title: Th2 chronic inflammation, biological repl 3

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

description: Gene expression data from lung-resident Th2cells isolated after 12 weeks of allergic airway inflammation.

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained in the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

data_processing: The data were analyzed via R using affy, limma and vsn packages. Since the probe information have not been updated by Affymetrix since December 22, 2010, PERL scripts were written to extract the updated information about mature miRs from miRBase (Kozomara and Griffiths-Jones, 2014) by using the probe sequences given by Affymetrix to pattern match them against “mature.fa” provided by miRBase (downloaded on April 29, 2015).  Reference: Kozomara, A., and Griffiths-Jones, S. (2014). miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic acids research 42, D68-73.

source_name: Mouse lung at day 104 after OVA-induced allergic airway inflammation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mice were sensitized by three intra peritoneal injections of 10 µg OVA adsorbed to 1.5 mg aluminum-hydroxide dissolved in 200µl phosphate buffered saline (PBS) at days 1, 14 and 21. OVA aerosol challenges (1 % [wt/v] OVA) were performed for 3 consecutive days (acute) or for 12 weeks (chronic) with two consecutive challenges per week.

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

treatment_protocol: Lungs were perfused with PBS, excised and digested with collagenase D and DNaseI for 30 min at 37 °C. CD4+ T cells were enriched using the magnetic bead separation from the resulting cell suspension. Cell sorting was performed targeting following surface molecules: naive CD4+ T cells (CD4+ CD62L+ CD44-), tissue-resident Th2 cells (CD4+ CD69+ ST2+). After sorting, cells were activated with anti-CD3/anti-CD28 for 8 hours.

tag: cell


title: mucosa next to tumor bottom crypt fraction, px 6

status: Public on Jun 18 2018

type: RNA

city: Singapore

first: Peh Yean

last: Cheah

address: 20 College Road

department: Colorectal Surgery

country: Singapore

institute: Singapore General Hospital

description: gene expression data from MT bottom crypt fraction for px6

hyb_protocol: Following fragmentation, target cRNAs were hybridized to GeneChip Human Gene 1.0 ST Arrays at 45C for 17hr. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Signals were analysed with the GeneChip operating system (GCOS) software. Quality assessment of the arrays was performed with Affymetrix Expression Console v1.1.  The CEL files were imported into Partek for further analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: colonic mucosa next to tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA

extract_protocol: Total RNA was extracted from each specimen using Qiagen RNA (tissue) extraction kit according to manufacturer's instructions.

tag: tissue

value: colonic mucosa next to tumor


title: control #1

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

hyb_protocol: Microarray hybridization was performed using the Affymetrix Fluidics Station 450 with  program FS450_0001.

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

data_processing: Data were preprocessed in the R v3.2.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

organism: Chlorocebus sabaeus

source_name: control-treated Vero cells

label_protocol: 100ng total RNA from each sample was processed with the IVT Express reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's protocol.

growth_protocol: Cells were cultured in RPMI medium containing 10% fetal calf serum and standard antibiotics at 37°C and 5% CO2.

extract_protocol: RNA was extrated with Trizol reagent.

tag: cell line

value: Vero

tag: group

value: control


title: mucosa next to tumor top crypt fraction, px7

description: gene expression data from MT top crypt fraction for px 7


title: APOBEC3G #1

source_name: APOBEC3G-overexpressing Vero cells

value: overexpression


title: Th2 chronic inflammation, biological repl 2

organism: Mus musculus


title: Th2 chronic inflammation, biological repl 1


title: ChIP: Input_LOUCY_012615 [lab: Look-DFCI]

type: SRA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

library_source: genomic

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

molecule: genomic DNA

source_name: Loucy

growth_protocol: T-ALL cells were maintained in RPMI-1640 medium supplemented with 10% FBS, L-glutamine, and penicillin/streptomycin

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using antibodies.

tag: cell type

value: T-ALL

value: Loucy

tag: chip antibody


title: ChIP: JDP2_sc-23456X_LOUCY_012615 [lab: Look-DFCI]

value: JDP2 (Santa Cruz sc-23456X)


title: KOPTK1_dox_3

library_source: transcriptomic

data_processing:
Reads were aligned to the hg19 revision of the human reference genome using tophat with parameters --library-type fr-firststrand --no-novel-juncs and a GTF of RefSeq transcripts downloaded 7/5/17.  Per-RefSeq-gene expression was calculated using htseq-count with parameters -i gene_id –stranded=reverse -f bam -m intersection-strict. Differential expression was determined using DESeq2
Supplementary_files_format_and_content: rc files contain numbers of reads assignable to each gene using htseq-count

molecule: polyA RNA

extract_protocol:
Purified RNA was reverse-transcribed with the Superscipt III RT kit (Invitrogen). Quantitative real-time PCR was performed with the Applied Biosystems ViiATM 7 using gene-specific primers and SYBR Green PCR Master Mix (Roche).
mRNA was extracted using the RNeasy Mini Kit (Qiagen).

tag: treatment

value: DOX (induced shJDP2)


title: mucosa top crypt fraction, px 6

description: gene expression data from M top crypt fraction for px 6

source_name: colonic mucosa

value: colonic mucosa


title: Th2 acute inflammation, biological repl 2

description: Gene expression data from lung-resident Th2cells isolated at an early stage (1 week) of allergic airway inflammation.

source_name: Mouse lung at day 29 after OVA-induced allergic airway inflammation


title: Th2 acute inflammation, biological repl 3


title: mucosa next to tumor bottom crypt fraction, px 5

description: gene expression data from MT bottom crypt fraction for px 5


title: Th2 acute inflammation, biological repl 1


title: mucosa next to tumor top crypt fraction, px 5

description: gene expression data from MT top crypt fraction for px 5


title: KOPTK1_dox_2


title: KOPTK1_ctrl_2

value: DMSO


title: KOPTK1_ctrl_1


title: naive CD4+ T cells, biological repl 2

description: Gene expression data from antigen-naive CD4+ T cells isolated from spleen.

source_name: Mouse spleen at day 29 of sham treatment


title: KOPTK1_ctrl_3


title: mucosa bottom crypt, px 6

description: gene expression data from M bottom crypt fraction for px6


title: LOUCY_dox_3


title: naive CD4+ T cells, biological repl 1


title: mucosa top crypt fraction, px 5

description: gene expression data from M top crypt fraction for px5


title: LOUCY_ctrl_2


title: LOUCY_ctrl_3


title: LOUCY_ctrl_1


title: LOUCY_dox_2


title: reChIP_Input_ESC

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Direct sequencing following sonication of x-linked chromatin

growth_protocol: ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for reChIP and ChIP assays.
reChIP and ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: ESC


title: LOUCY_dox_1


title: mucosa top crypt fraction, px 4

description: gene expression data from M top crypt fraction for px 4


title: naive CD4+ T cells, biological repl 3


title: mucosa next to tumor top crypt fraction, px4

description: gene expression data from MT top crypt fraction for px 4


title: reChIP_H4K20me3+H3K4me3_ESC

description: GAWSU27-TTAGGC-shLuc-ESC-H4K20me3-H3K4me3-reChIP

source_name: Sequential chromatin IP against H3K4me3

tag: antibody

value: Anti-H4K20me3 antibody (Millipore; 07-463), Anti-H3K4me3 antibody (Millipore; 17-614)


title: mucosa next to tumor top crypt fraction, px3

description: gene expression data from MT top crypt fraction for px 3


title: mucosa bottom crypt, px 4

description: gene expression data from M bottom crypt fraction for px 4


title: reChIP_H3K4me3+H4K20me3_ESC

description: GAWSU28-TGACCA-shLuc-ESC-H3K4me3-H4K20me3-reChIP

value: Anti-H3K4me3 antibody (Millipore; 17-614), Anti-H4K20me3 antibody (Millipore; 07-463)


title: C57BL/6 mice 3 days post infection with Salmonella and treated with Bacillus clausii vs reference

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

country: India

institute: National Institute of Science Education and Research Bhubaneswar

description: Common reference for all test groups

hyb_protocol: 825 ng each of test and reference Cy dye  labeled RNA was mixed together and was fragmented using Agilent fragmentation kit in the presence of blocking reagent for 30 minutes in 60 degree celsius. Equal volume of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture to stop the reaction. 100 μl of the mixture was added to each of the chamber of the hybridization gasket and the array slide was sandwitched over it. The hybridization reaction was done for 17 hours in 65 degree celsius with moist condition in a hybridization oven.

scan_protocol: Scanned on an Agilent G2505C scanner using Agilent Scan control (version 8.3.1.1). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Gut wall tissue from distal ileum and proximal colon

label_protocol: 500 ng of total RNA were primed with 1.2 µl (3rd dilution) of  T7 promoter primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of MMLV Rtase. The c-DNA was then transcribed by T7 RNA Polymerase in the presence of NTPs and labeled with Cy3-CTP (For Rererence) and Cy5-CTP (For test).

growth_protocol: Mice were grown in the animal house facility of the Institute of life science, Bhubaneswar. Mice were fed with normal Chow, filtered water and grown in 12 h light and 12 h dark period. The average room temperature was maintained at 24 degree celsius and humidity of 60-70%.

extract_protocol: Total RNA extracted using Qiagen RNEasy mini kit following manufacturer's instructions

value: gut wall from distal ileum and proximal colon

tag: Sex

value: male

tag: strain

tag: age

value: 7 weeks

source_name: pooled whole mouse gut wall tissue from all the test groups (Reference)

value: C57BL/6 and BALB/c


title: mucosa next to tumor bottom crypt fraction, px3

description: gene expression data from MT bottom crypt fraction for px 3

value: colonic mucosa next to tumor


title: mucosa next to tumor bottom crypt fraction, px 2

description: gene expression data from MT bottom crypt fraction for px 2


title: mucosa bottom crypt, px 3

description: gene expression data from M bottom crypt fraction for px 3


title: mucosa next to tumor bottom crypt fraction, px 4

description: gene expression data from MT bottom crypt fraction for px 4


title: C57BL/6 mice 3 days post treatment with Bacillus clausii vs reference

description: Common reference for all test groups


title: C57BL/6 mice 3 days post treatment with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: mucosa top crypt fraction, px 3

description: gene expression data from M top crypt fraction for px 3


title: C57BL/6 mice 5 days post treatment with Bacillus clausii vs reference

description: Common reference for all test groups


title: C57BL/6 mice 5 days post infection with Salmonella and treated with Bacillus clausii vs reference

description: Common reference for all test groups


title: C57BL/6 mice 10 days post infection with Salmonella and treated with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: C57BL/6 mice 5 days post infection with Salmonella vs reference

description: Common reference for all test groups


title: C57BL/6 mice 5 days post treatment with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: mucosa bottom crypt, px 5

description: gene expression data from M bottom crypt fraction for px 5


title: mucosa bottom crypt, px 2

description: gene expression data from M bottom crypt fraction for px 2


title: mucosa top crypt fraction, px2

description: gene expression data from M top crypt fraction for px 2


title: mucosa next to tumor top crypt fraction, px2

description: gene expression data from MT top crypt fraction for px 2


title: C57BL/6 mice 3 days post no treatment (NT) vs reference

description: Common reference for all test groups


title: C57BL/6 mice 3 days post infection with Salmonella and treated with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: mucosa next to tumor bottom crypt fraction, px 1

description: gene expression data from MT bottom crypt fraction for px 1


title: C57BL/6 mice 3 days post infection with Salmonella vs reference

description: Common reference for all test groups


title: C57BL/6 mice 5 days post infection with Salmonella and treated with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: BALB/c mice 5 days post treatment with Bacillus clausii vs reference

description: Common reference for all test groups

value: BALB/c


title: Identification of si-AP1S3_2 target genes in MDA-MB-231

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

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

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

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

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: breast cancer

tag: transfection

value: no transfection

source_name: si-AP1S3_2 transfected cell line


title: Identification of si-RACGAP_3 target genes in SW1990

value: pancreatic cancer

source_name: si-RACGAP_3 transfected cell line


title: mucosa bottom crypt, px 1

description: gene expression data from M bottom crypt fraction for px 1


title: BALB/c mice 3 days post treatment with Bacillus clausii vs reference

description: Common reference for all test groups


title: mucosa next to tumor top crypt fraction, px 1

description: gene expression data from MT top crypt fraction for px 1


title: BALB/c mice 3 days post infection with Salmonella and treated with Bacillus clausii vs reference

description: Common reference for all test groups


title: mucosa top crypt fraction, px 1

description: gene expression data from M top crypt fraction for px 1


title: SRSF2 P95H RNA-seq uninduced

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

description:
RNA-seq from HEL cells stably expressing mutant SRSF2 (P95H), uninduced
SRSF2_RNAseq_counts.txt

data_processing:
HITS-CLIP: adapter removal and collapse of duplicate reads were performed with FASTX-Toolkit (0.0.14). Reads were aligned to the human genome (GRCh38.p3) with Tophat (version 2.0.14), using the Gencode 23 transcript annotation as transcriptome guide. Candidate binding sites were collected from genomic positions with at least 1 crosslinking induced deletion and coverage in at least two of the four replicates. Differential analysis of WT vs P95H binding sites was performed with edgeR.  RNA-seq: read pairs were aligned to the human genome (GRCh38.p3) with STAR (version 2.5.3a, --quantMode GeneCounts), using the Gencode 23 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR package. Alternative splicing analysis was performed with rMATS.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: SRSF2_differential_RNA_interactome.txt: tab-delimited text file of SRSF2 differentially bound exonic RNA regions (P95H vs WT). The file contains the genomic coordinates (columns 1-4), differential binding analysis (columns 5-7) and annotation of the regions.  SRSF2_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-7) and sample-specific counts of aligned reads.

source_name: Human Erythroleukemia Cell Line (HEL)

growth_protocol: RPMI 10% FBS

extract_protocol:
HITS-CLIP: cells were UV-crosslinked (400mJ, Stratalinker 2400, Stratagene). RNA–protein complexes were immunoprecipitated with anti-Flag M2 Agarose beads (Sigma). RNA was partially digested with RNase A (Affymetrix) and P32-labeled (Perkin Elmer). SRSF2-RNA complexes were isolated by SDS-PAGE, treated with proteinase K, followed by RNA linker ligation.   RNA_seq: QIAGEN RNeasy minikit protocol
HITS-CLIP: Ilumina small RNA library protocol for linker ligation.   RNA-seq: rRNA depletion

treatment_protocol: uninduced cells

tag: sequencing method

value: RNA-seq

tag: stable transfection

value: SRSF2 P95H uninduced


title: BALB/c mice 5 days post treatment with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: Th2 chronic inflammation, biological repl 1

description: Gene expression data from lung-resident Th2cells isolated after 12 weeks of allergic airway inflammation.

data_processing: The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de). After the normalization by Robust Multi-array Average (RMA) and the application of moderate t-statitsics via the limma package, Transcript Cluster IDs that match that do not match to a gene or to multiple genes were discarded. Then, a standard deviation is calculated across samples. For a gene that matches to multiple Transcript Cluster IDs, the Transcript Cluster ID with the highest standard deviation was kept for further analysis.


title: SRSF2 P95H RNA-seq rep 2

description:
RNA-seq from HEL cells stably expressing mutant SRSF2 (P95H), biological replicate 2
SRSF2_RNAseq_counts.txt

treatment_protocol: Doxycycline 1mcg/ml x 48 hours

value: SRSF2 P95H


title: Th2 chronic inflammation, biological repl 3


title: Th2 chronic inflammation, biological repl 2


title: Identification of si-TNS4_3 target genes in A549

value: lung cancer

source_name: si-TNS4_3 transfected cell line


title: Identification of si-NCS1_1 target genes in SK-MES

value: SK-MES

source_name: si-NCS1_1 transfected cell line


title: Identification of si-AP1S3_1 target genes in MDA-MB-231

source_name: si-AP1S3_1 transfected cell line


title: KOPTK1_dox_1

value: T-ALL

value: DOX (induced shJDP2)


title: Th2 acute inflammation, biological repl 3

description: Gene expression data from lung-resident Th2cells isolated at an early stage (1 week) of allergic airway inflammation.


title: Identification of si-RACGAP_1 target genes in SW1990

source_name: si-RACGAP_1 transfected cell line


title: Identification of si-TNS4_2 target genes in A549

source_name: si-TNS4_2 transfected cell line


title: BALB/c mice 10 days post infection with Salmonella and treated with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: BALB/c mice 5 days post infection with Salmonella and treated with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: BALB/c mice 5 days post infection with Salmonella vs reference

description: Common reference for all test groups


title: SRSF2 P95H RNA-seq rep 1

description:
RNA-seq from HEL cells stably expressing mutant SRSF2 (P95H), biological replicate 1
SRSF2_RNAseq_counts.txt


title: Th2 acute inflammation, biological repl 2


title: SRSF2 WT RNA-seq rep 2

description:
RNA-seq from HEL cells stably expressing wild type SRSF2, biological replicate 2
SRSF2_RNAseq_counts.txt

value: SRSF2 wild type


title: BALB/c mice 5 days post no treatment (NT) vs reference

description: Common reference for all test groups

value: gut wall from distal ileum and proximal colon


title: BALB/c mice 5 days post infection with Salmonella and treated with Bacillus clausii vs reference

description: Common reference for all test groups

value: male


title: SRSF2 WT RNA-seq rep 1

description:
RNA-seq from HEL cells stably expressing wild type SRSF2, biological replicate 1
SRSF2_RNAseq_counts.txt


title: H1299 +Dox ChIP DNA

status: Public on Jun 17 2018

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare Control and Treatment ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.5
Genome_build: hg19
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-7 to identify BRG1 enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: H1299 Cell line

growth_protocol: H1299 cells were maintained in 10% FBS and pen/strep supplemented RPMI-1640 media

extract_protocol:
Histone-DNA complexes were isolated using antibodies described from -DOX and +DOX H1299 sonicated nuclei.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

treatment_protocol: pINDUCER20-SMARCA4 viral vector stably transduced in H1299 cell lines. Cells were then selected using G418 (0.4mg/ml). SMARCA4 induced using doxycycline (0.5microgram/ml) for 5 days and cells also treated with IACS-10759 (1000nM) for 24 hours prior to extraction

value: Human mammary epithelial cell line

tag: chip-antibody

value: Brg1 antibody Abcam ab110641


title: Th2 acute inflammation, biological repl 1


title: H1299 -Dox input

value: Input


title: H1299 +Dox input


title: 72h reduced - replicate 3

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
The original samples contained R2 to read inner barcodes and unique molelcular identifiers.
Base calling was performed with bcl2fastq (2.17).
Samples were demultiplexed using internal barcodes.
Reads were mapped to the yeast (sacCer3) genome using  bowtie2 default parameters.
Duplicated reads were filtered using UMI, to remove PCR bias.
To estimate the expression level of each gene we counted the number of reads that  mapped to the 3’ end of the gene (from 350bp upstream to 200bp downstream of  TTS). The read counts in each sample were normalized to PPM.
Genome_build: sacCer3
Supplementary_files_format_and_content: A table containing the normalized read counts for each yeast gene in each one of the 12 samples.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

extract_protocol:
Cells were incubated with Proteinase K (Epicentre MPRK092) and 1% SDS at  70 o C to release the RNA. Cell debris was precipitated by centrifugation in the  presence of KOAc precipitation solution. Finally, the RNA was purified from the  supernatant using nucleic acid binding plates (UNIFILTER plates, catalog #7700-  2810) and was stored with RNAse-inhibitor (Murine #M0314L) at -80°C.
Total RNA (~20ng per sample) was incubated with oligo-dT RT primers with a  7bp barcode and a 8bp UMI (Unique Molecular Identifier) at 72oC for 3 minutes  and transferred immediately to ice. RT reaction was performed with SmartScribe  enzyme (TaKaRa Lot# 1604343A) at 42°C for one hour followed by incubation at  70°C for 15 minutes. Barcoded samples were then pooled and purified using  SPRI beads X1.2 (AMPure XP). DNA-RNA molecules were tagmented using Tn5  transposase (loaded with oligo  TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG) and 0.2% SDS was used to  strip off the Tn5 from the DNA, followed by a SPRI X2 clean up. NGS sequences  were added to the tagmented DNA by PCR (KAPA HiFi HotStart ReadyMix 2X  (KAPA Biosystems KM2605), 12 cycles). Finally, DNA was purified using X0.65    SPRI beads followed by X0.8 SPRI beads. The library was sequenced using  Illumina NextSeq-500 sequencer.

tag: chronological age

tag: oxidation status

value: reduced


title: H1299 -Dox ChIP DNA


title: 72h reduced - replicate 2


title: THP1 SAMHD1 KO 1

city: Columbus

first: Serena

last: Bonifati

state: Ohio

address: 1900 Coffey Road

department: Veterinary Biosciences

institute: Ohio State University College of Veterinary Medicine

description: Replicate #1

hyb_protocol: Experiment performed at: Genomic Core Facility, The Ohio State University, Columbus, Ohio, USA.

data_processing: The data were normalized by RMA method with Affymetrix Expression Console software. Normalized data were filtered by keeping genes whose expression are above 6 (log2 scale) for at least 2 out of 3 samples in any condition. Linear model and moderated t-test was used for testing differentially expressed genes by using SAS and R packages.

source_name: Generated by using a CRISPR-Cas9 lentiviral vector expressing gRNA specific for SAMHD1

growth_protocol: Cells were grown in RPMI 1640 (ATCC) supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin and 1 μg/ml puromycin. 500,000 cells/well were seeded in 12-well plate in 1 ml/well, and harvested after 48 hours. Three replicates were prepared for each cell line.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen)

value: Patient-derived acute myeloid leukemia cells

tag: genotype/variation

value: SAMHD1 KO


title: THP1 SAMHD1 KO 3

description: Replicate #3

scan_protocol: Experiment performed at: Genomic Core Facility, The Ohio State University, Columbus, Ohio, USA.


title: BALB/c mice 3 days post treatment with Lactobacillus acidophilus vs reference

description: Common reference for all test groups

tag: tissue

value: BALB/c

value: 7 weeks

value: C57BL/6 and BALB/c


title: THP1 SAMHD1 KO 2

description: Replicate #2

label_protocol: Experiment performed at: Genomic Core Facility, The Ohio State University, Columbus, Ohio, USA.

tag: cell line


title: Identification of si-NCS1_3 target genes in SK-MES

value: no transfection

source_name: si-NCS1_3 transfected cell line


title: naive CD4+ T cells, biological repl 3

description: Gene expression data from antigen-naive CD4+ T cells isolated from spleen.

source_name: Mouse spleen at day 29 of sham treatment

tag: cell


title: 72h reduced - replicate 1


title: BALB/c mice 3 days post infection with Salmonella and treated with Lactobacillus acidophilus vs reference

description: Common reference for all test groups


title: BALB/c mice 3 days post infection with Salmonella vs reference

description: Common reference for all test groups


title: naive CD4+ T cells, biological repl 1


title: 72h oxidized - replicate 1

value: oxidized


title: 72h oxidized - replicate 3


title: 72h oxidized - replicate 2


title: 48h reduced - replicate 3


title: naive CD4+ T cells, biological repl 2


title: THP1 control 1

description: Replicate #1

source_name: THP-1 expressing endogenous SAMHD1 and transduced with an empty CRISPR-Cas9 vector

tag: cell type

value: control


title: THP1 control 3

description: Replicate #3


title: 48h oxidized - replicate 3


title: 48h oxidized - replicate 2


title: 48h reduced - replicate 1


title: 48h oxidized - replicate 1


title: THP1 control 2

description: Replicate #2


title: 48h reduced - replicate 2


title: WTHD11r

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description: tumor tissue of right kidney of patient WTHD11

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x GE hybridization buffer HI- RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (4x 44K) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) and air dried.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction V11.5.1.1 was used for background subtraction and LOWESS normalization. Control spots are removed, replicate oligos are averaged.

source_name: WTHD11 rumor right kidney

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

extract_protocol: RNA was prepared using the RNAeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations, with an included on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: kidney

tag: gender

value: 4 weeks


title: 12_1299+Dox -Glucose

first: Jennifer

last: Wang

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Standard Affymetrix hybridization protocol applicable to Clariom_S_Human platform

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Expression Console

label: Biotin

source_name: cells grown with 0.5ug/ml doxycycline, media changed to RPMI with No Glucose 24 hours prior to harvest

label_protocol: Biotinylated cRNA were prepared with the  kit for Affymetrix arrays

extract_protocol: RNA was extracted with RNAeasy Kit from Qiagen,Quality control was performed with Agilent Bioanalyser.

value: lung cancer cell line


title: WTHD2r

description: tumor tissue of right kidney of patient WTHD2

source_name: WTHD2 tumor right kidney

tag: treatment

value: 8 weeks chemo (including ADR)


title: Wilms11

description: tumor tissue of patient Wilms11

source_name: Wilms11 tumor

value: female


title: WTHD1l

description: tumor tissue of left kidney of patient WTHD1

source_name: WTHD1 tumor left kidney

value: 8 weeks chemo


title: 07_1299-Dox 100nM 10759

source_name: cells grown with no doxycycline, added 100nM of IACS-10759 for 24 hours, duplicate


title: Wilms8

description: tumor tissue of patient Wilms8

source_name: Wilms8 tumor

value: male

value: more than 7 weeks chemo


title: 11_1299-Dox -Glucose

source_name: cells grown with no doxycycline, media changed to RPMI with No glucose 24 hours prior to harvest


title: 09_1299 Reg -Dox

source_name: cells grown with no doxycycline


title: 10_1299 Reg +Dox

source_name: cells grown with 0.5ug/ml doxycycline


title: 02_H1299+Dox DMSO

source_name: cells grown with 0.5ug/ml doxycycline, added DMSO for 24 hours


title: 03_1299-Dox 100nM 10759

source_name: cells grown with no doxycycline, added 100nM of IACS-10759 for 24 hours


title: 06_1299+Dox DMSO

source_name: cells grown with 0.5ug/ml doxycycline, added DMSO for 24 hours duplicate


title: 05_1299-Dox DMSO

source_name: cells grown with no doxycycline, added DMSO for 24 hours biological duplicate


title: 04_1299+Dox 100nM 10759

source_name: cells grown with 0.5ug/ml doxycycline, added 100nM of IACS-10759 for 24 hours


title: 08_1299+Dox 100nM 10759

source_name: cells grown with 0.5ug/ml doxycycline, added 100nM of IACS-10759 for 24 hours, duplicate


title: Wilms1_2_r

description: tissue from second tumor of patient Wilms1 in right kidney

scan_protocol: Scanned on an Agilent G2505B scanner (batch A) or G2505C scanner (batch B).

data_processing: Scans were quantified using Agilent Feature Extraction Software (batch A: V10.1.1.1; batch B: V10.7.1.1) applying default parameters. Control spots were removed, replicate oligos averaged. Arrays were quantile normalized between chips using R-software (Limma).

source_name: Wilms1 tumor 2 right kidney

value: Wilms tumor kidney

tag: batch

value: B


title: Healthy subject 6

status: Public on Jun 16 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Extracellular vesicles were isolated from serum of a healthy subject. Total RNA was isolated and was subjected to microarray analysis.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

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

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

source_name: Serum extracellular vesicles

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan).

growth_protocol: There are no symptoms of diseases in healthy subjects.

extract_protocol: RNA samples were extracted from cells using miRNeasy mini kit (Qiagen).

treatment_protocol: 5 ml of each serum was isolated from 6 healthy subjects.

tag: disease status

value: Healthy

value: Serum extracellular vesicles


title: Wilms4

description: tumor tissue of patient Wilms4

source_name: Wilms4 tumor

value: A


title: Wilms1_2_l

description: tissue from second tumor of patient Wilms1 in left kidney

source_name: Wilms1 tumor 2 left kidney


title: Wilms3

description: tumor tissue of patient Wilms3

source_name: Wilms3 tumor

value: 4 weeks with actinomycin D + vincristine


title: Wilms1_1_r

description: tissue from first tumor of patient Wilms1 in right kidney

source_name: Wilms1 tumor 1 right kidney


title: Wilms6

description: tumor tissue of patient Wilms6

source_name: Wilms6 tumor

value: overall 8 weeks:4 weeks actinomycin D, vincristine and additionally 4 weeks doxorubicin


title: Wilms1_1_l

description: tissue from first tumor of patient Wilms1 in left kidney

source_name: Wilms1 tumor 1 left kidney


title: Wilms10_Met

description: lung nodule tissue of patient Wilms10

source_name: Wilms10 lung metastasis

value: Wilms tumor lung metastasis

value: NWTSG5 protocol, regimen DD-4A (actinomycin D, vincristine and doxorubicin, additionally radiation therapy, overall 6 months)


title: iPSC_CHMP1A_null_rep2

city: Santa Cruz

first: Ali

middle: S

last: Shariati

state: CA

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

data_processing:
Reads were trimmed using trimmomatic (0.36) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25. Then, reads were mapped using STAR (2.4.0)–outStd SAM–outReadsUnmapped Fastx–chimSegmentMin 18–chimScoreMin 12 and Bowtie2 (2.3.3.1)–local–very-sensitive-local -q–mm, output BAM file per tool were merged. To generate raw read counts per gene: htseq-count (0.6.1p1) -t exon -i exon_id -q. DESeq2 (2.11.39, Galaxy) was used to normalize read counts and do pairwise statistical analysis.
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Tab-delimited text files contain for each sample the raw counts per gene, or DESeq2 normalized counts per gene.

source_name: IMR90 CHMP1A null iPSC 27

growth_protocol: hIPSC were grown in mTeSR1 medium (Stemcell Technologies) on matrigel (Corning) coated plates for routine cell culture. For cortical organoid differentiation, hiPSC colonies were grown on a feeder layer of mouse MEFs MitC treated (35,000 MEFs/cm2) and cultured in W0 medium (DMEM/F12, 20% KOSR, 2mM L-glutamine, 1x NEAA, 1x P/S, 50 µM b-mercaptoethanol (Thermofisher) + 8 ng/ml FGF2 (added fresh daily, Sigma)). After iPSC colonies reached 2-3mm in diameter, they were lifted with a cell scraper and transferred to ultra-low attachment 60mm culture dishes (Corning), containing W0 + 1x sodium pyruvate (Differentiation medium, no FGF2). After 24 hours, initial embryoid bodies are formed and (day 0) 50% of medium was replaced with Differentiation medium + small molecule inhibitors to the following final concentrations: 10 µM SB-431542 (Sigma), 1 µM Dorsomorphin (Sigma), 3 µM IWR-1-Endo (Sigma) and 1 µM Cyclopamine (Sigma). Differentiation medium + small molecules was then replaced every other day. On day 4, 60mm plates containing organoids were placed on a hi/lo rocker inside the incubator. On day 18, medium was replaced with Neurobasal/N2 medium (Neurobasal, 1x N2 supplement, 2 mM L-glutamine, 1x P/S) supplemented with 1 µM Cyclopamine. On day 26 medium was replaced with Neurobasal/N2 medium without cyclopamine.

extract_protocol:
hIPSCs or cerebral organoids were homogenized in TRIzol solution. RNA was isolated according to TRIzol protocol, followed by DNAse I treatment and purified again using spin columns (Zymo)
hIPSC sample libraries were constructed using standard Illumina TruSeq protocol with Ribo-Zero rRNA removal. Cerebral organoid mRNA was isolated from total RNA using polyA selection Dynabeads mRNA DIRECT Micro Purification Kit (Thermofisher). Library was prepared using strand-specific Ion Total RNA-seq Kit v2 (Thermofisher) and Ion Xpress RNA-seq Barcode 1-16 (Thermofisher) to label different samples.

treatment_protocol: Day 35 cerebral organoids were treated 72 hours with DMSO or 1mM SAG. Medium was replaced daily.

value: hiPSC

tag: genotype

value: CHMP1A null


title: Cortical_organoid_day38_CHMP1A_null_SAG_rep1

source_name: Directed differentiation IMR90 CHMP1A null iPSC


title: Cortical_organoid_day38_CHMP1A_null_DMSO_rep1


title: Wilms2

description: tumor tissue of patient Wilms2

source_name: Wilms2 tumor


title: Cortical_organoid_day38_CHMP1A_null_DMSO_rep2


title: Cortical_organoid_day38_WT_SAG_rep2

source_name: Directed differentiation IMR90 iPSC

value: WT


title: Cortical_organoid_day38_CHMP1A_null_SAG_rep2


title: Healthy subject 2


title: Healthy subject 4


title: Healthy subject 5


title: Healthy subject 3


title: Healthy subject 1


title: Cortical_organoid_day38_WT_DMSO_rep2


title: iPSC_WT_rep2

source_name: IMR90 iPSC 30


title: Wilms10

description: tumor tissue of patient Wilms10

source_name: Wilms10 tumor


title: 01_H1299-Dox DMSO

source_name: cells grown with no doxycycline, added DMSO for 24 hours

value: lung cancer cell line


title: Cortical_organoid_day38_WT_SAG_rep1


title: Cortical_organoid_day38_WT_DMSO_rep1


title: Cortical_organoid_day14_CHMP1A_null_rep2


title: WTHD9

description: tumor tissue of patient WTHD9

source_name: WTHD9 tumor

value: kidney

value: 4 weeks


title: Cortical_organoid_day14_WT_rep1


title: Cortical_organoid_day14_WT_rep2


title: Cortical_organoid_day14_CHMP1A_null_rep1


title: SC_PCB_5

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Preprocessing using fastqc
Mapping the reads to the genome using tophat/cufflinks pipeline
Obtaining read counts using featureCount
Differential gene expression using DESeq. Batch was given as a covariate.
Genome_build: Killifish20130322asm.fa and kfish2rae5h_fc17_subupd4.gtf
Supplementary_files_format_and_content: text files containing raw read counts

organism: Fundulus heteroclitus

source_name: Whole Embryos

growth_protocol: F2 generation Killifish embryos from New Bedford Harbor and Scorton Creek were obtained and reared at 23 degrees in fresh seawater.

extract_protocol:
Total RNA from embryos was isolated using BioRad Aurum kit.
Library construction and sequencing were done at Tufts University Core facility. Libraries were prepared using Illumina library preparation kit.

treatment_protocol: At 10 days post-fertilization, Killifish embryos from New Bedford Harbor and Scorton Creek were exposed to either DMSO or PCB153 for 6 hours.

value: Whole Embryos

tag: location

value: Scorton creek, Sandwich MA

tag: developmental stage

value: 10 days post fertilization

tag: generation

value: F2 generation


title: SC_PCB_4


title: SC_PCB_3


title: SC_DMSO_5

value: DMSO


title: Control 3 (CP3) male young

city: Cardiff

first: Timothy

last: Bowen

address: Heath Park

country: United Kingdom

institute: Cardiff University

description: MicroRNA

data_processing:
The expression profiles of miRNAs in urine samples were determined using the Human TaqMan miRNA Arrays A v2.1 (Life Technlogies) following the manufacturer’s recommendations. qPCR was carried out on an Applied Biosystems 7900HT thermo cycler using the manufacturer’s recommended program
Statistical  analysis  Data  were  analyzed  using  DataAssistTM  Software,  NormFinder  Software  and  GraphPadPrism  5  version  5.0a.  The  NormFinder  algorithm was used for  identifying  the  optimal  normalization  gene  among  a  panel  of  putative  reference  genes by ranking  a  set  of  candidate  normalization  genes  according  to  their  expression  stability  in  a  given  sample  incorporated in the  experimental  design.

source_name: Pooled sample group (each group n=5)

extract_protocol:
RNA was isolated from all samples using the miRNeasy kit (Qiagen), according to the manufacturer’s recommendation
MiRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1, Life Technologies) with a predefined pool of up to 381 reverse transcription (RT) primers for each Megaplex Primer Pool. A fixed volume of 3 μl of RNA solution was used as input in each RT reaction. Each RT reaction was performed according to the manufacturer’s recommendations.
The RT reaction products were then amplified using Megaplex PreAmp Primers (Primers A v2.1, Life Technologies), the samples were then diluted to a final volume of 100 μl and then controls and DN products were pooled

value: male

tag: disease state

value: Healthy Control


title: Control 1 (CP1) female mature

description: MicroRNA

value: female


title: SC_DMSO_4


title: iPSC_WT_rep1


title: Patient 4 (PP4) ckd4523-27.3

description: MicroRNA

value: Chronic Kidney Disease; stage 4/5


title: Control 4 (CP4) man mature

description: MicroRNA


title: Patient 3 (PP3) ckd4512.9-22

description: MicroRNA


title: Patient 2 (PP2) ckd36-43.3

description: MicroRNA

value: Chronic Kidney Disease; stage 3


title: Patient 1 (PP1) ckd3135

description: MicroRNA


title: Control 2 (CP2) female young

description: MicroRNA


title: SC_DMSO_3


title: DHL-2-1

city: Guangzhou

first: Weijie

last: Zhong

state: Guangdong

address: Panfu road 1st

country: China

institute: Guangzhou First People's Hospital

description: Gene expression without IL-17A treatment 72hr in SU-DHL-2 cells

hyb_protocol: 1μg of each labeled cRNA was fragmented by adding 11μl 10 × Blocking Agent and 2.2μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned by using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.Quantile normalization and subsequent data processing were performed by using the GeneSpring GX v12.1 software package (Agilent Technologies).
After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: SU-DHL-2 cells without IL-17A for 72hr

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Hilden, Germany). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (Thermo).

growth_protocol: The SU-DHL-2 cell lines were cultured in RPMI 1640 medium containing 10% FBS, 4 mM L-glutamine (Gibco), 100 U/ ml of penicillin, and 100 U/ml of streptomycin.

extract_protocol: the total RNA of each sample was extracted by TRIzol reagent (Takara) following the manufacturer's recommendations.

treatment_protocol: Six samples of SU-DHL-2 cells (2×10^6 cells/ml) co-cultured with or without IL-17A (200pg/ml) for 72hr in vivo. Three samples of SU-DHL-2 cells were all co-cultured with IL-17A , other three samples of SU-DHL-2 cells without IL-17A treatment were used as controls.


title: NBH_PCB_4

value: New Bedford Harbor, Massachusetts


title: NBH_DMSO_5


title: mPFC Drd2+ cell mRNA, technical replicate 2

city: Toronto

first: Martin

last: Beaulieu

state: Ontario

address: 1 king's college circle room 4336

department: Pharmacology and Toxicology

country: Canada

institute: University of Toronto

description:
mRNA isolated from HA immunoprecipitated ribosomes
SAMPLE 2

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol

scan_protocol: Arrays were scanned using Affymetrix GCS 3000 7G and Gene-Chip Command Console Software (AGCC) (Affymetrix) to produce probe cell intensity data (CEL).

data_processing: Data is analysed by TAC4.0 program

source_name: Pool of 5 adult mouse mPFCs, technical replicate 2

label_protocol: RNA was labeled using the Affymetrix GeneChip® WT Plus Reagent  Kit protocol

extract_protocol: RNA is extracted by Trizol from HA immunoprecipitated ribisomes followed by RNA column purification

tag: strain

value: D2Cre::RiboTag mouse

tag: age

value: adult

value: medial prefrontal cortex

value: Drd2+ neurons


title: DHL-2-2

scan_protocol: The hybridized arrays were washed, fixed and scanned by using the Agilent DNA Microarray Scanner (part number G2505C).


title: DHL-2+IL17A-1

description: Gene expression after IL-17A treatment 72hr in SU-DHL-2 cells

source_name: SU-DHL-2 cells with IL-17A for 72hr

tag: treated with

value: IL-17A (200pg/ml) for 72hr


title: NBH_DMSO_4


title: DHL-2+IL17A-3


title: DHL-2-3


title: SC_DMSO_2


title: DHL-2+IL17A-2


title: mPFC Drd2+ cell mRNA, technical replicate 1

description:
mRNA isolated from HA immunoprecipitated ribosomes
SAMPLE 1

source_name: Pool of 5 adult mouse mPFCs, technical replicate 1


title: SC_DMSO_1


title: SC_PCB_1


title: NBH_PCB_2


title: NBH_PCB_5


title: NBH_PCB_3


title: SC_PCB_2


title: NBH_PCB_1


title: FaDu untreated control

city: Wuerzburg

first: Marianne

last: Schmidt

state: Outside U.S. & Canada

institute: University of Wuerzburg, Dept. of Otorhinolaryngology

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were processed with the Affymetrix Expression Console.

source_name: FaDu hypopharyngeal cell line

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix) with biotin; all steps were performed according to the manufacturers' protocols.

growth_protocol: FaDu cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum and standard antibiotics at 37°C and 5% CO2.

extract_protocol: RNA of FaDu cell cultures was isolated with the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated for 48 hrs with cell culture medium supplemented with 10µg/ml NSC-631570. Controls were incubated with corresponding volume of distilled water or for 48 hrs.

value: FaDu

value: hypopharyngeal cell line

value: untreated


title: FaDu untreated control 2


title: NBH_DMSO_2

value: Whole Embryos

value: 10 days post fertilization


title: C12-ECs

city: Baltimore

first: Sharon

last: Gerecht

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

data_processing: Global normalization was performed using three house-keeping genes (HKG): 18sRNA, GAPDH and ACTB. Normalization was conducted in the Thermo Fisher Cloud software according to the following manuscript: Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3: RESEARCH0034-10.1186/gb-2002-3-7-research0034.  Fold change is reported as 2^-ddCT where -ddCT = -(dCt_test -dCt control).

label: TaqMan

source_name: Human induced pluripotent stem cell derived endothelial cell

label_protocol: PCR assays were performed using a custom PCR assay panel from Thermo Fisher Scientific.  Revere transcription was performed from 1 µg of total RNA.

growth_protocol: hiPSC-ECs were grown in endothelial differentiation media.  BC1 and C12-ECs were grown on collagen IV coating plates, while hiPSC-ECFCs were expanded on collagen I coated surfaces.

extract_protocol: Total RNA was isolated using the TRIzol reagent according to the manufacturer’s instructions.

treatment_protocol: Prior to RNA extraction growth media conditions were switched to serum starvation media (DMEM) for 24 hours.

tag: sample type

value: Test

value: Stem cell derived endothelial cell


title: hiPSC-ECFCs

value: Control


title: BC1-ECs


title: NBH_DMSO_1

tag: tissue

value: DMSO

value: F2 generation


title: Primary hepatocyte-EdTx-6h-rep2

city: El Paso

first: Lihong

last: Wu

state: Texas

address: MSB1, Room 3105,5001 El Paso Drive

department: Department of Biomedical Sciences, Paul L. Foster School of Medicine

institute: Texas Tech University Health Sciences Center El Paso

description: gene expression data from EdTx treated primary hepatocytes

hyb_protocol: Samples were hybridized with GeneChip Mouse Transcriptome Arrays (Affymetrix) and scanned at the UTSW Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with Affymetrix Expression console software for background correction and normalization.

source_name: EdTx treated primary hepatocytes,6h

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT plus reagent kit. (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted according to the manufacturer's instructions of Qiagen Rneasy MiNi Kit.

treatment_protocol: Primary hepatocytes were exposed to 4 µg/ml EdTx for 6 h, with PBS as a negative control.

value: A/J

value: liver

value: primary hepatocytes


title: Primary hepatocyte-EdTx-6h-rep4


title: NBH_DMSO_3

value: New Bedford Harbor, Massachusetts


title: FaDu NSC-631570

tag: cell line


title: Primary hepatocyte-EdTx-6h-rep3


title: Primary hepatocyte-EdTx-6h-rep1


title: Primary hepatocyte-No EdTx-6h-rep3

description: gene expression data from No EdTx treated primary hepatocytes

source_name: No EdTx treated primary hepatocytes,6h


title: Primary hepatocyte-No EdTx-6h-rep1


title: Primary hepatocyte-No EdTx-6h-rep4


title: Primary hepatocyte-No EdTx-6h-rep2


title: Identification of miR-140-5p target genes in T24

status: Public on Jun 15 2018

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

value: bladder cancer

tag: transfection

value: no transfection

source_name: miR-140-5p transfected cell line


title: Differentially expressed genes by knocking down of PIR-2 in PC3

tag: cell type

value: prostate cancer

source_name: si-PIR-2 transfected cell line


title: Identification of miR-130-3p target genes in PANC1

value: pancreatic cancer

source_name: miR-130-3p transfected cell line


title: Identification of miR-144-3p target genes in SK-MES-1

value: lung squamous cell carcinoma

source_name: miR-144-3p transfected cell line


title: Identification of miR-204-5p target genes in MDA-MB-231

value: breast cancer

source_name: miR-204-5p transfected cell line


title: Differentially expressed genes by knocking down of PIR-3 in PC3

source_name: si-PIR-3 transfected cell line


title: siRNA_a_72h_rep2

city: Beijing

first: Jiao

last: Yuan

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Biological replicate 2 of 3

hyb_protocol: According to the Agilent lncRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images. The signal ratio of Cy5 intensity and Cy3 intensity on the same array was subjected to quantile normalization.

source_name: cells cultured in vitro untreated

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent lncRNA microarray, according to manufacturer's protocol.

growth_protocol: Human cells L02 were cultured in RPMI 1640 Medium (ATCC Modification), supplemented with 10% (v/v) FBS.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

source_name: cells cultured in vitro siRNA-a treated with 72h post induction


title: siRNA_b_72h_rep2

description: Biological replicate 2 of 3

source_name: cells cultured in vitro siRNA-b treated with 72h post induction


title: siRNA_a_72h_rep3

description: Biological replicate 3 of 3


title: Identification of bisamide24H target genes in PC3

first: Naohiko

last: Seki

institute: Chiba University

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

source_name: bisamide24H transfected cell line


title: Identification of miR-532-5p target genes in 786-O

value: renal cancer

source_name: miR-532-5p transfected cell line


title: WTHD6

description: tumor tissue of patient WTHD6

source_name: WTHD6 tumor

value: kidney

tag: gender

value: female

value: 4 weeks


title: siRNA_b_72h_rep1

description: Biological replicate 1 of 3


title: Identification of miR-130-5p target genes in PANC1

source_name: miR-130-5p transfected cell line


title: Identification of miR-144-5p target genes in SK-MES-1

source_name: miR-144-5p transfected cell line


title: Identification of miR-199-3p target genes in C4-2

source_name: miR-199-3p transfected cell line


title: Identification of miR-532-3p target genes in 786-O

source_name: miR-532-3p transfected cell line


title: Identification of miR-140-3p target genes in T24

source_name: mock

source_name: miR-140-3p transfected cell line


title: siRNA_b_72h_rep3

description: Biological replicate 3 of 3


title: Identification of miR-125b-1-3p target genes in PC3

source_name: miR-125b-1-3p transfected cell line


title: Identification of bisamide48H target genes in PC3

source_name: bisamide48H transfected cell line


title: Identification of miR-204-5p target genes in SW1990

source_name: miR-204-5p ransfected cell line


title: siRNA_a_72h_rep1

description: Biological replicate 1 of 3


title: siRNA_b_48h_rep3

description: Biological replicate 3 of 3

source_name: cells cultured in vitro siRNA-b treated with 48h post induction


title: siRNA_a_48h_rep2

description: Biological replicate 2 of 3

source_name: cells cultured in vitro siRNA-a treated with 48h post induction


title: siRNA_b_48h_rep2

description: Biological replicate 2 of 3

source_name: cells cultured in vitro untreated


title: siRNA_b_48h_rep1

description: Biological replicate 1 of 3


title: Sample 2- Biopsy 2h DMEM

city: Boston

first: Alessio

last: Fasano

address: 114 16th Street

institute: Massachusetts General Hospital

description:
Terminal Ileum Biopsy
Human_vs_Human_Typhi de_genes

data_processing:
The reads generated for each RNA sample were analyzed using an Ergatis-based RNA-Seq analysis pipeline
Quality control of the sequences was performed using FastQC (version 0.10.0)
Human sequencing reads were aligned to the Homo sapiens reference genome GRCh38.78 using TopHat (version 2.1.1). Bacterial reads were aligned to Salmonella enterica serovar Typhi strain Ty2 genome (NCBI Reference Sequence: NC_004631.1) using Bowtie (version 0.12.9). The number of reads that aligned to the predicted coding regions were determined using HTSeq (version 0.4.7) [5]. Differential gene expression was analyzed using DESeq (version 1.5.24)
Genome_build: Homo sapiens reference genome GRCh38.78, Salmonella enterica serovar Typhi strain Ty2 genome (NCBI Reference Sequence: NC_004631.1)

source_name: Tissue Biopsy

extract_protocol:
Zymo Direct-Zol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: uninfected tissue biopsy

value: human intestine ileum


title: Sample 1- Biopsy 2h DMEM


title: HC3_R1_001.fastq.gz - Biopsy 2h DMEM


title: Sample 3- Biopsy 2h DMEM


title: siRNA_b_24h_rep2

description: Biological replicate 2 of 3

source_name: cells cultured in vitro siRNA-b treated with 24h post induction


title: St_C_4W_43_153

city: Nottingham

first: Hernan

middle: Pablo

last: Fainberg

address: Derby Rd

department: Division of Child Health, Obstetrics & Gynaecology

institute: The University of Nottingham

description: Gene expression data from EAT age group 40 days to 1 year old

hyb_protocol: 10 μg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Detection used a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The raw image files (.DAT files) were analyzed using Affymetrix GeneChip Operating Software to generate .CEL files.Normalization and network analysis was performed, unless otherwise stated, using free and open source packages, from the R project (http://cran.r-project.org/). The open source Bioconductor community (http://www.bioconductor.org/), provides specific resources for microarray analysis including the Human Genome U133A plus 2 arrays (Affymetrix). We used the function “gcrma” embedded in the “affy” package for pre-processing data stages, including background correction, normalization and probe match verification.

organism: Ovis aries

source_name: Sternal adipose tissue 4 week

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A sample of each adipose depot (approximately 5 grams) was collected during the dissection as a part of the standard dissection procedure.

extract_protocol: 100-1000 mg of adipose tissue biopsies were dissected for analysis into 2ml of TRI® reagent (Sigma Chemical Co. Poole, UK). Total RNA was extracted using RNeasy Plus® kit (Qiagen, West Sussex, UK) according to the manufacturer’s instructions.

treatment_protocol: One (sex-matched) twin from each mother was randomly assigned to be humanely euthanased at 7 and 28 days and adipose tissues sampled from the epicardial, perirenal, sternal, subcutaneous and omental depots. Tissues were quickly dissected and weighed before being sectioned and snap frozen in liquid nitrogen for storage at −80°C.

value: Sternal adipose tissue

value: 28 days old


title: St_C_4W_44_155


title: Su_C_4W_25_155

source_name: Subcutaneous adipose tissue 4 week

value: Subcutaneous adipose tissue


title: siRNA_a_48h_rep1

description: Biological replicate 1 of 3


title: siRNA_b_24h_rep3

description: Biological replicate 3 of 3


title: Su_C_4W_24_153


title: St_C_4W_45_159


title: St_C_4W_42_146


title: Su_C_4W_23_146


title: Su_C_4W_21_136


title: NC

city: Jinan

first: Bo

middle: duan

last: Shi

address: Jinan wenhua xi road 44#

institute: Shandong university

description: Gene expression 48hr after negative control plasmids being transfected in human gastric cancer cells

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in Agilent hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - Agilent  Technologies,Inc. Waldbronn, Germany). Following hybridization, washing was performed using the  Agilent Wash Buffer kit ( Agilent  Technologies,Inc. Waldbronn, Germany). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into Agilent software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the  Agilent software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the Agilent Gene Expression Analysis protocol ( Agilent  Technologies,Inc. Waldbronn, Germany). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the epicentreTargetAmp 1-round aRNA amplification kit  was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol ( Agilent  Technologies,Inc. Waldbronn, Germany). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: BGC823/NC cells were cultrued with RPMI1640 medium and then transfected with PcDNA3,1-empty plasmids for 48h as negative control.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: BGC823/SPIN4 and BGC823/GAGE12I cells were cultrued with RPMI1640 medium and then transfected with PcDNA3,1-SPIN4 and  PcDNA3,1-GAGE12I for 48h for overexpressing SPIN4 and GAGE12I.

tag: differentiation

value: poorly differentiated


title: PrR_C_4W_33_153

source_name: Perirenal adipose tissue 4 week

value: Perirenal adipose tissue


title: siRNA_a_24h_rep3

description: Biological replicate 3 of 3

source_name: cells cultured in vitro siRNA-a treated with 24h post induction


title: GAGE12I

description: Gene expression 48hr after GAGE12I being overexpressed in human gastric cancer cells


title: Su_C_4W_22_141


title: siRNA_b_24h_rep1

description: Biological replicate 1 of 3


title: siRNA_a_24h_rep2

description: Biological replicate 2 of 3


title: PrR_C_4W_34_155


title: siRNA_a_24h_rep1

description: Biological replicate 1 of 3


title: ANS2

description: tumor tissue of patient ANS2

data_processing: Agilent Feature Extraction V11.5.1.1 was used for background subtraction and LOWESS normalization. Control spots are removed, replicate oligos are averaged.

source_name: ANS2 tumor

value: male

tag: treatment


title: siRNA_a_48h_rep3

description: Biological replicate 3 of 3


title: PrR_C_4W_35_150


title: St_C_4W_41_141


title: PrR_C_4W_32_146


title: SPIN4

description: Gene expression 48hr after SPIN4 being overexpressed in human gastric cancer cells


title: OM_C_4W_15_159

source_name: Omental adipose tissue 4 week

value: Omental adipose tissue


title: OM_C_4W_14_155


title: PrR_C_4W_31_141


title: Su_C_1W_110_126

source_name: Subcutaneous adipose tissue 1 week

value: 7 days old


title: EpC_C_4W_05_159

source_name: Epicardial adipose tissue 4 week

value: Epicardial adipose tissue


title: OM_C_4W_12_146


title: Su_C_1W_111_130


title: EpC_C_4W_04_155


title: EpC_C_4W_01_141


title: EpC_C_4W_02_146


title: OM_C_4W_13_153


title: Su_C_1W_108_105


title: OM_C_4W_11_141


title: Su_C_1W_114_122


title: PrR_C_1W_67_115

source_name: Perirenal adipose tissue 1 week


title: St_C_1W_81_130

source_name: Sternal adipose tissue 1 week


title: St_C_1W_79_117


title: St_C_1W_82_109


title: St_C_1W_80_126


title: EpC_C_4W_03_151


title: PrR_C_1W_66_109


title: PrR_C_1W_63_105


title: OM_C_1W_98_115

source_name: Omental adipose tissue 1 week


title: PrR_C_1W_64_117


title: OM_C_1W_96_130


title: PrR_C_1W_65_130


title: OM_C_1W_94_117


title: St_C_1W_84_122


title: EpC_C_1W_37_115

source_name: Epicardial adipose tissue 1 week


title: EpC_C_1W_38_122


title: OM_C_1W_93_105


title: iPSC_CHMP1A_null_rep1

source_name: IMR90 CHMP1A null iPSC 27

value: hiPSC

tag: genotype

value: CHMP1A null


title: EpC_C_1W_32_105


title: 9008_SGC_L_1 Lesional before treatment

city: Sophia Antipolis

first: CORINNE

last: MENIGOT

address: 2400 route des colles

country: France

institute: GALDERMA R & D

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Expression Console (Affymetrix) with RMA normalization.

source_name: Human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA).

extract_protocol: RNeasy Micro Kit_Qiagen RNA extraction was performed according to the manufacturer's instructions.

value: Whole skin

value: Lesional before treatment


title: 9008_SGC_PL_1 peri lesional before treatment

value: peri lesional before treatment


title: EpC_C_1W_35_130


title: 9008_SGC_L_18 Lesional after treatment

value: Lesional after treatment


title: 9006_J-G_L_1 Lesional before treatment


title: 9005_N-S_PL_1 peri lesional before treatment


title: 9006_J-G_H_1 Healthy

value: Healthy


title: 9007_D-H_H_1 Healthy


title: 9007_D-H_PL_1 peri lesional before treatment


title: 9006_J-G_PL_18 peri lesional after treatment

value: peri lesional after treatment


title: 9007_D-H_L_18 Lesional after treatment


title: 9006_J-G_PL_1 peri lesional before treatment


title: 9003_SAJ_PL_18 peri lesional after treatment


title: 9008_SGC_H_1 Healthy


title: 9007_D-H_PL_18 peri lesional after treatment


title: 9007_D-H_L_1 Lesional before treatment


title: 9005_N-S_H_1 Healthy


title: 9005_N-S_L_1 Lesional before treatment


title: 9006_J-G_L_18 Lesional after treatment


title: 9003_SAJ_PL_1 peri lesional before treatment


title: OM_C_1W_99_122


title: 9005_N-S_PL_18 peri lesional after treatment


title: 9003_SAJ_L_1 Lesional before treatment


title: 9003_SAJ_L_18 Lesional after treatment


title: 9003_SAJ_H_1 Healthy


title: EpC_C_1W_33_117


title: 9008_SGC_PL_18 peri lesional after treatment


title: 9002_M-G_L_18 Lesional after treatment


title: 9002_M-G_PL_18 peri lesional after treatment


title: 9002_M-G_PL_1 peri lesional before treatment


title: 9005_N-S_L_18 Lesional after treatment


title: 9001_LMD_PL_18 peri lesional after treatment


title: 9002_M-G_H_1 Healthy


title: 9001_LMD_L_18 Lesional after treatment


title: PV_504_AG2

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

institute: Roskilde Hospital

description: Gene expression data from patients with Polycythemia Vera (PV)

hyb_protocol: Fragmented aRNA was hybridized to Affymetrix HG-U133 Plus 2.0 chips

scan_protocol: The micorarrays were scanned with the Affymetrix GeneChip Scanner 3000-7G

data_processing: Data were analyzed in R using rma. The regularized t-test limma for pairwise data was used to calculate differences in gene expression between patients before and after treatment with IFN-alpha2.

source_name: Whole blood

label_protocol: total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

extract_protocol: Total RNA was extracted from whole-blood using the Paxgene Blood RNA Kit

value: PV

value: Whole blood


title: 9001_LMD_L_1 Lesional before treatment


title: PV_497_Y2


title: PV_405_Z2


title: PV_490_AD2


title: PV_467_T2


title: PV_507_AC2


title: 9001_LMD_H_1 Healthy


title: PV_510_AH2


title: PV_357_U2


title: PV_417_X2


title: 9002_M-G_L_1 Lesional before treatment


title: PV_373_M2


title: 9001_LMD_PL_1 peri lesional before treatment


title: PV_338_L2


title: PV_385_S2


title: PV_482_I2


title: PV_356_Q2


title: PV_319_P2


title: PV_330_R2


title: PMF_496_AE2

description: Gene expression data from patients with Primary Myelofibrosis (PMF)

value: PMF


title: PMF_369_AA2


title: PV_314_O2


title: ET_267_H2

description: Gene expression data from patients with Essentiel Thrombocythemia

value: ET


title: PV_275_K2


title: ET_246_E2


title: PV_316_B2


title: ET_255_C2


title: PV_328_F2


title: ET_252_A2


title: PV_250_D2


title: ET_470_AF2


title: ET_414_AB2


title: PMF_295_J2


title: ET_347_N2


title: PMF_450_V2


city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

description: Gene expression data from NHEK_080730 SM exposure 50 uM_16h timepoint

hyb_protocol: Spike controls were added to 15 µg fragmented cRNA before hybridization (36h) using 10 µg of cRNA.  Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Affymetrix GeneChip Scanner.

scan_protocol: After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. The 3'/5' ratios for GAPDH and B-actin were checked for quality. BioB, BioC, BioD and CreX spike controls were also examined to determine sample quality. All arrays were scaled to a target intensity of 150 using Affymetrix GeneChip Operating System (GCOS) software.

data_processing: Raw signal intensities were imported into Partek Genomics Solutions v6.5 (Partek, St. Louis, MO) and normalized using the robust multi-array averaging (RMA) algorithm.

label_protocol: Total RNA was processed for hybridization to GeneChip® Human Genome U133 Plus 2.0 oligonucleotide arrays (Affymetrix, Inc., Santa Clara, CA) using the BioArray Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Inc., Farmingdale, NY).  In brief, 10 µg of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer.  After second strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP for cRNA amplification.

growth_protocol: Normal human epidermal keratinocytes (NHEK) (Lonza, Walkersville, MD) were seeded at a density of 1.2 x103 cells per cm2 in 25 cm2 flasks, and grown to approximately 80 % confluency.  Cells were fed 24 hours prior to exposure with appropriate amount of media for final exposure concentration volume.  Cells were grown at 37◦C with 5% CO2.

extract_protocol: Cell lysates were collected in 400uL 1% beta-mercaptoethanol in RLT lysis buffer and processed through QIAshredder columns (QIAGEN, Valencia, CA) per the manufacturer's instructions.  Total RNA was extracted and DNase I-treated using the RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN) according to the manufacturer’s protocol.  The quantity and quality of the RNA was determined with a NanoDrop ND-1000 UV-vis spectrophotometer (Thermo Scientific, Wilmington, DE) and an Agilent bioanalyzer (Agilent Technologies, Santa Clara, CA) throughout sample processing.

treatment_protocol: On the day of exposure 1M stocks of either mechlorethamine hydrochloride (nitrogen mustard;NM) or 2-chloroethyl ethyl sulfide (CEES) were reconstituted in dimethyl sulphoxide (DMSO). From these stock solutions, 4 mM solutions in KGM Media (Lonza, Walkersville, MD) were made and immediately placed on ice prior to exposure.  A frozen aliquot of neat bis-(2-chloroethyl) sulfide (sulfur mustard;SM) in KGM was thawed and vortexed for 30 sec to generate a 4 mM stock SM solution. This solution was placed on ice immediately after generation prior to exposure.  Cells were exposed to 12.5µM, 25µM, 50uM, 100uM, 200uM, 400uM, 600uM, 800uM, and 1000uM NM or SM.  Cells were exposed to .1mM, .5mM, 1.0mM, 1.5mM, 2.0mM, 2.5mM, 3.0mM, 3.5 and 4.0mM CEES.  Post agent exposure cells were incubated in a chemical fume hood for one hour at 37◦C without CO2, and placed in tissue culture incubator at 37◦C with 5% CO2 for the remainder of the exposure period.  Exposure periods were 1hr, 2hr, 4hr, 8hr, 16hr, and 24hr.  Time matched controls were carried out with each exposure group.

value: primary human epidermal keratinocytes (NHEK)

tag: agent

value: SM

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

value: Qiacube

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

value: Rothwell

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_080813 NM exposure 1000 uM_8h timepoint

tag: cell type

value: NM

value: Manual


description: Gene expression data from NHEK_080730 NM exposure 400 uM_8h timepoint


description: Gene expression data from NHEK_080730 SM exposure 1000 uM_1h timepoint replicate B


description: Gene expression data from NHEK_080730 NM exposure 100 uM_8h timepoint


description: Gene expression data from NHEK_080730 NM exposure 200 uM_2h timepoint


description: Gene expression data from NHEK_080730 NM exposure 25 uM_24h timepoint


description: Gene expression data from NHEK_080730 CEES exposure control 0 uM_16h timepoint

value: CEES


description: Gene expression data from NHEK_080730 CEES exposure 3.5 uM_24h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.0 uM_16h timepoint


description: Gene expression data from NHEK_080730 SM exposure 1000 uM_1h timepoint replicate A


description: Gene expression data from NHEK_080730 CEES exposure 4.0 uM_16h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.5 uM_8h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.0 uM_8h timepoint


description: Gene expression data from NHEK_080730 SM exposure 25 uM_24h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 1.5 uM_24h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.5 uM_16h timepoint


description: Gene expression data from NHEK_080813 SM exposure 600 uM_2h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 2.5 uM_4h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 0.5 uM_4h timepoint

value: Phillips


description: Gene expression data from NHEK_080730 CEES exposure 3.0 uM_4h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.5 uM_4h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 2.0 uM_4h timepoint


description: Gene expression data from NHEK_080730 NM exposure 800 uM_8h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 1.0 uM_4h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 1.5 uM_4h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.5 uM_2h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 4.0 uM_2h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 4.0 uM_1h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.0 uM_2h timepoint


description: Gene expression data from NHEK_080129 SM exposure 100 uM_24h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 2.0 uM_2h timepoint_replicate C


description: Gene expression data from NHEK_080730 CEES exposure 1.5 uM_2h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 2.5 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 600 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 50 uM_24h timepoint


description: Gene expression data from NHEK_080129 SM exposure 25 uM_16h timepoint


description: Gene expression data from NHEK_080129 SM exposure 12.5 uM_16h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 1.0 uM_2h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.0 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 200 uM_16h timepoint


description: Gene expression data from NHEK_080129 SM exposure 200 uM_24h timepoint


description: Gene expression data from NHEK_080129 SM exposure 1000 uM_8h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 3.5 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 400 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 12.5 uM_24h timepoint


description: Gene expression data from NHEK_080129 SM exposure 50 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 200 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 800 uM_4h timepoint

value: Philips


description: Gene expression data from NHEK_080129 SM exposure 12.5 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 800 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 600 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 25 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 1000 uM_4h timepoint


title: ET_273_G2

description: Gene expression data from patients with Essentiel Thrombocythemia

tag: disease state

tag: tissue


description: Gene expression data from NHEK_080129 SM exposure 100 uM_8h timepoint


description: Gene expression data from NHEK_080129 SM exposure 400 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 50 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 12.5 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 100 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 100 uM_2h timepoint


description: Gene expression data from NHEK_080129 SM exposure 200 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 25 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 400 uM_2h timepoint


description: Gene expression data from NHEK_080129 SM exposure 12.5 uM_2h timepoint


description: Gene expression data from NHEK_080129 SM exposure 800 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 200 uM_2h timepoint


description: Gene expression data from NHEK_080129 SM exposure 800 uM_2h timepoint


description: Gene expression data from NHEK_080129 SM exposure 200 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 400 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 50 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 3.0 uM_24h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.5 uM_24h timepoint


description: Gene expression data from NHEK_080129 SM exposure 50 uM_2h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 4.0 uM_24h timepoint


description: Gene expression data from NHEK_080129 SM exposure 25 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 600 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 100 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 3.5 uM_24h timepoint


description: Gene expression data from NHEK_080129 SM exposure 12.5 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.0 uM_24h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.5 uM_16h timepoint

value: Davidson


description: Gene expression data from NHEK_080116 CEES exposure 0.5 uM_24h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.0 uM_24h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.0 uM_16h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.1 uM_24h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.1 uM_16h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.5 uM_8h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 4.0 uM_8h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.5 uM_16h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.0 uM_16h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.5 uM_16h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.0 uM_8h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.5 uM_8h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.5 uM_2h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 4.0 uM_4h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.0 uM_8h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.5 uM_24h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.1 uM_2h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.5 uM_8h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.1 uM_8h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 3.0 uM_4h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 3.5 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.5 uM_2h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 4.0 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 3.0 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.0 uM_2h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.5 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 2.0 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.5 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 0.1 uM_1h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.5 uM_24h timepoint


description: Gene expression data from NHEK_080129 SM exposure 1000 uM_2h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.5 uM_1h timepoint


description: Gene expression data from NHEK_080116 CEES exposure 1.0 uM_1h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.5 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.1 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.0 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.5 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.0 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.5 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.0 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.5 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 4.0 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.0 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.0 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.0 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.5 uM_16h timepoint


description: Gene expression data from NHEK_080730 CEES exposure 0.1 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.5 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 4.0 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.5 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.0 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.1 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.0 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.5 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 4.0 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.5 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.1 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.0 uM_4h timepoint


description: Gene expression data from NHEK_080129 SM exposure 25 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.5 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.0 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 4.0 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 4.0 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.1 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.5 uM_8h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.0 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.5 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.5 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.5 uM_1h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.0 uM_1h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.5 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.0 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 2.0 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.1 uM_1h timepoint


description: Gene expression data from NHEK_080129 SM exposure 600 uM_2h timepoint


description: Gene expression data from NHEK_080129 SM exposure 100 uM_16h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.5 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.5 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.5 uM_4h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 3.5 uM_2h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 1.0 uM_1h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.1 uM_2h timepoint


description: Gene expression data from NHEK_071107 CEES exposure control 0 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 4.0 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 2.5 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 2.0 uM_24h timepoint


description: Gene expression data from NHEK_071128 CEES exposure 0.5 uM_1h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.0 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 2.0 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.5 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 2.5 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 4.0 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure control 0 uM_8h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 3.5 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 0.5 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 3.0 uM_8h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 0.5 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 0.1 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 3.0 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 4.0 uM_8h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.5 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 0.1 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.0 uM_16h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 2.5 uM_8h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 3.5 uM_8h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.0 uM_8h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 2.0 uM_8h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.5 uM_8h timepoint


title: Pig skin_514h_post- sulfur mustard exposure_rep_2

description: Gene expression data for Pig skin, 514h post- sulfur mustard exposure

data_processing: Raw data was imported into Partek Genomic solutions (version 6.3; Partek Inc., St. Louis, MO) and normalized using robust multi-array averaging (RMA).  Normalized data was analyzed using principle component analysis (PCA) to determine the most significant sources of variation.  A two-way analysis of variance (ANOVA) was conducted on this data set using time and treatment as grouping variables.  Hierarchical cluster analysis was performed on genes significantly altered by HD exposure (Top 800 genes FDR p<0.00248).  A Pearson’s (linear) correlation between histopathology score and all microarray probe sets was calculated for the following histopathology scoring criteria: micro vesicle formation, short-term (24-72h) histopathology endpoints, and long term (7d-21d) histopathology endpoints.  A |r| ≥ 0.7 was used as a cutoff to identify genes highly correlated with histopathology scores.  Affymetrix porcine probe IDs were converted to the corresponding human gene accession number using a conversion tool based on the annotation of Tsai and coworkers (Tsai et al., 2010).  The accession number of each highly correlated gene was imported into Ingenuity Pathways Analysis suite (Ingenuity Systems, Inc., Redwood City, CA) to determine interactive canonical pathways correlated with HD-induced histopathology.

organism: Sus scrofa

label_protocol: Total RNA was processed for hybridization to GeneChip® Porcine Genome oligonucleotide arrays (Affymetrix, Inc., Santa Clara, CA) using the BioArray Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Inc., Farmingdale, NY).  In brief, 10 µg of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer.  After second strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP for cRNA amplification.

extract_protocol: Frozen skin biopsy tissue was homogenized in Tri reagent (Sigma-Aldrich Chemical Company, St. Louis, MO).  RNA was extracted according to the manufacturer’s protocol and purified using RNeasy columns (Qiagen, Valencia CA).

treatment_protocol: Female Yorkshire crossbred (SPF) pigs (Country View Farms, Shanksville, PA and Isler Genetics, Prospect, OH) were depiliated prior to exposure on the ventral surface to 400 microliters of neat sulfur mustard for 8 min.  An exposure template was used to obtain four uniform 3 cm skin lesions on the ventral abdomen, two sulfur mustard-exposed lesions and two unexposed controls. Sham animals were prepared for exposure but were not exposed to SM. 8 mm skin punch biopsies were collected in RNAlater (Applied Biosystems/Ambion, Austin, TX) from four animals at each time point (three animals for sulfur mustard exposed and unexposed controls, one animal for sham): 1h, 2h, 4h, 24h, 48h, 72h, 7d, 14d, or 21d post exposure.

value: skin

tag: time (h)

tag: treatment

value: HD

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: pustular epidermitis

tag: epidermal necrosis

tag: vesicle

tag: follicular damage

tag: dermal necrosis

tag: re-epithelialization complete?

tag: epidermal hyperplasia

tag: epidermal/dermal separation

tag: inflammatory cells

tag: hair follicles

tag: glands

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)