: SUM149_JQ1_10uM_12h_R1


title: SUM159_JQ1_12h_R1


title: SUM149_DMSO_12h_Replicate3


title: SUM149_DMSO_12h_Replicate2


title: SUM149_DMSO_12h_Replicate1


title: SUM149R_DMSO_12h_Replicate3

description: JQ1 starvation


title: SUM159R_JQ1_BRD4_R1

extract_protocol:
Cells (1x107) were grown in SUM Medium. The media were then removed and replaced with media containing 1% formaldehyde (EM grade; tebu-bio) and crosslinked for 8 min. Crosslinking was quenched by adding glycine to a final concentration of 0.2 M. The cells were washed with ice-cold PBS, harvested in PBS, and the cell pellet was washed with PBS. The nuclear fraction was extracted by first resuspending the pellet in 10 ml of LB1 buffer (50mM HEPES-KOH [pH 7.5], 140mMNaCl, 1mMEDTA, 10% glycerol, 0.5% NP-40 or Igepal CA-630, and 0.25% Triton X-100) for 10 min at 4C. Cells were pelleted, resuspended in 10 ml of LB2 buffer (10 mM Tris-HCL [pH 8.0], 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and mixed for 5 min. Cells were pelleted and resuspended in 1ml  LB3 buffer (10 mM Tris-HCl [pH 7.4], 1 mM EDTA, 0.1%SDS, 1%Triton X-100, 0.1% Na-deoxycholate, 1Mm DTT, 0.25% N-lauroylsarcosine, protease inhibitors and phosphatase inhibitors) and sonicated in a covaris sonicator for 10 min. A total of 30 l of 5M Nacl was added, and lysate was centrifuged for 10 min at 20,000 rcf to purify the debris. The supernatant was then incubated with 50 l of magnetic beads (Life Technologies) prebound with 20 g BRD4 antibody (Bethyl, A301-985A), and immunoprecipitation (IP) was conducted overnight in the cold room. The beads were washed ten times in 1 ml of RIPA buffer and twice in 100mM ammonium hydrogen carbonate (AMBIC) solution. DNA was eluted in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS). Cross-links were reversed overnight at 65C. RNA and protein were digested with 0.2 mg/mL RNase A for 2 hr followed by 0.2 mg/mL Proteinase K for 1 hr. DNA was purified with phenol chloroform extraction and ethanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

value: anti-BRD4 (Bethyl, A301-985A)

tag: replicate


title: SUM159R_JQ1_BRD2_R2

value: anti-BRD2 (Cell signaling, 5848)


title: SUM159R_Input


title: SUM159R_JQ1_BRD4_R2


title: SUM159R_DMSO_BRD4_R1


title: SUM159R_JQ1_BRD2_R1


title: SUM159R_DMSO_BRD2_R2


title: SUM159R_DMSO_BRD2_R1


title: SUM159R_H3K27Ac_R1

value: anti-H3K27ac (Abcam, ab4729)


title: SUM159_JQ1_BRD4_R1


title: SUM159R_DMSO_BRD4_R2


title: SUM159_JQ1_BRD4_R2


title: SUM159_JQ1_BRD2_R1


title: SUM149_JQ1_10uM_12h_R3


title: SUM159_DMSO_BRD4_R2


title: SUM159_DMSO_BRD2_R1


title: SUM159_DMSO_BRD4_R1


title: SUM159_DMSO_BRD2_R2


title: SUM149R_JQ1_BRD2_R2


title: SUM159_H3K27Ac_R1


title: SUM149R_JQ1_H3K27Ac_R1


title: SUM149R_JQ1_BRD2_R1


title: SUM149R_DMSO_H3K27Ac_R1


title: SUM149R_DMSO_BRD4_R1


title: SUM149R_Input


title: SUM149R_DMSO_BRD2_R2


title: SUM159_JQ1_BRD2_R2


title: SUM159_Input Sample


title: SUM149R_DMSO_BRD2_R1


title: SUM149_JQ1_BRD2_R2


title: DSGPFA_SUM159R_INPUT


title: DSGPFA_SUM159R_JQ1_INPUT


title: SUM149_DMSO_H3K27Ac_R1


title: SUM149_JQ1_BRD2_R1


title: SUM149_DMSO_BRD2_R2


title: SUM149_DMSO_BRD4_R1


title: SUM149_DMSO_BRD2_R1


title: DSGPFA_SUM159R_BRD7_DMSO_2

value: anti-BRD7 (Cell Signaling, 14910)


title: DSGPFA_SUM159R_BRD7_JQ1_1


title: SUM149R_JQ1_BRD4_R1


title: DSGPFA_SUM159_JQ1_INPUT


title: DSGPFA_SUM159_INPUT


title: DSGPFA_SUM159R_BRD7_DMSO_1


title: DSGPFA_SUM159_BRD7_DMSO_1


title: DSGPFA_SUM159_BRD7_JQ1_1


title: SUM159_P0_R1_001

data_processing:
Library strategy: Barcode-seq
We followed the method used in Bhang et al. 2015 with small modifications. In details, all sequencing reads are trimmed by using 3 prime adaptor sequence: AGCAGAGCTACGCACTCTATGCTAGTGCTAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCACGATCGTATCTCGTATGCCGTCTTCTGCTTG with minimum alignment length of 40-nt. The trimmed reads with Ns or less than 30-nt or without the WS x 15 pattern are removed. Then the 30-nt barcode sequences are extracted from the 3 prime end of the trimmed sequences. Barcodes with an estimated Phred quality score of at least 10 for all nucleotides and with an average Phred quality score greater than 30 are kept as qualified barcodes. The barcodes with only one count are excluded from the analyses to avoid the noise derived from the sequencing error.
Genome_build: hg19
Supplementary_files_format_and_content: tsv files contain the abundant of each barcode

growth_protocol: Cells were barcoded by lentiviral infection using high-complexity barcode library, ClonTracer. After a 24 h incubation with virus, infected cells were selected with 2 μg ml−1 puromycin. To ensure that the majority of cells were labeled with a single barcode per cell, for lentival infection we used a target m.o.i. of approximately 0.2, corresponding to 20% infectivity after puromycin selection. Infected cell populations were expanded in culture for the minimal time period to obtain a sufficient number of cells to set up replicate experiments. Cells were cultured in SUM medium for increasing dose of JQ1 and their corresponding control.

extract_protocol:
Genomic DNA was extracted from the frozen cell populations with a QIAamp DNA Midi Kit (Qiagen).
We used PCR to amplify the barcode sequence for NGS by introducing Illumina adaptors and 5-bp-long index sequences.

treatment_protocol: Barcoded cells were treated with JQ1. The control groups were treated with 0.1% DMSO. Each group was cultured in quadruplicate.

tag: agent

tag: passage


title: DSGPFA_SUM159_BRD7_JQ1_2


title: SUM159_JQ1_P20_4_R1_001


title: SUM159_JQ1_P20_2_R1_001


title: SUM159_JQ1_P20_1_R1_001


title: SUM159_JQ1_P20_3_R1_001


title: SUM149_JQ1_BRD4_R1


title: SUM149_JQ1_H3K27Ac_R1


title: SUM149_Input


title: SUM159_DMSO_P20_3_R1_001


title: SUM159_DMSO_P20_2_R1_001


title: DSGPFA_SUM159R_BRD7_JQ1_2


title: SUM149_P0_2_S10_R1_001


title: SUM159_DMSO_P20_1_R1_001


title: SUM149_JQ1_P25_3_S7_R1_001


title: SUM149_JQ1_P25_4_S8_R1_001


title: SUM149_JQ1_P25_1_S5_R1_001


title: SUM149_JQ1_P25_2_S6_R1_001


title: SUM149_DMSO_P25_2_S2_R1_001


title: Scramble-2-2-JQ1

data_processing:
ChiLin pipeline 2.0.0 (Qin et al., 2016) is used for QC and preprocess of the ATAC-seq. We use Burrows-Wheeler Aligner (BWA) (Li and Durbin, 2009) as a read mapping tool, and Model-based Analysis of ChIP-Seq (MACS2) (Zhang et al., 2008) as a peak caller, with a q-value (FDR) threshold of 0.01.Based on a dynamic Poisson distribution MACS2 can effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction of binding sites. Unique read for a position for peak calling is used to reduce false positive peaks, statically significant peaks are finally selected by calculated false discovery rate of reported peaks. Deeptools (Ramirez et al., 2016) is used for the heatmap plots. ATAC-seq Peaks from all study samples in were merged to create a union set of sites. Read densities were calculated for each peak for each sample, differential peaks between WT and KO were identified by DEseq2 (Love et al., 2014) with adjusted P ≤0.05, |log2fold change| ≥ 1.
Supplementary_files_format_and_content: bigwig of signals files

extract_protocol: 50,000 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at max speed for 5 min in a pre-chilled (4 C) fixed-angle centrifuge. After centrifugation supernatant was carefully aspirated.  Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 5 min at max speed in a pre-chilled (4 C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 μl of transposition mix (reference to OMNI paper) 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen columns. Libraries were amplified as described previously (Buenrostro et al., 2015).

treatment_protocol: SUM149, SUM159, SUM149R, SUM159R cells were incubated for 12 hr with 200nM JQ1 or DMSO treatment.

value: BRD7 wildtype

tag: clone


title: SUM149_DMSO_P25_1_S1_R1_001


title: SUM149_P0_1_S9_R1_001


title: Scramble-1-2-JQ1


title: Scramble-1-2-DMSO


title: Scramble-2-1-DMSO


title: Scramble-2-2-DMSO


title: Scramble-2-1-JQ1


title: Scramble-1-1-JQ1


title: Scramble-1-1-DMSO


title: SUM159_DMSO_P20_4_R1_001


title: BRD7-KO-2-2-JQ1

value: BRD7 knockout


title: BRD7-KO-2-2-DMSO


title: BRD7-KO-2-1-JQ1


title: BRD7-KO-2-1-DMSO


title: BRD7-KO-1-2-JQ1


title: BRD7-KO-1-2-DMSO


title: BRD7-KO-1-1-JQ1


title: BRD7-KO-1-1-DMSO


title: SUM149_DMSO_P25_3_S3_R1_001


title: SUM149_DMSO_P25_4_S4_R1_001


title: 66 WT D6 R3

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads were aligned to mouse genome (mm10) using STAR v2.7.0d.
2) Gene read coverages were computed with featureCounts v1.6.2 using GENCODE annotation release M21
3) Differential expression analysis was performed using edgeR v3.24.3 with "y ~ 0 + group + block" design while filtering low count reads using built-in function filterByExpr
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

extract_protocol:
Cell lysis and phase separation were performed using TRIzol Reagent (Invitrogen). The RNA was purified using RNeasy Kit (Qiagen).
Illumina TruSeq Stranded Total RNA Library Prep Gold, with RNAClean XP Kit (Agencourt) for RNA purification, AMPure XP Kit (Agencourt) for DNA purification, and SuperScript III Reverse Transcriptase (Invitrogen) for cDNA synthesis. High-throughput sequencing was performed using the NextSeq 500 Sequencing System (Illumina) and the NextSeq 500/550 High Output Kit v2 (75 cycles).

tag: cell type

value: brown pre-adipocyte

tag: genotype

value: WT

tag: cell culture id

tag: library pool

tag: day


title: 66 WT D2 R3


title: 66 SA D2 R3


title: 66 SA D6 R3


title: 66 WT D0 R3


title: 66 SA D0 R3


title: 66 WT D6 R2


title: 66 SA D2 R2


title: 66 WT D2 R1


title: 66 WT D6 R1


title: 66 WT D0 R2


title: 48 SA D6 R3


title: 66 SA D0 R1


title: 66 SA D0 R2


title: 66 SA D2 R1


title: 48 WT D6 R3


title: 66 SA D6 R2


title: 48 SA D2 R3


title: 48 WT D2 R3


title: 48 WT D0 R3


title: 48 SA D0 R3


title: 66 WT D2 R2


title: 66 WT D0 R1


title: 48 SA D6 R2


title: 66 SA D6 R1


title: 48 WT D6 R2


title: 48 SA D2 R2


title: 48 SA D0 R2


title: 48 WT D2 R2


title: 48 WT D0 R2


title: 48 SA D6 R1


title: 48 WT D6 R1


title: 48 SA D2 R1


title: 48 WT D2 R1

source_name: WT _D2


title: 48 WT D0 R1


title: WT-Copper-R2

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

data_processing:
RNA-sequencing data analysis Adaptor sequences and low quality score bases (Phred score < 30) were first trimmed using Trimmomatic.
The resulting reads were aligned to the C. albicans reference assembly SC5314 from Ensembl (http://fungi.ensembl.org/Candida_albicans_sc5314_gca_000182965/Info/Index), using STAR.
Read counts are obtained using HTSeq (Anders et al., 2015) and are represented as a table which reports, for each sample (columns), the number of reads mapped to a given gene (rows).
The R package limma (Ritchie et al., 2015) was used to identify differences in gene expression levels between treated and non-treated samples. Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method.
Genome_build: SC5314: http://fungi.ensembl.org/Candida_albicans_sc5314_gca_000182965/Info/Index
Supplementary_files_format_and_content: DEG.xlsx: Excel file includes differential expression analysis.

organism: Candida albicans

source_name: Yeast cells

growth_protocol: Overnight cultures of mac1 mutant and WT (SN250) strains were diluted to an OD600 of 0.1 in 40 147 ml of fresh YPD-uridine medium and grown at 30°C under agitation (200 rpm) to an OD600 of 0.4.

extract_protocol:
Total RNA was extracted using an RNeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater. Total RNA was eluted, assessed for integrity on an Agilent 4200 TapeStation System prior to cDNA library preparation.
The NEBNext® UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library following the manufacturer’s instruction. The quality, quantity and the size distribution of the libraries were determined using an Agilent Bioanalyzer. A 2x100 paired-end sequencing of cDNAs were performed using an Illumina Novaseq6000 sequencing system.

treatment_protocol: Cultures were then either left untreated or exposed to CuSO4 (2mM) and BCS (400µM), and incubated at 30°C for 30 min. Cells were then harvested by centrifugation at 3,000 x g for 5 min and the pellets were quick-frozen and stored at -80°C.

value: Yeast cells

tag: strain

tag: genotype/variation

tag: treatment


title: Mac1-R2


title: Mac1-R1


title: OldEx4

first: Ho

last: Ko

address: 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

country: China

institute: The Chinese University of Hong Kong

data_processing:
The multiple fastq files were aligned to mm10 reference genome by Cellranger software (v3.0.0)
Follow the stadard Seurat (v3.0.1) process pipeline, the batch effect was removed, and cells were undergo quality control by following criterias: 1. Lower than 5% or higher than 95% UMI count or gene count. 2. The proportion of mitochondrial genes > 20%.
The dimension reduction and clustering was finished by tSNE and Seurat FindNeighbors and FindClusters function on first components of PCA results.
The primary cell type was identified by well-known marker genes and endothelia and smooth muscle cells' subtypes were identfied by Cellassign algorithm
Genome_build: mm10
Supplementary_files_format_and_content: Standard 10X cellranger output files: 1. Sparse matrix (mtx), each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). 2.The meta file contained the batch, age, sample names, clustering results and cell type identified in Seurat.

source_name: Brain

growth_protocol: C57BL/6J mal mice were provided by the Laboratory Animal Service Center of CUHK and maintained at controlled temperature (22 – 23°C) with an alternating 12-hour light/dark cycle with free access to standard mouse diet and water

extract_protocol:
We adapted a previously described dissociation protocols optimized for single brain vascular cells isolation from both young and old mouse brains. Briefly, mice were deeply anesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). Mice were then rapidly decapitated, and whole brains were immersed in ice-cold Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific). The brain tissues were cut into small pieces and dissociated into single cells using a modified version of the Neural Tissue Dissociation kit (P) (130-092-628, Miltenyi Biotec). Myelin debris was removed using the Myelin Removal kit II (130-096-733, Miltenyi Biotec) according to the manufacturer’s manual. Cell clumps were removed by serial filtration through pre-wetted 70 μm (#352350, Falcon) and 40 μm (#352340, Falcon) nylon cell strainers. Centrifugation was performed at 300 xg for 5 minutes at 4°C. The final cell pellets were resuspended in 500 – 1000 μl FACS buffer (DMEM without phenol red (Thermo Fisher Scientific), supplemented with 2% fetal bovine serum (Thermo Fisher Scientific)).
Chromium Single Cell 3′ Reagent Kit v2
Drop-seq (10X Gemonic)

treatment_protocol: Exenatide (5 nmol/kg/day, Byetta, AstraZeneca LP) was intraperitoneally (I.P.) administered starting at 17 – 18 months old for 4 – 5 weeks respectively prior to single-cell RNA sequencing experiments.

tag: age

value: 18 – 20 months

tag: mice number


title: WT-R1


title: WT-BCS-R1

value: BCS


title: WT-R2


title: WT-BCS-R2


title: Old4


title: Mac1-BCS-R2


title: Mac1-BCS-R1


title: OldEx1


title: OldEx2


title: Young2

value: 2 – 3 months


title: Old1


title: Control Ptf1aCRE/+;Ai14

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Reads were mapped to annotated pre-mRNA sequences from mouse reference genome (mm10) using 10X genomics CellRanger (V3.1.0) tool
Raw expression UMI counts were obtained using 10X genomics CellRanger (V3.1.0) tool
Downstream analysis of snRNA-seq raw expression data was performed using Seurat R package (v3.1.1).
[snRNA_seq_neuron_average_expression.txt]  From the cellranger results, we filtered out the low quality nuclei and merged two samples together. After that, we identified the neuronal populations from the merged sample using Neuron markers such as Rbfox3 and Snhg11 and reclustered them to identify different neuronal sub-populations. The clustering analysis revealed 31 discrete clusters. This file has the information about the average expression of each gene in each of the 31 clusters.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized UMI counts

source_name: Cervical spinal cord nuclei

extract_protocol:
Nuclei from spinal cords were isolated as described in Matson, K.J.E., Sathyamurthy, A., Johnson, K.R., Kelly, M.C., Kelley, M.W., and Levine, A.J. (2018). Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing. J Vis Exp. PMCID: PMC6235529  DOI:10.3791/58413
10X Genomics Next GEM Single cell 3’ Reagent Kit v3.1.  Nuclei were loaded with Single Cell 3’ Gel Beads into a Next GEM Chip G and run on the Chromium™ Controller. GEM emulsions are incubated and then broken.  Silane magnetic beads are used to clean up GEM reaction mixture. Read 1 primer sequence is added during incubation and full-length, barcoded cDNA is then amplified by PCR after cleanup. Sample size is checked on the Agilent Tapestation 4200 using the DNAHS 5000 tape and concentration determined by the Qubit 4 Fluorometer (ThermoFisher) using the DNA HS assay. Samples are enzymatically fragmented and undergo size selection before proceeding to library construction.  During library preparation, Read 2 primer sequence, sample index and both Illumina adapter sequences are added.  Subsequently, samples are cleaned up using Ampure XP beads and post library preparation quality control is performed using the DNA 1000 tape on the Agilent Tapestation 4200. Final concentration is ascertained using the Qubit 4 Fluorometer (ThermoFisher) DNA HS assay. Samples are loaded at 1.6 pM and run on the Illumina NextSeq500 High Output Flowcell using V2.5 chemistry.  Run configuration is 28x98x8.

tag: Stage

value: mixed

tag: tissue

value: cervical spinal cords


title: Old2


title: Young1


title: ∆npf N8004 H3K27me2/3 ChIP-seq

city: Eugene

first: Eric

last: Selker

state: Oregon

address: 1370 Franklin Blvd.

department: Biology

institute: University of Oregon

description: CTCTGGAT_N8004_npf_H3K27me2me3_062419_S31_L007_R1_001

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
RNA-seq processing: Tools available on Galaxy (Afgan et al., 2018) were used to map mRNA-sequencing reads (intron size < 1kb) (Dobin et al, 2012) against the corrected N. crassa OR74A (NC12) genome (Galazka et al., 2016), count the number of reads per gene (Dobin et al., 2012) and determine differentially expressed genes with DESeq2 (Love et al, 2014).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp.
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 previously published replicates of wild type and ∆set-7 strains (both from Klocko et al. 2016; GSE82222). In addition they contain normalized counts for ∆pas replicates and an additional set of wild type replicates (totalling 4 wild type samples). We have also included the pairwise comparisons of wild type to ∆set-7 and wild type to ∆pas from DESeq2 (Love et al., 2014).

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and H3K27me2/3 antibody was added (typically 2uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

value: germinated conidia

value: mat a; Dnpf::hph

tag: chip antibody

value: H3K27me2/3 (Active motif #39536)


title: 48 SA D0 R1

tag: replicate


title: Mutant Ptf1aCre/AR-DNT1;Ai14


title: WT-Copper-R1


title: Young4


title: ∆pas N8002 H3K27me2/3 ChIP-seq

description: AGAGTCCA_N8002_NCU04278_H3K27me2me3_062419_S29_L007_R1_001

value: mat A; Dpas::nat-1


title: ∆pas N7999 H3K27me2/3 ChIP-seq

description: GTAGCGTA_N7999_NCU04278_H3K27me2me3_062419_S28_L007_R1_001

value: mat a; Dpas::nat-1


title: Series4_A549_IAV_2

status: Public on Mar 25 2020

city: New York

first: Daniel

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
3-9-wt2-16_S16
processed data file: RawReadCounts_Human.tsv

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.

source_name: IAV infected A549 cells

extract_protocol:
TruSeq RNA Library Prep Kit v2
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
TruSeq RNA Library Prep Kit v2 (A549) or TruSeq Stranded mRNA LP (NHBE) according to the manufacturer’s instructions

tag: cell line

value: Lung adenocarcinoma

value: IAV infected (MOI 5)

value: A/Puerto Rico/8/1934 (H1N1)

tag: time point

value: 9hrs after treatment


title: ADAR2-hiCLIP-rep2

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Demultiplex raw data by barcodes, remove PCR duplicates using fastx_toolkit_0.0.13, and trim adaptors with cutadapt v1.14
Step 1 mapping: map reads to hg19 transcripts (bowtie -f-S -v 3 -k 10 --best --strata) and discard the mapped reads
Step 2 mapping: map reads to hg19 genome (bowtie -f -S -v 3 -k 10 --best --strata) and discard the continuously mapped reads
Step 3 mapping: map reads to hg19 genome using STAR (--outSAMprimaryFlag AllBestScore --outSAMattributes All --outFilterMultimapNmax 100  --outFilterMismatchNmax 3 --alignEndsType EndToEnd  --outSAMunmapped Within --alignIntronMin 4)
Step 4 mapping: map reads to hg19 genome (bowtie --very-sensitive-local -f),  extract the swapped reads, and reorganize these reads
Step 5 mapping: map reads to hg19 genome using STAR version 020201 (--outSAMprimaryFlag  AllBestScore --outSAMattributes All  --outFilterMultimapNmax 100  --outFilterMismatchNmax 3  --alignEndsType EndToEnd  --outSAMunmapped Within --alignIntronMin 4)
Obtain hybrid reads from step 3 and step 5
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing hybrid reads of ADAR1, ADAR2 and ADAR3

source_name: HEK293 cell

growth_protocol: HEK293 cells were grown in DMEM containing 10% FBS and cultured in 37℃ with 5% CO2.

extract_protocol:
UV crosslinked RNA was extracted with phenol-chloroform.
Cells were collected, washed with 10 ml DPBS, and crosslinked on ice with UV-C. Cells were lysed with 4 ml ice-cold lysis buffer for 5 min on ice and collected into 15 ml tubes by scraping. The lysate was incubated for 10 min on ice and then centrifuged at 6400 g for 30 min at 4 ℃. The supernatant was transferred to a new tube and incubated with 50 ul protein G Dynabeads that were coated with 10 µg FLAG antibody with rotation for 3h at 4 ℃. The immunoprecipitate was washed with 1 ml LS-IgG buffer, 1 ml HS-IgG buffer twice, 1 ml LS-IgG buffer and 1 ml NT2 buffer, sequentially. On-beads digestion was performed with RNase I for 5 min at 37 ℃. 1 ml high-stringency buffer was added to stop the digestion reaction. The immunoprecipitate was washed twice with NT2 buffer, and then dephosphorylated with Thermosensitive Alkaline Phosphatase (TSAP) for 1 h at 37 ℃. Next, the 5’ end phosphorylation of RNA was performed with T4 PNK for 1h at 37 ℃. Inter-molecular RNA-RNA ligation was performed with T4 RNA ligase I overnight at 16 ℃. The supernatant was then washed with NT2 buffer. Fluorescent dye IR800 labeled preA-DNA-adaptor was ligated to the 3’ end of the RNA with T4 RNA ligase I at 16 ℃ overnight. The Immunoprecipitate was then washed with NT2 buffer, resolved by a 4-12% NuPAGE Bis-Tris gel, and transferred to NC membrane. Target regions were cut into 1 mm narrow strips and digested by 20 ul proteinase K. RNA fragments were purified by phenol-chloroform extraction. Reverse transcription was performed using SuperScript IV Reverse Transcriptase with RT primers according to the manufacturer’s instructions. RNA/cDNA hybrids were captured by Streptavidin Dynabeads. cDNA were circularized by Circligase-II after RNA degradation and cDNA elution. Circularized cDNA was captured by VAHTS DNA clean beads. library was amplified by two rounds of PCR and the final products were separated by 2.5% TAE gel. The PCR products ranging from 150 bp to 275 bp were cut and recovered using Zymoclean Gel DNA Recovery Kit.

treatment_protocol: HEK293 cells were transiently transfected with ADAR plasmids by Lipofectamine 3000

tag: passages

tag: irclash or hiclip antibody

value: anti-FLAG M2 antibody (Sigma-Aldrich, cat# F1804-1MG)

tag: experiment


title: HydroxyMeDIP-seq WT Tumor rep 2

status: Public on Mar 26 2020

city: Barcelona

first: Lorenzo

last: Rinaldi

state: Spain

address: Carrer Reixac Baldiri 10

department: Oncology

country: Spain

institute: IRB

description: No processed data was provided for the hydroxy-MeDIP-seq samples because only the enrichment of hydroxymethylation within certain genomic regions (the peaks of the ChIP-seq) was studied.

data_processing:
MeDIP-seq datasets were aligned to the mouse genome build mm10 using BowTie (version 1.0.1) (Langmead et al. 2009); the parameters used were –k 1, –m 1, and –n 2. UCSC browser tracks (Kent et al. 2002) were created from the mapped bam file after converting it to bedGraph (normalized to 10 million reads) and subsequently bigWig format. Peaks of the methylation and hydroxymethylation datasets were determined MACS version 1.4.1. MeDIP-seq peaks were annotated using the annotatePeaks.pl script of the HOMER suite (version 4.6).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Deseq2 for the differential methylated regions.

source_name: DNA hydroxymethylation profile of WT Itga6+ tumor cells

growth_protocol: Inbred male or female Dnmt3a flox/flox (C57/Bl6) backcrossed to Krt14-CRE-YFP (C57/Bl6) for 6-9 generations were used for all animal experiments.

extract_protocol:
Tumor cells (YFPbright/lineageneg cells), pre-cancerous epidermis of interfollicular epidermis (YFPpos/CD49fhigh/CD34neg cells), and bulge hair follicle stem cells (YFPbright/CD49fhigh/CD34pos cells) were FACS-sorted using a BD FACSAria Fusion flow cytometer (BD Biosciences). Approximately 3-20x10^4 cells were sorted and lysed in 1 ml of TRIzol for RNA and DNA isolation. After adding 200 µl chloroform, samples were vortexed for 30 second and then centrifuged at 12,000 g to separate the RNA-containing supernatant from the organic phase. RNA was precipitated with 1´ volume of isopropanol, washed twice with 70% ethanol, and then used for library preparation. The interphase of the TRIzol solution (after removal of the supernatant) was precipitated adding 1´ volume of isopropanol, centrifuged for 1 h at 4°C at 13,000 g, washed twice with ethanol, and digested overnight at 55°C with proteinase K (10 mg/ml) in TE 1´ buffer. The following day, digested material was incubated 1 h at 37°C with RNase A and purified using a conventional phenol/chloroform separation. The DNA pellet was quantified, and DNA was used for library preparation for MeDIP-seq and hMeDIP-seq experiments.
Purified genomic DNA (250 ng) from tumor cells was sonicated to obtain fragments of 300-700 bp. Adaptors from the NEBNext Ultra DNA Library Prep Kit for Illumina were added to the fragmented DNA. DNA was denatured for 10 min at 99°C and cooled to avoid re-annealing. Fragmented DNA was incubated overnight with 1 mg of antibodies (5-methylcytosine, Abcam cat. # ab10805; 5-hydroxymethylcytosine, Active Motif, cat. # 39769) previously cross-linked with 15 ml of Dynabeads Protein A (Life Technologies). Immunocomplexes were recovered using 8 ml for 2 h. The following morning, DNA was washed three times for 10 min each, and purified DNA was extracted using QIAquick MinElute (Qiagen). Amplified libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following the manufacturer's instructions.

treatment_protocol: Chemically-induced skin carcinogenesis was performed as previously described (Nassar et al. 2015; Abel et al. 2009), with a slight modification to yield high-frequency SCCs in the C57/Bl6 genetic background. Briefly, the back skin of 8-week-old mice -- at which time hair follicles are in their resting phase (telogen) -- was shaved and treated with the mutagen 7,12-dimethylbenz[a]anthracene (DMBA; 200 µl of 0.25 mg/ml solution in acetone) and the pro-inflammatory and pro-proliferation agent 12-O-tetradecanoyl phorbol-13-acetate (TPA; 200 µl of 0.02 mg/ml solution in acetone) once weekly for 6 weeks. Specifically, DMBA was given on Monday and TPA always on the Friday of the same week.

value: Itga6+ tumor cells

tag: genetic background

value: CU Black Six

value: Wild-Type

value: 6 months

tag: gender

value: Female

tag: medip antibody

value: 5-hydroxymethylcytosine (Active Motif, 39769)


title: HydroxyMeDIP-seq KO Tumor rep 2

source_name: DNA hydroxymethylation profile of Dnmt3a KO Itga6+ tumor cells

value: Dnmt3a Flox/Flox Krt14-CRE (Dnmt3a Krt14 KO)


title: Series4_A549_Mock_1

description:
3-9-mock1-13_S20
processed data file: RawReadCounts_Human.tsv

source_name: Mock treated A549 cells

tag: cell type

value: Mock treatment


title: ADAR2-hiCLIP-rep1


title: Series4_A549_IAV_1

description:
3-9-wt1-15_S2
processed data file: RawReadCounts_Human.tsv

tag: strain


title: Series4_A549_Mock_2

description:
3-9-mock2-14_S1
processed data file: RawReadCounts_Human.tsv

tag: treatment


title: forelimb bud at embryonic stage E11.5 WT

city: Montreal

first: Marie

last: Kmita

state: QC

address: 9730 Avenue de Lorimier

institute: IRCM (institut de Recherche Clinique de Montreal)

data_processing:
Sequencing reads were aligned on mm10 genome using Cellranger-atac version1.1.0 (from 10xGenomics®)
Sorted bam files were structured into hdf5 snapfiles (Single-Nucleus Accessibility Profiles) using snaptools version 1.4.1. Quality control analysis was performed using SnapATAC 1.0.0.. Cells with logUMI in [3.5-5] and fragment overlapping peaks above 25% were selected. They were cleaned by eliminating bins overlapping with ENCODE Blacklist regions, mitochondrial DNA as well as the top 5% of invariant features (house-keeping gene promoters).
Dimensionality reduction was performed using a non-linear diffusion map algorithm available in the SnapATAC 1.0.0 package to produce 50 eigen-vectors of which the first 26 were selected in order to generate K Nearst Neighbor graph with K=15.
The clustering was performed using Leiden Algorithm available in the package leidenalg version 0.7.0 with a resolution of 0.7 and  2 UMAP (uniform Manifold Approximation and Projection version 0.2.3.1) embedding were generated to visualize the data.
Fragments originating from the cells belonging to them same clusters were pooled using snaptools 1.4.1 and peak calling was performed using MACS2 version 2.1.2 for each of the clusters (see detailed code on Github, github.com/BCYasser/DigitMorphoScATAC).
Genome_build: mm10
Supplementary_files_format_and_content: Narrowpeaks, Bigwigs

source_name: Limb bud

extract_protocol:
Dissection of forelimb buds from wild type embryos and Hox13-/- embryos were performed at E11.5. Forelimbs were dissected in cold 1XPBS, after centrifugation at 300 rcf for 5 minutes at 4°C the forelimbs were incubated in dissociation buffer (450 μl of 0.25% Trypsine/EDTA (GIBCO), 50 μl 10% BSA, 1 μl DNAseI (NEB)) for 10 minutes at 37°C. After incubation limb cells were gently mixed by pipetting up and down 10-15 times until they were dissociated, then 10% final FBS was added. Dissociated cells were filtered using a cell strainer (40 μm Nylon, BD Falcon) and after centrifugation at 300 rcf for 5 minutes at 4°C the resulting pellet of cells was resuspended in 1XPBS, 0.1%BSA. Dissociated cells were counted and assessed for cell viability using 0.4% Trypan blue. After centrifugation at 300 rcf for 5 minutes at 4°C, the cell pellet was resuspended in 100 μl of ice-cold lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA) and incubated for 5 minutes on ice. Then 1 ml of wash buffer (10mM Tris-HCl, pH7.4, 10 mM NaCl, 3mM MgCl2, 0.1% Tween-20, 1% BSA) was added to the cells. After centrifugation at 300 rcf for 5 minutes at 4°C, the pellet of nuclei was re-suspended in diluted nuclei buffer in order to have 3500 nuclei/μl and processed using Chromium Single Cell ATAC Reagent Kits (10x Genomics, Pleasanton, CA) following the manufacturer recommendation.
nuclei were incubated in a Transposition Mix that includes a Transposase that preferentially fragments the DNA in open regions of the chromatin and simultaneously, adapter sequences were added to the ends of the DNA fragments. GEMs were then generated, using partitioning oil, in order to contain a single nucleus and a Master Mix to produce 10x barcoded single-stranded DNA after thermal cycling. The Chromium Single Cell ATAC Library was amplified and double sided size selected. Samples were controlled at multiple steps during the procedure by running on BioAnalyzer. Libraries were sequenced on Hiseq 4000 with 100 bp paired- end reads
scATACseq using 10x Chromium Single Cell ATAC Reagent Kit

tag: developmental stage

value: developmental stage E11.5

tag: genotype

value: WT

value: mesenchymal cells


title: H460 no radiation, biological replicate 3

city: Morgantown

first: Ivan

last: Martinez

state: WV

address: 1838 MBRCC PO Box 9300

department: Microbiology / Cancer Center

institute: West Virginia University

description: ACHI_HTA2_9_070214_(HTA-2_0).rma-gene-full-Signal

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray Suite version 5.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: H460 no radiation

label_protocol: standard Affymetrix protocol

extract_protocol: TRIzol

value: Non-Small Cell Lung Cancer (NSCLC) cell line

value: control


title: Series3_A549_RSV_2

description:
svRNA184-RSV-1-indexF4_S16
processed data file: RawReadCounts_Human.tsv

source_name: RSV infected A549 cells

value: Lung adenocarcinoma

value: RSV infected (MOI 15)

value: 24hrs after treatment


title: H460 radiated with 7Gy, biological replicate 3

description: ACHI_HTA2_12_070214_(HTA-2_0).rma-gene-full-Signal

source_name: H460 radiated with 7Gy

value: 7Gy of radiation


title: H460 radiated with 7Gy, biological replicate 2

description: ACHI_HTA2_11_070214_(HTA-2_0).rma-gene-full-Signal


title: H460 radiated with 7Gy, biological replicate 1

description: ACHI_HTA2_10_070214_(HTA-2_0).rma-gene-full-Signal


title: H460 no radiation, biological replicate 1

description: ACHI_HTA2_7_070214_(HTA-2_0).rma-gene-full-Signal


title: H460 no radiation, biological replicate 2

description: ACHI_HTA2_8_070214_(HTA-2_0).rma-gene-full-Signal


title: ADAR3-irCLASH-rep1

value: anti-FLAG M2 antibody (Sigma-Aldrich, cat# F1804-1MG)


title: Series3_A549_RSV_1

description:
svRNA184-RSV-3-indexH9_S18
processed data file: RawReadCounts_Human.tsv


title: ADAR3-irCLASH-rep2


title: ADAR2-irCLASH-rep1


title: ∆npf N8003 H3K27me2/3 ChIP-seq

description: GCTACTCT_N8003_npf_H3K27me2me3_062419_S30_L007_R1_001

value: germinated conidia

value: mat a; Dnpf::hph

value: H3K27me2/3 (Active motif #39536)


title: Series3_A549_Mock_2

description:
svRNA184-mock-1-indexF1_S13
processed data file: RawReadCounts_Human.tsv


title: HydroxyMeDIP-seq KO Tumor rep 1

value: Itga6+ tumor cells

value: CU Black Six

tag: genotype/variation

tag: age

value: 6 months

value: Female


title: Series3_A549_Mock_1

description:
svRNA184-mock-3-indexF3_S15
processed data file: RawReadCounts_Human.tsv

value: Mock treatment


title: Series2_A549_SARS-CoV-2_3

description:
CoV002-CoV2-1-indexG4_S4
processed data file: RawReadCounts_Human.tsv

source_name: SARS-CoV-2 infected A549 cells

value: SARS-CoV-2 infected (MOI 0.2)


title: ADAR1-irCLASH-rep3


title: ADAR1-irCLASH-rep2


title: ADAR2-irCLASH-rep2


title: Series2_A549_SARS-CoV-2_2

description:
CoV002-CoV2-2-indexG5_S5
processed data file: RawReadCounts_Human.tsv


title: forelimb bud at embryonic stage E11.5 Hox13-/-

value: developmental stage E11.5

value: Hox13 Knockout

value: mesenchymal cells


title: Series2_A549_SARS-CoV-2_1

description:
CoV002-CoV2-3-indexG6_S6
processed data file: RawReadCounts_Human.tsv

value: Lung adenocarcinoma


title: Series2_A549_Mock_3

description:
CoV002-mock1-indexG1_S1
processed data file: RawReadCounts_Human.tsv


title: ADAR1-irCLASH-rep1


title: Series2_A549_Mock_2

description:
CoV002-mock2-indexG2_S2
processed data file: RawReadCounts_Human.tsv


title: HydroxyMeDIP-seq WT Tumor rep 1

description: No processed data was provided for the hydroxy-MeDIP-seq samples because only the enrichment of hydroxymethylation within certain genomic regions (the peaks of the ChIP-seq) was studied.

tag: tissue

value: Wild-Type

value: 5-hydroxymethylcytosine (Active Motif, 39769)


title: Series2_A549_Mock_1

description:
CoV002-mock3-indexG3_S3
processed data file: RawReadCounts_Human.tsv

value: 24hrs after treatment


title: Series1_NHBE_SARS-CoV-2_2

description:
SARS004-CoV2-2_S5
processed data file: RawReadCounts_Human.tsv

source_name: SARS-CoV-2 infected NHBE cells

extract_protocol:
TruSeq Stranded mRNA LP
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
TruSeq RNA Library Prep Kit v2 (A549) or TruSeq Stranded mRNA LP (NHBE) according to the manufacturer’s instructions

value: NHBE

value: primary human bronchial epithelial cells

value: SARS-CoV-2 infected (MOI 2)


title: Series1_NHBE_SARS-CoV-2_1

description:
SARS004-CoV2-3_S6
processed data file: RawReadCounts_Human.tsv


title: Series1_NHBE_Mock_2

description:
SARS004-mock-2_S2
processed data file: RawReadCounts_Human.tsv

source_name: Mock treated NHBE cells


title: Series1_NHBE_Mock_3

description:
SARS004-mock-1_S1
processed data file: RawReadCounts_Human.tsv


title: Series1_NHBE_Mock_1

description:
SARS004-mock-3_S3
processed data file: RawReadCounts_Human.tsv


title: M-stress/treatment 4

status: Public on Mar 12 2020

city: New York City

first: Jun

last: Wang

address: 1 Gustave L. Levy Pl, New York

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
STAR(2.6.1d) maps the reads to the genome
samtools(1.9) indexes BAM files
featureCounts(subread/1.6.3) counts reads to genomic features
Data were filtered using sum(counts) in all samples >= 20
edgeR package to generate normalized expression data
Genome_build: mm10(Mus_musculus.GRCm38.83.gtf)
Supplementary_files_format_and_content: tab-delimited text file includes expression values for each Sample (row:genes, column:samples, first column is gene id)

source_name: M-stress/treatment

extract_protocol:
Total RNA was isolated using the Qiagen RNA-easy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were treated with vehicle or dihydrocaffeic acid/malvidin-glucoside two weeks prior to and throughout the social defeat paradigm

tag: Sex

value: male

value: PFC

value: 10 weeks

value: wild type

tag: stress

value: social defeat stress

value: dihydrocaffeic acid/malvidin-glucoside


title: M-stress/treatment 2


title: M-stress/treatment 1


title: Series1_NHBE_SARS-CoV-2_3

description:
SARS004-CoV2-1_S4
processed data file: RawReadCounts_Human.tsv

tag: cell line

tag: time point


title: M-stress/treatment 3


title: M-stress/vehicle 5

source_name: M-stress/vehicle

value: vehicle


title: P20P-405254A-T-RNA [S144]

status: Public on Mar 10 2020

city: Durham

first: David

last: Kirsch

state: NC

address: PO Box 96100

institute: Duke University

data_processing:
Base-calling was done on the instrument using RTA v3.3.3.
Demultiplexing was done using bcl2fatq v2.20.0.422
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic v0.36
Reads were mapped to mouse mm10 genome using STAR v5.5.4b and quantified to features using HT-Seq built in the STAR aligner.
Genome_build: mm10
Supplementary_files_format_and_content: csv file with read counts per gene

growth_protocol: Primary p53/MCA sarcomas were generated in mice between 6-10 weeks old by  intramuscular Adeno-Cre injection into the gastrocnemius of p53FL/FL mice, followed by injection of 300 µg MCA (Sigma-Aldrich) resuspended in sesame oil (SigmaAldrich) at 6 µg/µl. Allograft p53/MCA sarcomas were generated by injecting 50,000 cells resuspended in 100 uL DMEM (Gibco) and Corning matrigel from cell line 402230 into the gastrocnemius muscle of syngeneic mice.

extract_protocol:
Tumor specimens and matched liver control were harvested and stored in RNALater at -80° until all samples were collected. DNA and RNA extractions from each sample were performed using AllPrep DNA/RNA Mini Kit (Qiagen). Extracted total RNA quality and concentration was assessed on a 2100 Bioanalyzer (Agilent Technologies) and Qubit 2.0 (ThermoFisher Scientific), respectively. Only extracts with RNA Integrity Number (RIN) greater than 7 were processed for sequencing. DNA extraction was followed by RNAse treatment (Qiagen). Genomic DNA samples were quantified using fluorometric quantitation on the Qubit 2.0 (ThermoFisher Scientific). For each sample, 200 ng of DNA was sheared using focused-ultrasonicators (Covaris) to generate DNA fragments of about 300 bp in length.
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer’s protocol. In brief, mRNA transcripts were first captured using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed using random priming. During the 2nd strand synthesis, the cDNA:RNA hybrid was converted into to double-stranded cDNA (dscDNA) and dUTP incorporated into the 2nd cDNA strand, effectively marking the second strand. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. The strand marked with dUTP was not amplified, allowing strand-specificity sequencing.
Libraries were indexed using a dual indexing approach allowing for multiple libraries to be pooled and sequenced on the same sequencing Illumina sequencing flow cell.

treatment_protocol: Tumors were treated when volume reached ~150 mm3 and harvested 3 days later. Mice received  200 ug IP of either muDX400 (Merck, murine anti-PD-1) or isotype control followed immediately by 0 or 20 Gy radiation. For mice receiving radiation, the tumor-bearing hind limb of the mice was irradiated with 20 Gy using the X-RAD 225Cx small animal image-guided irradiator (Precision X-Ray). The irradiation field included the whole left hind limb and was defined using fluoroscopy with 40 kVp, 2.5 mA X-rays using a 2 mm Al filter. Irradiations were performed using parallel-opposed anterior and posterior fields with an average dose rate of 300 cGy/min prescribed to midplane with 225 kVp, 13 mA X-rays using a 0.3 mm Cu filter.

tag: strain background

tag: replicate group

tag: barcode

value: TCCGCGAA+CCTATCCT

tag: tumor type

value: Primary

tag: radiation dose


title: HepG2_RNASeq

city: Wako

first: Itoshi

last: Nikaido

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

data_processing:
(Fr-1 ~ Fr-5, and RNA) Sequenced reads were trimmed with retaining last 50 bps using fastx_trimmer (-l 50).
(Fr-1 ~ Fr-5) Sequenced reads were mapped to hg38 whole genome using hisat2 v2.0.4 (samtools 0.1.19)  with parameters -p 24, then sorted and converted to bed.
(Fr-1 ~ Fr-5) Sequence reads were scaled to their read counts using wiggletools "scale".
(Fr-1 ~ Fr-5) Bam data were converted to wig (bam2wig.py -t 8500000000 -u -s hg38.chrom.sizes) and evaluate Fr-5/Fr-1 ratio using wiggletools "ratio" and "log 2"
(RNA-seq) TPM of each gene was evaluated using sailfish (SailfishBeta-0.10.0_CentOS5) quant -p 20 -l SR, and -i "hg38 gene of ensembl76"
Genome_build: hg38
Supplementary_files_format_and_content: wig format data and tab-delimited text files include TPM of each gene

source_name: HepG2 cells

growth_protocol: HepG2 cells were cultured in a minimum essential medium with alpha-modification supplemented with 10% fetal bovine serum.

extract_protocol:
Cell extracts for the chromatin fractionation were prepared as follows: treatment with formaldehyde, solubilization, and fragmentation by sonication. Total RNA was prepared using an RNeasy MinElute Cleanup Kit (#74204, Qiagen).
The DNA in the fractions was sheared with an LE220 Focused-ultrasonicator (Covaris), and converted to a sequence library using a KAPA Hyper Library Preparation Kit (KAPA Biosystems). Total RNA from HepG2 cells was converted to a sequence library using a KAPA Stranded mRNA-seq Kit (KAPA Biosystems).

tag: cell type

value: hepatocyte carcinoma

tag: fractional distribution