title: B. cinerea in vitro replicate 3

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

institute: Consiglio Nazionale delle Ricerche (CNR)

description: B. cinerea mycelia from saprophytic growth in liquid nutrient medium in laboratory flasks

data_processing:
de-multiplexing: all raw reads related to the same sample (originally spread over multiple FASTQ files) were merged into a single FASTQ file of R1 or R2 reads for the given sample.
data filtering: raw reads were subjected to quality control by using the IlluQC software, that is part of the NGS QC Toolkit [Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619. doi: 10.1371/journal.pone.0030619. Epub 2012 Feb 1. PubMed PMID: 22312429; PubMed Central PMCID: PMC3270013.] with default parameters (i.e.: quality cutoff: 20; required % of nucleotides in reads with quality score at least equal to quality cutoff: 70%).
mapping: filtered reads were mapped against a mixed reference genome (Botrytis cinerea + Vitis vinifera) by using TopHat (version 2.0.11) [Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with  RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16. PubMed PMID: 19289445; PubMed Central PMCID: PMC2672628.].
gene-level summarization: mapped reads were summarized at the gene-level into a count-matrix by using the htseq-count tool from the HTSeq library [Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25. PubMed PMID: 25260700; PubMed Central PMCID: PMC4287950].
gene-level count matrices were then used to perform differential expression analyses by using edgeR [Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11. PubMed PMID: 19910308; PubMed Central PMCID: PMC2796818]. Only genes having at least 3 mapped reads in at least 3 samples of the above count matrix were tested for differential expression.
Genome_build: whole-genome sequences and annotations for Vitis vinifera (genome annotation release: V1) were obtained from the Grape genome database [Vitulo N, Forcato C, Carpinelli EC, Telatin A, Campagna D, D'Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M, Valle G. A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol. 2014 Apr 17;14:99. doi: 10.1186/1471-2229-14-99. PubMed PMID: 24739459; PubMed Central PMCID: PMC4108029]. Whole-genome sequences and annotations for Botrytis cinerea (Ensembl-fungi release 28; Botrytis cinerea strain: B05.10; Genome assembly: ASM15095v2) were obtained from the Ensembl Fungi data portal [Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K,  Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res. 2010 Jan;38(Database issue):D563-9. doi: 10.1093/nar/gkp871. Epub 2009 Nov 1. PubMed PMID: 19884133; PubMed Central PMCID: PMC2808935]. Both sets of genomic data were downloaded on August 5, 2015.
Supplementary_files_format_and_content: file “Gene_level_count matrix_Botrytis cinerea.xls”: Microsoft Excel file including 2 sheets: (1.) “rawCounts__allGenes” = gene-level raw counts matrix produced by the hts-count software for 11702 annotated Botrytis cinerea genes across all 9 samples assayed by RNA-Seq; (2) “normCounts__edgeR_testedGenes” = gene-level matrix of edgeR-normalized counts limited to 10881 genes passing abundance filter (ie: with at least 3 raw counts in at least 3 samples) across 6 samples (ie: 3 replicates of the two conditions under contrast). File “Gene_level_count matrix_Garganega.xls”: Microsoft Excel file including 2 sheets: (1.) “rawCounts__allGenes” = gene-level raw counts matrix produced by the hts-count software for 29970 annotated Vitis vinifera genes across all 9 samples assayed by RNA-Seq; (2) “normCounts__edgeR_testedGenes” = gene-level matrix of edgeR-normalized counts limited to 22253 genes passing abundance filter (ie: with at least 3 raw counts in at least 3 samples) across 6 samples (ie: 3 replicates of the two conditions under contrast).

organism: Botrytis cinerea

source_name: mycelia

growth_protocol: B. cinerea B05.10 liquid cultures were produced in three flasks inoculating 7 x 106 conidia/ml into 125 ml of potato dextrose broth (Formedium, Hunstanton, UK). After 7 days of incubation at 22°C and shaking at 120 rpm, B. cinerea mycelia were recovered by filtration, frozen and ground in liquid nitrogen. Vitis vinifera cv. Garganega bunches were harvested in October 2014 in Monteforte d’Alpone (Verona, Italy) and withered into the Pasqua Vigneti e Cantine winery facility located in Verona. Healthy grapes were collected at the commercial ripening stage (soluble solids content = 18.5 ± 0.25°Brix) and placed into perforated plastic boxes (plateaux, about 5 kg each) in a ventilated withering facility under natural conditions (17–20°C, 78–82% relative humidity).  Randomly selected replicates were subjected weekly to Brix degrees determination using a DBR35 digital refractometer (Giorgio Bormac, Carpi, Italy) while three dedicated plateaux were weighed weekly using a CH50K50 electronic balance (Kern, Balingen, Germany) in order to determine the weight loss of the berry bunches.  After one month of withering, berry Brix degree was about 26.6 and the percentage of weight loss was ~30% of the initial weigh. At this stage, 1000 Garganega berries (with pedicels) were sampled, surface sterilized for 5 minutes in 70% Ethanol and dried in sterility.

extract_protocol:
Infected/uninfected berry pericarps were ground into liquid nitrogen and total RNA was isolated from 200 mg of powders using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA). The RNA quantity, integrity and purity were controlled using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer Chip RNA 7500 serie II (Agilent).
For each sample, unstranded library was prepared from 2.5 µg of total RNA using the Illumina TruSeq Library Prep Kit v2 (Illumina, San Diego, CA).

treatment_protocol: Among the 1000 sterilized berries, 500 berries were inoculated with B. cinerea by syringae injection while the remaining 500 berries were injected with sterile water and were used as negative control.  Garganega berries were then incubated into sterile 24-well plates under controlled conditions (15°C/15h dark; 18°C/9h light) to induced noble rot.

value: mycelia

tag: sample type

value: saprophytic growth of B. cinerea

tag: strain/cultivar


title: B. cinerea in vitro replicate 2

status: Public on Jul 26 2019

type: SRA

country: Italy

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: B. cinerea in vitro replicate 1


title: 562157A10_Pa.ro

type: genomic

city: Portland

first: Suzy

middle: CP

last: Renn

state: Oregon

address: 3203 SE Woodstock Blvd., Biology Room B124

department: Biology

country: USA

institute: Reed College

description: multi-species aCGH

hyb_protocol: Arrays were hybridized for 64hrs at 42ºC in a NimbleGen Hybridization Station 4, then arrays were washed and dried according to manufactured protocol

scan_protocol: Arrays were scanned on the GenPix 4000 Scanner at a resolution of 5um/pixel

data_processing:
High-resolution pictures were processed with DEVA v.2.1 (NimbleGen). Dual-color signal-intensity matrices were exported and analyzed in R using the Ringo and limma packages
MA2C normalized data (ch1 bias = negative, ch2 bias = positive). More info on normalization method available at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375008/

label: AlexaFluor 555

molecule: genomic DNA

organism: Paralabidochromis sp.

label_protocol: Genomic DNA was labeled using dual-color labeling kits from NimbleGen, following standard protocol.

extract_protocol: For each species used in this study DNA was extracted from muscle or fin tissue from a single individual using a standard phenol-chloroform protocol.

tag: test

value: Paralabidochromis sp rock

label: AlexaFluor 647

organism: Haplochromis burtoni

source_name: Haplochromis burtoni pooled genomic DNA

tag: reference

value: Haplochromis burtoni


title: 562157A11_Sa.la

description: multi-species aCGH

organism: Sarotherodon lamprechti

value: Sarotherodon lamprechti


title: 562157A09_Bo.mi

description: multi-species aCGH

organism: Boulengerochromis microlepis

value: Boulengerochromis micro


title: 10uM ICA treatment root rep 1

type: RNA

city: Shizuoka

first: JAE-HOON

last: CHOI

address: 836 Ohya

department: Graduate School of Science and Technology

country: Japan

institute: Shizuoka University

description:
10uM ICA treatment rice-root1
10ICA-R-rep1

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Agilent Technologies Scanner G2505C

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.4.1).
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

source_name: control-root

label_protocol: Cy3-and Cy5-labeled cRNA were prepared from 200 ng total RNA using Low RNA Input Linear Amp Kit (Agilent) according to manufacturer's protocol .

growth_protocol: Seeds of rice (Oryza sativa L. ‘Nipponbare’) were germinated at 28 °C in a sterilized germination tray. The seedlings had been grown for 14 days at 28 °C.

extract_protocol: Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Germinaed rice was treated with ICA (2 and 10 uM) for 2 weeks in test-tube. After incubation for 2 weeks, rice seedlings were seperated into two parts, shoot and root.

tag: cultivar

value: Nipponbare

tag: age

value: root

tag: treatment

value: control

tag: dose

value: ICA


title: 10uM ICA treatment shoot rep 2

description:
10uM ICA treatment rice-shoot2
10ICA-S-rep2

value: shoot

source_name: control-shoot


title: antiTNF_NONResponder_2

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were log2 transformed and quantile normalized using R Bioconductor. Only microarray probes matching curated gene sequences from NCBI RefSeq database (release 51) were selected. A final number of 21,189 curated probes representing the expression of 18,524 different human genes were finally selected for analysis.

label: biotin

organism: Homo sapiens

extract_protocol: RNA was extracted using Quiagen Mini Kit Protocol in accordance with the described protocol. Dnase I treatment was used to remove genomic DNA traces.

treatment_protocol: Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ºC until extraction.

tag: disease

value: Rheumatoid Arthritis fulfilling ACR diagnostic criteria

tag: gender

value: male

tag: anti-tnf response 20 weeks

value: European League Against Rheumatoid Arthritis (EULAR) none responder


title: 10uM ICA treatment root rep 2

description:
10uM ICA treatment rice-root2
10ICA-R-rep2


title: 2uM ICA treatment root rep 1

description:
2uM ICA treatment rice-root1
2ICA-R-rep1


title: 2uM ICA treatment root rep 2

description:
2uM ICA treatment rice-root2
2ICA-R-rep2


title: MCF-7

city: Goyang-si

first: sung bin

last: park

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

department: Department of Life Science

country: South Korea

institute: Dongguk University-Seoul

description: biotin

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: Mammary Gland; Breast

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: RNA was extracted and purified from MCF-10A using ZR Dyet DNA/RNA kit (Zymo research) according

tag: cell line

tag: cell type

value: breast cancer epithelial cell

tag: treated with

value: none (control)


title: 562157A08_Hm.bi

description: multi-species aCGH

organism: Rubricatochromis bimaculatus

value: Hemichromis bimaculatus


title: antiTNF_Responder_2

scan_protocol: Standard Illumina hybridization protocol

value: female

value: European League Against Rheumatoid Arthritis (EULAR) responder


title: antiTNF_Responder_3

label_protocol: Standard Illumina hybridization protocol


title: 562157A06_Ti.ej

description: multi-species aCGH

organism: Coptodon ejagham

value: Tilapia ejagham


title: 562157A07_Ti.de

description: multi-species aCGH

organism: Coptodon deckerti

value: Tilapia deckerti

value: Haplochromis burtoni


title: antiTNF_Responder_6


title: antiTNF_NONResponder_3


title: antiTNF_Responder_8


title: CAP treated MCF-7

description: biotin

value: Cold atmospheric plasma (CAP)


title: antiTNF_Responder_5


title: antiTNF_Responder_1


title: antiTNF_Responder_7


title: 2uM ICA treatment shoot rep 1

description:
2uM ICA treatment rice-shoot1
2ICA-S-rep1

value: Nipponbare


title: 562157A05_Sa.kn

description: multi-species aCGH

organism: Sarotherodon knauerae

value: Sarotherodon knauerae


title: antiTNF_NONResponder_1


title: 10uM ICA treatment shoot rep 1

description:
10uM ICA treatment rice-shoot1
10ICA-S-rep1

value: control


title: 562157A04_St.ma

description: multi-species aCGH

organism: Stomatepia mariae

value: Stomatepia mariae


title: 562157A03_Pg.ma

description: multi-species aCGH

organism: Pungu maclareni

value: Pungu maclareni


title: 2uM ICA treatment shoot rep 2

description:
2uM ICA treatment rice-shoot2
2ICA-S-rep2

value: shoot

value: ICA


title: 562157A02_Ko.ei

description: multi-species aCGH

organism: Konia eisentrauti

value: Konia eisentrauti


title: 562157A01_Co.vi

description: multi-species aCGH

organism: Copadichromis virginalis

value: Copadichromis virginalis


title: 562149A12_Ti.ej

description: multi-species aCGH


title: Rbfox2 mutant_rep2 [RMC190_MUT]

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

data_processing:
Fastqc v0.11.4 was used to check the quality of the bases in the reads
Paired end fastq sequence reads from each sample were aligned to mouse reference genome (GRCm38) using ultrafast RNA-seq aligner STAR
Aligned reads were assembled and abundances estimated as FPKM via Cufflinks2
Differential expression of genes and transcripts between control and KO samples were estimated via Cuffdiff and MISO
The distribution of raw RNA-Seq densities mapped to the exons and splice junctions of gene isoforms across control and mutant samples were visualized by Sashimi plots
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited files with FPKM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Rbfox2 mutant_craniofacial tissue

growth_protocol: Not applicable

extract_protocol:
Craniofacial tissue was microdissected from E12.5 control and knockout embryos in cold PBS. Three independent biological replicates were used for each genotype group. Tissues were homogenized and RNA was isolated using a PureLink RNA Mini kit from Thermo Fisher (Cat. no. 12183018A).
Sequencing libraries of poly(A)+ RNA from 3 control and 3 mutant samples were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturer’s instructions. Biological replicates were individually barcoded and pooled for paired-end sequencing using Illumina HiSeq4000 platform at the Genome Institute of Singapore.

treatment_protocol: No treatment

tag: genotype/variation

value: Pax3Cre/+:Rbfox2 flox/flox

value: Craniofacial tissue


title: 562149A11_Co.vi

description: multi-species aCGH


title: Control_rep2 [RMC187_CNT]

source_name: Control_craniofacial tissue

value: Rbfox2 flox/flox


title: Rbfox2 mutant_rep3 [RMC191_MUT]


title: Rbfox2 mutant_rep1 [RMC189_MUT]


title: Control_rep3 [RMC188_CNT]


title: Control_rep1 [RMC186_CNT]


title: 562149A10_Co.bo

description: multi-species aCGH

organism: Copadichromis borleyi

value: Copadichromis borleyi


title: 562149A09_Sa.la

description: multi-species aCGH

value: Sarotherodon lamprechti


title: 562149A05_St.ma

description: multi-species aCGH


title: 562149A08_As.ca

description: multi-species aCGH

organism: Astatotilapia calliptera

value: Astatotilapia calliptera


title: 562149A06_Pg.ma

description: multi-species aCGH

value: Haplochromis burtoni


title: 562149A04_Hm.bi

description: multi-species aCGH

value: Hemichromis bimaculatus


title: 562149A07_Ap.nd

description: multi-species aCGH

organism: Oreochromis ndalalani

value: Alcolapia ndalalani


title: 562149A02_Ti.de

description: multi-species aCGH

value: Tilapia deckerti

organism: Haplochromis burtoni


title: 562149A01_Ko.ei

description: multi-species aCGH


title: 562149A03_Pa.ro

description: multi-species aCGH

organism: Paralabidochromis sp.

value: Paralabidochromis sp rock


title: UAS-klu Esg+ cell RNA-Seq rep3

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Raw reads were quality-trimmed and filtered for low complexity with the preprocess from SGA assembler (version 0.10.13, parameters -q 30 -m 50 --dust)
The quality filter-passed reads were mapped to the D. melanogaster reference genome (BDGP6)  with TopHat2 (version 2.1.0) using conservative settings (i.e. --b2-sensitive --no-coverage-search --no-novel-juncs --no-novel-indels --transcriptome-max-hits=1)
Mapping reads were assigned to genes using FeatureCounts (version 1.5.0, multi-mapping or multi-overlapping reads were not counted, stranded mode was set to “–s 1”, genome annotation: Ensembl release 87)
Genome_build: BDGP6
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

organism: Drosophila melanogaster

source_name: midgut

growth_protocol: Female Drosophila of genotypes listed above (5-7 days old) were shifted and treated with Ecc15

extract_protocol:
Esg+ GFP cells were isolated from 80-100 midguts/sample and cells were sorted and RNA- isolated immediately afterwards using the PicoPure kit (Arcturus), subsequently followed by RNA-amplification using the Arcturus™ RiboAmp™ HS PLUS Kit
TruSeq Stranded mRNA w/o polyA+ Enrichment (since polyA+ RNA was amplified in a prior step)

treatment_protocol: 2 days shift + 16 hrs Ecc15 infection

value: Esg+ stem-Progenitor cells

value: midgut

value: 2 days shift + 16 hrs Ecc15 infection

tag: genotype

value: esgts X UAS-klu

value: overexpression of klu


title: kluRNAi Esg+ cell RNA-Seq rep3

value: esgts X kluRNAi (BL28731)

value: RNAi against klu


title: kluRNAi Esg+ cell RNA-Seq rep1


title: kluRNAi Esg+ cell RNA-Seq rep2


title: UAS-klu Esg+ cell RNA-Seq rep1


title: UAS-klu Esg+ cell RNA-Seq rep2


title: Control Esg+ cell RNA-Seq rep3

value: esgts X w1118

value: control


title: 562102A11_St.ma

description: multi-species aCGH

value: Stomatepia mariae


title: 562102A12_Ti.ej

description: multi-species aCGH

value: Tilapia ejagham


title: Control Esg+ cell RNA-Seq rep2


title: Control Esg+ cell RNA-Seq rep1


title: antiTNF_Responder_4

value: Rheumatoid Arthritis fulfilling ACR diagnostic criteria

value: female

value: European League Against Rheumatoid Arthritis (EULAR) responder


title: 562102A10_Co.bo

description: multi-species aCGH

value: Copadichromis borleyi

value: Haplochromis burtoni


title: CAP treated MCF-7

description: biotin

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: RNA was extracted and purified from MCF-7 using ZR Dyet DNA/RNA kit (Zymo research) according

value: MCF-7 breast cancer cell line


title: MCF-7

description: biotin


title: 562102A09_Pa.ro

description: multi-species aCGH

value: Paralabidochromis sp rock


title: 562102A08_Ti.de

description: multi-species aCGH

value: Tilapia deckerti


title: 562102A05_Ko.ei

description: multi-species aCGH

value: Konia eisentrauti


title: 562102A06_Pg.ma

description: multi-species aCGH

value: Pungu maclareni


title: 562102A07_As.bl

description: multi-species aCGH

organism: Astatotilapia bloyeti

value: Astatotilapia bloyeti


title: 562102A04_Sa.kn

description: multi-species aCGH

value: Sarotherodon knauerae


title: 562102A02_Sa.la

description: multi-species aCGH

organism: Sarotherodon lamprechti

value: Sarotherodon lamprechti


title: Guo_144_wb_161

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

description: Gene expression from mouse blood

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical language version 3.0.0. RMA was used to fit log2 transformed expression values

source_name: blood

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

growth_protocol: Male C57BL/J6 mice (7 weeks old, average weight 21.19 g ± 0.06 g) were obtained from Jackson Laboratories (Bar Harbor, ME). Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitous viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus. Mice were maintained on Harlan Teklad Rodent Diet 7913 (Indianapolis, IN), and tap water was provided ad libitum. Animals were allowed to acclimate for at least 5 days before use.

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

treatment_protocol: A stock suspension of MWCNT (1.6 mg/mL) was prepared in DM (Ca2+ and Mg2+-free phosphate-buffered saline, pH 7.4, supplemented with 5.5 mM d-glucose, 0.6 mg/mL mouse serum albumin, and 0.01 mg/mL 1,2-dipalmitoyl-sn-glycero-3-phosphocholine) with sonication as previously described by Porter et al. (2008; 2010). Serial dilutions of MWCNT suspension were made using DM as the diluent. Crocidolite asbestos (2.4 mg/mL) was suspended in DM by brief vortexing. Mice were anesthetized with isoflurane (Abbott Laboratories, North Chicago, IL). When fully anesthetized, the mouse was positioned with its back against a slant board and suspended by the incisor teeth using a rubber band. The mouth was opened, and the tongue gently pulled aside from the oral cavity. A 50 μL aliquot of sample was pipetted at the base of the tongue, and the tongue was restrained until at least 2 deep breaths were completed (but for not longer than 15 sec). Following release of the tongue, the mouse was gently lifted off the board, placed on its left side, and monitored for recovery from anesthesia. Mice received either DM; 1, 10, 40 or 80 μg MWCNT; or 120 μg asbestos.

tag: treatment dose and postexposure time

value: 10ug MWCNT 12 month

tag: animal

tag: Sex

value: male

value: blood


title: 562102A01_Co.vi

description: multi-species aCGH

tag: test

value: Copadichromis virginalis


title: 562101A09_Hm.bi

description: multi-species aCGH

organism: Rubricatochromis bimaculatus

value: Hemichromis bimaculatus

tag: reference


title: 562101A08_Bo.mi

description: multi-species aCGH

organism: Boulengerochromis microlepis

value: Boulengerochromis micro


title: 562101A07_Ap.nd

description: multi-species aCGH

value: Alcolapia ndalalani


title: 562101A12_Ti.zi

description: multi-species aCGH

organism: Coptodon zillii

value: Tilapia zillii


title: 562101A11_Cc.lp

description: multi-species aCGH

organism: Cyprichromis leptosoma

value: Cyprichromis leptosoma

value: Haplochromis burtoni


title: 562101A05_Rh.lg

description: multi-species aCGH

organism: Rhamphochromis longiceps

value: Rhamphochromis longicep


title: 562101A02_Ti.fu

description: multi-species aCGH

organism: Coptodon fusiforme

value: Tilapia fusiforme


title: 562101A04_Ti.ko

description: multi-species aCGH

organism: Coptodon kottae

value: Tilapia kottae


title: Guo_143_wb_409

description: Gene expression from mouse blood

value: 40ug MWCNT 12 month

tag: tissue


title: Guo_134_wb_281

description: Gene expression from mouse blood

value: 40ug MWCNT 6 month


title: Guo_142_wb_23

description: Gene expression from mouse blood


title: 562101A10_Sa.me

description: multi-species aCGH

organism: Sarotherodon melanotheron

value: Sarotherodon melanothe


title: Guo_129_wb_35

description: Gene expression from mouse blood

organism: Mus musculus


title: Guo_131_wb_65

description: Gene expression from mouse blood

value: 80ug MWCNT 6 month


title: Guo_130_wb_11

description: Gene expression from mouse blood


title: Guo_133_wb_333

description: Gene expression from mouse blood

value: 10ug MWCNT 1 month


title: Guo_135_wb_49

description: Gene expression from mouse blood

value: 40ug MWCNT 1 month

value: male


title: Guo_139_wb_161

description: Gene expression from mouse blood

value: 10ug MWCNT 12 month

value: blood


title: Guo_138_wb_84

description: Gene expression from mouse blood

value: DM 6 month


title: Guo_132_wb_362

description: Gene expression from mouse blood


title: Guo_136_wb_409

description: Gene expression from mouse blood


title: Guo_137_wb_50

description: Gene expression from mouse blood

value: 80ug MWCNT 1 month


title: WIN-cocaine-ATAC

status: Public on Jul 27 2019

city: New York

first: Philippe

last: Melas

address: 1051 Riverside Drive

institute: Columbia University

description:
WIN+cocaine-treated
ATAC_4samples_ucsctracks.bed

library_source: genomic

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, and only reads mapping as matched pairs and being uniquely mapped (mapping quality >= 1) were used for further analysis. The 42 base pair (bp) length of the reads were used for peak-calling and the generic term “interval” was used to describe genomic regions with local enrichments in tag numbers. Intervals were defined by the chromosome number, and a start and end coordinate.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff p-value of 1e-7 and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
HISAT2 was used to map filtered sequenced reads to the reference rat genome, HTSeq was used to analyze gene expression levels (in union mode)
DESeq was used for differential gene expression analysis
rMATS (replicate multivariate analysis of transcript splicing) was used for detection of differential alternative splicing (AS)
Genome_build: RN6(Nacc-RNAseq and ATACseq), RN5(PFC-RNAseq)
Supplementary_files_format_and_content: xlsx files including FPKM value for each sample

organism: Rattus norvegicus

source_name: WIN+cocaine-treated

extract_protocol:
Total RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
ATAC-seq: Nuclei from flash frozen PFC tissue were extracted and 100,000 nuclei were tagmented. DNA were prepared using Nextera library prep kit.
RNA and DNA  libraries were prepared for sequencing using standard Illumina protocols

value: PFC

tag: strain

value: Sprague-Dawley


title: Control-ATAC

description:
control
ATAC_4samples_ucsctracks.bed

source_name: control


title: Guo_141_wb_235

description: Gene expression from mouse blood

value: 1ug MWCNT 1 month


title: 562100A12_Ca.ma

description: multi-species aCGH

organism: Callochromis macrops

value: Callochromis macrops

value: Haplochromis burtoni


title: 562101A01_Ap.la

description: multi-species aCGH

organism: Oreochromis latilabris

value: Alcolapia latilabris


title: 562100A10_Ju.or

description: multi-species aCGH

organism: Julidochromis ornatus

value: Julidochromis ornatus

organism: Haplochromis burtoni


title: 562100A09_Pb.mu

description: multi-species aCGH

organism: Pseudocrenilabrus multicolor victoriae

value: Pseudocreni m victoriae


title: Guo_140_wb_97

description: Gene expression from mouse blood

value: DM 12 month


title: 562100A08_Pd.to

description: multi-species aCGH

organism: Pallidochromis tokolosh

value: Pallidochromis tokolosh


title: Guo_127_wb_67

description: Gene expression from mouse blood

value: DM 1 month


title: Guo_126_wb_323

description: Gene expression from mouse blood

value: 120ug crocidolite 6 month


title: 562100A07_As.ca

description: multi-species aCGH

organism: Astatotilapia calliptera

value: Astatotilapia calliptera


title: Guo_128_wb_342

description: Gene expression from mouse blood

value: male


title: 562100A11_Ti.fu

description: multi-species aCGH

value: Tilapia fusiforme


title: 562100A05_Ao.al

description: multi-species aCGH

organism: Astatoreochromis alluaudi

value: Astatoreo alluaudi


title: 562100A06_Tr.mo

description: multi-species aCGH

organism: Tropheus moorii

value: Tropheus moori


title: Guo_125_wb_223

description: Gene expression from mouse blood

value: 80ug MWCNT 12 month

value: blood


title: Guo_124_wb_178

description: Gene expression from mouse blood

value: 1ug MWCNT 6 month


title: Guo_123_wb_312

description: Gene expression from mouse blood

value: 10ug MWCNT 1 month


title: 562100A04_Lo.la

description: multi-species aCGH

organism: Lobochilotes labiata

value: Lobochilotes labiatus

value: Haplochromis burtoni


title: 562100A03_Lp.el

description: multi-species aCGH

organism: Benthodesmus elongatus

value: Lepidiol elongatus


title: 562100A02_Xn.sp

description: multi-species aCGH

organism: Xenotilapia spiloptera

value: Xenotilapia spiloptera


title: 562100A01_Op.ve

description: multi-species aCGH

organism: Ophthalmotilapia ventralis

value: Ophthalmot ventralis


title: 562098A10_Tp.re

description: multi-species aCGH

organism: Tropheops sp. 'red cheek'

value: Tropheops redcheek


title: 562098A12_Xn.sp

description: multi-species aCGH


title: 562098A11_Va.mo

description: multi-species aCGH

organism: Variabilichromis moorii

value: Variabilichromis moori


title: 562098A09_Sa.me

description: multi-species aCGH

organism: Sarotherodon melanotheron

value: Sarotherodon melanothe


title: 562098A08_Pb.mu

description: multi-species aCGH

value: Pseudocreni m victoriae


title: Guo_122_wb_121

description: Gene expression from mouse blood

organism: Mus musculus

value: 80ug MWCNT 1 month

value: male


title: Guo_117_wb_101

description: Gene expression from mouse blood

value: 1ug MWCNT 1 month


title: Guo_120_wb_5

description: Gene expression from mouse blood

value: 1ug MWCNT 12 month


title: Guo_121_wb_257

description: Gene expression from mouse blood


title: Guo_113_wb_189

description: Gene expression from mouse blood

value: 40ug MWCNT 6 month


title: Guo_112_wb_23

description: Gene expression from mouse blood

value: 10ug MWCNT 12 month

value: blood


title: 562098A03_Cc.lp

description: multi-species aCGH

organism: Cyprichromis leptosoma

value: Cyprichromis leptosoma


title: 562098A07_Pd.to

description: multi-species aCGH

value: Pallidochromis tokolosh


title: 562098A06_Lp.el

description: multi-species aCGH

value: Haplochromis burtoni


title: 562098A05_Ju.or

description: multi-species aCGH

value: Julidochromis ornatus


title: 562098A02_Cp.fr

description: multi-species aCGH

organism: Cyphotilapia frontosa

value: Cyphotilapia frontosa


title: Guo_114_wb_286

description: Gene expression from mouse blood


title: Guo_115_wb_74

description: Gene expression from mouse blood

value: 10ug MWCNT 6 month


title: Guo_118_wb_118

description: Gene expression from mouse blood


title: Guo_109_wb_200

description: Gene expression from mouse blood

value: 80ug MWCNT 12 month


title: Guo_116_wb_417

description: Gene expression from mouse blood

value: 120ug crocidolite 12 month


title: Guo_111_wb_160

description: Gene expression from mouse blood


title: Guo_119_wb_217

description: Gene expression from mouse blood

value: 1ug MWCNT  12 month


title: 562098A01_Ca.ma

description: multi-species aCGH

organism: Callochromis macrops

value: Callochromis macrops


title: 562098A04_Er.cy

description: multi-species aCGH

organism: Eretmodus cyanostictus

value: Eretmodus cyanostictus

organism: Haplochromis burtoni


title: 562097A10_Hm.fa

description: multi-species aCGH

organism: Hemichromis fasciatus

value: Hemichromis fasciatus


title: Guo_110_wb_196

description: Gene expression from mouse blood

value: 80ug MWCNT  1 month

value: male


title: 562097A12_Lp.el

description: multi-species aCGH

value: Lepidiol elongatus


title: 562097A09_Ti.zi

description: multi-species aCGH

organism: Coptodon zillii

value: Tilapia zillii


title: 562097A11_Xn.sp

description: multi-species aCGH

value: Xenotilapia spiloptera


title: 562097A06_Lo.la

description: multi-species aCGH

value: Lobochilotes labiatus


title: 562097A03_Di.gr

description: multi-species aCGH

organism: Diplotaxodon greenwoodi

value: Diplotaxodon greenwoodi


title: 562097A07_Bo.mi

description: multi-species aCGH

organism: Boulengerochromis microlepis

value: Boulengerochromis micro

value: Haplochromis burtoni


title: 562097A05_Pa.ch

description: multi-species aCGH

organism: Haplochromis chilotes

value: Paralabidochromis chilot


title: Guo_108_wb_2

description: Gene expression from mouse blood

value: DM 12 month

value: blood


title: 562097A04_Ny.mi

description: multi-species aCGH

organism: Nyassachromis microcephalus

value: Nyassachromis microcep


title: 562097A02_Tp.re

description: multi-species aCGH

value: Tropheops redcheek


title: Guo_105_wb_288

description: Gene expression from mouse blood

value: 10ug MWCNT 12 month


title: 562097A01_Cx.fu

description: multi-species aCGH

organism: Cyathopharynx furcifer

value: Cyathopharynx furcifer


title: Guo_104_wb_135

description: Gene expression from mouse blood

value: 10ug MWCNT 6 month


title: Guo_107_wb_300

description: Gene expression from mouse blood

value: 40ug MWCNT 12 month


title: 562096A12_Cx.fu

description: multi-species aCGH


title: 562097A08_Sa.ga

description: multi-species aCGH

organism: Sarotherodon galilaeus

value: Sarotherodon galilaeus


title: 562096A11_La.fu

description: multi-species aCGH

organism: Labeotropheus fuelleborni

value: Labeotropheus fuelleborni


title: Guo_106_wb_337

description: Gene expression from mouse blood

value: 120ug crocidolite 12 month

value: male


title: Guo_097_wb_142

description: Gene expression from mouse blood

value: 80ug MWCNT 6 month


title: Guo_098_wb_116

description: Gene expression from mouse blood

value: DM 1 month


title: 562096A10_Tp.re

description: multi-species aCGH

organism: Tropheops sp. 'red cheek'


title: Guo_093_wb_372

description: Gene expression from mouse blood


title: Guo_094_wb_407

description: Gene expression from mouse blood


title: 562096A08_Ne.om

description: multi-species aCGH

organism: Neochromis omnicaeruleus

value: Neochromis omnicaeruleus


title: Guo_091_wb_376

description: Gene expression from mouse blood

organism: Mus musculus

value: 10ug MWNCT 6 month


title: Guo_099_wb_247

description: Gene expression from mouse blood

value: 1ug MWCNT 6 month


title: 562096A07_As.fl

description: multi-species aCGH

organism: Astatotilapia flaviijosephi

value: Astatotilapia flavijosephi

value: Haplochromis burtoni


title: Guo_092_wb_119

description: Gene expression from mouse blood

value: 10ug MWCNT 1 month

value: blood


title: 562096A06_As.ca

description: multi-species aCGH

organism: Astatotilapia calliptera

value: Astatotilapia calliptera


title: Guo_103_wb_399

description: Gene expression from mouse blood


title: Guo_100_wb_330

description: Gene expression from mouse blood

value: 1ug MWCNT 12 month


title: 562096A05_Tr.mo

description: multi-species aCGH

organism: Tropheus moorii

value: Tropheus moori


title: 562096A03_Cc.lp

description: multi-species aCGH

organism: Cyprichromis leptosoma

value: Cyprichromis leptosoma


title: 562096A09_Ap.gr

description: multi-species aCGH

organism: Oreochromis grahami

value: Alcolapia grahami

organism: Haplochromis burtoni


title: 562096A02_Sa.me

description: multi-species aCGH

organism: Sarotherodon melanotheron

value: Sarotherodon melanotheron


title: Guo_096_wb_216

description: Gene expression from mouse blood


title: 562096A01_Hm.fa

description: multi-species aCGH

organism: Hemichromis fasciatus

value: Hemichromis fasciatus


title: Guo_102_wb_355

description: Gene expression from mouse blood

value: 80ug MWCNT 12 month

value: male


title: Guo_095_wb_315

description: Gene expression from mouse blood

value: 80ug MWCNT 1 month


title: Guo_101_wb_275

description: Gene expression from mouse blood


title: Guo_089_wb_350

description: Gene expression from mouse blood

value: DM 1 month


title: Guo_090_wb_404

description: Gene expression from mouse blood

value: 40ug MWNCT 1 month


title: 561988A06_Tr.mo

description: multi-species aCGH


title: 561988A05_Ao.al

description: multi-species aCGH

organism: Astatoreochromis alluaudi

value: Astatoreochromis alluaudi


title: 562096A04_Op.ve

description: multi-species aCGH

organism: Ophthalmotilapia ventralis

value: Ophthalmotilapia ventralis


title: Guo_088_wb_263

description: Gene expression from mouse blood

value: 120ug crocidolite 6 month


title: 561988A04_Lo.la

description: multi-species aCGH

organism: Lobochilotes labiata

value: Lobochilotes labiatus

value: Haplochromis burtoni


title: 561988A03_Lp.el

description: multi-species aCGH

organism: Lepidiolamprologus elongatus

value: Lepidiolamprologus elongatus


title: 561987A10_Ap.gr

description: multi-species aCGH


title: Guo_082_wb_403

description: Gene expression from mouse blood

value: 1ug MWCNT 1 month

value: blood


title: Guo_085_wb_345

description: Gene expression from mouse blood

value: 40ug MWCNT 6 month


title: Guo_084_wb_319

description: Gene expression from mouse blood

value: 40ug MWCNT 1 month


title: 550971A12_As.bu

description: multi-species aCGH

value: Astatotilapia burtoni


title: 561988A01_Op.ve

description: multi-species aCGH


title: Guo_078_wb_425

description: Gene expression from mouse blood

value: 10ug MWCNT  1 month


title: Guo_081_wb_53

description: Gene expression from mouse blood

value: DM 6 month


title: Guo_086_wb_267

description: Gene expression from mouse blood

value: 10ug MWCNT 1 month

value: male


title: Guo_079_wb_174

description: Gene expression from mouse blood

value: 80ug MWCNT 6 month


title: 550971A06_Me.ze

description: multi-species aCGH

organism: Maylandia zebra

value: Maylandia zebra


title: Guo_087_wb_343

description: Gene expression from mouse blood


title: Guo_077_wb_429

description: Gene expression from mouse blood

value: 1ug MWCNT  12 month


title: Guo_083_wb_78

description: Gene expression from mouse blood

value: 120ug crocidolite 12 month


title: 561987A11_Tr.mo

description: multi-species aCGH

value: Tropheus moori


title: Guo_076_wb_36

description: Gene expression from mouse blood

value: 80ug MWCNT 12 month


title: Guo_075_wb_296

description: Gene expression from mouse blood

value: 10ug MWCNT 6 month


title: Guo_072_wb_70

description: Gene expression from mouse blood

value: DM 12 month


title: Guo_074_wb_231

description: Gene expression from mouse blood


title: 550971A08_Pu.ny

description: multi-species aCGH

organism: Pundamilia nyererei

value: Pundamilia nyererei

value: Haplochromis burtoni


title: 550971A10_Nl.br

description: multi-species aCGH

organism: Neolamprologus brichardi

value: Neolamprologus brichardi


title: 550971A02_Or.ni

description: multi-species aCGH

organism: Oreochromis niloticus

value: Oreochromis niloticus


title: Guo_080_wb_169

description: Gene expression from mouse blood

organism: Mus musculus

value: blood


title: Guo_073_wb_298

description: Gene expression from mouse blood

value: 1ug MWCNT 12 month


title: Guo_071_wb_133

description: Gene expression from mouse blood

value: DM 6 month


title: Guo_069_wb_410

description: Gene expression from mouse blood


title: 545445A12_Ti.zi

description: multi-species aCGH

organism: Coptodon zillii

value: Coptodon zillii


title: Guo_066_wb_306

description: Gene expression from mouse blood

value: male


title: 545445A11_Ti.fu

description: multi-species aCGH

organism: Coptodon ejagham

value: Coptodon ejagham


title: Guo_068_wb_412

description: Gene expression from mouse blood

value: 120ug crocidolite 6 month


title: 545445A10_Ap.gr

description: multi-species aCGH

value: Alcolapia grahami


title: 550971A04_As.bu

description: multi-species aCGH

value: Astatotilapia burtoni


title: 545445A09_Va.mo

description: multi-species aCGH

organism: Variabilichromis moorii

value: Variabilichromis moorii


title: Guo_067_wb_310

description: Gene expression from mouse blood

value: 1ug MWCNT 6 month


title: 545445A04_La.fu

description: multi-species aCGH

organism: Labeotropheus fuelleborni

value: Labeotropheus fuelleborni


title: Guo_065_wb_218

description: Gene expression from mouse blood

value: 120ug crocidolite 1 month


title: Guo_064_wb_265

description: Gene expression from mouse blood

value: DM 12 month


title: Guo_063_wb_225

description: Gene expression from mouse blood

value: 80ug MWCNT 6 month


title: 545445A07_Hp.th

description: multi-species aCGH

organism: Haplochromis thereuterion

value: Haplochromis thereuterion

value: Haplochromis burtoni


title: 545445A03_Di.gr

description: multi-species aCGH

organism: Diplotaxodon greenwoodi

value: Diplotaxodon greenwoodi

organism: Haplochromis burtoni


title: 545445A06_Pb.mu

description: multi-species aCGH

organism: Pseudocrenilabrus multicolor victoriae

value: Pseudocrenilabrus multicolor victoriae


title: 545445A08_Ju.or

description: multi-species aCGH

organism: Julidochromis ornatus

value: Julidochromis ornatus


title: 545445A02_Er.cy

description: multi-species aCGH

organism: Eretmodus cyanostictus

value: Eretmodus cyanostictus


title: Guo_070_wb_351

description: Gene expression from mouse blood

value: 40ug MWCNT  1 month

value: male

value: blood


title: 545445A05_Ao.al

description: multi-species aCGH

organism: Astatoreochromis alluaudi

value: Astatoreochromis alluaudi


title: 545445A01_Op.ve

description: multi-species aCGH

organism: Ophthalmotilapia ventralis

value: Ophthalmotilapia ventralis


title: 545427A11_As.ca

description: multi-species aCGH

organism: Astatotilapia calliptera

value: Astatotilapia calliptera


title: 545427A09_Pa.ch

description: multi-species aCGH

organism: Haplochromis chilotes

value: Paralabidochromis chilotes


title: 545427A12_As.fl

description: multi-species aCGH

organism: Astatotilapia flaviijosephi

value: Astatotilapia flaviijosephi


title: 545427A08_Ca.ma

description: multi-species aCGH

organism: Callochromis macrops

value: Callochromis macrops


title: 545427A07_Ap.nd

description: multi-species aCGH

organism: Oreochromis ndalalani

value: Alcolapia ndalalani


title: Guo_062_wb_52

description: Gene expression from mouse blood

organism: Mus musculus

value: 80ug MWCNT 1 month


title: 545427A06_Di.gr

description: multi-species aCGH


title: Guo_061_wb_111

description: Gene expression from mouse blood

value: 120ug crocidolite 1 month


title: Guo_060_wb_254

description: Gene expression from mouse blood

value: 40ug MWCNT 1 month


title: Guo_055_wb_98

description: Gene expression from mouse blood

value: 10ug MWCNT 12 month


title: 545427A03_Ap.la

description: multi-species aCGH

organism: Oreochromis latilabris

value: Alcolapia latilabris

value: Haplochromis burtoni


title: Guo_050_wb_69

description: Gene expression from mouse blood

value: 1ug  MWCNT 12 month


title: Guo_056_wb_138

description: Gene expression from mouse blood

value: 40ug MWCNT 6 month


title: Guo_047_wb_235

description: Gene expression from mouse blood

value: 1ug MWCNT 1 month

value: male


title: Guo_059_wb_391

description: Gene expression from mouse blood

value: DM 1 month

value: blood


title: 545427A02_Rh.lg

description: multi-species aCGH

organism: Rhamphochromis longiceps

value: Rhamphochromis longiceps


title: Guo_045_wb_97

description: Gene expression from mouse blood

value: DM 12 month


title: Guo_058_wb_72

description: Gene expression from mouse blood

value: 80ug MWCNT 12 month


title: Guo_054_wb_205

description: Gene expression from mouse blood


title: Guo_051_wb_152

description: Gene expression from mouse blood

value: 40ug MWCNT 12 month


title: Guo_048_wb_85

description: Gene expression from mouse blood


title: 545427A01_As.bl

description: multi-species aCGH

organism: Astatotilapia bloyeti

value: Astatotilapia bloyeti


title: Guo_057_wb_201

description: Gene expression from mouse blood

value: 10ug MWCNT 6 month


title: 545426A12_As.bl

description: multi-species aCGH


title: 545426A11_Rh.lg

description: multi-species aCGH


title: Guo_049_wb_31

description: Gene expression from mouse blood


title: Guo_053_wb_71

description: Gene expression from mouse blood


title: Guo_052_wb_54

description: Gene expression from mouse blood


title: 545427A05_Ne.om

description: multi-species aCGH

organism: Neochromis omnicaeruleus

value: Neochromis omnicaeruleus


title: 545426A10_Ap.la

description: multi-species aCGH


title: 545426A09_Ap.al

description: multi-species aCGH

organism: Oreochromis alcalicus

value: Alcolapia alcalicus


title: 545427A04_Ap.al

description: multi-species aCGH

organism: Haplochromis burtoni


title: Guo_044_wb_168

description: Gene expression from mouse blood

value: 120ug crocidolite 12 month


title: Guo_042_wb_301

description: Gene expression from mouse blood

value: 120ug crocidolite 1 month


title: 545426A08_Ne.om

description: multi-species aCGH

value: Haplochromis burtoni


title: Guo_043_wb_340

description: Gene expression from mouse blood


title: Guo_046_wb_366

description: Gene expression from mouse blood

value: 10ug MWCNT 12 month


title: 545426A07_Hm.fa

description: multi-species aCGH

organism: Hemichromis fasciatus

value: Hemichromis fasciatus


title: 545426A06_Er.cy

description: multi-species aCGH

value: Eretmodus cyanostictus


title: 545426A05_Hp.th

description: multi-species aCGH

organism: Haplochromis thereuterion

value: Haplochromis thereuterion


title: 545426A04_Pa.ch

description: multi-species aCGH

value: Paralabidochromis chilotes


title: 545426A03_Ny.mi

description: multi-species aCGH

organism: Nyassachromis microcephalus

value: Nyassachromis microcephalus


title: 545426A01_As.ca

description: multi-species aCGH

value: Astatotilapia calliptera


title: 545426A02_As.ca

description: multi-species aCGH


title: 545409A10_Nl.br

description: multi-species aCGH

organism: Neolamprologus brichardi

value: Neolamprologus brichardi


title: 545409A12_Sa.ga

description: multi-species aCGH

organism: Sarotherodon galilaeus

value: Sarotherodon galilaeus


title: 545409A08_Pu.ny

description: multi-species aCGH

organism: Pundamilia nyererei

value: Pundamilia nyererei


title: 545409A06_Me.ze

description: multi-species aCGH

organism: Maylandia zebra

value: Maylandia zebra


title: 545409A04_As.bu

description: multi-species aCGH

value: Astatotilapia burtoni


title: 545409A02_Or.ni

description: multi-species aCGH

organism: Oreochromis niloticus

value: Oreochromis niloticus


title: Guo_040_wb_143

description: Gene expression from mouse blood

value: male

value: blood


title: Guo_037_wb_347

description: Gene expression from mouse blood

value: 1ug MWCNT 6 month


title: Guo_035_wb_100

description: Gene expression from mouse blood


title: Guo_031_wb_164

description: Gene expression from mouse blood

value: DM 12 month


title: Guo_032_wb_314

description: Gene expression from mouse blood


title: Guo_039_wb_383

description: Gene expression from mouse blood

value: 120ug crocidolite 1 month


title: Guo_036_wb_402

description: Gene expression from mouse blood

value: 10ug MWCNT 12 month


title: Guo_034_wb_408

description: Gene expression from mouse blood


title: Guo_038_wb_214

description: Gene expression from mouse blood

value: 40ug MWCNT 12 month


title: Guo_033_wb_274

description: Gene expression from mouse blood

value: 80ug MWCNT 6 month


title: Guo_029_wb_240

description: Gene expression from mouse blood

value: 120ug crocidolite 6 month


title: Guo_028_wb_113

description: Gene expression from mouse blood

value: 1ug MWCNT 1 month


title: 545388A10_Nl.br

description: multi-species aCGH

value: Haplochromis burtoni


title: 545388A08_Pu.ny

description: multi-species aCGH


title: WT_R7947_CD11c_pos

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
Raw Illumina sequencing data was demultiplexed and fastq files were generated using 10X Genomics Cellranger mkfastq v2.2.0
Fastq files were aligned to the mm10 genome and unique UMI sums per gene were calculated using 10X Genomics Cellranger count v2.2.0
Genome_build: mm10
Supplementary_files_format_and_content: The three files per sample are 10X cellranger count output from non-empty droplets.  Cell barcodes and analyzed genes are present as tab-delimited files.  Unique UMI sums per gene per cell are recorded in market exchange format.

source_name: tumor microenvironment

extract_protocol: For the single cell drop-seq RNA expression profiling, GEM (Gel bead-in-EMulsions) generation & barcoding, post GEM-RT cleanup & cDNA amplification and the library construction were done according to manufacture procedures using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237), Chromium Single Cell A Chip Kit (PN-1000009) and Chromium i7 Multiplex Kit (PN-120262) by 10x Genomics (Pleasanton, California, USA).

value: myeloid cells


title: 545388A07_Pu.ny

description: multi-species aCGH


title: WT_R7945_CD11c_pos


title: 545388A12_Sa.ga

description: multi-species aCGH

value: Sarotherodon galilaeus


title: Th1_Vitro WT 24h_3

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

data_processing:
The abundance of transcripts from RNA-seq data was quantified through the Kallisto program. This program is based on pseudo alignment for rapidly determining the compatibility of reads with targets, without the need for alignment. The Kallisto transcript
Genome_build: mm10
Supplementary_files_format_and_content: csv

source_name: Naive T cells from WT spleen and lymph nodes

growth_protocol: CD4+ T naive cells were isolated from wild-type C57BL/6J mice. Differentiation were induced in RPMI culture medium complemented with 10% FBS,1% antibiotics in CD3/CD28 coating plates. Tfh (TILS) cells were isolated from tumor bearing mice.

extract_protocol:
Total RNA was extracted from 300,000 CD4+ T cells with Trireagent by following manufacturer protocol.
Libraries were prepared from 12 µl of total RNA with the TruSeq Stranded Total RNA using Ribo-Zero (Illumina) following manufacturer instructions. Once qualified, paired-end libraries were sequenced using 2 × 75 bp output on a NextSeq 500 device (Illumina

treatment_protocol: Th1 differentiation was induced with IL-12 (10ng/ml) in presence of IL-4 blocking antibody (10µg/ml) for 48h. Tfh differentition was induced with IL-6 (50ng/ml) and IL-21 (50ng/ml) in presence of IL-4 blocking antibody (10µg/ml), IFNγ blocking antibody (10µg/ml) and TGFβ blocking antibody (10µg/ml) for 48h.

tag: age

value: 7 weeks

value: Naive T cells

value: WT spleen and lymph nodes


title: 545388A06_Me.ze

description: multi-species aCGH

value: Maylandia zebra


title: Th1_Vitro WT 24h_1


title: Guo_026_wb_8

description: Gene expression from mouse blood

value: male


title: Guo_027_wb_384

description: Gene expression from mouse blood

value: 80ug MWCNT 1 month

value: blood


title: 545388A05_Me.ze

description: multi-species aCGH


title: Tfh_Vitro OT-II 48h_3

source_name: Naive T cells from OT-II spleen and lymph nodes

value: OT-II spleen and lymph nodes


title: Guo_041_wb_390

description: Gene expression from mouse blood

value: DM 12 month


title: 545388A04_As.bu

description: multi-species aCGH

value: Astatotilapia burtoni


title: 545388A03_As.bu

description: multi-species aCGH


title: Tfh_Vitro OT-II 48h_2


title: Guo_024_wb_43

description: Gene expression from mouse blood


title: Guo_025_wb_95

description: Gene expression from mouse blood


title: Th1_Vitro WT 24h_2


title: 545388A01_Or.ni

description: multi-species aCGH

value: Oreochromis niloticus


title: 545385A08_Pu.ny

description: multi-species aCGH

value: Pundamilia nyererei


title: 545385A10_Nl.br

description: multi-species aCGH

value: Neolamprologus brichardi


title: 545388A09_Nl.br

description: multi-species aCGH


title: Guo_030_wb_411

description: Gene expression from mouse blood

value: DM 6 month


title: Tfh_Vitro WT 24h_3


title: 545385A06_Me.ze

description: multi-species aCGH

value: Haplochromis burtoni


title: Guo_023_wb_346

description: Gene expression from mouse blood

value: 40ug MWCNT 6 month


title: 545385A02_Or.ni

description: multi-species aCGH


title: 545385A04_As.bu

description: multi-species aCGH


title: 545383A12_As.bu

description: multi-species aCGH


title: 545388A02_Or.ni

description: multi-species aCGH


title: 545383A10_Nl.br

description: multi-species aCGH


title: Tfh_Vitro OT-II 48h_1


title: Guo_022_wb_170

description: Gene expression from mouse blood

value: 120ug crocidolite 6 month


title: 545383A06_Me.ze

description: multi-species aCGH


title: Tfh_Vitro WT 24h_1

value: 7 weeks


title: 545383A08_Pu.ny

description: multi-species aCGH


title: Tfh_TILS_3

source_name: CD4+ CXCR5+ PD1+ (Tfh) cells from MC38 tumors

value: CD4+ CXCR5+ PD1+ (Tfh) cells

value: MC38 tumors


title: Tfh_Vitro WT 24h_2

value: Naive T cells

value: WT spleen and lymph nodes


title: 545383A04_As.bu

description: multi-species aCGH


title: 545383A02_Or.ni

description: multi-species aCGH


title: Infected Garganega berries 2

description: Healthy Garganega berries artificially inoculated with B. cinerea by injecting conidia under berry skin, in controlled conditions, reproducing the pourri plein stage of noble rot

organism:
Vitis vinifera
Botrytis cinerea

source_name: berries

value: berries

tag: sample type

value: noble rot

tag: strain/cultivar

value: Vitis vinifera cv. Garganega; B05.10


title: Tfh_TILS_1


title: Infected Garganega berries 3


title: Guo_021_wb_92

description: Gene expression from mouse blood

value: 120ug crocidolite 12 month

value: male

value: blood


title: Guo_019_wb_243

description: Gene expression from mouse blood

value: 10ug MWCNT 12 month


title: Guo_020_wb_76

description: Gene expression from mouse blood

value: DM 1 month


title: Infected Garganega berries 1


title: Guo_018_wb_34

description: Gene expression from mouse blood

value: 1ug MWCNT 6 month


title: Tfh_TILS_2


title: lung, 615D_600_Rm240

description:
raw data file: 2013-08-23_19718615_600PMT_5um_0532.txt
Array D (blocks 25-32)

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon Genepix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split into four subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 10240 features on each microarray by subtracting the median local background from the median local foreground for each spot. Visually flagged spots were removed prior to averaging and normalizing.The 95th percentile of the negative control spots was also calculated for each array. The spot intensities and 95th percentile of negative controls (TPT95) were transformed by taking the log (base 2) of each value. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The mean probe intensities for each of the probes on each array were then determined by averaging the triplicate spot intensities. Spots that have an average saturated signal were removed prior to normalization. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the non-saturated human probes above threshold in all samples. The log2-transformed spot intensities for all features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays.

label: Oyster-550 fluorescent dye

source_name: lung, 40ug MWCNT, 12 mo

label_protocol: The total RNA with was DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitous viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus.

extract_protocol: Total RNA was isolated from mouse lung tissue using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol.

treatment_protocol: Each component consisted of 8 mice per exposure group (dispersion media [DM, negative control]; 1, 10, 40, or 80 μg MWCNT; 120 μg crocidolite asbestos [positive control]) to be sacrificed at 1, 6 or 12 months post-exposure, for a total of 144 mice.

tag: treatment

value: 40ug MWCNT

tag: time

value: 12 mo

value: lung


title: lung, 616A_600_Rm275

description:
raw data file: 2013-08-23_19718616_600PMT_5um_0532.txt
Array A (blocks 1-8)

source_name: lung, 80ug MWCNT, 12 mo

value: 80ug MWCNT


title: lung, 616C_600_m429

description:
raw data file: 2013-08-23_19718616_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, 1ug MWCNT, 12 mo

value: 1ug MWCNT


title: TF1_C

city: Indianapolis

first: Chi

last: Zhang

state: IN

institute: INDIANA UNIVERSITY

data_processing:
The sequencing data was next assessed using FastQC (Babraham Bioinfomatics, Cambridge, UK) and then mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner with the parameter: “—outSAMmapqUNIQUE 60”.
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) .
Genes with readcount per million (CPM) >0.5 in more than 3 of the samples were kept.
The data were normalized using TMM (trimmed mean of M values) method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited count matrix file

source_name: Tet2-/-Flt3ITD with vehicle treatment

growth_protocol: Bone marrow cells were isolated from the hind limbs of C57BL/6 or Tet2-/-Flt3ITD mice and the lineage positive cells were removed using mouse hematopoietic progenitor cell enrichment kit (Stem Cell Technologies). The cells were expanded in a cytokine cocktail of IL-3, IL-6 and SCF for 5 days to generate myeloid blast like cells

extract_protocol:
Total RNA was isolated using the Qiagen RNA extraction kit.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library prep kit (Illumina).

treatment_protocol: The cells were treated for 24 hr with SHP099 for 24 h

tag: strain background

value: Bone marrow

value: vehicle


title: TF3_C

source_name: Tet2-/-Flt3ITD  with vehicle treatment


title: TF2_I

source_name: Tet2-/-Flt3ITD  with SHP099 treatment


title: TF2_C


title: TF3_1


title: WT3_C

source_name: wildtype with vehicle treatment

value: wildtype


title: TF1_I


title: Guo_015_wb_114

description: Gene expression from mouse blood

value: 120ug crocidolite 1 month


title: lung, 614D_600_m218

description:
raw data file: 2013-08-23_19718614_600PMT_5um_0532.txt
Array D (blocks 25-32)

source_name: lung, 120ug crocidolite, 1 mo

value: 120ug crocidolite

value: 1 mo


title: lung, 615A_600_m402

description:
raw data file: 2013-08-23_19718615_600PMT_5um_0532.txt
Array A (blocks 1-8)

source_name: lung, 10ug MWCNT, 12 mo

value: 10ug MWCNT


title: lung, 614B_600_m362

description:
raw data file: 2013-08-23_19718614_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 615B_600_m330

description:
raw data file: 2013-08-23_19718615_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 613C_600_m366

description:
raw data file: 2013-08-23_19718613_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 613D_600_m118

description:
raw data file: 2013-08-23_19718613_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 614A_600_m390

description:
raw data file: 2013-08-23_19718614_600PMT_5um_0532.txt
Array A (blocks 1-8)

source_name: lung, DM, 12 mo

value: DM


title: lung, 614C_600_Rm355

description:
raw data file: 2013-08-23_19718614_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 615C_600_Rm155

description:
raw data file: 2013-08-23_19718615_600PMT_5um_0532.txt
Array C (blocks17-24)


title: Guo_014_wb_238

description: Gene expression from mouse blood

source_name: blood

value: male

value: blood


title: Guo_013_wb_144

description: Gene expression from mouse blood

value: 120ug crocidolite 12 month


title: Guo_012_wb_132

description: Gene expression from mouse blood

value: 120ug crocidolite 6 month


title: Guo_016_wb_327

description: Gene expression from mouse blood

value: DM 12 month


title: Guo_011_wb_41

description: Gene expression from mouse blood


title: Guo_010_wb_185

description: Gene expression from mouse blood

value: 10ug MWCNT 1 month


title: Guo_008_wb_82

description: Gene expression from mouse blood

value: 1ug MWCNT 12 month


title: Guo_009_wb_380

description: Gene expression from mouse blood

value: 120ug crocidolite  6  month


title: lung, 613B_600_Rm14

description:
raw data file: 2013-08-23_19718613_600PMT_5um_0532.txt
Array B (blocks 9-16)

value: lung


title: lung, 613A_600_Rm72

description:
raw data file: 2013-08-23_19718613_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 80ug MWCNT

value: 12 mo


title: WT1_C

value: wildtype

value: Bone marrow

value: vehicle


title: lung, 612C_600_m164

description:
raw data file: 2013-08-22_19718612_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 612D_600_m71

description:
raw data file: 2013-08-22_19718612_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: 40ug MWCNT


title: lung, 612B_600_Rm257

description:
raw data file: 2013-08-22_19718612_600PMT_5um_0532.txt
Array B (blocks 9-16)

value: 1ug MWCNT


title: lung, 610D_600_m82

description:
raw data file: 2013-08-22_19718610_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 610B_600_Rm337

description:
raw data file: 2013-08-22_19718610_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 120ug crocidolite, 12 mo

value: 120ug crocidolite


title: lung, 612A_600_m98

description:
raw data file: 2013-08-22_19718612_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 10ug MWCNT


title: lung, 610C_600_m161

description:
raw data file: 2013-08-22_19718610_600PMT_5um_0532.txt
Array C (blocks17-24)


title: Guo_017_wb_140

description: Gene expression from mouse blood

value: 80ug MWCNT 1 month

value: male

value: blood


title: lung, 611D_600_Rm289

description:
raw data file: 2013-08-22_19718611_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: E7

first: Phyllis

last: Faust

state: NY

address: 630 W 168th Street

department: Pathology and Cell Biology

institute: Columbia Unversity

description:
mRNA pulldown
raw read counts.xlsx
Ctout_v_Etout.deseq2.xlsx

data_processing:
Aligned RNA-seq reads to the human genome and trascriptome annotation using STAR aligner (STAR v2.4.4a)
Quantified the reads that aligned uniquely to the transcriptome using the featureCounts program in the subread package (subread v1.4.6)
Identified differentially expressed genes using DEseq2
Genome_build: hg19 (UCSC annotation from Illumina iGenomes)
Supplementary_files_format_and_content: .xlsx raw read counts and DEseq2 readouts for ET vs. Control

organism: Homo sapiens

source_name: Cerebellar Cortex: anterior and posterior quadrangulate lobules

extract_protocol:
Whole anterior cerebellar cortex was cut at a cryostat for a total of 500-600um of sample. RNA was extracted using a QIASymphony auto-extractor. RNA was quantified using an Agilent bioanalyzer nano chip.
mRNA was isolated from 450ng of total RNA by incubation with streptavidin-coated C1 Dynabeads (ThermoFisher CAT#65001). Dynabeads were washed (20mM Tris pH 8.0, 50mM NaCl, 0.1% Tween-20/0.5mL per 20uL of beads), placed in hybridization buffer (20mM Tris pH 8.0, 1M NaCl, 0.1% Tween-20/20uL per 20uL of beads) and coated with 25uM biotinylated LNA-Oligo(dT) (Exiqon CAT#300100-03/4uL per 20uL of beads). LNA-Oligo(dT)-coated Dynabeads were incubated with each sample at 1:1 volume and RNase inhibitor was added (SUPERaseIN [ThermoFisher CAT#AM2694], 0.50 ul per sample). Libraries were constructed using SMARTer Stranded RNA-Seq kit (Clontech Laboratories CAT#634862) according to the manufacturer’s instructions. mRNA was fragmented for 4 minutes at 94°C and cDNA libraries were purified using AMPure XP beads (Beckman Coulter CAT#A63880). Libraries were amplified via 9 cycles of PCR and each sample indexed with unique barcodes for high-throughput sequencing. The RNA-seq library was purified again using AMPure XP beads. The cDNA quality in the sequencing libraries was determined using an Agilent Bioanalyzer 2100 High Sensitivity DNA assay and concentration determined in Qubit assay (ThermoFisher CAT#Q32851). The libraries were pooled (at equal concentrations) and 1x75 base-pair single-end sequenced in quadruplicate on an Illumina NextSeq 500 using 75-cycle High Output Kits (~30M reads per sample).
Samples were run in quadruplicate for more coverage. The chip used for the sequencing has 4 lanes, therefore there are files for each lane and each run on the machine.

value: Cerebellar Cortex:anterior and posterior quadrangulate lobules

tag: diagnosis

value: Control

tag: gender

value: Female


title: Guo_007_wb_250

description: Gene expression from mouse blood

organism: Mus musculus

value: DM 6 month


title: E5


title: Guo_005_wb_7

description: Gene expression from mouse blood

value: 1ug MWCNT 6 month


title: Guo_006_wb_33

description: Gene expression from mouse blood

value: 40ug MWCNT 6 month


title: E4

value: Male


title: WT2_C

tag: genotype/variation

value: wildtype


title: Guo_003_wb_123

description: Gene expression from mouse blood

value: DM 1 month


title: lung, 609D_600_m152

description:
raw data file: 2013-08-22_19718609_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: 12 mo

value: lung


title: lung, 609B_600_m397

description:
raw data file: 2013-08-22_19718609_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 1ug MWCNT, 6 mo

value: 1ug MWCNT

value: 6 mo


title: lung, 610A_600_m410

description:
raw data file: 2013-08-22_19718610_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 80ug MWCNT


title: lung, 609C_600_Rm306

description:
raw data file: 2013-08-22_19718609_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, DM, 6 mo

value: DM


title: lung, 609A_600_m23

description:
raw data file: 2013-08-22_19718609_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 10ug MWCNT


title: E2


title: lung, 608D_600_Rm417

description:
raw data file: 2013-08-22_19718608_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: 120ug crocidolite


title: Guo_004_wb_197

description: Gene expression from mouse blood

value: 1ug MWCNT 1 month

value: male

value: blood


title: E6

value: Cerebellar Cortex:anterior and posterior quadrangulate lobules

value: Control

value: Female


title: E1

value: Male


title: Guo_002_wb_187

description: Gene expression from mouse blood

value: 40ug MWCNT 1 month


title: E3


title: Guo_001_wb_184

description: Gene expression from mouse blood

value: 120ug crocidolite 1 month


title: FSKL_P4_3

city: Cleveland

first: Sam

last: Mesiano

state: OH

address: 11100 Euclid Avenue, MacDonald Women's Hospital, Mac 8129

institute: Case Western Reserve University

data_processing:
Transcripts were aligned using TopHat against the UCSC hg19 reference transcriptome.
Transcript assembly and abundance estimation was performed using CuffDiff
Gene expression matrix was obtained using the repFpkmMatrix() function in the cummeRbund R package
Genes having zero expression in three or more samples were removed
Genome_build: hg19
Supplementary_files_format_and_content: Normalized FPKM gene expression matrix for all 24 samples in CSV format

source_name: myometrium

growth_protocol: Studies were performed using the hTERT-HM^A/B telomerase-immortalized human myometrial cell line maintained at 37 °C in a 5% CO^2-humidified incubator in Dulbecco's modified eagle medium (DMEM)/Ham's F12 (1:1) supplemented with 5% charcoal-stripped fetal bovine serum (FBS), 1% penicillin-streptomycin, 0.1 mg/mL geneticin and 2 mM L-glutamine (Thermo Fisher Scientific, Waltham, MA). hTERT-HM^A/B is a sub-clone of the hTERT-HM (Condon et al., 2002) that was genetically modified to contain stably incorporated transgenes expressing PR-A and PR-B in response to independent inducers (Tan et al., 2012). hTERT-HM^A/B cells have minimal expression of PGR (encodes PR-A and PR-B) and PR-A and PR-B levels under basal conditions and are not responsive to P4. The cells express PR-A in response to doxycycline (DOX) and PR-B in response to diacylhydrazine (DAH), each in a concentration-dependent manner and PR-A and PR-B transgenes are silent in the absence of exposure to DOX and DAH.

extract_protocol: Total RNA was isolated using the Total RNA Isolation/NucleoSpin RNA II kit (Macherey-Nagel, Bethlehem, PA), treated with DNase (DNA- free; Thermo Fisher Scientific) and quantified by absorbance at 260 nM.  Quality control of total RNA samples was executed using Qubit (Invitrogen) for quantification and Agilent 2100 Bioanalyzer analysis to assess quality using a cut-off of RIN > 7.0 to select specimens for further analysis. For library preparation, the Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold for rRNA removal was used. This protocol starts by using the Ribo-Zero kit to remove ribosomal RNA (rRNA) from 0.10 - 1 µg of Total RNA using a hybridization/bead capture procedure that selectively binds rRNA species using biotinylated capture probes. The resulting purified mRNA is used as input for the Illumina TruSeq kit in which libraries are tagged with unique adapter-indexes. Final libraries were validated on the Agilent 2100 Bioanalyzer, quantified via qPCR and pooled at equimolar ratios. Pooled libraries were diluted, denatured and loaded onto the Illumina HiSeq 2500 using a paired-end Rapid Run flowcell.

treatment_protocol: hTERT-HM^A/B cells were maintained in the basal state (negligible PR levels and no PRE2-LUCFFresponse to P4) or induced to express equivalent amounts of PR-A and PR-B and then treated with P4 (100 nM; Sigma) or vehicle [dimethyl sulfoxide (DMSO)] for 24h. Media was then changed and the cells were exposed to IL-1β (1 ng/mL; Cell Signaling) in the presence and absence of P4 (replenished) and/or forskolin (10 μM; Sigma) for a further 24h.   Cells were induced to express PR-A (DOX: 100 ng/mL) and PR-B (DAH: 400 nM) prior to treatment.

tag: cell type

value: hTERT-HM^(A/B)

tag: p4 treatment

value: Yes

tag: fsk treatment

tag: il-1beta treatment

value: No


title: FSK_P4_IL-1beta_3


title: FSKL_P4_1


title: lung, 607D_600_m309

description:
raw data file: 2013-08-22_19718607_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: 1ug MWCNT

value: 6 mo

value: lung


title: lung, 608A_600_m97

description:
raw data file: 2013-08-22_19718608_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: DM

value: 12 mo


title: lung, 608B_600_Rm189

description:
raw data file: 2013-08-22_19718608_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 40ug MWCNT, 6 mo

value: 40ug MWCNT


title: FSKL_P4_2


title: D12

description:
mRNA pulldown
raw read counts.xlsx
Outlier sample: no processed data

value: Control **(Outlier)**


title: lung, 608C_600_m160

description:
raw data file: 2013-08-22_19718608_600PMT_5um_0532.txt
Array C (blocks17-24)

value: 80ug MWCNT


title: D10

value: Cerebellar Cortex:anterior and posterior quadrangulate lobules

value: Essential Tremor


title: lung, 607C_600_m243

description:
raw data file: 2013-08-22_19718607_600PMT_5um_0532.txt
Array C (blocks17-24)

value: 10ug MWCNT


title: FSK_P4_IL-1beta_2


title: D9

value: Female


title: lung, 607B_600_Rm78

description:
raw data file: 2013-08-22_19718607_600PMT_5um_0532.txt
Array B (blocks 9-16)

value: 120ug crocidolite


title: lung, 606C_600_m265

description:
raw data file: 2013-08-20_19718606_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 606D_600_m406

description:
raw data file: 2013-08-20_19718606_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 607A_600_Rm372

description:
raw data file: 2013-08-22_19718607_600PMT_5um_0532.txt
Array A (blocks 1-8)

source_name: lung, 80ug MWCNT, 6 mo


title: FSK_IL-1beta_3


title: FSK_P4_IL-1beta_1


title: D8

description:
mRNA pulldown
raw read counts.xlsx
Ctout_v_Etout.deseq2.xlsx


title: lung, 606B_600_m347

description:
raw data file: 2013-08-20_19718606_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 606A_600_m296

description:
raw data file: 2013-08-20_19718606_600PMT_5um_0532.txt
Array A (blocks 1-8)

source_name: lung, 10ug MWCNT, 6 mo


title: D7


title: lung, 605D_600_m41

description:
raw data file: 2013-08-20_19718605_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: D6


title: FSK_IL-1beta_2


title: FSK_IL-1beta_1


title: lung, 605C_600_Rm142

description:
raw data file: 2013-08-20_19718605_600PMT_5um_0532.txt
Array C (blocks17-24)


title: P4_IL-1beta_3


title: lung, 605A_600_m411

description:
raw data file: 2013-08-20_19718605_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 605B_600_m345

description:
raw data file: 2013-08-20_19718605_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: D5

value: Control


title: D4


title: P4_IL-1beta_2

value: hTERT-HM^(A/B)


title: P4_IL-1beta_1

value: Yes


title: D3


title: lung, 604C_600_m376

description:
raw data file: 2013-08-20_19718604_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 604D_600_m247

description:
raw data file: 2013-08-20_19718604_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: D2


title: lung, 603C_600_m343

description:
raw data file: 2013-08-20_19718603_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 604B_600_m168

description:
raw data file: 2013-08-20_19718604_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 603D_600_m220

description:
raw data file: 2013-08-20_19718603_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 604A_600_m223

description:
raw data file: 2013-08-20_19718604_600PMT_5um_0532.txt
Array A (blocks 1-8)

source_name: lung, 80ug MWCNT, 12 mo


title: FSK_3

value: No


title: FSK_2


title: C12

value: Male


title: D1


title: lung, 602D_600_Rm262

description:
raw data file: 2013-08-20_19718602_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 602C_600_m399

description:
raw data file: 2013-08-20_19718602_600PMT_5um_0532.txt
Array C (blocks17-24)

value: 6 mo


title: lung, 603A_600_m231

description:
raw data file: 2013-08-20_19718603_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: lung


title: lung, 602B_600_m281

description:
raw data file: 2013-08-20_19718602_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 603B_600_m175

description:
raw data file: 2013-08-20_19718603_600PMT_5um_0532.txt
Array B (blocks 9-16)

value: 1ug MWCNT


title: C11

description:
mRNA pulldown
raw read counts.xlsx
Ctout_v_Etout.deseq2.xlsx


title: C10


title: lung, 601D_600_m154

description:
raw data file: 2013-08-20_19718601_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: C9


title: IL-1beta_2


title: lung, 601C_600_m201

description:
raw data file: 2013-08-20_19718601_600PMT_5um_0532.txt
Array C (blocks17-24)


title: IL-1beta_1


title: lung, 601B_600_m412

description:
raw data file: 2013-08-20_19718601_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 120ug crocidolite, 6 mo


title: C8


title: FSK_1


title: C7


title: P4_2


title: C6


title: lung, 602A_600_m250

description:
raw data file: 2013-08-20_19718602_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: DM


title: C5

description:
mRNA pulldown
raw read counts.xlsx
Outlier sample: no processed data

value: Essential Tremor **(Outlier)**


title: lung, 600C_600_m169

description:
raw data file: 2013-08-16_19718600_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 599D_600_m336

description:
raw data file: 2013-08-16_19718599_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 600A_600_m135

description:
raw data file: 2013-08-16_19718600_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 600B_600_m100

description:
raw data file: 2013-08-16_19718600_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: IL-1beta_3


title: lung, 599B_600_m85

description:
raw data file: 2013-08-16_19718599_600PMT_5um_0532.txt
Array B (blocks 9-16)

value: 40ug MWCNT


title: lung, 599C_600_m274

description:
raw data file: 2013-08-16_19718599_600PMT_5um_0532.txt
Array C (blocks17-24)

value: 80ug MWCNT


title: lung, 598D_600_m7

description:
raw data file: 2013-08-16_19718598_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: Control_3


title: lung, 598C_600_m74

description:
raw data file: 2013-08-16_19718598_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 601A_600_m225

description:
raw data file: 2013-08-20_19718601_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 600D_600_m138

description:
raw data file: 2013-08-16_19718600_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: C4

value: Cerebellar Cortex:anterior and posterior quadrangulate lobules


title: Control_2


title: C3


title: P4_3


title: lung, 597C_600_m84

description:
raw data file: 2013-08-16_19718597_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 597D_600_m54

description:
raw data file: 2013-08-16_19718597_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 598B_600_m263

description:
raw data file: 2013-08-16_19718598_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 598A_600_m174

description:
raw data file: 2013-08-16_19718598_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: Control_1


title: P4_1


title: C2

description:
mRNA pulldown
raw read counts.xlsx
Ctout_v_Etout.deseq2.xlsx


title: lung, 599A_600_m133

description:
raw data file: 2013-08-16_19718599_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 597B_600_Rm101

description:
raw data file: 2013-08-16_19718597_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 1ug MWCNT, 1 mo

value: 1 mo


title: C1


title: B12

value: Essential Tremor


title: 33A

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg38 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each  gencode V22 gene.

source_name: Kidney Allograft Biopsy

growth_protocol: Biopsy tissue immersed in RNAlater and stored in -80C.

extract_protocol:
Total RNA isolated using miRNeasy mini kit (QIAGEN)
TruSeq sample preparation kit v2 (ILLUMINA)

tag: subject status

value: dult kidney transplant recipient

value: Normal/Non Specific

value: Kidney Allograft Biopsy


title: 31A


title: 36A


title: lung, 596D_600_m323

description:
raw data file: 2013-08-16_19718596_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: 120ug crocidolite


title: lung, 597A_600_m4

description:
raw data file: 2013-08-16_19718597_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 10ug MWCNT


title: 12A


title: B11

value: Control

value: Female


title: B10

value: Male


title: lung, 595D_600_m403

description:
raw data file: 2013-08-16_19718595_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: lung


title: lung, 596A_600_m48

description:
raw data file: 2013-08-16_19718596_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 6 mo


title: lung, 595C_600_Rm333

description:
raw data file: 2013-08-16_19718595_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, 10ug MWCNT, 1 mo


title: lung, 596B_600_m351

description:
raw data file: 2013-08-16_19718596_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 40ug MWCNT, 1 mo


title: B9


title: 11A


title: 10A


title: 9A


title: B8


title: lung, 595B_600_m170

description:
raw data file: 2013-08-16_19718595_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: B7


title: lung, 596C_600_m65

description:
raw data file: 2013-08-16_19718596_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 595A_600_m11

description:
raw data file: 2013-08-16_19718595_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: 8A


title: lung, 594C_600_Rm391

description:
raw data file: 2013-08-16_19718594_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, DM, 1 mo

value: DM


title: lung, 594D_600_m404

description:
raw data file: 2013-08-16_19718594_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 594B_600_m340

description:
raw data file: 2013-08-16_19718594_600PMT_5um_0532.txt
Array B (blocks 9-16)

value: 1ug MWCNT


title: lung, 593D_600_m132

description:
raw data file: 2013-08-16_19718593_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: B5


title: lung, 594A_600_m425

description:
raw data file: 2013-08-16_19718594_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 593C_600_Rm384

description:
raw data file: 2013-08-16_19718593_600PMT_5um_0532.txt
Array C (blocks17-24)

source_name: lung, 80ug MWCNT, 1 mo


title: 4A


title: B4

description:
mRNA pulldown
raw read counts.xlsx
Ctout_v_Etout.deseq2.xlsx


title: 7A


title: lung, 593B_600_m254

description:
raw data file: 2013-08-16_19718593_600PMT_5um_0532.txt
Array B (blocks 9-16)

value: 40ug MWCNT


title: lung, 592D_600_m286

description:
raw data file: 2013-08-14_19718592_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 592C_600_m312

description:
raw data file: 2013-08-14_19718592_600PMT_5um_0532.txt
Array C (blocks17-24)


title: 3A


title: 2A


title: B2


title: 1A


title: lung, 592A_600_Rm315

description:
raw data file: 2013-08-14_19718592_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 80ug MWCNT


title: lung, 592B_600_m55

description:
raw data file: 2013-08-14_19718592_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 591D_600_m319

description:
raw data file: 2013-08-14_19718591_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 591B_600_m197

description:
raw data file: 2013-08-14_19718591_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: B3

value: Cerebellar Cortex:anterior and posterior quadrangulate lobules


title: 52


title: B1


title: A12


title: lung, 591A_600_m185

description:
raw data file: 2013-08-14_19718591_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 1 mo


title: lung, 593A_600_Rm216

description:
raw data file: 2013-08-16_19718593_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 590D_600_m8

description:
raw data file: 2013-08-14_19718590_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: A11

value: Essential Tremor


title: B6


title: 51

value: dult kidney transplant recipient


title: lung, 589D_600_m235

description:
raw data file: 2013-08-14_19718589_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 590A_600_m350

description:
raw data file: 2013-08-14_19718590_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 590B_600_m187

description:
raw data file: 2013-08-14_19718590_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 590C_600_m342

description:
raw data file: 2013-08-14_19718590_600PMT_5um_0532.txt
Array C (blocks17-24)


title: A10


title: lung, 589B_600_Rm383

description:
raw data file: 2013-08-14_19718589_600PMT_5um_0532.txt
Array B (blocks 9-16)

source_name: lung, 120ug crocidolite, 1 mo


title: 49

value: Normal/Non Specific


title: 50

value: Kidney Allograft Biopsy


title: lung, 589C_600_m267

description:
raw data file: 2013-08-14_19718589_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 588D_600_m102

description:
raw data file: 2013-08-13_19718588_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: lung, 591C_600_Rm123

description:
raw data file: 2013-08-14_19718591_600PMT_5um_0532.txt
Array C (blocks17-24)


title: A8

description:
mRNA pulldown
raw read counts.xlsx
Ctout_v_Etout.deseq2.xlsx


title: lung, 588C_600_m217

description:
raw data file: 2013-08-13_19718588_600PMT_5um_0532.txt
Array C (blocks17-24)


title: A7


title: lung, 588B_600_m10

description:
raw data file: 2013-08-13_19718588_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: A6


title: 18A

source_name: ACR_Kidney Allograft Biopsy

value: Acute Cellular Rejection (ACR)


title: lung, 587C_600_m90

description:
raw data file: 2013-08-13_19718587_600PMT_5um_0532.txt
Array C (blocks17-24)


title: lung, 587B_600_m129

description:
raw data file: 2013-08-13_19718587_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: A5

source_name: Cerebellar Cortex: anterior and posterior quadrangulate lobules


title: lung, 587A_600_m13

description:
raw data file: 2013-08-13_19718587_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: A4


title: lung, 588A_600_m119

description:
raw data file: 2013-08-13_19718588_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: 10ug MWCNT


title: lung, 589A_600_m50

description:
raw data file: 2013-08-14_19718589_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 586C_600_m51

description:
raw data file: 2013-08-13_19718586_600PMT_5um_0532.txt
Array C (blocks17-24)


title: 16A


title: lung, 586D_600_m101

description:
raw data file: 2013-08-13_19718586_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: 14A


title: 48


title: A9


title: lung, 587D_600_Rm184

description:
raw data file: 2013-08-13_19718587_600PMT_5um_0532.txt
Array D (blocks 25-32)

value: 120ug crocidolite


title: lung, 586B_600_m114

description:
raw data file: 2013-08-13_19718586_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: lung, 586A_600_m121

description:
raw data file: 2013-08-13_19718586_600PMT_5um_0532.txt
Array A (blocks 1-8)


title: lung, 585D_600_m49

description:
raw data file: 2013-08-13_19718585_600PMT_5um_0532.txt
Array D (blocks 25-32)


title: 13A


title: A3

value: Female


title: 23


title: A2


title: lung, 585C_600_m67

description:
raw data file: 2013-08-13_19718585_600PMT_5um_0532.txt
Array C (blocks17-24)


title: A1

value: Male


title: 22


title: lung, 585A_600_m105

description:
raw data file: 2013-08-13_19718585_600PMT_5um_0532.txt
Array A (blocks 1-8)

value: lung


title: lung, 585B_600_m113

description:
raw data file: 2013-08-13_19718585_600PMT_5um_0532.txt
Array B (blocks 9-16)


title: 20


title: 19


title: ChIP-Seq A549 p-Babe LKB1 rep3

city: San Diego

first: Ezra

last: Wiater

state: CA

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

description: IP of CRTC2 bound DNA

data_processing:
Reads were aligned to the human (hg19) genome using bowtie2
Binding peaks were called using Homer
Homer peak files were converted to bedgraph files using Homer
Genome_build: hg19
Supplementary_files_format_and_content: homer peak files in bedgraph format

source_name: A549 cells

growth_protocol: DMEM 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody as indicated
ChIP-seq libraries were constructed with NEBNext ChIPseq library kit (NEB) according to manufacturer's instructions.

treatment_protocol: stable expression of pBabe vector or pBabe-LKB1 selected with puromycin

value: NSCLC cells

tag: transduction

value: retrovirus mediated transduction of pBabe-LKB1 (WT)

tag: expression

value: stable expression of pBabe-LKB1(WT) vector selected with puromycin

tag: chip-antibody

value: 6865 anti-CRTC2 rabbit serum


title: ChIP-Seq A549 p-Babe LKB1 rep1

description: input DNA without IP


title: 174D_550_wb 380

description: raw data file: 2013-10-02_19723174_550PMT_5um_0532.txt, Array D (blocks 25-32)

scan_protocol: The microarrays were scanned on an Axon GenePix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: Data for 4 arrays were extracted from a single microarray image into a single text file using GenePix version 4.1 software. The raw text files were split in to eighteen subfiles based on block assignment, namely blocks 1-8 contained data for array A, blocks 9-16 contained data for array B, blocks 17-24 contained data for array C, and blocks 25-32 contained data for array D. Spot intensities were obtained for the 10240 features on each microarray by subtracting the median local background from the median local foreground for each spot. Visually flagged spots were removed prior to averaging and normalizing. The 95th percentile of the negative control spots was also calculated for each array. The spot intensities and 95th percentile of negative controls (TPT95) were transformed by taking the log (base 2) of each value. The detection threshold (T) for each microarray was computed by summing five times the standard deviation of the background signal and the 10% trim mean of the negative control spots. The mean probe intensities for each of the probes on each array were then determined by averaging the triplicate spot intensities. Spots that have an average saturated signal were removed prior to normalization. The normalization factor (N) for each microarray was determined by obtaining the 20% trim mean of the non-saturated human probes above threshold in all samples. The log2-transformed spot intensities for all features were normalized, by subtracting N from each spot intensity, and scaled by adding the grand mean of N across all microarrays.

source_name: Month 6 120ug crocidolite

label_protocol: The total RNA was DNase digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitious viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus.

extract_protocol: Total RNA was isolated from mouse blood using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol.

tag: strain/background

tag: tissue

value: Blood

value: Month 6


title: 175D_550_wb 410

description: raw data file: 2013-10-03_19723175_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 12 80ug MWCNT

value: 80ug MWCNT

value: Month 12


title: 174C_550_wb 140

description: raw data file: 2013-10-02_19723174_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 1 80ug MWCNT

value: Month 1


title: 175C_550_wb 390

description: raw data file: 2013-10-03_19723175_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 12 DM

value: DM


title: 175B_550_wb 300

description: raw data file: 2013-10-03_19723175_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 12 40ug MWCNT

value: 40ug MWCNT


title: ChIP-Seq A549 p-Babe rep3

description: IP of CRTC2 bound DNA

value: retrovirus mediated trasduction of pBabe vector

value: stable expression of pBabe vector selected with puromycin


title: 175A_550_wb 257

description: raw data file: 2013-10-03_19723175_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 12 1ug MWCNT

value: 1ug MWCNT


title: 17

value: dult kidney transplant recipient

value: Acute Cellular Rejection (ACR)

value: Kidney Allograft Biopsy


title: 176A_550_wb 351

description: raw data file: 2013-10-03_19723176_550PMT_5um_0532.txt, Array A (blocks 1-8)

source_name: Month 1 40ug MWCNT

value: Male


title: 174B_550_wb 346

description: raw data file: 2013-10-02_19723174_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 6 40ug MWCNT


title: 12


title: ChIP-Seq A549 p-Babe rep2

description: IP of CREB bound DNA

value: NSCLC cells

value: 244 anti-CREB rabbit serum


title: 173D_550_wb 408

description: raw data file: 2013-10-02_19723173_550PMT_5um_0532.txt, Array D (blocks 25-32)

source_name: Month 6 1ug MWCNT


title: 174A_550R_wb 70

description: raw data file: 2013-10-02_19723174_550PMT_5um_redip_0532.txt, Array A (blocks 1-8)


title: ChIP-Seq A549 p-Babe rep1

description: input DNA without IP


title: 173C_550_wb 31

description: raw data file: 2013-10-02_19723173_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 6 10ug MWCNT

value: 10ug MWCNT


title: 9


title: ChIP-Seq A549 p-Babe LKB1 rep2

description: IP of CREB bound DNA

value: retrovirus mediated transduction of pBabe-LKB1 (WT)

value: stable expression of pBabe-LKB1(WT) vector selected with puromycin


title: 173B_550_wb 144

description: raw data file: 2013-10-02_19723173_550PMT_5um_0532.txt, Array B (blocks 9-16)

source_name: Month 12 120ug crocidolite

value: Blood

value: 120ug crocidolite


title: 18


title: 173A_550_wb 52

description: raw data file: 2013-10-02_19723173_550PMT_5um_0532.txt, Array A (blocks 1-8)

value: 80ug MWCNT

value: Month 1


title: 8


title: No-CAP H3K4me3_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
peaks were called using macs version 1.4
Genome_build: hg19
Supplementary_files_format_and_content: peak files with quantitative data, tag density files

source_name: No-CAP H3K4me3

growth_protocol: A breast cancer cell line MCF-7 was purchased from the American Type Culture Collection (ATCC) (Manassas, VA, USA) and cultured in RPMI-1640 medium (Gibco, Los Angeles, CA, USA) supplemented with 10% FBS (Gibco) and 2% Penicillin and Streptomycin (Gibco) maintained at 37 °C in 5% CO2

extract_protocol:
DNA was extracted using DNA Prep. Kit
construction of library was performed using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

treatment_protocol: The CAP device, a type of mesh - DBD (Dielectric Barrier Discharge), was manufactured at the Plasma Bioscience Research Center (Kwangwoon University, Korea). CAP was treated onto the cell in culture media for 600 sec at 0.12 kV, using argon gas flow of 1.5 L/min, with operation frequency 12.89 kHz.

tag: cell line

value: Mammary epithelial cell line

value: none (control)

tag: chip antibody

value: Histone H3K4me3 Polyclonal Antibody

tag: chip antibody vendor

value: Signalway Antibody

tag: chip antibody cat. #


title: 172C_550_wb 53

description: raw data file: 2013-10-02_19723172_550PMT_5um_0532.txt, Array C (blocks 17-24)

source_name: Month 6 DM

tag: treatment

value: DM

tag: time

value: Month 6


title: 172A_550R_wb 425

description: raw data file: 2013-10-02_19723172_550PMT_5um_redip_0532.txt, Array A (blocks 1-8)

source_name: Month 1 10ug MWCNT

tag: gender


title: 172B_550_wb 69

description: raw data file: 2013-10-02_19723172_550PMT_5um_0532.txt, Array B (blocks 9-16)

value: 1ug MWCNT

value: Month 12


title: 7

source_name: ACR_Kidney Allograft Biopsy

value: dult kidney transplant recipient

tag: diagnosis

value: Acute Cellular Rejection (ACR)

value: Kidney Allograft Biopsy