title: N2 Day 5 Control [LL31]


title: N2 Day 5 Control [LL30]

status: Public on Dec 31 2022

type: SRA

city: Providence

first: Louis

last: Lapierre

address: 185 Meeting St.

country: USA

institute: Brown

library_source: transcriptomic

data_processing:
 Illumina HiSeq, 2x150bp configuration, single index, per lane
Sequences were trimmed using Trimmomatic and mapped to the Caenorhabditis elegans reference genome available on ENSEMBL  using the STAR aligner
Unique gene hit counts were calculated by using feature Counts from the Subread package. Only unique reads that fell within exon regions were counted.
Assembly: WBcel235 (Ensembl Release 67)
Supplementary files format and content: Normalized counts are TMP

molecule: total RNA

organism: Caenorhabditis elegans

source_name: N2 Day 5 Control

growth_protocol: Nematodes were synchronized using hypochlorite and eggs were seeded on nematode growth media plates with E. coli OP50 and developed at 20°C

extract_protocol:
Total RNA was extracted from approximately 10-12000 worms after treatment using Trizol Reagent (Invitrogen) followed by purification using Qiagen RNeasy kit according to the manufacturers' protocols
Standard Illumina protocols were used for RNA library preparations

treatment_protocol: At Day 1 of adulthood, the nematodes were transferred onto nematode growth media plates with control bacteria or bacteria expressing dsRNA against atgl-1 and grown at 25°C for 4 days

tag: strain/genotype

value: N2 (Bristol)

tag: treatment

value: Control 4 days 25C


title: ER+ breast cancer 9

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

data_processing:
Basecalls performed using CASAVA version 1.7
Adapter and low-quality reads were removed using Trimmomatic v0.36
Aligning was done using TopHat v2.1.1
Quantification and normalization was done using cufflinks 2.2.1
Genome_build: hg37
Supplementary_files_format_and_content: Gene expression (FPKM) values for the 44 samples. Rows are genes, columns are samples, the column header is the sample name. The 7 BMI groups considered are as follows: 18.5 – 24.99, 25.00 – 27.99, 28.00 – 29.99, 30.00 – 31.99, 32.00 – 34.00, 34.01 – 39.99, ≥ 40.

organism: Homo sapiens

source_name: breast tissue

extract_protocol:
The Recoverall Nucleic Acid Isolation Kit for FFPE Tissue (Ambion, Austin, TX) was used to isolate RNA
Quantitation and fragmentation analysis were performed using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 and RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA). A Qubit fluorometric assay (Thermo Fisher Scientific) was used to quantitate and equalize dsDNA prepared using the Truseq RNA Access library preparation kit (Illu- mina, San Diego, CA). Libraries were randomized, indexed, multiplexed, and paired end sequenced (200 cycles total) on an Illumina Nextseq500.

tag: tissue

value: breast

tag: cancer type

value: ER +

tag: storage type

value: FFPE

value: untreated

tag: bmi group


title: N2 Day 5 atgl-1 RNAi [LL34]

source_name: N2 Day 5 atgl-1 RNAi

value: atgl-1 RNAi 4 days 25C


title: LMS45

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

country: France

institute: University of Bordeaux

data_processing:
Sequencing quality was assessed using FastQC from the Babraham Institute (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were then trimmed for adaptors using cutadapt version 1.10 with -q 30 and -m 18 parameters.
We aligned the reads with mature miRNA sequences from the miRbase Sequence database using, BWA-aln algorithm version 0.7.17 with -n 1 -o 0 -e 0 -k 1 -t 8 parameters and evaluated mapping quality using Qualimap version 2.2.2b.
We used Samtools version 1.9 to discard the reads with a mapping quality under 30 and to count mapped reads with the reference sequences (samtools idxstats)
We applied the EdgeR R package on raw counts to normalize data and define significantly differentially expressed genes with a generalized linear model fitting (glmQLFit), correcting the returned p-values using Holm’s method.
We kept as expressed any miRNAs (filterByExpr) with a summed raw count over all samples > 10 and represented by a minimum of five reads in at least one sample.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw or normalized mature miRNA counts for every samples

source_name: Primary tumor Leiomyosarcoma

extract_protocol: NEBNext Small RNA Library Prep Set for Illumina (E7330L, New England Biolabs Inc., Ipswich, MA, USA) according to the manufacturer’s recommendations.

treatment_protocol: Frozen tissue

value: Primary tumor Leiomyosarcoma

tag: metastasis

tag: os

tag: Sex

value: MALE

tag: differentiation

tag: location

value: Member

tag: age

tag: lms subtype

value: hLMS

tag: molecule subtype

value: small RNA


title: ATGL-1 OE Day 5 [LL26]

source_name: ATGL-1 OE Day 5

value: ATGL-1 OE


title: LMS44

value: FEMALE

value: Internal trunk

value: Not evaluable


title: Fertilized Egg Cell (~1 hap), biological rep 3

type: RNA

city: Norman

first: Scott

middle: D

last: Russell

state: OK

address: 770 Van Vleet Oval

department: Dept of Microbiology and Plant Biology

institute: University of Oklahoma

description: Gene expression data from pollen at anthesis

hyb_protocol: Fifteen ug of fragmented cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rice Genome oligonucleotide array. Subsequent GeneChip washing and staining steps were performed on a GeneChip Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Affymetrix MAS 5.0 processing, with all chips scaled to the same target value of 500.

label: biotin

organism: Oryza sativa Japonica Group

source_name: Greenhouse grown rice, cv Katy

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip Two-Cycle cDNA Synthesis Kit for target preparation with signal amplification according to the standard Affymetrix protocol from total RNA of three replicates each of 100 unfertilized egg cells, 100 fertilized egg cells and 100 zygotes, respectively. According to estimate of Onishi et al. 2010 (PMID: 21106719) each egg cell is estimated to contain 25 pg and zygote slightly more (with paternal contribution); total RNA is estimated to be 2.5 ng for each 100 cell collection.

growth_protocol: Oryza sativa ssp. japonica, cultivar Katy were grown in greenhouses of the University of Oklahoma, under long-day, disease free conditions

extract_protocol: Total RNA was purified using the RNeasy plant mini kit according to manufacturer’s instructions (Qiagen).  Yield per egg cell or zygote cell is estimated at 25 picogram (by Ohnishi et al., 2011, and our own estimates), so the total collection may represent ~2.5 ng Total RNA

treatment_protocol: Egg cells (unfertilized), egg cells (fertilized) and zygotes were collected from anthesis florets, ovaries isolated and ovules excised to remove egg and zygote cells from the micropylar female gametophyte using non-enzymatic method described in Zhang et al (2010) for isolation of rice female gametophyte cells.  Each biological technical replicate represents ~100 cells.

tag: subspecies

value: japonica

tag: cultivar

value: Katy

tag: genotype

value: Wild type

tag: developmental stage

value: Fertilized Egg Cell (~1 hap)


title: CONTROL_rep6 (antimony)

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: M. musculus vehicle control sample

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA). Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Affymetrix Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized across all three groups.

organism: Mus musculus

source_name: lung, vehicle control

label_protocol: One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3′ IVT Plus kit protocol. Fifteen micrograms of amplified biotin-aRNAs was fragmented, and 12.5 μg was hybridized to each array for 16 h at 45 °C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

growth_protocol: At the start of the study, the animals were 5–6 weeks of age. The animals were housed 2 per cage. Tap water and NTP-2000 diet (Zeigler Brothers, Inc. Gardners, PA) were made available ad libitum. The care of animals on this study was according to National Institutes of Health (NIH) procedures as described in the ‘‘The U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals,’’ available from the Office of Laboratory Animal Welfare, NIH, Department of Health and Human Services, RKLI, Bethesda, MD or online at http://grants.nih.gov/grants/olaw/olaw.htm#pol.

extract_protocol: The lung was harvested and weighed, and then, a representative sections are collected and fixed in 10 % neutral buffered formalin for histology. Hematoxylin and eosin (H&E)-stained sections (5 μm) were examined by a board certified pathologist. Selected lung tumors are dissected from the remaining lung parenchyma and flash-frozen in liquid nitrogen and stored at −80 °C until RNA extraction. RNA was extracted from frozen samples using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A, Carlsbad, CA) according to the manufacturer’s protocol. RNA concentration and quality were measured on a Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples were aliquoted and stored at −80 °C until they were analyzed for gene expression studies.

treatment_protocol: Antimony trioxide was obtained from 3N International, Inc. (Akron, OH), in one lot (3N-06159) that was used in the 2-week and 2-year studies. Groups of 60 male and 60 female mice were exposed by whole body inhalation to antimony trioxide aerosol at concentrations of 0, 3, 10, or 30 mg/m3 for 6 hours plus T90 (12 minutes) per day, 5 days per week for up to 105 weeks.

tag: group


title: ATGL-1 OE Day 5 [LL25]

tag: strain/genotype

tag: treatment

value: Control 4 days 25C


title: LMS40

tag: tissue

value: oLMS


title: Unfertilized Egg Cell, biological rep 2

description: Gene expression data from whole seedlings at 3rd collar leaf stage

value: Unfertilized Egg Cell


title: LRL147_37C_Rep3

source_name: LRL147 (hlh-30;NeuroHLH-30) 37C

treatment_protocol: At Day 1 of adulthood, the nematodes were transferred onto nematode growth media plates with E. Coli OP50 and grown at 20°C or 37°C for 3 hours

tag: strain

value: E. coli OP50 3hr. 37C


title: LRL147_37C_Rep4


title: TREATED_rep1 (antimony)

description: antimony treated tumor M. musculus sample

source_name: lung, antimony treated tumor

value: antimony_Treated Tumor


title: LMS39

value: Primary tumor Leiomyosarcoma

tag: metastasis


title: LRL147_37C_Rep2


title: LMS38

tag: os

value: Member


title: LRL147_20C_Rep4

source_name: LRL147 (hlh-30;NeuroHLH-30) 20C

value: E. coli OP50 3hr. 20C


title: LRL147_37C_Rep1


title: N2 Day 5 Control [LL29]

value: N2 (Bristol)


title: CONTROL_rep4 (antimony)

description: M. musculus vehicle control sample


title: LMS37

tag: Sex

value: hLMS

value: small RNA


title: MCF7_2

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

data_processing:
The RNA-seq data passed the quality control conducted using FastQC and MulitQC
Sequencing reads were mapped to the mouse reference genome GRCh38/hg38 using STAR software
Intron retention quantification was performed using IRFinder
Genome_build: hg38

molecule: polyA RNA

source_name: breast cancer cells

extract_protocol:
Total RNA was isolated from MCF7 and MCF10A cells using Trizol (Invitrogen). The RNA quality was assessed using RNA 6000 Nano Chips on an Agilent Bioanalyzer (Agilent Technologies) to confirm an RNA integrity score of >7.0.
RNA-seq libraries were prepared from > 1 μg of total RNA using TruSeq RNA sample prep kit (Illumina) according to the manufacturers’ instructions.

tag: cell line

tag: cell type

value: estrogen receptor positive (ER+) breast cancer cells

value: WT


title: LRL147_20C_Rep3


title: CONTROL_rep2 (antimony)

description: M. musculus vehicle control sample


title: CONTROL_rep3 (antimony)

description: M. musculus vehicle control sample


title: ATGL-1 OE Day 5 [LL27]

value: ATGL-1 OE


title: ATGL-1 OE Day 5 [LL28]


title: LRL147_20C_Rep2


title: CONTROL_rep1 (antimony)

description: M. musculus vehicle control sample


title: CONTROL_rep5 (antimony)

description: M. musculus vehicle control sample


title: MCF7_1


title: LRL147_20C_Rep1


title: TREATED_rep2 (antimony)


title: LMS36

value: FEMALE

tag: differentiation

tag: location

value: Internal trunk

tag: age


title: LRL31_37C_Rep4


title: MCF10a_2

source_name: breast epithelial cells

value: non-malignant breast epithelial cells


title: LMS35

tag: lms subtype

tag: molecule subtype


title: LMS34

value: MALE


title: LRL31_37C_Rep1


title: LRL31_37C_Rep3


title: LRL31_20C_Rep4


title: LRL31_20C_Rep3


title: MCF10a_1

tag: genotype


title: PBMC - patient 18 with Sezary syndrome [SS18]

city: Pittsburgh

first: Oleg

middle: E

last: Akilov

state: PA

address: 200 Lothrop Street

department: Dermatology

institute: University of Pittsburgh

data_processing:
Processed single-cell transcriptomic reads were examined by quality metrics and mapped to a reference human genome (GRCh38) using the Seven Bridges Genomic Platform (BD Rhapsody Bioinformatics) to quantify the total numbers of molecules of specific genes present per cell using distribution-based error corrections
Seurat (version 4.0.2) was used for clusters visualization using a uniform manifold approximation and projection (UMAP)
The downstream analysis was performed in R (version 4.0.3)
Genome_build: hg38
Supplementary_files_format_and_content: SSXX_rna.csv = targeted scRNAseq data
Supplementary_files_format_and_content: SSXX_tcr.csv = VDJ CDR3 scRNAseq data
Supplementary_files_format_and_content: SSXX_abseq.csv = scRNAseq AbSeq data

source_name: PBMC - patient with Sezary syndrome

extract_protocol:
Patient with Sezary syndrome donated 15 ml of peripheral blood, and the peripheral blood mononuclear cells were prepared by gradient purification.
BD Rhapsody VDJ CDR3, Sample Tag, BD AbSeq Library preparation protocol for targeted single-cell RNA sequencing with Human Immune Response panel enriched with genes specfic for Sezary syndrome

value: relapse

value: peripheral blood mononuclear cells


title: LMS33


title: LRL31_37C_Rep2

value: E. coli OP50 3hr. 37C


title: LRL31_20C_Rep1


title: LMS32


title: N2_37C_Rep4


title: PBMC - patient 16 with Sezary syndrome [SS16]


title: PBMC - patient 17 with Sezary syndrome [SS17]


title: LMS31


title: PBMC - patient 15 with Sezary syndrome [SS15]


title: N2_37C_Rep2


title: N2_37C_Rep1


title: N2_37C_Rep3


title: LRL31_20C_Rep2


title: N2_20C_Rep4


title: LMS23

value: oLMS


title: N2_20C_Rep3


title: PBMC - patient 13 with Sezary syndrome [SS13]


title: N2_20C_Rep1


title: PBMC - patient 14 with Sezary syndrome [SS14]


title: N2_20C_Rep2


title: pathogen rep3

city: Rindge

first: Shallee

middle: Tyler

last: Page

state: New Hampshire

address: 40 University Dr, Marcucella Hall

department: Coll. Health & Natural Sci.

institute: Franklin Pierce U

data_processing:
Illumina software used for basecalling.
Sequenced reads were assessed by FASTQC(v0.11.6), trimmed for adaptor sequence (Trimmomatic v.0.38), and low-quality sequence. Reads were then mapped using HISAT2(v.2.1.0) default parameters.
SAMTools (v.1.3.1) was used to convert SAM to BAM format.
Transcript assembly and quantification was done with Stringtie (v.1.3.4). DESeq2 (v.1.30.1) was used to calculate and visualize differential expression.
Genome_build: WBcel235.99
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole animal

growth_protocol: C. elegans were grown on NGM agar plates under standard conditions

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA isolation from the Trizol (Direct-zol, ZYMO) suspension was performed according to the manufacturer’s instructions with DNAse treatment on the spin column. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The library construction and sequencing were performed at the UNH Hubbard Genome Center core facility. RNA concentration and quality were assessed via Bioanalyzer nano. Ribosomal subtraction was performed using Illumina poly-A selection according to the manufacturer’s instructions. Library construction was completed using KapaRNA Hyperprep v5.17 and the adapters were the KAPA Dual-Indexed Adapters (KK8722), and Illumina Tru-Seq RNA sequencing (2 X 150bp) paired-end sequencing was performed on Illumina HiSeq2000. All reagents were utilized following the manufacturer's protocols.

treatment_protocol: Worms were grown with OP50, bir-2 or E. faecalis bacterial lawns; after 5 days were washed off with M9 three times and filtered to isolate L1 worms. Equal numbers were plated spread with OP50, bir-2 knockdown bacteria, or E. faecalis. Thus four treatments were: OP50/OP50, bir-2/bir-2, bir-2/EF, or EF/EF each in quadruplicate. Any L3 or L4 that ended up on the plates were removed manually. On day 3, plates were washed three times with M9 and pelleted. Volumes were adjusted to transfer 990 worms to Trizol at -20°C overnight.

value: Whole animal

value: wild type

tag: agent

value: E. faecalis


title: LMS20

value: Primary tumor Leiomyosarcoma


title: LMS21

value: hLMS


title: PBMC - patient 11 with Sezary syndrome [SS11]


title: pathogen rep2

value: N2 (Bristol)


title: bir-2knockdown pathogen rep4


title: pathogen rep4


title: pathogen rep1


title: LMS18_1

value: small RNA


title: bir-2knockdown pathogen rep3


title: bir-2knockdown pathogen rep2


title: PBMC - patient 09 with Sezary syndrome [SS09]

value: naïve


title: bir-2knockdown pathogen rep1


title: LMS24


title: PBMC - patient 10 with Sezary syndrome [SS10]


title: bir-2knockdown untreated rep4


title: LMS16

value: Member


title: PBMC - patient 08 with Sezary syndrome [SS08]


title: bir-2knockdown untreated rep3


title: bir-2knockdown untreated rep1


title: bir-2knockdown untreated rep2


title: LMS22


title: PBMC - patient 07 with Sezary syndrome [SS07]


title: LMS10

value: FEMALE


title: LMS14

value: Internal trunk


title: PBMC - patient 12 with Sezary syndrome [SS12]


title: untreated rep4


title: PBMC - patient 06 with Sezary syndrome [SS06]


title: untreated rep2


title: LMS7_1


title: untreated rep1


title: LMS9_1


title: LMS6


title: PBMC - patient 05 with Sezary syndrome [SS05]


title: PBMC - patient 04 with Sezary syndrome [SS04]


title: PBMC - patient 03 with Sezary syndrome [SS03]


title: LMS5


title: PBMC - patient 02 with Sezary syndrome [SS02]


title: LMS4


title: PBMC - patient 01 with Sezary syndrome [SS01]


title: untreated rep3


title: LMS3


title: USP7 KO#41 rep3

city: Houston

first: Litong

last: Nie

state: Texas

address: 6565 MD Anderson Blvd Unit, Desk Z6.2026

department: ERO

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data were filtered with FastQC. Salmon (version 0.14.1) was used to map read and assemble transcripts into genes.
DESeq2 (v 1.28.1) was used to analysis the fold change and adjusted p value of transcripts or genes.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: USP7 KO#41 rep3

extract_protocol:
The whole mRNA of four cells were extracted with RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: USP7 KO#41


title: USP7 KO#41 rep1

source_name: USP7 KO#41 rep1


title: USP7/MGA DKO rep2

source_name: USP7/MGA DKO rep2

value: USP7/MGA DKO


title: USP7 KO#41 rep2

source_name: USP7 KO#41 rep2


title: IonXpress_060

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description: Homozygous (GBA+/-) cells treated with low-dose rGCase (1ug/mL)

data_processing:
Base-calling, filtering, QC, and alignment was handled automatically by IonTorrent Server Suite (version 4.4.0)
Amplicon coverage is reported by IonTorrent Server Suite (version 4.0.2) as a tab-delimited file, which was converted into GCT format by in-house scripts.
Genome_build: hg19

extract_protocol:
Cell were harvested at day 30 following floor plate induction, DA differentiation, and DA maturation by removing the culture medium. Cell lysates in 50 µl RLT buffer (QIAGEN, Hombrechtikon, Switzerland) were immediately frozen and stored at -80°C.
10 ng of total RNA from each sample were reverse transcribed to cDNA by poly-A-priming followed by PCR pre-amplification (15 cycles) according to the protocol supplied with the Ion AmpliSeq™ RNA Library Kit (Life Technologies, Carlsbad, USA, Catalog number 4482335). After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. This library was amplified, purified and stored at -20°C. Amplicon size and DNA concentration were measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer’s recommendation.

value: dopaminergic (DA) neurons

tag: genotype/variation

value: GBA-/-

value: rGCase 1ug/mL


title: IonXpress_072

description: Homozygous (GBA+/-) cells treated with high-dose rGCase (10ug/mL)

value: rGCase 10ug/mL


title: IonXpress_004

description: Wild-type (GBA+/+) cells treated with low-dose rGCase (1ug/mL)

value: GBA+/+


title: IonXpress_036

description: Homozygous (GBA+/-) cells treated with vehicle control

value: Vehicle


title: IonXpress_005

description: Wild-type (GBA+/+) cells treated with high-dose rGCase (10ug/mL)


title: IonXpress_003


title: IonXpress_006


title: IonXpress_024


title: IonXpress_084


title: USP7/MGA DKO rep1

source_name: USP7/MGA DKO rep1


title: LMS2

value: MALE

value: oLMS


title: IonXpress_048


title: NK cells_expanded_replicate 4

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

description: gene expression analysis of T7-amplified polyA RNA

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K v1, Design ID 028004) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files.

source_name: purified human NK cells, after 14 days expansion

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from Buffy Coat of healthy donors by density gradient centrifugation (Ficoll, GE Healthcare) followed by untouched NK cell isolation using the NK Cell Isolation Kit (Miltenyi Biotec). Alternatively NK cells were purified using MACSxpress NK Cell Isolation Kit enabling direct isolation without prior PBMC preparation (Miltenyi Biotec). For microarray analysis, isolated primary cells or expanded cells from 5-7 donors were pooled (n=4, total number of donors: 24). From this pool, we cryopreserved 1x107 cells for microarray analysis and flow cytometry.

extract_protocol: RNA was extracted using NucleoSpin® RNA kit (Macherey & Nagel) following manufacturer's instructions.

treatment_protocol: Isolated primary NK cells were either directly used for further analysis or expanded for 14 days with cell sized magnetic particles loaded with CD2 and CD335 (NK Cell Activation and Expansion kit, Miltenyi Biotec). SCGM (Cell Genix) supplemented with 1000U/mL IL-2 (Proleukin, Novartis) and 5% AB Serum (Lonza) was used as cultivation medium.

tag: number of pooled donors

tag: stimulation

value: after 14 days expansion

tag: sample pairs


title: NK cells_primary_replicate 3

source_name: purified human NK cells, primary unstimulated

value: primary unstimulated


title: NK cells_expanded_replicate 2


title: NK cells_primary_replicate 1


title: USP7/MGA DKO rep3

source_name: USP7/MGA DKO rep3


title: NK cells_primary_replicate 4


title: TREATED_rep5 (antimony)

tag: group

value: antimony_Treated Tumor


title: NK cells_expanded_replicate 1


title: NK cells_primary_replicate 2


title: NK cells_expanded_replicate 3


title: MGA KO rep2

source_name: MGA KO rep2

value: MGA KO


title: MGA KO rep1

source_name: MGA KO rep1


title: WT rep3

source_name: WT rep3

value: WT


title: IonXpress_001

description: Wild-type (GBA+/+) cells treated with vehicle control

tag: treatment


title: WT rep2

source_name: WT rep2


title: WT rep1

source_name: WT rep1


title: USP7 KO rep3

source_name: USP7 KO rep3

value: USP7 KO


title: F2_D2 individual, grown at 4C [T4_P5.H7_F2_D2]

city: Vienna

first: Rahul

last: Pisupati

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

tag: tissue

value: leaf

tag: developmental stage

value: 7-10 leave rosette


title: F2_D1 individual, grown at 4C [T4_P5.H4_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P5.H6_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P5.H8_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P5.H5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P5.H9_F2_D1]


title: MCAO 12hr, biological rep3

city: Riverside

first: Byron

last: Ford

state: CA

address: 900 University Ave

institute: University of California-Riverside

description: Gene expression data from animals treated with 1% bovine serum albumin(BSA) in phosphate buffered saline (PBS) following MCAO

hyb_protocol: Per manufacturing guidelines, following fragmentation and Labeling Single-Stranded cDNA and 3.5 ug of cRNA was added to Affymetrix Hybridization Master Mix and hybridized for 16 hr at 45C on Affymetrix Rat Genome 2.0st GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using Affymetric TAC 4.0

organism: Rattus norvegicus

source_name: MCAO_12 hours

label_protocol: Fragmented DNA is labeled using an Affymetrix proprietary DNA Labeling Reagent which is covalently linked to biotin by terminal deoxynucleotidyl transferase (TdT), which is added to 5.5 ug total RNA. This and all steps were completed via manufacturing guidelines. (GeneChip® WT PLUS Reagent Kit Manual, 2013, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MCAO was induced by the intraluminal suture method.  A 4 cm length 4-0 surgical monofilament nylon suture coated with silicon (Doccol Corp., Sharon, MA, diameter 0.37 mm, length 2.3-2.5 mm) was inserted from the external carotid artery (ECA) into the internal carotid artery. (ICA) and then into the Circle of Willis, to occlude the origin of the left middle cerebral artery (MCA). Rats in the sham control group underwent the same procedure as those in the injury group, but a filament was not inserted into the ICA. Rats in the sham control group underwent the same procedure as those in the injury group, but a filament was not inserted into the ICA.

value: brain (cortex)

value: adult

tag: gender

value: male


title: MCAO + Vehicle treated, biological rep 5

description: Gene expression data from animals treated with NRG-1 following pMCAO

source_name: MCAO_12 hours + NRG treated


title: MCAO 12hr, biological rep2


title: MCAO + Vehicle treated, biological rep 4


title: MCAO + Vehicle treated, biological rep 3


title: MCAO 12hr, biological rep4


title: USP7 KO rep2

source_name: USP7 KO rep2


title: MCAO 6hr, biological rep2

source_name: MCAO_6 hours


title: MCAO + Vehicle treated, biological rep 2


title: USP7 KO rep1

source_name: USP7 KO rep1


title: P_6191 individual, grown at 4C [T4_P5.H3_P_6191]

tag: cell type


title: MCAO 12hr, biological rep1


title: MCAO 6hr, biological rep4


title: MCAO 6hr, biological rep3


title: MCAO + Vehicle treated, biological rep 1


title: MCAO 3hr, biological rep2

source_name: MCAO_3 hours


title: MCAO 3hr, biological rep3


title: MCAO 6hr, biological rep1


title: MCAO 3hr, biological rep1


title: F2_D2 individual, grown at 4C [T4_P5.H2_F2_D2]


title: 293A wildtype rep2

source_name: 293A wt rep2

value: 293A wt


title: F2_D1 individual, grown at 4C [T4_P5.H1_F2_D1]


title: 293A wildtype rep3

source_name: 293A wt rep3


title: sham control, biological repl 4

description: Gene expression data from sham control


title: F2_D2 individual, grown at 4C [T4_P5.H12_F2_D2]


title: sham control, biological repl 2

description: Gene expression data from sham control


title: 293A wildtype rep1

source_name: 293A wt rep1


title: F2_D1 individual, grown at 4C [T4_P5.H11_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P5.G9_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P5.H10_F2_D1]


title: RNA_seq_CD511_L001

city: Shanghai

first: Ying

last: Liang

state: Shanghai

address: Room 416, West Building 13, Dong'an Road 130, Xuhui District

country: China

institute: Fudan University

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

source_name: osteogenic sarcoma cells

growth_protocol: human osteosarcoma cell lines MNNG/HOS (MNNG)-RFP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, HyClone) supplemented with 10% fetal calf serum (HyClone). All cells were incubated in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP seq; Total RNA extract was harvested using Trizol reagent for RNA seq.
For ChIP-seq, libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Transfecting miR-1246 expression lentivirus into MNNG cells.

tag: strain

value: MNNG/HOS (MNNG)-RFP cells

value: control


title: sham control, biological repl 3

description: Gene expression data from sham control


title: F2_D1 individual, grown at 4C [T4_P5.G8_F2_D1]


title: case_AGO2_chip

tag: chip antibody

value: AGO2 (Santa Cruz, sc-8576)

value: overexpressing miR-1246


title: control_AGO2_chip


title: LV 1

city: Linz

first: Anna

middle: Regina

last: Tröscher

address: Krankenhausstraße 5

department: Center for Medical Research

institute: Johannes Kepler University Linz

description:
gene expression of GAD65-encephalitis short disease duration
SAMPLE 14

hyb_protocol: Affymetrix  human Gene 2.1 ST array plates were washed, stained and scanned according to the protocol described in GeneTitan®Instrument User Guide for Expression Arrays Plates (P/N 702933)

scan_protocol: Scanning was done on an Affymetrix GeneTitan (Single Channel ), software AGCC 3.2.4.1515W

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187

label: Biotin

source_name: Hippocampus

label_protocol: 2ng of total RNA were amplified and labeled using the GeneChip WT Pico Reagent Kit (Catalog Number 902622,Affymetrix, Santa Clara, CA)

extract_protocol: RNA was extracted using the High Pure FFPE RNA Micro Kit from Roche.

value: Hippocampus

tag: diagnosis

tag: disease stage

value: early


title: case_cd511_h3k27ac

value: H3K27ac(Sigma, F3165 )


title: sham control, biological rep 1

description: Gene expression data from sham control

tag: age


title: AST 22_i

description:
gene expression of GAD65-encephalitis long disease duration
SAMPLE 16

value: late


title: RNA_seq_miR1246_L001


title: LV 2

description:
gene expression of GAD65-encephalitis short disease duration
SAMPLE 15


title: F2_D2 individual, grown at 4C [T4_P5.G6_F2_D2]

tag: genotype


title: control_cd511_h3k27ac


title: AT 348

description:
gene expression of control
SAMPLE 13

value: epilepsy


title: AT 341

description:
gene expression of GAD65-encephalitis long disease duration
SAMPLE 10


title: case_1246_h3k4me1

value: H3K4me1(Sigma, A5838)


title: AT 340

description:
gene expression of control
SAMPLE 9


title: F2_D2 individual, grown at 4C [T4_P5.G5_F2_D2]


title: PB ATAC-seq

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

institute: INSERM

description: Tagmented DNA

data_processing:
Image analysis and base calling was performed using Illumina Real Time Analysis ( 2.7.7 ) with default parameters.
Sequencing quality was assessed by FastQC and reads were trimmed of adapter and over-represented sequences with cutadapt.
Reads were aligned on the human hg19 genome with bowtie1 and duplicate reads were removed with PICARD.
Open chromatin regions were called with MACS2 and no external background (macs2 callpeak -t $1 -n $name -f BAMPE -g hs --nomodel --broad --keep-dup 1 --slocal 10000 --outdir $dir), an union of open regions was created with bedtools by taking the largest coordinates for partially overlapping regions.
Read counts and densities were computed for each region and each sample with bedtools intersect and samtools (normalizing by library sequencing depth and region size for densities), counts were analyzed with DESeq2 for determining differentially opened regions.
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, a bigWig signal file, created with bam2wig.py, is provided.

source_name: In vitro differentiated human B cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) from healthy volunteers were obtained from the Etablissement Français du Sang (Rennes, France) after Ficoll density centrifugation (Sigma-Aldrich, St Louis, MO). Subjects were recruited under institutional review board approval and informed consent according to the Declaration of Helsinki. For in vitro differentiation, human naïve B cells were purified by negative selection using magnetic cell separation (Naive B Cell Isolation kit II, Miltenyi Biotech) following the manufacturer’s instructions, using the AutoMACS deplete-sensitive program. The purity of isolated CD19+/CD27- NBCs was routinely above 99%. Cell culture conditions, antibodies, as well as flow cytometry procedures, were as described in Le Gallou et al., 2012. All cultures were performed in complete medium consisting of RPMI 1640 (Invitrogen) supplemented with 10% FCS (Biowest) and antibiotics (Invitrogen). Briefly, purified human naive B cells were labeled with 1µM Violet Proliferation Dye 450 (VPD450, BD Biosciences) in PBS at 37oC for 10 min and washed in complete medium to follow cellular divisions, and enable cell sorting of VPD450hi/lo populations (D4hi/lo). Purified cells were cultured at 7.5.105 cells/ml in 24-well plates and stimulated during 4 days with cocktail 1 composed of 2.6 μg/ml F(ab’)2 fragment goat anti-human IgM (H+L) (Jackson ImmunoResearch Laboratories), 100 ng/ml recombinant human soluble CD40L (NCI), 1.0 mg/ml CpG oligodeoxynucleotide 2006 (Cayla Invivogen), and 50 U/ml recombinant IL-2 (SARL Pharmaxie). After 2 days, antigen-primed naive B cells received a 2-day 12.5 ng/ml IL-10 stimulation (R&D Systems). At day 4, activated B cells were washed, stained with surface markers and CaspGLOW kit (eBioscience) to exclude active caspase-3 cells according to the manufacturer’s instructions and sorted into D4hi/lo populations using FACsARIA cell sorter (BD Biosciences). D4lo cells were then cultured at 4 x 105 cells/ml for up to 3 days with cocktail 2 composed of 50 U/ml IL-2, 12.5 ng/ml IL-10, and 5 ng/ml IL-4 (R&D Systems).

extract_protocol:
Cells were stained with surface markers and sorted at day 0 as MBC IgG+ (CD27+/IgG+/IgM-), MBC IgG+ (CD27+/IgG-/IgM+), NBC (CD27--/IgG+/Ig+-) and at day 6 as PB (VPDlo/CD38hi) cells using a FACsARIA cell sorter (BD Biosciences).
50,000 live cells were manually counted immediately after sorting and ATAC-seq libraries were constructed according to the original ATAC-seq protocol (Buenrostro et al., 2013) with no further modification. No size selection was performed to keep a complete view the the open chromatin landscape. Quantity and quality of libraires were assessed by BioAnalyzer (Agilent) and qPCR (Kapa) analyses. Libraries were sequenced as a single equimolar pool on one lane of a paired end 2x100 bp run on the Illumina HiSeq4000 sequencer by an external provider (Integragen, Evry, France).

tag: days in culture

value: Day 6

tag: cell population

value: In vitro differentiated plasmablast


title: AT 338

description:
gene expression of control
SAMPLE 8


title: F2_D2 individual, grown at 4C [T4_P5.G7_F2_D2]

value: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 4C [T4_P5.G4_F2_D2]


title: NBC ATAC-seq

description: Tagmented DNA

source_name: FACS sorted human peripheral blood B cells

value: Day 0

value: Naive B cells


title: AT 336

description:
gene expression of GAD65-encephalitis short disease duration
SAMPLE 7


title: MBC_IgM ATAC-seq

description: Tagmented DNA

value: IgM+ memory B cells


title: AT 331

description:
gene expression of GAD65-encephalitis short disease duration
SAMPLE 6

source_name: Amygdala

value: Amygdala


title: AT 328

description:
gene expression of control
SAMPLE 5

value: control


title: AT 346

description:
gene expression of control
SAMPLE 12


title: AT 325

description:
gene expression of control
SAMPLE 4


title: AT 312

description:
gene expression of GAD65-encephalitis long disease duration
SAMPLE 3


title: AT 344

description:
gene expression of control
SAMPLE 11


title: F2_D2 individual, grown at 4C [T4_P5.G3_F2_D2]


title: AT 311

description:
gene expression of GAD65-encephalitis short disease duration
SAMPLE 2


title: control_cd511_h3k4me1

value: MNNG/HOS (MNNG)-RFP cells


title: Hep3B_treatA_2

first: Chunxiao

last: Liu

address: 7675 Phoenix Dr Apr623

institute: MD Anderson

data_processing:
Original data file from Illumina is transformed into sequenced reads (raw data, FASTQ formate files) by CASAVA base recognition.
Raw data is filtered by removal of reads with adaptor contamination,reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%),reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Sequencing is mapped to Homo_sapiens_hg19 by STAR software. The alignment by STAR performs precise and effective in positioning junction reads for RNA sequencing data analysis.
FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008).
For the samples with biological replicates, differential expression analysis of two conditions/groups was performed using the Limma R package.
Genome_build: Homo_sapiens_hg19

extract_protocol:
Flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample 5 and 6 was treated with 1 ug/mL RNase7 for 1 h. Sample 1-4 are controls without any treatment.

tag: cell line

value: hepatocellular carcinoma (HCC)

tag: genotype/variation

value: WT

value: RNase7 treatment


title: AT 309

description:
gene expression of GAD65-encephalitis long disease duration
SAMPLE 1

value: Hippocampus


title: WT-MRE11 rep1

city: Guangzhou City

first: Denghui

last: Chen

address: No. 74 Zhongshan 2nd Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

data_processing:
Library strategy: CUT&Tag
Raw data were first trimmed and filtered by TrimGalore with default parameter; then qualified read pairs were aligned to reference genome by Bowtie2 (release 2.4.1); after that biological and optical duplicates were removed with Sambamba (release 0.7.1); last we used MACS2 (release 2.2.7.1; parameters: -q 0.05 -g hs -f BAMPE) to call peaks. All Cut-Tag peaks were filtered with 5% FDR threshold.
We abolished the filtering step in which BLENDER (https://github.com/staciawyman/blender) compares the similarity known gRNA sequence and putative cut sites to discard some candidates. In our code, the cut sites with highest sequencing signal were retained and provided for downstream analyses and experimental validation.
Genome_build: hg38
Supplementary_files_format_and_content: BED format file (Cas9 and MRE11 CutTag peaks and putative cut sites of iCas9)

source_name: human embryonic stem cells

growth_protocol: hESCs were cultured in matrigel-coated plates in the Essential 8TM hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. hESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days.

extract_protocol:
A hyperactive pA-Tn5 transposon for the illumina platform was first generated. hESCWT, hESCiCas9 and hESCidCas9 were treated with 1 µg/ml doxycycline for 12 hours. Cells were harvested and washed twice. Then the nuclei were isolated by ice-cold NE1 buffer and re-suspended in wash buffer. 10 μl of activated concanavalin A beads were added per sample and incubated at room temperature for 10 minutes. Primary antibody (1:50 dilution of anti-IgG, anti-FLAG (Cas9), anti-HA (dCas9), anti-MRE11) incubation was performed on a rotator at 4°C overnight. To increase the number of protein A binding sites, a secondary antibody (such as guinea pig anti-Rabbit IgG antibody for a rabbit primary antibody, and rabbit anti-mouse IgG for a mouse primary antibody) was diluted 1:100 in wash buffer and incubated at RT for 1h. After removing unbound antibodies, cells were mixed with 1:100 dilution of pA-Tn5 (0.04 µM) and incubated at room temperature for 1 hour on rotator. Next, cells were re-suspended in 300 µl tagmentation buffer and incubated at 37 °C for 1 h. To stop tagmentation, 10 µl 0.5 M EDTA, 3µl 10% SDS and 2.5 µl of 20 mg/mL Proteinase K was added to sample, which was incubated overnight at 37 °C. DNA was extracted by PCI and dissolved in 30 μl TE buffer.
To amplify libraries, we added P5 primer, P7 primer (Vazyme, catalog. no. TD202), TruePrep Amplify Enzyme (Vazyme catalog. no. TD601) and performed PCR with the conditions below: 72°C for 3 minutes; 98°C for 30 seconds; 18 cycles of 98°C for 15 seconds, 63°C for 15 seconds; 72°C for 5 minutes. Post-PCR clean-up was performed by adding 1.2 volume of DNA clean beads (Vazyme, catalog. no. N411) and libraries were eluted in 20 μl nuclease-free water.

value: embryonic stem cells


title: WT-MRE11 rep2


title: MBC_IgG ATAC-seq

description: Tagmented DNA

value: IgG+ memory B cells


title: P_6191 individual, grown at 4C [T4_P5.G2_P_6191]


title: F2_D1 individual, grown at 4C [T4_P5.G1_F2_D1]


title: Hep3B_ctrlB_2


title: Hep3B_treatA_1


title: dCas9-MRE11 rep1


title: dCas9-MRE11 rep2


title: F2_D1 individual, grown at 4C [T4_P5.G12_F2_D1]


title: Hep3B_ctrlB_1


title: dCas9-IgG rep2


title: dCas9-IgG rep1


title: Hep3B_ctrlA_2

value: FIG-ROS1 fusion


title: WT-IgG rep2


title: Hep3B_ctrlA_1


title: iCas9-MRE11 rep1


title: dCas9-Cas9 rep1


title: F2_D1 individual, grown at 4C [T4_P5.G10_F2_D1]


title: BLEO/Curcumin_02

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: Sample 8 (E02)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Prostate stromal cell

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or curcumin.

extract_protocol:
Cells were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, the medicinal compound cucumin was applied to the media at 10 µM.

value: bleomycin/curcumin

value: Normal human prostate derived primary stromal cells

tag: passage


title: BLEO/Curcumin_03

description: Sample 9 (E03)


title: F2_D1 individual, grown at 4C [T4_P5.G11_F2_D1]

source_name: leaf

value: leaf


title: P_6191 individual, grown at 4C [T4_P5.F8_P_6191]

value: 7-10 leave rosette


title: iCas9-Cas9 rep2


title: iCas9-IgG rep2


title: F2_D2 individual, grown at 4C [T4_P5.F7_F2_D2]


title: iCas9-Cas9 rep1


title: P_6046 individual, grown at 4C [T4_P5.F9_P_6046]


title: Cas9 irCLIP-seq replicate 2

data_processing:
Library strategy: irCLIP-seq
Sequencing output reads were processed by fastx_collapser from the Fastx-toolkit (version 0.0.14) to remove the duplication on fastq level.
Remained reads were trimmed off the 3’ adapter by fastx_clipper and against reads less than 17 bp and the sequencing quality q25 by fastx_trimmer .
Trimmed reads were aligned to the PhiX genome using Bowtie2(version 2.3.5). Sequence reads that did not align to PhiX were retained for the subsequent analysis.
Trimmed reads were mapped to the rRNAs, snRNAs, miscRNAs, tRNAs(downloaded from RNAcentral release 16 (https://rnacentral.org/)) by bowtie2 (v2.3.5) .
Remained reads were mapped to the human genome  by STAR (v2.5.2). Sequences were then filtered based on mapping quality (Command: samtools view -bS -q 30).
UMI-tools were used to remove technical duplicates to keep uniquely mapped reads.
The binding sites of Cas9 were identified by PureCLIP using the default options.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage.
Supplementary_files_format_and_content: peak files were generated using pureCLIP.

source_name: H1 icas9 embryonic stem cells

growth_protocol: hESCs were cultured in matrigel-coated plates in the Essential 8 hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. hESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days.

extract_protocol:
Cas9-RNA complexes were isolated with anti-FLAG (Sigma F1804) antibody.
RNA libraries were prepared according to the irCLIP protocol (PMID: 27111506)

treatment_protocol: Cells were treated with Doxycyline (1 μg/ml) for 24 hours and then UV cross-linked at 254 for 300 mJ/cm2 to in vivo fix RNA-cas9 interactions.

tag: rip antibody

value: Flag antibody （F1804,sigma)


title: WT-IgG rep1


title: BLEO/Curcumin_01

description: Sample 7 (E01)

tag: treatment


title: BLEOMYCIN_03

description: Sample 6 (B03)

value: bleomycin


title: iCas9-IgG rep1


title: dCas9-Cas9 rep2


title: F2_D2 individual, grown at 4C [T4_P5.F6_F2_D2]

tag: tissue


title: BLEOMYCIN_02

description: Sample 5 (B02)


title: iCas9-MRE11 rep2


title: F2_D1 individual, grown at 4C [T4_P5.F3_F2_D1]

tag: developmental stage


title: F2_D2 individual, grown at 4C [T4_P5.F2_F2_D2]


title: CONTROL_03

description: Sample 3 (A03)


title: F2_D1 individual, grown at 4C [T4_P5.F1_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P5.F12_F2_D2]


title: CONTROL_01

description: Sample 1 (A01)


title: BLEO_03

description: Sample 6 (B03)

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or alpha-lipoic acid (ALA).

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, the medicinal compound ALA was applied to the media at 100 µM.


title: BLEO/ALA_01

description: Sample 7 (F01)

value: bleomycin/alpha-lipoic acid


title: CONTROL_02

description: Sample 2 (A02)


title: F2_D1 individual, grown at 4C [T4_P5.F5_F2_D1]


title: BLEO/ALA_02

description: Sample 8 (F02)


title: F2_D2 individual, grown at 4C [T4_P5.F10_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P5.E9_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P5.E7_F2_D2]


title: Cas9 irCLIP-seq replicate 1


title: F2_D1 individual, grown at 4C [T4_P5.E8_F2_D1]


title: BLEO_02

description: Sample 5 (B02)


title: CTRL_03

description: Sample 3 (A03)


title: MGA KO rep3

source_name: MGA KO rep3

value: MGA KO


title: F2_D2 individual, grown at 4C [T4_P5.F4_F2_D2]


title: IEL-NK cells, Day3_2

city: Serdang

first: Boo

last: Sook Yee

state: Selangor

address: Universiti Putra Malaysia

department: Institute of Bioscience

country: Malaysia

institute: Universiti Putra Malaysia

data_processing:
Fastq files were generated from BCL files using the MiSeq reporter
the fastq files were loaded inside the CLC Genomics Workbench for quality and adapter trimming
the filtered fastq files were proceeded for alignment to chicken genome and microRNA database using Oasis analysis platform v2.0
The differential expression analysis was conducted to find out the DE genes
Genome_build: Galgal4_ensembl, miRBase ver. 21 (released date: June 2014)
Supplementary_files_format_and_content: Read counts and expression value

organism: Gallus gallus

source_name: CD3-, 28.4+ IEL-NK cells isolated from duodenum

growth_protocol: specific-pathogen-free (SPF) embryonated chicken eggs were obtained from Veterinary Research Institute, Ipoh, Perak and hatched in our laboratory under sterile conditions. The chicken was transferred to the Biosafety level-2 facility at our animal house where they were fed with pelleted feed and supplied with water ad libitum.

extract_protocol:
Total RNA was extracted from enriched IEL-NK cells using the trizol reagent.
The total RNA sample was proceeded to the library prep using the TruSeq small RNA library prep kit

treatment_protocol: infected by vvIBDV (UPM0081) at a dosage of 10e3 EID50/0.1ml

value: Duodenum

value: CD3-, 28.4+ IEL-NK cells

tag: infection

tag: time


title: IEL-NK cells, Day3_3

tag: cell type


title: BLEO_01

description: Sample 4 (B01)


title: IEL-NK cells, Day3_1


title: F2_D2 individual, grown at 4C [T4_P5.E6_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P5.E5_F2_D1]


title: IonXpress_002

value: dopaminergic (DA) neurons

value: GBA+/+

value: Vehicle


title: BLEO/ALA_03

description: Sample 9 (F03)


title: IEL-NK cells, Day1_3


title: IEL-NK cells, Day1_2


title: CTRL_01

description: Sample 1 (A01)

value: control


title: F2_D1 individual, grown at 4C [T4_P5.E4_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P5.E3_F2_D2]


title: IEL-NK cells, Day1_1


title: BLEO/NMN 03

description:
Sample 12 (D03)
D.gene.count.matrix.annot

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or NAD+/NMN supplements

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To minimize the senescence-associated secretory phenotype (SASP) by a mechanism of targeting the NAMPT-NAD+ signaling, a metabolic molecule NAD+ or NMN was applied to the media at 10 mM.

value: bleomycin/NMN


title: IEL-NK cells, Control_2

value: uninfected


title: F2_D2 individual, grown at 4C [T4_P5.E2_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P5.E12_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P5.E1_F2_D1]


title: CTRL_02

description: Sample 2 (A02)


title: BLEO/NMN 02

description:
Sample 11 (D02)
D.gene.count.matrix.annot


title: BLEO/NMN 01

description:
Sample 10 (D01)
D.gene.count.matrix.annot


title: DE_27_093_DE_L

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

description: processed data file: DE_HisatCounts_all.csv

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60
All sequences were aligned to the Rattus norvegicus Rnor 6.0 genome from NCBI downloaded July 31, 2015 using HiSat2/2.1.0.
Raw gene counts were assigned using Samtools/1.8, Python/2.7.3 and HTSeq/0.6.1.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: DE_HisatCounts_all.csv: Comma-separated text file including raw counts in a matrix.

source_name: lung

growth_protocol: Male Sprague-Dawley rats (Hilltop Lab Animals, Scottdale, PA), weighing approximately 200-250 g were used in this study which was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in pairs and maintained on a 12-hour light-dark cycle in a temperature (68-72°F) and humidity (30-70%) controlled room with free access to filtered tap water and HaCXan Teklad Global 18% protein rodent diet (Harlan Teklad; Madison, WI).

extract_protocol:
Total RNA was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc, Valencia, CA) following the procedure provided by the manufacturer.
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep (Illumina, Inc., San Diego, CA) following the manufacturer's protocol. Briefly, following depletion of ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis. The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers. While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA. After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: The rats were exposed by whole-body inhalation to filtered air or an aerosol containing DEP at concentrations of 200 or 1000 ug/m3, 6 hours/day for 4 days. The control and DEP-exposed rats were euthanized at post-exposure time intervals of 1, 7, or 27 days.

tag: strain

value: Sprague-Dawley

tag: Sex

value: Male

value: Adult

value: Lung

tag: treatment chemical

value: Diesel exhaust

tag: dose of diesel exhaust

tag: treatment duration

value: 6hr/day for 4 days

tag: post-exposure timepoint

value: 27 days


title: DE_27_090_DE_L

tag: age


title: DE_27_089_DE_L


title: DE_27_091_DE_L


title: F2_D2 individual, grown at 4C [T4_P5.E10_F2_D2]

value: leaf

value: 7-10 leave rosette

tag: genotype


title: DE_27_087_AA_L

value: Air

value: 0 ug/m3


title: DE_27_094_DE_L


title: F2_D2 individual, grown at 4C [T4_P5.E11_F2_D2]


title: DE_27_092_DE_L


title: DE_27_086_AA_L


title: BLEO/NAD+ 02

description:
Sample 8 (C02)
C.gene.count.matrix.annot

value: bleomycin/NAD+

value: Normal human prostate derived primary stromal cells

tag: cell line


title: IEL-NK cells, Control_3

value: Duodenum

value: CD3-, 28.4+ IEL-NK cells


title: DE_27_085_AA_L


title: IEL-NK cells, Control_1

value: control


title: BLEO/NAD+ 01

description:
Sample 7 (C01)
C.gene.count.matrix.annot

tag: passage


title: F2_D2 individual, grown at 4C [T4_P5.D9_F2_D2]


title: DE_27_084_AA_L


title: BLEO 03

description:
Sample 6 (B03)
B.gene.count.matrix.annot

value: bleomycin


title: DE_27_083_AA_L

value: Sprague-Dawley


title: BLEO 02

description:
Sample 5 (B02)
B.gene.count.matrix.annot


title: BLEO/NAD+ 03

description:
Sample 9 (C03)
C.gene.count.matrix.annot


title: F2_D1 individual, grown at 4C [T4_P5.D8_F2_D1]


title: DE_27_046_DE_H

value: Male


title: DE_27_042_AA_H

value: Adult


title: BLEO 01

description:
Sample 4 (B01)
B.gene.count.matrix.annot


title: DE_27_045_DE_H

value: Lung


title: DE_27_041_AA_H


title: CTRL 02

description:
Sample 2 (A02)
A.gene.count.matrix.annot


title: F2_D1 individual, grown at 4C [T4_P5.D5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P5.D4_F2_D1]


title: DE_27_023_DE_H

value: Diesel exhaust


title: CTRL 01

description:
Sample 1 (A01)
A.gene.count.matrix.annot


title: DE_27_022_DE_H

value: 6hr/day for 4 days


title: F2_D1 individual, grown at 4C [T4_P5.D7_F2_D1]


title: CTRL 03

description:
Sample 3 (A03)
A.gene.count.matrix.annot


title: F2_D1 individual, grown at 4C [T4_P5.D3_F2_D1]


title: DE_27_019_AA_H

value: 27 days


title: Ctrl-Y2

first: Hailiang

address: NO 1239, siping road

institute: Tongji university

description: Cultured hADSC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg18 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: hg18
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: adipose

extract_protocol:
Total RNA was extracted using the TRIZOL following the manufacturer's instructions.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina

value: Human adipose-derived mesenchymal stem cells

value: China

value: adipose

value: Young

value: untreated


title: DE_27_021_DE_H


title: DE_27_081_AA_L

value: Air

value: 0 ug/m3


title: F2_D1 individual, grown at 4C [T4_P5.D2_F2_D1]

value: leaf

value: 7-10 leave rosette


title: DE_27_018_AA_H


title: DE_27_020_AA_H


title: DE_27_024_DE_H


title: DE_27_017_AA_H


title: Ctrl-Y1

description: Cultured hADSC


title: F2_D2 individual, grown at 4C [T4_P5.D1_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P5.D6_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P5.D12_F2_D2]


title: DE_07_076_DE_L

value: 7 days


title: Gdf-6-3

description: Cultured hADSC

value: Aged

value: rGDF11 treatment 6 days


title: DE_07_077_DE_L

value: Sprague-Dawley

value: Male

value: Adult


title: DE_07_075_DE_L

value: Lung

value: Diesel exhaust

value: 6hr/day for 4 days


title: F1_D2 individual, grown at 4C [T4_P5.D11_F1_D2]


title: DE_07_074_DE_L


title: Gdf-6-2

description: Cultured hADSC

value: Human adipose-derived mesenchymal stem cells

value: China


title: DE_07_073_DE_L


title: Gdf-6-1

description: Cultured hADSC

value: adipose


title: DE_07_069_AA_L


title: F2_D2 individual, grown at 4C [T4_P5.D10_F2_D2]


title: DE_07_068_AA_L


title: DE_07_070_AA_L


title: F2_D2 individual, grown at 4C [T4_P5.C9_F2_D2]


title: DE_07_067_AA_L


title: Gdf-2-2

description: Cultured hADSC

value: rGDF11 treatment 2 days


title: DE_07_078_DE_L


title: DE_07_066_AA_L

value: Air


title: DE_07_065_AA_L

value: 0 ug/m3


title: DE_07_038_DE_H


title: F2_D2 individual, grown at 4C [T4_P5.C8_F2_D2]

value: leaf


title: F2_D1 individual, grown at 4C [T4_P5.C7_F2_D1]

value: 7-10 leave rosette


title: Gdf-2-1

description: Cultured hADSC


title: Gdf-1-3

description: Cultured hADSC

value: rGDF11 treatment 1 day


title: DE_07_037_DE_H

value: 7 days


title: DE_07_034_AA_H


title: Gdf-1-2

description: Cultured hADSC

value: Aged


title: DE_07_016_DE_H

value: Sprague-Dawley


title: F2_D2 individual, grown at 4C [T4_P5.C5_F2_D2]


title: Gdf-1-1

description: Cultured hADSC


title: DE_07_014_DE_H

value: Male


title: Ctrl-A3

description: Cultured hADSC

value: untreated


title: DE_07_013_DE_H

value: Adult

value: Lung


title: P_6046 individual, grown at 4C [T4_P5.C4_P_6046]


title: Ctrl-A2

description: Cultured hADSC


title: DE_07_011_AA_H

value: 6hr/day for 4 days


title: Ctrl-A1

description: Cultured hADSC

value: Human adipose-derived mesenchymal stem cells


title: DE_07_009_AA_H


title: F2_D2 individual, grown at 4C [T4_P5.C2_F2_D2]


title: DE_01_062_DE_L

value: Diesel exhaust

value: 1 day


title: DE_07_010_AA_H


title: F2_D2 individual, grown at 4C [T4_P5.C1_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P5.C6_F2_D1]


title: Gdf-2-3

description: Cultured hADSC

value: China

value: adipose

value: rGDF11 treatment 2 days


title: HDX338

source_name: Human blood-derived peripheral blood mononuclear cell

tag: geography

value: PBMC


title: DE_07_033_AA_H

value: Air

value: 0 ug/m3


title: F2_D2 individual, grown at 4C [T4_P5.C12_F2_D2]

value: leaf

value: 7-10 leave rosette

tag: treatment


title: DE_01_060_DE_L

value: Sprague-Dawley

tag: tissue


title: DE_01_059_DE_L

value: Male


title: DE_07_015_DE_H

value: 7 days


title: DE_01_061_DE_L

value: Adult


title: DE_07_012_AA_H

value: Lung


title: F2_D1 individual, grown at 4C [T4_P5.C11_F2_D1]

tag: developmental stage


title: HDX312

value: Aged


title: DE_01_057_DE_L

value: 6hr/day for 4 days


title: DE_01_054_AA_L


title: HDX321


title: DE_01_058_DE_L

value: Diesel exhaust


title: F2_D1 individual, grown at 4C [T4_P5.C10_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P5.C3_F2_D1]


title: HDX220


title: F2_D1 individual, grown at 4C [T4_P5.B9_F2_D1]


title: DE_01_052_AA_L

value: 1 day


title: DE_01_051_AA_L


title: HDX141

value: China


title: DE_01_050_AA_L


title: DE_01_030_DE_H


title: F2_D1 individual, grown at 4C [T4_P5.B7_F2_D1]


title: BLEOMYCIN_01

description: Sample 4 (B01)

value: bleomycin

value: Normal human prostate derived primary stromal cells


title: HDX113

value: PBMC


title: F2_D2 individual, grown at 4C [T4_P5.B6_F2_D2]


title: DE_01_026_AA_H

value: Air


title: DE_01_025_AA_H

value: 0 ug/m3


title: HDX120


title: HDX84


title: DE_01_007_DE_H


title: DE_01_008_DE_H


title: DE_01_005_DE_H


title: F2_D2 individual, grown at 4C [T4_P5.B5_F2_D2]

value: leaf


title: HYS315

value: Young


title: DE_01_053_AA_L

value: Sprague-Dawley


title: DE_01_006_DE_H

value: Male


title: HYS33


title: DE_01_004_AA_H


title: F2_D1 individual, grown at 4C [T4_P5.B4_F2_D1]

value: 7-10 leave rosette


title: F2_D2 individual, grown at 4C [T4_P5.B3_F2_D2]


title: DE_01_003_AA_H

value: Adult


title: F2_D1 individual, grown at 4C [T4_P5.B8_F2_D1]


title: DE_01_002_AA_H

value: Lung


title: DE_01_049_AA_L


title: F2_D2 individual, grown at 4C [T4_P5.B2_F2_D2]


title: DE_01_029_DE_H


title: DE_01_001_AA_H


title: F2_D2 individual, grown at 4C [T4_P5.F11_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P5.B1_F2_D1]


title: HYS28


title: F2_D2 individual, grown at 4C [T4_P5.B12_F2_D2]


title: OV_16_28D_94_Lu_OV

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60
All sequences were aligned to the Rattus norvegicus Rnor 6.0 genome from NCBI downloaded July 31, 2015 using HiSat2/2.1.0.
Raw gene counts were assigned using Samtools/1.8, Python/2.7.3 and HTSeq/0.6.1.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: 2 csv files including raw counts in a matrix; one file for high dose samples; one file for low dose samples

growth_protocol: Male Sprague-Dawley rats (Hilltop Lab Animals, Scottdale, PA), weighing approximately 200-250 g were used in this study which was conducted in an Association for Assessment and Accreditation of Laboratory Animal Care International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Animal Care and Use Committee. The rats were housed in pairs and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and HaCXan Teklad Global 18% protein rodent diet (Harlan Teklad; Madison, WI).

extract_protocol:
Total RNA was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc, Valencia, CA) following the procedure provided by the manufacturer.
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep (Illumina, Inc., San Diego, CA) following the manufacturer's protocol.  Briefly, following depletion of ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis.  The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers.  While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA.  After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. The rats were exposed by inhalation to filtered air or oil vapor particles (300 ppm, 6 hours/day for 1 day or 300 ppm, 6 hours/day, 4 days/week for 4 weeks). At post exposure time intervals of 1 and 28 days, the air and oil vapor exposed rats were euthanized. n=6 for all groups.

value: oil vapor

tag: dose (oil vapor)

value: 28 day post-exposure

value: lung


title: HYS25


title: HYS27


title: OV_16_28D_96_Lu_OV

tag: time


title: OV_16_28D_92_Lu_OV


title: OV_16_28D_91_Lu_OV


title: OV_16_28D_93_Lu_OV


title: OV_16_28D_89_Lu_OV


title: HYS23


title: F2_D2 individual, grown at 4C [T4_P5.B10_F2_D2]

tag: cell type


title: HYS21


title: OV_16_28D_88_Lu_AA

value: air

tag: strain


title: F2_D1 individual, grown at 4C [T4_P5.B11_F2_D1]


title: OV_16_28D_87_Lu_AA


title: F2_D1 individual, grown at 4C [T4_P5.A9_F2_D1]


title: OV_16_28D_84_Lu_AA


title: HYS18

value: China


title: HYS29


title: OV_16_28D_83_Lu_AA


title: OV_16_28D_82_Lu_AA


title: HYS17


title: F2_D1 individual, grown at 4C [T4_P5.A8_F2_D1]


title: OV_16_01D_48_Lu_OV

value: 1 day post-exposure


title: OV_16_01D_46_Lu_OV


title: P_6046 individual, grown at 4C [T4_P5.A7_P_6046]


title: OV_16_01D_45_Lu_OV


title: OV_16_01D_47_Lu_OV


title: F1_D1 individual, grown at 4C [T4_P5.A6_F1_D1]


title: OV_16_01D_40_Lu_AA


title: OV_16_01D_43_Lu_OV


title: F2_D1 individual, grown at 4C [T4_P5.A4_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P5.A5_F2_D1]


title: OV_16_01D_37_Lu_AA


title: OV_16_01D_39_Lu_AA


title: OV_16_01D_44_Lu_OV


title: OV_16_01D_38_Lu_AA


title: OV_16_28D_86_Lu_AA


title: OV_16_01D_34_Lu_AA


title: OV_01_28D_32_Lu_OV


title: F2_D1 individual, grown at 4C [T4_P5.A3_F2_D1]


title: OV_16_01D_36_Lu_AA


title: F2_D2 individual, grown at 4C [T4_P5.A1_F2_D2]


title: OV_01_28D_29_Lu_OV


title: F2_D1 individual, grown at 4C [T4_P5.A2_F2_D1]


title: OV_01_28D_31_Lu_OV


title: F2_D2 individual, grown at 4C [T4_P5.A11_F2_D2]


title: OV_01_28D_27_Lu_OV


title: OV_01_28D_24_Lu_OV


title: OV_01_28D_28_Lu_OV


title: F2_D2 individual, grown at 4C [T4_P5.A10_F2_D2]


title: OV_01_28D_23_Lu_AA


title: OV_01_28D_22_Lu_AA


title: F2_D1 individual, grown at 4C [T4_P4.H9_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P4.H8_F2_D2]


title: OV_01_28D_19_Lu_AA


title: OV_01_28D_18_Lu_AA


title: OV_01_28D_17_Lu_AA


title: P_6046 individual, grown at 4C [T4_P4.H7_P_6046]


title: OV_01_01D_14_Lu_OV


title: OV_01_01D_16_Lu_OV


title: OV_01_01D_13_Lu_OV


title: OV_01_01D_07_Lu_OV


title: F2_D2 individual, grown at 4C [T4_P4.H5_F2_D2]


title: OV_01_01D_10_Lu_AA


title: OV_01_01D_06_Lu_OV


title: OV_01_28D_20_Lu_AA


title: F2_D1 individual, grown at 4C [T4_P5.A12_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P4.H4_F2_D1]


title: OV_01_01D_02_Lu_AA


title: OV_01_01D_09_Lu_AA


title: OV_01_01D_01_Lu_AA


title: SB-18-96

description: total RNA including microRNAs

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters  ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were mapped  to Rnor6.0 whole genome using tophat/2.0.9 and bowtie2/2.2.9.
Aligned sequences were identified using cufflinks/2.1.1
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including fpkm values in a matrix containing all samples

growth_protocol: This experiment was conducted in an animal facility (NIOSH, Morgantown, WV) accredited by AAALAC International following a protocol approved by the Institutional Animal Care and Use Committee (IACUC). Male Fischer (CDF®) rats (F344/DuCrl) 3 months of age were purchased from Charles River Laboratories (Wilmington, MA). Rats were housed 3 per cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and Teklad rodent diet (Envigo, Indianapolis, IN).

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold Kit   (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol. The samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. Groups (n=5*) were exposed to air (controls) or crystalline silica (6 hours/day, 5 days). Rats were maintained under conditions detailed in the grow protocol for 1, 3, 6, 9, 12, or 18 months following crystalline silica exposure. *for 9 month air, n=4

value: Fischer 344

tag: treatment group

value: silca

tag: crystalline silica concentration (mg/m3)

tag: post-exposure timepoint (months)


title: OV_01_01D_03_Lu_AA

tag: treatment chemical


title: OV_01_01D_05_Lu_OV


title: F2_D2 individual, grown at 4C [T4_P4.H12_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P4.H2_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P4.H1_F2_D1]


title: SB-18-95

description: total RNA including microRNAs


title: SB-18-94

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.H3_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P4.H11_F2_D1]


title: SB-18-93

description: total RNA including microRNAs


title: SB-18-83

description: total RNA including microRNAs


title: SB-18-91

description: total RNA including microRNAs


title: SB-18-82

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.H10_F2_D2]


title: OV_01_01D_04_Lu_AA


title: P_6191 individual, grown at 4C [T4_P4.H6_P_6191]


title: SB-18-81

description: total RNA including microRNAs


title: SB-12-48

description: total RNA including microRNAs


title: SB-12-44

description: total RNA including microRNAs


title: SB-12-38

description: total RNA including microRNAs


title: SB-18-79

description: total RNA including microRNAs


title: F1_D2 individual, grown at 4C [T4_P4.G7_F1_D2]


title: P_6191 individual, grown at 4C [T4_P4.G8_P_6191]


title: F2_D2 individual, grown at 4C [T4_P4.G6_F2_D2]


title: SB-12-35

description: total RNA including microRNAs


title: SB-12-34

description: total RNA including microRNAs


title: SB-12-37

description: total RNA including microRNAs


title: SB-12-28

description: total RNA including microRNAs


title: SB-12-33

description: total RNA including microRNAs


title: SB-09-70

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.G3_F2_D1]


title: SB-09-69

description: total RNA including microRNAs


title: SB-12-26

description: total RNA including microRNAs


title: SB-09-63

description: total RNA including microRNAs


title: SB-09-65

description: total RNA including microRNAs


title: SB-09-64

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.G2_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P4.G9_F2_D2]


title: F1_D1 individual, grown at 4C [T4_P4.G1_F1_D1]


title: SB-09-60

description: total RNA including microRNAs


title: SB-09-56

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.G12_F2_D1]


title: SB-12-40

description: total RNA including microRNAs


title: SB-09-53

description: total RNA including microRNAs


title: SB-09-50

description: total RNA including microRNAs


title: SB-18-80

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.G11_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P4.G5_F2_D2]


title: SB-06-119

description: total RNA including microRNAs


title: SB-06-120

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.F9_F2_D2]


title: SB-06-118

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.G4_F2_D2]


title: SB-06-117

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.G10_F2_D1]


title: SB-06-105

description: total RNA including microRNAs


title: SB-06-106

description: total RNA including microRNAs


title: SB-06-107

description: total RNA including microRNAs


title: P_6191 individual, grown at 4C [T4_P4.F8_P_6191]


title: SB-06-103

description: total RNA including microRNAs


title: SB-06-115

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.F7_F2_D1]


title: SB-03-160

description: total RNA including microRNAs


title: SB-03-159

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.F6_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P4.F4_F2_D1]


title: SB-03-158

description: total RNA including microRNAs


title: SB-03-157

description: total RNA including microRNAs


title: P_6046 individual, grown at 4C [T4_P4.F5_P_6046]


title: F2_D1 individual, grown at 4C [T4_P4.F3_F2_D1]


title: SB-03-150

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.F2_F2_D1]


title: SB-03-147

description: total RNA including microRNAs


title: SB-03-145

description: total RNA including microRNAs


title: SB-03-146

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.F1_F2_D2]


title: SB-01-137

description: total RNA including microRNAs


title: SB-01-135

description: total RNA including microRNAs


title: SB-01-136

description: total RNA including microRNAs


title: SB-06-104

description: total RNA including microRNAs


title: SB-01-134

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.F12_F2_D2]


title: SB-01-133

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.F10_F2_D1]


title: SB-03-161

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.F11_F2_D1]


title: SB-01-125

description: total RNA including microRNAs


title: SB-01-126

description: total RNA including microRNAs


title: SB-01-124

description: total RNA including microRNAs


title: F2_D2 individual, grown at 4C [T4_P4.E8_F2_D2]


title: SB-01-123

description: total RNA including microRNAs


title: SB-03-148

description: total RNA including microRNAs


title: MW_180_162_MW

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters  ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60
Sequences were mapped  to Rnor6.0 whole genome using Hisat2/2.1.0 with the following parameters: -q --downstream-transcriptome-assembly --dta-cufflinks --fr --no-mixed --time --met-file
Aligned sequences were identified, sorted, and counted using Samtools/1.8 and HTSeq/0.11.2
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the IlluminaTruSeq Stranded mRNA Library Prep Kit   (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol. The samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. Groups (n=6) were exposed to air (controls) or MWCNT (6 hours/day, 3 days) to result in cumulative doses of 180, 90, 45, 22.5, or 11.25 mg/m3.

value: MWCNT

tag: mwcnt concentration (mg/m3)

tag: outlier in subsequent analyses

value: no

tag: molecule subtyoe

value: total RNA including microRNAs


title: MW_180_161_MW


title: F2_D1 individual, grown at 4C [T4_P4.E7_F2_D1]

value: leaf

tag: genotype


title: F2_D1 individual, grown at 4C [T4_P4.E6_F2_D1]


title: MW_180_159_MW


title: MW_180_158_MW


title: MW_180_160_MW


title: MW_180_157_MW

value: yes


title: F2_D1 individual, grown at 4C [T4_P4.E5_F2_D1]


title: MW_180_150_AA


title: MW_180_149_AA


title: SB-01-127

description: total RNA including microRNAs


title: F2_D1 individual, grown at 4C [T4_P4.E3_F2_D1]


title: MW_180_147_AA


title: MW_180_146_AA


title: F2_D2 individual, grown at 4C [T4_P4.E2_F2_D2]


title: MW_180_145_AA


title: F1_D1 individual, grown at 4C [T4_P4.E9_F1_D1]


title: MW_011_111_MW


title: MW_011_112_MW


title: MW_011_114_MW


title: MW_011_113_MW


title: MW_011_110_MW


title: F2_D2 individual, grown at 4C [T4_P4.E1_F2_D2]


title: MW_011_109_MW


title: F2_D1 individual, grown at 4C [T4_P4.E11_F2_D1]


title: MW_011_102_AA


title: MW_011_101_AA


title: F2_D1 individual, grown at 4C [T4_P4.E10_F2_D1]


title: MW_011_097_AA


title: F2_D1 individual, grown at 4C [T4_P4.E4_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P4.D9_F2_D2]


title: MW_011_100_AA


title: MW_011_099_AA


title: MW_090_089_MW


title: MW_011_098_AA


title: MW_180_148_AA


title: F2_D2 individual, grown at 4C [T4_P4.D8_F2_D2]


title: MW_090_090_MW


title: MW_090_087_MW


title: MW_090_088_MW


title: MW_090_086_MW


title: F2_D2 individual, grown at 4C [T4_P4.D6_F2_D2]


title: MW_090_085_MW


title: F2_D2 individual, grown at 4C [T4_P4.D7_F2_D2]


title: MW_090_077_AA


title: MW_090_076_AA


title: F2_D2 individual, grown at 4C [T4_P4.D4_F2_D2]


title: MW_090_075_AA


title: F2_D1 individual, grown at 4C [T4_P4.D3_F2_D1]


title: MW_090_078_AA


title: MW_090_074_AA


title: MW_022_065_MW


title: MW_090_073_AA


title: MW_022_066_MW


title: MW_022_064_MW


title: MW_022_063_MW


title: F2_D2 individual, grown at 4C [T4_P4.D12_F2_D2]


title: MW_022_053_AA


title: MW_022_052_AA


title: MW_022_054_AA


title: MW_022_051_AA


title: MW_022_061_MW


title: Control_3

city: Cincinnati

first: Scott

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

description:
DK245
microRNA

data_processing:
Base calling software: Casava 1.8.
Preprocessing: Sequence reads were pre-processed to remove adapters and retain only 16-30 base pair- length reads.
Alignment: Reads were aligned to the reference human genome (hg19) using the Bowtie aligner.
Counts: The reads aligning to each known miRNA were counted using Bioconductor packages for next-generation sequencing data analysis based on miRNA definitions in miRBase database.
Normalized abundance measures: RPKM.
Assembly: hg19
Supplementary files format and content: Processed_Counts_HNSCC_HPVpos_cells.csv: The processed data file is in comma-separated format and contains a table of miRNA transcripts (rows) and normalized abundance (RPKM) data for each sample (columns).

source_name: primary gingival epithelial cells: small extracellular vesicles

growth_protocol: Cells were cultivated in supplier-recommended media with 10% fetal bovine serum (FBS) that was super-depleted of exosomes via 18 hour ultracentrifugation at 100,000g (verified via nanoparticle tracking analysis) and 1% penicillin/streptomycin at 37°C with 5% CO2 in 150 cm2 flasks with 25mL media. To achieve adequate volume for exosome isolation, cells were cultured in 2-pair sets of flasks in triplicate (6 flasks total per cell-line). Culture media were replaced approximately 48 hours prior to cells reaching 80-90% confluence; media and cells were respectively collected after 48 hours. The media from each 2-flask pair were combined (50mLtotal). After media was harvested, cells were detached from each flask and pooled for each cell-line.

extract_protocol:
Total RNA was extracted from each exosome pellet using the miRNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s suggested protocol.
The NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA) was used with 20 ng to 1 µg of total RNA in a 6-µL solution as input, following the manufacturer’s protocol with modification of library size selection.

tag: cell line

value: HGEPp

value: Primary gingival epithelial cells

tag: culture media

value: CnT-Prime

tag: source

value: small extracellular vesicles


title: F2_D1 individual, grown at 4C [T4_P4.D10_F2_D1]

tag: tissue

value: 7-10 leave rosette

tag: treatment


title: F2_D1 individual, grown at 4C [T4_P4.C9_F2_D1]

tag: developmental stage


title: MW_022_062_MW


title: P_6191 individual, grown at 4C [T4_P4.D1_P_6191]


title: MW_022_050_AA


title: F2_D2 individual, grown at 4C [T4_P4.D11_F2_D2]


title: Control_2

description:
DK244
microRNA


title: F2_D1 individual, grown at 4C [T4_P4.D5_F2_D1]


title: MW_045_041_MW


title: MW_022_049_AA


title: F2_D2 individual, grown at 4C [T4_P4.C8_F2_D2]


title: MW_045_040_MW


title: Control_1

description:
DK243
microRNA


title: MW_045_042_MW


title: F2_D2 individual, grown at 4C [T4_P4.C7_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P4.D2_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P4.C6_F2_D2]


title: UPCI:SCC152_3

description:
DK242
SCC152_3
microRNA

source_name: HNSCC cell line: small extracellular vesicles

value: HNSCC cell line

value: MEM


title: MW_045_038_MW

value: lung


title: F2_D1 individual, grown at 4C [T4_P4.E12_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P4.C5_F2_D2]


title: MW_045_027_AA

value: air


title: F2_D2 individual, grown at 4C [T4_P4.C2_F2_D2]


title: MW_045_029_AA


title: P_6046 individual, grown at 4C [T4_P4.C3_P_6046]


title: F2_D2 individual, grown at 4C [T4_P4.C4_F2_D2]


title: MW_045_030_AA


title: MW_045_025_AA


title: UPCI:SCC152_2

description:
DK241
SCC152_2
microRNA


title: UM-SCC104_3

description:
DK236
SCC104_3
microRNA

value: DMEM


title: MW_045_028_AA

value: Fischer 344


title: UPCI:SCC152_1

description:
DK240
SCC152_1
microRNA


title: UPCI:SCC090_1

description:
DK237
SCC090_1
microRNA


title: HFS_SO_09_138_Lu

description:
total RNA including small RNAs
HighFatDietSilica_09months
SO09Lu_tophat_counts.csv

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:adapters/TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 (for SL03Lu) or 60 (SL09Lu)
Sequences were mapped with the Rattus norvegicus Rnor 6.0 genome from NCBI downloaded July 31st, 2015 using Tophat/2.0.9 (Trapnell, C. et al., 2012) and Bowtie2/2.2.9 (Langmead B. and Salzberg S., 2012)
Aligned sequences were identified, sorted, and counted using Samtools/0.1.19 (Li, H. et al. 2009), Python/2.7.3 and HTSeq/0.6.1
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

growth_protocol: This experiment was conducted in an animal facility (NIOSH, Morgantown, WV) accredited by AAALAC International following a protocol approved by the Institutional Animal Care and Use Committee (IACUC). Male Fischer (CDF®) rats (F344/DuCrl) 3 months of age were purchased from Charles River Laboratories (Wilmington, MA). Rats were housed 3 per cage in a temperature (22-25C) and humidity (30-70%) controlled environment following a 12hr light-dark schedule with free access to Harlan Teklad Global 18% Protein Rodent Diet, 2918 irradiated rodent chow, (Harlan Laboratories, Frederick, MD, USA) and tap water.

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep with Ribo-Zero Gold  (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol with the exception of only 12 PCR cycles used to enrich the DNA fragments.

treatment_protocol: Acclimated rats were fed either a regular-fat diet (RFD; 18% kcal as fat) (Envigo, Indianapolis, IN) or a high-fat diet (HFD; 60% kcal as fat) (Envigo, Indianapolis, IN) for two weeks and then exposed by whole-body inhalation to either air or crystalline silica (15 mg/m3, 6 hours/day, 5 days). The respective diets were continued throughout the experiment, and at designated post-exposure time intervals (1, 3, 6, and 9 months) rats were euthanized and tissues collected.

tag: Sex

value: male

tag: diet

value: high 60% kcal as fat diet

value: silica, 15 mg/m3, 6 hours/day, 5 days

tag: post-exposure timepoint

value: 09 months


title: UPCI:SCC090_3

description:
DK239
SCC090_3
microRNA

tag: cell type


title: UM-SCC104_2

description:
DK235
SCC104_2
microRNA


title: MW_045_037_MW

tag: strain

value: MWCNT

value: no

value: total RNA including microRNAs


title: HFS_SO_09_134_Lu


title: HFS_SO_09_135_Lu


title: F2_D1 individual, grown at 4C [T4_P4.C11_F2_D1]

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

value: leaf


title: F2_D1 individual, grown at 4C [T4_P4.C10_F2_D1]


title: HFA_SO_09_129_Lu

description:
total RNA including small RNAs
HighFatDietAir_09months
SO09Lu_tophat_counts.csv


title: MW_045_039_MW


title: HFS_SO_09_133_Lu


title: MW_045_026_AA


title: HFS_SO_09_141_Lu


title: UPCI:SCC090_2

description:
DK238
SCC090_2
microRNA


title: UM-SCC104_1

description:
DK234
SCC104_1
microRNA


title: HFS_SO_09_137_Lu


title: F2_D2 individual, grown at 4C [T4_P4.C12_F2_D2]


title: HFA_SO_09_128_Lu


title: F2_D2 individual, grown at 4C [T4_P4.B9_F2_D2]


title: HFA_SO_09_127_Lu


title: F2_D2 individual, grown at 4C [T4_P4.B7_F2_D2]


title: HFA_SO_09_124_Lu


title: HFA_SO_09_122_Lu


title: UM-SCC47_3

description:
DK233
SCC47_3
microRNA


title: UM-SCC47_1

description:
DK231
SCC47_1
microRNA


title: UM-SCC47_2

description:
DK232
SCC47_2
microRNA


title: F2_D2 individual, grown at 4C [T4_P4.B8_F2_D2]


title: RDS_SO_09_118_Lu

description:
total RNA including small RNAs
RegularDietSilica_09months
SO09Lu_tophat_counts.csv

value: regular 18% kcal as fat diet


title: RDS_SO_09_119_Lu


title: HFA_SO_09_121_Lu


title: RDS_SO_09_115_Lu


title: RDS_SO_09_117_Lu


title: RDS_SO_09_120_Lu


title: RDA_SO_09_114_Lu

description:
total RNA including small RNAs
RegularDietAir_09months
SO09Lu_tophat_counts.csv


title: Control [DK859]

data_processing:
Base calling software: Casava 1.8
Preprocessing: Sequence reads were pre-processed to remove adapters and retain only 16-30 base pair- length reads
Alignment: Reads were aligned to the reference human genome (hg19) using the Bowtie aligner
Counts: The reads aligning to each known miRNA were counted using Bioconductor packages for next-generation sequencing data analysis based on miRNA definitions in miRBase database
Normalized abundance measures: RPKM
Assembly: hg19
Supplementary files format and content: The processed data file is in .csv format and contains a table of miRNA transcripts (rows) and normalized abundance (RPKM) data for each sample (columns)

source_name: serum small extracellular vesicles

extract_protocol:
Total RNA was extracted from each exosome pellet using the miRNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s suggested protocol.
The NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA) was used with 20 ng to 1 µg of total RNA in a 6-µL solution as input, following the manufacturer’s protocol with modification of library size selection

tag: age

value: Male

value: small extracellular vesicles

tag: tissue type

value: Benign - hamartoma

tag: molecule type

value: microRNA


title: F2_D2 individual, grown at 4C [T4_P4.B4_F2_D2]

value: 7-10 leave rosette


title: RDA_SO_09_113_Lu

value: lung

value: air


title: aged mouse 6 (72 weeks) [Sequel II]

city: NORWICH

first: Laura

last: mincarelli

state: County (optional)

address: Norwich Research Park, Colney Lane, Colney

country: United Kingdom

institute: Earlham Institute

description: single cell fulllenght cDNA (10x Genomics)

data_processing:
Illumina data
Raw Illumina sequencing data were analysed with the 10X Genomics CellRanger pipeline (version 3.0.2) to obtain a single-cell expression matrix object.
Using Seurat v3 in R data were normalised using NormalizeData
data from multiple samples were merged using the FindIntegrationAnchors and IntegrateData commands
count matrices produced by short-read sequencing for individual libraries were combined in Seurat using FindIntegrationAnchors and IntegrateData functions
Illumina and PacBio reads were integrated in Seurat using the CreateAssayObject command to add the long-read data to an existing Seurat object already containing the short-read data
Pacbio data
Circular Consensus reads (CCS) were generated using smrtlink-6.0.0.47841 amnd the command "ccs --numThreads=24 --noPolish --minLength=50 --maxLength=15000 --minPasses=1 --minPredictedAccuracy=0.8"
Reads with identified polydA or polydT were demultiplexed using bbduk and the 10X genomics barcodes identified from the short-read analysis
Long-reads were mapped to the mouse genome (mm10) using Minimap 2 (v2.17), and to the gencode (vM19) transcriptome. De novo transcript annotation was performed with TALON  v.5 was used to generate custom transcriptome using gencode v.M24 and GRCm38.p6. Minimum identity threshold 0.9, coverage 0.8. Novel features filtered with N=5 reads in K=3 samples. Transcriptome then filtered for mis-called antisense transcripts. Novel features were merged with v.M24 reference to make custom annotation. Count matrices were generated using HTSeq, the alignments to the genome (GRCm38.p6, Minimap2) and the TALON annotation
Novel exons were identified by investigating the alignment of the reads to the transcriptome
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: gene level counts
Supplementary_files_format_and_content: de novo annotation
Supplementary_files_format_and_content: gene levels counts

source_name: bone marrow cells

extract_protocol:
Bone marrow was isolated from spine, femora, tibiae, and ilia,blood cell depletion was performed with ammonium chloride lysis  and lineage negative cells were isolated using the EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit
3’ end single cell RNA-Seq using the 10X Genomics Chromium (V2 Kit) according to manufacturer’s protocol
Libraries compatible for Illumina platform and for Pacific Biosciences Sequel/Sequel II systems were prepared from input cDNA

value: Lineage negative, cKit (Cd117) positive (LK) cell fraction

value: female

value: 72 weeks


title: Control [DK857]

value: Female

value: Benign - serous cystadenoma


title: F1_D2 individual, grown at 4C [T4_P4.B3_F1_D2]


title: RDA_SO_09_112_Lu

value: Fischer 344

value: male

value: 09 months


title: Control [DK856]

value: Benign - mucinous cystadenoma


title: young  mouse 5 ( 8 weeks) [Sequel II]

value: 8 weeks


title: F2_D1 individual, grown at 4C [T4_P4.B6_F2_D1]

value: leaf


title: RDA_SO_09_110_Lu

value: regular 18% kcal as fat diet


title: Control [DK855]

value: small extracellular vesicles


title: aged mouse 4 (72 weeks) [Sequel II]


title: F2_D2 individual, grown at 4C [T4_P4.B2_F2_D2]


title: Control [DK858]

value: Benign - granuloma

value: microRNA


title: F2_D1 individual, grown at 4C [T4_P4.B12_F2_D1]

value: 7-10 leave rosette


title: F2_D1 individual, grown at 4C [T4_P4.B5_F2_D1]