title: Pig skin_514h_exposure control_rep_3

description: Gene expression data for Pig skin, 514h exposure control

source_name: Pig skin, 514h exposure control

tag: tissue

tag: time (h)

tag: treatment

value: Control

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: scan date

tag: pustular epidermitis


title: Pig skin_514h_post- sulfur mustard exposure_rep_1

status: Public on Jun 15 2018

type: RNA

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

country: USA

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

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

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 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.

label: biotin

molecule: total RNA

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

value: HD

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)


title: Pig skin_514h_exposure control_rep_2

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: scan date

tag: pustular epidermitis


title: Pig skin_514h_exposure control_rep_1

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


title: Pig skin_514h_post- sulfur mustard exposure_rep_3

source_name: Pig skin, 514h post- sulfur mustard exposure

tag: hair follicles

tag: glands

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_514h_sham

description: Gene expression data for Pig skin, 514h sham

source_name: Pig skin, 514h sham

tag: tissue

tag: time (h)

tag: treatment

value: SHAM

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: scan date

tag: pustular epidermitis


description: Gene expression data from NHEK_071107 CEES exposure 0.5 uM_8h timepoint

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.

organism: Homo sapiens

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.

tag: cell type

value: primary human epidermal keratinocytes (NHEK)

tag: agent

value: CEES

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

value: Manual

tag: rna extraction technician

value: Rothwell

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


description: Gene expression data from NHEK_071107 CEES exposure 0.1 uM_8h timepoint


title: Pig skin_72h_sham

description: Gene expression data for Pig skin, 72h sham

source_name: Pig skin, 72h sham

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

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)


title: Pig skin_72h_exposure control_rep_3

description: Gene expression data for Pig skin, 72h exposure control

source_name: Pig skin, 72h exposure control

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: scan date

tag: pustular epidermitis


title: Pig skin_72h_post- sulfur mustard exposure_rep_3

description: Gene expression data for Pig skin, 72h post- sulfur mustard exposure

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


description: Gene expression data from NHEK_071107 CEES exposure control 0 uM_4h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_72h_exposure control_rep_1

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: scan date

tag: pustular epidermitis

tag: epidermal necrosis

tag: vesicle

tag: follicular damage

tag: dermal necrosis

tag: hair follicles

tag: glands

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


description: Gene expression data from NHEK_071107 CEES exposure 4.0 uM_4h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


description: Gene expression data from NHEK_071107 CEES exposure 2.5 uM_4h timepoint

tag: scan date


description: Gene expression data from NHEK_071107 CEES exposure 3.5 uM_4h timepoint


description: Gene expression data from NHEK_071107 CEES exposure control 0 uM_2h timepoint


title: Pig skin_72h_post- sulfur mustard exposure_rep_1

source_name: Pig skin, 72h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

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


title: Pig skin_72h_post- sulfur mustard exposure_rep_2

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_48h_sham

description: Gene expression data for Pig skin, 48h sham

source_name: Pig skin, 48h sham

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?


title: Pig skin_4h_post- sulfur mustard exposure_rep_3

description: Gene expression data for Pig skin, 4h post- sulfur mustard exposure

tag: epidermal hyperplasia

tag: epidermal/dermal separation

tag: inflammatory cells

tag: hair follicles

tag: glands

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Pig skin_4h_exposure control_rep_1

description: Gene expression data for Pig skin, 4h exposure control

source_name: Pig skin, 4h exposure control

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


description: Gene expression data from NHEK_071107 CEES exposure 1.0 uM_4h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_4h_sham

description: Gene expression data for Pig skin, 4h sham

source_name: Pig skin, 4h sham

tag: tissue

tag: time (h)

tag: treatment

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


title: Pig skin_4h_exposure control_rep_3

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_48h_exposure control_rep_3

description: Gene expression data for Pig skin, 48h exposure control

source_name: Pig skin, 48h exposure control

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?


title: Pig skin_4h_exposure control_rep_2

tag: epidermal hyperplasia

tag: epidermal/dermal separation

tag: inflammatory cells

tag: hair follicles

tag: glands

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Pig skin_72h_exposure control_rep_2

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_4h_post- sulfur mustard exposure_rep_2

source_name: Pig skin, 4h post- sulfur mustard exposure

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?


description: Gene expression data from NHEK_071107 CEES exposure 3.0 uM_2h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


description: Gene expression data from NHEK_071107 CEES exposure 1.5 uM_4h timepoint

tag: scan date


title: Pig skin_4h_post- sulfur mustard exposure_rep_1

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: pustular epidermitis

tag: epidermal necrosis

tag: vesicle

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)


description: Gene expression data from NHEK_071107 CEES exposure 2.0 uM_4h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_071107 CEES exposure 4.0 uM_2h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 3.0 uM_4h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 0.5 uM_4h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 0.1 uM_4h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 3.5 uM_2h timepoint


title: Pig skin_48h_post- sulfur mustard exposure_rep_3

description: Gene expression data for Pig skin, 48h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

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


description: Gene expression data from NHEK_071107 CEES exposure 2.5 uM_2h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_071107 CEES exposure 1.0 uM_2h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.5 uM_2h timepoint


title: Pig skin_48h_exposure control_rep_2

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_48h_post- sulfur mustard exposure_rep_2

source_name: Pig skin, 48h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


description: Gene expression data from NHEK_071107 CEES exposure 2.0 uM_2h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_48h_post- sulfur mustard exposure_rep_1

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_336h_sham

description: Gene expression data for Pig skin, 336h sham

source_name: Pig skin, 336h sham

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Pig skin_336h_exposure control_rep_3

description: Gene expression data for Pig skin, 336h exposure control

source_name: Pig skin, 336h exposure control

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?


description: Gene expression data from NHEK_071107 CEES exposure 0.1 uM_2h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_336h_post- sulfur mustard exposure_rep_3

description: Gene expression data for Pig skin, 336h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: scan date

tag: pustular epidermitis

tag: epidermal necrosis

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)


description: Gene expression data from NHEK_071107 CEES exposure 3.5 uM_1h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


description: Gene expression data from NHEK_071107 CEES exposure 0.5 uM_2h timepoint

tag: scan date


title: Pig skin_48h_exposure control_rep_1

description: Gene expression data for Pig skin, 48h exposure control

tag: tissue

tag: time (h)

tag: treatment

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


description: Gene expression data from NHEK_071107 CEES exposure 4.0 uM_1h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_071107 CEES exposure 2.5 uM_1h timepoint


title: Pig skin_336h_exposure control_rep_2

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_2h_exposure control_rep_3

description: Gene expression data for Pig skin, 2h exposure control

source_name: Pig skin, 2h exposure control

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Pig skin_336h_exposure control_rep_1

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?


title: Pig skin_2h_sham

description: Gene expression data for Pig skin, 2h sham

source_name: Pig skin, 2h sham

tag: epidermal hyperplasia

tag: epidermal/dermal separation

tag: inflammatory cells

tag: hair follicles

tag: glands

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


description: Gene expression data from NHEK_071107 CEES exposure 2.0 uM_1h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_071107 CEES exposure control 0 uM_1h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 3.0 uM_1h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 1.5 uM_1h timepoint


title: Pig skin_336h_post- sulfur mustard exposure_rep_1

source_name: Pig skin, 336h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

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


title: Pig skin_2h_post- sulfur mustard exposure_rep_3

description: Gene expression data for Pig skin, 2h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_2h_post- sulfur mustard exposure_rep_2

source_name: Pig skin, 2h post- sulfur mustard exposure

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?


title: Pig skin_336h_post- sulfur mustard exposure_rep_2

tag: epidermal hyperplasia

tag: epidermal/dermal separation

tag: inflammatory cells

tag: hair follicles

tag: glands

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Pig skin_2h_exposure control_rep_1

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


description: Gene expression data from NHEK_071107 CEES exposure 0.5 uM_1h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


description: Gene expression data from NHEK_071107 CEES exposure 1.0 uM_1h timepoint


description: Gene expression data from NHEK_071003 SM exposure 200 uM_24h timepoint

value: SM

value: Davidson

value: Phillips


title: Pig skin_2h_post- sulfur mustard exposure_rep_1

tag: tissue

tag: time (h)

tag: treatment

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


description: Gene expression data from NHEK_071107 CEES exposure 3.0 uM_24h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


title: Pig skin_24h_sham

description: Gene expression data for Pig skin, 24h sham

source_name: Pig skin, 24h sham

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_2h_exposure control_rep_2

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


description: Gene expression data from NHEK_071003 SM exposure 12.5 uM_24h timepoint

tag: cell type

tag: agent

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

tag: hybridization date

tag: hybridization technician


description: Gene expression data from NHEK_071003 SM exposure 50 uM_24h timepoint


description: Gene expression data from NHEK_071107 CEES exposure 0.1 uM_1h timepoint


description: Gene expression data from NHEK_071003 SM exposure 25 uM_24h timepoint


description: Gene expression data from NHEK_071003 SM exposure 100 uM_24h timepoint


description: Gene expression data from NHEK_071003 SM exposure 200 uM_16h timepoint


description: Gene expression data from NHEK_071003 SM exposure 50 uM_16h timepoint


title: Pig skin_24h_exposure control_rep_2

description: Gene expression data for Pig skin, 24h exposure control

source_name: Pig skin, 24h exposure control

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_24h_post- sulfur mustard exposure_rep_3

description: Gene expression data for Pig skin, 24h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


description: Gene expression data from NHEK_071003 SM exposure 25 uM_16h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_24h_exposure control_rep_1

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_1h_exposure control_rep_3

description: Gene expression data for Pig skin, 1h exposure control

source_name: Pig skin, 1h exposure control

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Pig skin_1h_sham

description: Gene expression data for Pig skin, 1h sham

source_name: Pig skin, 1h sham

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?


title: Pig skin_1h_post- sulfur mustard exposure_rep_2

description: Gene expression data for Pig skin, 1h post- sulfur mustard exposure

tag: epidermal hyperplasia

tag: epidermal/dermal separation

tag: inflammatory cells

tag: hair follicles

tag: glands

tag: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_24h_exposure control_rep_3

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


description: Gene expression data from NHEK_071003 SM exposure 800 uM_8h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_24h_post- sulfur mustard exposure_rep_1

source_name: Pig skin, 24h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_1h_exposure control_rep_2

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Pig skin_24h_post- sulfur mustard exposure_rep_2

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?


description: Gene expression data from NHEK_071003 SM exposure 1000 uM_8h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_1h_post- sulfur mustard exposure_rep_3

source_name: Pig skin, 1h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: scan date

tag: pustular epidermitis

tag: epidermal necrosis

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)


title: Pig skin_1h_exposure control_rep_1

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: vesicle

tag: follicular damage

tag: dermal necrosis

tag: re-epithelialization complete?


description: Gene expression data from NHEK_071003 SM exposure 12.5 uM_16h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


title: Pig skin_1h_post- sulfur mustard exposure_rep_1

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: rna extraction date

tag: ivt processing date

tag: pustular epidermitis

tag: epidermal necrosis

tag: vesicle

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)


description: Gene expression data from NHEK_071003 SM exposure 100 uM_16h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_071003 SM exposure 50 uM_8h timepoint


description: Gene expression data from NHEK_071003 SM exposure 200 uM_8h timepoint


description: Gene expression data from NHEK_071003 SM exposure 600 uM_8h timepoint


title: Pig skin_168h_sham

description: Gene expression data for Pig skin, 168h sham

source_name: Pig skin, 168h sham

tag: tissue

tag: time (h)

tag: treatment

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


description: Gene expression data from NHEK_071003 SM exposure 100 uM_8h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_071003 SM exposure 1000 uM_4h timepoint


description: Gene expression data from NHEK_071003 SM exposure 12.5 uM_8h timepoint


description: Gene expression data from NHEK_071003 SM exposure 400 uM_8h timepoint


description: Gene expression data from NHEK_071003 SM exposure 600 uM_4h timepoint


title: Pig skin_168h_exposure control_rep_2

description: Gene expression data for Pig skin, 168h exposure control

source_name: Pig skin, 168h exposure control

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_168h_post- sulfur mustard exposure_rep_3

description: Gene expression data for Pig skin, 168h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


description: Gene expression data from NHEK_071003 SM exposure 800 uM_4h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Pig skin_168h_post- sulfur mustard exposure_rep_2

source_name: Pig skin, 168h post- sulfur mustard exposure

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


description: Gene expression data from NHEK_071003 SM exposure 25 uM_8h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


title: Pig skin_168h_exposure control_rep_1

tag: tissue

tag: time (h)

tag: treatment

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


description: Gene expression data from NHEK_071003 SM exposure 100 uM_4h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician

tag: scan date


description: Gene expression data from NHEK_071003 SM exposure 400 uM_4h timepoint


title: Pig skin_168h_exposure control_rep_3

tag: tissue

tag: time (h)

tag: treatment

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: vascular proliferation

tag: hemorrhage

tag: total (normal=13)


title: Pig skin_168h_post- sulfur mustard exposure_rep_1

tag: tissue

tag: time (h)

tag: treatment

tag: sac date

tag: scan date

tag: smooth muscles

tag: collagen orientation

tag: fibroplasia


title: Liver_IUGR_Insulin_0.9Gestation_rep1

city: Aurora

first: Stephanie

middle: R

last: Wesolowski

state: Colorado

address: MS F441

institute: Dr

description: Hepatic gene expression data from control or IUGR fetal sheep after acute hyperinsulinemic clamp or saline infusion conditions

hyb_protocol: 10ug of cRNA was hybridized on the Affymetrix Bovine Gene Chip with rotation at 60rpm for 16 hours at 45C. Chips were washed and scanned using a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000.

data_processing: Data were analyzed and normalized with the robust multi-array average (RMA) method using Affymetrix Expression ConsoleTM Software.  Normalized data were analyzed using a 2-way ANOVA with the main effects of IUGR (Control, IUGR), infusion (INSULIN, SALINE), and the interaction using GeneSpring Software.

organism: Ovis aries

source_name: Ovine liver right lobe at 0.9 gestation in IUGR conditions and hyperinsulinemic-euglycemic clamp

label_protocol: Total RNA (300ng) was primed with T7 oligo primer to synthesize cDNA. Single-stranded cDNA was converted to double stranded cDNA template for transcription. The cDNA was used directly in the In Vitro Transcription reaction to synthesize Biotin-Modified cRNA.

growth_protocol: Intrauterine growth restricted (IUGR) fetuses were studied at 0.9 gestation.

extract_protocol: RNA was isolated from powedered liver tissue from the right liver lobe using Qiazol and the Rneasy mini-kit with on-column deoxyribonuclease I treatment (Qiagen).

treatment_protocol: A fetal hyperinsulinemic-isoglycemic clamp or saline infusion was performed. After the infusion period (~3hr), the ewe and fetus were euthanized and a necropsy was performed to collect liver sample from the right lobe. Liver tissues were snap frozen in liquid nitrogen.

value: Liver right lobe

tag: gestational age

value: 132 days gestation


title: Liver_IUGR_Insulin_0.9Gestation_rep3


description: Gene expression data from NHEK_071003 SM exposure 1000 uM_2h timepoint

tag: cell type

tag: agent

tag: exposure date

tag: dose (um)

tag: timepoint (h)

tag: date of rna extraction

tag: rna extraction method

tag: rna extraction technician

tag: cdna processing date

tag: cdna processing technician

tag: hybridization date

tag: hybridization technician


title: Liver_Control_Insulin_0.9Gestation_rep3

source_name: Ovine liver right lobe at 0.9 gestation in control conditions and hyperinsulinemic-euglycemic clamp

tag: tissue


title: Liver_IUGR_Insulin_0.9Gestation_rep2


description: Gene expression data from NHEK_071003 SM exposure 50 uM_4h timepoint

tag: scan date


description: Gene expression data from NHEK_071003 SM exposure 200 uM_2h timepoint


title: Liver_IUGR_Saline_0.9Gestation_rep2

source_name: Ovine liver right lobe at 0.9 gestation in IUGR conditions and saline infusion


title: Liver_IUGR_Saline_0.9Gestation_rep3


title: Liver_Control_Insulin_0.9Gestation_rep1


title: Liver_IUGR_Saline_0.9Gestation_rep1


description: Gene expression data from NHEK_071003 SM exposure 200 uM_4h timepoint


description: Gene expression data from NHEK_071003 SM exposure 100 uM_2h timepoint


description: Gene expression data from NHEK_071003 SM exposure 800 uM_2h timepoint


title: Liver_Control_Saline_0.9Gestation_rep3

source_name: Ovine liver right lobe at 0.9 gestation in control conditions and saline infusion


title: Liver_Control_Insulin_0.9Gestation_rep2


description: Gene expression data from NHEK_071003 SM exposure 800 uM_1h timepoint


description: Gene expression data from NHEK_071003 SM exposure 12.5 uM_4h timepoint


title: Liver_Control_Saline_0.9Gestation_rep2


description: Gene expression data from NHEK_071003 SM exposure 50 uM_2h timepoint


title: Liver_Control_Saline_0.9Gestation_rep1


description: Gene expression data from NHEK_071003 SM exposure 400 uM_2h timepoint


description: Gene expression data from NHEK_071003 SM exposure 12.5 uM_2h timepoint


description: Gene expression data from NHEK_071003 SM exposure 400 uM_1h timepoint


description: Gene expression data from NHEK_071003 SM exposure 200 uM_1h timepoint


description: Gene expression data from NHEK_071003 SM exposure 25 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 50 uM_16h timepoint

value: NM


description: Gene expression data from NHEK_070926 NM exposure 50 uM_24h timepoint


description: Gene expression data from NHEK_071003 SM exposure 600 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 600 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 12.5 uM_8h timepoint


description: Gene expression data from NHEK_071003 SM exposure 50 uM_1h timepoint


description: Gene expression data from NHEK_071003 SM exposure 100 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 200 uM_8h timepoint


description: Gene expression data from NHEK_070926 NM exposure 200 uM_24h timepoint


description: Gene expression data from NHEK_070926 NM exposure 100 uM_16h timepoint


description: Gene expression data from NHEK_070926 NM exposure 200 uM_16h timepoint


description: Gene expression data from NHEK_070926 NM exposure 800 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 100 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 25 uM_24h timepoint


description: Gene expression data from NHEK_071003 SM exposure 12.5 uM_1h timepoint


description: Gene expression data from NHEK_071003 SM exposure 25 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 100 uM_24h timepoint


description: Gene expression data from NHEK_070926 NM exposure 200 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 25 uM_8h timepoint


description: Gene expression data from NHEK_070926 NM exposure 600 uM_8h timepoint


description: Gene expression data from NHEK_070926 NM exposure 1000 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 50 uM_8h timepoint


description: Gene expression data from NHEK_070926 NM exposure 12.5 uM_16h timepoint


description: Gene expression data from NHEK_070926 NM exposure 50 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 400 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 800 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 25 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 600 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 12.5 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 12.5 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 100 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 200 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 1000 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 400 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 50 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 600 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 800 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 200 uM_24h timepoint


description: Gene expression data from NHEK_070919 NM exposure 100 uM_24h timepoint


description: Gene expression data from NHEK_070926 NM exposure 100 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 25 uM_2h timepoint


description: Gene expression data from NHEK_071003 SM exposure 25 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 200 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 25 uM_1h timepoint


description: Gene expression data from NHEK_070926 NM exposure 400 uM_2h timepoint


description: Gene expression data from NHEK_070926 NM exposure 1000 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 200 uM_16h timepoint


description: Gene expression data from NHEK_070926 NM exposure 12.5 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 12.5 uM_24h timepoint


description: Gene expression data from NHEK_070919 NM exposure 50 uM_24h timepoint


description: Gene expression data from NHEK_070926 NM exposure 50 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 50 uM_16h timepoint


description: Gene expression data from NHEK_070919 NM exposure 25 uM_16h timepoint


description: Gene expression data from NHEK_070919 NM exposure 12.5 uM_16h timepoint


description: Gene expression data from NHEK_070919 NM exposure 200 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 25 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 800 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 100 uM_16h timepoint


description: Gene expression data from NHEK_070919 NM exposure 800 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 200 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 12.5 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 1000 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 50 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 100 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 1000 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 400 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 1000 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 50 uM_4h timepoint


description: Gene expression data from NHEK_070926 NM exposure 25 uM_16h timepoint


description: Gene expression data from NHEK_070919 NM exposure 12.5 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 400 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 600 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 400 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 600 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 600 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 25 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 200 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 800 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 25 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 50 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 12.5 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 100 uM_4h timepoint


description: Gene expression data from NHEK_070919 NM exposure 100 uM_2h timepoint


description: Gene expression data from NHEK_070919 NM exposure 1000 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 800 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 200 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 600 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 100 uM_1h timepoint


description: Gene expression data from NHEK_070919 NM exposure 12.5 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 100 uM_24h timepoint


description: Gene expression data from NHEK_070919 NM exposure 400 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 200 uM_16h timepoint


description: Gene expression data from NHEK_070919 NM exposure 25 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 200 uM_24h timepoint


description: Gene expression data from NHEK_070912 NM exposure 50 uM_24h timepoint


description: Gene expression data from NHEK_070912 NM exposure 50 uM_16h timepoint


description: Gene expression data from NHEK_070912 NM exposure 100 uM_16h timepoint


description: Gene expression data from NHEK_070912 NM exposure 25 uM_16h timepoint


description: Gene expression data from NHEK_070912 NM exposure 12.5 uM_16h timepoint


description: Gene expression data from NHEK_070912 NM exposure 1000 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 25 uM_24h timepoint


description: Gene expression data from NHEK_070912 NM exposure 400 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 50 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 100 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 12.5 uM_24h timepoint


description: Gene expression data from NHEK_070926 NM exposure 12.5 uM_24h timepoint


description: Gene expression data from NHEK_070912 NM exposure control 0 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 200 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 800 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 12.5 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure control 0 uM_16h timepoint


description: Gene expression data from NHEK_070912 NM exposure 25 uM_8h timepoint


description: Gene expression data from NHEK_070919 NM exposure 50 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure control 0 uM_24h timepoint


description: Gene expression data from NHEK_070912 NM exposure control 0 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 1000 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 800 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 600 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 1000 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 12.5 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 50 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 800 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure control 0 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 600 uM_8h timepoint


description: Gene expression data from NHEK_070912 NM exposure 25 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 400 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 400 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 600 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 25 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure 200 uM_4h timepoint


description: Gene expression data from NHEK_070912 NM exposure control 0 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 50 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 600 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 100 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 12.5 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 100 uM_2h timepoint


description: Gene expression data from NHEK_070912 NM exposure 1000 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 200 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 800 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 50 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 25 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 12.5 uM_1h timepoint


description: Gene expression data from NHEK_070912 NM exposure 400 uM_1h timepoint


description: Gene expression data from NHEK_070829 SM exposure control 0 uM_24h timepoint


description: Gene expression data from NHEK_070912 NM exposure 100 uM_4h timepoint


description: Gene expression data from NHEK_070829 SM exposure 200 uM_24h timepoint


description: Gene expression data from NHEK_070829 SM exposure 100 uM_24h timepoint


description: Gene expression data from NHEK_070829 SM exposure 50 uM_24h timepoint


description: Gene expression data from NHEK_070829 SM exposure 50 uM_16h timepoint


description: Gene expression data from NHEK_070829 SM exposure 25 uM_24h timepoint


description: Gene expression data from NHEK_070829 SM exposure 12.5 uM_24h timepoint


description: Gene expression data from NHEK_070829 SM exposure control 0 uM_16h timepoint


description: Gene expression data from NHEK_070829 SM exposure 100 uM_16h timepoint


description: Gene expression data from NHEK_070829 SM exposure 100 uM_8h timepoint


description: Gene expression data from NHEK_070829 SM exposure 600 uM_8h timepoint


description: Gene expression data from NHEK_070829 SM exposure 12.5 uM_16h timepoint


description: Gene expression data from NHEK_070829 SM exposure 25 uM_8h timepoint


description: Gene expression data from NHEK_070829 SM exposure control 0 uM_8h timepoint


description: Gene expression data from NHEK_070829 SM exposure 800 uM_8h timepoint


description: Gene expression data from NHEK_070829 SM exposure 12.5 uM_8h timepoint


title: Retinocytoma 31

city: Atlanta

first: Hans

middle: E

last: Grossniklaus

state: Georgia

address: 1365 Clifton Rd

institute: Emory Eye Center

description:
RC 31
Gene expression data from matched retinocytoma sample.

hyb_protocol: Standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocols.

data_processing: Data was processed, normalized by robust multi-array average (RMA), and log2 transformed using the Oligo Bioconductor R package.

label: Biotin

source_name: Matched retinocytoma

label_protocol: Standard Affymetrix protocols.

growth_protocol: Not applicable.

extract_protocol: AllPrep DNA/RNA FFPE (Qiagen) and Mag-Bind XP FFPE RNA (Omega Bio-tek) kits.

value: Retinocytoma


description: Gene expression data from NHEK_070829 SM exposure 200 uM_8h timepoint


title: Retinocytoma 33

description:
RC 33
Gene expression data from matched retinocytoma sample.


description: Gene expression data from NHEK_070829 SM exposure 400 uM_8h timepoint


title: Retinocytoma 32

description:
RC 32
Gene expression data from matched retinocytoma sample.


description: Gene expression data from NHEK_070829 SM exposure 50 uM_8h timepoint


description: Gene expression data from NHEK_070829 SM exposure 1000 uM_8h timepoint


description: Gene expression data from NHEK_070829 SM exposure control 0 uM_4h timepoint


description: Gene expression data from NHEK_070829 SM exposure 200 uM_16h timepoint


title: Normal retina 33

description:
NR 33
Gene expression data from matched normal retina sample.

source_name: Matched normal retina

value: Normal retina


title: Normal retina 19

description:
NR 19
Gene expression data from matched normal retina sample.


description: Gene expression data from NHEK_070829 SM exposure 600 uM_4h timepoint


description: Gene expression data from NHEK_070829 SM exposure 800 uM_4h timepoint


description: Gene expression data from NHEK_070829 SM exposure 1000 uM_4h timepoint


title: Normal retina 9

description:
NR 9
Gene expression data from matched normal retina sample.


description: Gene expression data from NHEK_070829 SM exposure 200 uM_4h timepoint


description: Gene expression data from NHEK_070829 SM exposure 400 uM_4h timepoint


title: Retinoblastoma 33

description:
RB 33
Gene expression data from retinoblastoma sample.

source_name: Retinoblastoma

value: Retinoblastoma

tag: anaplasia

value: Severe


description: Gene expression data from NHEK_070829 SM exposure 100 uM_4h timepoint


title: Retinoblastoma 32

description:
RB 32
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 24

description:
RB 24
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 25

description:
RB 25
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 30

description:
RB 30
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure control 0 uM_2h timepoint


title: Retinoblastoma 21

description:
RB 21
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 28

description:
RB 28
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 600 uM_2h timepoint


description: Gene expression data from NHEK_070829 SM exposure 50 uM_4h timepoint


description: Gene expression data from NHEK_070829 SM exposure 400 uM_2h timepoint


description: Gene expression data from NHEK_070829 SM exposure 100 uM_2h timepoint


title: Retinoblastoma 26

description:
RB 26
Gene expression data from retinoblastoma sample.

value: Moderate


title: Retinoblastoma 12

description:
RB 12
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 13

description:
RB 13
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 31

description:
RB 31
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 200 uM_2h timepoint


description: Gene expression data from NHEK_070829 SM exposure 25 uM_4h timepoint


description: Gene expression data from NHEK_070829 SM exposure 25 uM_16h timepoint


description: Gene expression data from NHEK_070829 SM exposure 1000 uM_2h timepoint


description: Gene expression data from NHEK_070829 SM exposure 800 uM_2h timepoint


title: Retinoblastoma 22

description:
RB 22
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 12.5 uM_4h timepoint


title: Retinoblastoma 18

description:
RB 18
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 14

description:
RB 14
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 50 uM_2h timepoint


description: Gene expression data from NHEK_070829 SM exposure 25 uM_2h timepoint


title: Retinoblastoma 16

description:
RB 16
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 11

description:
RB 11
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 12.5 uM_2h timepoint


title: Retinoblastoma 2

description:
RB 2
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 9

description:
RB 9
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 8

description:
RB 8
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 6

description:
RB 6
Gene expression data from retinoblastoma sample.

value: Mild


description: Gene expression data from NHEK_070829 SM exposure control 0 uM_1h timepoint

value: primary human epidermal keratinocytes (NHEK)


title: Retinoblastoma 19

description:
RB 19
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 1

description:
RB 1
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 23

description:
RB 23
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 100 uM_1h timepoint


title: Retinoblastoma 5

description:
RB 5
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 1000 uM_1h timepoint


description: Gene expression data from NHEK_070829 SM exposure 400 uM_1h timepoint


title: Retinoblastoma 3

description:
RB 3
Gene expression data from retinoblastoma sample.


description: Gene expression data from NHEK_070829 SM exposure 600 uM_1h timepoint


description: Gene expression data from NHEK_070829 SM exposure 50 uM_1h timepoint


description: Gene expression data from NHEK_070829 SM exposure 12.5 uM_1h timepoint


description: Gene expression data from NHEK_070829 SM exposure 200 uM_1h timepoint


description: Gene expression data from NHEK_070829 SM exposure 800 uM_1h timepoint


description: Gene expression data for NHEK exposed 081001, 8 hour timepoint, 0 uM SM control, biological replicate 3

source_name: NHEK 8h 0 uM SM Control

label_protocol: Total RNA was processed for hybridization to GeneChip® Human 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: Cell lines were seeded at 1.2x103 cells per cm2 in 25 cm2 flasks (30,000 cells per flask), and grown to approximately 80% confluency.  Cells were kept in a standard biological incubator at 37°C with 5% CO2.  Cells were fed 5 mL each day prior to exposure using appropriate media, KGM Complete (for NHEK) or DMEM (for HaCaT) (Lonza, Walkersville, MD).

extract_protocol: Cell lysates were collected in 400uL 1% beta-mercaptoethanol in RLT lysis buffer and processed through QIAshredder columns (QIAGEN, Valencia, CA) according to 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: Cells were exposed to 0 uM, 25 uM, or 200 uM SM in a chemical surety hood.  Cells remained in the hood in a 37°C incubator for 30 min post exposure.  Cells were returned to a standard biological incubator and harvested at 1h or 8h post exposure.  Time matched controls were included for each group.

value: skin

value: Primary normal human epidermal keratinocytes (NHEKs)

tag: timepoint

tag: sulfur mustard dose (um)


description: Gene expression data for NHEK exposed 081001, 8 hour timepoint, 25 uM SM, biological replicate 3

source_name: NHEK 8h 25 uM SM

tag: cell type


description: Gene expression data for NHEK exposed 081001, 8 hour timepoint, 200 uM SM, biological replicate 3

source_name: NHEK 8h 200 uM SM


description: Gene expression data for NHEK exposed 081009, 1 hour timepoint, 200 uM SM, biological replicate 4

source_name: NHEK 1h 200 uM SM


title: Retinoblastoma 7

description:
RB 7
Gene expression data from retinoblastoma sample.


title: Retinoblastoma 17

description:
RB 17
Gene expression data from retinoblastoma sample.


title: Neutron_100%_day7_rep 6

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: blood

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 purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia at day 7 post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: treatment

value: 0.75 Gy neutron exposures

tag: Sex

value: male

tag: strain


description: Gene expression data from NHEK_070829 SM exposure 25 uM_1h timepoint

tag: agent

value: SM

tag: exposure date

tag: dose (um)

tag: timepoint (h)

value: Rothwell


title: Neutron_100%_day7_rep 4


title: Neutron_100%_day7_rep 5


title: Neutron_100%_day7_rep 3


description: Gene expression data for NHEK exposed 081001, 1 hour timepoint, 0 uM SM control, biological replicate 3

source_name: NHEK 1h 0 uM SM Control


title: Neutron_100%_day7_rep 1


title: Neutron_25%_day7_rep 4

value: 3 Gy mixed-field irradiation of x-rays with neutrons contributing 25 percent


title: Neutron_25%_day7_rep 5


description: Gene expression data for NHEK exposed 081001, 1 hour timepoint, 25 uM SM, biological replicate 3

source_name: NHEK 1h 25 uM SM


description: Gene expression data for NHEK exposed 080923, 8 hour timepoint, 25 uM SM, biological replicate 2


description: Gene expression data for NHEK exposed 080923, 8 hour timepoint, 200 uM SM, biological replicate 2


description: Gene expression data for NHEK exposed 081001, 1 hour timepoint, 200 uM SM, biological replicate 3


description: Gene expression data for NHEK exposed 080923, 1 hour timepoint, 200 uM SM, biological replicate 2


title: Neutron_25%_day7_rep 1


title: Neutron_25%_day7_rep 2


title: Neutron_25%_day7_rep 6


title: Neutron_15%_day7_rep 6

value: 3 Gy mixed-field irradiation of x-rays with neutrons contributing 15 percent


title: Neutron_25%_day7_rep 3


description: Gene expression data for NHEK exposed 080917, 8 hour timepoint, 200 uM SM, biological replicate 1


description: Gene expression data for NHEK exposed 080917, 8 hour timepoint, 0 uM SM control, biological replicate 1


description: Gene expression data for NHEK exposed 080923, 1 hour timepoint, 25 uM SM, biological replicate 2


description: Gene expression data for NHEK exposed 080923, 1 hour timepoint, 0 uM SM control, biological replicate 2


title: Neutron_15%_day7_rep 5


title: Neutron_15%_day7_rep 4


title: Neutron_15%_day7_rep 3


title: Neutron_15%_day7_rep 2


description: Gene expression data for NHEK exposed 080917, 8 hour timepoint, 25 uM SM, biological replicate 1


description: Gene expression data for NHEK exposed 080917, 1 hour timepoint, 25 uM SM, biological replicate 1


title: Neutron_5%_day7_rep 5

value: 3 Gy mixed-field irradiation of x-rays with neutrons contributing 5 percent


title: Neutron_5%_day7_rep 6


title: Neutron_5%_day7_rep 1


description: Gene expression data for NHEK exposed 080917, 1 hour timepoint, 0 uM SM control, biological replicate 1


title: Neutron_5%_day7_rep 4


title: Neutron_5%_day7_rep 3


title: Neutron_5%_day7_rep 2


description: Gene expression data for NHEK exposed 080917, 1 hour timepoint, 200 uM SM, biological replicate 1


title: X-ray_3Gy_day7_rep 4

value: 3 Gy x-ray exposures


title: X-ray_3Gy_day7_rep 3


title: Neutron_15%_day7_rep 1


title: X-ray_3Gy_day7_rep 2


title: X-ray_3Gy_day7_rep 6


description: Gene expression data for HaCaT exposed 081009, 8 hour timepoint, 25 uM SM, biological replicate 3

source_name: HaCaT 8h 25 uM SM

value: HaCaT human keratinocyte cell line


description: Gene expression data for HaCaT exposed 081009, 1 hour timepoint, 200 uM SM, biological replicate 3

source_name: HaCaT 1h 200 uM SM


description: Gene expression data for HaCaT exposed 081002, 8 hour timepoint, 0 uM SM control, biological replicate 2

source_name: HaCaT 8h 0 uM SM Control


description: Gene expression data for HaCaT exposed 081002, 1 hour timepoint, 0 uM SM control, biological replicate 2

source_name: HaCaT 1h 0 uM SM Control


description: Gene expression data for HaCaT exposed 081009, 1 hour timepoint, 0 uM SM control, biological replicate 3


description: Gene expression data for HaCaT exposed 081009, 8 hour timepoint, 0 uM SM control, biological replicate 3


description: Gene expression data for HaCaT exposed 081009, 8 hour timepoint, 200 uM SM, biological replicate 3

source_name: HaCaT 8h 200 uM SM


description: Gene expression data for HaCaT exposed 081009, 1 hour timepoint, 25 uM SM, biological replicate 3

source_name: HaCaT 1h 25 uM SM


description: Gene expression data for HaCaT exposed 081002, 8 hour timepoint, 25 uM SM, biological replicate 2


description: Gene expression data for NHEK exposed 080923, 8 hour timepoint, 0 uM SM control, biological replicate 2


title: X-ray_3Gy_day7_rep 1


description: Gene expression data for HaCaT exposed 081002, 1 hour timepoint, 200 uM SM, biological replicate 2


description: Gene expression data for HaCaT exposed 081002, 8 hour timepoint, 200 uM SM, biological replicate 2


description: Gene expression data for HaCaT exposed 081002, 1 hour timepoint, 25 uM SM, biological replicate 2


title: Control_day7_rep 1


title: Control_day7_rep 5


description: Gene expression data for HaCaT exposed 080925, 1 hour timepoint, 25 uM SM, biological replicate 1


title: Control_day7_rep 6


title: Control_day7_rep 3


description: Gene expression data for HaCaT exposed 080925, 1 hour timepoint, 0 uM SM control, biological replicate 1


title: Control_day7_rep 2


description: Gene expression data for HaCaT exposed 080925, 8 hour timepoint, 200 uM SM, biological replicate 1


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 2

description: Gene expression data from NHEK exposed with 200 uM SM and no drug on 090819, harvested at 8 hour

growth_protocol: Primary human epidermal keratinocytes (Lonza, Walkersville, MD) were seeded at passage 3 at 1.2x103 cells per cm2 in 25 cm2 flasks (30,000 cells/flask), and grown to approximately 80% confluency.  Cells were kept in a standard biological incubator at 37°C with 5% CO2.  Cells were fed 5 mL each day prior to exposure using KGM Complete media (Lonza, Walkersville, MD).

treatment_protocol: Small molecule inhibitors SB 203580 (p38 inhibitor), PD 98059 (Erk inhibitor), and SP 600125 (JNK inhibitor) were prepared as 10 mM stock solutions in water or DMSO, depending on manufacturer's recommendations (Tocris Bioscience, Ellisville, MO).  One hour prior to exposure, inhibitor was added to each flask to a final concentration of 10 uM and incubated at 37°C with 5% CO2.  Cells were exposed to 0 uM or 200 uM SM in a chemical surety hood.  Cells remained in the hood in a 37°C incubator for 30 min post exposure.  Cells were returned to a standard biological incubator and harvested at 1h, 4h, or 8h post exposure.  Time matched controls were included for each group.

tag: time point (hrs)

tag: drug inhibitor

tag: sm dose (um)


title: Retinoblastoma 4

description:
RB 4
Gene expression data from retinoblastoma sample.


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 1

source_name: NHEK exposed with 200 uM SM and no drug on 090819, harvested at 8 hour


description: Gene expression data for HaCaT exposed 080925, 8 hour timepoint, 0 uM SM control, biological replicate 1


title: Control_day7_rep 4


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 3


title: X-ray_3Gy_day7_rep 5


title: Dermal fibroblast 1, biological rep 1

city: amman

first: DANA

last: HATTAB

address: queen rania street

country: Jordan

institute: CELL THERAPY CENTER

description: Gene expression data from dermis derived fibroblasts

hyb_protocol: Following fragmentation and labeling, 5.2 ug of ss-DNA were hybridized for 16 hr at 45C on Human Transcriptome Analysis 2 (HTA 2) chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix® GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software and  Affymetrix® Transcriptome Analysis Console (TAC®) Software V4.

source_name: fibroblast from dermis

label_protocol: The fragmented cDNA was biotin labelled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent ( Manual target preperation for GeneChip whole trascript expression array, 2013, Affymetrix).

growth_protocol: For all studied MSCs, the culture medium consisted of: α-modified minimum essential medium (α-MEM; GIBCO, ThermoFisher, USA) supplemented with 5 % platelet lysate, 1% (w/v) Penicillin/Streptomycin (P/S) and 2mM L-glutamine (GIBCO, ThermoFisher, USA).

extract_protocol: RNA was extracted using the mixed Trizol- Qiagen® RNeasy Mini kit (Qiagen, USA) , according to the manufacturer's instructions.

treatment_protocol: MSCs from all different sources at passage three were cultured in 6 well plates. At 80-90% confluence, the cells were washed with PBS and lysed using Trizol® reagent (Ambion, ThermoFisher scientific, USA)

value: foreskin dermis

value: fibroblast


description: Gene expression data for HaCaT exposed 080925, 1 hour timepoint, 200 uM SM, biological replicate 1


title: Dermal fibroblast 2, biological rep 2


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 1

description: Gene expression data from NHEK exposed with 0 uM SM and no drug on 090819, harvested at 8 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 2

source_name: NHEK exposed with 0 uM SM and no drug on 090819, harvested at 8 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 3


title: placenta 3, biological rep 3

description: Gene expression data from placenta derived mesenchymal stem cells

source_name: mesenchymal stem cells from placenta

value: placenta

value: mesenchymal stem cells


title: Dermal fibroblast 3, biological rep 3


title: umbilical cord 4, biological rep 4

description: Gene expression data from umbilical cord derived mesenchymal stem cells

source_name: mesenchymal stem cells from umbilical cord

value: umbilical cord


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 2

description: Gene expression data from NHEK exposed with 200 uM SM and no drug on 090819, harvested at 4 hour

value: primary human epidermal keratinocytes (NHEK)


title: Neutron_100%_day7_rep 2


title: placenta 1. biological rep 1


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 1

source_name: NHEK exposed with 200 uM SM and no drug on 090819, harvested at 4 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 3

description: Gene expression data from NHEK exposed with 0 uM SM and no drug on 090819, harvested at 4 hour


title: umbilical cord 2, biological rep 2


title: umbilical cord 1, biological rep 1


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 2

source_name: NHEK exposed with 0 uM SM and no drug on 090819, harvested at 4 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 3

description: Gene expression data from NHEK exposed with 200 uM SM and no drug on 090819, harvested at 1 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 2

source_name: NHEK exposed with 200 uM SM and no drug on 090819, harvested at 1 hour


title: adipose tissue 2, biological rep 2

description: Gene expression data from adipose tissue derived mesenchymal stem cells

source_name: mesenchymal stem cells from adipose tissue

value: adipose tissue


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 3


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 1


title: bone marrow 2, biological rep 5

description: Gene expression data from bone marrow derived mesenchymal stem cells

source_name: mesenchymal stem cells from bone marrow

value: bone marrow


title: umbilical cord 3, biological rep 3


title: adipose tissue 3, biological rep 3


title: bone marrow 2, biological rep 4


title: bone marrow 2, biological rep 3


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 1


title: adipose tissue 1, biological rep 1


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 2

description: Gene expression data from NHEK exposed with 0 uM SM and no drug on 090819, harvested at 1 hour


title: bone marrow 2, biological rep 2


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 1

source_name: NHEK exposed with 0 uM SM and no drug on 090819, harvested at 1 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 3


title: bone marrow 1, biological rep 1


description: Gene expression data for HaCaT exposed 080925, 8 hour timepoint, 25 uM SM, biological replicate 1

source_name: HaCaT 8h 25 uM SM

value: skin


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, with PD98059 drug pre-tx, biological replicate 2

description: Gene expression data from NHEK exposed with 200 uM SM and PD98059 pre-tx on 090819, harvested at 8 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, with PD98059 drug pre-tx, biological replicate 2

description: Gene expression data from NHEK exposed with 0 uM SM and PD98059 pre-tx on 090819, harvested at 8 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, with PD98059 drug pre-tx, biological replicate 2

description: Gene expression data from NHEK exposed with 200 uM SM and PD98059 pre-tx on 090819, harvested at 4 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, with PD98059 drug pre-tx, biological replicate 1

source_name: NHEK exposed with 200 uM SM and PD98059 pre-tx on 090819, harvested at 4 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, with PD98059 drug pre-tx, biological replicate 1

source_name: NHEK exposed with 0 uM SM and PD98059 pre-tx on 090819, harvested at 8 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, with PD98059 drug pre-tx, biological replicate 1

description: Gene expression data from NHEK exposed with 0 uM SM and PD98059 pre-tx on 090819, harvested at 4 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, with PD98059 drug pre-tx, biological replicate 1

source_name: NHEK exposed with 200 uM SM and PD98059 pre-tx on 090819, harvested at 8 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, with PD98059 drug pre-tx, biological replicate 2

source_name: NHEK exposed with 0 uM SM and PD98059 pre-tx on 090819, harvested at 4 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, with PD98059 drug pre-tx, biological replicate 1

description: Gene expression data from NHEK exposed with 200 uM SM and PD98059 pre-tx on 090819, harvested at 1 hour


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, with PD98059 drug pre-tx, biological replicate 1

description: Gene expression data from NHEK exposed with 0 uM SM and PD98059 pre-tx on 090819, harvested at 1 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, with PD98059 drug pre-tx, biological replicate 3


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, with PD98059 drug pre-tx, biological replicate 3


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, with PD98059 drug pre-tx, biological replicate 3


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, with PD98059 drug pre-tx, biological replicate 3


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, with PD98059 drug pre-tx, biological replicate 3

source_name: NHEK exposed with 0 uM SM and PD98059 pre-tx on 090819, harvested at 1 hour


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, with PD98059 drug pre-tx, biological replicate 2

source_name: NHEK exposed with 200 uM SM and PD98059 pre-tx on 090819, harvested at 1 hour


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 1

description: Gene expression data from NHEK exposed with 0 uM SM and no drug on 090805, harvested at 8 hour


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 2

description: Gene expression data from NHEK exposed with 200 uM SM and no drug on 090805, harvested at 8 hour


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 2

source_name: NHEK exposed with 0 uM SM and no drug on 090805, harvested at 8 hour


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 3

description: Gene expression data from NHEK exposed with 200 uM SM and no drug on 090805, harvested at 4 hour


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 3


title: 090819 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, with PD98059 drug pre-tx, biological replicate 3


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 3

source_name: NHEK exposed with 200 uM SM and no drug on 090805, harvested at 8 hour


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 2

source_name: NHEK exposed with 200 uM SM and no drug on 090805, harvested at 4 hour


title: N129-T244

type: SRA

city: Berkeley

first: Paul

last: Yaswen

state: California

address: One Cyclotron Road, Building 977

institute: LBNL

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.9
Reads  were checked for per base/per tile sequence quality, per sequence GC content, adapter content etc. using FASTQC software
HISAT2/htseq-count pipeline with default parameters for PE reads alignments was applied assuming that a gene is an union of its exons
Raw count table was pre-filtered removing rows with all zeros through all samples. R environment and package DESeq2(Bioconductor) were used to quantify candidate genes with cutoffs for non-specific filtering and p-values = 0.1
Normalizing filtered raw counts using variance-stabilizing transformation
Genome_build: hg38
Supplementary_files_format_and_content: csv-files(comma-delimited) were generated with R

source_name: breast

growth_protocol: The wells of a 24-well cell culture plate were uniformly coated with 50µl lrECM (BME, Matrigel Basement Membrane Matrix Growth Factor Reduced, Corning) /well and allowed to polymerize at 37°C for 20 min. Organoid aliquots were thawed, diluted in baseline medium: Advanced DMEM/F12 (ThermoFisher) containing 30mM HEPES (Sigma), 1x GlutaMAX (ThermoFisher), 140 nM hydrocortisone (Sigma), 10 ng/ml EGF (Sigma), 1% PenStrep (ThermoFisher), and centrifuged twice before resuspension in 600 µl lrECM. 50µl portions were plated at the centers of the pre-coated wells. Following 1h polymerization, 500µl of pre-warmed culture medium was added to each well and organoids were incubated for 2 days at 37°C, 5% CO2 in a humidified incubator. Organoids were retrieved from lrECM by removing medium and adding 500µl of Cell Harvesting Buffer/Dispase (Corning) to each well and incubating for 1h at 37°C. Organoids were then collected and mixed with an equal volume of 0.5 mM EDTA in phosphate buffered saline (PBS), and incubated for an additional 15 minutes at room temperature before centrifugation. Organoids were then dissociated to single cells using 1ml of TryPLE (ThermoFisher) for 10 min at 37°C, while shaking. Following dissociation, the suspension was filtered through 35µm nylon mesh to obtain single cells. The cells were then washed in baseline medium, resuspended in lrECM and replated in pre-coated 24-well plates at a density of 25,000 cells/well. Following lrECM polymerization for 1 h, 500 µl medium was added per well, with indicated additional factors including EGF (50 ng/ml, Sigma), Noggin (100 ng/ml, PeproTech), R-Spondin-1 (500 ng/ml, PeproTech), Neuregulin1 (100 ng/ml, PeproTech), Jagged-1 (1 µM, AnaSpec), A 83-01 (500 nM, Tocris), SB 431542 (10 µM, Sigma), RepSox (25 µM, Sigma). ROCK inhibitor Y-27632 (10 µM, Tocris) was added to all the cultures during dissociation and for the first 2-3 days of culture. Cells were incubated for 8 to 14 days (until the mean diameter of colonies was > 100 µm) and medium was changed every other day.

extract_protocol:
RNA was isolated directly from intact cultures using RNA STAT-60 (Amsbio) following the manufacturer’s instructions, and quantitated using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher).
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) from 1 µg of total RNA input per sample, following the manufacturer’s instructions.

treatment_protocol: 3D cultures from 3 specimens were exposed to 10nM estradiol or vehicle alone for 6 or 24 hours.

value: epithelial

value: estradiol

tag: time

value: 24 hr


title: N129

value: primary organoid


title: N129-T243


title: endometrium30_cancer_G1

city: Sosnowiec

first: Urszula

last: Mazurek

address: Jedności 8

department: Department of Molecular Biology

country: Poland

institute: Medical University of Silesia

hyb_protocol: 15ug of fragmented cRNA were hybridized on HGU133A microarray (Affymetrix). Hybrydization was performed for 16h at 45C. Gene chip was washed and stained with use  GeneChip® Fluidics Station 450 - protocol EukGE-WS2v4 .

scan_protocol: Scan was made with use of GeneArray Scanner G2500A

data_processing: The data were analyzed with Affymetrix GeneChip Command Console (AGCC) Software,  PL-Grid (http://www.plgrid.pl/) , GeneSpring 13.0 (Agilent Technologies UK Limited, South Queensferry, UK)

source_name: endometrium cancer G1

label_protocol: Biotinylated cRNA were prepared according to Affymetrix protocol  from 5-8ug of total RNA (Gene Expression Analysis Technical Manual, Affymertix).

extract_protocol: Total RNA was extracted with Trizol Reagend according to the manufacturer's instructions.

tag: tissue

value: endometrium cancer

tag: grade


title: endometrium27_cancer_G2

source_name: endometrium cancer G2


title: endometrium29_cancer_G2


title: endometrium19_cancer_G2


title: endometrium28_cancer_G2


title: endometrium25_cancer_G2


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 1


title: endometrium31_cancer_G1


title: endometrium26_cancer_G2


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 3

description: Gene expression data from NHEK exposed with 0 uM SM and no drug on 090805, harvested at 4 hour


title: endometrium21_cancer_G2


title: endometrium24_cancer_G1


title: placenta 2, biological rep 2

description: Gene expression data from placenta derived mesenchymal stem cells

source_name: mesenchymal stem cells from placenta


title: endometrium20_cancer_G2


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 2

description: Gene expression data from NHEK exposed with 200 uM SM and no drug on 090805, harvested at 1 hour


title: endometrium17_cancer_G3

source_name: endometrium cancer G3


title: endometrium18_cancer_G3


title: endometrium22_cancer_G2


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 1

source_name: NHEK exposed with 0 uM SM and no drug on 090805, harvested at 4 hour


title: endometrium16_cancer_G1


title: N129-T241


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 4 hour timepoint, no drug, biological replicate 2


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 3

description: Gene expression data from NHEK exposed with 0 uM SM and no drug on 090805, harvested at 1 hour


title: N129-T63

value: 6 hr


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 3

source_name: NHEK exposed with 200 uM SM and no drug on 090805, harvested at 1 hour


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 1


title: N129-T64


title: N129-T242


title: N129-T62


title: N129-T61


title: N129-C4

value: control

value: 0 hr


title: H3K27Ac-ChIP-seq

city: Seattle

first: Karol

last: Bomsztyk

state: WA

address: 850 Republican Street

department: Medicine

institute: University of Washington

library_source: genomic

data_processing:
Base Calling was performed using bcl2fastq (v2.20.0.442), alignment was performed using BWA-mem (0.7.12), filtering was performed using Samtools (0.1.19), and peak calling was performed using MACS (1.4.2).
Genome_build: h19

molecule: genomic DNA

source_name: colon-derived

extract_protocol:
Human HCT116 cells were grown to 200,000 cells per well, crosslinked, and sheared using 96-well plate PIXUL sonicator. Fragmented chromatin was used in ChIP assays with the listed antibodies.
ChIP and library prep was performed for each factor from a single well using Active Motif’s Low Cell ChIP-Seq Kit (Catalog number 53084). Libraries were sequenced on a NextSeq 500 as PE75 or SE75 with dual 8bp indexing, allowing for PCR de-duplication with molecular identifiers at the i5 position (see product manual).

tag: cell line

value: HCT116 colorectal carcinoma

value: colon-derived

tag: chip antibody

value: H3K27Ac antibody 39133 Active Motif


title: CTCF-ChIP-seq

value: CTCF antibody 61311 Active Motif


title: H3K27me3-ChIP-seq

value: H3K27me3  antibody 39155 Active Motif


title: H3K36me3-ChIP-seq

value: H3K36me3 antibody 61101 Active Motif


title: N129-C3


title: endometrium13_cancer_G3


title: endometrium15_cancer_G2


title: H3K9Ac-ChIP-seq

value: H3K9Ac antibody 91103 Active Motif


title: endometrium12_cancer_G3


title: endometrium9_cancer_G3


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, with SP600125 drug pre-tx, biological replicate 3

description: Gene expression data from NHEK exposed with 200 uM SM and SP600125 pre-tx on 090805, harvested at 8 hour

value: primary human epidermal keratinocytes (NHEK)


title: 090819 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, with PD98059 drug pre-tx, biological replicate 2


title: 090805 date of exposure, NHEK 200 uM sulfur mustard, 8 hour timepoint, no drug, biological replicate 1


title: N129-C2


title: N129-C1


title: H3K4me3-ChIP-seq

value: H3K4me3 antibody 39159 Active Motif


title: endometrium14_cancer_G2


title: H3K4me1-ChIP-seq

value: H3K4me1 antibody 39297 Active Motif


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 1

source_name: NHEK exposed with 0 uM SM and no drug on 090805, harvested at 1 hour


title: 090805 date of exposure, NHEK 0 uM sulfur mustard, 1 hour timepoint, no drug, biological replicate 2


title: N88

value: epithelial


title: endometrium7_cancer_G1


title: endometrium8_cancer_G3


title: endometrium5_control

source_name: endometrium control

value: endometrium


title: endometrium6_control