title: Brain_PH3_1H_Rat716

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: Genotyping data for sample 1600G

status: Public on Jun 01 2021

type: genomic

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software

hyb_protocol: Standard Illumina protocol for Infinium 2.5M  Beadchip

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina 2.5M platform we used QuantiSNP, iPattern, PennCNV.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from whole blood

extract_protocol: Genomic DNA extracted using the Qiagen DNA micro kit (QIAgen, Hilden, Germany)

tag: gender

value: Male

tag: ethnicity

value: North-Central European ancestry

tag: celltype

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_2_DC35_E17

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

molecule: total RNA

organism: Mus musculus

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_E21

value: F

value: Mac III


title: Genotyping data for sample 1599G

scan_protocol: Standard Illumina protocol for Infinium 2.5M  Beadchip

value: Roma ancestry


title: Liver_PH3_1H_Rat712

type: RNA

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

country: USA

institute: USAMRICD

description: 660 ppm  x 32.2 min (21,252 ppm x min)

hyb_protocol: The complimentary RNA (cRNA) produced from the isolated total RNA was then fragmented and hybridized to GeneChip HT RG-230PM array plates (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The HT RG-230PM array plates were scanned using an Affymetrix GeneTitan system.

data_processing: Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)

label: Biotin

organism: Rattus norvegicus

label_protocol: The isolated RNA was amplified and biotinylated using the GeneChip 3’ in vitro transcription (IVT) Plus reagent kit (Affymetrix; Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: Male Sprague-Dawley rats (300-400 g, Charles-River Laboratories, Wilmington, MA) were individually housed under standard conditions (12 hour light/dark cycle) with standard rodent chow and water provided ad libitum.

extract_protocol: Following eutanasia (ketamine (90 mg/kg) and xylazine (10 mg/kg)  by im followed by exsanguination), tissues were flash frozen in liquid nitrogen and stored at -80 until processing. Tissues were cryopulverized and total RNA isolated using RNeasy Plus mini kits (Qiagen; Germantown, MD) according to manufacturer's instructions with a DNase digestion step. Blood samples were collected via heart stick. RNA was isolated from collected blood samples and processed using the RNeasy Protect Animal Blood System (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Whole-body PH3 inhalation exposures were conducted as described in Wong et al., 2017. PH3 concentration was 21,252 ppm x minute (660 ppm x 32.2 minutes), representing a “high” concentration Ct.

tag: tissue

value: Liver

tag: time point

tag: exposure


title: F_P7_hyperoxia_CD45_2_DC35_E16

value: Mac II


title: M_P7_hyperoxia_CD45_1_DC35_I7

value: Mac V


title: Genotyping data for sample 2291G

label_protocol: Standard Illumina protocol for Infinium 2.5M  Beadchip


title: M_P7_hyperoxia_CD45_1_DC35_M16


title: Kidney_PH3_1H_Rat712

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: Blood_PH3_1H_Rat713

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: Genotyping data for sample 1594G


title: F_P7_hyperoxia_CD45_2_DC35_G3


title: Lung_PH3_1H_Rat712

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Genotyping data for sample 1226G


title: M_P7_hyperoxia_CD45_2_DC35_A8


title: F_P7_hyperoxia_CD45_2_DC35_E10

value: neutrophil


title: F_P7_hyperoxia_CD45_2_DC35_M21


title: Genotyping data for sample 1224G

value: Male


title: Genotyping data for sample 1222G

value: North-Central European ancestry


title: F_P7_hyperoxia_CD45_2_DC35_I10

value: basophil


title: Heart_PH3_1H_Rat712

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: Brain_Air_1H_Rat720

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain

value: Air


title: F_P7_hyperoxia_CD45_2_DC35_A4

value: hyperoxia

value: immune


title: Genotyping data for sample 1221G

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_J2

value: M

value: B cell


title: Genotyping data for sample 1233G

value: Roma ancestry


title: M_P7_hyperoxia_CD45_2_DC35_E1

value: Mac III


title: M_P7_hyperoxia_CD45_1_DC35_I9

value: mast cell II


title: Genotyping data for sample 1220G


title: Kidney_PH3_1H_Rat710

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: F_P7_hyperoxia_CD45_2_DC35_H19

value: F

value: Mac IV


title: Brain_PH3_1H_Rat712

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Genotyping data for sample 1219G

value: Male


title: M_P7_hyperoxia_CD45_1_DC35_F5

value: neutrophil


title: Heart_PH3_1H_Rat710

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_P14


title: F_P7_hyperoxia_CD45_2_DC35_M11

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_O17

value: DC I


title: M_P7_hyperoxia_CD45_1_DC35_O20


title: Lung_PH3_1H_Rat710

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Genotyping data for sample 1217G

value: North-Central European ancestry


title: Liver_PH3_1H_Rat710

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: M_P7_hyperoxia_CD45_2_DC35_E8

value: hyperoxia

value: immune


title: F_P7_hyperoxia_CD45_2_DC35_I7


title: M_P7_hyperoxia_CD45_2_DC35_N19

value: M


title: Genotyping data for sample 1214G

value: DNA extracted from whole blood


title: F_P7_hyperoxia_CD45_2_DC35_O20


title: F_P7_hyperoxia_CD45_2_DC35_M7


title: Brain_PH3_1H_Rat710

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_1_DC35_I4

value: mast cell


title: Genotyping data for sample 1213G

value: Roma ancestry


title: F_P7_hyperoxia_CD45_2_DC35_C5


title: M_P7_hyperoxia_CD45_1_DC35_D20

value: basophil


title: OlfacBulb_Air_6H_Rat526

description: 0ppm  x 25 min (0 ppm x min)

source_name: Olfac Bulb_Air_6H

treatment_protocol: Whole-body PH3 inhalation exposures were conducted as described in Wong et al., 2017. PH3 concentration was 16,500 ppm x minute (660 ppm x 25 minutes), representing a “medium” concentration Ct.

value: Olfac Bulb

value: Air


title: OlfacBulb_PH3_6H_Rat522

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Olfac Bulb_PH3_6H


title: OlfacBulb_PH3_3H_Rat517

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Olfac Bulb_PH3_3H


title: Genotyping data for sample 1121G

value: Male


title: F_P7_hyperoxia_CD45_2_DC35_K4

value: F

value: B cell


title: M_P7_hyperoxia_CD45_1_DC35_O19

value: neutrophil


title: Genotyping data for sample 1215G


title: M_P7_hyperoxia_CD45_2_DC35_L13

value: Mac III


title: M_P7_hyperoxia_CD45_2_DC35_F13

value: Mac V


title: OlfacBulb_PH3_3H_Rat516

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_L19


title: Genotyping data for sample 1103G


title: Genotyping data for sample 1119G

value: North-Central European ancestry


title: Genotyping data for sample 1101G


title: OlfacBulb_Air_3H_Rat520

description: 0ppm  x 25 min (0 ppm x min)

source_name: Olfac Bulb_Air_3H


title: F_P7_hyperoxia_CD45_2_DC35_D13

value: hyperoxia


title: OlfacBulb_Air_3H_Rat514

description: 0ppm  x 25 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_K13

value: immune


title: M_P7_hyperoxia_CD45_2_DC35_K1

value: M


title: Genotyping data for sample 1098G

value: DNA extracted from whole blood


title: OlfacBulb_Air_1H_Rat509

description: 0ppm  x 25 min (0 ppm x min)

source_name: Olfac Bulb_Air_1H


title: OlfacBulb_PH3_3H_Rat512

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 1096G


title: M_P7_hyperoxia_CD45_1_DC35_J14

value: Mac IV


title: M_P7_hyperoxia_CD45_1_DC35_N16

value: DC III


title: M_P7_hyperoxia_CD45_1_DC35_C2


title: Genotyping data for sample 1120G


title: OlfacBulb_PH3_1H_Rat508

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Olfac Bulb_PH3_1H


title: Genotyping data for sample 1093G

value: Roma ancestry


title: M_P7_hyperoxia_CD45_1_DC35_C4


title: M_P7_hyperoxia_CD45_2_DC35_L14


title: OlfacBulb_PH3_1H_Rat506

description: 660ppm  x 25 min (16,500 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_J7


title: OlfacBulb_Air_1H_Rat507

description: 0ppm  x 25 min (0 ppm x min)


title: Genotyping data for sample 1092G


title: M_P7_hyperoxia_CD45_2_DC35_J6


title: F_P7_hyperoxia_CD45_2_DC35_L18


title: M_P7_hyperoxia_CD45_2_DC35_M4


title: F_P7_hyperoxia_CD45_2_DC35_I5


title: BrainStem_Air_24H_Rat502

description: 0ppm  x 25 min (0 ppm x min)

source_name: Brain Stem_Air_24H

value: Brain Stem


title: Genotyping data for sample 1090G


title: F_P7_hyperoxia_CD45_2_DC35_A10

value: mast cell II


title: Genotyping data for sample 1070G


title: F_P7_hyperoxia_CD45_2_DC35_D2

value: basophil


title: M_P7_hyperoxia_CD45_1_DC35_A9


title: Genotyping data for sample 1069G

value: Male


title: M_P7_hyperoxia_CD45_2_DC35_H10


title: M_P7_hyperoxia_CD45_1_DC35_D1


title: M_P7_hyperoxia_CD45_1_DC35_A7


title: Genotyping data for sample 1068G


title: M_P7_hyperoxia_CD45_2_DC35_J11

value: T cell


title: Genotyping data for sample 1067G


title: M_P7_hyperoxia_CD45_1_DC35_H14

value: IL cell


title: OlfacBulb_Air_24H_Rat502

description: 0ppm  x 25 min (0 ppm x min)

source_name: Olfac Bulb_Air_24H

value: Olfac Bulb

value: Air


title: M_P7_hyperoxia_CD45_1_DC35_M22

value: Mac III


title: M_P7_hyperoxia_CD45_1_DC35_P5


title: Heart_Air_24H_Rat502

description: 0ppm  x 25 min (0 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_1_DC35_F14

value: hyperoxia


title: Genotyping data for sample 1066G


title: Genotyping data for sample 1065G

value: North-Central European ancestry


title: F_P7_hyperoxia_CD45_2_DC35_G22

value: F

value: immune


title: F_P7_hyperoxia_CD45_2_DC35_B11


title: Genotyping data for sample 1064G

value: DNA extracted from whole blood


title: Lung_Air_24H_Rat502

description: 0ppm  x 25 min (0 ppm x min)

value: Lung


title: F_P7_hyperoxia_CD45_2_DC35_D3


title: Genotyping data for sample 1063G

value: Roma ancestry


title: M_P7_hyperoxia_CD45_1_DC35_K19

value: M

value: Mac V


title: M_P7_hyperoxia_CD45_2_DC35_G12


title: Kidney_Air_24H_Rat502

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney


title: OlfacBulb_Air_3H_Rat490

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_A22


title: M_P7_hyperoxia_CD45_1_DC35_I2

value: neutrophil


title: M_P7_hyperoxia_CD45_1_DC35_J13

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_I17


title: Genotyping data for sample 1062G

value: Male


title: Genotyping data for sample 1061G


title: M_P7_hyperoxia_CD45_2_DC35_E9

value: mast cell


title: OlfacBulb_Air_24H_Rat491

description: 0ppm  x 25 min (0 ppm x min)

value: Olfac Bulb

value: Air


title: Kidney_Air_3H_Rat490

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_H22


title: M_P7_hyperoxia_CD45_2_DC35_H14


title: OlfacBulb_PH3_24H_Rat489

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Olfac Bulb_PH3_24H


title: Genotyping data for sample 1060G


title: OlfacBulb_PH3_24H_Rat488

description: 660ppm  x 25 min (16,500 ppm x min)


title: OlfacBulb_Air_1H_Rat485

description: 0ppm  x 25 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_K5

value: Mac III


title: Genotyping data for sample 1058G


title: F_P7_hyperoxia_CD45_2_DC35_B6

value: hyperoxia

value: B cell


title: OlfacBulb_PH3_1H_Rat483

description: 660ppm  x 25 min (16,500 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_F2

value: F


title: OlfacBulb_Air_1H_Rat484

description: 0ppm  x 25 min (0 ppm x min)


title: Genotyping data for sample 1056G

value: North-Central European ancestry


title: M_P7_hyperoxia_CD45_1_DC35_C10

value: immune


title: Genotyping data for sample 7707

value: DNA extracted from whole blood


title: F_P7_hyperoxia_CD45_2_DC35_F5

value: Mac II


title: M_P7_hyperoxia_CD45_1_DC35_K17

value: M


title: OlfacBulb_Air_24H_Rat479

description: 0ppm  x 25 min (0 ppm x min)


title: OlfacBulb_Air_24H_Rat478

description: 0ppm  x 25 min (0 ppm x min)


title: Genotyping data for sample 7706


title: Genotyping data for sample 7705


title: M_P7_hyperoxia_CD45_1_DC35_A6


title: M_P7_hyperoxia_CD45_2_DC35_B17


title: F_P7_hyperoxia_CD45_2_DC35_P16

value: Mac V


title: OlfacBulb_PH3_24H_Rat476

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_M15


title: M_P7_hyperoxia_CD45_2_DC35_I6

value: mast cell II


title: F_P7_hyperoxia_CD45_2_DC35_I13


title: OlfacBulb_PH3_1H_Rat482

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_P7


title: Genotyping data for sample 7704


title: OlfacBulb_PH3_24H_Rat475

description: 660ppm  x 25 min (16,500 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_G11

value: basophil


title: M_P7_hyperoxia_CD45_1_DC35_A23


title: Genotyping data for sample 7702


title: M_P7_hyperoxia_CD45_1_DC35_G10

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_N20


title: F_P7_hyperoxia_CD45_2_DC35_O16


title: Genotyping data for sample 7700

value: Male


title: Genotyping data for sample 7699


title: F_P7_hyperoxia_CD45_2_DC35_M23


title: OlfacBulb_Air_1H_Rat472

description: 0ppm  x 25 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_I2

value: mast cell


title: M_P7_hyperoxia_CD45_1_DC35_C7


title: M_P7_hyperoxia_CD45_1_DC35_E14


title: Lung_Air_3H_Rat400

description: 0ppm  x 25 min (0 ppm x min)

value: Lung


title: Genotyping data for sample 7698


title: Kidney_Air_3H_Rat400

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney

value: Air


title: Genotyping data for sample 7678


title: F_P7_hyperoxia_CD45_2_DC35_O13

value: hyperoxia


title: M_P7_hyperoxia_CD45_2_DC35_B7


title: Genotyping data for sample 7703


title: M_P7_hyperoxia_CD45_1_DC35_I23

value: neutrophil


title: Heart_Air_3H_Rat400

description: 0ppm  x 25 min (0 ppm x min)

value: Heart


title: Genotyping data for sample 7677

value: North-Central European ancestry


title: M_P7_hyperoxia_CD45_1_DC35_B8

value: immune

value: T cell


title: M_P7_hyperoxia_CD45_2_DC35_O17


title: Genotyping data for sample 7676

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_E11

value: M

value: Mac III


title: M_P7_hyperoxia_CD45_2_DC35_F17


title: M_P7_hyperoxia_CD45_2_DC35_M21


title: Genotyping data for sample 7673


title: Genotyping data for sample 7674


title: M_P7_hyperoxia_CD45_1_DC35_G17

value: DC II


title: OlfacBulb_Air_3H_Rat400

description: 0ppm  x 25 min (0 ppm x min)

value: Olfac Bulb


title: F_P7_hyperoxia_CD45_2_DC35_N4

value: F


title: M_P7_hyperoxia_CD45_2_DC35_I9


title: F_P7_hyperoxia_CD45_2_DC35_A21


title: BrainStem_Air_3H_Rat400

description: 0ppm  x 25 min (0 ppm x min)

source_name: Brain Stem_Air_3H

value: Brain Stem


title: Lung_PH3_3H_Rat399

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_E14

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_A3


title: OlfacBulb_PH3_3H_Rat399

description: 660ppm  x 25 min (16,500 ppm x min)


title: Kidney_PH3_3H_Rat399

description: 660ppm  x 25 min (16,500 ppm x min)


title: Heart_PH3_3H_Rat399

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 7669

value: Male


title: M_P7_hyperoxia_CD45_2_DC35_A6


title: M_P7_hyperoxia_CD45_2_DC35_H22

value: basophil


title: M_P7_hyperoxia_CD45_2_DC35_E18


title: Genotyping data for sample 7640


title: F_P7_hyperoxia_CD45_2_DC35_H7


title: Blood_Air_3H_Rat400

description: 0ppm  x 25 min (0 ppm x min)

value: Blood

value: Air


title: M_P7_hyperoxia_CD45_1_DC35_F12

value: hyperoxia


title: Genotyping data for sample 7672


title: Genotyping data for sample 7639


title: Blood_PH3_3H_Rat399

description: 660ppm  x 25 min (16,500 ppm x min)


title: OlfacBulb_Air_6H_Rat394

description: 0ppm  x 25 min (0 ppm x min)


title: BrainStem_PH3_3H_Rat399

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Brain Stem_PH3_3H


title: Kidney_Air_6H_Rat394

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney


title: F_P7_hyperoxia_CD45_2_DC35_K23

value: mast cell


title: M_P7_hyperoxia_CD45_1_DC35_K21

value: immune

value: neutrophil


title: Genotyping data for sample 7671

value: North-Central European ancestry

value: DNA extracted from whole blood


title: F_P7_hyperoxia_CD45_2_DC35_H12


title: M_P7_hyperoxia_CD45_1_DC35_G6

value: M

value: Mac III


title: M_P7_hyperoxia_CD45_1_DC35_E8

value: B cell


title: M_P7_hyperoxia_CD45_1_DC35_J7

value: Mac V


title: Genotyping data for sample 7636


title: Lung_Air_6H_Rat394

description: 0ppm  x 25 min (0 ppm x min)

value: Lung


title: M_P7_hyperoxia_CD45_2_DC35_C15


title: F_P7_hyperoxia_CD45_2_DC35_M5

value: F


title: Genotyping data for sample 7635

value: Male


title: F_P7_hyperoxia_CD45_2_DC35_O9


title: Heart_Air_6H_Rat394

description: 0ppm  x 25 min (0 ppm x min)

value: Heart


title: Genotyping data for sample 7634


title: Genotyping data for sample 7637


title: BrainStem_Air_6H_Rat394

description: 0ppm  x 25 min (0 ppm x min)

source_name: Brain Stem_Air_6H

value: Brain Stem


title: M_P7_hyperoxia_CD45_2_DC35_F9


title: OlfacBulb_PH3_6H_Rat391

description: 660ppm  x 25 min (16,500 ppm x min)

value: Olfac Bulb


title: Lung_PH3_6H_Rat391

description: 660ppm  x 25 min (16,500 ppm x min)


title: Blood_Air_6H_Rat394

description: 0ppm  x 25 min (0 ppm x min)

value: Blood

value: Air


title: Genotyping data for sample 7633


title: M_P7_hyperoxia_CD45_1_DC35_K3

value: hyperoxia

value: DC III


title: M_P7_hyperoxia_CD45_1_DC35_D8

value: immune


title: M_P7_hyperoxia_CD45_1_DC35_L22

value: neutrophil


title: M_P7_hyperoxia_CD45_2_DC35_F5

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_A12

value: M


title: M_P7_hyperoxia_CD45_1_DC35_G7


title: Genotyping data for sample 7625

value: North-Central European ancestry

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_M23

value: Mac III


title: F_P7_hyperoxia_CD45_2_DC35_M8

value: basophil


title: F_P7_hyperoxia_CD45_2_DC35_L10

value: F


title: Genotyping data for sample 7623

value: Male


title: BrainStem_PH3_6H_Rat391

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Brain Stem_PH3_6H


title: F_P7_hyperoxia_CD45_2_DC35_J23


title: F_P7_hyperoxia_CD45_2_DC35_P11


title: Genotyping data for sample 7622


title: Genotyping data for sample 7630


title: Genotyping data for sample 7626


title: Blood_PH3_6H_Rat391

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_E19

value: mast cell


title: Lung_Air_6H_Rat388

description: 0ppm  x 25 min (0 ppm x min)

value: Lung


title: M_P7_hyperoxia_CD45_2_DC35_O19


title: Heart_PH3_6H_Rat391

description: 660ppm  x 25 min (16,500 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_2_DC35_M23


title: OlfacBulb_Air_6H_Rat388

description: 0ppm  x 25 min (0 ppm x min)

value: Olfac Bulb


title: F_P7_hyperoxia_CD45_2_DC35_M6


title: Genotyping data for sample 7619


title: Kidney_PH3_6H_Rat391

description: 660ppm  x 25 min (16,500 ppm x min)

value: Kidney


title: Genotyping data for sample 7618


title: Kidney_Air_6H_Rat388

description: 0ppm  x 25 min (0 ppm x min)

value: Air


title: M_P7_hyperoxia_CD45_2_DC35_M14

value: hyperoxia

value: T cell


title: F_P7_hyperoxia_CD45_2_DC35_M14

value: immune

value: Mac V


title: M_P7_hyperoxia_CD45_1_DC35_J8

value: M


title: F_P7_hyperoxia_CD45_2_DC35_J16


title: F_P7_hyperoxia_CD45_2_DC35_E2

value: Mac IV


title: Genotyping data for sample 7596

value: North-Central European ancestry

value: DNA extracted from whole blood


title: Genotyping data for sample 7620


title: Heart_Air_6H_Rat388

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_O16

value: basophil


title: BrainStem_Air_6H_Rat388

description: 0ppm  x 25 min (0 ppm x min)

value: Brain Stem


title: Genotyping data for sample 7595

value: Male


title: Blood_Air_6H_Rat388

description: 0ppm  x 25 min (0 ppm x min)

value: Blood


title: F_P7_hyperoxia_CD45_2_DC35_J12

value: F

value: B cell


title: F_P7_hyperoxia_CD45_2_DC35_G21

value: Mac II


title: M_P7_hyperoxia_CD45_2_DC35_O4

value: neutrophil


title: OlfacBulb_PH3_6H_Rat387

description: 660ppm  x 25 min (16,500 ppm x min)

value: Olfac Bulb


title: Genotyping data for sample 7593


title: M_P7_hyperoxia_CD45_2_DC35_A16

value: hyperoxia

value: Mac III


title: Lung_PH3_6H_Rat387

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: Genotyping data for sample 7592


title: M_P7_hyperoxia_CD45_1_DC35_P22

value: immune

value: DC I


title: M_P7_hyperoxia_CD45_2_DC35_C23

value: M

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_M4


title: F_P7_hyperoxia_CD45_2_DC35_D21


title: Genotyping data for sample 7617

value: North-Central European ancestry

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_B16


title: Kidney_PH3_6H_Rat387

description: 660ppm  x 25 min (16,500 ppm x min)

value: Kidney


title: M_P7_hyperoxia_CD45_1_DC35_B9


title: M_P7_hyperoxia_CD45_2_DC35_G17


title: Genotyping data for sample 7590

value: Male


title: Heart_PH3_6H_Rat387

description: 660ppm  x 25 min (16,500 ppm x min)

value: Heart


title: F_P7_hyperoxia_CD45_2_DC35_P14

value: F

value: Mac IV


title: Genotyping data for sample 7589


title: Genotyping data for sample 7588


title: M_P7_hyperoxia_CD45_1_DC35_K20

value: B cell


title: M_P7_hyperoxia_CD45_2_DC35_L15


title: F_P7_hyperoxia_CD45_2_DC35_I14

value: T cell


title: Genotyping data for sample 7587


title: M_P7_hyperoxia_CD45_2_DC35_B14

value: DC II


title: M_P7_hyperoxia_CD45_2_DC35_O13

value: hyperoxia


title: F_P7_hyperoxia_CD45_2_DC35_C15

value: Mac III


title: OlfacBulb_Air_6H_Rat382

description: 0ppm  x 25 min (0 ppm x min)

value: Olfac Bulb

value: Air


title: BrainStem_PH3_6H_Rat387

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: Genotyping data for sample 7583


title: M_P7_hyperoxia_CD45_2_DC35_C12

value: M

value: immune

value: DC I


title: Blood_PH3_6H_Rat387

description: 660ppm  x 25 min (16,500 ppm x min)

value: Blood


title: Genotyping data for sample 7591

value: North-Central European ancestry

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_O12

value: neutrophil


title: M_P7_hyperoxia_CD45_1_DC35_C15


title: Genotyping data for sample 7579

value: Male


title: M_P7_hyperoxia_CD45_1_DC35_C14


title: M_P7_hyperoxia_CD45_1_DC35_N18


title: M_P7_hyperoxia_CD45_1_DC35_B13

value: Mac IV


title: Heart_Air_6H_Rat382

description: 0ppm  x 25 min (0 ppm x min)

value: Heart


title: Genotyping data for sample 7578


title: BrainStem_Air_6H_Rat382

description: 0ppm  x 25 min (0 ppm x min)


title: Genotyping data for sample 7577


title: F_P7_hyperoxia_CD45_2_DC35_P4

value: F

value: B cell


title: Blood_Air_6H_Rat382

description: 0ppm  x 25 min (0 ppm x min)


title: OlfacBulb_PH3_6H_Rat381

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_G23

value: hyperoxia

value: Mac V


title: Genotyping data for sample 7576


title: Genotyping data for sample 7581


title: M_P7_hyperoxia_CD45_1_DC35_M6

value: Mac III


title: Lung_Air_6H_Rat382

description: 0ppm  x 25 min (0 ppm x min)

value: Lung

value: Air


title: Kidney_Air_6H_Rat382

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney


title: M_P7_hyperoxia_CD45_2_DC35_O22

value: M

value: immune


title: Lung_PH3_6H_Rat381

description: 660ppm  x 25 min (16,500 ppm x min)


title: Kidney_PH3_6H_Rat381

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_N7


title: Genotyping data for sample 7574


title: Genotyping data for sample 7575


title: F_P7_hyperoxia_CD45_2_DC35_J1


title: M_P7_hyperoxia_CD45_1_DC35_B18


title: M_P7_hyperoxia_CD45_2_DC35_H20

value: NK cell


title: Genotyping data for sample 7572

value: North-Central European ancestry


title: M_P7_hyperoxia_CD45_1_DC35_H4


title: F_P7_hyperoxia_CD45_2_DC35_F8

value: mast cell


title: F_P7_hyperoxia_CD45_2_DC35_A6


title: M_P7_hyperoxia_CD45_1_DC35_H7


title: F_P7_hyperoxia_CD45_2_DC35_L3

value: T cell


title: M_P7_hyperoxia_CD45_2_DC35_L20


title: BrainStem_PH3_6H_Rat381

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: Genotyping data for sample 7570

value: Male

value: DNA extracted from whole blood


title: Lung_Air_6H_Rat377

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_N9


title: Blood_PH3_6H_Rat381

description: 660ppm  x 25 min (16,500 ppm x min)

value: Blood


title: Genotyping data for sample 7569


title: Kidney_Air_6H_Rat377

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_K15


title: F_P7_hyperoxia_CD45_2_DC35_K19

value: F


title: M_P7_hyperoxia_CD45_2_DC35_N14

value: hyperoxia

value: Mac II


title: M_P7_hyperoxia_CD45_2_DC35_C18

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_C10

value: basophil


title: M_P7_hyperoxia_CD45_2_DC35_N23

value: Mac IV


title: Genotyping data for sample 7568


title: Genotyping data for sample 7567


title: Genotyping data for sample 7571


title: Genotyping data for sample 7565


title: F_P7_hyperoxia_CD45_2_DC35_L21

value: Mac III


title: M_P7_hyperoxia_CD45_2_DC35_L17

value: M


title: Genotyping data for sample 7560


title: M_P7_hyperoxia_CD45_1_DC35_O10

value: immune


title: Heart_PH3_6H_Rat381

description: 660ppm  x 25 min (16,500 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_1_DC35_M12


title: F_P7_hyperoxia_CD45_2_DC35_E22


title: BrainStem_Air_6H_Rat376

description: 0ppm  x 25 min (0 ppm x min)

value: Air


title: Lung_PH3_6H_Rat375

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: Blood_Air_6H_Rat377

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_N21


title: Genotyping data for sample 7557

value: North-Central European ancestry


title: Heart_Air_6H_Rat377

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_L2


title: M_P7_hyperoxia_CD45_2_DC35_K8


title: Genotyping data for sample 7555


title: Heart_PH3_6H_Rat375

description: 660ppm  x 25 min (16,500 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_C16


title: F_P7_hyperoxia_CD45_2_DC35_F11


title: F_P7_hyperoxia_CD45_2_DC35_N15


title: Genotyping data for sample 7553


title: F_P7_hyperoxia_CD45_2_DC35_M12

value: neutrophil


title: Genotyping data for sample 7552

value: Male


title: M_P7_hyperoxia_CD45_1_DC35_B10


title: BrainStem_PH3_6H_Rat375

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: Genotyping data for sample 7559

value: DNA extracted from whole blood


title: F_P7_hyperoxia_CD45_2_DC35_I16

value: F


title: M_P7_hyperoxia_CD45_2_DC35_P23

value: hyperoxia


title: M_P7_hyperoxia_CD45_1_DC35_A16


title: M_P7_hyperoxia_CD45_2_DC35_A14


title: Genotyping data for sample 7549


title: M_P7_hyperoxia_CD45_1_DC35_E21


title: Genotyping data for sample 7546


title: Kidney_PH3_6H_Rat375

description: 660ppm  x 25 min (16,500 ppm x min)

value: Kidney


title: Blood_PH3_6H_Rat375

description: 660ppm  x 25 min (16,500 ppm x min)

value: Blood


title: Genotyping data for sample 7545


title: Genotyping data for sample 7542


title: M_P7_hyperoxia_CD45_2_DC35_C8


title: M_P7_hyperoxia_CD45_1_DC35_N17


title: M_P7_hyperoxia_CD45_2_DC35_K13


title: Heart_Air_3H_Rat370

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_F15

value: DC III


title: M_P7_hyperoxia_CD45_2_DC35_F18


title: M_P7_hyperoxia_CD45_1_DC35_I16


title: BrainStem_Air_3H_Rat370

description: 0ppm  x 25 min (0 ppm x min)


title: Blood_Air_3H_Rat370

description: 0ppm  x 25 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_C7


title: Lung_Air_3H_Rat370

description: 0ppm  x 25 min (0 ppm x min)


title: Lung_PH3_3H_Rat368

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 7551


title: Heart_PH3_3H_Rat368

description: 660ppm  x 25 min (16,500 ppm x min)


title: BrainStem_PH3_3H_Rat368

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 7538

value: Roma ancestry


title: M_P7_hyperoxia_CD45_2_DC35_P8


title: M_P7_hyperoxia_CD45_2_DC35_J5

value: Mac IV


title: Blood_PH3_3H_Rat368

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_D5

value: M

value: Mac III


title: Lung_Air_3H_Rat365

description: 0ppm  x 25 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_A23

value: immune


title: M_P7_hyperoxia_CD45_2_DC35_C9

value: NK cell


title: Genotyping data for sample 7540


title: Heart_Air_3H_Rat365

description: 0ppm  x 25 min (0 ppm x min)

value: Heart

value: Air


title: Genotyping data for sample 7526


title: Genotyping data for sample 7525


title: Genotyping data for sample 7515


title: M_P7_hyperoxia_CD45_2_DC35_F23

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_P5


title: F_P7_hyperoxia_CD45_2_DC35_B10

value: mast cell


title: Genotyping data for sample 7539

value: Male


title: F_P7_hyperoxia_CD45_2_DC35_C3


title: Genotyping data for sample 7536

value: DNA extracted from whole blood


title: Genotyping data for sample 7523


title: M_P7_hyperoxia_CD45_2_DC35_F16

value: basophil


title: M_P7_hyperoxia_CD45_1_DC35_G9

value: hyperoxia


title: M_P7_hyperoxia_CD45_2_DC35_H16


title: M_P7_hyperoxia_CD45_2_DC35_G2


title: F_P7_hyperoxia_CD45_2_DC35_C20

value: F

value: B cell


title: M_P7_hyperoxia_CD45_2_DC35_N8

value: neutrophil


title: M_P7_hyperoxia_CD45_2_DC35_O18


title: BrainStem_Air_3H_Rat365

description: 0ppm  x 25 min (0 ppm x min)

value: Brain Stem


title: F_P7_hyperoxia_CD45_2_DC35_N12


title: Genotyping data for sample 7514

value: Roma ancestry


title: F_P7_hyperoxia_CD45_2_DC35_D4


title: F_P7_hyperoxia_CD45_2_DC35_J8


title: Genotyping data for sample 7512


title: Blood_Air_3H_Rat365

description: 0ppm  x 25 min (0 ppm x min)

value: Blood


title: Kidney_Air_3H_Rat365

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney


title: Kidney_PH3_3H_Rat363

description: 660ppm  x 25 min (16,500 ppm x min)


title: Lung_PH3_3H_Rat361

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: Kidney_PH3_3H_Rat361

description: 660ppm  x 25 min (16,500 ppm x min)


title: Heart_PH3_3H_Rat361

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_D3

value: M

value: immune


title: M_P7_hyperoxia_CD45_1_DC35_C13

value: Mac III


title: M_P7_hyperoxia_CD45_2_DC35_M7

value: DC II


title: Genotyping data for sample 7511


title: Genotyping data for sample 7510


title: Genotyping data for sample 7507


title: F_P7_hyperoxia_CD45_2_DC35_H17


title: F_P7_hyperoxia_CD45_2_DC35_N13


title: M_P7_hyperoxia_CD45_2_DC35_J23


title: M_P7_hyperoxia_CD45_1_DC35_D14


title: M_P7_hyperoxia_CD45_1_DC35_K4


title: M_P7_hyperoxia_CD45_2_DC35_G8


title: Genotyping data for sample 7505


title: M_P7_hyperoxia_CD45_1_DC35_B6


title: Lung_PH3_3H_Rat359

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 7504


title: F_P7_hyperoxia_CD45_2_DC35_B12


title: Blood_PH3_3H_Rat361

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_C8

value: Mac V


title: Genotyping data for sample 7503

value: Male


title: Heart_PH3_3H_Rat359

description: 660ppm  x 25 min (16,500 ppm x min)

value: Heart


title: Blood_PH3_3H_Rat359

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_L18


title: BrainStem_PH3_3H_Rat359

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 7501

value: DNA extracted from whole blood


title: Genotyping data for sample 7506


title: F_P7_hyperoxia_CD45_2_DC35_D6

value: hyperoxia


title: Genotyping data for sample 7500


title: F_P7_hyperoxia_CD45_2_DC35_I8

value: F


title: Genotyping data for sample 7499


title: M_P7_hyperoxia_CD45_1_DC35_O17


title: M_P7_hyperoxia_CD45_2_DC35_N15

value: DC I


title: Genotyping data for sample 7498


title: M_P7_hyperoxia_CD45_2_DC35_L10

value: NK cell


title: F_P7_hyperoxia_CD45_2_DC35_F19

value: mast cell


title: BrainStem_PH3_3H_Rat358

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: BrainStem_PH3_1H_Rat357

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Brain Stem_PH3_1H


title: Kidney_PH3_1H_Rat357

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 7490

value: Roma ancestry


title: M_P7_hyperoxia_CD45_2_DC35_M19


title: M_P7_hyperoxia_CD45_1_DC35_K8

value: Mac IV


title: Heart_PH3_1H_Rat357

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_I11


title: M_P7_hyperoxia_CD45_1_DC35_J19


title: Genotyping data for sample 7489


title: Genotyping data for sample 7488


title: M_P7_hyperoxia_CD45_1_DC35_N5


title: F_P7_hyperoxia_CD45_2_DC35_A5

value: IL cell


title: Lung_PH3_1H_Rat357

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: F_P7_hyperoxia_CD45_2_DC35_M10

value: immune


title: M_P7_hyperoxia_CD45_1_DC35_G22

value: M

value: Mac III


title: F_P7_hyperoxia_CD45_2_DC35_A11

value: neutrophil


title: F_P7_hyperoxia_CD45_2_DC35_F9


title: Kidney_PH3_3H_Rat359

description: 660ppm  x 25 min (16,500 ppm x min)

value: Kidney


title: Genotyping data for sample 7487

value: Male


title: F_P7_hyperoxia_CD45_2_DC35_H21


title: F_P7_hyperoxia_CD45_2_DC35_C2

value: mast cell II


title: F_P7_hyperoxia_CD45_2_DC35_L4

value: hyperoxia

value: Mac V


title: Genotyping data for sample 7476

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_J17


title: M_P7_hyperoxia_CD45_1_DC35_L21


title: Genotyping data for sample 7473


title: Blood_PH3_1H_Rat357

description: 660ppm  x 25 min (16,500 ppm x min)

value: Blood


title: M_P7_hyperoxia_CD45_1_DC35_P20


title: Genotyping data for sample 7472


title: Lung_Air_3H_Rat355

description: 0ppm  x 25 min (0 ppm x min)

value: Air


title: Genotyping data for sample 7471


title: M_P7_hyperoxia_CD45_2_DC35_I20

value: B cell


title: Genotyping data for sample 7470

value: Roma ancestry


title: M_P7_hyperoxia_CD45_1_DC35_K10


title: M_P7_hyperoxia_CD45_1_DC35_P10

value: DC III


title: M_P7_hyperoxia_CD45_2_DC35_H13


title: M_P7_hyperoxia_CD45_1_DC35_O2

value: T cell


title: M_P7_hyperoxia_CD45_2_DC35_B4


title: Genotyping data for sample 7469


title: Kidney_Air_3H_Rat355

description: 0ppm  x 25 min (0 ppm x min)


title: Blood_Air_3H_Rat355

description: 0ppm  x 25 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_B4

value: F

value: Mac IV


title: Genotyping data for sample 7467


title: Heart_Air_3H_Rat355

description: 0ppm  x 25 min (0 ppm x min)

value: Heart


title: Lung_Air_1H_Rat354

description: 0ppm  x 25 min (0 ppm x min)

value: Lung


title: genomic DNA from cultured airway epithelial cells (basal cells) [8f70_40b0-1A]

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

description:
200516380117_R08C01
8f70_40b0-1A

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard Illumina scanner settings

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 90% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5% in either African Americans or European Americans) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
normalized data: Average Beta

label: cy3, cy5

source_name: Cultred airway epithelial cells

label_protocol: Standard Illumina protocol.

value: RV

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Never

value: Hispanic

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [8f70_40b0-2A]

description:
200526210086_R01C01
8f70_40b0-2A

value: vehicle

tag: gender

value: Male

tag: ethnicity


title: Heart_Air_1H_Rat354

description: 0ppm  x 25 min (0 ppm x min)


title: BrainStem_Air_3H_Rat355

description: 0ppm  x 25 min (0 ppm x min)

value: Brain Stem


title: Blood_Air_1H_Rat354

description: 0ppm  x 25 min (0 ppm x min)

value: Blood


title: BrainStem_Air_1H_Rat354

description: 0ppm  x 25 min (0 ppm x min)

source_name: Brain Stem_Air_1H

value: Air


title: genomic DNA from cultured airway epithelial cells (basal cells) [6f90_420d-2A]

description:
200517480202_R06C01
6f90_420d-2A

tag: treatment

value: Oral

value: Female

value: Black


title: Genotyping data for sample 7463

source_name: genomic DNA from whole blood

value: Roma ancestry

tag: celltype

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_2_DC35_C4

source_name: distal lung

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac III


title: Lung_Air_1H_Rat353

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Lung

tag: time point

tag: exposure


title: genomic DNA from cultured airway epithelial cells (basal cells) [6f90_420d-1A]

description:
200517480194_R07C01
6f90_420d-1A

value: RV

tag: crs

value: CRS

tag: asthma

tag: steroid

value: Never


title: Kidney_Air_1H_Rat354

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney


title: Genotyping data for sample 7462

value: Male


title: M_P7_hyperoxia_CD45_2_DC35_P11

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: Genotyping data for sample 7468

tag: gender

tag: ethnicity


title: M_P7_hyperoxia_CD45_2_DC35_E20

tag: sequencing run

tag: treatment

value: DC I


title: genomic DNA from cultured airway epithelial cells (basal cells) [b2d6_4e63-1A]

description:
200514040156_R05C01
b2d6_4e63-1A

value: No

value: Nasal

tag: smoking

value: Prior

value: White

tag: age

tag: array


title: Genotyping data for sample 7461

value: Roma ancestry

tag: celltype

value: DNA extracted from whole blood


title: Genotyping data for sample 7460


title: Heart_Air_1H_Rat353

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Heart

value: Air


title: Kidney_Air_1H_Rat353

description: 0ppm  x 25 min (0 ppm x min)

tag: time point


title: M_P7_hyperoxia_CD45_2_DC35_C7

value: M

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: T cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [1413_4602-2A]

description:
200526210086_R08C01
1413_4602-2A

value: vehicle

tag: crs

value: CRS

tag: asthma

tag: steroid

value: Never

value: Hispanic


title: F_P7_hyperoxia_CD45_2_DC35_D18

tag: gender

value: F

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Genotyping data for sample 7457

value: Male

tag: ethnicity


title: genomic DNA from cultured airway epithelial cells (basal cells) [1413_4602-1A]

description:
200517480194_R06C01
1413_4602-1A

tag: treatment

value: RV

tag: smoking

tag: age

tag: array


title: F_P7_hyperoxia_CD45_2_DC35_D19

tag: sequencing run

tag: plate

value: Mac IV


title: genomic DNA from cultured airway epithelial cells (basal cells) [b2d6_4e63-2A]

description:
200526210092_R02C01
b2d6_4e63-2A

value: No

value: Nasal

value: Prior

value: White


title: Genotyping data for sample 7455

value: Roma ancestry

tag: celltype

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_K15

value: M

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune


title: M_P7_hyperoxia_CD45_1_DC35_L10

tag: cell subtype

value: neutrophil


title: Genotyping data for sample 7456


title: M_P7_hyperoxia_CD45_1_DC35_L16


title: Genotyping data for sample 7453


title: genomic DNA from cultured airway epithelial cells (basal cells) [0ebb_471b-1A]

description:
200516380199_R01C01
0ebb_471b-1A

tag: crs

value: CRS

tag: asthma

tag: steroid


title: genomic DNA from cultured airway epithelial cells (basal cells) [c9d1_4237-2A]

description:
200526210086_R04C01
c9d1_4237-2A

value: vehicle

value: nonCRS

value: Never

tag: gender

value: Female


title: genomic DNA from cultured airway epithelial cells (basal cells) [c9d1_4237-1A]

description:
200514040119_R01C01
c9d1_4237-1A

value: RV


title: F_P7_hyperoxia_CD45_2_DC35_F6

value: F

value: B cell

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_N22

tag: treatment

value: T cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [16ac_4246-2A]

description:
200514030067_R05C01
16ac_4246-2A

value: No

value: Nasal

tag: smoking

value: Prior

value: Male

tag: ethnicity

tag: age


title: M_P7_hyperoxia_CD45_2_DC35_E2

tag: sequencing run

value: M

tag: plate

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [0ebb_471b-2A]

description:
200517480083_R03C01
0ebb_471b-2A

value: White

tag: array


title: Blood_Air_1H_Rat353

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Blood

tag: time point

tag: exposure

value: Air


title: BrainStem_Air_1H_Rat353

description: 0ppm  x 25 min (0 ppm x min)

value: Brain Stem


title: genomic DNA from cultured airway epithelial cells (basal cells) [16ac_4246-1A]

description:
200526210060_R07C01
16ac_4246-1A

tag: crs

value: CRS


title: Kidney_Air_1H_Rat352

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney


title: Lung_Air_1H_Rat352

description: 0ppm  x 25 min (0 ppm x min)

value: Lung


title: BrainStem_Air_1H_Rat352

description: 0ppm  x 25 min (0 ppm x min)


title: Blood_Air_1H_Rat352

description: 0ppm  x 25 min (0 ppm x min)


title: Genotyping data for sample 7414

value: Roma ancestry

tag: celltype

value: DNA extracted from whole blood


title: Heart_Air_1H_Rat352

description: 0ppm  x 25 min (0 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_1_DC35_K18

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype


title: Genotyping data for sample 7454

tag: gender


title: Genotyping data for sample 7413


title: genomic DNA from cultured airway epithelial cells (basal cells) [5399_4680-2A]

description:
200526210086_R05C01
5399_4680-2A

tag: treatment

value: vehicle

value: nonCRS

tag: asthma

value: No

tag: steroid

value: Nasal

value: Never


title: M_P7_hyperoxia_CD45_2_DC35_N21

value: M

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Lung_PH3_1H_Rat351

description: 660ppm  x 25 min (16,500 ppm x min)


title: Genotyping data for sample 7412

value: Male

tag: ethnicity

value: North-Central European ancestry


title: genomic DNA from cultured airway epithelial cells (basal cells) [5399_4680-1A]

description:
200512330148_R06C01
5399_4680-1A

value: RV

tag: smoking

value: White

tag: age

tag: array


title: Kidney_PH3_1H_Rat351

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Kidney

tag: time point

tag: exposure


title: Genotyping data for sample 7411

tag: celltype


title: genomic DNA from cultured airway epithelial cells (basal cells) [e109_4585-2A]

description:
200514030104_R05C01
e109_4585-2A

tag: crs

value: Current


title: Genotyping data for sample 7416

value: Roma ancestry

value: DNA extracted from whole blood


title: Heart_PH3_1H_Rat351

description: 660ppm  x 25 min (16,500 ppm x min)

value: Heart


title: BrainStem_PH3_1H_Rat351

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: Genotyping data for sample 7339


title: M_P7_hyperoxia_CD45_2_DC35_H18

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype


title: Genotyping data for sample 7336

tag: gender


title: Genotyping data for sample 7337


title: M_P7_hyperoxia_CD45_2_DC35_E13

tag: treatment

value: T cell

tag: mousename

tag: coverage

tag: number of genes


title: Lung_PH3_1H_Rat350

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: M_P7_hyperoxia_CD45_2_DC35_G11

value: mast cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [21f6_4a02-1A]

description:
200517480051_R08C01
21f6_4a02-1A

value: nonCRS

tag: asthma

value: No

tag: steroid

value: Inhaled

tag: smoking

value: Prior

value: Female

tag: ethnicity

value: Black

tag: age

tag: array


title: Blood_PH3_1H_Rat351

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Blood

tag: time point

tag: exposure


title: genomic DNA from cultured airway epithelial cells (basal cells) [21f6_4a02-2A]

description:
200517480051_R07C01
21f6_4a02-2A

value: vehicle

tag: crs


title: genomic DNA from cultured airway epithelial cells (basal cells) [c47b_49c5-2A]

description:
200526210060_R04C01
c47b_49c5-2A

value: Never

value: Male

value: Hispanic


title: Genotyping data for sample 7019

value: North-Central European ancestry

tag: celltype

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_I17

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_P4

tag: gender

tag: treatment

value: DC II

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [c47b_49c5-1A]

description:
200517480020_R01C01
c47b_49c5-1A

value: RV

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_J23

tag: sequencing run


title: Genotyping data for sample 6998

tag: celltype


title: M_P7_hyperoxia_CD45_1_DC35_E6

tag: plate

tag: well


title: Genotyping data for sample 7022


title: genomic DNA from cultured airway epithelial cells (basal cells) [e109_4585-1A]

description:
200517480189_R06C01
e109_4585-1A

tag: crs

value: Current

value: White


title: genomic DNA from cultured airway epithelial cells (basal cells) [d2ad_4e13-2A]

description:
200516380203_R08C01
d2ad_4e13-2A

value: Nasal

value: Female


title: F_P7_hyperoxia_CD45_2_DC35_K21

value: F

tag: timepoint

tag: cell type

tag: cell subtype

value: neutrophil


title: INS1 cells, uninduced, vehicle treated, at 24 hours, replicate 3

city: San Francisco

first: Vincent

last: Auyeung

state: CA

department: Medicine

institute: University of California, San Francisco

data_processing:
Filtering: Removed reads that mapped to adaptors, have >10% N, have >50% bases with quality <20
Mapping: HISAT2 to the Rattus norvegicus genome (Ensemble release 79)
Gene read count assignment: HTSeq (union mode)
Genome_build: Rattus norvegicus Ensembl release 79
Supplementary_files_format_and_content: Un-normalized read counts in CSV format

source_name: Cell line

extract_protocol:
RNeasy Mini (Qiagen)
NEBNext Ultra II RNA Library Prep for Illumina (NEB)
PolyA enrichment on oligo dT beads, followed by reverse transcription, adaptor ligation, amplification, and sequencing.

tag: cell line

tag: dox-inducible transgene

value: IRE1alpha (Ern1)

tag: induction

tag: treatment

value: Vehicle

tag: time


title: genomic DNA from cultured airway epithelial cells (basal cells) [d2ad_4e13-1A]

description:
200514030067_R01C01
d2ad_4e13-1A

tag: asthma

tag: steroid

tag: smoking

value: Never

tag: gender

value: Hispanic


title: Kidney_PH3_1H_Rat350

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Kidney

tag: time point

tag: exposure


title: Blood_PH3_1H_Rat350

description: 660ppm  x 25 min (16,500 ppm x min)

value: Blood


title: genomic DNA from cultured airway epithelial cells (basal cells) [fcd5_4862-2A]

description:
200514040052_R02C01
fcd5_4862-2A

value: vehicle

value: Prior

tag: ethnicity

value: Black

tag: age

tag: array


title: BrainStem_PH3_1H_Rat350

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: INS1 cells, uninduced, vehicle treated, at 24 hours, replicate 1


title: Lung_Air_1H_Rat345

description: 0ppm  x 25 min (0 ppm x min)

value: Lung

value: Air


title: INS1 cells, uninduced, vehicle treated, at 24 hours, replicate 2


title: F_P7_hyperoxia_CD45_2_DC35_L7

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

value: mast cell

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [fcd5_4862-1A]

description:
200514030112_R05C01
fcd5_4862-1A

tag: treatment

value: RV

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

value: Female


title: Heart_PH3_1H_Rat350

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Heart

tag: time point


title: Kidney_Air_1H_Rat345

description: 0ppm  x 25 min (0 ppm x min)

tag: exposure


title: M_P7_hyperoxia_CD45_2_DC35_I7

tag: gender

value: M

tag: cell subtype


title: INS1 cells, uninduced, vehicle treated, at 4 hours, replicate 3

tag: cell line

tag: dox-inducible transgene

value: IRE1alpha (Ern1)

tag: induction

value: Vehicle

tag: time


title: F_P7_hyperoxia_CD45_2_DC35_J15

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type


title: Heart_Air_1H_Rat345

description: 0ppm  x 25 min (0 ppm x min)


title: INS1 cells, uninduced, vehicle treated, at 4 hours, replicate 2

tag: treatment


title: M_P7_hyperoxia_CD45_2_DC35_D17

value: DC III

tag: mousename

tag: coverage

tag: number of genes


title: BrainStem_Air_1H_Rat345

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

tag: time point


title: M_P7_hyperoxia_CD45_1_DC35_K11

tag: gender

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [bf8a_4f2b-2A]

description:
200517480083_R06C01
bf8a_4f2b-2A

value: vehicle

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Never

tag: ethnicity

value: Black

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [bf8a_4f2b-1A]

description:
200517480052_R01C01
bf8a_4f2b-1A


title: INS1 cells, uninduced, vehicle treated, at 4 hours, replicate 1

tag: cell line

tag: dox-inducible transgene

tag: induction

tag: time


title: INS1 cells, doxycyline induced IRE1α overexpression, vehicle treated, at 4 hours, replicate 3

value: Doxycycline

tag: treatment


title: F_P7_hyperoxia_CD45_2_DC35_N23

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage


title: genomic DNA from cultured airway epithelial cells (basal cells) [2189_4c08-2A]

description:
200517480051_R03C01
2189_4c08-2A

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

tag: gender

value: Male


title: Blood_Air_1H_Rat345

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Blood

tag: time point

tag: exposure

value: Air


title: genomic DNA from cultured airway epithelial cells (basal cells) [16e4_494f-2A]

description:
200517480083_R05C01
16e4_494f-2A

tag: treatment

value: Prior

value: Female

tag: ethnicity

value: White

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [16e4_494f-1A]

description:
200514030156_R06C01
16e4_494f-1A

value: RV


title: INS1 cells, doxycyline induced IRE1α overexpression, vehicle treated, at 4 hours, replicate 2

tag: cell line

tag: dox-inducible transgene

value: IRE1alpha (Ern1)

tag: induction

value: Vehicle

tag: time


title: INS1 cells, doxycyline induced IRE1α overexpression, vehicle treated, at 4 hours, replicate 1


title: F_P7_hyperoxia_CD45_2_DC35_F15

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Kidney_PH3_1H_Rat343

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Kidney

tag: time point

tag: exposure


title: F_P7_hyperoxia_CD45_2_DC35_F23

tag: gender

tag: treatment

value: hyperoxia

value: Mac V


title: INS1 cells, doxycyline induced IRE1α overexpression, vehicle treated, at 24 hours, replicate 3

tag: cell line

tag: dox-inducible transgene

value: Doxycycline


title: genomic DNA from cultured airway epithelial cells (basal cells) [bcf7_46c2-2A]

description:
200516380117_R07C01
bcf7_46c2-2A

value: vehicle

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Never

tag: ethnicity

value: Black

tag: age

tag: array


title: INS1 cells, doxycyline induced IRE1α overexpression, vehicle treated, at 24 hours, replicate 2

tag: induction

tag: time


title: M_P7_hyperoxia_CD45_2_DC35_G14

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [bcf7_46c2-1A]

description:
200514040156_R02C01
bcf7_46c2-1A

tag: treatment

tag: crs

tag: asthma

value: No

tag: gender

value: Female


title: genomic DNA from cultured airway epithelial cells (basal cells) [2189_4c08-1A]

description:
200526210024_R05C01
2189_4c08-1A

value: RV

tag: steroid

tag: smoking

value: Male

tag: ethnicity

tag: age


title: INS1 cells, doxycyline induced IRE1α overexpression, vehicle treated, at 24 hours, replicate 1

tag: cell line

tag: dox-inducible transgene

value: IRE1alpha (Ern1)

tag: induction

value: Vehicle

tag: time


title: F_P7_hyperoxia_CD45_2_DC35_O14

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: B cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [3f1a_423c-2A]

description:
200516380117_R06C01
3f1a_423c-2A

tag: treatment

value: White

tag: array


title: INS1 cells, doxycyline induced IRE1α overexpression, KIRA9 treated, at 24 hours, replicate 3

value: Doxycycline


title: Lung_PH3_1H_Rat343

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Lung

tag: time point

tag: exposure


title: genomic DNA from cultured airway epithelial cells (basal cells) [3f1a_423c-1A]

description:
200514030073_R02C01
3f1a_423c-1A

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

tag: gender


title: genomic DNA from cultured airway epithelial cells (basal cells) [9145_49d8-2A]

description:
200512330148_R08C01
9145_49d8-2A

value: vehicle

value: Nasal

value: Never

tag: ethnicity

tag: age


title: F_P7_hyperoxia_CD45_2_DC35_K11

tag: sequencing run

value: hyperoxia

value: immune

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: INS1 cells, doxycyline induced IRE1α overexpression, KIRA9 treated, at 24 hours, replicate 2

tag: cell line

tag: dox-inducible transgene

tag: induction

tag: treatment

tag: time


title: M_P7_hyperoxia_CD45_1_DC35_K14

value: M

tag: plate

tag: well

tag: timepoint

tag: cell type

value: Mac III


title: Heart_PH3_1H_Rat343

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Heart

tag: time point

tag: exposure


title: BrainStem_PH3_1H_Rat343

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: INS1 cells, doxycyline induced IRE1α overexpression, KIRA9 treated, at 24 hours, replicate 1

value: IRE1alpha (Ern1)


title: BrainStem_PH3_24H_Rat341

description: 660ppm  x 25 min (16,500 ppm x min)

source_name: Brain Stem_PH3_24H


title: Blood_PH3_24H_Rat341

description: 660ppm  x 25 min (16,500 ppm x min)

value: Blood


title: Lung_PH3_24H_Rat341

description: 660ppm  x 25 min (16,500 ppm x min)


title: Kidney_PH3_24H_Rat341

description: 660ppm  x 25 min (16,500 ppm x min)

value: Kidney


title: Blood_PH3_1H_Rat343

description: 660ppm  x 25 min (16,500 ppm x min)


title: Lung_Air_24H_Rat340

description: 0ppm  x 25 min (0 ppm x min)

value: Air


title: Heart_PH3_24H_Rat341

description: 660ppm  x 25 min (16,500 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_J9

tag: sequencing run

tag: gender

value: Mac I


title: genomic DNA from cultured airway epithelial cells (basal cells) [9145_49d8-1A]

description:
200517480083_R01C01
9145_49d8-1A

value: RV

tag: crs

tag: asthma

value: No

tag: steroid

tag: smoking

value: Female

tag: ethnicity

value: Black

tag: age

tag: array


title: F_P7_hyperoxia_CD45_2_DC35_N14

value: F

tag: treatment

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_I3

tag: plate

tag: well

tag: timepoint

tag: cell type

value: Mac II


title: genomic DNA from cultured airway epithelial cells (basal cells) [7240_43f5-2A]

description:
200512330148_R01C01
7240_43f5-2A

value: vehicle

value: nonCRS

value: Prior

tag: gender

value: Male


title: genomic DNA from cultured airway epithelial cells (basal cells) [2f11_490d-2A]

description:
200526210023_R04C01
2f11_490d-2A

tag: crs

value: Never

value: White


title: genomic DNA from cultured airway epithelial cells (basal cells) [2f11_490d-1A]

description:
200526210060_R06C01
2f11_490d-1A

tag: asthma


title: M_P7_hyperoxia_CD45_1_DC35_G19

tag: sequencing run

value: M

value: hyperoxia

value: immune

value: Mac III


title: INS1 cells, doxycyline induced IRE1α overexpression, KIRA9 treated, at 4 hours, replicate 2

tag: cell line

tag: dox-inducible transgene

value: IRE1alpha (Ern1)

tag: induction

value: Doxycycline

tag: time


title: M_P7_hyperoxia_CD45_1_DC35_F16

tag: treatment


title: Heart_Air_24H_Rat340

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Heart

tag: time point

tag: exposure

value: Air


title: INS1 cells, doxycyline induced IRE1α overexpression, PAIR1 treated, at 24 hours, replicate 3


title: genomic DNA from cultured airway epithelial cells (basal cells) [7240_43f5-1A]

description:
200526210023_R01C01
7240_43f5-1A

value: RV

value: No

tag: steroid

tag: smoking

tag: ethnicity

value: Black

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_F1

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: basophil

tag: mousename

tag: coverage

tag: number of genes


title: Kidney_Air_24H_Rat340

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Kidney


title: M_P7_hyperoxia_CD45_2_DC35_H6

tag: sequencing run

tag: treatment

value: Mac V


title: INS1 cells, doxycyline induced IRE1α overexpression, KIRA9 treated, at 4 hours, replicate 3

tag: cell line

tag: dox-inducible transgene

tag: induction

tag: time


title: INS1 cells, doxycyline induced IRE1α overexpression, PAIR1 treated, at 24 hours, replicate 1


title: genomic DNA from cultured airway epithelial cells (basal cells) [acb0_4eb2-1A]

description:
200517480189_R07C01
acb0_4eb2-1A

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Male

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [acb0_4eb2-2A]

description:
200517480189_R03C01
acb0_4eb2-2A

value: vehicle

value: Never

tag: gender


title: M_P7_hyperoxia_CD45_2_DC35_M18

value: M

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage


title: F_P7_hyperoxia_CD45_2_DC35_H20

tag: sequencing run

value: F

tag: treatment

value: immune

value: Mac III

tag: number of genes


title: Blood_Air_24H_Rat340

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Blood

tag: time point

tag: exposure

value: Air


title: INS1 cells, doxycyline induced IRE1α overexpression, PAIR1 treated, at 24 hours, replicate 2

tag: cell line

tag: dox-inducible transgene

value: IRE1alpha (Ern1)

tag: induction

value: Doxycycline

tag: time


title: INS1 cells, doxycyline induced IRE1α overexpression, KIRA9 treated, at 4 hours, replicate 1


title: genomic DNA from cultured airway epithelial cells (basal cells) [89cb_44b7-2A]

description:
200514030112_R01C01
89cb_44b7-2A

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Prior

tag: gender

tag: ethnicity

value: White

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_E15

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

value: mast cell II

tag: mousename

tag: coverage


title: INS1 cells, doxycyline induced IRE1α overexpression, PAIR1 treated, at 4 hours, replicate 3

tag: cell line

tag: dox-inducible transgene

tag: induction

tag: time


title: INS1 cells, doxycyline induced IRE1α overexpression, PAIR1 treated, at 4 hours, replicate 2


title: F_P7_hyperoxia_CD45_2_DC35_B9

tag: gender

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [1b8e_429b-2A]

description:
200517480111_R01C01
1b8e_429b-2A

tag: crs

tag: asthma

tag: steroid

tag: smoking

value: Male

tag: ethnicity

value: Hispanic

tag: age


title: INS1 cells, doxycyline induced IRE1α overexpression, PAIR1 treated, at 4 hours, replicate 1

tag: treatment


title: genomic DNA from cultured airway epithelial cells (basal cells) [89cb_44b7-1A]

description:
200514030112_R03C01
89cb_44b7-1A

value: RV

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [1b8e_429b-1A]

description:
200517480108_R01C01
1b8e_429b-1A

value: Never


title: F_P7_hyperoxia_CD45_2_DC35_L5

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

tag: cell subtype


title: Lung_Air_24H_Rat335

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Lung

tag: time point

tag: exposure


title: genomic DNA from cultured airway epithelial cells (basal cells) [fcc4_4f9f-2A]

description:
200526210092_R06C01
fcc4_4f9f-2A

value: vehicle

tag: crs

value: CRS

value: No

tag: gender


title: genomic DNA from cultured airway epithelial cells (basal cells) [fcc4_4f9f-1A]

description:
200517480194_R02C01
fcc4_4f9f-1A

tag: asthma

tag: steroid


title: M_P7_hyperoxia_CD45_1_DC35_E22

value: M

value: immune

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: Kidney_Air_24H_Rat335

description: 0ppm  x 25 min (0 ppm x min)

value: Kidney

value: Air


title: genomic DNA from cultured airway epithelial cells (basal cells) [1f5f_4d4f-2A]

description:
200517480194_R03C01
1f5f_4d4f-2A

tag: treatment

tag: smoking

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [1f5f_4d4f-1A]

description:
200526210024_R01C01
1f5f_4d4f-1A


title: M_P7_hyperoxia_CD45_2_DC35_O21

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

value: Mac II


title: M_P7_hyperoxia_CD45_2_DC35_A23

tag: cell subtype

value: neutrophil


title: M_P7_hyperoxia_CD45_2_DC35_I2

tag: gender


title: BrainStem_Air_24H_Rat340

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Brain Stem

tag: time point

tag: exposure


title: genomic DNA from cultured airway epithelial cells (basal cells) [d89d_472e-2A]

description:
200514030104_R08C01
d89d_472e-2A

tag: crs

tag: asthma

tag: steroid

value: Current

value: Male

value: White


title: F_P7_hyperoxia_CD45_2_DC35_P6

value: F

tag: treatment

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: BrainStem_Air_24H_Rat335

description: 0ppm  x 25 min (0 ppm x min)


title: Lung_PH3_24H_Rat333

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: F_P7_hyperoxia_CD45_2_DC35_H4

tag: sequencing run

value: hyperoxia

value: T cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [d89d_472e-1A]

description:
200526210024_R04C01
d89d_472e-1A

value: RV

value: CRS

tag: smoking

tag: ethnicity

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_M1

value: M

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: basophil


title: genomic DNA from cultured airway epithelial cells (basal cells) [9bfe_41f4-2A]

description:
200514030073_R08C01
9bfe_41f4-2A

value: vehicle

tag: crs

value: Never

tag: gender

value: Asian


title: Heart_Air_24H_Rat335

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Heart

tag: time point

tag: exposure

value: Air


title: M_P7_hyperoxia_CD45_2_DC35_M2

tag: treatment

value: Mac V

tag: mousename

tag: coverage


title: Blood_Air_24H_Rat335

description: 0ppm  x 25 min (0 ppm x min)

value: Blood


title: Kidney_PH3_24H_Rat333

description: 660ppm  x 25 min (16,500 ppm x min)

value: Kidney


title: genomic DNA from cultured airway epithelial cells (basal cells) [9bfe_41f4-1A]

description:
200517480052_R08C01
9bfe_41f4-1A

tag: asthma

tag: steroid

tag: smoking

value: Male


title: Blood_PH3_24H_Rat333

description: 660ppm  x 25 min (16,500 ppm x min)


title: BrainStem_PH3_24H_Rat333

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: Lung_Air_24H_Rat328

description: 0ppm  x 25 min (0 ppm x min)

value: Lung


title: M_P7_hyperoxia_CD45_2_DC35_J17

tag: sequencing run

value: hyperoxia

value: Mac III

tag: number of genes


title: Heart_PH3_24H_Rat333

description: 660ppm  x 25 min (16,500 ppm x min)


title: Heart_Air_24H_Rat328

description: 0ppm  x 25 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_P23

tag: plate

tag: well

value: Mac IV


title: s7A.TL1H2.Cy3

city: Urbana

first: Eunsoo

last: Choe

state: Illinois

address: s-306 Turner hall 1102 S. Goodwin Ave.

institute: USDA-ARS

description:
biological replication 4 of 4
raw data in Cy3 channel of 10007_A.gpr

hyb_protocol: Samples were hybridized to custom designed Agilent maize 4x44k array.

scan_protocol: Axon 4000B microarray scanner (Molecular Devices, Sunnyvale, CA) at 5 μm resolution. Spotfinding was carried out using GenePix 6.1 image analysis software (Molecular Devices, Sunnyvale, CA).

data_processing: R (R Development Core Team, 2014) (v 3.1.0) using the Limma package (v 3.20.1) were used for data processing. Median foreground values from the 16 arrays were read into R, and any spots that had been manually flagged (-100 values) were given a weight of zero (Smyth and Speed, 2003). The individual Cy5 and Cy3 values were all normalized together using the quantile method and then log2-transformed. The mixed effects statistical model were used and accounted for dye as fixed, array as random and labeling efficiency as a covariate. The expression values from the probes were compared with the positive and negative controls and selected based on expression values > 6.25 on the log2 scale in at least 4 samples out of 32 samples.

organism: Zea mays

source_name: DMC21-84 planted in Vegetable Farm at High plant density

label_protocol: Seventy-five ng of total RNA was labeled using the Agilent 2-color Low Input Quickamp Whole Transcriptome Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's protocols.

growth_protocol: Two shrunken2 (sh2) sweet corn hybrids, GSS2259P and DMC21-84, were planted in two environments, Vegetable Farm and Fruit Farm, at the University of Illinois Crop Sciences Research and Education Center, Urbana, IL.

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, North Rhine-Westphalia, Germany).

treatment_protocol: Each environment received two plant density treatments with 4 replications, which were targeted at low (51,500 plants ha-1) and high (96,100 plants ha-1) densities

tag: environment

value: Vegetable Farm

tag: hybrid

tag: density

value: High

value: leaf at R1


title: s7C.SL1L1.Cy3

description:
biological replication 4 of 4
raw data in Cy3 channel of 10007_C.gpr

source_name: GSS2259P planted in Vegetable Farm at Low plant density

value: Low


title: BrainStem_Air_24H_Rat328

description: 0ppm  x 25 min (0 ppm x min)


title: s7D.SL2H1.Cy3

description:
biological replication 4 of 4
raw data in Cy3 channel of 10007_D.gpr

source_name: GSS2259P planted in Fruit Farm at High plant density

value: Fruit Farm


title: s6B.SL1H1.Cy3

description:
biological replication 4 of 4
raw data in Cy3 channel of 10006_B.gpr

source_name: GSS2259P planted in Vegetable Farm at High plant density


title: F_P7_hyperoxia_CD45_2_DC35_I23

tag: gender

value: F

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: DC II


title: genomic DNA from cultured airway epithelial cells (basal cells) [d1be_4099-1A]

description:
200517480052_R05C01
d1be_4099-1A

tag: treatment

value: RV

tag: crs

value: nonCRS

value: No

value: Nasal

value: Never

value: Female

tag: ethnicity

value: White

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [71cb_4385-2A]

description:
200526210024_R06C01
71cb_4385-2A

value: vehicle

value: CRS

tag: asthma

tag: steroid

value: Inhaled

tag: smoking

value: Prior


title: genomic DNA from cultured airway epithelial cells (basal cells) [71cb_4385-1A]

description:
200514030104_R04C01
71cb_4385-1A


title: s6D.SL1L2.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10006_D.gpr

value: Vegetable Farm

tag: tissue

value: leaf at R1


title: genomic DNA from cultured airway epithelial cells (basal cells) [d1be_4099-2A]

description:
200514030104_R06C01
d1be_4099-2A


title: M_P7_hyperoxia_CD45_2_DC35_B11

tag: sequencing run

value: M

tag: plate

tag: well

value: hyperoxia

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_P9

tag: gender

value: F

tag: timepoint

tag: cell type

value: immune

value: DC II


title: genomic DNA from cultured airway epithelial cells (basal cells) [a7dc_4ab3-2A]

description:
200514040052_R03C01
a7dc_4ab3-2A

tag: treatment

tag: crs

value: nonCRS

value: No


title: s7B.TL2L2.Cy3

description:
biological replication 4 of 4
raw data in Cy3 channel of 10007_B.gpr

source_name: DMC21-84 planted in Fruit Farm at Low plant density

tag: environment

value: Fruit Farm

tag: hybrid

tag: density

value: Low


title: s6C.TL2H2.Cy3

description:
biological replication 4 of 4
raw data in Cy3 channel of 10006_C_image.gpr

source_name: DMC21-84 planted in Fruit Farm at High plant density

value: High


title: s6A.TL2L1.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10006_A.gpr


title: Blood_Air_24H_Rat328

description: 0ppm  x 25 min (0 ppm x min)

value: Blood

tag: time point

tag: exposure

value: Air


title: Kidney_Air_24H_Rat328

description: 0ppm  x 25 min (0 ppm x min)

tag: tissue

value: Kidney


title: Lung_PH3_24H_Rat326

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: s5D.SL2H2.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10005_D.gpr


title: s5C.SL2L2.Cy3

description:
biological replication 4 of 4
raw data in Cy3 channel of 10005_C.gpr

source_name: GSS2259P planted in Fruit Farm at Low plant density


title: Kidney_PH3_24H_Rat326

description: 660ppm  x 25 min (16,500 ppm x min)


title: s5A.TL1L2.Cy3

description:
biological replication 4 of 4
raw data in Cy3 channel of 10005_A.gpr

source_name: DMC21-84 planted in Vegetable Farm at Low plant density

value: Vegetable Farm


title: s5B.TL1H1.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10005_B.gpr

value: leaf at R1


title: Heart_PH3_24H_Rat326

description: 660ppm  x 25 min (16,500 ppm x min)

value: Heart


title: genomic DNA from cultured airway epithelial cells (basal cells) [a7dc_4ab3-1A]

description:
200517480202_R03C01
a7dc_4ab3-1A

value: RV

tag: asthma

tag: steroid

value: Nasal

tag: smoking

value: Never

value: Female

tag: ethnicity

value: White

tag: age

tag: array


title: s4D.SL2L1.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10004_D.gpr


title: M_P7_hyperoxia_CD45_1_DC35_H19

tag: sequencing run

tag: gender

value: M

tag: plate

tag: well

value: hyperoxia

value: immune

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: s4C.SL1H2.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10004_C.gpr

tag: environment

tag: hybrid

tag: density

value: High


title: F_P7_hyperoxia_CD45_2_DC35_D22

value: F

tag: timepoint

tag: treatment

tag: cell type

value: basophil


title: genomic DNA from cultured airway epithelial cells (basal cells) [ac28_4568-1A]

description:
200514030156_R02C01
ac28_4568-1A

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

tag: ethnicity


title: genomic DNA from cultured airway epithelial cells (basal cells) [ac28_4568-2A]

description:
200517480051_R01C01
ac28_4568-2A

value: vehicle

tag: gender

tag: age

tag: array


title: Blood_PH3_24H_Rat326

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Blood

tag: time point

tag: exposure


title: BrainStem_PH3_24H_Rat326

description: 660ppm  x 25 min (16,500 ppm x min)

value: Brain Stem


title: F_P7_hyperoxia_CD45_2_DC35_C17

tag: sequencing run

tag: plate

tag: well

tag: cell subtype

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [48c7_4117-2A]

description:
200526210023_R03C01
48c7_4117-2A

tag: treatment

tag: crs

tag: asthma

value: Current

value: Male


title: Lung_PH3_24H_Rat325

description: 660ppm  x 25 min (16,500 ppm x min)

value: Lung


title: s4B.TL2H1.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10004_B.gpr

tag: environment

value: Fruit Farm

tag: hybrid

tag: density

value: leaf at R1


title: M_P7_hyperoxia_CD45_2_DC35_K19

tag: gender

value: M

tag: timepoint

value: hyperoxia

tag: cell type

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [61eb_4fc3-2A]

description:
200512330148_R03C01
61eb_4fc3-2A

value: CRS

tag: steroid

tag: smoking

value: Never

tag: ethnicity

value: White

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_H13

tag: sequencing run

tag: plate

tag: well

value: immune

tag: cell subtype

value: T cell

tag: mousename


title: M_P7_hyperoxia_CD45_1_DC35_H9

tag: treatment

tag: coverage

tag: number of genes


title: 2495_STC1_G

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

description: Input-DNA

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline https://github.com/crazyhottommy/pyflow-ChIPseq. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2 (Langmead et al., 2009). Duplicate reads were removed using SAMBLASTER (Faust and Hall, 2014) before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5 (Li et al., 2009). To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0 (Ramirez et al., 2014) to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Cell Line

growth_protocol: Melanoma tumors were obtained from the Melcore tumor bank at MD Anderson Cancer Center. Tissue was disassociated (50 mg of tissue; ~8 mg per histone modification antibody) manually in 2 mL of Hanks' Balanced Salt Solution (HBSS) using a sterile razor blade. Mince the tissue into 3 to 4 mm pieces for approximately 5 min in a sterile tissue culture dish. Transfer the tissue and HBSS solution into a dissociator tube and add another 8 mL of HBSS. Further disassociate the tissue using a dissociator until homogenized. For melanoma tumors, place the tubes in a dissociator and run the following cycles each one time in this order: h_tumor_01.01, h_tumor_02.01, h_tumor_03.01 and m_heart_02.01.

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing. Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

tag: chip-antibody

value: melanoma short-term patient culture cell line

tag: cell genotype

value: NRAS mutation


title: genomic DNA from cultured airway epithelial cells (basal cells) [61eb_4fc3-1A]

description:
200516380157_R01C01
61eb_4fc3-1A

value: RV

tag: crs

tag: asthma

value: No

tag: gender


title: M_P7_hyperoxia_CD45_2_DC35_I15

tag: timepoint

tag: cell type


title: M_P7_hyperoxia_CD45_1_DC35_B3


title: genomic DNA from cultured airway epithelial cells (basal cells) [d76f_4712-2A]

description:
200516380174_R01C01
d76f_4712-2A

value: vehicle

tag: steroid

tag: smoking

tag: ethnicity

value: Hispanic

tag: age


title: BrainStem_PH3_24H_Rat325

description: 660ppm  x 25 min (16,500 ppm x min)

tag: tissue

value: Brain Stem

tag: time point

tag: exposure


title: F_P7_hyperoxia_CD45_2_DC35_O4

tag: sequencing run

value: F

tag: plate

tag: well

tag: treatment

tag: cell subtype

value: IL cell

tag: mousename


title: 2495_STC1_E

description: ChIP-DNA

tag: chip-antibody

tag: cell genotype


title: F_P7_hyperoxia_CD45_2_DC35_E19

tag: gender

tag: timepoint

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [d76f_4712-1A]

description:
200517480051_R04C01
d76f_4712-1A

tag: crs

tag: asthma

tag: steroid

tag: smoking

value: Male

tag: ethnicity

tag: array


title: s4A.TL1L1.Cy3

description:
biological replication 3 of 4
raw data in Cy3 channel of 10004_A.gpr

tag: environment

value: Vegetable Farm

tag: hybrid

tag: density

value: Low

tag: tissue

value: leaf at R1


title: genomic DNA from cultured airway epithelial cells (basal cells) [7fee_4d30-2A]

description:
200516380157_R02C01
7fee_4d30-2A

tag: treatment

value: CRS

value: Never

tag: age


title: DIPGXIII_EPZ_3_Quant-Seq

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
RNA-Seq data was processed using hisat2 (v2.1.0) to align reads to the hg38 genome and featureCounts (v1.6.4) to quantify gene abundance. DESeq2 (v1.24.0) was used to identify differentially expressed genes.
QuantSeq data were process using Lexogens Quantseq 3' mRNA-seq analysis pipeline hosted on Bluebee
genome build: hg38

source_name: Glioma

growth_protocol: DIPGXIII cell cultures were maintained in TSM serum-free basal medium supplemented with B27 (Life Technologies), laminin (Sigma), growth factors EGF, FGF2, PDGF-AA and PDGF-BB (Peprotech) and Heparin (Sigma)

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy preparation kit in accordance with the manufacturers instructions
Libraries were constructed using the Lexogen QuantSeq 3' mRNA-Seq library prep kit FWD for Illumina 015.24. in accordance with the manufacturers instructions.

treatment_protocol: Cells were treated with DMSO or Tazemetostat (EPZ6438) at 2uM for 24hrs

tag: cell type

value: DIPGXIII

tag: genotype

value: EPZ treated


title: DIPGXIII_EPZ_2_Quant-Seq


title: s7D.SL2L3.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10007_D.gpr

value: Fruit Farm


title: s7C.SL1H3.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10007_C.gpr

value: High


title: Kidney_PH3_24H_Rat325

description: 660ppm  x 25 min (16,500 ppm x min)

value: Kidney

tag: time point

tag: exposure


title: Heart_PH3_24H_Rat325

description: 660ppm  x 25 min (16,500 ppm x min)

value: Heart


title: s6D.SL2L4.Cy5

description:
biological replication 1 of 4
raw data in Cy5 channel of 10006_D.gpr


title: s6B.TL1H4.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10006_B.gpr


title: s7A.TL1L4.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10007_A.gpr


title: 2495_STC1_F

description: ChIP-DNA

tag: chip-antibody

value: melanoma short-term patient culture cell line

tag: cell genotype

value: NRAS mutation


title: F_P7_hyperoxia_CD45_2_DC35_K12

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: s7B.TL2H4.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10007_B.gpr

tag: environment

tag: hybrid

tag: density

tag: tissue


title: Blood_PH3_24H_Rat325

description: 660ppm  x 25 min (16,500 ppm x min)

value: Blood

tag: time point


title: DIPGXIII_EPZ_1_Quant-Seq

tag: cell type

tag: genotype

tag: treatment


title: genomic DNA from cultured airway epithelial cells (basal cells) [7fee_4d30-1A]

description:
200514030067_R07C01
7fee_4d30-1A

value: RV

tag: crs

tag: asthma

tag: steroid

tag: smoking

value: Male

tag: ethnicity

value: White

tag: age

tag: array


title: s6C.SL2H4.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10006_C_image.gpr

value: leaf at R1


title: genomic DNA from cultured airway epithelial cells (basal cells) [bbd0_41ec-2A]

description:
200517480194_R04C01
bbd0_41ec-2A

value: vehicle

value: CRS

value: No

value: Nasal

value: Never

tag: gender

value: Black


title: DIPGXIII_DMSO_3_Quant-Seq

value: DIPGXIII

value: DMSO treated


title: genomic DNA from cultured airway epithelial cells (basal cells) [bbd0_41ec-1A]

description:
200514030112_R02C01
bbd0_41ec-1A


title: DIPGXIII_DMSO_2_Quant-Seq


title: M_P7_hyperoxia_CD45_1_DC35_J18

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: s6A.TL1L3.Cy5

description:
biological replication 1 of 4
raw data in Cy5 channel of 10006_A.gpr

tag: environment

value: Vegetable Farm

tag: hybrid

tag: density

value: Low

tag: tissue


title: genomic DNA from cultured airway epithelial cells (basal cells) [4cb0_4702-2A]

description:
200517480045_R01C01
4cb0_4702-2A

tag: treatment

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Prior


title: M_P7_hyperoxia_CD45_1_DC35_L1

tag: sequencing run

tag: gender

value: hyperoxia

tag: cell type

value: immune

value: neutrophil


title: DIPGXIII_DMSO_1_Quant-Seq

tag: genotype


title: genomic DNA from cultured airway epithelial cells (basal cells) [4cb0_4702-1A]

description:
200514030067_R02C01
4cb0_4702-1A

value: RV

value: Male

tag: ethnicity

value: White

tag: age

tag: array


title: s5B.TL2H3.Cy5

description:
biological replication 1 of 4
raw data in Cy5 channel of 10005_B.gpr

value: Fruit Farm

value: High

value: leaf at R1


title: s5C.TL2L4.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10005_C.gpr


title: M_P7_hyperoxia_CD45_1_DC35_J5

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_B16

tag: treatment


title: genomic DNA from cultured airway epithelial cells (basal cells) [d2bb_43a4-2B]

description:
200526210092_R04C01
d2bb_43a4-2B

value: vehicle

tag: crs

value: CRS

tag: asthma

tag: steroid

value: Nasal

value: Female


title: M_P7_hyperoxia_CD45_2_DC35_K4

tag: sequencing run

tag: gender

value: M


title: genomic DNA from cultured airway epithelial cells (basal cells) [d2bb_43a4-1B]

description:
200514030034_R03C01
d2bb_43a4-1B

tag: smoking


title: HCT116 Re-replication p139-MCM2 Replicate 1 (ChIPSeq)

city: Bethesda

first: Christophe

middle: E

last: Redon

address: 37 Convent Drive

institute: NIH

description:
HCT116 36h MLN4924-treated pS139-MCM2 ChipSeq
HCT116 re-replication p139-MCM2-1

data_processing:
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

source_name: Colon carcinoma

growth_protocol: Cancer cells were grown in DMEM medium, 10% FBS

extract_protocol:
DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest. Re-replicated DNA was isolated by by Brdu-cesium chloride gradient
Enriched ChIPed DNA molecules were sequenced by Illumina NextSeq 75 cycle High Output kit with single ennd of 75bp. For nascent  DNA, re-replicated DNA, paired-end libraries of genomic DNA (gDNA) were prepared using Illumina TruSeq Nano DNA Library Prep kits. Control genomic DNA was fragmented to ~ 400 bp insert size on the Covaris which generates dsDNA fragments with 3' or 5' overhangs. The sheared DNA was blunt-ended and library size selection was done using sample purification beads. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to each other during the adapter ligation reaction. A corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. The indexed adapters were ligated to the ends of the DNA fragments and then PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated by qPCR before cluster generation and sequencing.

treatment_protocol: Cells were treated with MLN4924 or doxyclcline to induce re-replication.

tag: strain

tag: cell type

value: Cultured cancer cell line

tag: chip antibody

value: pS139-MCM2 (Cell Signaling, 12958)

tag: molecule subtype

value: ChipSeq DNA


title: HCT116 Re-replication p139-MCM2 Replicate 2 (ChIPSeq)

description:
HCT116 36h MLN4924-treated pS139-MCM2 ChipSeq
HCT116 re-replication p139-MCM2-2


title: HCT116 control p139-MCM2 Replicate 2 (ChIPSeq)

description:
HCT116 no treatment pS139-MCM2 ChipSeq
HCT116 control p139-MCM2-2


title: genomic DNA from cultured airway epithelial cells (basal cells) [bd64_4344-2A]

description:
200517480202_R04C01
bd64_4344-2A

source_name: Cultred airway epithelial cells

value: Prior

tag: ethnicity

tag: age

tag: array


title: HCT116 control p139-MCM2 Replicate 1 (ChIPSeq)

description:
HCT116 no treatment pS139-MCM2 ChipSeq
HCT116 control p139-MCM2-1


title: M_P7_hyperoxia_CD45_1_DC35_L9

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: IL cell

tag: mousename


title: M_P7_hyperoxia_CD45_1_DC35_F23

tag: treatment

value: DC II

tag: coverage

tag: number of genes


title: s5D.SL1H4.Cy5

description:
biological replication 1 of 4
raw data in Cy5 channel of 10005_D.gpr

tag: environment

value: Vegetable Farm

tag: hybrid

tag: density

tag: tissue


title: genomic DNA from cultured airway epithelial cells (basal cells) [bd64_4344-1A]

description:
200526210024_R02C01
bd64_4344-1A

value: RV

tag: crs

tag: asthma

tag: steroid

tag: smoking

tag: gender

value: Male

value: White


title: F_P7_hyperoxia_CD45_2_DC35_N16

tag: sequencing run

value: F

tag: plate

tag: cell type

value: B cell


title: HCT116 Re-replication CDT1 Replicate 1 (ChIPSeq)

description:
HCT116 36h MLN4924-treated CDT1 ChipSeq
HCT116 re-replication CDT1-1

tag: strain

tag: chip antibody

value: CDT1 antibody (Cell Signaling, 8064)

tag: molecule subtype


title: s4C.SL1L4.Cy5

description:
biological replication 1 of 4
raw data in Cy5 channel of 10004_C.gpr

value: Low

value: leaf at R1


title: minus_toxIN_20min_T7_rep2

city: Cambridge

first: Chantal

middle: K

last: Guegler

state: MA

address: 31 Ames Street

department: Biology

institute: MIT

data_processing:
Paired-end reads mapped to MG1655 and T7 genomes using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment, at all aligned positions a count was added (fragment density mapping).
For each uniquely mapped fragment, a count was added to the middle of each fragment (middle fragment mapping).
Counts were depth normalized to a pseudo-reference sample calculated from all samples (fragment density mapping) or by rpkm in each individual sample (middle fragment mapping).
Counts at all positions were log2 transformed and a cleavage ratio was calculated (+ toxIN: - toxIN) for assessing ToxN cleavage in transcripts; this analysis was conducted separately for the E. coli and T7 transcriptomes.
Genome_build: NCBI reference sequence: NC_000913.2 (E. coli); V01146.1 (T4)
Supplementary_files_format_and_content: t7_phage_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for the T7 genome for every genomic position at both strands for each sample as well as the average cleavage ratio for each timepoint calculated from both replicates.
Supplementary_files_format_and_content: t7_host_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for the E. coli genome for every genomic position at both strands for each sample as well as the average cleavage ratio for each timepoint calculated from both replicates.
Supplementary_files_format_and_content: t7_ERCCspikein_sum.csv.gz is the list of the sum of raw counts for the ERCC spike-in controls for each sample.
Supplementary_files_format_and_content: t7_phage_rpkm.csv.gz is the list of the rpkm per T7 mRNA for every sample at every timepoint calculated from both replicates.
Supplementary_files_format_and_content: t7_host_rpkm.csv.gz is the list of the rpkm per E. coli CDS for every sample at every timepoint calculated from both replicates.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterial liquid culture

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM.

extract_protocol:
RNA was extracted using two rounds of hot acid-phenol extraction at 67°C, followed by one round of hot acid-phenol-chloroform extraction at 67°C, followed by isopropanol precipitation.
See publication for complete protocol. Briefly, samples were treated with a custom rRNA depletion kit. Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

treatment_protocol: Cultures were back-diluted to OD600 = 0.2 and grown at 30 °C for 30 min before being infected with T7 at MOI = 5. At each timepoint post-infection, 500 μL infected cells was mixed with 500 μL lysis buffer (SDS 2%, 4 mM EDTA pH = 8) and boiled at 100 °C for 5 min before being flash-frozen.

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard

value: Prior to extraction


title: HCT116 Re-replication CDT1 Replicate 2 (ChIPSeq)

description:
HCT116 36h MLN4924-treated CDT1 ChipSeq
HCT116 re-replication CDT1-2

value: Cultured cancer cell line

value: ChipSeq DNA


title: s4D.SL2H3.Cy5

description:
biological replication 1 of 4
raw data in Cy5 channel of 10004_D.gpr

tag: environment

value: Fruit Farm

tag: hybrid

tag: density

value: High


title: genomic DNA from cultured airway epithelial cells (basal cells) [4d6c_4f66-2B]

description:
200517480051_R05C01
4d6c_4f66-2B

tag: treatment

value: vehicle

tag: crs

value: nonCRS

tag: asthma

value: Current

value: Female

tag: ethnicity

tag: age

tag: array


title: s5A.SL1L3.Cy5

description:
biological replication 2 of 4
raw data in Cy5 channel of 10005_A.gpr

value: Vegetable Farm

tag: tissue


title: s4B.TL2L3.Cy5

description:
biological replication 1 of 4
raw data in Cy5 channel of 10004_B.gpr