title: HepG2 cells, 2,4-D treated at 3uM, rep.3

city: Research Triangle Park

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_311_P3_2-4-D-HepG2

hyb_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit, page40-42 and GeneTitan® Instrument User Guide for Expression Array Plates

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6 (each group normalized independently)

source_name: ATCC (Manassas, VA)

growth_protocol: HepG2 cells were purchased from ATCC (Manassas, VA).   HepG2 cells were cultured in DMEM (cellgro) containing 10% FBS, 1X pen/strep, and 1X NEAA and plated at 18,000 cells/well in 96 well plates.

extract_protocol: Trizol® (ThermalFisher) organic extraction with Phase Lock Gel™ -Heavy- tubes (5Prime).  Aqueous phase placed in RB(QiaCube sample) tubes and loaded into QiaCube, the RNeasy Mini Protocol used.

treatment_protocol: Cells were exposed in 96-well plates 24hrs after plating to allow attachment.  2,4-dichlorophenoxyacetic acid, fenbuconazole, and imazalil were purchased from Sigma-Aldrich (St. Louis, MO).  Stock solutions of 2,4-D, fenbuconazole, and imazilil were diluted in DMSO and added to culture media to a final DMSO concentration of 0.2%.  The cells were exposed for 24hrs to the DMSO vehicle (0.2%) or one of the following chemical concentrations: 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10uM.

tag: cell line

tag: cell type

value: Cell culture

tag: time of exposure

value: 24 hours

tag: agent

tag: dose (um)


title: 0 (control) for 7 days, biological rep2

status: Public on Dec 21 2018

type: RNA

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

country: Japan

institute: Sumitomo Chemical Co., Ltd.

description: Gene expression data from lung of mice fed diets containing 0 (control) ppm chemical for 7 days

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained with Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with a Genechip Scanner 3000 (Affymetrix) and the image files were obtained.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotin-labeled cRNA were prepared from 100 ng of total RNA using 3’IVT Express Kit (Affymetrix) following the manufacturer's protocol.

growth_protocol: Crlj:CD1(ICR) female mice aged 9 weeks were purchased, quarantined for 7 days and maintained at 22 - 26°C and a relative humidity range of 40 - 70% with frequent ventilation. A powdered diet and water were provided ad libitum.

extract_protocol: The lungs were stored in RNA stabilization solution (Ambion, Austin, TX) at –20°C. Total RNA samples were extracted from lung using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Animals were fed diets containing 0 (control), 5000 and 10000 ppm permethrin and 2500 ppm isoniazid (positive control for tumor induction) for periods of 7 and 14 days.

tag: strain

tag: gender

value: female

tag: tissue

value: lung

tag: age

value: age of 11 weeks


title: TNY12_TG6_67B

type: SRA

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG

library_source: transcriptomic

data_processing:
HiSeq 2500 standard base-calling
A published small RNAseq pipeline, "rnaworld", PMID: 22836126
Genome_build: hg19
Supplementary_files_format_and_content: Excel worksheet: microRNA read counts in all study samples

organism: Homo sapiens

source_name: ex-vivo FNAB

extract_protocol:
TRIzol extraction followed by glycogen-fascilitated isopropanol precipitation
ligation & gel-based small RNA cDNA library (see PMID: 24489795)

tag: malignancy

value: male

tag: group

value: FL

tag: barcode


title: HepG2 cells, 2,4-D treated at 3uM, rep.2

first: Michael

country: USA

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_283_P2_2-4-D-HepG2

label_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit


title: HepG2 cells, 2,4-D treated at 10uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_282_P2_2-4-D-HepG2


title: 5000 ppm permethrin for 7 days, biological rep1

description: Gene expression data from lung of mice fed diets containing 5000 ppm permethrin for 7 days


title: HepG2 cells, 2,4-D treated at 3uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_255_P1_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 10uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_310_P3_2-4-D-HepG2


title: TNY12_TG4_56A

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG

value: malignant


title: TNY12_TG13_149N1

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG

value: benign


title: TNY12_TG3_49B

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: TNY12_TG10_145FL2

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: TNY12_TG5_64B

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: TNY12_TG2_181N1

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: TNY12_TG1_174T1

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: TNY12_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG

source_name: cell-line


title: HepG2 cells, 2,4-D treated at 1uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_312_P3_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 1uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_284_P2_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.3uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_257_P1_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.1uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_314_P3_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.3uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_313_P3_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 1uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_256_P1_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.3uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_285_P2_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 10uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_254_P1_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.1uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_286_P2_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.03uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_287_P2_2-4-D-HepG2


title: TNY12_TG23_152FL2

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: HepG2 cells, 2,4-D treated at 0.1uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_258_P1_2-4-D-HepG2


title: TNY12_TG20_151Fl1

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: TNY12_TG21_151FL2

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY12_TG19_150FL2

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY12_TG22_151FL3

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: TNY12_TG17_150N3

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY11_TG16_139N2

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: TNY11_TG15_153T3

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: TNY11_TG14_139N3

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: TNY11_TG12_171N2

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: TNY11_TG11_153T2

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: HepG2 cells, 2,4-D treated at 0.03uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_259_P1_2-4-D-HepG2


title: 5000 ppm permethrin for 14 days, biological rep5

description: Gene expression data from lung of mice fed diets containing 5000 ppm permethrin for 14 days

value: age of 12 weeks


title: HepG2 cells, 2,4-D treated at 0.01uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_260_P1_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.01uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_288_P2_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.003uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_261_P1_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.003uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_289_P2_2-4-D-HepG2


title: HepG2 common DMSO control 3, RMA normalized with 2-4-D samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_309_P3_DMSO-HepG2-2-4-D

value: control


title: HepG2 cells, 2,4-D treated at 0.01uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_316_P3_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.001uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_262_P1_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.003uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_317_P3_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.03uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_315_P3_2-4-D-HepG2


title: HepG2 cells, 2,4-D treated at 0.001uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_318_P3_2-4-D-HepG2


title: TNY11_TG8_147T1

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: HepG2 common DMSO control 1, RMA normalized with 2-4-D samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_253_P1_DMSO-HepG2-2-4-D


title: TNY11_TG9_143FL3

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY11_TG13_177N1

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY11_TG7_144T1

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: HepG2 common DMSO control 2, RMA normalized with 2-4-D samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_281_P2_DMSO-HepG2-2-4-D


title: TNY11_TG6_138N1

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: HepG2 cells, 2,4-D treated at 0.001uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_290_P2_2-4-D-HepG2


title: TNY11_TG10_168N3

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 3uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_273_P1_IMAZ-HepG2

value: Imazalil


title: HepG2 cells, Imazalil treated at 3uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_329_P3_IMAZ-HepG2


title: TNY11_TG4_197FL3

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY11_TG3_80

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: TNY11_TG2_164N1

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 10uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_328_P3_IMAZ-HepG2


title: TNY11_TG1_153T1

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 3uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_301_P2_IMAZ-HepG2


title: TNY11_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 10uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_300_P2_IMAZ-HepG2


title: TNY11_TG22_187N1

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 1uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_330_P3_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 10uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_272_P1_IMAZ-HepG2


title: TNY11_TG21_76B

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY11_TG19_83

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY11_TG20_147T2

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 1uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_302_P2_IMAZ-HepG2


title: TNY11_TG18_160FL1

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY11_TG17_143FL1

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY10_TG16_141N3

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: TNY11_TG23_14A

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.1uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_276_P1_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.3uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_303_P2_IMAZ-HepG2


title: TNY10_TG13_170T2

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY10_TG14_198FL1

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: TNY10_TG11_58A

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: TNY10_TG12_81B

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.01uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_334_P3_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.1uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_304_P2_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.03uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_333_P3_IMAZ-HepG2


title: TNY10_TG10_200N2

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.3uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_275_P1_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.1uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_332_P3_IMAZ-HepG2


title: TNY10_TG9_183T2

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.03uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_277_P1_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.03uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_305_P2_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.01uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_278_P1_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.01uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_306_P2_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.003uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_307_P2_IMAZ-HepG2


title: TNY10_TG8_165N1

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: TNY10_TG15_144T1

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.001uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_336_P3_IMAZ-HepG2


title: TNY10_TG7_52

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.001uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_308_P2_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.003uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_335_P3_IMAZ-HepG2


title: TNY10_TG6_146FL1

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: TNY10_TG5_190FL1

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: HepG2 common DMSO control 3, RMA normalized with IMAZ samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_309_P3_DMSO-HepG2-IMAZ


title: TNY10_TG4_178N2

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY10_TG3_71A

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.003uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_279_P1_IMAZ-HepG2


title: TNY10_TG1_180T2

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: HepG2 cells, Imazalil treated at 0.001uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_280_P1_IMAZ-HepG2


title: HepG2 cells, Imazalil treated at 0.3uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_331_P3_IMAZ-HepG2


title: TNY10_TG2_150FL3

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: TNY10_TG23_185N3

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: HepG2 common DMSO control 1, RMA normalized with IMAZ samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_253_P1_DMSO-HepG2-IMAZ


title: TNY10_TG22_13

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: TNY12_TG18_150FL1

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY10_TG20_62

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: HepG2 common DMSO control 2, RMA normalized with IMAZ samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_281_P2_DMSO-HepG2-IMAZ


title: TNY10_TG19_164N2

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY10_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 10uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_263_P1_FENB-HepG2

value: Fenbuconazole


title: HepG2 cells, Fenbuconazole treated at 3uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_292_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 1uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_293_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 10uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_291_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 10uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_10_24h_319_P3_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 3uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_264_P1_FENB-HepG2


title: TNY10_TG18_65


title: TNY10_TG17_149N2

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 0.3uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_322_P3_FENB-HepG2


title: TNY9_TG15_50

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: TNY10_TG21_154N2

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY9_TG14_69A

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 1uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_321_P3_FENB-HepG2


title: TNY9_TG13_157N1

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY9_TG12_147T3

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: TNY9_TG16_28

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 3uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_3_24h_320_P3_FENB-HepG2


title: TNY9_TG11_59

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 1uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_265_P1_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.1uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_295_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.1uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_323_P3_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.1uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_01_24h_267_P1_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.3uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_294_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.03uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_296_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.03uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_324_P3_FENB-HepG2


title: TNY9_TG10_178N3

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 0.3uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_03_24h_266_P1_FENB-HepG2


title: TNY9_TG9_153N1

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY9_TG8_169N3

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: TNY9_TG7_142T3

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: TNY9_TG6_183T1

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 0.01uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_325_P3_FENB-HepG2


title: TNY9_TG4_78A

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY9_TG5_174T3

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: TNY9_TG1_16B

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: TNY9_TG2_163FL1

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: TNY9_TG3_201N3

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 0.01uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_269_P1_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.01uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_001_24h_297_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.003uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_326_P3_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.001uM, rep.3

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_327_P3_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.03uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_003_24h_268_P1_FENB-HepG2


title: TNY11_TG5_174T2


title: HepG2 cells, Fenbuconazole treated at 0.003uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_270_P1_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.003uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_0003_24h_298_P2_FENB-HepG2


title: HepG2 cells, Fenbuconazole treated at 0.001uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_271_P1_FENB-HepG2


title: TNY9_TG23_154N3

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: TNY9_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: HepG2 cells, Fenbuconazole treated at 0.001uM, rep.2

description:
Gene Expression data from HepG2 cell culture
BW_0001_24h_299_P2_FENB-HepG2


title: HepG2 cells, Imazalil treated at 1uM, rep.1

description:
Gene Expression data from HepG2 cell culture
BW_1_24h_274_P1_IMAZ-HepG2


title: TNY9_TG20_166N2

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: TNY9_TG22_199N2

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: HepG2 common DMSO control 3, RMA normalized with FENB samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_309_P3_DMSO-HepG2-FENB


title: TNY8_TG16_78B

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: TNY8_TG14_164N3

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 3uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_3_P1_2-4-D-HepaRG

source_name: Thermo Fisher Scientific (Waltham, MA).

growth_protocol: HepaRG cells and media were purchased from Thermo Fisher Scientific (Waltham, MA).   HepaRG cells thawed and plated according to the manufacturer’s protocol onto a collagen type 1 coated (2.5ug/well) 96 well plates (day 0) and allowed to attach for 24hrs at 37C in a humidified chamber with 95% relative humidity and 5% CO2.  On Day 1, 3, and 5, the media was removed from the wells and replaced with 100uL/well of maintenance/metabolism supplemented media.  On day 7, the media was removed and replaced with 100uL/well of induction supplemented media.  On day 8, the cells were treated with chemical.

treatment_protocol: Cells were exposed in 96-well plates.  2,4-dichlorophenoxyacetic acid, fenbuconazole, and imazalil were purchased from Sigma-Aldrich (St. Louis, MO).  Stock solutions of 2,4-D, fenbuconazole, and imazilil were diluted in DMSO and added to culture media to a final DMSO concentration of 0.2%.  The cells were exposed for 24hrs to the DMSO vehicle (0.2%) or one of the following chemical concentrations: 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10uM.

value: HepaRG


title: TNY9_TG19_146FL2

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY9_TG17_54

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY9_TG21_174N1

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY8_TG13_170N1

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY8_TG11_145FL1

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: TNY8_TG15_72

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 3uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_59_P3_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 3uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_31_P2_2-4-D-HepaRG


title: TNY9_TG18_38

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY8_TG10_164T2

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 10uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_58_P3_2-4-D-HepaRG


title: HepG2 common DMSO control 1, RMA normalized with FENB samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_253_P1_DMSO-HepG2-FENB


title: HepaRG cells, 2,4-D treated at 0.3uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_61_P3_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 10uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_2_P1_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 10uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_30_P2_2-4-D-HepaRG


title: HepG2 common DMSO control 2, RMA normalized with FENB samples

description:
Gene Expression data from HepG2 cell culture
BW_0_24h_281_P2_DMSO-HepG2-FENB


title: TNY8_TG12_171N1

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 1uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_60_P3_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 1uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_32_P2_2-4-D-HepaRG


title: TNY8_TG9_153N2

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY8_TG4_175T3

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY8_TG6_61B

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 0.3uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_33_P2_2-4-D-HepaRG


title: TNY8_TG8_176N2

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: TNY8_TG3_146FL3

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: TNY8_TG2_82B

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: TNY8_TG1_143N2

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: TNY8_TG23_169N2

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: TNY8_TG7_172N3

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 0.1uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_62_P3_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.1uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_34_P2_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.1uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_6_P1_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.3uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_5_P1_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 1uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_4_P1_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.03uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_63_P3_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.01uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_64_P3_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.03uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_7_P1_2-4-D-HepaRG


title: TNY8_TG19_197FL1

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY8_TG18_159N2

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY8_TG5_153N3

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: TNY8_TG17_46

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY8_TG24_BCPUP

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: TNY8_TG22_177N2

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 0.003uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_66_P3_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.03uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_35_P2_2-4-D-HepaRG


title: TNY8_TG21_141N1

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY8_TG20_164T1

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: TNY7_TG14_47A

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 0.003uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_10_P1_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.003uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_37_P2_2-4-D-HepaRG


title: TNY7_TG13_32

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 0.001uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_9_P1_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.001uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_37_P2_2-4-D-HepaRG


title: HepaRG cells, 2,4-D treated at 0.001uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_65_P3_2-4-D-HepaRG


title: HepaRG common DMSO control 2, RMA normalized with 2-4-D samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_29_P2_DMSO-HepaRG_2-4-D


title: HepaRG common DMSO control 3, RMA normalized with 2-4-D samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_57_P3_DMSO-HepaRG_2-4-D


title: HepaRG cells, 2,4-D treated at 0.01uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_8_P1_2-4-D-HepaRG


title: TNY7_TG11_167N1

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: TNY7_TG16_179N2

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: TNY7_TG15_169N1

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: TNY7_TG12_143L2

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: TNY7_TG9_55

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: HepaRG cells, Imazalil treated at 3uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_49_P2_IMAZ-HepaRG


title: TNY7_TG10_61A

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: TNY7_TG7_176N3

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: HepaRG cells, Imazalil treated at 3uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_77_P3_IMAZ-HepaRG


title: TNY7_TG8_139N1

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: TNY7_TG6_29

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: TNY7_TG5_200N1

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: TNY7_TG4_45

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY7_TG3_182N3

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: HepaRG cells, Imazalil treated at 10uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_48_P2_IMAZ-HepaRG


title: TNY7_TG2_182N2

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: HepaRG cells, 2,4-D treated at 0.01uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_36_P2_2-4-D-HepaRG


title: HepaRG common DMSO control 1, RMA normalized with 2-4-D samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_1_P1_DMSO-HepaRG_2-4-D


title: HepaRG cells, Imazalil treated at 10uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_76_P3_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 10uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_20_P1_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 1uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_78_P3_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 3uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_21_P1_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 1uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_22_P1_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.3uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_79_P3_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 1uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_50_P2_IMAZ-HepaRG


title: TNY7_TG1_63

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: TNY7_TG23_64A

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: TNY7_TG21_73A

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY7_TG22_66B

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: TNY7_TG24_BCPUP

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: HepaRG cells, Imazalil treated at 0.3uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_23_P1_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.1uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_52_P2_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.3uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_51_P2_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.1uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_80_P3_IMAZ-HepaRG


title: TNY7_TG18_167N3

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY7_TG20_138N3

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: TNY7_TG17_170N3

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY7_TG19_179T

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY6_TG16_179N1

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: HepaRG cells, Imazalil treated at 0.1uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_24_P1_IMAZ-HepaRG


title: TNY6_TG15_81A

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: HepaRG cells, Imazalil treated at 0.03uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_25_P1_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.01uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_54_P2_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.01uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_82_P3_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.01uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_26_P1_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.03uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_81_P3_IMAZ-HepaRG


title: TNY6_TG14_60B

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: HepaRG cells, Imazalil treated at 0.003uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_56_P2_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.03uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_53_P2_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.003uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_84_P3_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.003uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_28_P1_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.001uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_83_P3_IMAZ-HepaRG


title: HepaRG cells, Imazalil treated at 0.001uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_55_P2_IMAZ-HepaRG


title: TNY6_TG12_27B

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: TNY6_TG11_22

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: TNY6_TG10_176N1

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: TNY6_TG7_143N3

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: TNY6_TG9_183T1

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY6_TG8_183T3

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: TNY6_TG13_66A

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY6_TG6_79A

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: HepaRG common DMSO control 3, RMA normalized with IMAZ samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_57_P3_DMSO-HepaRG-IMAZ


title: TNY6_TG4_199N3

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY6_TG2_76

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: TNY6_TG1_175T

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: TNY6_TG24_BCPUP

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 3uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_12_P1_FENB-HepaRG


title: HepaRG common DMSO control 1, RMA normalized with IMAZ samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_1_P1_DMSO-HepaRG-IMAZ


title: TNY6_TG22_201N2

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: HepaRG common DMSO control 2, RMA normalized with IMAZ samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_29_P2_DMSO-HepaRG-IMAZ


title: TNY6_TG23_71B

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 10uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_39_P2_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 3uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_68_P3_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 10uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_67_P3_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 10uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_10_24h_11_P1_FENB-HepaRG


title: HepaRG cells, Imazalil treated at 0.001uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_27_P1_IMAZ-HepaRG


title: HepaRG cells, Fenbuconazole treated at 3uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_3_24h_40_P2_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.3uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_42_P2_FENB-HepaRG


title: TNY6_TG19_175N3

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY6_TG20_194T3

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 1uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_69_P3_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 1uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_41_P2_FENB-HepaRG


title: TNY6_TG18_149N3

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.3uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_70_P3_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.3uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_03_24h_14_P1_FENB-HepaRG


title: TNY6_TG3_159N1

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.1uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_43_P2_FENB-HepaRG


title: TNY6_TG5_138T1

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.1uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_71_P3_FENB-HepaRG


title: TNY6_TG21_143T

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG

value: omitted


title: TNY6_TG17_192N1

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY5_TG16_188T2

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: TNY5_TG15_70

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: TNY5_TG13_193N3

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY5_TG12_42

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.1uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_01_24h_15_P1_FENB-HepaRG


title: TNY5_TG11_190N1

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.03uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_16_P1_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.03uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_44_P2_FENB-HepaRG


title: TNY5_TG10_87N2

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.03uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_003_24h_72_P3_FENB-HepaRG


title: TNY5_TG9_85

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY5_TG8_174N2

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.01uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_73_P3_FENB-HepaRG


title: TNY5_TG7_35B

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 1uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_1_24h_13_P1_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.003uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_47_P2_FENB-HepaRG


title: TNY5_TG6_82A

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.003uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_75_P3_FENB-HepaRG


title: TNY5_TG14_44

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: HepaRG cells, Fenbuconazole treated at 0.003uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_0003_24h_19_P1_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.01uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_45_P2_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.001uM, rep.3

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_74_P3_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.001uM, rep.2

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_46_P2_FENB-HepaRG


title: TNY5_TG3_186N3

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: TNY5_TG4_143N1

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY5_TG2_186N2

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: TNY5_TG5_37

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: TNY5_TG24_BCPAP

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: TNY5_TG23_144T3

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: TNY5_TG22_198N3

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: HepaRG common DMSO control 1, RMA normalized with FENB samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_1_P1_DMSO-HepaRG-FENB


title: TNY5_TG20_190N2

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: MCF7 cells, 2,4-D treated at 3uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_143_P3_2-4-D-MCF7

growth_protocol: MCF7 cells were purchased from ATCC (Manassas, VA).   MCF7 cells were cultured in MEM containing 10% FBS, 1X pen/strep, 2mM Glutamax, 1mM sodium pyruvate, and 1X NEAA and plated at 32,000 cells/well in a 96-well plate.

treatment_protocol: Cells were exposed in 96-well plates 24hrs after plating to allow attachment.  Stock solutions of 2,4-D, fenbuconazole, and imazilil were diluted in DMSO and added to culture media to a final DMSO concentration of 0.2%.  The cells were exposed for 24hrs to the DMSO vehicle (0.2%) or one of the following chemical concentrations: 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10uM.


title: HepaRG common DMSO control 2, RMA normalized with FENB samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_29_P2_DMSO-HepaRG-FENB


title: TNY5_TG19_168N2

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY5_TG21_49A

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: MCF7 cells, 2,4-D treated at 3uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_87_P1_2-4-D-MCF7


title: HepaRG common DMSO control 3, RMA normalized with FENB samples

description:
Gene Expression data from HepaRG cell culture
BW_0_24h_57_P3_DMSO-HepaRG-FENB


title: MCF7 cells, 2,4-D treated at 10uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_86_P1_2-4-D-MCF7


title: HepaRG cells, Fenbuconazole treated at 0.01uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_001_24h_17_P1_FENB-HepaRG


title: HepaRG cells, Fenbuconazole treated at 0.001uM, rep.1

description:
Gene Expression data from HepaRG cell culture
BW_0001_24h_18_P1_FENB-HepaRG


title: MCF7 cells, 2,4-D treated at 10uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_114_P2_2-4-D-MCF7


title: TNY5_TG17_125N1

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY4_TG16_198N1

description: 3' adapter sequence:TTACATCGTATGCCGTCTTCTG


title: TNY5_TG18_193FL2

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY4_TG15_199T3

description: 3' adapter sequence:TGATGTCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 3uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_115_P2_2-4-D-MCF7


title: TNY4_TG14_192N2

description: 3' adapter sequence:TATCATCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 1uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_88_P1_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 10uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_142_P3_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 1uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_144_P3_2-4-D-MCF7


title: TNY5_TG1_35A

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: MCF7 cells, 2,4-D treated at 0.3uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_89_P1_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.3uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_145_P3_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 1uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_116_P2_2-4-D-MCF7


title: TNY4_TG13_193FL1

description: 3' adapter sequence:TAGAGTCGTATGCCGTCTTCTG


title: TNY4_TG12_194FL3

description: 3' adapter sequence:TAATATCGTATGCCGTCTTCTG


title: TNY4_TG11_194FL1

description: 3' adapter sequence:TAACGTCGTATGCCGTCTTCTG


title: TNY4_TG9_195FL2

description: 3' adapter sequence:TCTCCTCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.1uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_90_P1_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.1uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_118_P2_2-4-D-MCF7


title: TNY4_TG10_194N3

description: 3' adapter sequence:TTAAGTCGTATGCCGTCTTCTG


title: TNY4_TG7_196N3

description: 3' adapter sequence:TCGCGTCGTATGCCGTCTTCTG


title: TNY4_TG6_196T

description: 3' adapter sequence:TCGATTCGTATGCCGTCTTCTG


title: TNY4_TG5_196N1

description: 3' adapter sequence:TCCTATCGTATGCCGTCTTCTG


title: TNY4_TG3_195T1

description: 3' adapter sequence:TCCACTCGTATGCCGTCTTCTG


title: TNY4_TG2_194FL2

description: 3' adapter sequence:TCATCTCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.3uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_117_P2_2-4-D-MCF7


title: TNY4_TG1_194N2

description: 3' adapter sequence:TCACTTCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.1uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_146_P3_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.03uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_91_P1_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.03uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_119_P2_2-4-D-MCF7


title: TNY4_TG22_127N3

description: 3' adapter sequence:TTGTATCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.03uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_147_P3_2-4-D-MCF7


title: TNY4_TG23_127N1

description: 3' adapter sequence:TGTTATCGTATGCCGTCTTCTG


title: TNY4_TG4_196N2

description: 3' adapter sequence:TCCGTTCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.003uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_149_P3_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.003uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_93_P1_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.001uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_94_P1_2-4-D-MCF7


title: TNY4_TG21_34

description: 3' adapter sequence:TTGACTCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.001uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_122_P2_2-4-D-MCF7


title: TNY4_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.001uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_150_P3_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.01uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_92_P1_2-4-D-MCF7


title: TNY4_TG20_30A

description: 3' adapter sequence:TTCATTCGTATGCCGTCTTCTG


title: MCF7 cells, 2,4-D treated at 0.01uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_148_P3_2-4-D-MCF7


title: MCF7 cells, 2,4-D treated at 0.01uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_120_P2_2-4-D-MCF7


title: TNY4_TG19_199N2

description: 3' adapter sequence:TTATTTCGTATGCCGTCTTCTG


title: TNY4_TG18_197FL

description: 3' adapter sequence:TAGCCTCGTATGCCGTCTTCTG


title: TNY4_TG17_200N2

description: 3' adapter sequence:TACTCTCGTATGCCGTCTTCTG


title: MCF7 common DMSO control 1, RMA normalized with 2-4-D samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_113_P2_DMSO-MCF7-2-4-D


title: MCF7 common DMSO control 2, RMA normalized with 2-4-D samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_141_P3_DMSO-MCF7-2-4-D


title: MCF7 cells, Imazalil treated at 3uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_161_P3_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 3uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_105_P1_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 3uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_133_P2_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 10uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_132_P2_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 10uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_160_P3_IMAZ-MCF7


title: TNY3_TG16_191FL2

description: 3' adapter sequence:TTACATCGTATGCCGTCTTCTG


title: TNY3_TG15_188N1

description: 3' adapter sequence:TGATGTCGTATGCCGTCTTCTG


title: TNY3_TG14_191FL1

description: 3' adapter sequence:TATCATCGTATGCCGTCTTCTG


title: TNY3_TG12_180N2

description: 3' adapter sequence:TAATATCGTATGCCGTCTTCTG


title: TNY3_TG10_188N3

description: 3' adapter sequence:TTAAGTCGTATGCCGTCTTCTG


title: TNY3_TG11_187N3

description: 3' adapter sequence:TAACGTCGTATGCCGTCTTCTG


title: MCF7 common DMSO control 3, RMA normalized with 2-4-D samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_85_P1_DMSO-MCF7-2-4-D


title: TNY3_TG9_188T3

description: 3' adapter sequence:TCTCCTCGTATGCCGTCTTCTG


title: MCF7 cells, Imazalil treated at 10uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_104_P1_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 1uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_162_P3_IMAZ-MCF7


title: TNY3_TG8_189N2

description: 3' adapter sequence:TCTAGTCGTATGCCGTCTTCTG


title: MCF7 cells, Imazalil treated at 1uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_134_P2_IMAZ-MCF7


title: TNY3_TG5_191FL2

description: 3' adapter sequence:TCCTATCGTATGCCGTCTTCTG


title: TNY3_TG13_184N2

description: 3' adapter sequence:TAGAGTCGTATGCCGTCTTCTG


title: TNY3_TG6_188T1

description: 3' adapter sequence:TCGATTCGTATGCCGTCTTCTG


title: TNY3_TG7_190N3

description: 3' adapter sequence:TCGCGTCGTATGCCGTCTTCTG


title: MCF7 cells, Imazalil treated at 1uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_106_P1_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.3uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_163_P3_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.1uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_164_P3_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.1uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_108_P1_IMAZ-MCF7


title: TNY3_TG4_188N1

description: 3' adapter sequence:TCCGTTCGTATGCCGTCTTCTG


title: MCF7 cells, Imazalil treated at 0.03uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_165_P3_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.3uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_135_P2_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.3uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_107_P1_IMAZ-MCF7


title: TNY3_TG2_191FL3

description: 3' adapter sequence:TCATCTCGTATGCCGTCTTCTG


title: TNY3_TG3_189N3

description: 3' adapter sequence:TCCACTCGTATGCCGTCTTCTG


title: TNY3_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCCGTCTTCTG


title: TNY3_TG23_189N1

description: 3' adapter sequence:TGTTATCGTATGCCGTCTTCTG


title: TNY3_TG1_191FL1

description: 3' adapter sequence:TCACTTCGTATGCCGTCTTCTG


title: MCF7 cells, Imazalil treated at 0.1uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_136_P2_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.01uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_166_P3_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.01uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_110_P1_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.03uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_137_P2_IMAZ-MCF7


title: TNY3_TG22_187N3

description: 3' adapter sequence:TTGTATCGTATGCCGTCTTCTG


title: TNY3_TG21_188N3

description: 3' adapter sequence:TTGACTCGTATGCCGTCTTCTG


title: TNY3_TG20_188T3

description: 3' adapter sequence:TTCATTCGTATGCCGTCTTCTG


title: TNY3_TG19_189N2

description: 3' adapter sequence:TTATTTCGTATGCCGTCTTCTG


title: TNY3_TG18_190N3

description: 3' adapter sequence:TAGCCTCGTATGCCGTCTTCTG


title: MCF7 cells, Imazalil treated at 0.03uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_109_P1_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.01uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_138_P2_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.003uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_139_P2_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.003uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_167_P3_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.003uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_111_P1_IMAZ-MCF7


title: MCF7 cells, Imazalil treated at 0.001uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_168_P3_IMAZ-MCF7


title: TNY2_TG16_84

description: 3' adapter sequence:TTACATCGTATGCCGTCTTCTG


title: TNY2_TG15_145FL3

description: 3' adapter sequence:TGATGTCGTATGCCGTCTTCTG


title: TNY2_TG13_67A

description: 3' adapter sequence:TAGAGTCGTATGCCGTCTTCTG


title: TNY2_TG14_69B

description: 3' adapter sequence:TATCATCGTATGCCGTCTTCTG


title: MCF7 common DMSO control 2, RMA normalized with IMAZ samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_141_P3_DMSO-MCF7-IMAZ


title: MCF7 cells, 2,4-D treated at 0.003uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_121_P2_2-4-D-MCF7


title: MCF7 cells, Imazalil treated at 0.001uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_112_P1_IMAZ-MCF7


title: MCF7 common DMSO control 1, RMA normalized with IMAZ samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_113_P2_DMSO-MCF7-IMAZ


title: MCF7 common DMSO control 3, RMA normalized with IMAZ samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_85_P1_DMSO-MCF7-IMAZ


title: MCF7 cells, Imazalil treated at 0.001uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_140_P2_IMAZ-MCF7


title: TNY2_TG12_60A

description: 3' adapter sequence:TAATATCGTATGCCGTCTTCTG


title: TNY2_TG11_58B

description: 3' adapter sequence:TAACGTCGTATGCCGTCTTCTG


title: TNY2_TG10_57

description: 3' adapter sequence:TTAAGTCGTATGCCGTCTTCTG


title: TNY2_TG8_48

description: 3' adapter sequence:TCTAGTCGTATGCCGTCTTCTG


title: TNY2_TG6_43

description: 3' adapter sequence:TCGATTCGTATGCCGTCTTCTG


title: TNY3_TG17_188T1

description: 3' adapter sequence:TACTCTCGTATGCCGTCTTCTG


title: TNY2_TG9_53

description: 3' adapter sequence:TCTCCTCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 3uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_152_P3_FENB-MCF7


title: TNY2_TG7_47B

description: 3' adapter sequence:TCGCGTCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 3uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_96_P1_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 10uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_151_P3_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 3uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_3_24h_124_P2_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 10uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_123_P2_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 10uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_10_24h_95_P1_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 1uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_97_P1_FENB-MCF7


title: TNY4_TG8_195T3


title: TNY2_TG4_40

description: 3' adapter sequence:TCCGTTCGTATGCCGTCTTCTG


title: TNY2_TG3_33A

description: 3' adapter sequence:TCCACTCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 1uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_125_P2_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 1uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_1_24h_153_P3_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 0.3uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_98_P1_FENB-MCF7


title: TNY2_TG5_41

description: 3' adapter sequence:TCCTATCGTATGCCGTCTTCTG


title: TNY2_TG2_31B

description: 3' adapter sequence:TCATCTCGTATGCCGTCTTCTG


title: TNY2_TG1_30B

description: 3' adapter sequence:TCACTTCGTATGCCGTCTTCTG


title: TNY2_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 0.3uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_154_P3_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 0.3uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_03_24h_126_P2_FENB-MCF7


title: TNY2_TG23_182N1

description: 3' adapter sequence:TGTTATCGTATGCCGTCTTCTG


title: PTCL/NOS 23

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

hyb_protocol: Standard Illumina Whole Genome DASL hybridization protocol.

scan_protocol: Illumina's BeadArray Reader was used to scan the BeadChips using the standard Illumina Whole Genome DASL scanning protocol.

data_processing: The data were log2-transformed and then quantile normalized using the lumi Bioconductor package. Normalized data coming from 2 different arrays (HumanRef-8 WG-DASL v3.0, HumanHT-12 WG-DASL V4.0 R2) were joined together considering only those genes in common to both versions of the array.

source_name: lymph node peripheral T-cell lymphoma not otherwise specified

label_protocol: Standard Illumina Whole Genome DASL labeling protocol.

extract_protocol: RNA from FFPE samples was extracted with the Ambion RecoverAll Extraction Kit. Normal cells from healthy donors were isolated by the Qiagen RNeasy Mini kit.

tag: tumor type

value: PTCL/NOS


title: PTCL/NOS 25


title: PTCL/NOS 24


title: MCF7 cells, Fenbuconazole treated at 0.1uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_155_P3_FENB-MCF7


title: TNY2_TG22_184N2

description: 3' adapter sequence:TTGTATCGTATGCCGTCTTCTG


title: PTCL/NOS 21


title: PTCL/NOS 22


title: PTCL/NOS 18


title: PTCL/NOS 19


title: MCF7 cells, Fenbuconazole treated at 0.1uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_99_P1_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 0.03uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_156_P3_FENB-MCF7


title: PTCL/NOS 20


title: PTCL/NOS 12


title: PTCL/NOS 13


title: TNY2_TG20_173N1

description: 3' adapter sequence:TTCATTCGTATGCCGTCTTCTG


title: TNY2_TG21_175N2

description: 3' adapter sequence:TTGACTCGTATGCCGTCTTCTG


title: TNY2_TG19_175N1

description: 3' adapter sequence:TTATTTCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 0.1uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_01_24h_127_P2_FENB-MCF7


title: TNY2_TG18_183_N1

description: 3' adapter sequence:TAGCCTCGTATGCCGTCTTCTG


title: PTCL/NOS 14


title: MCF7 cells, Fenbuconazole treated at 0.03uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_100_P1_FENB-MCF7


title: PTCL/NOS 17


title: PTCL/NOS 15


title: TNY2_TG17_173N2

description: 3' adapter sequence:TACTCTCGTATGCCGTCTTCTG


title: PTCL/NOS 11


title: MCF7 cells, Fenbuconazole treated at 0.03uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_003_24h_128_P2_FENB-MCF7


title: PTCL/NOS 10


title: PTCL/NOS 16


title: PTCL/NOS 8


title: MCF7 cells, Fenbuconazole treated at 0.01uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_129_P2_FENB-MCF7


title: PTCL/NOS 9


title: MCF7 cells, Fenbuconazole treated at 0.01uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_157_P3_FENB-MCF7


title: PTCL/NOS 2


title: PTCL/NOS 7


title: PTCL/NOS 1


title: TNY1_TG16_19B

description: 3' adapter sequence:TTACATCGTATGCCGTCTTCTG


title: PTCL/NOS 4


title: MCF7 cells, Fenbuconazole treated at 0.01uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_001_24h_101_P1_FENB-MCF7


title: PTCL/NOS 6


title: PTCL/NOS 3


title: PTCL/NOS 5


title: TNY1_TG15_19A

description: 3' adapter sequence:TGATGTCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 0.003uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_130_P2_FENB-MCF7


title: MCF7 cells, Fenbuconazole treated at 0.003uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_102_P1_FENB-MCF7


title: TNY1_TG14_18

description: 3' adapter sequence:TATCATCGTATGCCGTCTTCTG


title: ALCL ALK+ 6

source_name: lymph node anaplastic large-cell lymphoma ALK positive

value: ALCL ALK positive


title: TNY1_TG13_17B

description: 3' adapter sequence:TAGAGTCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 0.003uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_0003_24h_158_P3_FENB-MCF7

value: Cell culture


title: TNY1_TG12_17A

description: 3' adapter sequence:TAATATCGTATGCCGTCTTCTG


title: MCF7 cells, Fenbuconazole treated at 0.001uM, rep.3

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_159_P3_FENB-MCF7

value: 24 hours


title: TNY1_TG11_16A

description: 3' adapter sequence:TAACGTCGTATGCCGTCTTCTG

value: female


title: ALCL ALK+ 1


title: TNY1_TG10_15

description: 3' adapter sequence:TTAAGTCGTATGCCGTCTTCTG


title: ALCL ALK+ 5


title: ALCL ALK+ 2


title: ALCL ALK- 5

source_name: lymph node anaplastic large-cell lymphoma ALK negative

value: ALCL ALK negative


title: ALCL ALK- 4


title: ALCL ALK+ 4


title: ALCL ALK- 6


title: TNY1_TG9_14B

description: 3' adapter sequence:TCTCCTCGTATGCCGTCTTCTG


title: MCF7 common DMSO control 3, RMA normalized with FENB samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_85_P1_DMSO-MCF7-FENB


title: ALCL ALK+ 3


title: MCF7 cells, Fenbuconazole treated at 0.001uM, rep.1

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_103_P1_FENB-MCF7


title: ALCL ALK- 1


title: AITL 10

source_name: lymph node angioimmunoblastic T-cell lymphoma

value: AITL


title: ALCL ALK- 2


title: ALCL ALK- 3


title: AITL 8


title: MCF7 cells, Fenbuconazole treated at 0.001uM, rep.2

description:
Gene Expression data from MCF7 cell culture
BW_0001_24h_131_P2_FENB-MCF7


title: AITL 6


title: AITL 9


title: AITL 7


title: MCF7 common DMSO control 2, RMA normalized with FENB samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_141_P3_DMSO-MCF7-FENB


title: A673 cells, 2,4-D treated at 3uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_3_24h_227_P3_2-4-D-A673

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6 (each strain normalized independently)

growth_protocol: A673 cells were purchased from ATCC (Manassas, VA).   A673 cells were cultured in DMEM (hyclone) containing 10% FBS and 1X pen/strep and plated at 26,000 cells/well in a 96-well plate.


title: TNY1_TG8_136N2

description: 3' adapter sequence:TCTAGTCGTATGCCGTCTTCTG


title: A673 cells, 2,4-D treated at 3uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_3_24h_199_P2_2-4-D-A673


title: AITL 5


title: AITL 4


title: MCF7 common DMSO control 1, RMA normalized with FENB samples

description:
Gene Expression data from MCF7 cell culture
BW_0_24h_113_P2_DMSO-MCF7-FENB


title: TNY1_TG7_136N1

description: 3' adapter sequence:TCGCGTCGTATGCCGTCTTCTG


title: A673 cells, 2,4-D treated at 3uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_3_24h_171_P1_2-4-D-A673


title: TNY1_TG6_132N1

description: 3' adapter sequence:TCGATTCGTATGCCGTCTTCTG


title: TNY1_TG5_126N1

description: 3' adapter sequence:TCCTATCGTATGCCGTCTTCTG


title: TNY1_TG3_123N1

description: 3' adapter sequence:TCCACTCGTATGCCGTCTTCTG


title: TNY1_TG4_124N3

description: 3' adapter sequence:TCCGTTCGTATGCCGTCTTCTG

value: male


title: TNY1_TG2_122N2

description: 3' adapter sequence:TCATCTCGTATGCCGTCTTCTG


title: AITL 2


title: AITL 1


title: A673 cells, 2,4-D treated at 10uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_10_24h_226_P3_2-4-D-A673


title: RA(+) no.2

city: Kyoto

first: Hiroyuki

last: Yoshitomi

address: 53, Kawahara-Cho, Shogoin,

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the RMA16 algorithm.

source_name: Osteogenic differentiation from hiPSC with RA

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: iPSC were cultured in mTESR and induced in osteogenic medium for two days with or without retinoic acid

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

treatment_protocol: Osteogenic differentiation from hiPSC for two days with retinoic acid or without retinoic acid

value: induced osteogenic cells

tag: treatment

value: retinoic acid


title: RA(+) no.1


title: AITL 3


title: RA(-) no.2

source_name: Osteogenic differentiation from hiPSC without RA


title: A673 cells, 2,4-D treated at 10uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_10_24h_198_P2_2-4-D-A673


title: TNY1_TG1_121N2

description: 3' adapter sequence:TCACTTCGTATGCCGTCTTCTG

value: benign


title: RA(+) no.3


title: Day0 no.3

source_name: Osteogenic differentiation from hiPSC day0

value: iPSC


title: RA(-) no.3


title: TNY1_TG24_TPC1

description: 3' adapter sequence:TGCCATCGTATGCCGTCTTCTG


title: RA(-) no.1


title: A673 cells, 2,4-D treated at 1uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_1_24h_200_P2_2-4-D-A673


title: A673 cells, 2,4-D treated at 1uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_1_24h_228_P3_2-4-D-A673


title: MSTN-KO rep3_mRNA

city: Changchun

first: Wenni

last: You

address: No 5333 Xi`an road

country: China

institute: Jilin University

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

source_name: myoblasts

extract_protocol:
Myoblasts were cellected in a centrifugal tube,and RNA was harvested using Trizol reagent. Quantscript RT Kit from TIANGEN(Beijing) (Cat#KR103-03) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skeletal muscle

tag: genotype

value: MSTN-KO

value: myoblasts


title: A673 cells, 2,4-D treated at 10uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_10_24h_170_P1_2-4-D-A673


title: Day0 no.1


title: A673 cells, 2,4-D treated at 0.3uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_03_24h_229_P3_2-4-D-A673


title: TNY1_TG23_27A

description: 3' adapter sequence:TGTTATCGTATGCCGTCTTCTG


title: A673 cells, 2,4-D treated at 1uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_1_24h_172_P1_2-4-D-A673


title: MSTN-KO rep1_mRNA


title: WT rep3_mRNA

value: WT


title: Day0 no.2


title: TNY1_TG22_26A

description: 3' adapter sequence:TTGTATCGTATGCCGTCTTCTG


title: A673 cells, 2,4-D treated at 0.3uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_03_24h_201_P2_2-4-D-A673


title: TNY1_TG21_25

description: 3' adapter sequence:TTGACTCGTATGCCGTCTTCTG

value: malignant


title: WT rep1_mRNA


title: MSTN-KO rep3_miRNA


title: TNY1_TG20_23B

description: 3' adapter sequence:TTCATTCGTATGCCGTCTTCTG


title: MSTN-KO rep1_miRNA


title: MSTN-KO rep2_mRNA


title: TNY1_TG19_23A

description: 3' adapter sequence:TTATTTCGTATGCCGTCTTCTG


title: WT rep2_miRNA


title: WT rep3_miRNA


title: A673 cells, 2,4-D treated at 0.3uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_03_24h_173_P1_2-4-D-A673


title: K562 vehicle treated

city: Boston

last: Xiang

state: MA

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from K562 cells treated with vehicle (DMSO) for 5 hours

hyb_protocol: The fragmented cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C (Source: DFCI Microarray Core website).

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured (Source: DFCI Microarray Core website).

data_processing: The data were analyzed using dChip (build Dec 5 2011), using the default normalization and analysis settings.

label_protocol: Biotinylated cRNA was generated by the Dana-Farber Cancer Institute Microarray Core according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: Cells were maintained in RPMI-1640 + 10% FBS and passaged every 3 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by additional purification using the RNeasy spin column (QIAgen) according to the manufacturer's instructions.

treatment_protocol: The day before treatment, cells were suspended in fresh growth media at a concentration of 0.5x10^5/ml. On the day of treatment, vehicle or drug was added to the existing media at the indicated dose and time lengths.

value: chronic myeloid leukemia cells

tag: treated with

value: DMSO for 5hr


title: U266 atovaquone treated

description: Gene expression data from U266 cells treated with atovaquone (15 micromolar) for 2 hours

value: multiple myeloma cells

value: 15µM atovaquone for 2hr


title: U266 vehicle treated

description: Gene expression data from U266 cells treated with vehicle (DMSO) for 2 hours

value: DMSO for 2hr


title: WT rep1_miRNA


title: TNY1_TG18_21

description: 3' adapter sequence:TAGCCTCGTATGCCGTCTTCTG

value: female


title: A673 cells, 2,4-D treated at 0.1uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_01_24h_230_P3_2-4-D-A673

value: Cell culture

value: 24 hours


title: K562 atovaquone treated

description: Gene expression data from K562 cells treated with atovaquone (20 micromolar) for 5 hours

value: 20µM atovaquone for 5hr


title: A673 cells, 2,4-D treated at 0.1uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_01_24h_202_P2_2-4-D-A673


title: WT rep2_mRNA


title: DN3-wt3: wildtype replicate 3

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

description: wildtype replicate 3

data_processing:
Alignment using STAR v2.4.2a
Gene counting using featureCounts
DE analysis with LIMMA
Genome_build: mm10

source_name: DN3 Thymocyte Cells

extract_protocol:
Rneasy Extraction Kit (Qiagen)
mRNA - Poly A capture

value: DN3 Thymocyte Cells


title: A673 cells, 2,4-D treated at 0.1uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_01_24h_174_P1_2-4-D-A673


title: A673 cells, 2,4-D treated at 0.03uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_003_24h_231_P3_2-4-D-A673


title: DN3-wt2: wildtype replicate 2

description: wildtype replicate 2


title: TNY1_TG17_20

description: 3' adapter sequence:TACTCTCGTATGCCGTCTTCTG

value: benign


title: MSTN-KO rep2_miRNA


title: A673 cells, 2,4-D treated at 0.03uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_003_24h_203_P2_2-4-D-A673


title: DN3-P21KO3: p21 KO replicate 3

description: p21 KO replicate 3


title: DN3-wt1: wildtype replicate 1

description: wildtype replicate 1


title: DN3-P21KO1: p21 KO replicate 1

description: p21 KO replicate 1


title: DN3-P21KO2: p21 KO replicate 2

description: p21 KO replicate 2


title: DN3-LMO2TgP21KO2: LMO2-p21 KO replicate 2

description: LMO2-p21 KO replicate 2


title: Healthy17 VisitH4

city: Stanford

first: Lisa

middle: K

last: Blum

state: CA

address: 269 Campus Drive

institute: Stanford University

description:
HC17_VH4
Amplicon mixture

data_processing:
Matching files from the two HiSeq lanes were concatenated together (e.g., Sample1_Read1_Lane1+Sample1_Read1_Lane2).
Reads were filtered and assembled within UMI groups using MIGEC.
Explanation of the cumulative quality score (CQS) in migec-processed fastq files, and the relationship between CQS and Phred scores is described in the initial migec publication (Shugay et al. 2014, Nature Methods), and further illustrated in Turchaninova et al. 2016, Nature Protocols).
Paired-ends were merged with MITOOLS.
Genome_build: NA
Supplementary_files_format_and_content: *fastq: Fastq files of stitched reads, assembled and collapsed by UMI read group. These processed fastq files represent sequences that were assembled based on unique molecular identifiers (UMIs). The Q scores in these files are calculated based on the number of reads per UMI, as well as the quality of each base in each read.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA from PBMCs was extracted with Trizol and purified using RNA Clean & Concentrator-5 (Zymo Research) according to the manufacturer’s procedure.
cDNA was tagged with unique-molecular identifier sequences during RT. After a preliminary amplification step (specific for immunoglobulin constant regions), samples were divided into two aliquots and tagged with sequencing adapters in opposing directions (i.e., P5-Gene-P7 and P5-eneG-P7 for each sample), to allow for high quality assembly of UMI contigs. Library was sequenced across two separate HiSeq2500 lanes.

value: Peripheral Blood Mononuclear Cells

tag: timepoint

value: 1 year after initial visit

tag: disease group

value: Healthy control

tag: treatment response


title: Healthy17 VisitH3

description:
HC17_VH3
Amplicon mixture

tag: cell type

value: 6 months after initial visit


title: DN3-LMO2TgP21KO1: LMO2-p21 KO replicate 1

description: LMO2-p21 KO replicate 1


title: A673 cells, 2,4-D treated at 0.03uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_003_24h_175_P1_2-4-D-A673

tag: cell line

tag: time of exposure

tag: agent


title: DN3-LMO2Tg3: LMO2-transgenic replicate 3

description: LMO2-transgenic replicate 3

tag: strain


title: Healthy17 VisitH2

description:
HC17_VH2
Amplicon mixture

value: Initial Visit


title: A673 cells, 2,4-D treated at 0.01uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_001_24h_232_P3_2-4-D-A673

tag: dose (um)


title: DN3-LMO2Tg2: LMO2-transgenic replicate 2

description: LMO2-transgenic replicate 2

tag: tissue


title: A673 cells, 2,4-D treated at 0.01uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_001_24h_204_P2_2-4-D-A673


title: Healthy16 VisitH4

description:
HC16_VH4
Amplicon mixture


title: GFP_LO3: DN3 GFP Low cells replicate 3


title: A673 cells, 2,4-D treated at 0.01uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_001_24h_176_P1_2-4-D-A673


title: GFP_LO2: DN3 GFP Low cells replicate 2


title: Healthy16 VisitH2

description:
HC16_VH2
Amplicon mixture


title: Healthy16 VisitH3

description:
HC16_VH3
Amplicon mixture


title: GFP_HI3: DN3 GFP Hi cells replicate 3


title: GFP_HI1: DN3 GFP Hi cells replicate 1


title: Healthy10 VisitH4

description:
HC10_VH4
Amplicon mixture


title: Healthy10 VisitH3

description:
HC10_VH3
Amplicon mixture


title: GFP_HI2: DN3 GFP Hi cells replicate 2


title: GFP_LO1: DN3 GFP Low cells replicate 1


title: A673 cells, 2,4-D treated at 0.003uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_0003_24h_233_P3_2-4-D-A673


title: A673 cells, 2,4-D treated at 0.003uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_0003_24h_177_P1_2-4-D-A673


title: Healthy10 VisitH2

description:
HC10_VH2
Amplicon mixture


title: Healthy8 VisitH4

description:
HC8_VH4
Amplicon mixture


title: A673 cells, 2,4-D treated at 0.003uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_0003_24h_205_P2_2-4-D-A673


title: Col_DPI_Control_Systemic Leaf_rep3

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: Column name in processed data file: ZM22

data_processing:
Basecalling performed using Standard Illumina Base Caller (Bustard)
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample

organism: Arabidopsis thaliana

source_name: Col_DPI_Control_Systemic Leaf

growth_protocol: Arabidopsis thaliana Col (WT) plants were grown in peat pellets (Jiffy-7, Jiffy, http://www.jiffygroup.com/en/) at 23°C under short day growth conditions (8-hour light/16-hour dark, 50 µmol m−2 s−1).

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen Life Technologies) according to the manufacturer’s instructions and purified using NucleoSpin RNA Clean-up kit (Macherey-Nagel).
TruSeqHT

treatment_protocol: To inhibit the propagation of the ROS wave from the local to the systemic leaf, a drop of 0.3% agarose-containing water or 50 mM diphenyleneiodonium (DPI), was placed at the midpoint between the local and systemic leaves of 4– to 5-week-old Col-0 plants for 15 min. Local leaves of 4– to 5-week-old Col were exposed to a light intensity of 2000 µmol m-2 sec-1 for 8 min using a gooseneck light source (ACE I; Schott)

tag: ecotype

value: Col

value: DPI

tag: repeat

value: wild type

tag: stress

value: Control

value: Systemic Leaf


title: Healthy8 VisitH3

description:
HC8_VH3
Amplicon mixture


title: Col_DPI_Control_Local Leaf_rep3

description: Column name in processed data file: ZM21

source_name: Col_DPI_Control_Local Leaf

value: Local Leaf


title: Col_H2O_Highlight 8min_Local Leaf_rep3

description: Column name in processed data file: ZM19

source_name: Col_H2O_Highlight 8min_Local Leaf

value: Highlight 8min


title: Col_H2O_Control_Systemic Leaf_rep3

description: Column name in processed data file: ZM18

source_name: Col_H2O_Control_Systemic Leaf


title: Col_H2O_Control_Local Leaf_rep3

description: Column name in processed data file: ZM17

source_name: Col_H2O_Control_Local Leaf


title: Healthy7 VisitH4

description:
HC7_VH4
Amplicon mixture


title: Col_DPI_Highlight 8min_Systemic Leaf_rep3

description: Column name in processed data file: ZM24

source_name: Col_DPI_Highlight 8min_Systemic Leaf


title: Col_DPI_Highlight 8min_Systemic Leaf_rep2

description: Column name in processed data file: ZM16


title: Col_DPI_Highlight 8min_Local Leaf_rep2

description: Column name in processed data file: ZM15

source_name: Col_DPI_Highlight 8min_Local Leaf


title: Healthy7 VisitH3

description:
HC7_VH3
Amplicon mixture


title: Col_DPI_Highlight 8min_Local Leaf_rep3

description: Column name in processed data file: ZM23


title: Col_DPI_Control_Systemic Leaf_rep2

description: Column name in processed data file: ZM14


title: A673 cells, 2,4-D treated at 0.001uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_0001_24h_178_P1_2-4-D-A673

source_name: ATCC (Manassas, VA)

value: Cell culture


title: A673 cells, 2,4-D treated at 0.001uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_0001_24h_234_P3_2-4-D-A673

value: 24 hours


title: Wild type_rep2

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

description: 9234549016_C (Wild type_rep2)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Data was background corrected in Genome studio

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Breast cancer cell line

tag: genotype/variation


title: A673 cells, 2,4-D treated at 0.001uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_0001_24h_206_P2_2-4-D-A673


title: Wild type_rep1

description: 9234549016_A (Wild type_rep1)


title: A673 common DMSO control 2, RMA normalized with 2-4-D samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_197_P2_DMSO-A673-2-4-D

value: control


title: A673 cells, Imazalil treated at 3uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_3_24h_245_P3_IMAZ-A673

value: Imazalil


title: Col_DPI_Control_Local Leaf_rep2

description: Column name in processed data file: ZM13

tag: treatment


title: mH2A1.2_KO_rep1

description: 9234549016_B (mH2A1.2_KO_rep1)

value: mH2A1.2 knockout


title: mH2A1.2_KO_rep2

description: 9234549016_D (mH2A1.2_KO_rep2)


title: Healthy7 VisitH2

description:
HC7_VH2
Amplicon mixture

value: Peripheral Blood Mononuclear Cells


title: Col_H2O_Highlight 8min_Systemic Leaf_rep3

description: Column name in processed data file: ZM20

source_name: Col_H2O_Highlight 8min_Systemic Leaf

tag: genotype


title: A673 cells, Imazalil treated at 3uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_3_24h_217_P2_IMAZ-A673


title: Healthy8 VisitH2

description:
HC8_VH2
Amplicon mixture

value: Healthy control


title: Col_H2O_Highlight 8min_Systemic Leaf_rep2

description: Column name in processed data file: ZM12


title: A673 common DMSO control 3, RMA normalized with 2-4-D samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_225_P3_DMSO-A673-2-4-D


title: Col_H2O_Highlight 8min_Local Leaf_rep2

description: Column name in processed data file: ZM11


title: Col_H2O_Control_Systemic Leaf_rep2

description: Column name in processed data file: ZM10


title: Healthy5 VisitH4

description:
HC5_VH4
Amplicon mixture

value: 1 year after initial visit


title: Col_H2O_Control_Local Leaf_rep2

description: Column name in processed data file: ZM9


title: Healthy5 VisitH3

description:
HC5_VH3
Amplicon mixture

value: 6 months after initial visit


title: Col_DPI_Control_Systemic Leaf_rep1

description: Column name in processed data file: ZM6

value: Col


title: Healthy5 VisitH2

description:
HC5_VH2
Amplicon mixture

value: Initial Visit


title: A673 common DMSO control 1, RMA normalized with 2-4-D samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_169_P1_DMSO-A673-2-4-D


title: Col_DPI_Highlight 8min_Local Leaf_rep1

description: Column name in processed data file: ZM7

value: DPI

value: wild type


title: Healthy3 VisitH4

description:
HC3_VH4
Amplicon mixture


title: Col_H2O_Highlight 8min_Local Leaf_rep1

description: Column name in processed data file: ZM3


title: Healthy3 VisitH3

description:
HC3_VH3
Amplicon mixture


title: Col_H2O_Highlight 8min_Systemic Leaf_rep1

description: Column name in processed data file: ZM4

value: Systemic Leaf


title: Col_H2O_Control_Local Leaf_rep1

description: Column name in processed data file: ZM1

value: Control

value: Local Leaf


title: Col_DPI_Control_Local Leaf_rep1

description: Column name in processed data file: ZM5


title: A673 cells, Imazalil treated at 10uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_10_24h_188_P1_IMAZ-A673

value: Cell culture


title: Healthy3 VisitH2

description:
HC3_VH2
Amplicon mixture


title: A673 cells, Imazalil treated at 3uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_3_24h_189_P1_IMAZ-A673

value: 24 hours


title: Col_DPI_Highlight 8min_Systemic Leaf_rep1

description: Column name in processed data file: ZM8

value: Highlight 8min


title: Col_2min_H2O2_seedling_rep3

description: Column name in processed data file: 2-58

data_processing:
Basecalling performed using Standard Illumina Base Caller (Bustard)
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated file includes mean normalized counts for each sample

growth_protocol: Col-0 seedlings were grown in 100 mL of sterile 0.5 × MS media on a shaker under constant light (50 µmol m-2 sec-1) for 5 days

treatment_protocol: H2O2 treatment was conducted by adding 1 mM H2O2 to 5-day-old Col seedlings growing in 0.5 × MS media. Distilled water was added to control seedlings at time point 0. Seedlings were immediately frozen in liquid nitrogen after 2, 4 and 8 min of H2O2 treatment. About 100-150 seedlings were used for each time point and the experiment was repeated three times.

tag: time (min)

value: seedlings


title: Col_8min_H2O2_seedling_rep3

description: Column name in processed data file: 2-60


title: A673 cells, Imazalil treated at 10uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_10_24h_244_P3_IMAZ-A673

value: Imazalil


title: Col_4min_H2O2_seedling_rep3

description: Column name in processed data file: 2-59


title: A673 cells, Imazalil treated at 10uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_10_24h_216_P2_IMAZ-A673


title: Healthy1 VisitH4

description:
HC1_VH4
Amplicon mixture

tag: timepoint


title: Healthy1 VisitH3

description:
HC1_VH3
Amplicon mixture

tag: disease group


title: A673 cells, Imazalil treated at 1uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_1_24h_218_P2_IMAZ-A673


title: A673 cells, Imazalil treated at 1uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_1_24h_246_P3_IMAZ-A673


title: Col_8min_H2O2_seedling_rep2

description: Column name in processed data file: 2-56


title: Col_4min_H2O2_seedling_rep2

description: Column name in processed data file: 2-55


title: Col_2min_H2O2_seedling_rep2

description: Column name in processed data file: 2-54


title: A673 cells, Imazalil treated at 0.3uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_03_24h_247_P3_IMAZ-A673


title: Healthy1 VisitH2

description:
HC1_VH2
Amplicon mixture

tag: treatment response


title: Col_H2O_Control_Systemic Leaf_rep1

description: Column name in processed data file: ZM2


title: Col_0min_H2O_seedling_rep2

description: Column name in processed data file: 2-53


title: LymeDisease Pt26 Visit7

description:
LD26_V7
Amplicon mixture

tag: cell type

value: 2 years post-treatment

value: Lyme disease

value: Responder


title: A673 cells, Imazalil treated at 0.3uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_03_24h_191_P1_IMAZ-A673

tag: cell line


title: A673 cells, Imazalil treated at 0.3uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_03_24h_219_P2_IMAZ-A673

tag: time of exposure


title: LymeDisease Pt26 Visit5

description:
LD26_V5
Amplicon mixture

value: Peripheral Blood Mononuclear Cells

value: 6 months post-treatment


title: Col_0min_H2O_seedling_rep3

description: Column name in processed data file: 2-57

value: Col


title: Col_2min_H2O2_seedling_rep1

description: Column name in processed data file: 2-50


title: Col_4min_H2O2_seedling_rep1

description: Column name in processed data file: 2-51


title: LymeDisease Pt26 Visit3

description:
LD26_V3
Amplicon mixture

value: 1 month post-treatment


title: A673 cells, Imazalil treated at 0.1uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_01_24h_248_P3_IMAZ-A673

tag: agent


title: Col_0min_H2O_seedling_rep1

description: Column name in processed data file: 2-49


title: A673 cells, Imazalil treated at 1uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_1_24h_190_P1_IMAZ-A673


title: rbohd_Highlight_8min_Systemic Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-48

data_processing:
Basecalling performed using Standard Illumina Base Caller (Bustard)
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included normalized counts for each sample

source_name: rbohd_Highlight_8min_Systemic Leaf

growth_protocol: Arabidopsis thaliana Col (WT) and rbohD knockout plants were grown in peat pellets (Jiffy-7, Jiffy, http://www.jiffygroup.com/en/) at 23°C under short day growth conditions (8-hour light/16-hour dark, 50 µmol m−2 s−1).

treatment_protocol: Local leaves of 4– to 5-week-old Col (WT) and rbohD plants were exposed to a light intensity of 2000 µmol m-2 sec-1 for periods of 0, 2, 4 and 8 min using a gooseneck light source (ACE I; Schott)

value: Highlight

value: rbohd mutant


title: rbohd_Highlight_8min_Local Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-47

source_name: rbohd_Highlight_8min_Local Leaf


title: LymeDisease Pt26 Visit1

description:
LD26_V1
Amplicon mixture

value: Untreated


title: rbohd_Highlight_4min_Systemic Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-46

source_name: rbohd_Highlight_4min_Systemic Leaf

value: Systemic Leaf


title: A673 cells, Imazalil treated at 0.1uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_01_24h_220_P2_IMAZ-A673


title: LymeDisease Pt25 Visit7

description:
LD25_V7
Amplicon mixture


title: rbohd_Highlight_4min_Local Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-45

source_name: rbohd_Highlight_4min_Local Leaf

value: Local Leaf


title: rbohd_Highlight_2min_Local Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-43

source_name: rbohd_Highlight_2min_Local Leaf


title: A673 cells, Imazalil treated at 0.1uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_01_24h_192_P1_IMAZ-A673

value: Cell culture


title: LymeDisease Pt25 Visit5

description:
LD25_V5
Amplicon mixture


title: rbohd_Highlight_2min_Systemic Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-44

source_name: rbohd_Highlight_2min_Systemic Leaf


title: rbohd_Control_0min_Systemic Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-42

source_name: rbohd_Control_0min_Systemic Leaf

value: Control


title: rbohd_Control_0min_Local Leaf_rep_3

description:
Experiment2
Column name in processed data file: 2-41

source_name: rbohd_Control_0min_Local Leaf


title: Col_8min_H2O2_seedling_rep1

description: Column name in processed data file: 2-52

value: wild type


title: A673 cells, Imazalil treated at 0.03uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_003_24h_249_P3_IMAZ-A673

value: 24 hours


title: A673 cells, Imazalil treated at 0.03uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_003_24h_221_P2_IMAZ-A673

value: Imazalil


title: LymeDisease Pt25 Visit3

description:
LD25_V3
Amplicon mixture

source_name: Peripheral Blood Mononuclear Cells


title: rbohd_Highlight_8min_Systemic Leaf_rep_2

description:
Experiment2
Column name in processed data file: 2-40


title: LymeDisease Pt25 Visit1

description:
LD25_V1
Amplicon mixture


title: LymeDisease Pt24 Visit7

description:
LD24_V7
Amplicon mixture

value: 2 years post-treatment


title: LymeDisease Pt24 Visit5

description:
LD24_V5
Amplicon mixture

value: Lyme disease


title: rbohd_Highlight_4min_Systemic Leaf_rep_2

description:
Experiment2
Column name in processed data file: 2-38


title: LymeDisease Pt24 Visit1

description:
LD24_V1
Amplicon mixture

value: Responder