title: OMP_Day6_3

description: 6 day treatment

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38)
Supplementary_files_format_and_content: Tab-delimited text file includes rpkm normalized table for each sample

source_name: Leukemic cell

growth_protocol: Nras(G12D)/MLL–AF9 cells were cultured in RPMI medium supplemented with 10 % Fetal Bovine Serum (FBS), L-glutamine, penicillin streptomycin, recombinant mouse SCF, IL-3, and IL-6.

extract_protocol:
Total RNA were extracted using RNeasy Mini Kit (Qiagen).
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

treatment_protocol: Nras(G12D)/MLL-AF9 cells were treated with 100 micro molar OMP for 6 days, while the same volume of PBS was used as vehicle.

value: Blood

value: OMP 100 micro molar


title: GS1499_1acute_DHF_DN_100

status: Public on Jan 13 2020

type: SRA

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Research Center

library_source: transcriptomic

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to GRCh38 reference genome and Gencode 27 annotations using TopHat v1.4.1 (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite v0.20.3 (Schmieder and Edwards, 2011) and low-complexity reads (DUST > 4) were removed from the BAM files. The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (Anders et al., 2015) using the “union” option. After removing absent features (zero counts in all samples), the raw counts were then imported to DESeq2 to identify differentially expressed genes between groups (Love et al., 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file containing DESeq2 counts with variance stabilizing transformation

molecule: polyA RNA

organism: Homo sapiens

source_name: Cryopreserved PBMC

extract_protocol:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
For each condition, 100 cells were collected at 4 ˚C in 8 μL of lysis buffer composed by 0.2% Triton X-100, 2 U/ul of recombinant RNase inhibitor (Clontech/Takara), 5 mM dNTP mix (Life Technologies) in 0.2 ml PCR tube (Maxymum recovery, Axygen). Right after sort, tubes were vortexed at medium speed, spun for 5 minutes at >2000 g and stored at -80˚C until the completion of the whole set of samples. Purified total RNA (≈5 ng) was amplified following the Smart-seq2 protocol (Picelli et al., 2014; Rosales et al., 2018). Briefly, mRNA was captured using poly-dT oligos and directly reverse-transcribed into full-length cDNA using the described template-switching oligo (Picelli et al., 2014; Rosales et al., 2018). cDNA was amplified by PCR for 18 cycles and purified using AMPure XP magnetic bead (0.9:1 (vol:vol) ratio, Beckman Coulter).
For each sample, 1 ng of cDNA was used to prepare a standard NextEra XT sequencing library (NextEra XT DNA library prep kit and index kits; Illumina). Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR preamplification cycles, and fragment library size. Samples that failed quality controls were eliminated from downstream steps. Library that passed strict quality controls were pooled at equimolar concentration, loaded and sequenced on the Illumina Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina) mapping uniquely to mRNA reference, generating a total of about 204.3 million mapped reads (median of about 8.6 million filtered mapped reads per sample).

treatment_protocol: Human PBMCs were rested overnight at 37 °C and subsequently stimulated with DENV CD4 T cell peptide pool (1 μg/ml for individual peptides) for 3 h at 37 °C. IFN-g- and IL-10-producing cells were labeled using IFN-γ Secretion Assay – Detection Kit (PE), human (catalog# 130-054-202, Miltenyi Biotech) and IL-10 Secretion Assay – Detection Kit (APC), human (catalog# 130-090-761, Miltenyi Biotech), respectively, according to the manufacturer’s instructions. Subsequently, PBMCs were stained with anti-human CD3, CD4, CD8, CD14, CD19, CD45RA, and CCR7. CD4 IL-10-IFN-g- DN, IL-10+IFN-g- IL-10 SP and IL-10-IFN-g+ IFN-g SP, and IL-10+IFN-g+ DP cells were sorted into 8 μL of lysis buffer consisting of Triton X-100 (Sigma-Aldrich), recombinant ribonuclease inhibitor (Takara), and dNTP mix (Thermo Fisher Scientific).

tag: disease group

value: DHF

tag: donor

tag: cell type

value: PBMC

tag: cell subset

value: DN


title: OMP_Day6_2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: 6 day treatment

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: treatment


title: M_02_7d_750: Rv2558

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description: Rats were gavaged daily with acetamide in water vehicle

data_processing:
Illumina NextSeq 500 control software v2.1.0 with BCL files uploaded to Illumina BaseSpace for FASTQ file generation
Sequences trimmed from both based on QC (TRIMMOMATIC, min. retained read length 50bp), and mapped to Illumina iGenomes UCSC Rn6 using BOWTIE2
SAM files to BAM, and gene counts extracted from BAM files with HTSeq
Genome_build: UCSC Rn6 (Illumina iGenomes)
Supplementary_files_format_and_content: Tab delimited text files of gene counts

organism: Rattus norvegicus

source_name: Liver (left lobe)

extract_protocol:
Total RNA was isolated using the Maxwell RSC Simply RNA Tissue Kit (Promega, Cat No: AS1340).
Library preparation was accomplished using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, CatNo: RS-122-2103)

treatment_protocol: Rat were gavaged daily with water vehicle or acetamide, and the left lobe of the liver collected (at 7 or 28 days) for RNA-seq analysis.

value: Liver (left lobe)

tag: strain

tag: Sex

value: Male

tag: age

tag: age unit

value: weeks

value: Acetamide

tag: treatment cas

tag: dose

tag: dose unit

value: mg/kg/day

tag: treatment duration

tag: duration unit

value: days

tag: replicate

tag: exposure series

value: Exposure Experiment 2


title: Air_D21_rep3 [Lung miRNA]

type: RNA

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

description: Gene expression from rat blood

hyb_protocol: Following Labeling procedure, .88 ug were hybridized at 45C on miRNA-4.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: TAC 4.0 was used with annotation miRNA-4_1-st-v1.annotations.20160922.csv to generate RMA expression values. Linear models were fit using the limma package of bioconductor in R version 3.4

label: biotin

source_name: lung, control, 21 days

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: One hundred thirty-four healthy, male, 9 weeks old Sprague-Dawley rats, weighing an average of 300 grams were purchased from Taconic Farms Inc. (Hudson, NY). The rats were allowed to acclimatize for 1 week before the studies were initiated. Baseline data was collected for 1 week before the exposures occurred. The rats were maintained on a 12-hour light/dark cycle and food and water were provided ad libitum. Upon arrival, animals were randomly assigned a unique identification number, which determines the exposure group for the animal. There were two treatment groups: a) Control group: high efficiency particulate air (HEPA) filtered air, and b) PEPs Exposure group. All the animals were treated humanely in accordance with the guiding principles on the Use of Animals in Toxicology and the Animal Care and Use Committee of Harvard University (Ethical permit No.- 04623).

extract_protocol: Total RNA was isolated from rat blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol. Rat lungs were initially disrupted by transferring them to a 2 mL microcentrifuge tube containing 400 μL silica beads and 600 μL Lysis/Binding Solution.

treatment_protocol: The exposed group consisted of rats housed in individual cages and exposed via full body inhalation to PEPs and gaseous pollutants emitted by laser printer B1 using the Printer Exposure Generation System (PEGS) described in detail in a previous publication (Pirela et al, 2014). (Supplementary Material, Figure S1). In summary, printer B1 was used to generate PEPs emissions by printing a 5%-page coverage monochrome document using standardized settings (Pirela et al 2014). The laser printer B1 was selected based on exposure profiles reported in our previous studies (Pirela et al., 2014). In parallel, another group of rats was exposed to HEPA filtered air. The system was configured for twelve chambers (one animal per chamber), each equipped with a port for aerosol delivery and temperature and humidity measurement, a water bottle port, and a gas sampling port.   The whole exposure experiment was repeated twice, in 2016 and 2017. Animals were placed in their chambers for 1-5 hours for 5 days prior to the exposures to ensure they gradually acclimated to exposure chambers before the exposures occurred. The following week, animals were exposed to PEPs pollutants and the room HEPA-filtered air 5 hours/day for 21 consecutive days.

value: 9 weeks old

value: male

value: Sprague-Dawley

value: lung


title: M_01_7d_750: Rv2557


title: OMP_Day6_1

description: 6 day treatment


title: Vehicle_Day6_3

description: 6 day treatment

value: Vehicle


title: GS1435_1acute_DF_IL10_pos_48

tag: disease group

value: DF

tag: donor


title: GS1430_1acute_DF_DP_100

tag: cell type

tag: cell subset

value: DP


title: Vehicle_Day6_2

description: 6 day treatment

tag: tissue

value: Blood

tag: cell line


title: F_05_7d_500: Rv2555

tag: strain

value: Female

tag: treatment


title: F_04_7d_500: Rv2554

tag: Sex

tag: age


title: GS1448_1acute_DF_IFNg_pos_29

value: PBMC


title: GS1441_1acute_DF_IFNg_pos_100


title: Air_D21_rep1 [Lung miRNA]

description: Gene expression from rat blood


title: F_03_7d_500: Rv2553

value: Liver (left lobe)

tag: age unit

tag: treatment cas


title: Control tissue_3

city: Ithaca

first: Alexander

middle: Yu.

last: Nikitin

state: NY

address: 618 Tower Road T6 018A VRT

institute: Cornell Universty

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts for annotated genes (UCSC mm10).
cuffnorm v2.2.1 was used to generate FPKM values for annotated genes (UCSC mm10).
Genome_build: Mouse mm10 (UCSC)

source_name: Gastric squamous-columnar junction tissue

extract_protocol:
Indicated tissue were collected, washed by sterile PBS twice, and RNA was extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560).
Library construction protocol: Directional RNA-seq libraries were prepared from 800ng total RNA using the NEBNext Directional Ultra RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

tag: genotype/variation

value: wild type

value: Gastric squamous-columnar junction

tag: tissue subtype

value: control tissue


title: Vehicle_Day6_1

description: 6 day treatment


title: GS1435_1acute_DF_IFNg_pos_100


title: F_02_7d_500: Rv2552

value: weeks

value: Acetamide

tag: dose

tag: dose unit

value: mg/kg/day

tag: treatment duration

tag: duration unit


title: PEP_D21T_rep3 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 21 days, implanted with radio telemetry system

label_protocol: Biotinylated total RNA were prepared according to the Affymetrix Flashtag Biotin HSR RNA Labeling Kit protocol from 1 ug total RNA (Affymetrix Flashtag Biotin HSR RNA Labeling Kit Manual, P/N 703095 Rev. 2)

value: 9 weeks old

value: blood


title: Air_D21T_rep4 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, control, 21 days, implanted with radio telemetry system

value: male

value: Sprague-Dawley


title: GS1430_1acute_DF_IFNg_pos_100

tag: disease group

tag: donor


title: F_01_7d_500: Rv2551

value: days

tag: replicate

tag: exposure series

value: Exposure Experiment 2


title: Control tissue_2

tag: tissue


title: Air_D21T_rep3 [Blood miRNA]

description: Gene expression from rat blood

tag: strain


title: PEP_D21T_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D21T_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D21T_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: GS1448_1acute_DF_DN_100

value: DF

tag: cell type

tag: cell subset

value: DN


title: Cancer_5

source_name: Gastric squamous-columnar junction cancer

value: cancer tissue


title: Air_D21T_rep2 [Blood miRNA]

description: Gene expression from rat blood

tag: age

tag: Sex


title: M_04_7d_500: Rv2548

value: Male

tag: age unit

tag: treatment

tag: treatment cas


title: GS1441_1acute_DF_DN_100

value: PBMC


title: GS1435_1acute_DF_DN_100


title: Cancer_4

tag: genotype/variation

tag: tissue subtype


title: PEP_D1_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 1 day


title: Air_D21T_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: GS1430_1acute_DF_DN_100


title: PEP_D1_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D1_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: M_02_7d_500: Rv2546

value: Liver (left lobe)

tag: dose

tag: dose unit

tag: treatment duration


title: Cancer_2

value: Gastric squamous-columnar junction


title: PEP_D1_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: Cancer_1


title: STRIPEseq_S288C_100ng_diamide_3

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
Library strategy: STRIPE-seq
Human and yeast STRIPE-seq samples were processed from .fastq to coordinate sorted .bam files using the GoSTRIPEs computational workflow (https://github.com/BrendelGroup/GoSTRIPES)
TSSs and TSRs were called using TSRchitect (v1.8.9) as part of the GoSTRIPES workflow. TSSs with less than 3 reads were filtered out, and TSSs within 40 bases were clustered into TSRs.
TSS bedgraphs and TSR beds derived from TSRchitect were CPM normalized via edgeR (v3.28.0) and exported with rtracklayer (v1.42.1)
For human and yeast RNA-seq samples, rRNA reads were first removed using tagdust (v2.33.0) with additional settings -fe 3 -dust 97
STAR (v2.7.0e) was used to generate genome indices (with the additional setting --genomeSAindexNbases 10 for yeast) and align reads to coordinate sorted bam files.
Rsubread (v1.6.4) featureCounts was utilized to count fragments overlapping annotated exons.
RNA-seq bigwigs were generated with deepTools (3.3.0) bamCoverage using the settings -bs 1 --normalizeUsing CPM --smoothLength 25. RNA-seq libraries were constructed using the dUTP method, so coverage of positively-stranded transcripts was obtained with --filterRNAstrand forward, which excludes positively-stranded reads, as negatively-stranded reads correspond to positively-stranded transcripts in the dUTP protocol. Similarly, coverage of negatively-stranded transcripts was obtained with --filterRNAstrand reverse.
Genome_build: human (GRCh38.p13), yeast (R64-1-1)
Supplementary_files_format_and_content: CPM-normalized RNA-seq signal (.bw), CPM-normalized TSS signal (.bedgraph), CPM-normalized TSR signal (.bed).

organism: Saccharomyces cerevisiae

growth_protocol: YPD to mid-log phase at 30°C

extract_protocol:
Lucigen MasterPure Yeast RNA Purification Kit
STRIPE-seq
stripe-seq-library-construction-2ivgce6.pdf

value: 0.5 mM diamide (1 hour)

tag: input to technology


title: GS1416_1acute_DF_DN_100

tag: disease group

tag: donor


title: F_05_7d_300: Rv2543

tag: tissue

value: Female

value: weeks

tag: duration unit

tag: replicate

tag: exposure series


title: KA_control_3

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description: counts.xls

data_processing:
Illumina's bcl2fastq  v1.8.4 software used for extraction of FASTQ files
Reads were mapped using Tophat (v1.4.1) to the mm10 genome taken the refFlat annotation (version 2014-04-25) into account:  tophat -o OUTPUTDIR -G mm10_refFlat_2014_04_25.gtf -T -x 1 --no-novel-juncs mm10_genome fastq-file
Counting of reads per gene was done using htseq-count (v0.6.1): htseq-count --stranded=no --mode=union MAPPING_OUTPUT mm10_refFlat_2014_04_25.gtf > OUTPUTFILE
Genome_build: mm10, refFlat annotation (version 2014-04-25)
Supplementary_files_format_and_content: Excel file contains raw counts

source_name: primary neurons

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Quiagen).
Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit v2 following the manufacturer’s instruction.

tag: strain

tag: cell type

value: primary neurons


title: Air_D1_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, control, 1 day

tag: age

value: 9 weeks old

tag: Sex


title: F_04_7d_300: Rv2542

tag: age unit

tag: treatment

value: Acetamide

tag: treatment cas

value: mg/kg/day


title: KA_control_2

description: counts.xls


title: M_03_7d_500: Rv2547

tag: dose


title: STRIPEseq_S288C_100ng_diamide_1


title: STRIPEseq_S288C_100ng_diamide_2


title: Cancer_3

tag: genotype/variation

tag: tissue subtype


title: M_01_7d_500: Rv2545

tag: dose unit

tag: treatment duration


title: KA_control_1

description: counts.xls


title: F_03_7d_300: Rv2541


title: Air_D1_rep3 [Blood miRNA]

description: Gene expression from rat blood

value: male

value: Sprague-Dawley

value: blood


title: STRIPEseq_S288C_250ng_untreated_3

value: untreated

tag: input to technology


title: F_02_7d_300: Rv2540

tag: tissue

value: days

value: Exposure Experiment 2


title: Air_D1_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: Air_D1_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: STRIPEseq_S288C_250ng_untreated_2


title: Air_D5_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, control, 5 days


title: KA_2

description: counts.xls

value: Kainac acid (100 μM in culture medium)


title: M_05_7d_300: Rv2537

value: Male

tag: duration unit


title: Control tissue_1

value: wild type

value: control tissue


title: KA_1

description: counts.xls


title: M_04_7d_300: Rv2536

value: Liver (left lobe)

tag: replicate


title: OGD_control_3

description: counts.xls


title: M_03_7d_300: Rv2535

tag: exposure series


title: STRIPEseq_S288C_100ng_untreated_2

tag: strain


title: OGD_control_2

description: counts.xls

tag: cell type


title: Air_D5_rep4 [Blood miRNA]

description: Gene expression from rat blood

tag: age


title: M_02_7d_300: Rv2534

tag: Sex


title: Air_D1_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: OGD_control_1

description: counts.xls


title: F_01_7d_300: Rv2539

value: Female

tag: age unit


title: M_01_7d_300: Rv2533

value: weeks

tag: treatment


title: STRIPEseq_S288C_50ng_untreated_3

value: 50 ng


title: STRIPEseq_S288C_250ng_untreated_1


title: STRIPEseq_S288C_100ng_untreated_3


title: Air_D5_rep3 [Blood miRNA]

description: Gene expression from rat blood

value: 9 weeks old


title: F_05_7d_0: Rv2531

value: Acetamide

tag: treatment cas


title: OGD_2

description: counts.xls

value: primary neurons

value: OGD (oxygen-glucose deprivation)


title: OGD_3

description: counts.xls


title: F_04_7d_0: Rv2530

tag: dose

value: mg/kg/day


title: STRIPEseq_S288C_50ng_untreated_1


title: STRIPEseq_S288C_100ng_untreated_1


title: RNAseq_S288C_10ug_diamide_3

data_processing:
Human and yeast STRIPE-seq samples were processed from .fastq to coordinate sorted .bam files using the GoSTRIPEs computational workflow (https://github.com/BrendelGroup/GoSTRIPES)
TSSs and TSRs were called using TSRchitect (v1.8.9) as part of the GoSTRIPES workflow. TSSs with less than 3 reads were filtered out, and TSSs within 40 bases were clustered into TSRs.
TSS bedgraphs and TSR beds derived from TSRchitect were CPM normalized via edgeR (v3.28.0) and exported with rtracklayer (v1.42.1)
For human and yeast RNA-seq samples, rRNA reads were first removed using tagdust (v2.33.0) with additional settings -fe 3 -dust 97
STAR (v2.7.0e) was used to generate genome indices (with the additional setting --genomeSAindexNbases 10 for yeast) and align reads to coordinate sorted bam files.
Rsubread (v1.6.4) featureCounts was utilized to count fragments overlapping annotated exons.
RNA-seq bigwigs were generated with deepTools (3.3.0) bamCoverage using the settings -bs 1 --normalizeUsing CPM --smoothLength 25. RNA-seq libraries were constructed using the dUTP method, so coverage of positively-stranded transcripts was obtained with --filterRNAstrand forward, which excludes positively-stranded reads, as negatively-stranded reads correspond to positively-stranded transcripts in the dUTP protocol. Similarly, coverage of negatively-stranded transcripts was obtained with --filterRNAstrand reverse.
Genome_build: human (GRCh38.p13), yeast (R64-1-1)
Supplementary_files_format_and_content: CPM-normalized RNA-seq signal (.bw), CPM-normalized TSS signal (.bedgraph), CPM-normalized TSR signal (.bed).

extract_protocol:
Lucigen MasterPure Yeast RNA Purification Kit
RNA-seq (Illumina TruSeq Stranded mRNA Library Prep Kit)
stripe-seq-library-construction-2ivgce6.pdf

value: 0.5 mM diamide (1 hour)

value: 10 ug


title: OGD_1

description: counts.xls


title: F_03_7d_0: Rv2529

value: days


title: RNAseq_S288C_10ug_diamide_2


title: STRIPEseq_S288C_50ng_untreated_2

value: untreated


title: F_02_7d_0: Rv2528

value: Exposure Experiment 2


title: RNAseq_S288C_10ug_diamide_1


title: F_01_7d_0: Rv2527


title: Air_D5_rep2 [Blood miRNA]

description: Gene expression from rat blood

value: male

value: Sprague-Dawley

value: blood


title: RNAseq_S288C_10ug_untreated_3


title: M_05_7d_0: Rv2525

value: Liver (left lobe)

value: Male


title: RNAseq_S288C_10ug_untreated_2


title: S4B_NS: postoperative plasmas 4

city: Wuhan

first: Wen

last: Xiao

address: 1277 Jiefang Avenue

department: Department of Urology

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Gene expression postoperative

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The miRNA expression profiling was performed using the Agilent Human miRNA microarray 18.0 (Agilent Technolo-gies, Santa Clara, USA),  The fluorescent intensities were calculated using Feature extraction software(Agilent Technologies, Santa Clara, USA).

source_name: postoperative plasmas 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Plasma samples were extracted from EDTA-K 2 tubes and centrifuged at 800g, for 10 minutes at 40C to remove cells and centrifuged again,at 12,000g for 15 minutes at 40C to remove cellular debris, and then stored in a deep freezer at -80°C.  All plasmas were obtained within 4 hours after drawing blood and stored at -80°C for further RNA extraction.

treatment_protocol: 5 patients plasma samples  with ccRCC preoperatively and at day 7 postoperatively

value: whole blood


title: S5B_NS: postoperative plasmas 5

description: Gene expression postoperative

source_name: postoperative plasmas 5


title: M_04_7d_0: Rv2524

value: weeks


title: PEP_D5_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 5 days

value: 9 weeks old


title: PEP_D5_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: Air_D5_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: RNAseq_S288C_10ug_untreated_1


title: S2B_NS: postoperative plasmas 2

description: Gene expression postoperative

source_name: postoperative plasmas 2


title: S3B_NS: postoperative plasmas 3

description: Gene expression postoperative

source_name: postoperative plasmas 3


title: PEP_D9_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 9 days


title: M_03_7d_0: Rv2523

value: Acetamide


title: PEP_D5_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: S1B_NS: postoperative plasmas 1

description: Gene expression postoperative

source_name: postoperative plasmas 1


title: M_02_7d_0: Rv2522

source_name: Liver (left lobe)


title: S5A_NS: preoperative plasmas 5

description: Gene expression preoperative

source_name: preoperative plasmas 5


title: PEP_D5_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D5_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D9_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: S4A_NS: preoperative plasmas 4

description: Gene expression preoperative

source_name: preoperative plasmas 4


title: Hi-C chl4Δ - No tension

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

library_source: genomic

data_processing:
Fastq reads aligned to sacCer3 using HiC-Pro v2.11.1 , bowtie2 v2.3.4.1 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder), removing singleton, multi hit and duplicated reads.
Valid interaction pairs were converted into the .cool contact matrix format using cooler (1 kb resolution)
Matrixes balanced using Iterative correction
Genome_build: SacCer3
Supplementary_files_format_and_content: Cooler .cool matrix 1kb binned, balanced with iterative correction

molecule: genomic DNA

source_name: Hi-C chl4Δ - No tension

growth_protocol: Cells were diluted to OD(600)=0.2 and arrested G1 with alpha factor for 3 hours, then released into a metaphase arrest by depletion of Cdc20 for 2 hours. "No tension" condition included addition of nocodazole and benomyl, "Tension" condition did not.

extract_protocol:
Lysates were prepared by grinding the frozen pellet in a chilled mortar with a pestle for 15 minutes and 1/10th of the initial pellet weight (~0.5 g) was taken for further processing. Restriction enzyme digestion (DpnII), filling-in, ligation, crosslink reversal, DNA concentration and purification and biotin removal were carried out as described in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038. DNA was then fragmented on a Bioruptor Plus sonication device (Diagenode) for a total of 2x 30 cycles 30 seconds on/off at High setting.
DNA end repair and A-tailing using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I were carried out as in Schalbetter et al., 2018. Hi-C libraries were fractionated using Ampure XP beads as previously described in Belton et al. (2015) DOI: 10.1101/pdb.prot085209. Biotin pull-down, adapter ligation (NextFlex, Bioo Scientific) and sequencing (EMBL Core Genomics Facility, Heidelberg, Germany) were carried as in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038.

treatment_protocol: Cells were fixed and lysed as in Belton & Dekker (2015) DOI: 10.1101/pdb.prot085209. Briefly, 200 ml of cells at OD~0.6 carrying pMET-CDC20 were arrested in metaphase at 25 ˚C in the presence and absence of tension as described above, fixed with 3% formaldehyde for 20 minutes at 25 ˚C at 250 rpm and the reaction was quenched for 5 minutes by the addition of 0.35 M glycine (final concentration). Cells were washed with cold water, resuspended in 5 ml 1x NEBuffer 2 and frozen in liquid nitrogen.

tag: target

tag: cell cycle stage

value: Metaphase

tag: tension / no tension

value: No tension (Nocodazole treatment)


title: TpFp3

city: Barcelona

middle: Eduardo

last: Rech

address: Passeig Marítim de la Barceloneta 37-49

country: Spain

institute: Consejo Superior de Investigaciones Cientificas - Institute of Evolutionary Biology (CSIC-UPF)

data_processing:
BCL base call files were converted to FASTQ per sample using CASAVA v1.8.2 (default parameters).
Trimming of Illumina reads was performed using the tool Trimmomatic V0.30, whit the following options: LEADING: 11 TRAILING: 11 SLIDINGWINDOW: 4:20 MINLEN: 24.
We used Tophat v2.0.8, which uses Bowtie v2, to map RNA-seq reads to the reference genome. We used the B73 Zea mays genome (version 3.27) downloaded from the MAIZEDB site (http://www.maizegdb.org/). We used default parameters in Tophat, except in the following cases: --mate-inner-dist 60; --mate-std-dev 50; --library-type fr-secondstrand; --no-discordant; --no-mixed; -g 2.
Using BAM files obtained from mapping all reads per sample and the GTF file B73 Zea mays genome (version 3.27) downloaded from the MAIZEDB, we applied featureCounts (http://bioinf.wehi.edu.au/featureCounts/) to count how many reads map to each feature using the following parameters: -s 1 -p -t exon -g gene_id
Genome_build: B73 Zea mays genome (version 3.27) ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/zea_mays/dna/
Supplementary_files_format_and_content: Tab-delimited text files include ROW COUNTS reads for each sample.

organism: Zea mays

source_name: maize silk samples

growth_protocol: B73 maize seeds were planted in pots with soil and grown in greenhouse under controlled conditions. Ten days after germination the incipient roots were inoculated with 2 ml of trichoderma atroviride spores/ml. Four days after maize silks appearence, they were inoculated with 2 ml of Fusarium verticillioides spores/ml. 24 ours after infection the silks were collected and storaged until their usage.

extract_protocol:
RNA was extracted with Trizol according the manufacturing instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA seq (paired- ends (PE) 2x100bp Illumina Hiseq 1500)

treatment_protocol: Samples inoculated with Trichoderma and infected with Fusarium and the respective controls were maintained at -80 until the total RNA extraction moment.

tag: cultivar

value: maize silk

tag: developmental stage

value: 4 days post emergency

tag: inoculation-infection

value: Trichoderma and Fusarium


title: S3A_NS: preoperative plasmas 3

description: Gene expression preoperative

source_name: preoperative plasmas 3

tag: tissue


title: Hi-C sgo1Δ - No tension

source_name: Saccharomyces cerevisiae cells

tag: genotype


title: Hi-C sgo1-3A - No tension


title: Air_D9_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, control, 9 days


title: PEP_D9_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: TpFp2


title: PEP_D9_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: Hi-C reoriented - Tension

source_name: Hi-C reoriented - Tension

value: RE

value: Tension


title: Hi-C chl4Δ - Tension


title: S2A_NS: preoperative plasmas 2

description: Gene expression preoperative

source_name: preoperative plasmas 2


title: RNASeq_KO

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description: Mitochondria were isolated from homogenized hearts or skeletal muscle and isolated by differential centrifugation as described previously  (Rackham et al., 2016; Richman et al., 2016a).

data_processing:
Supplementary_files_format_and_content: Strand-specific coverage for each sample in wiggle format, normalised by total library size (RPM). BED files of ribosome profiling peaks for each sample, with normalised coverage scores (RPM).
wig files: Strand-specific coverage of the primary alignments of properly paired, full-length RNA fragments (excluding those with a length > 500 nt) across the mitochondrial genome was calculated with samtools v1.7  (Li et al., 2009)  and bedtools genomecov v2.26.0  (Quinlan and Hall, 2010) normalised to library size.
Supplementary_files_format_and_content: Strand-specific coverage for each sample in wiggle format, normalised by total library size (RPM).

source_name: Heart mitochondria

growth_protocol: Mice were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-h light/dark schedule (lights on 7 am to 7 pm) in controlled environmental conditions of 22 ± 2 °C and 50 + 10% relative humidity and fed a normal chow diet and water were provided ad libitum.

extract_protocol:
RNA was isolated from total hearts or heart mitochondria using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Total RNA libraries were prepared according to the Illumina TruSeq protocol, using random hexamer primers for cDNA generation and the Ribo-Zero rRNA removal kit for cytoplasmic RNA deptetion. RNA sequencing libraries for ribosome profiling were prepared using the Illumina Small RNA Sample Prep Kit, with a size selection step for 15-90 nt RNAs.

value: Heart

value: 25 weeks

value: Mtif3loxP/loxPloxP/loxP, +/Ckmm


title: Air_D9_rep4 [Blood miRNA]

description: Gene expression from rat blood

value: male

value: Sprague-Dawley

value: blood


title: S1A_NS: preoperative plasmas 1

description: Gene expression preoperative

source_name: preoperative plasmas 1

value: whole blood


title: PEP_D9_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: Hi-C Wild type - Tension

value: Wild type


title: M_01_7d_0: Rv2521

value: Liver (left lobe)

value: Male

value: weeks

tag: dose unit

value: mg/kg/day

tag: treatment duration

tag: duration unit

value: days

tag: replicate

tag: exposure series

value: Exposure Experiment 2


title: Air_D9_rep1 [Blood miRNA]

description: Gene expression from rat blood

tag: age

value: 9 weeks old

tag: Sex

tag: strain


title: TpFm3

value: maize silk

value: 4 days post emergency

value: Trichoderma


title: Air_D9_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: RNASeq_WT

value: Heart

value: 25 weeks


title: Air_D17_rep4 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, control, 17 days

value: male


title: Hi-C Wild type - No tension

description: WT-NT

value: Metaphase

tag: treatment

value: No tension (Nocodazole treatment)


title: BAR5: AM1105_tension_WT

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 10, min. length 30, standard illumina adapter AGATCGGAAGAG)
Reads were mapped to sacCer3 with STAR
parameters(--outReadsUnmapped Fastx, --outFilterIntronMotifs RemoveNoncanonicalUnannotated)
samtools was used to filter primary and unique alignments
chrMito was excluded using bedtools
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization)

source_name: Saccharomyces cerevisiae cell

growth_protocol: Cells were arrested G1 with alpha factor then releases into a metaphase arrest by depletion of Cdc20. "No tension" condition included addition of nocodazole and benomyl. Tension condition included addition of DMSO.

extract_protocol:
RNA seq library with RNA depletion prep.
All samples were prepared using a liquid handling robot (Hamilton) by Bianka Baying (EMBL, Heidelberg, Germany). 10ng of each sample mixed with library preparation were assessed according to manufacturer's recommendation (NEBNext Ultra™ DNA Library Prep Kit for Illumina, (#E7370S/L)). Library preparation was done according to manufacturer. Briefly, the Adapter in the Adapter Ligation step was diluted 1:30 in water. The size selection step was performed with Ampure XP Beads from Beckman Coulter (insert size 200-250bp). The PCR amplification was performed in 15 cycles. Finally NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (#E7335S/L) were used for the Indexing. The quality and quantity of the libraries was checked using the Agilent BioAnalyzer and the Qubit dsDNA HS Assay kit (Invitrogen).
Sequencing was performed  Illumina NextSeq 500 Sequencer with Requested Read Length 75, paired end.

treatment_protocol: RNA was prepared

value: Tension

value: WT


title: Ribo_F11_KO

value: Mtif3loxP/loxPloxP/loxP, +/Ckmm


title: Ribo_F9_KO


title: TpFm1


title: BAR1: AM1105_no_tension_WT

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 10, min. length 30, standard illumina adapter AGATCGGAAGAG)
Reads were mapped to sacCer3  with STAR
parameters(--outReadsUnmapped Fastx, --outFilterIntronMotifs RemoveNoncanonicalUnannotated)
samtools was used to filter primary and unique alignments
chrMito was excluded using bedtools
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization)

value: No tension (Nocodazol treatment)


title: Air_D9_rep3 [Blood miRNA]

description: Gene expression from rat blood

value: Sprague-Dawley

value: blood


title: TmFp3

value: Fusarium


title: Ribo_F7_KO


title: TpFp1

value: Trichoderma and Fusarium


title: WM278-shCDR1as_rep-002

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

description:
RNAseq_processed_FPKM.tsv
WM278_shCDR1as_rep2

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg38. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Read counting: STAR aligner version 2.5.0c integrated counting method (specific paramter --quantMode GeneCounts) was applied using gene level annotations downloaded from Ensembl Genes V85.
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V85 was used to calculate FPKM values for filtered genes (edgeR function 'rpkm').
Genome_build: hg38
Supplementary_files_format_and_content: FPKM table (tsv)

source_name: melanoma cell line

growth_protocol: Cultured melanocytes were grown in manufacturer supplied/recommended media. Media was changed every other day and cells were passaged/harvested for RNA extraction at ~80% confluence. Melanoma STCs were isolated as described in De Miera et al. PMID: 22404973 and cultured in DMEM supplemented with 10% FBS, Non-essential amino acids, and Pen-Strep. Established melanoma cell lines were cultured in DMEM supplemented with 10% FBS and Pen-Strep (501MEL, SK-MEL-147, SK-MEL-239, A375) or TU2% (80% MCDB153 pH7.5/20% L15 supplemented with 2% FBS, Insulin (5ug/mL), and 1.68mM CaCl2 (WM278 and WM1361a).

extract_protocol:
Total RNA extraction was performed using Qiagen miRNeasy mini kits following manufacturer's recommended protocol, including on-column DNAse treatment.
Total RNA was depleted of rRNA by Ribo-zero gold. Stranded libraries were prepared by Illumina ScriptSeq Complete Gold/TruSeq Stranded following manufacturer's recommendations.

treatment_protocol: All cells were harvested for RNA extraction between 60-80% confluence. Briefly, cells were washed 1X with PBS, detached from culture vessels by trypsinzation or cell dissociation buffer, quenched with growth media, then placed on ice. Cell suspensions were washed 1X with PBS, pelleted, and lysed in Qiazol. If indicated, cells were infected with lentiviral contstructs and selected with antibiotics. WM278 shNTC and shCDR1as cells were treated with 1ug/mL Doxycycline for 72hrs prior to cell harvest, RNA extraction, and RNA-seq.

tag: commercial or academic source

value: Rockland, Inc.

value: TetON pLKO shCDR1as (B) + 1ug/mL Doxycycline


title: TmFp2

value: maize silk

value: 4 days post emergency


title: Air_D17_rep1 [Blood miRNA]

description: Gene expression from rat blood

value: 9 weeks old


title: WM278-shCDR1as_rep-001

description:
RNAseq_processed_FPKM.tsv
WM278_shCDR1as_rep1


title: Ribo_F11_WT

value: Heart

value: 25 weeks


title: Air_D17_rep2 [Blood miRNA]

description: Gene expression from rat blood

value: male


title: TmFp1


title: Ribo_F9_WT


title: WM278-shNTC_rep-002

description:
RNAseq_processed_FPKM.tsv
WM278_shNTC_rep2

value: TetON pLKO shNTC + 1ug/mL Doxycycline


title: PEP_D17_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 17 days


title: TpFm2

value: Trichoderma


title: TmFm3


title: TmFm2


title: WM278-shNTC_rep-001

description:
RNAseq_processed_FPKM.tsv
WM278_shNTC_rep1


title: PEP_D17_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D17_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: Melanocytes_NHM_N6

description:
RNAseq_processed_FPKM.tsv
NHEM_pd10

source_name: melanocytes

value: Promocell


title: Air_D17_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D17_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: Melanocytes_NHM_N5

description:
RNAseq_processed_FPKM.tsv
NHEM_M2_juv


title: Melanocytes_NHM_N4

description:
RNAseq_processed_FPKM.tsv
NHEM_juv


title: Melanocytes_NHM_N3

description:
RNAseq_processed_FPKM.tsv
HEM_dark_P2

value: Sciencell


title: PEP_D17_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: KA_3

description: counts.xls

source_name: primary neurons

tag: cell type

value: primary neurons

value: Kainac acid (100 μM in culture medium)


title: Melanocytes_NHM_N2

description:
RNAseq_processed_FPKM.tsv
HEM_adult_P2


title: Ribo_F7_WT


title: allogeneic3 [A3]

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16   --quantMode GeneCounts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

growth_protocol: Recipient balb/c mice were lethally irradiated and transplanted with either syngeneic or allogeneic bone marrow (5 million cells) and T cells (300000). The mice were sacrificed by perfusion on day 14 and RNA was isolated from microglia. Four mice were analyzed per group

extract_protocol:
Microglia were sorted by FACS and RNA was isolated using the Picopure RNA extraction Kit as per manufacturer's instructions.RNA quality was accessed by bio-analyzer. The samples with an RNA integrity value of 8 and above were considered for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Post transplantation mouse were regularly checked until day 14 which is the peak stage of GvHD

tag: strain background

value: Balb/c

tag: genotype/variation

value: WT

value: Allogeneic Bone Marrow and T cell Transplantation

value: brain

value: sorted microglia cells


title: TmFm1

tag: cultivar

value: maize silk

tag: developmental stage


title: allogeneic4 [A4]

tag: tissue


title: bicuculline 3

city: Heidelberg

first: Carlos

last: Bas Orth

address: Im Neuenheimer Feld 307

department: Anatomy and Cell Biology

institute: Ruprecht-Karls-University Heidelberg

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent Feature Extraction software protocol

source_name: primary hippocampal neurons, stimulated with 50µM bicuculline for 4h

label_protocol: Labeling, hybridization and scanning were performed according to the standard Agilent hybridization protocol (miRNA Complete Labeling and Hyb Kit Protocol, Version 2.2)

growth_protocol: Primary mouse hippocampal neurons were prepared on postnatal day 1 and grown in 35mm petri dishes for 10 days in vitro (DIV).

extract_protocol: Total RNA was isolated with miRNeasy kit (QIAGEN, Hilden, Germany), according to the manufacturer's recommendations.

treatment_protocol: On DIV10 neurons were either left untreated (control), treated with 20µM N-methly-D-aspartate (NMDA) for 4h, or treated with 50µM bicuculline for 4h.

value: hippocampal neurons

value: bicuculline


title: bicuculline 2


title: NMDA 3

source_name: primary hippocampal neurons, stimulated with 20µM NMDA for 4h

value: NMDA


title: bicuculline 1


title: allogeneic2 [A2]


title: NMDA 2


title: NMDA 1


title: control 2

source_name: primary hippocampal neurons, untreated control

value: control


title: control 3


title: PEP_D13_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 13 days

value: 9 weeks old

value: male

value: Sprague-Dawley

value: blood


title: control 1


title: PEP_D13_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: Syngeneic2 [S2]

value: Syngeneic Bone Marrow and T cell Transplantation


title: Syngeneic3 [S3]


title: Control4 [C4]

value: Untransplanted


title: PEP_D13_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: Control3 [C3]


title: Air_D13_rep3 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, control, 13 days


title: PEP_D13_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: Air_D13_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D13_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: Syngeneic4 [S4]


title: Control2 [C2]


title: Air_D13_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: Air_D13_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: Air_D13_rep5 [Blood miRNA]

description: Gene expression from rat blood


title: Control1 [C1]


title: PEP_D21_rep5 [Blood miRNA]

description: Gene expression from rat blood

source_name: blood, exposed, 21 days


title: PEP_D21_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: liver_MSE-supplemented diet_biological replicate5

city: Gunma

first: Tsudoi

last: Toyoda

address: 54 Nakaorui-machi, Takasaki-shi

country: Japan

institute: Tkasaki University of Health and Welfare

description: no additional information

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to a Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) with the GeneChip 3' IVT Express kit (Thermo Fisher Scientific). The array was stained using the GeneChip Hybridization, Wash and Stain kit and on a GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: The fluorescence signals of probes were scanned with a GeneChip Scanner 3000 7G (Thermo Fisher Scientific) and converted to an intensity value with Affymetrix GeneChip Command Console software (Thermo Fisher Scientific).

data_processing: Probe sets with a false discovery rate < 0.05 were obtained as showing significant differences in gene expression by the rank products method. Probe sets counted among both up- and downregulated were excluded, and the genes for the remaining probe sets were regarded as differentially expressed genes. The above data processing was performed with R v.3.2.2 (https://cran.r-project.org/) and Bioconductor v.3.1 (http://www.bioconductor.org/).

source_name: MSE-supplemented diet

label_protocol: Biotinylated cRNA was prepared from purified total RNA with the GeneChip 3' IVT Express kit (Thermo Fisher Scientific).

extract_protocol: Total RNA was isolated from the liver with TRIzol reagent (Thermo Fisher Scientific) and purified with an RNeasy Mini kit and RNase-Free DNase Set (Qiagen, Venlo, the Netherlands).

treatment_protocol: The liver was treated with RNAlater (Thermo Fisher Scientific, Waltham, MA, USA) at 4°C overnight and stored at −80°C until use.

value: KK-Ay

tag: gender

value: 11 weeks old

tag: organ

value: liver


title: liver_MSE-supplemented diet_biological replicate8

description: no additional information


title: liver_MSE-supplemented diet_biological replicate7

description: no additional information


title: liver_MSE-supplemented diet_biological replicate4

description: no additional information


title: liver_MSE-supplemented diet_biological replicate3

description: no additional information


title: liver_MSE-supplemented diet_biological replicate6

description: no additional information


title: PEP_D21_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: liver_MSE-supplemented diet_biological replicate2

description: no additional information


title: PEP_D21_rep4 [Blood miRNA]

description: Gene expression from rat blood


title: B6 PAM CD45 2 biological replicate 2 [B6_PAM_CD45_2_R2]

city: London

last: Wack

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 11th December 2017. The parameters used were “--star-output-genome-bam --forward-prob 0.5”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: B6 PAM CD45

growth_protocol: Alveolar macrophages were enriched from whole lung using a postive selection using anti-Siglec F MACS selection. Enriched Ams were then FACS sorted based on Siglec F+ CD11c+ double positivity, and separated into resident and recruited using congenic markers (CD45.2 and CD45.1 respectively)

extract_protocol:
RNA was isolated using RLT buffer + beta-mercaptoethanol and the RNeasy Micro-Kit (Qiagen).
non strand-specific RNA-Seq; A total of <50ng of RNA was used to prepare the RNA library using Kapa mRNA Library Prep Kit  (Illumina) according to the manufacturer’s recommendations.

treatment_protocol: 50,000 cells retrieved from sorting were stimulated with 100ng/ml Pam3CSK4 (EnzoBiosciences) for 16 hours at 37°C and 5% CO2

tag: origin

value: C57BL/6 AM - PBS control lung

value: Alveolar macrophages

value: Pam3CSK4 stimulation


title: B6 PAM CD45 2 biological replicate 3 [B6_PAM_CD45_2_R3]


title: PEP_D21_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: B6 PAM CD45 2 biological replicate 1 [B6_PAM_CD45_2_R1]


title: liver_normal diet_biological replicate8

description: no additional information

source_name: normal diet


title: GFP-negative rep2

city: Iowa City

first: Robert

last: Cornell

state: Iowa

address: 1-400 D Bowen Science Bldg. 51 Newton Road

institute: University of Iowa

data_processing:
Sequencing reads were trimmed with Trimmomatic (0.35) using NexteraPE sequences.
Trimmed paired reads were mapped with Bowtie2 (default parameters). Sorting, removal of PCR duplicates and conversion from SAM to BAM files were performed using SAMtools
We employed DeepTools (v 2.0) to check the reproducibility of the biological replicates and generate bigWig coverage files for visualization
Peaks were called using MACS2 (v2.1.1) (parameter: --nomodel --nolambda --gsize 1.4e9 --keep-dup all --slocal 10000 ).
Genome_build: danRer10
Supplementary_files_format_and_content: bw, peaks bed

organism: Danio rerio

source_name: Tg(krt4:GFP) embryos

extract_protocol:
Sorted cells were lysed with 50 µL cold lysis buffer (10 mM Tris-‐HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40; all components purchased from Sigma) in a centrifuge at 500 x g for 15 minutes at 4°C.
Pelleted nuclei were resuspended in 50 µL tagmentation reaction mix (25 µL Nextera TD Buffer, 2.5 µL Nextera TD Enzyme, and 22.5 µL H2O, all from the Nextera DNA Sample Preparation Kit (Illumina). Immediately after Tn5 tagmentation, DNA samples were purified and indexed using NEBNext® High-Fidelity 2x PCR Master Mix (New England Biolabs) with a customized Nextera PCR primer pair, according to the following program: 72°C for 5 minutes; 98°C for 30 seconds; 11 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute; and hold at 4°C. All DNA libraries that exhibited a nucleosome pattern in the BioAnalyzer 2100 Assay passed the pre-sequencing QC process and were pooled for high-throughput sequencing.

treatment_protocol: FACS sorted GFP-positive and GFP-negative cells

value: 4-somite stage

tag: gfp

value: negative

value: non-periderm


title: Air_D21_rep4 [Blood miRNA]

description: Gene expression from rat blood

data_processing: TAC 4.0 was used with annotation miRNA-4_1-st-v1.annotations.20160922.csv to generate RMA expression values. Linear models were fit using the limma package of bioconductor in R version 3.4

source_name: blood, control, 21 days


title: liver_normal diet_biological replicate6

description: no additional information


title: Air_D21_rep1 [Blood miRNA]

description: Gene expression from rat blood


title: B6 MOCK CD45 2 biological replicate 3 [B6_MOCK_CD45_2_R3]

source_name: B6 MOCK CD45

value: Mock stimulation


title: liver_normal diet_biological replicate5

description: no additional information


title: liver_normal diet_biological replicate3

description: no additional information


title: Air_D21_rep5 [Blood miRNA]

description: Gene expression from rat blood


title: PEP_D21_rep6 [Blood miRNA]

description: Gene expression from rat blood


title: Air_D21_rep6 [Blood miRNA]

description: Gene expression from rat blood


title: liver_MSE-supplemented diet_biological replicate1

description: no additional information


title: Air_D21_rep3 [Blood miRNA]

description: Gene expression from rat blood


title: Air_D21_rep2 [Blood miRNA]

description: Gene expression from rat blood


title: GFP-negative rep1


title: liver_normal diet_biological replicate7

description: no additional information


title: B6 MOCK CD45 2 biological replicate 2 [B6_MOCK_CD45_2_R2]


title: GFP-positive rep2

value: positive

value: periderm


title: B6 MOCK CD45 2 biological replicate 1 [B6_MOCK_CD45_2_R1]


title: IgG ChIP-seq in NSCs without Rnase

city: Beijing

first: Yang

last: Yu

address: Dong Dan San Tiao #5

institute: Chinese Academy of Medical Sciences

description: IgG

data_processing:
reads quality were checked with FastQC
reads were mapped to mm10 with Bowtie2.2.5 with default parameters
Peaks were defined with MACS2 with default parameters
Peaks overlapped with ENCODE mouse blacklist were filtered
Peak summits were annotated to genes with the nearest transcription start site (within 2 million base pair) using Refseq release 72
Genome_build: mm10
Supplementary_files_format_and_content: tdf: tdf files were generated with IGV from bdg files, which were generated with MACS2

source_name: neural stem cells

growth_protocol: NSCs are cultured with NeuroCult Proliferation Kit (Stemcell Technologies, 05702) according to manufacturer’s manual. Briefly, adult SVZ is dissected from 6-8 week mice. Chopped tissue was enzymatically dissociated with Accutase (Stemcell Technologies, 07920), mechanically dissociated by pipetting, and cultured with NeuroCult medium containing EGF (20ng/ml, Peprotech) and FGF2 (10ng/ml, Peprotech). For differentiation assay, cells were seeded on poly-D-lysine coated glass coverslips and cultured in medium without EGF.

extract_protocol:
2X107 NSCs were harvested, washed and cross-linked with 4% PFA for sonication. Immunoprecipitation was performed with 4 μg rabbit or goat anti-Ars2 antibody. Normal rabbit or goat IgG was used as control. For ChIP with RNase treatment, RNase A (Roche 11579681001) was added to cell pellet and/or chromatin extract to 100 μg/ml.
DNA libraries were made using the Illumina ChIP-seq library preparation kit and sequenced as individual lanes on the Illumina GAII.

value: primary neural stem cells

tag: primary source

value: SVZ

tag: treatment of chip material

value: without RNase


title: GFP-positive rep1

tag: age


title: Ars2 ChIP-seq in differentiating neurospheres without RNase

source_name: differentiating neural stem cells

value: differentiating primary neural stem cells


title: PBS PAM 2M CD45 2 biological replicate 3 [PBS_PAM_2M_CD45_2_R3]

source_name: PBS PAM 2M CD45

value: Resident AM - PBS control lung


title: PBS PAM 2M CD45 2 biological replicate 2 [PBS_PAM_2M_CD45_2_R2]


title: liver_normal diet_biological replicate1

description: no additional information

value: KK-Ay

value: male


title: liver_normal diet_biological replicate4

description: no additional information

value: 11 weeks old

value: liver


title: Ars2 ChIP-seq in NSCs with RNase

value: with RNase


title: liver_normal diet_biological replicate2

description: no additional information


title: Ars2 ChIP-seq in NSCs without RNase


title: Single cell mRNA-seq_PC9_OSI-TRAM_invivo

city: Boston

first: Kari

last: Kurppa

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
cellranger 3.0.2 was used to process bcl files and convert them all to fastq files followed by aligning the fastq files to human GRCh38 transcriptome using standard cellranger pipeline
The filtered features matrix was used to perform downstream  analysis using Seurat V3. The following preprocessings were performed. First we filtered out cells with mitochondria percentages greater than 20 or expressed less than  200 genes
Raw counts was normalized using LogNormalize method with scaling factor 10000
Genome_build: GRCh38
Supplementary_files_format_and_content: tab deliminated, row names and column names corresponding to gene name amd cell barcodes, respectivley.

source_name: EGFR-mutant NSCLC cell line

extract_protocol:
Single cell isolation form tumors: Fresh tumor specimens (n=3) were pooled and minced in a 15 mL conical tube with media (DMEM + 10% FBS), penicillin–streptomycin (Fisher Scientific), 100 U/mL collagenase type IV (Life Technologies) and 2.5 mg/mL DNAse I (Sigma Aldrich), then incubated for 45min at 37°C.  Single cell suspensions were isolated by straining through a 40μm filters.  Cells were incubated with  Zombie Green™ Fixable Viability Kit (BioLegend), blocked with Human TruStain FcX™ (BioLegend), and stained with human anti-EpCAM (clone 9C4).  Viable EpCAM+ tumor cells were isolated via FACS Melody instrument (BD Biosciences). Cells were loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions.
Single-cell RNA libraries were generated using the Single Cell 3’ Reagent Kit (10X Genomics) per user guide.  Quality control of the completed libraries was performed using Bioanalyzer High Sensitivity DNA Kit (Agilent)

treatment_protocol: PC-9 were harvested and 5 x 106 cells with 50% Matrigel (Fisher Scientific) were implanted subcutaneously in the right flank of the NCr nude mice. Tumors were allowed to establish to 200 ± 50 mm3 in size before randomization using Studylog software (San Francisco, CA) into treatment groups (3 mice / group). Osimertinib (10 mg/kg once daily) and trametinib (1 mg/kg once daily) were administered orally as a suspension using 0.5% hydroxypropyl methylcellulose (HPMC; Sigma, St. Louis, MO) or 0.5% HPMC with 0.2% Tween 80 as vehicle, respectively. Mice were treated for 21 days, after which the tumors were harvested.

value: EGFR-mutant NSCLC cell line

tag: cell line

value: osimertinib + trametinib

tag: condition

value: in vivo


title: PBS MOCK 2M CD45 2 biological replicate 1 [PBS_MOCK_2M_CD45_2_R1]

source_name: PBS MOCK 2M CD45

value: Alveolar macrophages

tag: treatment


title: Single cell mRNA-seq_PC9_OSI_invivo

treatment_protocol: PC-9 were harvested and 5 x 106 cells with 50% Matrigel (Fisher Scientific) were implanted subcutaneously in the right flank of the NCr nude mice. Tumors were allowed to establish to 200 ± 50 mm3 in size before randomization using Studylog software (San Francisco, CA) into treatment groups (3 mice / group). Osimertinib (10 mg/kg once daily) was administered orally as a suspension using 0.5% hydroxypropyl methylcellulose (HPMC; Sigma, St. Louis, MO). Mice were treated for 21 days, after which the tumors were harvested.

value: osimertinib


title: PBS MOCK 2M CD45 2 biological replicate 2 [PBS_MOCK_2M_CD45_2_R2]

value: Mock stimulation


title: FLU PAM 2M CD45 2 biological replicate 3 [FLU_PAM_2M_CD45_2_R3]

source_name: FLU PAM 2M CD45

value: Resident AM - IAV d28 lung

value: Pam3CSK4 stimulation


title: Single cell mRNA-seq_PC9_DMSO_invivo

treatment_protocol: PC-9 were harvested and 5 x 106 cells with 50% Matrigel (Fisher Scientific) were implanted subcutaneously in the right flank of the NCr nude mice. Tumors were allowed to establish to 200 ± 50 mm3 in size before randomization using Studylog software (San Francisco, CA) into treatment groups. Mice received 0.5% HPMC with 0.2% Tween 80 administered orally. Mice were treated for 21 days, after which the tumors were harvested.

value: Vehicle


title: PBS PAM 2M CD45 2 biological replicate 1 [PBS_PAM_2M_CD45_2_R1]


title: Hindgut (1:3) Day 16 IM [H9]

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

description: Hindgut (1:3) Day 16 IM

data_processing:
Alignment with STAR
Summarization of reads per gene / exon provided by Broad Institute pipeline for DGE processing
SmartSeq_StarBasedPipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab separated counts per exon

source_name: Wells Protocol

extract_protocol: Trugrade_96_set3, Digital Gene Expression 3' RNA-seq

tag: protocol

value: Hindgut Protocol in various media conditions after sort

value: iPSC derived intestinal organoids


title: FLU PAM 2M CD45 2 biological replicate 2 [FLU_PAM_2M_CD45_2_R2]

tag: cell type


title: FLU PAM 2M CD45 2 biological replicate 1 [FLU_PAM_2M_CD45_2_R1]


title: AM16144_Scc1-6HA_CEN3del_tension_IP

description:
All samples were prepared using a liquid handling robot (Hamilton) by Bianka Baying (EMBL, Heidelberg, Germany). 10ng of each sample mixed with library preparation were assessed according to manufacturer's recommendation (NEBNext Ultra™ DNA Library Prep Kit for Illumina, (#E7370S/L)). Library preparation was done according to manufacturer. Briefly, the Adapter in the Adapter Ligation step was diluted 1:30 in water. The size selection step was performed with Ampure XP Beads from Beckman Coulter (insert size 200-250bp). The PCR amplification was performed in 15 cycles. Finally NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (#E7335S/L) were used for the Indexing. The quality and quantity of the libraries was checked using the Agilent BioAnalyzer and the Qubit dsDNA HS Assay kit (Invitrogen).
ChIP-Seq was performed using Illumina HiSeq 2000 Sequencer with Requested Read Length HiSeq50 SE.

data_processing:
Basecalls performed using CASAVA
ChIP-Seq reads were mapped with bwa (aln/samse) to sacCer3 and alternative reference (ref_CEN3del) using parameters (q 15)
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII/chrMito using bedtools (saturated with reads)
Genome_build: sacCer3 & strain with centromere on chromosome III at ectopic (ref_CEN3del)
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization)

source_name: Saccharomyces cerevisiae cell

extract_protocol: Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 30 seconds three times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with Roche 12CA5 anti-HA antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.

treatment_protocol: Cells were fixed in 1% formaldehyde for 30 minutes before washing twice in TBS and once in FA lysis buffer with 0.1% SDS. ChIP was performed using anti-HA antibodies

tag: chip antibody

tag: target

tag: cell cycle stage

value: Metaphase

tag: tension/no tension

value: Tension


title: AM16144_Scc1-6HA_CEN3del_no_tension_IP

value: No tension (Nocodazol treatment)


title: PBS MOCK 2M CD45 2 biological replicate 3 [PBS_MOCK_2M_CD45_2_R3]

value: Resident AM - PBS control lung


title: AM16144_Scc1-6HA_CEN3del_no_tension_input


title: AM16144_Scc1-6HA_CEN3del_tension_input


title: Hindgut Day 16 IM [H6]

description: Hindgut Day 16 IM


title: Hindgut (1:3) Day 16 CK+DCI [H7]

description: Hindgut (1:3) Day 16 CK+DCI


title: HepG2-nc-rep1

city: Shanghai

first: mengchao

last: wang

state: China

address: No225, Changhai Rd,

institute: second military medical university

description: Gene expression data from HepG2 cells with empty virus infected

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by RMA algorithm, Affy packages in R.

source_name: HepG2 cells with empty virus infected

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells was cultured with DMEM with 10% of fetal bovine serum in the incubator. The temperature was set at 37℃ and the concentration of CO2 is 5%.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by NucleoSpin RNA Clean-up XS kit (Cat#740903, MN, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: HepG2 cells was respectively infected with empty virus or virus containing shSox9 to build a Sox9-knock down HepG2 cell clone and the respecting clone of negative control.

tag: tissue

value: liver cancer cell line

tag: genotype/variation

value: control


title: HepG2-nc-rep2


title: HepG2-shSox9-rep2

source_name: HepG2 cells with virus containing shSox9 infected

value: SOX-9 knockdown


title: HepG2-shSox9-rep3


title: Hindgut Day 16 CK+DCI [H4]

description: Hindgut Day 16 CK+DCI


title: FLU PAM 2M CD45 1 biological replicate 2 [FLU_PAM_2M_CD45_1_R2]

value: Recruited AM - IAV d28 lung


title: Hindgut Day 16 CK+DCI [H3]

description: Hindgut Day 16 CK+DCI


title: Hindgut Day 16 IM [H5]

description: Hindgut Day 16 IM


title: HepG2-shSox9-rep1


title: FLU PAM 2M CD45 1 biological replicate 1 [FLU_PAM_2M_CD45_1_R1]


title: FLU MOCK 2M CD45 2 biological replicate 3 [FLU_MOCK_2M_CD45_2_R3]

source_name: FLU MOCK 2M CD45


title: Hindgut (GFP+ive) Day 16 CK+DCI [H12]

description: Hindgut (GFP+ive) Day 16 CK+DCI


title: WTInput-ten

data_processing:
Basecalls performed using CASAVA
ChIP-Seq reads were mapped with bwa (aln/samse) to sacCer3 and alternative reference (ref_CEN3del) using parameters (q 15)
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII/chrMito using bedtools (saturated with reads)
Genome_build: sacCer3 & strain with centromere on chromosome III at ectopic site (ref_CEN3del)
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization)

extract_protocol:
Input and ChIP DNA were sent for sequencing.
All samples were prepared using a liquid handling robot (Hamilton) by Bianka Baying (EMBL, Heidelberg, Germany). 10ng of each sample mixed with library preparation were assessed according to manufacturer's recommendation (NEBNext Ultra™ DNA Library Prep Kit for Illumina, (#E7370S/L)). Library preparation was done according to manufacturer. Briefly, the Adapter in the Adapter Ligation step was diluted 1:30 in water. The size selection step was performed with Ampure XP Beads from Beckman Coulter (insert size 200-250bp). The PCR amplification was performed in 15 cycles. Finally NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (#E7335S/L) were used for the Indexing. The quality and quantity of the libraries was checked using the Agilent BioAnalyzer and the Qubit dsDNA HS Assay kit (Invitrogen).
ChIP-Seq was performed using Illumina HiSeq 2000 Sequencer with Requested Read Length HiSeq50 SE.

treatment_protocol: ChIP was performed using anti-FLAG, anti-HA or anti-PK antibodies

tag: genotype

value: WT


title: WTChip+ten


title: WTChip-ten


title: HepG2-nc-rep3


title: Hindgut (1:3) Day 16 CK+DCI [H8]

description: Hindgut (1:3) Day 16 CK+DCI


title: FLU PAM 2M CD45 1 biological replicate 3 [FLU_PAM_2M_CD45_1_R3]

tag: origin

value: Alveolar macrophages


title: Hindgut (GFP+ive) Day 16 CK+DCI [H11]

description: Hindgut (GFP+ive) Day 16 CK+DCI


title: Hindgut (1:3) Day 16 IM [H10]

description: Hindgut (1:3) Day 16 IM


title: FLU MOCK 2M CD45 1 biological replicate 2 [FLU_MOCK_2M_CD45_1_R2]


title: BA7: 6390_Sgo1-6HA_WT-tension_Input

data_processing:
Basecalls performed using CASAVA
ChIP-Seq reads were mapped with bwa (aln/samse) to sacCer3
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII using bedtools (saturated with reads)
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM)

treatment_protocol: Cells were fixed in 1% formaldehyde for 30 minutes before washing twice in TBS and once in FA lysis buffer with 0.1% SDS.

tag: strain


title: FLU MOCK 2M CD45 1 biological replicate 3 [FLU_MOCK_2M_CD45_1_R3]


title: WTInput+ten


title: BA8: 6390_Sgo1-6HA_WT-tension_ChIP


title: BA6: 6390_Sgo1-6HA_WT+tension_ChIP


title: FLU MOCK 2M CD45 1 biological replicate 1 [FLU_MOCK_2M_CD45_1_R1]


title: FLU MOCK 2M CD45 2 biological replicate 1 [FLU_MOCK_2M_CD45_2_R1]


title: PBS PAM 2M CD45 2 biological replicate 2 [ATAC-seq]

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters “-a CTGTCTCTTATA -A CTGTCTCTTATA --minimum-length=25 –quality-cutoff=20 -u -50 -U -50”.
BWA (version 0.6.2) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the mouse mm10 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Read group addition, duplicate marking and insert size assessment was performed using the picard tools AddOrReplaceReadGroups, MarkDuplicates and CollectMultipleMetrics, respectively (version 2.1.1).
Reads mapped to mitochondrial DNA were removed using the pairToBed command from BEDTools (version 2.26.0) (Quinlan & Hall, 2010).
Additional filtering was performed to only include uniquely mapped, properly-paired reads with insert size <= 2kb, and mismatches <= 1 in both reads.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph coverage tracks representing the accessibility signal per million mapped paired-reads were generated using BEDTools genomeCoverageBed with the parameters “-bg -pc -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).

extract_protocol:
DNA was isolated as previously described (Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218, 2013).
50,000 cells were used for the transposition reaction, that was carried out for 4h at 37°C. Library fragments were amplified using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers. using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min - this was done for 13 cycles. Transposed DNA fragments were then PCR amplified for 13 cycles and purified by the ChargeSwitch PCR clean-up kit (Invitrogen)

treatment_protocol: 50,00 cells retrieved from FACs sorting were stimulated with 100ng/ml Pam3CSK4 (EnzoBiosciences) for 2 hours at 37°C and 5% CO2

value: Resident AM - PBS-control lung


title: BA5: 6390_Sgo1-6HA_WT+tension_Input


title: PBS PAM 2M CD45 2 biological replicate 1 [ATAC-seq]


title: Day 42 (GFP+ CD47-) IM [F8]

description: Day 42 (GFP+ CD47-) IM

source_name: Lung Differentiaton-Based Protocol

value: Dual inhibition organoids in various media conditions after sort


title: Day 42 (GFP+ CD47-) BMP2 IM [F6]

description: Day 42 (GFP+ CD47-) BMP2 IM


title: PBS MOCK 2M CD45 2 biological replicate 2 [ATAC-seq]

value: Mock stimulation


title: Parr_skin_8

city: Helsinki

first: Johanna

last: Kurko

state: --Please select--

address: Biocenter 1, Viikinkaari 9

country: Finland

institute: University of Helsinki

hyb_protocol: First, CodeSet Master Mix was prepared by adding 70 µl of Hybridization Buffer to the Reporter Codeset tube and mixing. Then 8 µl of Master Mix was aliquoted to each well of a sample strip tube containing 100 ng (20 ng/ul) RNA, mixed and spinned gently. 2 µl of Capture ProbeSet was added to each well of a strip tube, mixed  and spinned gently. Next, tubes were immediately transferred to PCR cycler heated to 65 °C and incubated o/n.

scan_protocol: After hybridization, the sample strip was transferred to the nCounter Prep Station for purification and immobilization in a sample cartridge. After immobilization, the cartridge was analyzed with the nCounter Digital Analyzer by taking images of the immobilized fluorescent reporters. The number of images taken corresponded to the number of reporters counted. The raw count data was exported as a csv file.

data_processing: The raw count data was normalized by RNA content normalization factor for each sample calculated from geometric mean count values of six genes selected from the panel. These genes (ef1ac, prkar1aa, rps20, rxrbaa, vdraa and vdrab) were chosen as they exhibited a low coefficient of variation and average count values across samples. Genes included two (ef1ac and rps20) of the nine genes originally included in the panel as potential normalization candidates, as well as four additional genes (prkar1aa, rxrbaa, vdraa and vdrab). After normalization and quality control, two samples, N.4.M and I.1.L, were observed to have too high RNA content normalization factor values (> 3.0) and they were not used in the further analyses. Quality control and normalization of the data was performed using the nSolver Analysis Software (v3.0) (NanoString Technologies). Background correction was not performed, but in further analyses a normalized count value of 20 was set as a background signal threshold.

organism: Salmo salar

source_name: Atlantic salmon developmental stages

extract_protocol: Dissected tissue samples or whole individuals (embryos, alevin, fry) were disrupted and homogenized in the presence of NucleoZOL (Macherey-Nagel, Düren, Germany) for lysis in 2 ml safe-lock tubes containing one 5 mm stainless steel bead (Qiagen) for 2.5-3 minutes at 30 Hz using TissueLyzer II (Qiagen). Total RNA was extracted from the lysate using NucleoSpin RNA Set for NucleoZOL (Macherey-Nagel) according to the manufacturer’s instructions. After the elution step, RNA was treated with rDNase using the rDNase Set (Macherey-Nagel) to remove any residual DNA and, subsequently, purified with either NucleoSpin RNA clean-up or NucleoSpin RNA clean-up XS kit (Macherey-Nagel) according to the RNA yield. Blood samples were lysed in the RNAprotect Animal Blood Tubes (Qiagen) and total RNA was extracted using the RNeasy Protect Animal Blood System kit (Qiagen) according to the manufacturer’s protocol followed by concentration of RNA using NucleoSpin RNA clean-up XS kit (Macherey-Nagel). The quantity and quality of RNA was determined using both NanoDrop Spectrophotometer ND-1000 (Thermo Scientific, Wilmington, DE, USA) and 2100 BioAnalyzer system (Agilent Technologies, Santa Clara, CA, USA).

value: skin

tag: Sex

value: M

tag: developmental stage

value: parr

tag: maturity stage

value: mature

tag: habitat

value: wild

tag: population origin

value: Inarijoki

tag: diet


title: Day 42 (GFP- CD47+) CK+DCI [F9]

description: Day 42 (GFP- CD47+) CK+DCI

tag: protocol

value: iPSC derived intestinal organoids


title: PBS MOCK 2M CD45 2 biological replicate 1 [ATAC-seq]

tag: cell type

tag: treatment


title: FLU MOCK 2M CD45 2 biological replicate 2 [FLU_MOCK_2M_CD45_2_R2]

value: Resident AM - IAV d28 lung


title: Parr_liver_8

value: liver


title: Day 42 (GFP+ CD47-) IM [F7]

description: Day 42 (GFP+ CD47-) IM


title: Trans1_rep2

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

description:
processed data file:
Transgender_combined_UMI.txt.gz
column header naming format:
Trans1-barcode_sequence-2

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Testicular cells

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane.

value: Testicle

tag: age


title: Day 42 (GFP+ CD47-) BMP2 IM [F5]

description: Day 42 (GFP+ CD47-) BMP2 IM


title: Hindgut Day 8 (GFP+ive) [F2]

description: Hindgut Day 8 (GFP+ive)

value: Hindgut Protocol in various media conditions after sort


title: Parr_muscle_8

value: muscle


title: Trans2

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina NovaSeq instrument. Each sample was sequenced in one separate sequencing lane.


title: FLU PAM 2M CD45 1 biological replicate 2 [ATAC-seq]

value: Recruited AM - IAV d60 lung

value: Pam3CSK4 stimulation


title: Day 42 (GFP+ CD47-) CK+DCI [F4]

description: Day 42 (GFP+ CD47-) CK+DCI


title: Day 42 (GFP+ CD47-) CK+DCI [F3]

description: Day 42 (GFP+ CD47-) CK+DCI


title: FLU PAM 2M CD45 2 biological replicate 2 [ATAC-seq]

value: Resident AM - IAV d60 lung

value: Alveolar macrophages


title: Parr_kidney_8

value: kidney


title: Sox2 ChIP-seq in NSCs without RNase

value: primary neural stem cells

tag: primary source

value: SVZ

tag: treatment of chip material

value: without RNase


title: FLU PAM 2M CD45 2 biological replicate 1 [ATAC-seq]


title: Trans1_rep1

description:
processed data file:
Transgender_combined_UMI.txt.gz
column header naming format:
Trans1-barcode_sequence-1

tag: tissue


title: circulating miRNA [67]

city: Lodz

first: Konrad

last: Pagacz

address: Mazowiecka 15

department: Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: Sampled 7 days

data_processing:
No normalization was performed
matrix non-normalized values

label: SYBR

source_name: serum

label_protocol: Each microRNA sample was reverse transcribed into cDNA and run on the miRCURY LNA™ Universal RT miRNA PCR Human panel I and II. SYBR green was used to label PCR products according to the manufactturer's guidelines.

extract_protocol: miRNA was extracted from the samples usingmiRCURY RNA Isolation kit (Qiagen) according to the manufacturer's handbook.

tag: protocols

value: no irradiation


title: circulating miRNA [29]

description: Sampled 7 days


title: FLU MOCK 2M CD45 2 biological replicate 2 [ATAC-seq]

value: Mock stimulation


title: Day 42 (GFP- CD47+) CK+DCI [F10]

description: Day 42 (GFP- CD47+) CK+DCI

value: Dual inhibition organoids in various media conditions after sort


title: Parr_heart_8

value: heart

value: M

value: parr

value: mature

value: wild

value: Inarijoki


title: circulating miRNA [5]

description: Sampled 7 days


title: Parr_eye_8

value: eye


title: FLU PAM 2M CD45 1 biological replicate 1 [ATAC-seq]

value: Recruited AM - IAV d60 lung

value: Pam3CSK4 stimulation


title: Hindgut Day 8 (GFP+ive) [F1]

description: Hindgut Day 8 (GFP+ive)

value: Hindgut Protocol in various media conditions after sort

value: iPSC derived intestinal organoids


title: Parr_gonad_8

value: gonad


title: circulating miRNA [20]

description: Sampled 7 days


title: FLU MOCK 2M CD45 2 biological replicate 1 [ATAC-seq]

value: Resident AM - IAV d60 lung

value: Alveolar macrophages


title: FLU MOCK 2M CD45 1 biological replicate 2 [ATAC-seq]


title: Parr_skin_7

value: skin


title: FLU MOCK 2M CD45 1 biological replicate 1 [ATAC-seq]

value: Mock stimulation


title: circulating miRNA [4]

description: Sampled 7 days

value: no irradiation


title: Day 30 (GFP- CD47+) IM [D6]

description: Day 30 (GFP- CD47+) IM

value: Dual inhibition organoids in various media conditions after sort


title: Day 30 (GFP- CD47-) IM [D7]

description: Day 30 (GFP- CD47-) IM


title: Day 30 (GFP- CD47-) IM [D8]

description: Day 30 (GFP- CD47-) IM


title: circulating miRNA [27]

description: Sampled 7 days


title: Day 30 (GFP- CD47+) IM [D5]

description: Day 30 (GFP- CD47+) IM


title: Parr_muscle_7

value: muscle

value: M


title: circulating miRNA [23]

description: Sampled 7 days


title: PBS PAM CD45 2 biological replicate 3 (RNA-seq)

source_name: PBS PAM CD45 2

extract_protocol:
RNA was isolated using RLT buffer + beta-mercaptoethanol and the RNeasy Micro-Kit (Qiagen).
A total of <50ng of RNA was used to prepare the RNA library using Kapa mRNA Library Prep Kit  (Illumina) according to the manufacturer’s recommendations.
non strand-specific RNA-Seq

value: Resident AM - PBS control lung


title: Parr_kidney_7

value: kidney

value: parr

value: mature

value: wild


title: Day 30 (GFP- CD47+) BMP2IM [D4]

description: Day 30 (GFP- CD47+) BMP2IM


title: circulating miRNA [11]

description: Sampled 7 days


title: Day 30 (GFP- CD47+) BMP2IM [D3]

description: Day 30 (GFP- CD47+) BMP2IM


title: PBS PAM CD45 2 biological replicate 2 (RNA-seq)

value: Pam3CSK4 stimulation


title: Parr_heart_7

value: hert

value: Inarijoki


title: Parr_gonad_7

value: gonad


title: PBS PAM CD45 2 biological replicate 1 (RNA-seq)


title: circulating miRNA [7]

description: Sampled 7 days


title: Day 30 (GFP- CD47+) CK+DCI [D2]

description: Day 30 (GFP- CD47+) CK+DCI

value: iPSC derived intestinal organoids


title: Parr_gill_7

value: gill


title: circulating miRNA [16]

description: Sampled 7 days


title: Parr_liver_7

value: liver


title: PBS MOCK CD45 2 biological replicate 3 (RNA-seq)

source_name: PBS MOCK CD45 2

value: Mock stimulation

value: Alveolar macrophages


title: Parr_eye_7

value: eye


title: circulating miRNA [55]

description: Sampled 7 days

value: no irradiation


title: circulating miRNA [36]

description: Sampled 7 days


title: PBS MOCK CD45 2 biological replicate 1 (RNA-seq)


title: FLU PAM CD45 2 biological replicate 5 (RNA-seq)

source_name: FLU PAM CD45 2

value: Resident AM - IAV d28 lung


title: Parr_skin_6

value: skin

value: M

value: immature


title: Day 14 (GFP+) [C12]

description: Day 14 (GFP+)

value: Dual inhibition organoids in various media conditions after sort


title: circulating miRNA [61]

description: Sampled 7 days


title: Day 14 (GFP+) [C11]

description: Day 14 (GFP+)


title: Parr_muscle_6

value: muscle

value: parr

value: wild


title: circulating miRNA [17]

description: Sampled 7 days


title: FLU PAM CD45 2 biological replicate 3 (RNA-seq)

value: Pam3CSK4 stimulation


title: circulating miRNA [58]

description: Sampled 7 days


title: Parr_kidney_6

value: kidney

value: Inarijoki


title: FLU PAM CD45 2 biological replicate 2 (RNA-seq)


title: Day 3 (DE) [B9]

description: Day 3 (DE)

source_name: Common

value: Early Differentiation Time Points up through Day 8

value: iPSC derived intestinal organoids


title: Day 30 (GFP- CD47+) CK+DCI [D1]

description: Day 30 (GFP- CD47+) CK+DCI


title: circulating miRNA [8]

description: Sampled 7 days


title: circulating miRNA [47]

description: Sampled 7 days


title: FLU PAM CD45 2 biological replicate 1 (RNA-seq)


title: Parr_heart_6

value: heart


title: Parr_gill_6

value: gill


title: PBS MOCK CD45 2 biological replicate 2 (RNA-seq)

value: Resident AM - PBS control lung

value: Mock stimulation

value: Alveolar macrophages


title: Day 6 (DS/SB) [B11]

description: Day 6 (DS/SB)


title: Day 8 (CBRA) [C2]

description: Day 8 (CBRA)


title: Day 6 (DS/SB) [B12]

description: Day 6 (DS/SB)


title: Parr_eye_6

value: eye


title: circulating miRNA [30]

description: Sampled 7 days

value: no irradiation


title: Day 3 (DE) [B10]

description: Day 3 (DE)


title: circulating miRNA [13]

description: Sampled 7 days


title: FLU PAM CD45 2 biological replicate 4 (RNA-seq)

value: Resident AM - IAV d28 lung


title: Parr_liver_6

value: liver

value: M

value: immature


title: Parr_liver_5

value: parr

value: wild


title: FLU PAM CD45 1 biological replicate 4 (RNA-seq)

source_name: FLU PAM CD45 1

value: Pam3CSK4 stimulation


title: Parr_muscle_5

value: muscle

value: Inarijoki


title: Day 8 (CBRA) [C1]

description: Day 8 (CBRA)

value: Dual inhibition organoids in various media conditions after sort

value: iPSC derived intestinal organoids


title: circulating miRNA [18]

description: Sampled 7 days


title: Parr_kidney_5

value: kidney


title: FLU PAM CD45 1 biological replicate 2 (RNA-seq)

value: Recruited AM - IAV d28 lung


title: circulating miRNA [50]

description: Sampled 7 days


title: circulating miRNA [9]

description: Sampled 7 days


title: FLU PAM CD45 1 biological replicate 1 (RNA-seq)


title: FLU MOCK CD45 2 biological replicate 5 (RNA-seq)

source_name: FLU MOCK CD45 2

value: Mock stimulation


title: FLU MOCK CD45 2 biological replicate 4 (RNA-seq)

value: Alveolar macrophages


title: circulating miRNA [2]

description: Sampled 7 days


title: Parr_gill_5

value: gill


title: Parr_heart_5

value: heart


title: C14C

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

institute: Shandong university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: cell

growth_protocol: Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated, evaluated the quality, reverse-transcribed to cDNA,
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were
converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min
followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: Cells were treated  with F. nucleatum at a multiplicity of infection (MOI) of F. nucleatum : cell =10:1, and culured at 3d, 7d, 14d and 21d

value: Human gingival-derived mesenchymal stem cells

tag: donor

value: donor 3

tag: culture time


title: C14F


title: C21F


title: C21C


title: FLU MOCK CD45 2 biological replicate 3 (RNA-seq)

tag: origin

value: Resident AM - IAV d28 lung


title: FLU PAM CD45 1 biological replicate 3 (RNA-seq)


title: C7C


title: circulating miRNA [63]

description: Sampled 7 days

value: no irradiation


title: Parr_eye_5

value: eye

tag: Sex

value: M

value: parr

value: immature


title: circulating miRNA [45]

description: Sampled 7 days


title: Parr_spleen_4

value: spleen

value: F

tag: developmental stage

value: hatchery

value: Neva

value: normal diet


title: FLU MOCK CD45 2 biological replicate 2 (RNA-seq)

value: Mock stimulation


title: circulating miRNA [48]

description: Sampled 7 days


title: Parr_skin_4

value: skin

tag: maturity stage


title: C7F


title: Parr_pyloric caeca_4

value: pyloric caeca

tag: habitat


title: FLU MOCK CD45 2 biological replicate 1 (RNA-seq)

value: Alveolar macrophages


title: circulating miRNA [12]

description: Sampled 7 days


title: FLU MOCK CD45 1 biological replicate 3 (RNA-seq)

source_name: FLU MOCK CD45 1

value: Recruited AM - IAV d28 lung


title: Parr_muscle_4

value: muscle

tag: population origin


title: B21F

value: Human gingival-derived mesenchymal stem cells

value: donor 2


title: circulating miRNA [69]

description: Sampled 7 days

value: no irradiation


title: B21C


title: Parr_liver_4

value: liver

tag: diet


title: FLU MOCK CD45 1 biological replicate 2 (RNA-seq)


title: B14F


title: circulating miRNA [21]

description: Sampled 7 days


title: FLU PAM CD45 2 biological replicate 2 (ATAC-seq)

value: Resident AM - IAV d28 lung

value: Pam3CSK4 stimulation


title: circulating miRNA [6]

description: Sampled 7 days


title: FLU PAM CD45 2 biological replicate 1 (ATAC-seq)


title: Parr_kidney_4

value: kidney

value: parr

value: immature


title: B7F


title: Parr_gonad_4

value: gonad

value: F

value: hatchery

value: Neva


title: circulating miRNA [43]

description: Sampled 7 days


title: Parr_gill_4

value: gill

value: normal diet


title: B14C


title: C3F

value: donor 3


title: circulating miRNA [25]

description: Sampled 7 days


title: C3C


title: B7C


title: circulating miRNA [56]

description: Sampled 7 days


title: Parr_eye_4

value: eye


title: B3F

value: Human gingival-derived mesenchymal stem cells


title: FLU PAM CD45 1 biological replicate 1 (ATAC-seq)

value: Recruited AM - IAV d28 lung

value: Alveolar macrophages


title: PEP_D1_rep4 [Blood miRNA]

city: Morgatown

first: Nancy

address: 2816 Health Sciences Center

institute: West Virginia University

description: Gene expression from rat blood

source_name: blood, exposed, 1 day

extract_protocol: Total RNA was isolated from rat blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol. Rat lungs were initially disrupted by transferring them to a 2 mL microcentrifuge tube containing 400 μL silica beads and 600 μL Lysis/Binding Solution.

treatment_protocol: The exposed group consisted of rats housed in individual cages and exposed via full body inhalation to PEPs and gaseous pollutants emitted by laser printer B1 using the Printer Exposure Generation System (PEGS) described in detail in a previous publication (Pirela et al, 2014). (Supplementary Material, Figure S1). In summary, printer B1 was used to generate PEPs emissions by printing a 5%-page coverage monochrome document using standardized settings (Pirela et al 2014). The laser printer B1 was selected based on exposure profiles reported in our previous studies (Pirela et al., 2014). In parallel, another group of rats was exposed to HEPA filtered air. The system was configured for twelve chambers (one animal per chamber), each equipped with a port for aerosol delivery and temperature and humidity measurement, a water bottle port, and a gas sampling port.   The whole exposure experiment was repeated twice, in 2016 and 2017. Animals were placed in their chambers for 1-5 hours for 5 days prior to the exposures to ensure they gradually acclimated to exposure chambers before the exposures occurred. The following week, animals were exposed to PEPs pollutants and the room HEPA-filtered air 5 hours/day for 21 consecutive days.

value: 9 weeks old

value: male

tag: strain

value: Sprague-Dawley

value: blood


title: circulating miRNA [1]

description: Sampled 7 days

value: no irradiation


title: B3C

tag: cell type

value: donor 2


title: FLU MOCK CD45 1 biological replicate 1 (RNA-seq)

tag: treatment

value: Mock stimulation


title: Parr_adipose tissue_4

value: adipose

value: F

value: parr

value: immature


title: Parr_brain_4

value: brain

value: hatchery

value: Neva

value: normal diet


title: FLU MOCK CD45 2 biological replicate 1 (ATAC-seq)

value: Resident AM - IAV d28 lung


title: circulating miRNA [57]

description: Sampled 7 days