title: THP-1_24h_50µg/mL_of_empty_ENP_rep3

description: Gene expression in THP-1 cells after 24 h in presence of empty ENP exposure (50 µg/mL)

source_name: THP-1, 24 h, 50 µg/mL of empty ENP, replicate 3

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with 50 µg / mL of empty polymeric Eudragit® RL nanoparticles (empty ENP; 50 µg/mL) for 24 h. Eudragit® RL PO [CAS number: 33434-24-1], an acrylic polycationic copolymer of acrylic and methacrylic acid esters with a proportion of quaternary ammonium groups (0.5-0.8%), was a gift from Evonik polymers (Darmstadt, Germany).

value: 50 µg/mL of empty ENP


title: control H1 cells at passage 56

status: Public on Dec 19 2013

type: genomic

city: Stockholm

first: Sergey

last: Rodin

address: Scheelesvag 2, Plan 4:B1

country: Sweden

institute: Karolinska institute

description: H1 p56

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000/G

data_processing:
The array image was acquired using Affymetrix GeneChip®Command Console 3.1. The CEL files were analyzed using Affymetrix Genotyping Console version 4.1.4.840. Copy Number/LOH analysis was performed according to the Genotyping Console manual, using a set of 75 healthy individuals as a reference (75_samples_ref.REF).
CNCHP files containing information on the observed copy number of genomic segments. One REF file produced by the Batch Sample Mode of copy number analysis in the Affymetrix Genotyping Console.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: human ES cells line H1

label_protocol: According to Affymetrics instructions

growth_protocol: Human Es cells were grown on laminin-521

extract_protocol: DNA was extracted using Qiagen DNA Mini Kit

tag: cell line

value: H1 (control)

tag: cell type

value: human ES cells

tag: passage

value: passage 56


title: Wild-type control mouse rep3

type: RNA

city: Houston

first: Horatiu

last: Voicu

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: Gene expression data from brain

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C, 60 RPM on GeneChip Mouse Expression 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 and the Affymetrix Command Console v3.0 (AGCC) software.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method.

molecule: total RNA

organism: Mus musculus

source_name: P0 injected mouse analyzed at 4 months of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Affymetrix 3'IVT Express Manual, 2008-2010, RevB, Affymetrix).

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

tag: strain

value: Wild-type

tag: treatment

value: control mouse

tag: tissue

value: hippocampus


title: Wild-type control mouse rep2

description: Gene expression data from brain


title: Wild-type mouse injected with AAVTFEB rep4

description: Gene expression data from brain

value: injected with AAVTFEB


title: Tg4510 control mouse rep3

description: Gene expression data from brain


title: VezoM11

city: Cambridge

first: Luca

last: Pagani

state: UK

address: Henry Wellcome Building, Fitzwilliam Street

department: Biological Anthropology

country: United Kingdom

institute: University of Cambridge

description:
188
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: Blood

label_protocol: Followed Illumina standard protocol

extract_protocol: Extraction of genomic DNA from saliva was performed using standard extraction protocols.

tag: gender

value: F

value: Blood

tag: population

value: Vezo

tag: region

value: Madagascar


title: HS1001 cells at passage 15

description: HS1001 p15

source_name: human ES cells line HS1001

value: passage 15


title: VezoM10

description:
187
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Wild-type control mouse rep4

description: Gene expression data from brain


title: Tg4510 control mouse rep4

description: Gene expression data from brain


title: Tg4510 control mouse rep2

description: Gene expression data from brain


title: THP-1_24h_0µg/mL_of_empty_ENP_rep5 control

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

description: Gene expression in THP-1 cells after 24 h in absence of empty ENP exposure (0 µg/mL)

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA (specific activity > 10 pmol Cy3 / µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent), and immediately dried by brief immersion in acetonitrile.

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20120628) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

source_name: THP-1, 24 h, 0 µg/mL of empty ENP, replicate 5

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: THP-1 human monocyte cell line is derived from a blood sample of a one-year old child suffering from acute monocytic leukemia and was obtained from American Type Culture Collection (ATCC, TIB-202TM, Manassas, VA, USA). Cells were grown in RPMI 1640 medium (GIBCO, Invitrogen, Cergy Pontoise, France) supplemented with 10 % of heat-inactivated fetal bovine serum (Eurobio, Les Ullis, France), as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma, Saint Quentin Fallavier, France). Cells were incubated at 37°C to an atmosphere composed of 95 % air, 5 % CO2 and diluted by half every 3 days.

extract_protocol: The quality of the RNA extracted by TRIzol® Reagent (Invitrogen, La Jolla, CA) was determined by spectrophotometry (A260nm/A280nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 9, Agilent 2100 Bioanalyser, Santa Clara, CA, USA).

value: peripheral blood

value: male

tag: age

tag: time

value: 0 µg/mL of empty ENP


title: VezoM12

description:
189
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: M


title: Wild-type control mouse rep1

description: Gene expression data from brain


title: Tg4510 mouse injected with AAVTFEB rep4

description: Gene expression data from brain


title: VezoM9

description:
186
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: HS999 cells at passage 10

description: HS999 p10

source_name: human ES cells line HS999

value: passage 10


title: control HS401 cells at passage 25

description: HS401 p25

source_name: human ES cells line HS401

value: HS401 (control)

value: passage 25


title: THP-1_24h_50µg/mL_of_empty_ENP_rep2

source_name: THP-1, 24 h, 50 µg/mL of empty ENP, replicate 2

value: 50 µg/mL of empty ENP


title: THP-1_24h_50µg/mL_of_empty_ENP_rep1

source_name: THP-1, 24 h, 50 µg/mL of empty ENP, replicate 1


title: THP-1_24h_0µg/mL_of_empty_ENP_rep4 control

source_name: THP-1, 24 h, 0 µg/mL of empty ENP, replicate 4


title: VezoM6

description:
183
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: HS181 at passage 20 on laminin-521/E-cadherin after the transfer

description: HS181 p20 ECad

source_name: human ES cells line HS181

value: human ES cells


title: VezoM7

description:
184
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Wild-type mouse injected with AAVTFEB rep2

description: Gene expression data from brain

value: Wild-type


title: Tg4510 control mouse rep1

description: Gene expression data from brain

value: control mouse

value: hippocampus


title: HS1001 cells at passage 5

description: HS1001 p5

value: passage 5


title: VezoM8

description:
185
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: Blood


title: THP-1_24h_0µg/mL_of_empty_ENP_rep3 control

source_name: THP-1, 24 h, 0 µg/mL of empty ENP, replicate 3


title: Wild-type mouse injected with AAVTFEB rep3

description: Gene expression data from brain

value: injected with AAVTFEB


title: Tg4510 mouse injected with AAVTFEB rep1

description: Gene expression data from brain


title: Tg4510 mouse injected with AAVTFEB rep2

description: Gene expression data from brain


title: Tg4510 mouse injected with AAVTFEB rep3

description: Gene expression data from brain


title: HS181 just transfered from feeders (at different passage on feeeders)

description: HS181 p0 ECad


title: THP-1_24h_0µg/mL_of_empty_ENP_rep1 control

source_name: THP-1, 24 h, 0 µg/mL of empty ENP, replicate 1


title: VezoM5

description:
182
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: Vezo

value: Madagascar


title: THP-1_4h_50µg/mL_of_empty_ENP_rep3

description: Gene expression in THP-1 cells after 4 h in presence of empty ENP exposure (50 µg/mL)

source_name: THP-1, 4 h, 50 µg/mL of empty ENP, replicate 3

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with 50 µg / mL of empty polymeric Eudragit® RL nanoparticles (empty ENP; 50 µg/mL) for 4 h. Eudragit® RL PO [CAS number: 33434-24-1], an acrylic polycationic copolymer of acrylic and methacrylic acid esters with a proportion of quaternary ammonium groups (0.5-0.8%), was a gift from Evonik polymers (Darmstadt, Germany).

value: peripheral blood

value: 4 h


title: THP-1_24h_0µg/mL_of_empty_ENP_rep2 control

source_name: THP-1, 24 h, 0 µg/mL of empty ENP, replicate 2

value: male

value: 0 µg/mL of empty ENP


title: Wild-type mouse injected with AAVTFEB rep1

description: Gene expression data from brain


title: THP-1_4h_200µg/mL_of_GSNO_loaded_ENP_rep2

description: Gene expression in THP-1 cells after 4 h in presence of GSNO-loaded ENP exposure (200 µg/mL)

source_name: THP-1, 4 h, 200 µg/mL of GSNO-loaded ENP, replicate 2

value: 200 µg/mL of GSNO-loaded ENP


title: VezoM4

description:
181
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: M


title: THP-1_4h_200µg/mL_of_GSNO_loaded_ENP_rep4

source_name: THP-1, 4 h, 200 µg/mL of GSNO-loaded ENP, replicate 4


title: THP-1_4h_50µg/mL_of_empty_ENP_rep2

source_name: THP-1, 4 h, 50 µg/mL of empty ENP, replicate 2


title: THP-1_4h_50µg/mL_of_empty_ENP_rep1

source_name: THP-1, 4 h, 50 µg/mL of empty ENP, replicate 1


title: THP-1_4h_200µg/mL_of_GSNO_loaded_ENP_rep1

source_name: THP-1, 4 h, 200 µg/mL of GSNO-loaded ENP, replicate 1

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with 200 µg / mL of S-Nitrosoglutathione-loaded polymeric Eudragit® RL nanoparticles (GSNO-loaded ENP; 200 µg/mL) for 4 h. Eudragit® RL PO [CAS number: 33434-24-1], an acrylic polycationic copolymer of acrylic and methacrylic acid esters with a proportion of quaternary ammonium groups (0.5-0.8%), was a gift from Evonik polymers (Darmstadt, Germany). GSNO [CAS number: 57564-91-7] was synthesized by Dr F. Aldeek and Prof. R. Schneider in LRGP UPR-CNRS 3349 laboratories (Lorraine University, France).


title: VezoM2

description:
180
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

source_name: Blood

value: F


title: THP-1_4h_50µg/mL_of_GSNO_loaded_ENP_rep1

description: Gene expression in THP-1 cells after 4 h in presence of GSNO-loaded ENP exposure (50 µg/mL)

source_name: THP-1, 4 h, 50 µg/mL of GSNO-loaded ENP, replicate 1

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with 50 µg / mL of S-Nitrosoglutathione-loaded polymeric Eudragit® RL nanoparticles (GSNO-loaded ENP; 50 µg/mL) for 4 h. Eudragit® RL PO [CAS number: 33434-24-1], an acrylic polycationic copolymer of acrylic and methacrylic acid esters with a proportion of quaternary ammonium groups (0.5-0.8%), was a gift from Evonik polymers (Darmstadt, Germany). GSNO [CAS number: 57564-91-7] was synthesized by Dr F. Aldeek and Prof. R. Schneider in LRGP UPR-CNRS 3349 laboratories (Lorraine University, France).

value: 50 µg/mL of GSNO-loaded ENP


title: Mikea242

description:
224
Genomic DNA extracted from buccal cells was genotyped using OmniExpress 720K Bead Chip (Illumina).

source_name: buccal cells

value: buccal cells

value: Mikea


title: THP-1_4h_50µg/mL_of_GSNO_loaded_ENP_rep3

source_name: THP-1, 4 h, 50 µg/mL of GSNO-loaded ENP, replicate 3


title: THP-1_4h_50µg/mL_of_GSNO_loaded_ENP_rep2

source_name: THP-1, 4 h, 50 µg/mL of GSNO-loaded ENP, replicate 2


title: THP-1_4h_200µg/mL_of_GSNO_loaded_ENP_rep3

source_name: THP-1, 4 h, 200 µg/mL of GSNO-loaded ENP, replicate 3


title: THP-1_4h_50µM_of_GSNO_rep3

description: Gene expression in THP-1 cells after 4 h in presence of GSNO exposure (50 µM)

source_name: THP-1, 4 h, 50 µM of GSNO, replicate 3

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with S-Nitrosoglutathione (GSNO, 50 µM) for 4 h. GSNO [CAS number: 57564-91-7] was synthesized by Dr F. Aldeek and Prof. R. Schneider in LRGP UPR-CNRS 3349 laboratories (Lorraine University, France).

value: 50 µM of GSNO


title: THP-1_4h_50µM_of_GSNO_rep4

source_name: THP-1, 4 h, 50 µM of GSNO, replicate 4


title: Mikea193

description:
223
Genomic DNA extracted from buccal cells was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea155

description:
219
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea159

description:
220
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea176

description:
221
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea178

description:
222
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: THP-1_4h_50µM_of_GSNO_rep2

source_name: THP-1, 4 h, 50 µM of GSNO, replicate 2


title: THP-1_4h_0µM_of_GSNO_rep1 control

description: Gene expression in THP-1 cells after 4 h in absence of GSNO exposure (0 µM)

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 1

value: 0 µM of GSNO


title: THP-1_4h_0µM_of_GSNO_rep4 control

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 4


title: THP-1_4h_50µM_of_GSNO_rep1

source_name: THP-1, 4 h, 50 µM of GSNO, replicate 1


title: THP-1_4h_0µM_of_GSNO_rep3 control

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 3


title: THP-1_4h_0µM_of_GSNO_rep2 control

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 2


title: Mikea84

description:
217
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: THP-1_4h_0µM_of_GSNO_rep5 control

source_name: THP-1, 4 h, 0 µM of GSNO, replicate 5


title: C. botulinum strain CDC54079

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

hyb_protocol: Labeled DNA was hybridized with microarrays at 42 degrees C for 16 hours.

scan_protocol: Arrays were scanned with a GenePix 4000B.

data_processing: The log10 (average 635 nm median signal intensity for triplicate probes/average signal intensity for all empty spots on the array) was determined.

organism: Clostridium botulinum

source_name: soil

label_protocol: Genomic DNA was labeled with Klenow fragment and Cy5-labeled random primers at 37 degrees C for 2 hours.

growth_protocol: Bacteria were grown under anaerobic conditions at 35 degrees C for 24-48 hours prior to genomic DNA extraction.

extract_protocol: DNA was isolated using the PureLink Genomic DNA kit (Life Technologies, Grand Island, NY).

tag: bontf subtype

tag: year isolated


title: Mikea82

description:
216
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea81

description:
215
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain CDC54090

source_name: stool


title: Mikea152

description:
218
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

source_name: Blood


title: Mikea76

description:
211
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain CDC54075


title: Mikea77

description:
212
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea80

description:
214
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea79

description:
213
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain CDC54096


title: C. botulinum strain CDC54085


title: C. botulinum strain CDC54074


title: C. botulinum strain CDC54084


title: C. botulinum strain CDC54093


title: C. botulinum strain 54091


title: Mikea53

description:
204
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Mikea54

description:
205
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA451

description:
646
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).

source_name: Saliva

tag: sample type

value: Saliva

value: Temoro (Antemoro)


title: Mikea58

description:
207
Genomic DNA extracted from buccal cells was genotyped using OmniExpress 720K Bead Chip (Illumina).

source_name: buccal cells


title: Mikea62

description:
208
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: Blood


title: MadMA419

description:
643
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA422

description:
645
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA420

description:
644
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain CDC54089

source_name: anchovies


title: DLC1_TGFb

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health

hyb_protocol: According to Affymetrix instruction

scan_protocol: According to Affymetrix instruction

data_processing: The raw data were processed with the RMA algorithm.

label: biotin

source_name: DLC1 Overexpression, Treated with TGFbeta

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen)

extract_protocol: Cancer Cells were cultured and harvested with trypsinization. RNA was extracted with Trizol.

value: breast cancer


title: Mikea75

description:
210
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: Madagascar


title: DLC1

source_name: DLC1 Overexpression


title: Mikea56

description:
206
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain CDC54078

source_name: chamomile

value: unknown


title: MadMA358

description:
641
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA469

description:
647
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain CDC54076


title: Mikea63

description:
209
Genomic DNA extracted from buccal cells was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain CDC54088

source_name: dust


title: MadMA418

description:
642
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Vector

source_name: Vector Control


title: C. botulinum strain CDC54087


title: Vector_TGFb

source_name: Vector Control, Treated with TGFbeta


title: C. botulinum strain 8g

source_name: crab


title: C. botulinum strain CDC49930

source_name: honey


title: C. botulinum strain 4BVII

source_name: unknown


title: MadMA351

description:
636
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA357

description:
640
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA350

description:
635
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain Pcrab

source_name: pasteurized crab

value: Pcrab


title: PBMCs  vs. PBMCs treated with TNF-a and EPO-a from 10 pooled healthy donors - technical replicate 3

city: Chieti

first: Mirko

last: Pesce

address: Via Vestini

country: Italy

institute: University G. D'Annunzio

description: Biological replicate 3; technical replicate 3

hyb_protocol: Microarrays were dehydrated in ethanol for 2 minutes at room temperature, and dried using compressed air. Microarrays were rehydrated by soaking in prehybridization solution (5x SSPE pH 7, 0.1% SDS, 1% BSA) for 2 hours at 42°C, then were washed in deionized water twice for 1 minute each, and dried by briefly spinning in a centrifuge. Labeled aRNA was denatured at 95°C for 5 minutes, and applied to microarray slide. Microarrays and labeled aRNA were then covered with cover slips (Knittel Glass), placed in Hyb chamber (Gene Machine) and hybridized for 14-16 hours at 42°C. Microarray slides were washed in 2x SSPE, 0.1% SDS at 42°C for 5 minutes, then in 0.1x SSPE, 0.1% SDS once for 2 minutes at room temperature. Slides were then washed three times for 1 minute each at room temperature in 0.1x SSPE, immediately dried by briefly spinning in a centrifuge, and stored in a dark box.

scan_protocol: After hybridization, Cy5-Cy3 fluorescent signals were captured by a Confocal Laser Scanner ScanArray Express (Packard BioScience) and analysed using the software ScanArray Express - MicroArray Analysis System version 3.0 (Perkin Elmer).

data_processing: The values of the median signal intensity from each spot were subtracted by the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for raw data normalization to evaluate the signal-to-noise ratio of test sample vs. reference signal with the software ScanArray Express - MicroArray Analysis System version 3.0 (Perkin Elmer).

source_name: PBMCs from pooled 10 healthy donors

label_protocol: Five to twenty microgram of amplified aRNA was fluorescently labelled with Cy5 (Amersham, Pharmacia Biotech, Buckinghamshire, UK).

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

tag: primary culture

value: ex vivo PBMCs from pooled 10 healthy donors

source_name: PBMCs treated with TNF-a and EPO-a from pooled 10 healthy donors

value: ex vivo PBMCs


title: MadMA353

description:
637
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA356

description:
639
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: PBMCs  vs. PBMCs treated with TNF-a and EPO-a from 10 pooled healthy donors - technical replicate 2

description: Biological replicate 3; technical replicate 2

value: treated with TNF-a and EPO-a from pooled 10 healthy donors


title: PBMCs  vs. PBMCs treated with TNF-a and EPO-a from 10 pooled healthy donors - technical replicate 1

description: Biological replicate 3; technical replicate 1


title: PBMCs  vs. PBMCs treated with EPO-a from 10 pooled healthy donors - technical replicate 3

description: Biological replicate 2; technical replicate 3

source_name: PBMCs treated with EPO-a from pooled 10 healthy donors


title: MadMA354

description:
638
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: M


title: C. botulinum strain 4VI


title: MadMA349

description:
634
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: C. botulinum strain 12F


title: C. botulinum strain Af84

source_name: soil


title: MadMA347

description:
633
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).

source_name: Saliva


title: PBMCs  vs. PBMCs treated with EPO-a from 10 pooled healthy donors - technical replicate 2

description: Biological replicate 2; technical replicate 2

value: treated with EPO-a from pooled 10 healthy donors


title: PBMCs  vs. PBMCs treated with EPO-a from 10 pooled healthy donors - technical replicate 1

description: Biological replicate 2; technical replicate 1


title: C. botulinum strain Langeland

source_name: Liver paste

value: Langeland


title: MadMA343

description:
632
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA338

description:
629
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: MadMA342

description:
631
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: PBMCs  vs. PBMCs treated with TNF-a from 10 pooled healthy donors - technical replicate 2

description: Biological replicate 1; technical replicate 2

source_name: PBMCs treated with TNF-a from pooled 10 healthy donors


title: MadMA340

description:
630
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Haloferax mediterranei ΔdeoR2 with induction by fructose vs without induction replicate 3

status: Public on Dec 18 2013

city: Beijing

first: Lei

last: Cai

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

description: compare gene expression profiles of strain DF50 delta deoR2 under the induction by fructose

hyb_protocol: standard CapitalBio Methods

scan_protocol: Agilent G2565C

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, lowess normalized log2 ratio (test/control) was calculated.

organism: Haloferax mediterranei

source_name: ΔdeoR2_induced by fructose

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells of H. mediterranei DF50 or DF50 delta deoR2 were grown at 37°C until OD600 reached 1.5 in AS-168SYL medium,

extract_protocol: Total RNA extracted using Trizol (invitrogen) following manufacturer's instructions

treatment_protocol: fructose (soluted in TBSL buffer) was added into the culture to a final concentration of 50mM, and a same volume TBSL buffer was added into the other culture, both two were incubated for 45 before harvested.

tag: genotype/variation

tag: induced by

value: fructose (at final conc. 50mM)

value: control (no induction)


title: Haloferax mediterranei ΔdeoR2 with induction by fructose vs without induction replicate 2


title: PBMCs  vs. PBMCs treated with TNF-a from 10 pooled healthy donors - technical replicate 3

description: Biological replicate 1; technical replicate 3

value: treated with TNF-a from pooled 10 healthy donors


title: Haloferax mediterranei DF50 with induction by fructose vs without induction replicate 3

description: compare gene expression profiles of DF50 under the induction by fructose

source_name: DF50_induced by fructose

value: wild type


title: Ad-TRb infected liver, PTU fed and saline treated, biological replicate 1

city: Boston

first: Preeti

last: Ramados

address: 3 Blackfan Cir

institute: Beth Israel Deaconess Medical Center

description:
Gene expression from mouse liver infected with Ad-TRb virus, PTU-fed and saline treated.
Jackson Labs' male FVB;129P2-Gt(ROSA)26Sortm1(birA)Mejr/J homozygotes were crossed to pure FVB female mice, and the heterozygote offspring were used for experiments/subsequent breeding.

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.2.1.20.

source_name: Mouse liver, Ad-TRb, saline

label_protocol: 100ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix GeneChip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA).

growth_protocol: 9- to 10-week-old heterozygous BirA-expressing mice were housed in individual cages, fed a PTU diet, administered either Ad-GFP or Ad-TRb virus and then treated with either saline or T3.

extract_protocol: Total RNA was extracted using Perfect Pure RNA Tissue kit from 5 Prime.

treatment_protocol: Mice were fed PTU diet for 3 weeks, followed by adenoviral injections through the tail vein. Mice were then injected intraperitoneally with saline or T3 for 4 days and then euthanized and tissues were collected.

tag: strain/background

value: FVB

value: BirA+/-

value: liver

tag: infection

value: Ad-TRb virus

value: saline


title: Ad-TRb infected liver, PTU fed and T3 treated, biological replicate 2

description:
Gene expression from mouse liver infected with Ad-TRb virus, PTU-fed and T3 treated.
Jackson Labs' male FVB;129P2-Gt(ROSA)26Sortm1(birA)Mejr/J homozygotes were crossed to pure FVB female mice, and the heterozygote offspring were used for experiments/subsequent breeding.

source_name: Mouse liver, Ad-TRb, T3


title: MadMA320

description:
626
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: F

value: Saliva

value: Temoro (Antemoro)

value: Madagascar


title: MadMA318

description:
625
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: Ad-TRb infected liver, PTU fed and T3 treated, biological replicate 3


title: Haloferax mediterranei ΔdeoR2 with induction by fructose vs without induction replicate 1


title: Ad-GFP infected liver, PTU fed and T3 treated, biological replicate 3

description:
Gene expression from mouse liver infected with Ad-GFP virus, PTU-fed and T3 treated.
Jackson Labs' male FVB;129P2-Gt(ROSA)26Sortm1(birA)Mejr/J homozygotes were crossed to pure FVB female mice, and the heterozygote offspring were used for experiments/subsequent breeding.

source_name: liver, Ad-GFP, T3

value: Ad-GFP virus


title: Ad-TRb infected liver, PTU fed and saline treated, biological replicate 2


title: Ad-GFP infected liver, PTU fed and saline treated, biological replicate 3

description:
Gene expression from mouse liver infected with Ad-GFP virus, PTU-fed and saline treated.
Jackson Labs' male FVB;129P2-Gt(ROSA)26Sortm1(birA)Mejr/J homozygotes were crossed to pure FVB female mice, and the heterozygote offspring were used for experiments/subsequent breeding.

source_name: liver, Ad-GFP, saline


title: Ad-GFP infected liver, PTU fed and T3 treated, biological replicate 2


title: PBMCs  vs. PBMCs treated with TNF-a from 10 pooled healthy donors - technical replicate 1

description: Biological replicate 1; technical replicate 1

value: ex vivo PBMCs from pooled 10 healthy donors

value: ex vivo PBMCs


title: MadMA317

description:
624
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: 10-0439D_512751_A03_11192011

city: Oklahoma city

first: Xianfu

last: Wang

state: OK

address: 1122 Ne 13th ST

department: Pediatrics

institute: OUHSC

description: array CGH with high resolutin on acute myeloid leukemia-M5 patients

hyb_protocol: The labled DNA were hybridized on the chip via incubating in the MAUI hybridization system (BioMicro Systems, Salt Lake City, UT) at 42°C for 40 hours depending on the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: The slides were washed and scanned using Roche MS 2000 0.5 uM scanner with parameter was setup at autogain and the gain ratio of laser 532 and 635 is 100%.

data_processing:
NimbleScan version 2.6 and the SignalMap version 1.9 were applied for data analysis (NimbleGen System Inc, Madison, WI). The genomic locations were retrieved from National Center for Biotechnology Information (NCBI) build 36 (hg 18). Frequently affected regions recently detected as copy number polymorphisms were excluded from data analysis according to the Chromosome Number Variation (CNV) database in our lab and genomic variants in human genome (Build 36: Mar. 2006).
Log2 ratio: the log2 ratio of the test minus the log2 ratio of control. Positive gain or lost is four continuous probes ≥ ±0.15.

source_name: 10-0439D DNA from bone marrow blasts

label_protocol: The patients and the reference DNA were labeled by Random primer labeled with Cyanine 3 (Cy-3) or Cyanine 5 (Cy-5) (Trilink Biotechnologies, San Diego, CA) through PCR  depending on the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Bone marrow mononuclear cells (MNCs) were isolated by Ficoll-paque gradient centrifugation (TAKARA Biotechnology, Dalian, China), DNA was extracted with phenol-chloroform, and precipitated with ammonium acetate, ethanol and glycogen.

value: female

tag: blast ratio in bone marrow

value: bone marrow

source_name: DNA from commercially available pooled normal control

tag: reference

value: pooled normal control (Promega Inc. Female genomic DNA Catalog#G1521, Male genomic DNA Catalog# G1471)


title: 09-0406D-Hud,T-449240-A03-02232011

source_name: 09-0406D DNA from bone marrow blasts


title: 10-0681D_463797_A01_01292011

source_name: 10-0681D DNA from bone marrow blasts


title: Haloferax mediterranei DF50 with induction by fructose vs without induction replicate 2

tag: strain

value: fructose (at final conc. 50mM)

value: control (no induction)


title: Ad-GFP infected liver, PTU fed and saline treated, biological replicate 1

value: FVB

tag: tissue

tag: treatment


title: Ad-GFP infected liver, PTU fed and T3 treated, biological replicate 1

value: BirA+/-


title: 10-0118D_463797_A03_01292011

source_name: 10-0118D DNA from bone marrow blasts

tag: gender

value: male


title: Haloferax mediterranei DF50 with induction by fructose vs without induction replicate 1

value: wild type


title: 10-0679D_463677_A03_01222011

source_name: 10-0679D DNA from bone marrow blasts


title: 10-0680D_459036_A03_01282011

source_name: 10-0680D DNA from bone marrow blasts


title: 10-0676D_463676_A01_01272011

source_name: 10-0676D DNA from bone marrow blasts


title: 10-0673D_463677_A01_01222011

source_name: 10-0673D DNA from bone marrow blasts


title: 10-0678D_463677_A02_01222011

source_name: 10-0678D DNA from bone marrow blasts


title: 10-0473D-391870-A01-09092010

source_name: 10-0473D DNA from bone marrow blasts


title: 10-0469D-389165-A01-09092010

source_name: 10-0469D DNA from bone marrow blasts


title: MadMA337

description:
628
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).

source_name: Saliva

value: M

tag: population

tag: region


title: 10-0470D-389165-A02-09092010

source_name: 10-0470D DNA from bone marrow blasts

tag: age


title: 10-0472D-389165-A03-09092010

source_name: 10-0472D DNA from bone marrow blasts


title: 10-0468D-389159-A03-09092010

source_name: 10-0468D DNA from bone marrow blasts


title: 10-0474D-391870-A02-09092010

source_name: 10-0474D DNA from bone marrow blasts


title: Ad-TRb infected liver, PTU fed and saline treated, biological replicate 3

source_name: Mouse liver, Ad-TRb, saline

value: liver

value: Ad-TRb virus

value: saline


title: 10-0604D_502916_A02_Slot2_08142011

source_name: 10-0604D DNA from bone marrow blasts

source_name: DNA from commercially available pooled normal control


title: Ad-GFP infected liver, PTU fed and saline treated, biological replicate 2

source_name: liver, Ad-GFP, saline


title: 10-0458D-389158-A02-09032010

source_name: 10-0458D DNA from bone marrow blasts


title: 10-0463D-389159-A01-09092010

source_name: 10-0463D DNA from bone marrow blasts


title: 10-0461D-389158-A03-09032010

source_name: 10-0461D DNA from bone marrow blasts


title: 10-0456D-389151 A03-09032010

source_name: 10-0456D DNA from bone marrow blasts


title: 10-0457D-389158-A01-09032010

source_name: 10-0457D DNA from bone marrow blasts


title: 10-0455D_459036_A02_01282011

source_name: 10-0455D DNA from bone marrow blasts


title: MadMA335

description:
627
Genomic DNA extracted from saliva was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: Saliva

value: Temoro (Antemoro)

value: Madagascar


title: 10-0453D-389151-A01-09032010

source_name: 10-0453D DNA from bone marrow blasts


title: 10-0464D-389159-A02-09092010

source_name: 10-0464D DNA from bone marrow blasts


title: Fruit 182 DAFB replicate 1-3

city: Tsukuba

first: Kenji

last: Nashima

state: Ibaraki

address: Fujimoto 2-1

country: Japan

institute: NARO institute for fruit tree science

hyb_protocol: The labeled samples were hybridized to the oligoarray slides using Gene Expression Hybridization Kit (Agilent) as a hybridization buffer at 65°C for 17 h in a hybridization chamber. After hybridization, arrays were washed with Gene Expression Wash Buffer (Agilent) according to the manufacturer’s instructions.

scan_protocol: The dried slides were scanned by Agilent scanner. Raw data from scanning of the array was captured using Agilent Feature Extraction Ver. 10.7.1.1 (with Linear & Lowess normalization).

data_processing: Expression for each gene was calculated as the centered value of three biological replicates and the standard error of Global normalization settings were used with Subio platform with basic plug-in. See http://www.subio.jp/ for details. Briefly, the values were log transformed, performed global normalization with 75 percentile value and then centering.

organism: Pyrus communis

source_name: Fruit 182 DAFB

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 10 to 50 ng (-7 and 0 DAFB) or 500 ng (30 to 182 DAFB) RNA using the One-Color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Pyrus communis ‘La France’ fruits were harvested in farmer's orchard in Kaminoyama, Yamagata prefecture, Japan.

extract_protocol: For -7 DAFB and 0 DAFB RNA extraction, total RNAs were extracted from each sample using the method described in GEO series GSE38550. For 30 DAFB to 182 DAFB,  total RNAs were extracted from each sample using the method described in Wan et al. (1994).

treatment_protocol: For 182 DAFB, harvested 150 DAFB fruit were incubated at 2°C for 12 days and then incubated at room temperature (15°C to 20°C) for 20 days.  Other samples were not treated.

tag: Stage

value: 182 DAFB

tag: year

value: fruit flesh


title: Fruit 0 DAFB replicate 1-3

source_name: Fruit 0 DAFB

value: 0 DAFB

value: fruit receptacle (young flesh)


title: Fruit 120 DAFB replicate 1-3

source_name: Fruit 120 DAFB

value: 120 DAFB


title: Ad-TRb infected liver, PTU fed and T3 treated, biological replicate 1

source_name: Mouse liver, Ad-TRb, T3


title: Fruit 30 DAFB replicate 1-3

source_name: Fruit 30 DAFB

value: 30 DAFB


title: Hu1153_24hr_0uM

city: Research Triangle Park

first: Patrick

middle: D

last: McMullen

state: North Carolina

address: 6 Davis Drive, P.O. Box 12137

institute: The Hamner Institutes for Health Sciences

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_24hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization using Partek Genomics Suite

source_name: Human Hepatocyte cell

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: mirvana (AM1560)

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 24, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: rna integrity number

tag: units of age

value: years


title: Fruit 150 DAFB replicate 1-3

source_name: Fruit 150 DAFB

value: 150 DAFB


title: Hu1153_12hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_12hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: Hu1153_12hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_12hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: Fruit 60 DAFB replicate 1-4

source_name: Fruit 60 DAFB

value: 60 DAFB


title: Hu1153_12hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_12hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 12, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: Hu1153_24hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_24hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: Fruit -7 DAFB replicate 1-3

source_name: Fruit -7 DAFB

value: -7 DAFB


title: Hu1153_24hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_24hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Hu1153_24hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_24hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1153_2hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_2hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: Hu1153_6hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_6hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Hu1153_12hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_12hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: Hu1153_6hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_6hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: Fruit 90 DAFB replicate 1-3

source_name: Fruit 90 DAFB

value: 90 DAFB


title: Hu1153_2hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_2hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: Female thorax

city: Sao Paulo

first: Maria

last: Vibranovski

address: Rua do Matao, 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: Universidade de Sao Paolo

description:
3 biological replicates
The resulting BAR files were created using the Affymetrix Tiling Analysis Software v1.1.02 with quantile normalization and a local smooting window of 50 bp. Signal files provide the normalized probe intensity values. P-value files provide the statistical evidence for probe calls.

hyb_protocol: Samples were hybridized to the Affymetrix Drosophila Tiling Array 1.0R according to the manufacturer's protocol.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's protocol.

data_processing: Affymetrix Tiling Analysis Software (TAS v1.1.02) was used to process raw tiling array data (Cheng et al. 2005; Manak et al. 2006). Raw data were normalized by quantile normalization and the median of target intensities was scaled to 100. As suggested in Affymetrix TAS user manual, each probe position was analyzed in a local smoothing window with bandwidth equal to 50 bp (resulting in a window width of 101 bp) for better statistical power.

organism: Drosophila melanogaster

source_name: Female thorax

label_protocol: Samples were labeled using the GeneChip® WT Sense Target Labeling and Control Reagents Kit (Affymetrix Part # 900652) according the manufacturer's protocol.

growth_protocol: Flies were grown at room temperature and ~50% humidity on natural dark-light cycles

extract_protocol: Tissues were dissected and immediately used for extraction with the QIAgen RNeasy Mini Kit according to the manufacturer's protocol, with optional on-column DNase digestion.

treatment_protocol:
none
Virgin flies were collected and aged 1-6 days post-eclosion before dissections.

value: female

value: Oregon-R

value: thorax

tag: genotype

value: wild type


title: Male thorax

source_name: Male thorax

value: male


title: Hu1153_72hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_72hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: Hu1154_12hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_12hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Hu1154_12hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_12hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1153_6hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_6hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1153_72hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_72hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: Hu1154_24hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_24hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: Hu1153_72hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_72hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Testis

source_name: Testes

extract_protocol: Prior to extraction with the QIAgen RNeasy Mini Kit, RNAlater was removed by 1) filling the storage tube with RNase-free PBS, 2) centrifuging at 5,000 x g for 5 minutes, 3) removing the supernatant, and 4) repeating steps 1-3. Tissues were immediately resuspended in buffer RLT and RNA extracted according to the manufacturer's protocol with optional on-column DNase digestion.

treatment_protocol:
Tissues were stored in RNAlater ® (Ambion) at -20 C until RNA extraction.
Virgin flies were collected and aged 1-6 days post-eclosion before dissections.

value: testis


title: Hu1154_24hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_24hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: Hu1154_24hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_24hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: Hu1153_72hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_72hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 72, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: Hu1154_24hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_24hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1153_72hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_72hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: Hu1154_24hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_24hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: Hu1154_24hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_24hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 24, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: Hu1153_72hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1153_72hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1154_2hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_2hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 2, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: Ovary

description:
3 biological replicates
The resulting BAR files were created using the Affymetrix Tiling Analysis Software v1.1.02 with quantile normalization and a local smooting window of 50 bp. Signal files provide the normalized probe intensity values. P-value files provide the statistical evidence for probe calls.

source_name: Ovaries

value: ovary


title: Hu1154_2hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_2hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Male whole body

description:
2 biological replicates, 1 technical replicate
The resulting BAR files were created using the Affymetrix Tiling Analysis Software v1.1.02 with quantile normalization and a local smooting window of 50 bp. Signal files provide the normalized probe intensity values. P-value files provide the statistical evidence for probe calls.

source_name: Male whole body

treatment_protocol:
none
Virgin flies were collected and aged 1-6 days post-eclosion before dissections.

value: whole body


title: Female gut

description:
4 biological replicates
The resulting BAR files were created using the Affymetrix Tiling Analysis Software v1.1.02 with quantile normalization and a local smooting window of 50 bp. Signal files provide the normalized probe intensity values. P-value files provide the statistical evidence for probe calls.

source_name: Female gut

value: gut


title: Hu1154_2hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_2hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: Female whole body

source_name: Female whole body


title: Accessory gland

source_name: Accessory gland

value: accessory gland


title: Male gut

source_name: Male gut


title: Hu1154_2hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_2hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1154_72hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_72hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: Hu1156_12hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_12hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: GBA-PD 2 iPSc clone 1

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

description: iPS MK088-1

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: iPS_PD patient [GBA N370S]

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: subject group

value: Parkinson's Disease patients with heterozygous glucocerebrosidase mutations (GBA N370S) mutations

tag: subject id

value: GBA-PD 2

value: Male

tag: cell type

value: induced pluripotent stem cell line derived from dermal fibroblasts (iPS)

tag: culture conditions

value: mTeSR-1 + matrigel


title: Hu1154_2hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_2hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM

value: ul

value: years


title: Hu1154_6hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_6hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: GBA-PD 1 fibroblasts

description: NHDF MK071

source_name: DF_PD patient [GBA N370S]

value: GBA-PD 1

tag: gender

value: Female

value: dermal fibroblasts (DF)

value: ADMEM + 10% FCS


title: Hu1154_72hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_72hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: Hu1154_6hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_6hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 6, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: Hu1154_6hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1154_6hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: IDI-PD 1 fibroblasts

description: NHDF MK024

source_name: DF_idiopathic PD patient

value: idiopathic Parkinson's Disease patients.

value: IDI-PD 1


title: Hu1156_12hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_12hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

source_name: Human Hepatocyte cell

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1156_12hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_12hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Hu1156_12hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_12hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: Hu1156_12hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_12hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: GBA-PD 2 fibroblasts

description: NHDF MK088


title: IDI-PD 2 fibroblasts

description: NHDF JR023

value: IDI-PD 2


title: IDI-PD 1 iPSc clone 3

description: iPS MK024-3

source_name: iPS_idiopathic PD patient


title: Hu1156_24hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_24hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: IDI-PD 2 iPSc clone 3

description: iPS JR023-2


title: Hu1156_12hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_12hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 12, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: GBA-PD 1 iPSc clone 1

description: iPS MK071-1


title: Hu1156_24hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_24hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%, Route of Exposure: Williams\' E Medium, Units of Amount of Vehicle: v/v, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: Hu1156_24hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_24hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 24, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: GBA-PD 1 iPSc clone 3

description: iPS MK071-3


title: Hu1156_2hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_2hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: Hu1156_2hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_2hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: Hu1156_2hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_2hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Hu1156_6hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_6hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: Hu1156_2hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_2hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: Hu1156_2hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_2hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: placenta, PROM 10

city: Staten Island

first: Nanbert

last: Zhong

state: NY

address: 1050 Forest Hill Road

department: Human Genetics

institute: New York State Institute fro Basic Research in Developmental Disabilities

description: PROM 10

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, Santa Clara, CA) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, NE). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (Agilent Technology, Santa Clara, CA).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies, Santa Clara, CA). After normalization of the raw data, lncRNAs and mRNAs that have flags (“All Targets Value”) were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (Version 12.1). Both “GO analysis” and “Pathway analysis” were performed in the standard enrichment computation method.

source_name: PROM

extract_protocol: Total RNA isolated with Trizol.  mRNA was purified from total RNA after removal of rRNA with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, NE).

tag: tissue

value: placenta

tag: tissue source

value: Fresh tissue delivered from premature rupture of membrane

tag: gestation


title: Hu1156_6hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_6hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

tag: age


title: Hu1156_6hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_6hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: Hu1156_6hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_6hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: Hu1156_24hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_24hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: placenta, PROM 9

description: PROM 9

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, Santa Clara, CA) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, NE). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (Agilent Technology, Santa Clara, CA).


title: Hu1156_6hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_6hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: placenta, PROM 8

description: PROM 8


title: placenta, PROM 7

description: PROM 7


title: Hu1156_6hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_6hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: placenta, PROM 6

description: PROM 6


title: Hu1156_72hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_72hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 72, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: CHC1461T

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

description: Hepatocellular adenoma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol. Log R Ratios exported from the Beadstudio software.

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from 3 mm3 frozen tumor samples using high salt precipitation (as described in PMID: 3344216).

tag: Sex

value: F

tag: pathological diagnosis

value: non dysplastic hepatocellular adenoma


title: CHC1437T

description: Hepatocellular adenoma


title: CHC1358T

description: Hepatocellular adenoma


title: CHC1386T

description: Hepatocellular adenoma


title: CHC1391T

description: Hepatocellular adenoma

value: M


title: Hu1156_72hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_72hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%, Route of Exposure: Williams\' E Medium, Units of Amount of Vehicle: v/v, Dose or Concentration: 10, Units of Dose or Concentration: uM

tag: array type

tag: amount to core


title: CHC1398T

description: Hepatocellular adenoma


title: CHC1419T

description: Hepatocellular adenoma


title: placenta, PROM 5

description: PROM 5


title: CHC2321T

description: Hepatocellular carcinoma

value: hepatocellular carcinoma developed on an adenoma


title: CHC1351T

description: Hepatocellular adenoma


title: CHC1377T

description: Hepatocellular adenoma


title: CHC1343T

description: Hepatocellular adenoma


title: CHC1259T

description: Hepatocellular adenoma


title: CHC1365T

description: Hepatocellular adenoma


title: CHC1382T

description: Hepatocellular adenoma


title: CHC1374T

description: Hepatocellular adenoma


title: Hu1156_72hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1156_72hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM

tag: units of amount

tag: ratio


title: CHC1383T

description: Hepatocellular adenoma


title: placenta, PROM 3

description: PROM 3


title: placenta, PROM 4

description: PROM 4


title: CHC1380T

description: Hepatocellular adenoma


title: CHC1346T

description: Hepatocellular adenoma

value: dysplastic hepatocellular adenoma


title: CHC1342T

description: Hepatocellular adenoma


title: CHC1123T

description: Hepatocellular adenoma


title: Hu1164_12hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_12hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM

tag: rna integrity number

tag: units of age


title: CHC1121T

description: Hepatocellular adenoma


title: Hu1164_12hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_12hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: placenta, PROM 2

description: PROM 2


title: CHC979T

description: Hepatocellular adenoma


title: Hu1164_12hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_12hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: placenta, PTB 10

description: PTB 10

source_name: PTB

value: Fresh tissue delivered from preterm birth


title: Hu1164_12hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_12hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%, Route of Exposure: Williams\' E Medium, Units of Amount of Vehicle: v/v, Dose or Concentration: 1, Units of Dose or Concentration: uM

value: ul


title: CHC967T

description: Hepatocellular adenoma


title: placenta, PROM 1

description: PROM 1


title: Hu1164_12hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_12hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 12, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%

value: years


title: CHC966T

description: Hepatocellular adenoma


title: CHC954T

description: Hepatocellular adenoma


title: Hu1164_24hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_24hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: CHC874T

description: Hepatocellular adenoma


title: placenta, PTB 9

description: PTB 9


title: Hu1164_24hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_24hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC854T

description: Hepatocellular adenoma


title: placenta, PTB 8

description: PTB 8


title: CHC870T

description: Hepatocellular adenoma


title: placenta, PTB 7

description: PTB 7


title: Hu1164_24hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_24hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 24, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: Hu1164_24hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_24hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: CHC761T

description: Hepatocellular adenoma


title: placenta, PTB 5

description: PTB 5


title: Hu1164_2hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_2hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: Hu1164_2hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_2hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hrs, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: placenta, PTB 4

description: PTB 4


title: CHC756T

description: Hepatocellular adenoma


title: placenta, PTB 3

description: PTB 3


title: CHC663T

description: Hepatocellular adenoma


title: placenta, PTB 2

description: PTB 2


title: Hu1164_2hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_2hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO control, Treatment Duration: 2, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: placenta, PTB 6

description: PTB 6


title: CHC621T

description: Hepatocellular adenoma


title: placenta, PTB 1

description: PTB 1


title: CHC635T

description: Hepatocellular adenoma


title: CHC483T

description: Hepatocellular adenoma


title: CHC535T

description: Hepatocellular adenoma


title: CHC537T

description: Hepatocellular adenoma


title: CHC584T

description: Hepatocellular adenoma


title: Hu1164_6hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_6hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: CHC543T

description: Hepatocellular adenoma


title: CHC582T

description: Hepatocellular adenoma


title: CHC754T

description: Hepatocellular adenoma


title: CHC467T

description: Hepatocellular adenoma


title: CHC473T

description: Hepatocellular adenoma


title: Hu1164_6hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_6hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC480T

description: Hepatocellular adenoma


title: CHC1490T

description: Hepatocellular adenoma


title: CHC1331T

description: Hepatocellular adenoma


title: Hu1164_6hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_6hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: CHC1124T

description: Hepatocellular adenoma


title: Hu1164_6hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_6hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: DMSO Control, Treatment Duration: 6, Units of Duration: hrs, Vehicle for Chemical: DMSO, Amount of Vehicle: 0.10%


title: CHC950T

description: Hepatocellular adenoma


title: CHC362T

description: Hepatocellular adenoma


title: placenta, FTB 9

description: FTB 9

source_name: FTB

value: Fresh tissue delivered from full term birth


title: CHC478T

description: Hepatocellular adenoma


title: CHC1666T

description: Hepatocellular adenoma


title: CHC1426T

description: Hepatocellular adenoma


title: Hu1164_72hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_72hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: Hu1164_72hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_72hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: placenta, FTB 10

description: FTB 10


title: CHC1665T

description: Hepatocellular adenoma


title: CHC627T

description: Hepatocellular adenoma


title: placenta, FTB 6

description: FTB 6


title: placenta, FTB 7

description: FTB 7