title: IR64 panicle treated with 0.5FTSW rep3

description: Biological replication 3 of 3, comparison between 0.5FTSW-treated and well-watered IR64 panicle


title: IR64 panicle treated with 0.2FTSW rep1

status: Public on Jul 01 2012

type: RNA

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 1 of 3, comparison between 0.2FTSW-treated and well-watered IR64 panicle

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing: Software: Feature Extraction ver 9.5

molecule: total RNA

organism: Oryza sativa Indica Group

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (PPV pipe D: 180mm x H: 1050mm)
Grwoth media :10 kg of soil and sand (2:1) mixture and 12 g of complete fertilizer
No of seedling per pot : 2
Light condition: Natural conditions
Tempareture: Day/Night = 29/21℃
Water content: 1.0 FTSW

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: TRIzol (Invitrogen)
manual: Invitrogen

treatment_protocol:
Growth environment: greenhouse study
growth stage: about 10 days before flowering
Light condition: Natural conditions
Tempareture: Day/Night = 29/21℃
drought stress: 0.2 FTSW
Length of treatment: 17 days
growth stage: about 10 days before flowering

tag: cultivar

tag: tissue

value: panicle

tag: treatment

treatment_protocol:
Growth environment: greenhouse study
Light condition: Natural conditions
Tempareture: Day/Night = 29/21℃
drought stress: 1.0 FTSW (well watered)
Length of treatment: 17 days


title: IR64 panicle treated with 0.5FTSW rep1

description: Biological replication 1 of 3, comparison between 0.5FTSW-treated and well-watered IR64 panicle

treatment_protocol:
Growth environment: greenhouse study
growth stage: about 10 days before flowering
Light condition: Natural conditions
Tempareture: Day/Night = 29/21℃
drought stress: 0.5 FTSW
Length of treatment: 17 days
growth stage: about 10 days before flowering


title: IR77298-14-1-2-B-10 panicle treated with 0.5FTSW rep2

description: Biological replication 2 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-10 panicle


title: IR77298-5-6-B-11 shoot treated with 0.2FTSW rep3

description: Biological replication 3 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-5-6-B-11 shoot

value: shoot

value: Shoot


title: IR77298-5-6-B-11 shoot treated with 0.5FTSW rep3

description: Biological replication 3 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-5-6-B-11 shoot


title: IR77298-5-6-B-11 shoot treated with 0.2FTSW rep2

description: Biological replication 2 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-5-6-B-11 shoot


title: IR64 panicle treated with 0.2FTSW rep3

description: Biological replication 3 of 3, comparison between 0.2FTSW-treated and well-watered IR64 panicle


title: IR77298-5-6-B-11 shoot treated with 0.5FTSW rep2

description: Biological replication 2 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-5-6-B-11 shoot


title: IR77298-5-6-B-18 shoot treated with 0.5FTSW rep1

description: Biological replication 1 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-5-6-B-18 shoot


title: IR77298-14-1-2-B-13 shoot treated with 0.5FTSW rep3

description: Biological replication 3 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-13 shoot


title: IR77298-5-6-B-18 shoot treated with 0.2FTSW rep1

description: Biological replication 1 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-5-6-B-18 shoot


title: IR77298-5-6-B-11 shoot treated with 0.5FTSW rep1

description: Biological replication 1 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-5-6-B-11 shoot


title: IR77298-14-1-2-B-13 shoot treated with 0.5FTSW rep2

description: Biological replication 2 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-13 shoot


title: IR77298-5-6-B-18 shoot treated with 0.2FTSW rep3

description: Biological replication 3 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-5-6-B-18 shoot


title: IR77298-5-6-B-18 shoot treated with 0.5FTSW rep3

description: Biological replication 3 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-5-6-B-18 shoot


title: IR77298-14-1-2-B-13 shoot treated with 0.2FTSW rep2

description: Biological replication 2 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-14-1-2-B-13 shoot


title: IR77298-5-6-B-18 shoot treated with 0.5FTSW rep2

description: Biological replication 2 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-5-6-B-18 shoot


title: IR77298-5-6-B-18 shoot treated with 0.2FTSW rep2

description: Biological replication 2 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-5-6-B-18 shoot


title: IR77298-14-1-2-B-13 shoot treated with 0.2FTSW rep3

description: Biological replication 3 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-14-1-2-B-13 shoot


title: IR77298-14-1-2-B-13 shoot treated with 0.5FTSW rep1

description: Biological replication 1 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-13 shoot


title: IR77298-5-6-B-11 shoot treated with 0.2FTSW rep1

description: Biological replication 1 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-5-6-B-11 shoot


title: IR77298-14-1-2-B-13 shoot treated with 0.2FTSW rep1

description: Biological replication 1 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-14-1-2-B-13 shoot


title: IR77298-14-1-2-B-10 shoot treated with 0.5FTSW rep3

description: Biological replication 3 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-10 shoot


title: IR77298-14-1-2-B-10 shoot treated with 0.2FTSW rep2

description: Biological replication 2 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-14-1-2-B-10 shoot


title: IR77298-14-1-2-B-10 root treated with 0.5FTSW rep1

description: Biological replication 1 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-10 root

value: root


title: IR77298-14-1-2-B-10 shoot treated with 0.2FTSW rep3

description: Biological replication 3 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-14-1-2-B-10 shoot


title: IR64 shoot treated with 0.2FTSW rep1

description: Biological replication 1 of 3, comparison between 0.2FTSW-treated and well-watered IR64 shoot


title: IR64 shoot treated with 0.5FTSW rep3

description: Biological replication 3 of 3, comparison between 0.5FTSW-treated and well-watered IR64 shoot


title: IR77298-14-1-2-B-10 shoot treated with 0.5FTSW rep2

description: Biological replication 2 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-10 shoot


title: IR64 shoot treated with 0.5FTSW rep2

description: Biological replication 2 of 3, comparison between 0.5FTSW-treated and well-watered IR64 shoot


title: IR77298-14-1-2-B-10 shoot treated with 0.2FTSW rep1

description: Biological replication 1 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-14-1-2-B-10 shoot


title: IR64 shoot treated with 0.2FTSW rep3

description: Biological replication 3 of 3, comparison between 0.2FTSW-treated and well-watered IR64 shoot


title: ETS2-null EB 2

city: Houston Road

first: Robert

middle: Joel

last: Schwartz

state: Texas

address: 4800 Calhoun

department: Biology and Biochemistry

country: USA

institute: University of Houston

description: 144 day 10 embryoid bodies of Ets2-null ES cells

hyb_protocol: Phalanx Hybridization Protocol (http://www.phalanxbiotech.com/)

scan_protocol: Scanned by Phalanx Biotech Group (http://www.phalanxbiotech.com/)

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

organism: Mus musculus

source_name: day 10 embryoid body

label_protocol: AminoAllyl aRNA labeling. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA with the NHS-CyDye.

extract_protocol: total RNA was extracted follow the Invitrogen trizol protocol, and further purified with the Qiagen RNeasy minicolumn.

tag: cell type

value: ES derived embryoid bodies

tag: genotype

tag: background strain


title: IR64 shoot treated with 0.5FTSW rep1

description: Biological replication 1 of 3, comparison between 0.5FTSW-treated and well-watered IR64 shoot


title: IR64 shoot treated with 0.2FTSW rep2

description: Biological replication 2 of 3, comparison between 0.2FTSW-treated and well-watered IR64 shoot


title: IR77298-14-1-2-B-10 shoot treated with 0.5FTSW rep1

description: Biological replication 1 of 3, comparison between 0.5FTSW-treated and well-watered IR77298-14-1-2-B-10 shoot


title: Control Wildtype EB 1

description: 144 day 10 embryoid bodies of wildtype ES cells

value: wild type


title: pet_ommo_F3_105d [fw dataset]

city: Raleigh

first: Heather

last: Hines

state: NC

address: Campus Box 7614

department: Genetics

institute: North Carolina State University

description: hwfwdatanobpest_lnm.txt, fwdatanobpest_lnm.txt

hyb_protocol: Hybridization of samples was performed according to NimbleGen protocols (2008): for the forewings this was performed at the City of Hope Functional Genomics Core, while the hindwings were run separately at NCSU. See www.nimblegen.com.

scan_protocol: Scanning of samples was performed on the GenePix 4000B scanner according to NimbleGen protocols (2008): for the forewings this was performed at the City of Hope Functional Genomics Core, while the hindwings were run separately at NCSU. See www.nimblegen.com.

data_processing: As an initial quality control measure we examined the distribution of probe intensities across each array. Regions with uneven intensities were removed from the dataset and treated as missing data. Arrays with large regions of uneven intensities or with inconsistent intensity distributions from other samples were rerun. To examine the effects of normalization, we used hierarchical clustering and principal components analyses to compare array clustering across raw and normalized datasets and examined the influence on distribution of intensities of all probes and random probes. Quality control procedures and microarray data analyses were performed using JMP Genomics 4.0 (SAS Institute). Forewing and hindwing datasets were normalized separately, except for the combined color ANOVA, where they were normalized together. Each of these normalized datasets are presented in a separate file. Similar intensity distributions across arrays of both studies prevented normalization methods from having a strong impact on intensities. Data were log2 transformed and Loess normalized using all transcript probes. Expression for each transcript was then summarized as a mean of the probes representing it.

organism: Heliconius erato petiverana

source_name: Heliconius erato petiverana pupal forewing, apical section, ommochrome stage

label_protocol: Total RNA was reverse transcribed and amplified using the TransPlex Whole Transcriptome Amplification Kit 2 (Sigma-Aldrich, St. Louis, Missouri, United States). Cy3-labeling of samples was performed according to NimbleGen protocols (2008): for the forewings this was performed at the City of Hope Functional Genomics Core, while the hindwings were run separately at NCSU. See www.nimblegen.com.

growth_protocol: H. e. petiverana (Panama) and the Peruvian stocks were developed from wild-caught individuals and the hybrid H. himera and H. e. etylus stocks were generated from Ecuadorian individuals that were crossed and selected across several generations to create a stock with a consistently homozygous phenotype. Specimens were reared from stocks maintained at the STRI Heliconius Rearing Facility in Gamboa, Panama. Each larva was reared separately on Passiflora hostplant and monitored for the time of pupation. Pupae for forewings were reared at ambient temperature (~28°C), while pupae for hindwings were kept indoors at 25°C.  In the forewings, Days 1, 3, and 5 were at 12, 36, and 60 hours post-pupation. In the hindwings these stages were sampled at 24, 48, and 72 hours.

extract_protocol: Dissected tissues were stored in RNAlater (Qiagen) at -80˚C until RNA extraction. Tissues were lysed using a Tissuelyser. Total RNA was purified using the RNAqueous Kit (Applied Biosystems, Carlsbad, California, United States) followed by DNA removal using the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: developmental stage

value: ommochrome

tag: wing

value: Forewing

tag: wing section

value: Apical

tag: wing section color

value: Black

tag: slide number

tag: sample id


title: Control Wildtype EB 2


title: pet_ommo_F3_102d [fw dataset]


title: pet_ommo_F1_16b [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, ommochrome stage

value: Basal


title: pet_ommo_F2_102c [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, ommochrome stage

value: Medial

value: Red


title: pet_ommo_F1_105b [fw dataset]


title: IR77298-14-1-2-B-10 panicle treated with 0.2FTSW rep1

description: Biological replication 1 of 3, comparison between 0.2FTSW-treated and well-watered IR77298-14-1-2-B-10 panicle


title: pet_mel_F1_15d [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, melanin stage

value: melanin


title: pet_ommo_F2_16c [fw dataset]


title: pet_ommo_F3_16d [fw dataset]


title: pet_mel_F3_15f [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, melanin stage


title: pet_mel_F2_15e [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, melanin stage


title: pet_mel_F3_126c [fw dataset]


title: pet_mel_F2_123c [fw dataset]


title: pet_ommo_F1_102b [fw dataset]


title: pet_mel_F3_123d [fw dataset]


title: pet_day5_F3_11c [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, 5 Days post-pupation

value: Day 5


title: pet_mel_F2_126b [fw dataset]


title: pet_mel_F1_126a [fw dataset]


title: pet_day5_F3_10d [fw dataset]


title: pet_day5_F2_1c [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, 5 Days post-pupation


title: pet_day5_F2_10c [fw dataset]


title: pet_day5_F3_1d [fw dataset]


title: pet_day5_F2_11b [fw dataset]


title: pet_mel_F1_123b [fw dataset]


title: pet_day5_F1_11a [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, 5 Days post-pupation


title: pet_day5_F1_1b [fw dataset]


title: pet_day5_F1_10b [fw dataset]


title: pet_day3_F2_7b [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, 3 Days post-pupation

value: Day 3


title: pet_day3_F3_5d [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, 3 Days post-pupation


title: pet_day3_F3_7c [fw dataset]


title: pet_day3_F2_5c [fw dataset]


title: pet_day3_F1_5b [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, 3 Days post-pupation


title: pet_day3_F2_4c [fw dataset]


title: pet_day3_F3_4d [fw dataset]


title: pet_day3_F1_7a [fw dataset]


title: pet_day1_F3_104d [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, 1 Day post-pupation

value: Day 1


title: pet_day1_F3_109c [fw dataset]


title: pet_day1_F3_6c [fw dataset]


title: pet_day3_F1_4b [fw dataset]


title: pet_day1_F1_6a [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, 1 Day post-pupation


title: pet_day1_F2_104c [fw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, 1 Day post-pupation


title: pet_ommo_F2_105c [fw dataset]


title: papa_ommo_F3_74c [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, ommochrome stage


title: pet_day1_F2_6b [fw dataset]


title: pet_day1_F1_109a [fw dataset]


title: papa_ommo_F3_82c [fw dataset]

organism: Heliconius erato etylus x Heliconius himera


title: pet_day1_F1_104b [fw dataset]


title: papa_ommo_F3_70d [fw dataset]


title: papa_ommo_F2_70c [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, ommochrome stage

value: Yellow


title: papa_ommo_F2_74b [fw dataset]


title: pet_day1_F2_109b [fw dataset]


title: papa_ommo_F1_70b [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, ommochrome stage


title: papa_ommo_F2_82b [fw dataset]


title: papa_ommo_F1_74a [fw dataset]


title: papa_mel_F3_88d [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, melanin stage


title: papa_ommo_F1_82a [fw dataset]


title: papa_day5_F3_69d [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, 5 Days post-pupation


title: papa_mel_F3_75c [fw dataset]


title: papa_mel_F2_88c [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, melanin stage


title: papa_mel_F2_80c [fw dataset]


title: papa_mel_F1_80b [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, melanin stage


title: papa_day5_F1_91b [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, 5 Days post-pupation


title: papa_mel_F1_75a [fw dataset]


title: papa_day3_F1_90b [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, 3 Days post-pupation


title: papa_mel_F3_80d [fw dataset]


title: papa_day5_F1_69b [fw dataset]


title: papa_day5_F3_91d [fw dataset]


title: papa_day3_F3_71d [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, 3 Days post-pupation


title: papa_day3_F3_84d [fw dataset]


title: papa_mel_F2_75b [fw dataset]


title: papa_day5_F1_79b [fw dataset]


title: papa_day3_F2_71c [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, 3 Days post-pupation


title: papa_day5_F2_79c [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, 5 Days post-pupation


title: papa_day3_F3_90d [fw dataset]


title: papa_mel_F1_88b [fw dataset]


title: papa_day5_F3_79d [fw dataset]


title: papa_day3_F2_90c [fw dataset]


title: papa_day1_F3_83d [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, 1 Day post-pupation


title: papa_day5_F2_69c [fw dataset]


title: papa_day3_F1_84b [fw dataset]


title: papa_day3_F2_84c [fw dataset]


title: papa_day3_F1_71b [fw dataset]


title: papa_day5_F2_91c [fw dataset]


title: ETS2-null EB 1

source_name: day 10 embryoid body


title: papa_day1_F3_85d [fw dataset]


title: papa_day1_F2_83c [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, 1 Day post-pupation


title: B07_favDay3 [hw dataset]

description: hwfwdatanobpest_lnm.txt, hwdatanobpest_lnm.txt

organism: Heliconius erato favorinus

source_name: Heliconius erato favorinus pupal hindwing, 3 Days post-pupation

value: Hindwing


title: E10_favommo [hw dataset]

source_name: Heliconius erato favorinus pupal hindwing, ommochrome stage


title: C04_favmela [hw dataset]

source_name: Heliconius erato favorinus pupal hindwing, melanin stage


title: papa_day1_F1_83b [fw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, 1 Day post-pupation


title: papa_day1_F2_85c [fw dataset]


title: A10_favDay5 [hw dataset]

source_name: Heliconius erato favorinus pupal hindwing, 5 Days post-pupation


title: A01_favDay1 [hw dataset]

source_name: Heliconius erato favorinus pupal hindwing, 1 Day post-pupation


title: F10_favDay1 [hw dataset]


title: D10_favmela [hw dataset]


title: C01_favDay5 [hw dataset]


title: papa_day1_F1_85b [fw dataset]


title: F1_favDay5 [hw dataset]


title: D4_favDay5 [hw dataset]


title: G4_favommo [hw dataset]


title: C07_favDay3 [hw dataset]


title: A09_emaommo [hw dataset]

organism: Heliconius erato emma

source_name: Heliconius erato emma pupal hindwing, ommochrome stage


title: A07_favmela [hw dataset]


title: F7_favmela [hw dataset]


title: E1_favDay1 [hw dataset]


title: F12_emaommo [hw dataset]


title: G3_emamela [hw dataset]

source_name: Heliconius erato emma pupal hindwing, melanin stage


title: F6_emamela [hw dataset]


title: D7_favDay3 [hw dataset]


title: B04_favommo [hw dataset]


title: D3_emaommo [hw dataset]


title: B10_favDay1 [hw dataset]


title: A04_favommo [hw dataset]


title: C06_emaommo [hw dataset]


title: F4_favDay3 [hw dataset]


title: G6_emaDay3 [hw dataset]

source_name: Heliconius erato emma pupal hindwing, 3 Days post-pupation


title: D9_emaDay5 [hw dataset]

source_name: Heliconius erato emma pupal hindwing, 5 Days post-pupation


title: C11_ampommo [hw dataset]

organism: Heliconius erato amphitrite

source_name: Heliconius erato amphitrite pupal hindwing, ommochrome stage


title: C09_emamela [hw dataset]


title: D5_ampmela [hw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, melanin stage


title: C12_emaDay5 [hw dataset]


title: D6_emaDay1 [hw dataset]

source_name: Heliconius erato emma pupal hindwing, 1 Day post-pupation


title: F2_ampommo [hw dataset]


title: D8_ampommo [hw dataset]


title: B02_emaDay3 [hw dataset]


title: F9_emaDay3 [hw dataset]


title: C03_emaDay1 [hw dataset]


title: B09_ampommo [hw dataset]


title: B05_emaDay5 [hw dataset]


title: F11_ampDay5 [hw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, 5 Days post-pupation


title: A02_ampmela [hw dataset]


title: A12_emaDay1 [hw dataset]


title: E5_ampDay5 [hw dataset]


title: fibroblasts 2

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

department: Medicine

institute: University of Minnesota

hyb_protocol: cRNA was hybridized onto a HumanHT-12 v.4.0 Expression Beadchip (Illumina) following the Direct Hybridization Gene Expression protocol.

scan_protocol: The Beadchips were scanned using an Illumina’s iScan instrument.

data_processing: Data were created using Illumina's GenomeStudio software and processed with Spotfire DecisionSite for Functional Genomics software.

label: biotin

organism: Homo sapiens

source_name: fibroblasts

label_protocol: Biotin-labeled cRNA was synthesized with a TotalPrep-96 RNA Amplification Kit (Life Technologies/Applied Biosystems #4393543) following the instruction of the manufacturer.

extract_protocol: RNA was prepared with the PureLink RNA total RNA purification system (Life Technologies). RNA quality was evaluated with a NanoDrop 8000 and an Agilent Bioanalyzer 2100.

value: primay fibroblasts


title: A06_emaDay3 [hw dataset]


title: B06_ampmela [hw dataset]


title: E12_emaDay5 [hw dataset]


title: LF-iPSCs 2

source_name: LF-iPS cells

value: LF-iPS cells

tag: parental cell line


title: G5_ampDay5 [hw dataset]


title: E3_emamela [hw dataset]


title: A05_ampDay5 [hw dataset]


title: E9_emaDay1 [hw dataset]


title: fibroblasts


title: G11_ampmela [hw dataset]


title: E8_ampDay3 [hw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, 3 Days post-pupation


title: L-iPSCs 2

source_name: L-iPS cells

value: L-iPS cells


title: F-iPSCs 2

source_name: F-iPS cells

value: F-iPS cells


title: ESCs 2

source_name: ES cells

value: ES cells

tag: cell line


title: C08_ampDay1 [hw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, 1 Day post-pupation


title: D2_ampDay3 [hw dataset]


title: PC9 GR Gef 1uM

city: Tokyo

first: Junko

last: Hamamoto

address: 35 Shinanomachi, Shinjuku-ku

department: Pulmonary Medicine

institute: School of Medicine, Keio University

description: Gene expression after 48hrs in 1uM Gefitinib human lung cancer cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 8x60K human array (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PC9 GR gefitinib 1uM

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 175 ng RNA using Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: PC9 cell lines were cultured by RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

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

treatment_protocol: For RNA collection, 8 × 10^4 cells were seeded per well in 6-well plates and allowed to attach for 24 hours. The cells were then treated with 1uM gefitinib, 48hrs later we collected total RNA from these cell line.

tag: gefitinib-resistant

value: yes

value: 1uM Gefitinib


title: A11_ampDay3 [hw dataset]

value: Black


title: D11_ampDay1 [hw dataset]


title: F-iPSCs


title: pet_ommo_F3_16d [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, ommochrome stage

value: ommochrome

value: Forewing

value: Apical


title: PC9 GR DMSO

description: Gene expression after 48hrs in 0uM Gefitinib human lung cancer cell line

source_name: PC9 GR

value: DMSO


title: B03_ampDay1 [hw dataset]


title: G8_ampDay1 [hw dataset]


title: pet_ommo_F3_105d [hwfw dataset]


title: LF-iPSCs


title: ESCs


title: pet_ommo_F3_102d [hwfw dataset]


title: C02_ampDay3 [hw dataset]


title: pet_ommo_F2_102c [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, ommochrome stage

value: Medial

value: Red


title: pet_ommo_F1_16b [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, ommochrome stage

value: Basal


title: pet_ommo_F2_16c [hwfw dataset]


title: PC9 GR3 DMSO

source_name: PC9 GR3


title: PC9 GR3 Gef 1uM

source_name: PC9 GR3 Gefitinib 1uM


title: L-iPSCs


title: PC9 GR1 Gef 1uM

source_name: PC9 GR1 Gefitinib 1uM


title: pet_ommo_F1_105b [hwfw dataset]


title: PC9 na Gef 1uM

source_name: PC9 na Gefitinib 1uM

value: no


title: PC9 GR1 DMSO

source_name: PC9 GR1


title: pet_mel_F2_15e [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, melanin stage

value: melanin


title: ZT16 elf4 3

city: Pohang

first: Hee Jung

last: Koo

address: Hyojadong San 31

country: South Korea

institute: Pohang University of Science and Technology

description: 7-day-old seedlings of elf4-209 mutant grown under LD were harvested at ZT16 [rep3]

hyb_protocol: Standard Agilent  hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.10.0 (R2010a)

organism: Arabidopsis thaliana

source_name: Arabidopsis 7-day-old seedlings

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: 16L/8D-grown seedlings for 7 days

extract_protocol: Total mRNA was extracted using WelPrepTM (JOIN BIO-INNOVATION, Daegu, Korea), and DNA was digested by treatment with DNase I (Ambion, Austin, TX).

treatment_protocol: Seven-day-old seedlings grown under LD were harvested at ZT1 and ZT16.

value: seedling

tag: age

value: 7 d

value: elf4-209 mutant

tag: sampling time


title: pet_day5_F3_10d [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, 5 Days post-pupation

value: Day 5


title: pet_mel_F3_123d [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, melanin stage


title: ZT16 gi-2.elf4 2

description: 7-day-old seedlings of gi-2 elf4-209 double mutant grown under LD were harvested at ZT16 [rep2]

tag: cultivar

value: gi-2 elf4-209 double mutant


title: pet_mel_F1_15d [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, melanin stage


title: pet_mel_F1_126a [hwfw dataset]


title: pet_mel_F3_15f [hwfw dataset]


title: ZT16 elf4 2

description: 7-day-old seedlings of elf4-209 mutant grown under LD were harvested at ZT16 [rep2]

tag: tissue


title: pet_mel_F1_123b [hwfw dataset]


title: pet_ommo_F2_105c [hwfw dataset]


title: ZT16 gi-2.elf4 3

description: 7-day-old seedlings of gi-2 elf4-209 double mutant grown under LD were harvested at ZT16 [rep3]


title: pet_mel_F2_126b [hwfw dataset]


title: pet_ommo_F1_102b [hwfw dataset]


title: pet_mel_F3_126c [hwfw dataset]


title: pet_day5_F2_1c [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, 5 Days post-pupation


title: PC9 na DMSO

source_name: PC9 na

tag: treatment


title: ZT16 gi-2.elf4 1

description: 7-day-old seedlings of gi-2 elf4-209 double mutant grown under LD were harvested at ZT16 [rep1]


title: pet_mel_F2_123c [hwfw dataset]


title: pet_day5_F2_10c [hwfw dataset]


title: pet_day5_F3_11c [hwfw dataset]


title: ZT16 elf4 1

description: 7-day-old seedlings of elf4-209 mutant grown under LD were harvested at ZT16 [rep1]


title: pet_day5_F3_1d [hwfw dataset]


title: ZT1 gi-2.elf4 3

description: 7-day-old seedlings of gi-2 elf4-209 double mutant grown under LD were harvested at ZT1 [rep3]


title: pet_day5_F1_11a [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, 5 Days post-pupation


title: pet_day3_F3_5d [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, 3 Days post-pupation

value: Day 3


title: pet_day3_F3_4d [hwfw dataset]


title: pet_day5_F1_1b [hwfw dataset]


title: pet_day5_F2_11b [hwfw dataset]


title: ZT1 elf4 3

description: 7-day-old seedlings of elf4-209 mutant grown under LD were harvested at ZT1 [rep3]


title: ZT1 gi-2.elf4 1

description: 7-day-old seedlings of gi-2 elf4-209 double mutant grown under LD were harvested at ZT1 [rep1]


title: ZT1 gi-2.elf4 2

description: 7-day-old seedlings of gi-2 elf4-209 double mutant grown under LD were harvested at ZT1 [rep2]


title: pet_day3_F3_7c [hwfw dataset]


title: pet_day5_F1_10b [hwfw dataset]


title: pet_day3_F2_5c [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, 3 Days post-pupation


title: ZT1 elf4 2

description: 7-day-old seedlings of elf4-209 mutant grown under LD were harvested at ZT1 [rep2]


title: pet_day3_F1_7a [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, 3 Days post-pupation


title: 6 h cis-cinnamic acid-treated seedlings vs control: replicate 2

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

institute: Tokyo University of Agriculture & Technology

description: Biological replicate 2 of 2

hyb_protocol: Mixtures of 0.825 µg of Cy3-labeled and Cy5-labeled cRNAs were co-hybridized at 65 °C for 17 h on an Agilent Technologies 4 × 44K Arabidopsis 3 60-mer oligo-microarray.

scan_protocol: The slides were then washed and scanned with an Agilent G2505B Scanner to detect fluorescence intensity.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Data represent the log ratio (treated/control). Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field), saturated (IsSaturated field) or low signal (IsWellAboveBG field) were omitted.

source_name: 6 h cis-cinnamic acid-treated seedlings

label_protocol: Two-color spike mix was added to the total RNA, and the RNA was labeled with a Quick Amp Labeling Kit, two-color (Agilent Technologies), according to the manufacturer’s protocol. Fluorescent cRNA was generated from total RNA: 500 ng of RNA was reverse-transcribed with MMLV reverse transcriptase and an oligo(dT) primer containing the T7 promoter, and subsequently transcribed in vitro using T7 RNA polymerase, resulting in Cy3-labeled (control) and Cy5-labeled (cis-CA-treated) cRNAs. The cRNAs were purified through RNeasy Mini Spin columns (Qiagen) and then quantified with a NanoDrop ND-1000 UV-VIS spectrophotometer

growth_protocol: The sterilized seeds were placed on 0.8% agar (Nakalai Tesque, Inc., Kyoto, Japan) with Murashige and Skoog Plant Salt Mixture (Nihon Pharmaceutical Co., Ltd., Tokyo, Japan) and 1% sucrose (Wako Pure Chemical Industries, Osaka, Japan) in a sterilized Petri dish (90-mm diameter). The seeds were held at 4 °C overnight in darkness and then transferred to a growth chamber. Emerging plants were maintained in the growth chamber under a schedule of 16-h light (22 °C) and 8-h dark (20 °C).

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

treatment_protocol: After 14 d in the growth chamber, seedlings were removed from the agar and equilibrated for 1 h at 22 °C in 20 ml deionized water, and then transferred to 20 ml of deionized water containing 20 µM cis-cinnamic acid and 0.0125% dimethyl sulfoxide, and then incubated under light. Plants were collected at 0 (control), 2, and 6 h and immediately frozen in liquid nitrogen, and then stored at –80 °C before analysis.

tag: time point

value: 6 h

tag: agent

value: cis-cinnamic acid

value: day 14

source_name: control seedlings

value: none, control


title: 2 h cis-cinnamic acid-treated seedlings vs control: replicate 2

description: Biological replicate 2 of 2

source_name: 2 h cis-cinnamic acid-treated seedlings

value: 2 h


title: pet_day1_F3_6c [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, apical section, 1 Day post-pupation

value: Day 1

value: Forewing

value: Apical

value: Black


title: pet_day3_F2_4c [hwfw dataset]

value: Medial

value: Red


title: pet_day1_F2_6b [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, medial section, 1 Day post-pupation


title: 2 h cis-cinnamic acid-treated seedlings vs control: replicate 1

description: Biological replicate 1 of 2

value: seedling


title: 132431

city: Indianapolis

first: Sunil

last: Badve

state: IN

address: 350 West 11th street

department: Pathology

institute: Indiana University

hyb_protocol: Illumina Default WG-DASL Protocol

scan_protocol: Illumina Default WG-DASL Protocol

data_processing: Image files from Illumina WG-DASL beadchips were processed using Illumina GenomeStudio to get non-normalized and average normalized probe profiles.

source_name: Thymus

label_protocol: Illumina Default WG-DASL Protocol

extract_protocol: RNA was extracted using TRIzol® Reagent method (Invitrogen, Carlsbad, CA) according to the manufacturer?s instructions. All RNA samples were treated with Turbo DNase® (Ambion/Applied Biosystems, Foster City, CA).

value: Fresh Frozen Human Tumors

tag: type

value: AB

tag: category

value: GI

tag: batch group

value: BATCH 3

tag: stage i/ii, iii/iv, or na = not applicable/unknown

tag: relapse no, yes, or na = not applicable/unknown

tag: metastasis no, yes, or na = not applicable/unknown

value: NO


title: pet_day3_F1_4b [hwfw dataset]

tag: developmental stage

value: Day 3

tag: wing

tag: wing section

value: Basal

tag: wing section color

tag: slide number

tag: sample id


title: pet_day3_F2_7b [hwfw dataset]


title: 132472

value: GII


title: pet_day3_F1_5b [hwfw dataset]


title: 6 h cis-cinnamic acid-treated seedlings vs control: replicate 1

description: Biological replicate 1 of 2

value: 6 h

value: cis-cinnamic acid

tag: cultivar

tag: age

value: day 14

value: none, control


title: 132478

tag: tissue

value: A


title: 132415

value: GIII

value: YES


title: 132459


title: 132408


title: 132463


title: pet_day1_F3_104d [hwfw dataset]

value: Day 1

value: Forewing

value: Apical

value: Black


title: papa_ommo_F3_74c [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, ommochrome stage

value: ommochrome


title: papa_ommo_F3_82c [hwfw dataset]


title: 132227

value: Fresh Frozen Human Tumors

value: AB

value: GI

value: BATCH 3


title: pet_day1_F1_6a [hwfw dataset]

source_name: Heliconius erato petiverana pupal forewing, basal section, 1 Day post-pupation

value: Basal


title: pet_day1_F3_109c [hwfw dataset]


title: pet_day1_F2_104c [hwfw dataset]

value: Medial

value: Red


title: 132479

value: Mixed AB


title: pet_day1_F1_109a [hwfw dataset]


title: pet_day1_F2_109b [hwfw dataset]


title: ZT1 elf4 1

description: 7-day-old seedlings of elf4-209 mutant grown under LD were harvested at ZT1 [rep1]

source_name: Arabidopsis 7-day-old seedlings

value: seedling

value: 7 d

tag: genotype

value: elf4-209 mutant

tag: sampling time


title: papa_ommo_F3_70d [hwfw dataset]

description: hwfwdatanobpest_lnm.txt, fwdatanobpest_lnm.txt


title: pet_day1_F1_104b [hwfw dataset]


title: 132430

tag: type

value: GII

value: NO


title: 132468

tag: category


title: papa_ommo_F2_70c [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, ommochrome stage

value: Forewing

value: Yellow


title: papa_ommo_F2_74b [hwfw dataset]


title: 132410

tag: batch group


title: 132397

tag: stage i/ii, iii/iv, or na = not applicable/unknown


title: 132285

tag: relapse no, yes, or na = not applicable/unknown


title: papa_ommo_F1_82a [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, ommochrome stage


title: papa_ommo_F2_82b [hwfw dataset]


title: 132409

tag: metastasis no, yes, or na = not applicable/unknown


title: 132404


title: 132490

value: YES


title: 132268


title: papa_ommo_F1_74a [hwfw dataset]

tag: developmental stage

value: ommochrome


title: 132395

value: Fresh Frozen Human Tumors

value: A/B

value: BATCH 2


title: 132269

value: BATCH 3


title: papa_mel_F3_80d [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, melanin stage

value: melanin

tag: wing

value: Apical

value: Black


title: papa_mel_F2_80c [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, melanin stage

tag: wing section

value: Medial


title: 132236


title: papa_mel_F1_88b [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, melanin stage

value: Basal

tag: wing section color

value: Red


title: papa_mel_F2_75b [hwfw dataset]

tag: slide number


title: papa_mel_F3_88d [hwfw dataset]

tag: sample id


title: papa_ommo_F1_70b [hwfw dataset]


title: 132475

value: GIII


title: papa_mel_F2_88c [hwfw dataset]


title: papa_mel_F3_75c [hwfw dataset]


title: 132400

value: AB

value: GI


title: 132484-Dupl.

value: Mixed AB

value: NO


title: papa_mel_F1_80b [hwfw dataset]

value: Forewing


title: 132411

value: YES


title: 132420

value: Fresh Frozen Human Tumors

value: GII


title: 132484

value: BATCH 2


title: 132429


title: papa_day5_F3_69d [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, 5 Days post-pupation

value: Day 5


title: papa_day5_F1_91b [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, 5 Days post-pupation


title: 132426


title: TThy6-6-Dupl

value: Cell Line

value: CL

value: BATCH 1


title: papa_mel_F1_75a [hwfw dataset]

value: melanin


title: 132454


title: 132434


title: papa_day5_F3_79d [hwfw dataset]

value: Apical

value: Black


title: papa_day5_F2_91c [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, 5 Days post-pupation

value: Medial

value: Yellow


title: papa_day5_F3_91d [hwfw dataset]


title: papa_day5_F2_69c [hwfw dataset]


title: papa_day5_F2_79c [hwfw dataset]


title: papa_day5_F1_69b [hwfw dataset]

value: Basal

value: Red


title: 132419

value: NO


title: papa_day3_F3_84d [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, 3 Days post-pupation

value: Day 3

value: Forewing


title: 132467

value: Fresh Frozen Human Tumors

value: Mixed AB

value: GI


title: 132413

value: AB

value: BATCH 2


title: TThy6-2

value: Cell Line

value: CL


title: TThy6-3

value: BATCH 1


title: papa_day3_F3_90d [hwfw dataset]

value: Apical


title: papa_day5_F1_79b [hwfw dataset]

value: Day 5


title: papa_day3_F3_71d [hwfw dataset]

value: Black


title: 132477

value: GII

value: BATCH 3


title: 132427


title: TThy6-6


title: papa_day3_F2_90c [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, 3 Days post-pupation

value: Medial

value: Yellow


title: papa_day1_F2_85c [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, medial section, 1 Day post-pupation

value: Day 1


title: 132401

value: NO

value: YES


title: papa_day3_F1_71b [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, 3 Days post-pupation

value: Day 3

value: Forewing

value: Basal

value: Red


title: papa_day3_F2_84c [hwfw dataset]


title: papa_day3_F1_84b [hwfw dataset]


title: papa_day3_F1_90b [hwfw dataset]


title: papa_day1_F3_85d [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, apical section, 1 Day post-pupation


title: papa_day1_F3_83d [hwfw dataset]


title: E10_favommo [hwfw dataset]

source_name: Heliconius erato favorinus pupal hindwing, ommochrome stage

value: ommochrome

value: Hindwing


title: papa_day3_F2_71c [hwfw dataset]


title: papa_day1_F2_83c [hwfw dataset]


title: papa_day1_F1_85b [hwfw dataset]

source_name: Heliconius erato etylus x Heliconius himera pupal forewing, basal section, 1 Day post-pupation


title: B04_favommo [hwfw dataset]


title: G4_favommo [hwfw dataset]


title: F4_favDay3 [hwfw dataset]

source_name: Heliconius erato favorinus pupal hindwing, 3 Days post-pupation


title: papa_day1_F1_83b [hwfw dataset]


title: A10_favDay5 [hwfw dataset]

source_name: Heliconius erato favorinus pupal hindwing, 5 Days post-pupation


title: F7_favmela [hwfw dataset]

source_name: Heliconius erato favorinus pupal hindwing, melanin stage

value: melanin


title: A04_favommo [hwfw dataset]


title: F1_favDay5 [hwfw dataset]


title: D10_favmela [hwfw dataset]


title: A07_favmela [hwfw dataset]


title: C04_favmela [hwfw dataset]


title: F10_favDay1 [hwfw dataset]

source_name: Heliconius erato favorinus pupal hindwing, 1 Day post-pupation


title: B07_favDay3 [hwfw dataset]


title: D4_favDay5 [hwfw dataset]


title: F12_emaommo [hwfw dataset]

source_name: Heliconius erato emma pupal hindwing, ommochrome stage


title: E1_favDay1 [hwfw dataset]


title: D7_favDay3 [hwfw dataset]


title: A01_favDay1 [hwfw dataset]


title: A09_emaommo [hwfw dataset]


title: C01_favDay5 [hwfw dataset]


title: D9_emaDay5 [hwfw dataset]

source_name: Heliconius erato emma pupal hindwing, 5 Days post-pupation


title: F9_emaDay3 [hwfw dataset]

source_name: Heliconius erato emma pupal hindwing, 3 Days post-pupation


title: C07_favDay3 [hwfw dataset]


title: G3_emamela [hwfw dataset]

source_name: Heliconius erato emma pupal hindwing, melanin stage


title: F6_emamela [hwfw dataset]


title: E3_emamela [hwfw dataset]


title: D3_emaommo [hwfw dataset]


title: D6_emaDay1 [hwfw dataset]

source_name: Heliconius erato emma pupal hindwing, 1 Day post-pupation


title: E12_emaDay5 [hwfw dataset]


title: B02_emaDay3 [hwfw dataset]


title: C09_emamela [hwfw dataset]


title: C06_emaommo [hwfw dataset]


title: C12_emaDay5 [hwfw dataset]


title: B10_favDay1 [hwfw dataset]


title: F2_ampommo [hwfw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, ommochrome stage


title: G6_emaDay3 [hwfw dataset]


title: E9_emaDay1 [hwfw dataset]


title: B05_emaDay5 [hwfw dataset]


title: A06_emaDay3 [hwfw dataset]


title: C03_emaDay1 [hwfw dataset]


title: A12_emaDay1 [hwfw dataset]


title: B09_ampommo [hwfw dataset]


title: C11_ampommo [hwfw dataset]


title: D8_ampommo [hwfw dataset]


title: B06_ampmela [hwfw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, melanin stage


title: D5_ampmela [hwfw dataset]


title: microRNA profile of case normal13

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

source_name: normal nasopharyngeal tissue

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: survival status  (1-death,0-survival)

value: no information

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case normal12


title: microRNA profile of case normal14


title: microRNA profile of case normal15


title: A02_ampmela [hwfw dataset]


title: E5_ampDay5 [hwfw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, 5 Days post-pupation

value: Day 5


title: microRNA profile of case normal9


title: microRNA profile of case normal16


title: microRNA profile of case normal18


title: microRNA profile of case normal8


title: microRNA profile of case normal10


title: microRNA profile of case normal17


title: microRNA profile of case normal11


title: E8_ampDay3 [hwfw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, 3 Days post-pupation

value: Black


title: G11_ampmela [hwfw dataset]


title: C08_ampDay1 [hwfw dataset]

source_name: Heliconius erato amphitrite pupal hindwing, 1 Day post-pupation


title: C02_ampDay3 [hwfw dataset]


title: G5_ampDay5 [hwfw dataset]


title: G8_ampDay1 [hwfw dataset]


title: A11_ampDay3 [hwfw dataset]


title: F11_ampDay5 [hwfw dataset]


title: D11_ampDay1 [hwfw dataset]


title: A05_ampDay5 [hwfw dataset]


title: B03_ampDay1 [hwfw dataset]


title: D2_ampDay3 [hwfw dataset]


title: microRNA profile of case normal6


title: microRNA profile of case normal5


title: microRNA profile of case normal1


title: microRNA profile of case normal4


title: microRNA profile of case NPC362992

source_name: Nasopharyngeal carcinoma


title: microRNA profile of case NPC362996


title: microRNA profile of case NPC362997


title: microRNA profile of case normal2


title: microRNA profile of case NPC362987


title: microRNA profile of case normal7


title: microRNA profile of case NPC362925


title: microRNA profile of case NPC362538


title: microRNA profile of case NPC362726


title: microRNA profile of case NPC362434


title: microRNA profile of case NPC362697


title: microRNA profile of case NPC362656


title: microRNA profile of case NPC362791


title: microRNA profile of case NPC362427


title: microRNA profile of case NPC362696


title: microRNA profile of case NPC362068


title: microRNA profile of case NPC362424


title: microRNA profile of case NPC362188


title: microRNA profile of case NPC362066


title: microRNA profile of case NPC361575


title: microRNA profile of case NPC361888


title: microRNA profile of case NPC362010


title: microRNA profile of case NPC361829


title: microRNA profile of case normal3


title: microRNA profile of case NPC362933


title: microRNA profile of case NPC362790


title: microRNA profile of case NPC361452


title: microRNA profile of case NPC361300


title: microRNA profile of case NPC361418


title: microRNA profile of case NPC361196


title: microRNA profile of case NPC361141


title: microRNA profile of case NPC360845


title: microRNA profile of case NPC360844


title: microRNA profile of case NPC360784


title: microRNA profile of case NPC360763


title: microRNA profile of case NPC361198


title: H1975 MP

city: Tampa

first: Jonathan

last: Nguyen

state: FL

department: Tumor Biology

institute: Moffitt Cancer Centre & Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 algorithm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.  Additional analysis was performed by log2 transformation of the expression values, and the mean center expression level for each gene was determined.

label: Biotin

source_name: H1975 main population

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocol using 100 ng of total RNA (Ambion).

growth_protocol: Side population analysis: The cell suspensions were labeled with Hoechst 33342 dye (Invitrogen) using the methods described by Goodell et al. with modifications. Briefly, cells were resuspended at 1 x 10^6/mL in pre-warmed DMEM (Invitrogen-Life Technologies) with 2% FBS (Invitrogen-Life Technologies) and 10 mmol/L HEPES buffer (Invitrogen- Life Technologies). Hoechst 33342 dye was added at a final concentration of 5 mg/mL and the cells were incubated at 37°C for 90 min with intermittent shaking. At the end of the incubation, the cells were washed with ice-cold HBSS (Invitrogen-Life Technologies) with 2% FBS and 10 mmol/L HEPES, centrifuged down at 4C, and resuspended in ice-cold HBSS containing 2% FBS and 10 mmol/L HEPES. Propidium iodide (Molecular Probes- Invitrogen) at a final concentration of 2 mg/mL was added to the cells to gate viable cells. Analyses and sorting were done on a FACSVantage SE (Becton Dickinson). The Hoechst 33342 dye was excited at 357 nm and its fluorescence was dual-wavelength analyzed (blue, 402–446 nm; red, 650–670 nm).

extract_protocol: Isolation of total RNA was performed using the Qiagen RNeasy column according to the manufacturer's instructions.

tag: cell line

tag: population

value: main


title: H460 MP

source_name: H460 main population


title: H1975 SP

source_name: H1975 side population

value: side


title: H1650 SP

source_name: H1650 side population


title: PNET cell line 5 treated

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

country: Netherlands

institute: Erasmus MC

description:
Gene expression data of PNET cell line
Sample name: PNET 5_t
KGK_IG_290307_PNET5_B.CHP
KGK_IG_290307_PNET5_B.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU 133 Plus2.0 arrays. GeneChips were washed and stained according to Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (TGT value 500) as normalization method.

source_name: PNET cell line 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cultured in DMEM or RPMI at 37 C and 5% CO2 in non-hypoxic conditions

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

treatment_protocol: untreated, daily change of culture medium; treated, 72 hours 30 nM DAC with addition of 25 nM TSA during the last 48 hours, daily refreshal of culture media containing drugs

value: PNET

tag: agent

value: DAC and TSA combination

tag: gender

value: female

tag: mycn status

value: EWS-FLI translocation


title: A549 MP

source_name: A549 main population


title: PNET cell line 3 treated

description:
Gene expression data of PNET cell line
Sample name: PNET 3_t
KGK_IG_290307_PNET3_B.CHP
KGK_IG_290307_PNET3_B.CEL

source_name: PNET cell line 3


title: PNET cell line 1 treated

description:
Gene expression data of PNET cell line
Sample name: PNET 1_t
KGK_IG_27032007_PNET1_B.CHP
KGK_IG_27032007_PNET1_B.CEL

source_name: PNET cell line 1


title: NBL 13 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL13_t
KGK_IG_28032007_NBL13_B.CHP
KGK_IG_28032007_NBL13_B.CEL

source_name: NBL cell line 13

value: NBL

value: MYCN amplified


title: NBL 17 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL17_t
KGK_IG_28032007_NBL17_B.CHP
KGK_IG_28032007_NBL17_B.CEL

source_name: NBL cell line 17


title: H460 SP

source_name: H460 side population


title: NBL 15 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL15_t
KGK_IG_28032007_NBL15_2.CHP
KGK_IG_28032007_NBL15_B_2.CEL

source_name: NBL cell line 15


title: microRNA profile of case NPC360058


title: NBL 14 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL14_t
KGK_IG_290307_NBL14_B.CHP
KGK_IG_290307_NBL14_B.CEL

source_name: NBL cell line 14

value: male


title: NBL 12 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL12_t
KGK_IG_28032007_NBL12_B.CHP
KGK_IG_28032007_NBL12_B.CEL

source_name: NBL cell line 12

value: no MYCN amplification


title: H1650 MP

source_name: H1650 main population


title: microRNA profile of case NPC360042


title: A549 SP

source_name: A549 side population


title: PNET cell line 2 treated

description:
Gene expression data of PNET cell line
Sample name: PNET 2_t
KGK_IG_28032007_PNET2_B.CHP
KGK_IG_28032007_PNET2_B.CEL

source_name: PNET cell line 2


title: NBL 8 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL8_t
KGK_IG_270307_NBL8_B.CHP
KGK_IG_270307_NBL8_B.CEL

source_name: NBL cell line 8


title: NBL 10 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL10_t
KGK_IG_27032007_NBL10_B.CHP
KGK_IG_27032007_NBL10_B.CEL

source_name: Derivative NBL16


title: NBL 11 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL11_t
KGK_IG_28032007_NBL11_B.CHP
KGK_IG_28032007_NBL11_B.CEL


title: PNET cell line 4 treated

description:
Gene expression data of PNET cell line
Sample name: PNET 4_t
KGK_IG_28032007_PNET4_B.CHP
KGK_IG_28032007_PNET4_B.CEL

source_name: PNET cell line 4


title: NBL 16 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL16_t
KGK_IG_290307_NBL16_B.CHP
KGK_IG_290307_NBL16_B.CEL

source_name: NBL cell line 16


title: NBL 9 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL9_t
KGK_IG_290307_NBL9_B.CHP
KGK_IG_290307_NBL9_B.CEL

source_name: NBL cell line 9


title: microRNA profile of case NPC359939

source_name: Nasopharyngeal carcinoma


title: microRNA profile of case NPC359846


title: microRNA profile of case NPC359784


title: microRNA profile of case NPC359745


title: NBL 6 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL6_t
KGK_IG_27032007_NBL6_B.CHP
KGK_IG_27032007_NBL6_B.CEL

source_name: NBL cell line 6


title: microRNA profile of case NPC360267


title: microRNA profile of case NPC359858


title: NBL 2 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL2_t
KGK_IG_290307_NBL2_B.CHP
KGK_IG_290307_NBL2_B.CEL

source_name: NBL cell line 2


title: NBL 7 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL7_t
KGK_IG_290307_NBL7_B.CHP
KGK_IG_290307_NBL7_B.CEL

source_name: NBL cell line 7


title: NBL 4 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL4_t
KGK_IG_290307_NBL4-B.CHP
KGK_IG_290307_NBL4-B.CEL

source_name: NBL cell line 4


title: NBL 2 cell line (Derivative NBL16)

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL2
KGK_IG_290307_NBL2_C.CHP
NBL2.CEL

value: untreated


title: NBL 1 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL1_t
KGK_IG_270307_NBL1_B.CHP
KGK_IG_270307_NBL1_B.CEL

source_name: NBL cell line 1


title: microRNA profile of case NPC359744


title: NBL 5 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL5_t
KGK_IG_27032007_NBL5_B.CHP
KGK_IG_27032007_NBL5_B.CEL

source_name: NBL cell line 5


title: NBL 3 cell line treated

description:
Gene expression data of neuroblastoma cell line
Sample name: NBL3_t
KGK_IG_27032007_NBL3_B.CHP
KGK_IG_27032007_NBL3_B.CEL

source_name: NBL cell line 3


title: microRNA profile of case NPC359594


title: microRNA profile of case NPC359592


title: microRNA profile of case NPC359463


title: microRNA profile of case NPC359591


title: microRNA profile of case NPC359462


title: A2058, GCD0941 treat, max conc, biol rep 4

city: Basel

first: Saskia

middle: Maria

last: Brachmann

address: Klybeckstrasse 141

department: Oncology Basel

country: Switzerland

institute: NIBR

hyb_protocol: Following fragmentation and labeling, 3.4 µg of cRNA were hybridized to the arrays following the manufaturer's instructions. Arrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Immortalized cell line

label_protocol: 50 ng of total RNA were amplified with the Nugen Ovation RNA Amplification System followed by a Ovation WB treatment. Biotinilated cRNA were then prepared using the FL cDNA Biotin Module V2 kit.

growth_protocol: A2058 cell lines are grown in DMEM, high glucose, 10% FCS, 1% pyruvate, 2% glutamine

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen: RNAeasy).

treatment_protocol: treatment frequency: 1; treatment duration: 24h

value: A2058 melanoma cell line

tag: agent (pi3k inhibitor)

tag: concentration

value: max


title: microRNA profile of case NPC359252


title: A2058, GCD0941 treat, IC90 conc, biol rep 4


title: A2058, GCD0941 treat, max conc, biol rep 2


title: A2058, GCD0941 treat, IC90 conc, biol rep 3


title: A2058, GCD0941 treat, IC50 conc, biol rep 3


title: A2058, GCD0941 treat, IC90 conc, biol rep 1


title: A2058, GCD0941 treat, max conc, biol rep 1


title: A2058, GCD0941 treat, IC90 conc, biol rep 2


title: A2058, GCD0941 treat, max conc, biol rep 3


title: A2058, GCD0941 treat, IC50 conc, biol rep 2


title: A2058, GCD0941 treat, IC50 conc, biol rep 4


title: microRNA profile of case NPC359112


title: A2058, GCD0941 treat, IC50 conc, biol rep 1


title: A2058, BEZ235 treat, max conc, biol rep 4


title: microRNA profile of case NPC358932


title: microRNA profile of case NPC358929


title: microRNA profile of case NPC358925


title: Huh7-JFH1-40µM-CQd-48h

city: Marseille

first: Claire

last: Camus

address: 163, avenue de Luminy - Case 928

department: GENOMIC

country: France

institute: TAGC UMRs928

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60C for 30 minutes in a reaction volume of 55µl containing Agilent fragmentation buffer 25X and Agilent blocking agent 10X following the manufacturer’s instructions. On completion of the fragmentation reaction, 55µl of Agilent 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture. 100µl of this mixture was hybridized to Whole Human Genome Microarray Kit, 4x44k (G4112F) for 17 hours at 65C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 supplemented with 0,005% Triton (Agilent) and 1 minute with 37C GE Wash buffer 2 supplemented with 0,005% Triton (Agilent), then dried using a10 sec washing in acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan settings for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters and Grid 014850_D_F_20060807. For HCV replicon based experiments: Feature Extraction Software version 9.5.3.1, protocol GE1-v5_95_Feb07), for HCVcc based experiments (Feature Extraction Software version 10.5.1.1, protocol GE1_105_Jan09 or GE1_105_Dec08). Feature Extraction software calculates background and subtracted it and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were normalized by the quantile method performed using R free software (http://www.r-project.org/).Normalized gene expression data were then  filtered according to intensities above the average background signal.

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 40µMCQd, 48h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The Huh7 derived GS4.3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen), 2 mM L-glutamine, nonessential amino acids, 500 µg/mL of G418, and 10% heat-inactivated fetal bovine serum (FBS).  Huh7 cells used for HCVcc were grown in DMEM, 100 nmol non-essential amino acids and 10 % FBS.

extract_protocol: Total cellular RNA was extracted with TRIzol reagent (Invitrogen) following the manufacturer’s direction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Huh7 cells harboring HCV replicon were treated during 6h, 12h or 24h with 10µM of CQd (derivative of chloroquine). HuH7 JFH1/CS-N6-A4 infected cells were treated during 12h and 48h with 40µM of CQ or CQd, or with 100 IU IFN alpha during 48h. Infection modulations were studied using HuH7 JFH1/CS-N6-A4 infected cells cultured at 6h, 24h and 48h postinfection.

tag: hcv infection model

value: HCVcell culture with JFH1/CS-N6-A4 virus strain


title: microRNA profile of case NPC358874


title: microRNA profile of case NPC358793


title: Huh7-JFH1-40µM-CQd-12h

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 40µMCQd, 12h


title: A2058, BEZ235 treat, max conc, biol rep 3


title: Huh7-JFH1-40µM-CQ-48h

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 40µMCQ, 48h


title: Huh7-JFH1-40µM-CQ-12h

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 40µMCQ, 12h


title: A2058, BEZ235 treat, max conc, biol rep 1


title: microRNA profile of case NPC358704


title: A2058, BEZ235 treat, max conc, biol rep 2


title: microRNA profile of case NPC358792


title: Huh7-JFH1-12h-CTRL-0CQ

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 0CQ, 12h


title: A2058, BEZ235 treat, IC90 conc, biol rep 3


title: microRNA profile of case NPC358633


title: A2058, BEZ235 treat, IC90 conc, biol rep 1


title: microRNA profile of case NPC358521


title: Huh7-JFH1-100IU-IFN-48h

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 100 IU IFN, 48h


title: Huh7-JFH1-48h

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 48h


title: microRNA profile of case NPC358236


title: Huh7-JFH1-48h-CTRL-0CQ

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 0CQ, 48h


title: A2058, BEZ235 treat, IC90 conc, biol rep 2


title: A2058, BEZ235 treat, IC90 conc, biol rep 4


title: A2058, BEZ235 treat, IC50 conc, biol rep 3


title: A2058, BEZ235 treat, IC50 conc, biol rep 4


title: microRNA profile of case NPC357740

source_name: Nasopharyngeal carcinoma


title: microRNA profile of case NPC357894


title: Huh7-JFH1-6h

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 6h


title: Huh7-uninfected-24h

source_name: Huh7 cells, uninfected, 24h


title: Huh7-uninfected-48h

source_name: Huh7 cells, uninfected, 48h


title: Huh7-JFH1-24h

source_name: Huh7 cells, HCV JFH1/CS-N6-A4 infected, 24h


title: A2058, BEZ235 treat, IC50 conc, biol rep 2


title: A2058, BKM120 treat, max conc, biol rep 4

value: IC90 (max)


title: Huh7REP24h-10µM-CQd-rep2

source_name: Huh7 cells harboring HCV replicon 1b, 10µM CQd treated, 24h

value: Huh7 GS4.3 cells

value: HCV replicon 1b


title: microRNA profile of case NPC357739


title: microRNA profile of case NPC357586


title: microRNA profile of case NPC357737


title: A2058, BEZ235 treat, IC50 conc, biol rep 1


title: A2058, BKM120 treat, max conc, biol rep 1


title: A2058, BKM120 treat, max conc, biol rep 3


title: A2058, BKM120 treat, max conc, biol rep 2


title: Huh7REP12h-10µM-CQd-rep2

source_name: Huh7 cells harboring HCV replicon 1b, 10µM CQd treated, 12h


title: Huh7REP24h-10µM-CQd-rep1


title: A2058, BKM120 treat, IC50 conc, biol rep 4


title: Huh7REP6h-10µM-CQd-rep2

source_name: Huh7 cells harboring HCV replicon 1b, 10µM CQd treated, 6h


title: microRNA profile of case NPC357426


title: A2058, BKM120 treat, IC50 conc, biol rep 3

source_name: Immortalized cell line


title: Huh7-uninfected-6h

source_name: Huh7 cells, uninfected, 6h


title: microRNA profile of case NPC357183


title: microRNA profile of case NPC357095


title: microRNA profile of case NPC357511


title: microRNA profile of case NPC357427


title: microRNA profile of case NPC357178


title: Huh7REP6h-10µM-CQd-rep1


title: A2058, BKM120 treat, IC50 conc, biol rep 2


title: A2058, BKM120 treat, IC50 conc, biol rep 1


title: A2058, BKM120 treat, IC30 conc, biol rep 3


title: A2058, BKM120 treat, IC30 conc, biol rep 4


title: A2058, BKM120 treat, IC30 conc, biol rep 2


title: microRNA profile of case NPC356984


title: Huh7REP12h-10µM-CQd-rep1


title: Huh7REP-0CQd-rep1

source_name: Huh7 cells harboring HCV replicon 1b,  untreated, 24h


title: Huh7REP-0CQd-rep2


title: microRNA profile of case NPC356965


title: A2058, BKM120 treat, IC30 conc, biol rep 1


title: microRNA profile of case NPC356942


title: cauda of epididymides from 47 years old man

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: RS_norm-tete-47ans_(miRNA-1_0_2Xgain).CEL

hyb_protocol: One ug of each total RNA samples were labeled using the FlashTag Biotin HSR (Genisphere, Hatfield, PA), and hybridized O/N on the GeneChip miRNA Array v1.0 (Affimetrix, Santa Clara, CA), according to the manufacturer’s recommendations.Wash and stain was made with Fluidics Station 450, using fluidics script FS450_00(Affymetrix).

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: Data were analyzed using the miRNA QC Tool software for quality control (www.affymetrix.com <http://www.affymetrix.com> ) and CEL files were imported and analyzed with the Partek Genomics Suite 6.5 software (Partek Incorporated, St Louis, MO).Signals were RMA normalized.

label_protocol: Briefly, 1 mg of each total RNA samples were labeled using the FlashTag Biotin HSR (Genisphere, Hatfield, PA) according to the manufacturer’s recommendations

growth_protocol: human epididymides were obtained through our local organ transplantation program (Québec Transplant, QC, Canada) from three donors of 26–50 years of age, with no known pathologies that could affect reproductive function.

extract_protocol: Total RNAs were extracted as previously described (Thimon et al, 2007) using Trizol reagent (Invitrogen, Burlington, ON, Canada). Total RNA was purified on RNeasy mini kit column (Qiagen, Mississauga, ON, Canada).

treatment_protocol: Artificial circulation was maintained during the surgery to preserve organ’s integrity. Epididymides were collected and processed within 3 hours after surgery.  Tissues were dissected into 3 anatomical regions (caput, corpus and cauda), immediately frozen in liquid nitrogen and stored at -80oC until use.

tag: age

value: 47 years old

tag: tissue

value: epididymis

tag: anatomical region

value: cauda


title: caput of epididymides from 47 years old man

description: RS_norm-queue-47ans_(miRNA-1_0_2Xgain).CEL

value: caput


title: cauda of epididymides from 50 years old man

description: RS_norm-tete-50ans_(miRNA-1_0_2Xgain).CEL

value: 50 years old


title: cauda of epididymides from 26 years old man

description: RS_norm-tete-26ans_(miRNA-1_0_2Xgain).CEL

value: 26 years old


title: A2058, DMSO treat, biol rep 4

value: control (DMSO)

value: control


title: microRNA profile of case NPC356663


title: microRNA profile of case NPC356907


title: caput of epididymides from 50 years old man

description: RS_norm-queue-50ans_(miRNA-1_0_2Xgain).CEL


title: caput of epididymides from 26 years old man

description: RS_norm-queue-26ans_(miRNA-1_0_2Xgain).CEL


title: microRNA profile of case NPC356964


title: microRNA profile of case NPC356661


title: microRNA profile of case NPC356659


title: microRNA profile of case NPC356601


title: microRNA profile of case NPC356355


title: microRNA profile of case NPC356389


title: microRNA profile of case NPC356273


title: A2058, DMSO treat, biol rep 2


title: microRNA profile of case NPC356226


title: microRNA profile of case NPC356227


title: microRNA profile of case NPC356064


title: A2058, DMSO treat, biol rep 3


title: corpus of epididymides from 47 years old man

description: RS_norm-corps-47ans_(miRNA-1_0_2Xgain).CEL

value: corpus


title: microRNA profile of case NPC356596


title: microRNA profile of case NPC356062


title: corpus of epididymides from 50 years old man

description: RS_norm-corps-50ans_(miRNA-1_0_2Xgain).CEL


title: MCF7-SNCA, biological rep1

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

description: Gene expression data from MCF7 cell line transfected with SNCA.

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

data_processing: The data were analyzed with Partek Genomics Suite using GC-RMA as the normalization method.

source_name: MCF7 cell line transfected with SNCA

label_protocol: FL-Ovation cDNA Biotin Module V2 from NuGen Technologies Inc.

growth_protocol: Cells were cultured and maintained in RPMI medium containing 10% FBS and 2 mM glutamine.

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

treatment_protocol: MCF7 cells were transfected with EmGFP or EmGFP-SNCA expression constructs (pcDNA6.2/N-EmGFP-DEST, Invitrogen) and selected with blasticidin.

tag: cell type

value: breast cancer

tag: transfection

value: α-synuclein (SNCA)


title: MCF7-SNCA, biological rep2

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).


title: HCT116 WT High glucose replicate2

city: Stanford

last: Sweet-Cordero

state: CA

address: CCSR-1215B, 269 Campus Dr

department: Pediatrics

institute: Stanford University

hyb_protocol: Standard Affymetrix processing

scan_protocol: Standard Affymetrix processing

data_processing: MAS 5.0

source_name: HCT116 WT High glucose replicate2

label_protocol: Standard Affymetrix processing

growth_protocol: Cells were cultured in DMEM with either 25 or 1 mM glucose

extract_protocol: Trizol followed by Rneasy cleanup

treatment_protocol: Cells were plated in the corresponding medium for seven days, with one passage on day three. Media with 1 mM glucose was changed daily.

tag: genotype

value: wild-type Kras

tag: treatment

value: 25 mM glucose


title: HCT116 G13D High glucose replicate1

source_name: HCT116 G13D High glucose replicate1

value: Kras G13D


title: MCF7 control, biological rep2

description: Gene expression data from MCF7 cell line transfected with GFP.

source_name: MCF7 cell line transfected with GFP

value: GFP control


title: HCT116 G13D High glucose replicate2

source_name: HCT116 G13D High glucose replicate2


title: HCT116 G13D Low glucose replicate2

source_name: HCT116 G13D Low glucose replicate2

value: 1 mM glucose


title: A2058, DMSO treat, biol rep 1

value: A2058 melanoma cell line


title: corpus of epididymides from 26 years old man

description: RS_norm-corps-26ans_(miRNA-1_0_2Xgain).CEL


title: microRNA profile of case NPC355992

source_name: Nasopharyngeal carcinoma

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)


title: microRNA profile of case NPC355856

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: HCT116 G13D Low glucose replicate1

source_name: HCT116 G13D Low glucose replicate1

tag: cell line


title: microRNA profile of case NPC355697


title: microRNA profile of case NPC355295


title: MCF7 control, biological rep1


title: microRNA profile of case NPC354788


title: microRNA profile of case NPC355031


title: microRNA profile of case NPC354952


title: microRNA profile of case NPC355191


title: HCT116 WT Low glucose replicate2

source_name: HCT116 WT Low glucose replicate2


title: microRNA profile of case NPC354280


title: microRNA profile of case NPC354600


title: microRNA profile of case NPC354528


title: microRNA profile of case NPC354276


title: HCT116 WT Low glucose replicate1

source_name: HCT116 WT Low glucose replicate1


title: Expt 1 & Expt 2 - Control 0 hr - repeat 5 - mAdbID:71439

city: University Park

first: A.

middle: Catharine

last: Ross

state: PA

address: 110 Chandlee Laboratory

department: Nutritional Sciences

institute: Penn State

description: mAdb experiment ID: 71439

hyb_protocol: Affymetrix Hybridization Protocol: The arrays were hybridized overnight at 45°C and washed using the fluidics station, then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol (GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

scan_protocol: Affymetrix Scanning Protocol: The arrays were scanned at 488 nm at 11-micron resolution using an Affymetrix Gene Chip Scanner.

data_processing: Data were acquired using Genechip Operating Software (GCOS, Affymetrix) and uploaded onto the NCI website mAdb (http://nciarray.nci.nih.gov/). Data were analyzed by setting the signal floor value to 1 and centering each array to the median signal intensity. The results were expressed as log 2-transformed signal intensities and the log 2 of the median intensity for each array was set to 0.

source_name: THP-1 Untreated

label_protocol: Affymetrix labeling protocol: cDNA was synthesized, labeled, and purified according to vendor's (Affymetrix Inc., Santa Clara, CA) instructions.

extract_protocol: RNA was prepared using Trizol extraction.

treatment_protocol:
Treatment type: compound
Agent: ethanol
Treatment dose: 0.1%
Treatment time: 40 hr
In-vitro treatment: THP-1 cells treated with 0.1% ethanol only. All cells were harvested at the 40 hour time point.

value: bone marrow

value: THP-1 cells

value: human myeloid cells


title: Expt 1 - RA and TNF - repeat 4 - mAdbID:71432

description: mAdb experiment ID: 71432

source_name: THP-1 RA and TNF

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid); TNF-alpha (tumor necrosis factor)
Treatment dose: 20 nM; 5ng/ml
Treatment time: 40 hours
In-vitro treatment: THP-1 cells were treated with 20 nM of RA for 16 hours, followed by treatment with 20nM of RA and 5 ng/ml of TNF-alpha for 24 hours. All cells were harvested at the 40 hour time point.


title: Expt 2 - 16 hr after RA - repeat 2 - mAdbID:71438

description: mAdb experiment ID: 71438

source_name: THP-1 16 hr after RA

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 20 nM
Treatment time: 16 hours
In-vitro treatment: THP-1 cells were treated with 20 nM RA at 0 hours. After 16 hours, these cells were harvested.


title: Expt 1 - TNF only - repeat 4 - mAdbID:71430

description: mAdb experiment ID: 71430

source_name: THP-1 TNF-only

treatment_protocol:
Treatment type: compound
Agent: TNF-alpha (tumor necrosis factor)
Treatment dose: 5 ng/ml
Treatment time: 24 hr
In-vitro treatment: THP-1 cells treated with TNF-alpha 5 ng/ml for 24 hours.


title: HCT116 WT High glucose replicate1

source_name: HCT116 WT High glucose replicate1


title: Expt 2 - Control 0 hr - repeat 4 - mAdbID:71434

description: mAdb experiment ID: 71434

source_name: THP-1 Control 0 hr

treatment_protocol:
Treatment type: compound
Agent: ethanol as a vehicle control
Treatment dose: 0.1%
Treatment time: 16 hours
In-vitro treatment: THP-1 cells were treated with 0.1% ethanol at 0 hours. After 16 hours, these cells were harvested.


title: Expt 1 & Expt 2 - RA only 40 hr - repeat 4 - mAdbID:71429

description: mAdb experiment ID: 71429

source_name: THP-1 RA-only

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 20 nM
Treatment time: 40 hours
In-vitro treatment: THP-1 cells were treated with 20 nM RA for 16 hours, followed by re-treatment for 24 hours for a total time of 40 hours. All cells were harvested at the 40 hour time point.


title: Expt 1 & Expt 2 - Control 0 hr - repeat 4 - mAdbID:71426

description: mAdb experiment ID: 71426


title: microRNA profile of case NPC354070


title: microRNA profile of case NPC354651


title: Expt 2 - Control 0 hr - repeat 3 - mAdbID:71424

description: mAdb experiment ID: 71424


title: Expt 1 - RA and TNF - repeat 5 - mAdbID:71415

description: mAdb experiment ID: 71415


title: Expt 2 - 16 hr after RA - repeat 1 - mAdbID:71425

description: mAdb experiment ID: 71425


title: microRNA profile of case NPC353730


title: Expt 2 - 2 hr after RA - repeat 1 - mAdbID:71418

description: mAdb experiment ID: 71418

source_name: THP-1 2 hr after RA

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 20 nM
Treatment time: 2 hours
In-vitro treatment: THP-1 cells were treated with 20 nM RA at 0 hours. After 2 hours, these cells were harvested.


title: Expt 2 - Control 0 hr - repeat 2 - mAdbID:71416

description: mAdb experiment ID: 71416


title: Expt 2 - 6 hr after RA - repeat 1 - mAdbID:71421

description: mAdb experiment ID: 71421

source_name: THP-1 6 hr after RA

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 20 nM
Treatment time: 6 hours
In-vitro treatment: THP-1 cells were treated with 20 nM RA at 0 hours. After 6 hours, these cells were harvested.


title: microRNA profile of case NPC353680


title: microRNA profile of case NPC353558


title: microRNA profile of case NPC353529


title: microRNA profile of case NPC353058


title: microRNA profile of case NPC352934


title: microRNA profile of case NPC352803


title: cDNA of starved cells versus non-starved cells exp 1

city: Groningen

first: Imke

last: de Jong

address: Nijenborgh 7

department: GBB, Molecular Genetics

institute: University of Groningen

description: Ch1 = control = 0.1% glucose. Ch2 = target = no glucose. Target with high signal => upregulation. Control with high signal => downregulation

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (ref. van Hijum, S. A., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244.).

organism: Bacillus subtilis

source_name: non-starved_cells_Net intensity (tr.mean) {A}

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

growth_protocol: Precultures were inoculated from single colonies on LB agar plates and grown at 37°C in LB medium at 225 rpm. At an OD600 between 0.3 and 1.0, the cells were diluted 2500x – 7500x in M9 medium supplemented with 0.1% glucose and 0.1% malate and grown overnight at 37°C and 300 rpm. The following morning, cells with an OD600 cultures with an OD600 between 0.2 and 1.0 were diluted to OD600 = 0.05 in M9 medium supplemented with glucose only, and grown to mid-exponential phase at 37°C and 300 rpm. At an OD600 of 0.5, the cells were centrifuged (5000 rcf, 3 min, RT) in an Eppendorf 5810 R centrifuge prior to resuspension in M9 medium with 0.1 % glucose or M9 medium without glucose. After one washing step, fresh medium was used for further growth. Samples for RNA isolation were taken after 20 min of incubation.

extract_protocol: RNA was isolated from 50 ml of cells grown to midexponential phase of growth (A600 = 0.5). Cells were harvested by centrifugation for 3 min at 5,000 rcf at room temperature. Cell pellets were immediately frozen in liquid nitrogen and stored at -80 °C. Pellets were resuspended in 500 µl of 10 mM Tris-HCl, 1 mM EDTA (T10E1), pH 8.0, after which 50 µl of 10% SDS, 500 µl of phenol/chloroform, 500 mg of glass beads (75-150 µm), and 175 µl of Macaloid suspension (Bentone) were added. Further purification was done using the High Pure RNA isolation (Roche), using the suppliers protocol.

tag: strain

value: 0.1% glucose (control)

source_name: glc_starved_Net intensity (tr.mean) {B}

value: no glucose (target)


title: cDNA of starved cells versus non-starved cells exp 2 (dye-swap)

source_name: non-starved_cells_Net intensity (tr.mean) {B}

source_name: glc_starved_Net intensity (tr.mean) {A}


title: microRNA profile of case NPC352931

source_name: Nasopharyngeal carcinoma


title: microRNA profile of case NPC352731


title: cDNA of starved cells versus non-starved cells exp 3


title: microRNA profile of case NPC352717


title: Expt 1 & Expt 2 - Control 0 hr - repeat 6 - mAdbID:71412

description: mAdb experiment ID: 71412


title: Expt 1 & Expt 2 - RA only 40 hr - repeat 5 - mAdbID:71413

description: mAdb experiment ID: 71413


title: Expt 1 - TNF only - repeat 5 - mAdbID:71414

description: mAdb experiment ID: 71414


title: Expt 2 - 16 hr after RA - repeat 3 - mAdbID:71411

description: mAdb experiment ID: 71411


title: microRNA profile of case NPC352711


title: Expt 2 - Control 0 hr - repeat 5 - mAdbID:71410

description: mAdb experiment ID: 71410


title: Expt 1 - RA and TNF - repeat 3 - mAdbID:68685

description: mAdb experiment ID: 68685


title: microRNA profile of case NPC352543


title: Expt 2 - 6 hr after RA - repeat 2 - mAdbID:71409

description: mAdb experiment ID: 71409


title: Expt 2 - Control 0 hr - repeat 1 - mAdbID:71407

description: mAdb experiment ID: 71407


title: microRNA profile of case NPC352389


title: Expt 1 - TNF only - repeat 3 - mAdbID:68678

description: mAdb experiment ID: 68678


title: gastrointestinal stromal tumor T1 vs blood reference

type: genomic

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

hyb_protocol: Cy3- and Cy5-labeled DNA samples were combined in a total volume of 79 μl and mixed with 6.5 μg Cot-1 DNA (Invitrogen), 25.5 μl of 10× blocking agent (Agilent Technologies), 130 μl of 2× hybridization buffer (Agilent Technologies), and 15.5 μl MilliQ water. The hybridization mixture was heated for 3 min at 95°C and immediately incubated for 30 min at 37°C. After centrifugation for 60 sec at 14,000 rpm, the hybridization mixture was applied to the 2x 105K array slide and placed in an assembly chamber for 24 hr at 65°C and 20 rpm (Agilent Technologies). After hybridization, slides were washed in the following steps; 1 min with wash buffer 1 at room temperature (RT), 5 min with wash buffer 1 at RT with rotation speed (750 rpm), 1 min with wash buffer 2 at 37°C with rotation speed (750 rpm), and finally a 1 min wash step with acetonitrile at RT.

scan_protocol: Images of the arrays were acquired using a microarray scanner G2505B (Agilent technologies) and image analysis was performed using feature extraction software (version 9.1; Agilent Technologies). The Agilent CGH-v4_91 protocol was applied using default settings. Spot intensities were corrected for local background, and only spots with intensities at least twofold above the background signal intensities were included in the analysis.

data_processing:
image analysis was performed using feature extraction software (version 9.1; Agilent Technologies). Spot intensities were corrected for local background, and only spots with intensities at least twofold above the background signal intensities were included in the analysis.
Two samples were excluded based on their noisy profiles and high Median Absolute Deviation value (>0.5). The data from the remaining 47 samples had their background deducted and were normalized by median centering. Inherent wave bias using the Smoothing Waves algorithm was used to correct the profiles [35]. The data was then segmented using the DNACopy algorithm to find fragments of copy number increase or decrease [36]. Copy number states were deduced by using the CGHCall algorithm [37]. 85% tumor tissue was specified as parameter for the calling and for all other parameters default values was used.  The oligonucleotides were mapped according to the human genome build NCBI 36 for the 2 × 105 K array format. Of both Cy3 and Cy5 channels, local background was subtracted from the median intensities. The log2 tumor to normal ratio was calculated for each spot and normalized against the median of the ratios of all autosomes. When two or more neighbouring oligonucleotides showed significant copy number differences from zero, this was considered to be a possible CNA (copy number aberration).

molecule: genomic DNA

source_name: T1 GIST

label_protocol: Labelling was performed using the Enzo Genomic DNA Labeling kit according to the manufacturer's instructions (Enzo Life Sciences). Briefly, 500 ng genomic DNA was combined with a mixture of primers and reaction buffer to a final volume of 39 μl. The DNA was denatured at 99°C for 10 min, and placed on ice. While on ice, 10 μl cyanine 3-dUTP and cyanine 5-dUTP nucleotide mixture was added to the test and reference DNA, respectively, and finally 1 μl Klenow DNA polymerase was added to each sample to extend the primers. After 4 hr incubation at 37°C, 5 μl stop buffer was added to stop the reaction. Label was purified using the QIAquick PCR Purification Kit (Qiagen, Westburg, Leusden, NL).

extract_protocol: Qiagen’s QIAamp DNA Micro kit (Qiagen, Hilden, Germany)

value: gastrointestinal stromal tumor

source_name: Pooled blood reference

value: normal pooled blood reference


title: Expt 2 - 2 hr after RA - repeat 2 - mAdbID:71408

description: mAdb experiment ID: 71408


title: Expt 1 - RA and TNF - repeat 1 - mAdbID:68681

description: mAdb experiment ID: 68681


title: gastrointestinal stromal tumor T12 vs blood reference

source_name: T12 GIST


title: microRNA profile of case NPC352387


title: Expt 1 - RA and TNF - repeat 2 - mAdbID:68683

description: mAdb experiment ID: 68683


title: Expt 1 - TNF only - repeat 2 - mAdbID:68677

description: mAdb experiment ID: 68677


title: gastrointestinal stromal tumor T4 vs blood reference

source_name: T4 GIST


title: STAT pcn male 5

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

description: mRNA from total RNA converted to cRNA

hyb_protocol: labeled and fragmented cRNA hybridized to MG-430 2.0 Affymetrix GeneChips using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent Genespring GX11 program. No further adjustments were made to the data in the table.

source_name: low dose penicillin

label_protocol: Labeled target cRNA population was generated with the Affymetrix 3’-IVT Express kit

growth_protocol: C57BL6 mice obtained from Jackson Labs. Given ad libitum access to food and water. 12h/12h light/dark cycles.

extract_protocol: Total RNA extractions performed by RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: 6 mice were controls and not given any antibiotics. 6 mice given low dose penicillin via drinking water. Sacrificed after 7 weeks of intervention and liver specimens resected.

tag: strain gender

tag: gender

value: male

value: liver


title: microRNA profile of case NPC352113


title: gastrointestinal stromal tumor T186 vs blood reference

source_name: T186 GIST


title: microRNA profile of case NPC351998


title: gastrointestinal stromal tumor T17 vs blood reference

source_name: T17 GIST


title: STAT pcn male 4

description: mRNA from total RNA converted to cRNA


title: gastrointestinal stromal tumor T70 vs blood reference

source_name: T70 GIST


title: STAT pcn male 6

description: mRNA from total RNA converted to cRNA


title: microRNA profile of case NPC351996


title: microRNA profile of case NPC351990


title: STAT pcn male 3

description: mRNA from total RNA converted to cRNA


title: Expt 1 - TNF only - repeat 1 - mAdbID:68675

description: mAdb experiment ID: 68675

source_name: THP-1 TNF-only


title: STAT pcn male 2

description: mRNA from total RNA converted to cRNA


title: Expt 1 - RA only - repeat 3 - mAdbID:68670

description: mAdb experiment ID: 68670

source_name: THP-1 RA-only


title: STAT control male 6

description: mRNA from total RNA converted to cRNA

source_name: control


title: gastrointestinal stromal tumor T54 vs blood reference

source_name: T54 GIST


title: Expt 1 - RA only - repeat 2 - mAdbID:68661

description: mAdb experiment ID: 68661


title: microRNA profile of case NPC351792


title: gastrointestinal stromal tumor T184 vs blood reference

source_name: T184 GIST


title: gastrointestinal stromal tumor T49 vs blood reference

source_name: T49 GIST


title: microRNA profile of case NPC351752


title: STAT control male 5

description: mRNA from total RNA converted to cRNA


title: microRNA profile of case NPC351592


title: Expt 1 - Control - repeat 2 - mAdbID:68655

description: mAdb experiment ID: 68655

source_name: THP-1 Untreated


title: STAT control male 3

description: mRNA from total RNA converted to cRNA


title: gastrointestinal stromal tumor T45 vs blood reference

source_name: T45 GIST


title: Expt 1 - Control - repeat 3 - mAdbID:68656

description: mAdb experiment ID: 68656


title: gastrointestinal stromal tumor T32 vs blood reference

source_name: T32 GIST


title: microRNA profile of case NPC351715

source_name: Nasopharyngeal carcinoma


title: STAT pcn male 1

description: mRNA from total RNA converted to cRNA


title: Expt 1 - RA only - repeat 1 - mAdbID:68658

description: mAdb experiment ID: 68658


title: STAT control male 2

description: mRNA from total RNA converted to cRNA


title: microRNA profile of case NPC351406


title: gastrointestinal stromal tumor T34 vs blood reference

source_name: T34 GIST

source_name: Pooled blood reference


title: microRNA profile of case NPC351401


title: Expt 1 - Control - repeat 1 - mAdbID:68653

description: mAdb experiment ID: 68653


title: gastrointestinal stromal tumor T28 vs blood reference

source_name: T28 GIST


title: STAT control male 4

description: mRNA from total RNA converted to cRNA


title: STAT control male 1

description: mRNA from total RNA converted to cRNA


title: gastrointestinal stromal tumor T8 vs blood reference

source_name: T8 GIST


title: STAT3-deficient naïve T cells stimulated for 3 hours with IL-27 3

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description: Gene expression data from STAT3KO naïve CD4+ T cells stimulated for 3 hours with IL-27

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1. The trimmed mean target intensity of each array was set to 500.

source_name: primary CD4+ T cells from spleen and lymph nodes

label_protocol: RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

growth_protocol: Control and STAT-deficient naïve CD4+CD44-CD62L+CD25- T cells were isolated and sorted on the flow cytometer. Cells were stimulated with IL-6 (20 ng/ml), IL-27 (20 ng/ml) or no stimulation for 3 hours.

extract_protocol: Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

treatment_protocol: After 3hours stimulation in vitro, cells were hervasted.

value: CD4+ T

tag: genotype/variation

value: Cd4-Cre_C57BL6-STAT3<tm1Dlv> (STAT3KO)

value: stimulated for 3 hours with IL-27 (20 ng/ml)


title: microRNA profile of case NPC351260


title: microRNA profile of case NPC351186


title: STAT3-deficient naïve T cells stimulated for 3 hours with IL-27 2