title: Chicken Embryo Breast sample C10_19

description:
ChiEmBrC10_19
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

tag: incubated sample

value: pectoralis major muscle


title: induced sputum_severe_rep46

status: Public on Dec 31 2016

type: RNA

city: London

first: Chih-hsi

middle: Scott

last: Kuo

address: South Kensington Campus

department: Department of Computing

country: United Kingdom

institute: Imperial College London

description: induced sputum_severe asthma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: The data were quality controlled and pre-processed using R code of Affymetric Analysis QC workflow from ArrayAnalysis.org with Robust Multichip Average (RMA) as normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: induced sputum_severe asthma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip Expression Analysis Technical Manual, Copyright 2005-2009, Affymetrix)

extract_protocol: column-based extraction of total RNA was performed according to the manufacturer's instructions

tag: gender

value: female

tag: age

tag: oral corticosteroid use

value: yes


title: Gastric tumor tissue KG107C

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Group Gene Profile option of this software was used.

label: Biotin

source_name: Gastric tumor tissue

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: adjuvant chemotherapy (1=yes, 0=no, na=not available)

tag: patient

tag: tumor type

value: GC

value: F

tag: location

value: Body

tag: lauren classification

value: Intestinal

tag: ajcc stage

tag: tissue

value: Gastric tumor tissue


title: induced sputum_severe_rep45

description: induced sputum_severe asthma

value: male


title: induced sputum_severe_rep44

description: induced sputum_severe asthma


title: Heat stress treatment for 2h, biological rep1 [sad1 1F]

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

description: Gene expression data from Arabidopsis sad1 seedling after heat stress for 2h

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 0.7 mm resolution using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization.
The intensities of (PM-MM) were used in all subsequent data analyses.

organism: Arabidopsis thaliana

label_protocol:
Eight to fifteen mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.
Biotin-labeled cRNA was generated from the cDNA by in vivo transcription using the GeneChIP IVT Labeling Kit (Affymetrix).

growth_protocol: Arabidopsis seedlings were grown for 10 days on 1% agar plates containing 1/2MS and 0.5% sucrose at 22°C and were subjected to 37°C for 0, 2 and 6h.

extract_protocol: Total RNA from seedling was isolated using ISOGEN　(Nippon Gene) according to manufacturer’s protocol.

tag: ecotype

value: Ten-day-old seedling

tag: protocol

value: heat stress

tag: timpe point


title: Heat stress treatment for 2h, biological rep2 [sad1 2F]

source_name: Arabidopsis sad1 seedling after heat stress for 2h


title: induced sputum_severe_rep43

description: induced sputum_severe asthma


title: Control seedling, biological rep3 [sad1 3F]

description: Gene expression data from Arabidopsis sad1 seedling

source_name: Arabidopsis sad1 seedling

value: Control


title: Chicken Embryo Breast sample C10_18

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description:
ChiEmBrC10_18
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix Chicken Gene 1.0 ST Array. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Gallus gallus

source_name: Chicken Embryo Breast sample C10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: hatching eggs were incubated at 37.8°C  except for the treatment interval; post-hatch chicken were kept in barn system and fed a standard diet ad libitum

extract_protocol: Total RNA of frozen individual tissue samples was isolated with Tri-Reagent-extraction (Sigma-Aldrich, Taufkirchen, Germany), after DNase treatment a column-based purification using the RNeasy Mini Kit (Qiagen, Hilden, Germany) was done

treatment_protocol: treatment intervals embryonic day (ED) 7-10 and 10-13; incubation temperature during treatment interval: high 38.8°C, control 37.8°C, low 36.8°C

value: Broiler eggs

tag: incubation temperature in treatment interval

value: Control 37.8°C

tag: developmental interval of incubation temperature

tag: stage/age of sampling


title: Chicken Embryo Breast sample H10_14

description:
ChiEmBrH10_14
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample H10

tag: incubated sample

value: High 38.8°C


title: induced sputum_severe_rep42

description: induced sputum_severe asthma

tag: gender


title: Control seedling, biological rep2 [sad1 2F]


title: Control seedling, biological rep1 [sad1 1F]


title: Chicken Embryo Breast sample C10_17

description:
ChiEmBrC10_17
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_severe_rep40

description: induced sputum_severe asthma

tag: age


title: Heat stress treatment for 6h, biological rep3 [WT 3F]

description: Gene expression data from Arabidopsis WT seedling after heat stress for 6h


title: Gastric tumor tissue KG106C

value: M

value: Antrum


title: Gastric tumor tissue KG103C


title: Gastric tumor tissue KG102C

value: Diffuse


title: induced sputum_severe_rep41

description: induced sputum_severe asthma

value: female

tag: oral corticosteroid use


title: Chicken Embryo Breast sample H10_16

description:
ChiEmBrH10_16
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: pectoralis major muscle


title: induced sputum_severe_rep38

description: induced sputum_severe asthma

value: no


title: Gastric tumor tissue KG104C

tag: adjuvant chemotherapy (1=yes, 0=no, na=not available)

value: GC

value: F


title: Heat stress treatment for 6h, biological rep2 [WT 2F]

source_name: Arabidopsis WT seedling after heat stress for 6h


title: Chicken Embryo Breast sample H10_13

description:
ChiEmBrH10_13
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Embryo Breast sample H10_11

description:
ChiEmBrH10_11
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KG100C

tag: patient


title: Chicken Embryo Breast sample H10_9

description:
ChiEmBrH10_9
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_severe_rep37

description: induced sputum_severe asthma


title: Gastric tumor tissue KG101C

tag: tumor type

value: Intestinal


title: Heat stress treatment for 6h, biological rep1 [WT 1F]


title: Chicken Embryo Breast sample H10_6

description:
ChiEmBrH10_6
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KG099C

tag: location

value: Body

value: Gastric tumor tissue


title: induced sputum_severe_rep36

description: induced sputum_severe asthma


title: induced sputum_severe_rep35

description: induced sputum_severe asthma


title: Heat stress treatment for 2h, biological rep3 [WT 3F]

description: Gene expression data from Arabidopsis WT seedling after heat stress for 2h

value: Ten-day-old seedling


title: Chicken Embryo Breast sample H10_4

description:
ChiEmBrH10_4
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Heat stress treatment for 2h, biological rep1 [WT 1F]

source_name: Arabidopsis WT seedling after heat stress for 2h

value: heat stress


title: induced sputum_severe_rep39

description: induced sputum_severe asthma

value: male


title: Control seedling, biological rep2 [WT 2F]

description: Gene expression data from Arabidopsis WT seedling

source_name: Arabidopsis WT seedling

value: Control


title: Control seedling, biological rep1 [WT 1F]


title: Chicken Mature Leg sample L13_180

description:
ChiMaLegL13_180
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

data_processing: Data were analyzed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

source_name: Chicken Mature Leg sample L13

value: Broiler eggs

value: Low 36.8°C

value: gastrocnemius muscle


title: Gastric tumor tissue KG105C

value: M

value: Antrum

tag: lauren classification


title: Gastric tumor tissue KG098C

value: Cardia

tag: ajcc stage


title: induced sputum_severe_rep34

description: induced sputum_severe asthma

value: female


title: Control seedling, biological rep3 [WT 3F]

tag: tissue


title: Gastric tumor tissue KG097C

value: Diffuse


title: Chicken Mature Leg sample L13_163

description:
ChiMaLegL13_163
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample L10_155

description:
ChiMaLegL10_155
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Mature Leg sample L10


title: Chicken Mature Leg sample L13_178

description:
ChiMaLegL13_178
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: induced sputum_severe_rep33

description: induced sputum_severe asthma

value: no


title: Gastric tumor tissue KG092C

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

value: GC


title: Gastric tumor tissue KG095C

value: Intestinal


title: Gastric tumor tissue KG096C


title: induced sputum_severe_rep30

description: induced sputum_severe asthma


title: induced sputum_severe_rep32

description: induced sputum_severe asthma


title: Chicken Mature Leg sample L10_170

description:
ChiMaLegL10_170
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG093C


title: Chicken Mature Leg sample L13_179

description:
ChiMaLegL13_179
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: induced sputum_severe_rep28

description: induced sputum_severe asthma


title: Chicken Mature Breast sample C13_68

description:
ChiMaBrC13_68
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample C13

value: Control 37.8°C

value: pectoralis major muscle


title: induced sputum_severe_rep29

description: induced sputum_severe asthma


title: Gastric tumor tissue KG091C

value: Body

value: Gastric tumor tissue


title: induced sputum_severe_rep31

description: induced sputum_severe asthma


title: Chicken Mature Leg sample L13_161

description:
ChiMaLegL13_161
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Breast sample H10_12

description:
ChiEmBrH10_12
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: High 38.8°C


title: Chicken Mature Leg sample L10_145

description:
ChiMaLegL10_145
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: induced sputum_severe_rep27

description: induced sputum_severe asthma

value: male


title: Chicken Mature Leg sample L10_153

description:
ChiMaLegL10_153
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Broiler eggs


title: induced sputum_severe_rep26

description: induced sputum_severe asthma


title: Chicken Mature Leg sample L13_122

description:
ChiMaLegL13_122
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Low 36.8°C


title: induced sputum_severe_rep25

description: induced sputum_severe asthma


title: Gastric tumor tissue KG087C


title: Gastric tumor tissue KG090C

value: F


title: Gastric tumor tissue KG089C

value: M


title: Chicken Mature Leg sample L10_116

description:
ChiMaLegL10_116
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: gastrocnemius muscle


title: Chicken Mature Leg sample L13_91

description:
ChiMaLegL13_91
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG094C

value: Antrum


title: Gastric tumor tissue KG086C


title: Gastric tumor tissue KG085C


title: Chicken Mature Leg sample C13_81

description:
ChiMaLegC13_81
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Mature Leg sample C13


title: induced sputum_severe_rep24

description: induced sputum_severe asthma

value: female


title: Chicken Mature Leg sample C13_83

description:
ChiMaLegC13_83
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG088C


title: induced sputum_severe_rep23

description: induced sputum_severe asthma


title: induced sputum_severe_rep22

description: induced sputum_severe asthma


title: Gastric tumor tissue KG084C


title: induced sputum_severe_rep21

description: induced sputum_severe asthma


title: Chicken Mature Leg sample L10_76

description:
ChiMaLegL10_76
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample C13_68

description:
ChiMaLegC13_68
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample C13_70

description:
ChiMaLegC13_70
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG082C

value: Diffuse


title: Gastric tumor tissue KG080C


title: induced sputum_severe_rep19

description: induced sputum_severe asthma

value: no


title: Chicken Mature Leg sample C10_90

description:
ChiMaLegC10_90
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Mature Leg sample C10


title: Chicken Mature Leg sample L13_6

description:
ChiMaLegL13_6
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: induced sputum_severe_rep20

description: induced sputum_severe asthma


title: Gastric tumor tissue KG083C

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

value: GC


title: Chicken Mature Leg sample L10_64

description:
ChiMaLegL10_64
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG077C


title: induced sputum_severe_rep17

description: induced sputum_severe asthma


title: YPK102/1 zcf32 null mutant (replicate-1)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Whole cell
zcf32 /zcf32-1

hyb_protocol: 600ng of labeled cRNA were hybridized on the array (AMADID: 26377) using the Agilent Gene Expression Hybridization kit (Part Number 5190-0404) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software (Agilent).

organism: Candida albicans

source_name: YPD, 30°C grown zcf32 null mutant

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Candida albicans strains were grown in YPD liquid medium at 30°C till the start of the stationary phase.

extract_protocol: Total RNA was extracted from Candida albicans strains using Qiagen RNeasy Mini RNA isolation kit (Catalogue no. 74104).

treatment_protocol: No traetment was given.

tag: genotype

value: zcf32 null mutant

tag: strain

value: YPK102/1 (parental:SC5314)


title: Chicken Mature Leg sample C13_77

description:
ChiMaLegC13_77
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Control 37.8°C


title: Gastric tumor tissue KG079C

value: Intestinal


title: induced sputum_severe_rep18

description: induced sputum_severe asthma


title: induced sputum_severe_rep15

description: induced sputum_severe asthma


title: induced sputum_severe_rep12

description: induced sputum_severe asthma


title: induced sputum_severe_rep14

description: induced sputum_severe asthma


title: YPK102/2 zcf32 null mutant (replicate-2)

description:
Whole cell
zcf32 /zcf32-2

value: YPK102/2 (parental:SC5314)


title: Gastric tumor tissue KG081C

value: Gastric tumor tissue


title: induced sputum_severe_rep16

description: induced sputum_severe asthma


title: Chicken Mature Leg sample L10_51

description:
ChiMaLegL10_51
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample H10_74

description:
ChiMaLegH10_74
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Mature Leg sample H10

value: High 38.8°C


title: Gastric tumor tissue KG076C


title: induced sputum_severe_rep13

description: induced sputum_severe asthma

value: male


title: Gastric tumor tissue KG075C


title: Chicken Mature Leg sample H10_72

description:
ChiMaLegH10_72
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Broiler eggs


title: ba_d7 miRNA array

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

country: China

institute: Tsinghua University

hyb_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). For C3H10T1/2: Array product number 208500, Array version 7th Gen, Array batch number 35001, miRBase version 18. For 3T3-L1 Array product number 208200, Array version 4th Gen, Array batch number 31028.

scan_protocol: For C3H10T1/2: After hybridization the microarrayslides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb)   order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark). For 3T3-L1: microarrayslides were scanned using GenePix 4000P.

data_processing:
The microRNA array signals were quantile normalized and then log2 transformation
R was used for quantile normalization

organism: Mus musculus

source_name: C3H10T1/2 cells

label_protocol: For C3H10T1/2: 550 ng total RNA from samples was labeled with Hy3™ fluorescent label, respectively, using  miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™ (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3™-labeled samples were hybridized to the miRCURY LNA™ microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. For 3T3-L1: for labelling the miRCURY LNA™ microRNA Power Labeling Kit (Hy3) was used follwoing the manufatorer's instructions and hybridized to the miRCURY LNA™ microRNA Array 4th Gen (Exiqon, Denmark).

growth_protocol: For C3H10T1/2: Growth medium: DMEM (high glucose), 10% Fetalclone III serum, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3; Differentiation medium (d2-d7): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3. Before differentiation cells were seeded at 70% confluency and growth medium was supplemented with 8.3nM human recombinant BMP7 for 3 days.For 3T3-L1: Growth medium: DMEM (high glucose), 10% BCS, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% FBS, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin; Differentiation medium (d2-d7): DMEM (high glucose), 10% FBS, PenStrep, 0.12ug/ml Insulin. Before differentiation cells were seeded at 70% confluency (d-4).

extract_protocol: Total RNA was extrated using Trizol reagent following the manufactorer's instructions and treated with DnaseI.

tag: day of differentiation


title: Gastric tumor tissue KG078C

value: Body


title: SC5314 wild type (replicate-2)

description:
Whole cell
SC5314-2

source_name: YPD, 30°C grown wild type

value: wild type


title: ba_d2 miRNA array

description: Growth medium: DMEM (high glucose), 10% Fetalclone III serum, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3; Differentiation medium (d2-d7): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3. Before differentiation cells were seeded at 70% confluency and growth medium was supplemented with 8.3nM human recombinant BMP7 for 3 days.

value: day 2


title: ba_6h miRNA array

value: day 0, 6h


title: ba_d0 miRNA array

value: day 0


title: Chicken Mature Leg sample H13_60

description:
ChiMaLegH13_60
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Mature Leg sample H13

tag: incubation temperature in treatment interval

value: gastrocnemius muscle


title: Gastric tumor tissue KG074C

source_name: Gastric tumor tissue

value: M

value: Antrum


title: Chicken Mature Leg sample H10_67

description:
ChiMaLegH10_67
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

tag: developmental interval of incubation temperature


title: Gastric tumor tissue KG073C

value: GC

value: F


title: Chicken Mature Leg sample H10_66

description:
ChiMaLegH10_66
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

tag: stage/age of sampling


title: induced sputum_severe_rep10

description: induced sputum_severe asthma

source_name: induced sputum_severe asthma

value: no


title: ba_d-3 miRNA array

value: day -3


title: induced sputum_severe_rep11

description: induced sputum_severe asthma

value: female


title: Gastric tumor tissue KG071C

value: Diffuse

value: Gastric tumor tissue


title: Gastric tumor tissue KG072C

value: Intestinal


title: SC5314 wild type (replicate-1)

description:
Whole cell
SC5314-1


title: Heat stress treatment for 2h, biological rep2 [WT 2F]

description: Gene expression data from Arabidopsis WT seedling after heat stress for 2h

tag: ecotype

value: Ten-day-old seedling

tag: protocol

value: heat stress

tag: timpe point


title: Chicken Mature Leg sample H13_58

description:
ChiMaLegH13_58
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

tag: incubated sample

value: Broiler eggs

value: High 38.8°C


title: Chicken Mature Leg sample H13_50

description:
ChiMaLegH13_50
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG068C

tag: adjuvant chemotherapy (1=yes, 0=no, na=not available)

tag: gender

tag: age

value: Body


title: Gastric tumor tissue KG069C

tag: patient

tag: tumor type

tag: location


title: Gastric tumor tissue KG070C

tag: lauren classification

tag: ajcc stage

tag: tissue


title: wa_d8 miRNA array

description: Growth medium: DMEM (high glucose), 10% BCS, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% FBS, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin; Differentiation medium (d2-d7): DMEM (high glucose), 10% FBS, PenStrep, 0.12ug/ml Insulin. Before differentiation cells were seeded at 70% confluency (d-4).

source_name: 3T3-L1 cells

tag: day of differentiation


title: induced sputum_severe_rep7

description: induced sputum_severe asthma

tag: oral corticosteroid use


title: induced sputum_severe_rep9

description: induced sputum_severe asthma


title: wa_d2 miRNA array

value: day 2


title: wa_6h miRNA array

value: day 0, 6h


title: induced sputum_severe_rep8

description: induced sputum_severe asthma

value: male


title: induced sputum_severe_rep5

description: induced sputum_severe asthma


title: Gastric tumor tissue KG067C

value: Antrum


title: wa_d0 miRNA array

value: day 0


title: induced sputum_severe_rep6

description: induced sputum_severe asthma


title: Chicken Mature Leg sample H13_43

description:
ChiMaLegH13_43
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

tag: incubation temperature in treatment interval

tag: developmental interval of incubation temperature

value: gastrocnemius muscle


title: Chicken Mature Leg sample H13_34

description:
ChiMaLegH13_34
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

tag: stage/age of sampling


title: Chicken Mature Leg sample H13_31

description:
ChiMaLegH13_31
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample H13_39

description:
ChiMaLegH13_39
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG066C

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

value: GC

value: F


title: Chicken Mature Leg sample C10_30

description:
ChiMaLegC10_30
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Control 37.8°C


title: Gastric tumor tissue KG064C

value: M

value: Diffuse


title: Gastric tumor tissue KG063C

value: Gastric tumor tissue


title: Gastric tumor tissue KG065C

value: Intestinal


title: induced sputum_severe_rep4

description: induced sputum_severe asthma

value: no


title: induced sputum_severe_rep3

description: induced sputum_severe asthma

value: female


title: Chicken Mature Leg sample H10_15

description:
ChiMaLegH10_15
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Broiler eggs

value: High 38.8°C


title: induced sputum_severe_rep2

description: induced sputum_severe asthma


title: Gastric tumor tissue KG061C


title: Gastric tumor tissue KG062C

value: Cardia


title: induced sputum_severe_rep1

description: induced sputum_severe asthma


title: Chicken Mature Leg sample C13_29

description:
ChiMaLegC13_29
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample H10_13

description:
ChiMaLegH10_13
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample H10_3

description:
ChiMaLegH10_3
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Mature Leg sample H13_53

description:
ChiMaLegH13_53
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG058C


title: Gastric tumor tissue KG060C


title: Chicken Mature Leg sample H10_11

description:
ChiMaLegH10_11
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 QUE DMSO r5

city: Research Triangle Park

first: Rebecca

middle: A

last: Clewell

state: NC

address: 6 Davis Drive

department: Institute for Chemical Safety Sciences

institute: The Hamner Institutes for Health Sciences

description: HT 1080 Human Fibrosarcoma Cell Line

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Analysis of gene expression data was performed using Partek software (Partek Inc., St. Louis, MO) utlising GC-RMA normalisation. A 1-way ANOVA with interactions was performed to compare gene expression between the treated and control cells. Probability values were adjusted for multiple comparisons using a false discovery rate of 5%

source_name: ATCC CCL121 (HT-1080 Cells)

label_protocol: RNA samples were prepared for microarray hybridization using the GeneAtlas™ 3’ IVT Express Kit according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).  Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA. The cDNA was then converted into a double-stranded DNA template for transcription. Amplified cRNA (aRNA) was transcribed in vitro, with incorporation of a biotin-congugated nucleotide.  The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate, and samples were fragmented to prepare the biotin-labeled aRNA samples for hybridization onto Affymetrix® GeneChip™

growth_protocol: HT1080 cells were grown under the conditions recommended by ATCC:  Eagle’s Minimum Essential media (EMEM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 100 mg/L streptomycin and 100 U/mL of penicillin G at 37 °C in a humidified atmosphere of 95% air and 5% CO2

extract_protocol: total RNA was collected from the treated cells using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA).  A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA (Qiagen)

treatment_protocol: Cells were plated in complete media containing 10% heat-inactivated FBS and allowed to attach overnight. Stock solutions of chemicals were prepared in DMSO at 1,000-fold higher concentrations than the final target doses.  Stock solutions were aliquoted and stored at -20oC for up to 1 week. Dosing solutions were prepared immediately prior to treatment of the cells by diluting stock solutions 1:200 in complete media.  24 hrs after seeding the cells, the media in each well was supplemented with the dosing solutions (1:5 v/v), for a final chemical dilution of 1:1000 (0.1% vehicle). Cells were maintained in original complete media throughout the course of the experiment.  Immediately following treatment, media was removed and the cells were washed with PBS and prepared for subsequent analyses

tag: cell line

tag: cell type

value: Fibrosarcoma


title: HT1080 QUE DMSO r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG057C

value: Body


title: HT1080 QUE DMSO r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C13_91

description:
ChiEmLegC13_91
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Embryo Leg sample C13

tag: incubated sample


title: Chicken Embryo Leg sample C13_88

description:
ChiEmLegC13_88
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 QUE DMSO r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 QUE DMSO r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG055C

tag: adjuvant chemotherapy (1=yes, 0=no, na=not available)


title: HT1080 QUE DMSO r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C13_87

description:
ChiEmLegC13_87
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG054C

tag: gender

value: Antrum


title: HT1080 QUE 30uM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 QUE 30uM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L13_83

description:
ChiEmLegL13_83
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Embryo Leg sample L13

value: Low 36.8°C


title: Chicken Embryo Leg sample C13_89

description:
ChiEmLegC13_89
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: gastrocnemius muscle


title: HT1080 QUE 30uM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L13_77

description:
ChiEmLegL13_77
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG056C

value: GC

tag: age


title: HT1080 QUE 30uM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG053C

tag: patient

value: F


title: Gastric tumor tissue KG052C

tag: tumor type


title: Chicken Embryo Leg sample L13_79

description:
ChiEmLegL13_79
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample L13_76

description:
ChiEmLegL13_76
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 QUE 30uM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG051C

tag: location


title: Gastric tumor tissue KG050C

tag: lauren classification


title: Gastric tumor tissue KG049C

tag: ajcc stage


title: HT1080 QUE 30uM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 ETP DMSO r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 ETP DMSO r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG047C

tag: tissue


title: Gastric tumor tissue KG048C


title: HT1080 ETP DMSO r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L13_73

description:
ChiEmLegL13_73
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 ETP DMSO r2-2

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L13_75

description:
ChiEmLegL13_75
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 ETP DMSO r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG045C

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

value: Mixed


title: Gastric tumor tissue KG046C

value: M


title: Chicken Embryo Leg sample L13_72

description:
ChiEmLegL13_72
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample C10_65

description:
ChiEmLegC10_65
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Embryo Leg sample C10

value: Control 37.8°C


title: HT1080 ETP DMSO r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C10_70

description:
ChiEmLegC10_70
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample L13_74

description:
ChiEmLegL13_74
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG043C

value: Gastric tumor tissue


title: HT1080 ETP DMSO r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C10_64

description:
ChiEmLegC10_64
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample C10_63

description:
ChiEmLegC10_63
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG042C

value: Intestinal


title: Gastric tumor tissue KG044C

value: Diffuse


title: Gastric tumor tissue KG038C


title: HT1080 ETP 0.3uM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L10_61

description:
ChiEmLegL10_61
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Embryo Leg sample L10


title: Gastric tumor tissue KG035C


title: Chicken Embryo Leg sample L10_60

description:
ChiEmLegL10_60
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 ETP 0.3uM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L10_57

description:
ChiEmLegL10_57
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG041C

value: GIST


title: HT1080 ETP 0.3uM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 ETP 0.3uM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 ETP 0.3uM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG037C


title: Chicken Embryo Leg sample L10_56

description:
ChiEmLegL10_56
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Broiler eggs


title: HT1080 ETP 0.3uM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L10_59

description:
ChiEmLegL10_59
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample L10_54

description:
ChiEmLegL10_54
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG028C


title: HT1080 CuR DMSO r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L10_55

description:
ChiEmLegL10_55
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG033C


title: HT1080 CuR DMSO r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample L10_51

description:
ChiEmLegL10_51
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric Surrounding normal tissue KG034N

source_name: Gastric Surrounding tumor tissue

value: Gastric Surrounding normal tissue


title: Gastric tumor tissue KG030C


title: Gastric tumor tissue KG027C


title: HT1080 CuR DMSO r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 CuR DMSO r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 CuR DMSO r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG023C


title: Chicken Embryo Leg sample C13_42

description:
ChiEmLegC13_42
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 CuR DMSO r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C13_41

description:
ChiEmLegC13_41
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Bacteria_salt_rep3

city: Evora

first: Marta

last: Laranjo

address: Apartado 94

department: ICAAM

country: Portugal

institute: Universidade de Evora

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol

data_processing: The signal intensity for each spot was extracted using QuantArray Analysis Software (GSI Lumonics). Analysis of raw data was performed using BRB-ArrayTools v3.4.0, where each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. The normalized dataset was then subjected to statistical analysis and clustering using MeV software to identified the diferencially expressed genes. The same dataset was also used to calculate the M-value and Fold-change variation.

organism: Mesorhizobium japonicum MAFF 303099

source_name: bacterial cells, salt shock

label_protocol:
aRNA amplification protocol: MessageAmp™ II-Bacteria Kit (Ambion) - Manufacturer's protocol
Quick Amp Labeling Kit (Agilent) - Manufacturer's protocol

growth_protocol: 10 ml of cells with an OD(540 nm)=0.3, which corresponds to approximately 6x10exp8 cells per ml were used.

extract_protocol:
RNeasy Mini Kit (Qiagen) manufacturer's protocol
mRNA enrichment protocol: MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) - Manufacturer's protocol

treatment_protocol: Cells grown overnight at 28 ºC and maintained at 28 ºC for the 30 min were used as control.For salt shock experiments, cells grown overnight at 28 ºC were subjected to a salt shock of 10% NaCl at 28 ºC for 30 min.

tag: treatment

value: salt shock


title: Chicken Embryo Leg sample C13_40

description:
ChiEmLegC13_40
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG020C

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

value: Cardia


title: Chicken Embryo Leg sample C13_39

description:
ChiEmLegC13_39
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 CUR 10uM r5

description: HT 1080 Human Fibrosarcoma Cell Line

value: Fibrosarcoma


title: HT1080 CUR 10uM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric Surrounding normal tissue KG011N


title: HT1080 CUR 10uM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Bacteria_salt_rep2

scan_protocol: One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol


title: Chicken Embryo Leg sample H13_36

description:
ChiEmLegH13_36
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Embryo Leg sample H13

value: High 38.8°C


title: Bacteria_salt_rep1


title: Gastric tumor tissue KG019C

value: Body


title: HT1080 CUR 10uM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric Surrounding normal tissue KG010N


title: Chicken Embryo Leg sample H13_30

description:
ChiEmLegH13_30
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: gastrocnemius muscle


title: Chicken Embryo Leg sample H13_29

description:
ChiEmLegH13_29
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG006C

value: GC

value: Antrum


title: Gastric Surrounding normal tissue KG008N.1


title: Gastric tumor tissue KG015C


title: Chicken Embryo Leg sample H13_32

description:
ChiEmLegH13_32
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: KG1a8Gy_48hr_0Gy_rep1

city: Delhi

first: Gangenahalli

middle: Ugraiah

last: Gurudutta

state: Delhi

address: Lucknow Road, Timarpur

department: Division of Stem Cell & Gene Therapy

institute: Institute of Nuclear Medicine and Allied Sciences (INMAS)

description:
KG1a8Gy_1
Gene expression after 48hr in 8Gy-irradiated KG1a cells

hyb_protocol: Hybridized to Human Whole Genome Arrary Chip (Human 8x60K Array AMAID: 039494/ GPL17077).

scan_protocol: Images were scanned and signaled data was acquired using feature extraction software (V/0.5 Agilent Tech). The images were manually verified and found to be devoid of uneven hybridization, strikes, blobs, and other artifacts.

data_processing: Inta-Array normalization was done using GeneSpring GX 12.1 software. The gProcessed signal (dye normalized background subtracted signal intensity) was log transformed and then for each of the array the 75th percentile value was calculated. In each sample the log transformed intensity values for each probe was subtracted by the calculated 75th percentile value of the respective array and expression values were obtained.

label_protocol: Following reverse transcription of RNA into cDNA, Cy3 labelled cRNA was produced by in vitro transcription.

growth_protocol: KG1a cells were grown in IMDM medium containing 20% fetal bovine serum and antibiotic and antimycotic solution, in 5% CO2 atmosphere at 37°C.

extract_protocol: RNA isolated using RNeasy Minikit (Qiagn, #74104) and quantified in Nanodrop spectrophotometer. RNA sample purity ratio was more than 1.9 for 260/280 nm, and RIN values were greater than 9.0 as evaluated on Bioanalyzer (Agilent Tech).

treatment_protocol: For irradiation of cells, Bhabhatron Teletherapy unit (Co60 as radiation source) was used.

tag: tissue source

value: bone marrow

tag: disease

value: acute myelogenous leukemia

value: promyeloblast, macrophage

tag: treated with

value: 8Gy of radiation


title: HT1080 MMS CTL r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: KG1a8Gy_48hr_0Gy_rep3

description:
KG1a8Gy_3
Gene expression after 48hr in 8Gy-irradiated KG1a cells


title: Chicken Embryo Leg sample H13_27

description:
ChiEmLegH13_27
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

tag: incubation temperature in treatment interval

tag: developmental interval of incubation temperature

tag: stage/age of sampling


title: KG1a8Gy_48hr_0Gy_rep2

description:
KG1a8Gy_2
Gene expression after 48hr in 8Gy-irradiated KG1a cells

tag: cell line

tag: cell type


title: Chicken Embryo Leg sample H13_28

description:
ChiEmLegH13_28
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

tag: incubated sample


title: HT1080 MMS CTL r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample H13_26

description:
ChiEmLegH13_26
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: KG1a_48hr_0Gy_rep3

description:
KG1a_3
Gene expression after 48hr in 0Gy-irradiated KG1a cells

value: none (0Gy)


title: HT1080 CUR 10uM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample H13_25

description:
ChiEmLegH13_25
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 CUR 10uM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: KG1a_48hr_0Gy_rep2

description:
KG1a_2
Gene expression after 48hr in 0Gy-irradiated KG1a cells


title: KG1a_48hr_0Gy_rep1

description:
KG1a_1
Gene expression after 48hr in 0Gy-irradiated KG1a cells


title: Gastric Surrounding normal tissue KG002N

tag: adjuvant chemotherapy (1=yes, 0=no, na=not available)


title: HT1080 MMS CTL r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C10_21

description:
ChiEmLegC10_21
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Control 37.8°C


title: HT1080 MMS CTL r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric tumor tissue KG024C

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

tag: patient

value: GIST

tag: gender

value: F

tag: age

value: Gastric tumor tissue


title: Chicken Embryo Leg sample C10_18

description:
ChiEmLegC10_18
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: Broiler eggs


title: Patient 7

city: Madrid

first: Ana

last: Del Rio

state: Madrid

address: Calle Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

description: Gene expression

hyb_protocol: Hybridization was performed according to the manufacturer’s protocol (Agilent One-Color Microarray-Based Gene Expression Analysis v6.5) using 600 ng cy3-labeled cRNA per sample and SurePrint G3 Human Gene Expression 8x60K Microarrays.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent).

data_processing: Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction

source_name: Bone marrow

label_protocol: 0.9 ug total RNA was labeled with cy3-CTP following Agilent Low Input Quick Amplification Labeling Kit protocol for One-Color Microarray-Based Gene Expression Analysis

growth_protocol: Human Hematopoietic Progenitors (hHP; CD34+) were purified using immunomagnetic beads (Miltenyi Biotech, Germany) from human umbilical cord blood (CB). They were cultured in Iscove’s modified Dulbecco’s media (IMDM) containing 20% BIT 9500 Serum substitute (STEMCELL Technologies), 1% penicillin-streptomycin (Invitrogen), 0.2% β-mercaptoethanol, 10 ng/ml SCF, megakaryocyte growth and development factor (TPO), FLT3 ligand (FLT3L), IL-3, and IL-6.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) following the manufacturer's recommendations.

tag: tissue/cell type

value: Bone marrow


title: Gastric tumor tissue KG001C

tag: tumor type

value: M

tag: location

tag: lauren classification

value: Intestinal

tag: ajcc stage


title: Gastric Surrounding normal tissue KG022N

tag: tissue

value: Gastric Surrounding normal tissue


title: HT1080 MMS 200uM r6

description: HT 1080 Human Fibrosarcoma Cell Line

value: Fibrosarcoma


title: HT1080 MMS CTL r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C10_19

description:
ChiEmLegC10_19
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

value: gastrocnemius muscle


title: HT1080 MMS 200uM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric Surrounding normal tissue KG021N


title: Gastric tumor tissue KG018C

value: GC

value: Antrum

value: Diffuse


title: Patient 6

description: Gene expression


title: Patient 5

description: Gene expression


title: HT1080 MMS 200uM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample C10_17

description:
ChiEmLegC10_17
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample H10_16

description:
ChiEmLegH10_16
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature

source_name: Chicken Embryo Leg sample H10

value: High 38.8°C


title: HT1080 MMS 200uM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: Patient 4

description: Gene expression


title: HT1080 MMS 200uM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Patient 3

description: Gene expression


title: Patient 2

description: Gene expression


title: Chicken Embryo Leg sample H10_14

description:
ChiEmLegH10_14
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric Surrounding normal tissue KG017N


title: Gastric Surrounding normal tissue KG014N


title: Chicken Embryo Leg sample H10_13

description:
ChiEmLegH10_13
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: hHP-NUP98-HOXA9 clone 2

description: Gene expression

source_name: Hematopoietic progenitors (CD34+) from cord blood


title: Patient 1

description: Gene expression


title: Gastric tumor tissue KG013C


title: HT1080 MMS 200uM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: hHP-NUP98-HOXA9 clone 1

description: Gene expression

value: Hematopoietic progenitors (CD34+) from cord blood


title: Gastric Surrounding normal tissue KG016N


title: Chicken Embryo Leg sample H10_12

description:
ChiEmLegH10_12
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Gastric tumor tissue KG012C


title: Gastric tumor tissue KG005C

value: Fundus


title: HT1080 BRO DMSO r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric Surrounding normal tissue KG008N


title: Gastric tumor tissue KG009C


title: Chicken Embryo Leg sample H10_6

description:
ChiEmLegH10_6
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: HT1080 BRO DMSO r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 BRO DMSO r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Chicken Embryo Leg sample H10_9

description:
ChiEmLegH10_9
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample H10_11

description:
ChiEmLegH10_11
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Chicken Embryo Leg sample H10_4

description:
ChiEmLegH10_4
gene level expression of broiler Musculus gastrocnemius after variation of incubation temperature


title: Root segment upon WD at T+2, biological rep.2

city: Louvain-la-Neuve

first: Xavier

last: Draye

address: Croix du Sud 2- L7.05.11

department: Earth and Life Institute

country: Belgium

institute: Université catholique de Louvain

description: Barley root segments that are likely to contain four LR initiation engaged in asymetric divisions (sample A), against zero in the B samples where these sites have been repressed.

hyb_protocol: The samples were hybridized to the arrays  for 16 h at 45°C and washed on GeneChip Fluids Station (Affymetrix).

scan_protocol: Gene chips were scanned on GeneChip Scanner (Affymetrix).

data_processing: The expression values were normalized using the robust multi-array average method (Irizarry et al. 2003) with R and affy package (www.r-project.org)

organism: Hordeum vulgare

source_name: Barley root segments (sample B) after 6h-long WD

label_protocol: 5.3 μg of total RNA was used for cRNA synthesis, labelling and fragmantation  acocrding  to  One  Cycle  Target  Labelling  kit  (Affymetrix),  as  for manufacture protocol.

growth_protocol: Seeds of barley cv. Derkado were wetted in 70% ethanol (v/v), placed in 5% (v/v) sodium hypochlorite for 15 min on a shaker and were washed several times with SDW (steril destilled water). Seeds were then stratified at 4°C for 2 d on a filter paper and were partially covered in SDW. Then, seeds were attached to a filter paper on a vertical plexi-glass plate with a sterile tape (Milipore, 3M) and left to germinate for two days in a dark, humid and closed box. Seedlings were then transferred to the aeroponics system where roots were sprayed with nutrient solution for 15 s every 5 min. Half-strength Hewitt solution (Hewitt 1966) was used for barley and consist of 2 mM Ca(NO3)2 · 4H2O, 2 mM KNO3, 0.75 mM MgSO4 · 7H2O, 0.67 mM NaH2PO4 · 2H2O, 0.05 mM FeEDTANa, 0.03 µM (NH4)6Mo7O24 · 4H2O, 50 µM NaCl, 25 µM H3BO3, 5 µM MnCl2 · 4H2O, 0.5 µM CuSO4 · 5H2O, 0.5 µM ZnSO4 · 7H2O, 0.6 mM Na2SiO3 · 5H2O; pH 5.8). In each experiment, half of the seeds were subjected to a transient WD treatment 3 days after the transfer to the aeroponic system.

extract_protocol: RNA was isolated from frozen root segments according to the SV Total RNA Isolation Systems (Promega). After DNAse treatment (Promega), RNA samples were quantified by using  Nanodrop  spectrophotometer  (Nanodrop Technologies)  and  then  confirmed  by RNA electrophorese.

treatment_protocol: The water deficit (WD) treatment was applied by interrupting the nutrient supply for 8 h during the night phase. The sampling strategy was designed to monitor gene expression at -4, -2, 0, 2 and 4 hours relative to the first asymetric division, in conditions that enable (A) or repress (B) LR formation. 5-mm long segments were sampled such that the first sampling (-4h position) targets a region distal to the first asymetric divisions, and the last sampling (+4h position) targets a region proximal to the first asymetric division.

value: root segment

tag: time (hours)

tag: treatment

value: Water Deficit

tag: cultivar

value: Derkado


title: Gastric tumor tissue KG004C

value: Body

value: Gastric tumor tissue


title: HT1080 BRO DMSO r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 BRO DMSO r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 BRO DMSO r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: Root segment upon WD at T+2, biological rep.1


title: HT1080 BRO 600uM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 BRO 600uM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 BRO 600uM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 BRO 600uM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: Root segment upon WD at T-2, biological rep.2

description: Barley root segments that are likely to contain one LR initiation engaged in asymetric divisions (sample A), against zero in the B samples where these sites have been repressed.

source_name: Barley root segments (sample B) after 2h-long WD


title: Root segment upon WD at T0, biological rep.1

description: Barley root segments that are likely to contain two-three LR initiation engaged in asymetric divisions (sample A), against zero in the B samples where these sites have been repressed.

source_name: Barley root segments (sample B) after 4h-long WD


title: Transgenic BnCRY2aOE leaf, Biological replicate 1

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

institute: University of Delhi South Campus

description:
Gene expression data of transgenic
BnCRY2aOE I
Brassica juncea var. RLM-198

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040). The purified cRNA (600ng) was fragmented with fragmentation blocking mix by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturer’s instructions (G2534-90001). Once loaded into the hybridization chamber, samples were placed in the hybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Hybridized microarray slides were scanned at a resolution of 5 μm using an Agilent Microarray scanner (G2565CA) with scan control software as per the manufacturer's instructions (G2505-90020).

data_processing: Raw data from the Feature Extraction software were obtained in .txt (Tab delimited) format and were normalized using GeneSpring GX v12.0. Normalization was performed by taking the 50th percentile for each sample. A baseline correction was applied to the median of all samples. The expected versus observed measurements of the hybridization control probes were compared for hybridization quality control for each sample. Hybridization quality control for replicate samples was performed by measuring the correlation co-efficient, performing a principle component analysis (PCA), creating scatter plots and creating an unsupervised condition tree of samples using the Pearson uncentered algorithm with average linkage rule.

organism: Brassica juncea

source_name: 45-d-old transgenic plant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Quick Amplification Labelling kit (Agilent Technologies, G4140-90040) 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: Seeds of wild-type Brassica juncea var. RLM-198 and BnCRY2aOE transgenics were sown in well-drained moist soil. After 45 days of sowing, the leaf samples were harvested from two replicates of wild-type and transgenics.

extract_protocol: Total RNA was extracted using the QIAgen RNeasy Plant Mini Kit as per the manufacturer’s instructions (Qiagen). The quality check of total RNA was done using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: No special treatment was given to plants before harvesting.

tag: genotype

value: BnCRY2a overexpression

value: leaf


title: Root segment upon WD at T0, biological rep.2


title: Root segment upon WD at T-2, biological rep.1


title: Wild-type leaf, Biological replicate 2

description:
Gene expression data of control
Wild-type II
Brassica juncea var. RLM-198

source_name: 45-d-old wild-type plant

value: wild type


title: HT1080 DMSO pooled r6

description: HT 1080 Human Fibrosarcoma Cell Line

tag: cell line


title: HT1080 BRO 600uM r2

description: HT 1080 Human Fibrosarcoma Cell Line

tag: cell type


title: Transgenic BnCRY2aOE leaf, Biological replicate 2

description:
Gene expression data of transgenic
BnCRY2aOE II
Brassica juncea var. RLM-198


title: Root segment at T+2, biological rep.1

source_name: Barley root segments (sample A) after 6h normal watering

value: control


title: HT1080 DMSO pooled r5

description: HT 1080 Human Fibrosarcoma Cell Line

source_name: ATCC CCL121 (HT-1080 Cells)

value: Fibrosarcoma


title: Root segment at T+2, biological rep.2


title: Wild-type leaf, Biological replicate 1

description:
Gene expression data of control
Wild-type I
Brassica juncea var. RLM-198


title: HT1080 BRO 600uM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 DMSO pooled r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gastric Surrounding normal tissue KG003N

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-12 beadChip ver. 3 were used.

value: Gastric Surrounding normal tissue


title: Root segment upon WD at T-4, biological rep.2

description: Barley root segments that do not contain any first asymetric divisions (samples A and B)

source_name: Barley root segment at the onset of the time course


title: Root segment at T-2, biological rep.2

source_name: Barley root segments (sample A) after 2h normal watering


title: HT1080 DMSO pooled r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Root segment at T0, biological rep.2

source_name: Barley root segments (sample A) after 4h normal watering


title: HT1080 MMS CTL r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Root segment at T0, biological rep.1


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Li_D5_3

city: New York

first: Angela

last: Rasmussen

state: NY

department: Center for Infection and Immunity

institute: Columbia University

hyb_protocol: ). Individual cRNA samples were hybridized to Agilent mouse whole-genome oligonucleotide 4-by-44 microarrays (approximately 39,000 unique mouse genes) according to the manufacturer's instructions. To enable examination of animal-to-animal variation as part of the data analysis, samples from individual animals were not pooled; included were samples from three animals per time point for each virus (60 animals total). Select samples were hybridized a second time (n = 2 technical replicates) to verify the quality of the process.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and the resulting images were analyzed using Agilent Feature Extractor version 8.1.1.1. This software was used to perform image analysis, including significance of signal and spatial detrending and to apply a universal error model. For these hybridizations, the most conservative error model was applied.

data_processing: standard Agilent protocol

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color LowInput Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA).

growth_protocol: Six to nine week-old male mice (C57Bl/6J, MAVS-/-) were used in all experiments.  Mice were housed in microisolator cages and allowed to acclimatize to the BSL4 environment for a least 5 days prior to use in experiments.

extract_protocol: RNA was extracted from mouse spleens and livers using a Qiagen RNeasy Minikit with RNAlater solution (Qiagen, Valencia, CA) according to the manufacturer's instructions. RNA was further purified using RNeasy columns (Qiagen, Valencia, CA). RNA samples were spectroscopically verified for purity, and the quality of the intact RNA was assessed using an Agilent 2100 Bioanalyzer. For each set of treatment conditions, three of the five RNA samples exhibiting the highest RNA integrity number (RIN) determined using the Bioanalyzer were used for microarray analysis.

treatment_protocol: Mice were infected by intraperitoneal (i.p.) injection with 100 focus-forming units (ffu) of either MA-ZEBOV or WT ZEBOV diluted in 0.2 ml of Dulbecco’s minimum essential medium (DMEM).  Mock-infected mice were i.p. inoculated with DMEM alone. Mice were humanely euthanized on days 3 and 5 post-infection, and spleens and livers removed and incubated in RNAlater (Qiagen, Valencia, CA). Tissues were then homogenized in Trizol reagent (ThermoFisher Scientific, Waltham, MA) to both inactivate virus and stabilize RNA, and stored at -80 C until RNA extraction.

value: Microarray


title: HT1080 tBHQ 200uM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 tBHQ 200uM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: Root segment at T-2, biological rep.1


title: HT1080 DMSO pooled r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 tBHQ 200uM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 DMSO pooled r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 tBHQ 200uM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Li_D5_2


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D5_1


title: HT1080 GAD 2mM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 tBHQ 200uM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Sp_D5_2


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Sp_D5_3


title: Root segment upon WD at T-4, biological rep.1


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Li_D3_3


title: HT1080 GAD 2mM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 tBHQ 200uM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Sp_D5_2


title: HT1080 GAD 2mM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 GAD 2mM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 GAD 2mM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Li_D3_2


title: HT1080 ENU 2mM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Sp_D3_3


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Sp_D5_3


title: HT1080 GAD 2mM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 ENU 2mM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D5_3


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Sp_D5_3


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Li_D3_2


title: HT1080 ENU 2mM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Li_D5_2


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Li_D5_1


title: HT1080 ENU 2mM r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 ENU 2mM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Li_D3_1


title: HT1080 ENU 2mM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_MAVSKO_Mu_Mock_Sp_D3_1


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Sp_D3_1


title: EBV_M_2015_1_MAVSKO_Mu_Mock_Li_D3_1


title: HT1080 H2O2 100uM r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Li_D3_1


title: HT1080 NCS 10ng/ml r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Sp_D3_2


title: HT1080 NCS 10ng/ml r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Sp_D5_1


title: EBV_M_2015_1_MAVSKO_Mu_Mock_Li_D5_2


title: HT1080 MMC 0.1uM  r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 H2O2 100uM r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 H2O2 100uM r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Li_D3_2


title: HT1080 NCS 10ng/ml r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_MAVSKO_Mu_Mock_Li_D5_1


title: HT1080 NCS 10ng/ml r1

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Li_D3_3


title: HT1080 NCS 10ng/ml r6

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D3_1


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D5_2


title: HT1080 H2O2 100uM r5

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gonad_HTE2_rep4

city: Barcelona

first: Noelia

middle: T

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

institute: Institute of Marine Sciences (ICM-CSIC)

description: Estradiol administration from 90 to 154 days post hatch

hyb_protocol: Each sample (1.65 μg) was hybridized to D. labrax array (Agilent ID 023790) at 65 °C for 17 h using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. The microarray platform GPL17917 has been validated and uploaded to the Gene Expression Omnibus (GEO)-NCBI database.

data_processing: Raw data was taken from the Feature Extraction output files and was corrected for background noise using the normexp (Ritchie et al., 2007) method. To assure comparability across samples quantile normalization (Bolstad, 2001) was used. A probe was considered reliable if its raw foreground intensity was at least two times higher than the respective background intensity and if it was neither saturated nor flagged by the Feature Extraction software. On our custom array design, most probes (78%) were represented in two (or in some cases more) identical copies. Median intensities of respective probe replicates were taken in order to yield only one expression value per probe. A probe was considered reliable if at least half of its replicates were reliable, as defined above. Differential expression analysis was carried out on all non-control probes with an empirical Bayes approach on linear models (limma) (Smyth, 2004). Results were corrected for multiple testing according to the False Discovery Rate (FDR) method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed if they had adjusted P-value < 0.05, absolute fold change > 1.2 and were reliable in all samples.  All statistical analyses were performed with the Bioconductor project (http://www.bioconductor.org/) in the R statistical environment (http://cran.rproject.org/) (Gentleman et al., 2004).

organism: Dicentrarchus labrax

source_name: Half gonad, 170 days post hatch, early high water temperature (HT) and Estradiol treatment from 90 to 154 dph

label_protocol: RNA labelling, hybridizations, and scanning were performed according to manufacturer’s instructions. Briefly, total RNA (100 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit. After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen), quantified with the Nanodrop ND- 1000 and verified using the Bioanalyzer 2100.

growth_protocol: Rearing conditions and handling methods were as described at (Díaz et al., 2013). Both experimental groups followed the same feeding protocol; larvae were fed three times a day with Artemia AF and then with amino acid enriched Artemia EG (INVE Aquaculture, Belgium). Juveniles and adults were fed ad libitum two times a day with dry food (ProAqua S.A., Spain) of different diameters according to fish size.

extract_protocol: Total RNA was purified from 170 dph European sea bass isolated gonads by homogenizing the tissue with Trizol reagent (Invitrogen- Live Technologies, Scotland, UK). Briefly, samples were then separated into phases by chloroform, precipitated with isopropanol and washed in 75% Ethanol. The quality and concentration of the RNA were assessed by ND-1000 spectrophotometer (NanoDrop Technologies) based on A260 absorbance and checked on a 1% agarose/formaldehyde gel. Integrity of the total RNA was then verified analyzing 1 µl/sample with a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent, Spain) before processing for microarrays to assure consistency across samples. RNA samples of 100-200 ng/µl and RINs higher than 7 were used to perform the hybridizations. Two hundred nanograms of total RNA were treated with E.coli RNAse H in order to remove complementary RNA. From this RNA 100 ng were used for the cDNA synthesis using SuperScript III RNase Transcriptase (Invitrogen, Spain) and Random hexamer (Invitrogen, Spain) following manufacturer’s instructions.

treatment_protocol: Larvae were divided in two tanks and maintained at 17ºC, a temperature known to avoid temperature effects on sex ratio (Piferrer et al., 2005; Navarro-Martín et al., 2009), for the first 20 dph. Then the thermal regime differed between the two groups. While in one tank temperature was increased to 21ºC (high temperature, HT group) in the other was decreased to 15 ºC (low temperature, LT group); in both cases temperature changes were achieved at a ratio of 0.5ºC/day. These temperatures were maintained until 60 dph when temperature in LT group was gradually raised to 21ºC to allow fish growth at normal rates. Finally, at ~220 dph, temperature started to follow the natural fluctuations to allow gonad. Also from 90 to 154 dph individuals were fed with an Estradiol-vaporized dry food (known to be a feminizing agent).

value: putative females

tag: growth

value: reared at high temperature (21°C)


title: Gonad_HTE2_rep5

value: Estradiol administration from 90 to 154 days post hatch


title: HT1080 NCS 10ng/ml r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gonad_HTE2_rep3


title: HT1080 H2O2 100uM r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: HT1080 MMC 0.1uM  r4

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Li_D5_2


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Sp_D3_2


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Sp_D5_1


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Sp_D3_2


title: Gonad_LTE2_rep5

source_name: Half gonad, 170 days post hatch, early low water temperature (LT) and Estradiol treatment from 90 to 154 dph

value: reared at low temperature (15°C)


title: HT1080 MMC 0.1uM  r3

description: HT 1080 Human Fibrosarcoma Cell Line


title: Gonad_HTE2_rep1


title: HT1080 MMC 0.1uM  r2

description: HT 1080 Human Fibrosarcoma Cell Line


title: EBV_M_2015_1_MAVSKO_Mu_Mock_Sp_D5_2


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Li_D5_1


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Sp_D3_2


title: Gonad_HTE2_rep2


title: Gonad_LTE2_rep4


title: Gonad_LTE2_rep3


title: Gonad_LTE2_rep2


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Sp_D3_1


title: 535233A10

city: Addlestone

first: Helen

middle: Elizabeth

last: Everett

state: Surrey

address: New Haw

department: Virology

institute: Animal and Plant Health Agency (APHA)

description: sorted porcine PBMC

hyb_protocol: Hybridization was performed according to the NimbleGen array users guide v6 Chapter 3. See www.nimblegen.com.

scan_protocol: Scanning was performed at 2um using an Agilent array scanner.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization  and background correction as implemented in the Limma  package.

organism: Sus scrofa

label_protocol: Labeling was performed using a one-color labeleing kit (NimbleGen)

growth_protocol: primary porcine PBMC

extract_protocol: Rneasy Plus mini kt (Qiagen)

treatment_protocol: FACS with lineage-specific markers

value: CD1+ dendritic cells


title: 535233A11

description: sorted porcine PBMC

value: CD1- dendritic cells


title: 535233A12

description: sorted porcine PBMC

value: plasmocytoid DC


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Li_D3_1


title: 535233A09

description: sorted porcine PBMC

value: monocytes


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Li_D5_2


title: Gonad_LTE2_rep1


title: 04_S1_biological rep1.

city: Kyoto

first: Kentaro

last: Abe

state: Kyoto

address: Yoshidakonoe, Sakyo-ku

department: Graduate School of Biostudies, Department of Molecular and Systems Biology

institute: Kyoto University

description: Gene expression data from zebrafinch 60 days post hatch

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip Zebra Finch Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Robust Multichip analysis (RMA) using Affymetrix default analysis settings.

organism: Taeniopygia guttata

source_name: Forebrain of the finch 60 days post hatch

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Six zebrafinches were reared with or without male tutor form 30-60 days post hatch (dph).

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

treatment_protocol: Finches were quickly anesthetized with isoflurane and decapitated. Brains were rinsed with ice cold PBS and the right forebrain was placed on ice in the Trizol solution (Invitrogen).

value: Entire forebrain

tag: male tutor

value: no


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Sp_D5_1


title: 05_S2_biological rep2


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Sp_D5_1


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Li_D3_2


title: 06_S3_biological rep3.


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Sp_D5_2


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Li_D5_3


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Li_D3_3


title: 03_N3_biological rep3

value: yes


title: 535233A08

description: sorted porcine PBMC


title: 535233A06

description: sorted porcine PBMC


title: Total Tissue Samples, biological rep 2

city: Ribeirão Preto

first: Daniel

middle: Guimarães

last: Tiezzi

state: São Paulo

address: Av. Bandeirantes, 3900 - Monte Alegre

department: Gynecology and Obstetrics

country: Brazil

institute: Ribeirão Preto Medical School - University of São Paulo

description: Total RNA expression information acquired with Affymetrix Human Gene 2.0 ST Array chip and associated protocols.

hyb_protocol: We used the Affymetrix GeneChip Human Gene 2.0 ST array. Preparation of cRNA, hybridizations, washes and detection were done as recommended by the supplier.

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

data_processing: Expression data were analyzed by the Robust Multi-array Average method (RMA) in R using Bioconductor, oligo package and associated R packages.

source_name: human breast tumor

label_protocol: We used 50 ng total RNA and Ambion WT Expression Kit and  Affymetrix GeneChip Eukaryotic Poly-A RNA Control Kit according with the manufacturer protocol

extract_protocol: Total RNA was extracted from fresh cell sorted ALDEFLUOR-positive cells and frozen total tissue using Mirvana Kit (Thermo Fisher Scientific), according to the manufacturer's instructions.

treatment_protocol: We prospectively sampled breast tumors from patients prior to any systemic therapy , at the Hospital das Clínicas, in the city of Ribeirão Preto, Brazil. The local ethics committee in has approved the study with the protocol number: 2467/09. All the patients were informed of the objectives of the study and signed a free and informed consent document before their inclusion. One patient refused to be part of the study for religious reasons. All samples were obtained by percutaneous ultrasound-guided biopsy as a routine procedure in the hospital. One core fragment per patient was used in this study. The fragments were separated into halves. One group for purification of bCSC and the other used the total tissue for comparison.

tag: sample

value: Tissue sample of breast cancer patient

tag: tnm

tag: clinical stage

value: IV

tag: histological grade

tag: er status ihc

value: Negative

tag: pr status ihc

tag: her2 status

value: Positive


title: 535233A05

description: sorted porcine PBMC


title: 01_N2_biological rep2


title: Total Tissue Samples, biological rep 3

tag: age

value: IIA


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Li_D3_1

value: Microarray


title: 535233A03

description: sorted porcine PBMC


title: 01_N1_biological rep1.

tag: tissue


title: ALDH1+ flow sorted cells, biological rep 3

source_name: human breast tumor_ALDH1+

value: ALDH1+ cell population of breast cancer patient


title: Total Tissue Samples, biological rep 1


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Sp_D3_1


title: 535233A02

description: sorted porcine PBMC


title: 535233A04

description: sorted porcine PBMC


title: app1Δpah1Δdpp1Δlpp1Δ(QM)

first: Malathi

last: Srinivasan

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

institute: Central Food Technological Research Institute

description: Stationary Phase cells

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Platform Custom Saccharomyces cerevisiae 8x15k designed by Genotypic Technology Private Limited (AMADID: 016333) 600ng of cy3 labeled samples were  fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift ( Gene based Analysis was performed)

organism: Saccharomyces cerevisiae

source_name: Cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: synthetic minimal medium (SM) (6.7g/L of Yeast Nitrogen Base (Difco), 1.92 g/L of Yeast Synthetic Drop-out (Sigma) and 2% Dextrose

extract_protocol: Cells pelleted and washed. Finally resuspended in RNAlater until further use. RNA was extracted using the TRIzol (Invitrogen) method with glass beads (Sigma, 425-600um, Cat #G8772) for homogenization following the manufacturer's recommendations.

treatment_protocol: 24 h grown cells at 30 ˚C


title: 535233A01

description: sorted porcine PBMC


title: ALDH1+ flow sorted cells, biological rep 2


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Sp_D3_1


title: 535233A07

description: sorted porcine PBMC


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Sp_D3_3


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Li_D3_3


title: syncytiotrophoblast (ST) Replicate 4

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

country: France

institute: INSERM UMRS-1139

description:
Biological replicate 4 of 5. Syncytiotrophoblast vs placenta
amplfied RNA

hyb_protocol: The labeled cDNA mixtures were hybridized according to the protocol described at http://cmgm.stanford.edu/pbrown/protocols/index

scan_protocol: The arrays were immediately scanned using a GenePix 4000A confocal Scanner (Axon Instruments). Images were analyzed using GenePix pro 3 software

data_processing: A print-tip loess normalization of the microarray experiments was performed after the log-transformation of the background-corrected expression measurements

source_name: term placenta 4

label_protocol: Three micrograms of amplified RNA  (aRNA) was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit  (Amersham Biosciences)

growth_protocol: VCT were isolated from term placenta by trypsin and purified on percoll gradient, then plated onto  Petri dishes in DMEM/10% FBS, cultured for 12h (VCT) or 72h (ST). VCT/ST pellets were then snap-frozen and stored at -80°C until RNA extraction.

extract_protocol:
Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions
amplification protocol: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit  (Ambion)

tag: culture time

value: total placental extract


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Sp_D3_3


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Li_D5_1


title: syncytiotrophoblast (ST) Replicate 5

description:
Biological replicate 5 of 5. Syncytiotrophoblast vs placenta
amplfied RNA

source_name: term placenta 5


title: P (H2)

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

hyb_protocol: Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Scanning was performed with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (channels: Green, resolution: 3µm, TIFF: 20 bit)

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots and spots not significantly different from background (k=5) were flagged using the Agilent GeneSpring GX software (v.10.0.2). Probes were considered valid when corresponding spots remained present in at least 80% of the replicates of each experimental condition after the flagging procedure. Data were subsequently scale-normalized using the median value of each array.

source_name: High quality_eggs

label_protocol: 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop. 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array.

growth_protocol: For the experiment 16 egg batches obtained from cultured European seabass (with average weight of 3.24 kg ±1.2 SD) resulting from a standard protocol including female stimulation, artificial spawning, artificial fertilization and incubation of the embryos as follows.

extract_protocol: RNA was extracted from 16 egg batches collected using Tri-reagent as previously described for rainbow trout (Bonnet et al., 2007). A NanoDrop® NP-1000 spectrophotometer (NanoDrop technologies, Wilmington, DE, USA) was used to measure the quantity and quality of the RNA samples. The quality of the RNA samples was checked also using a 2100 Bioanalyzer (Agilent Technologies Inc. Santa Clara, USA), and samples with RIN value higher than 8.5 were used for further analysis.

treatment_protocol: During spawning season, female genital state was regularly controlled through the observation of an ovarian biopsy. Only females at postvitellogenic stage were chosen for further procedures and subject to intraperitoneally injection of LHRHa (D-Trp6, SIGMA) solution at a dose of 10 µg kg-1. After induction, females were individually kept  indoor in 1m3 tanks at a temperature of 12.9-13.5°C, salinity of 34.8-36.2 ppt , pH 7.9-8.1 and photoperiod 8/16 (light/dark). After ovulation occurring between 68 and 75 h following hormonal injection) the eggs from each female separately were stripped exhaustively into dry containers the time after stimulation and the total volume of the collected egg batch was recorded. Then eggs were dispatched into aliquots for different treatments. One portion of 500 µl (approx. 500 eggs) was deep frozen in duplicate in liquid nitrogen and stored at -80°C until molecular analysis. Batches of 5 ml of eggs were fertilized in triplicates with an aliquot of a large pool (n=20) cryopreserved sperm created to cover the needs for all the crosses in order to exclude possible paternal effect in the analysis of embryonic development course [33]. During fertilization the amount of sperm was always adjusted to 2 105 of spermatozoa per egg. Fertilization was performed with sea water as an activating solution.

value: eggs

tag: egg quality

value: High quality


title: Q (L7)

source_name: Low quality_eggs

value: Low quality


title: ALDH1+ flow sorted cells, biological rep 1


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D3_2


title: N (H3)


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Sp_D5_2


title: W303-1A

description: Stationary Phase cells


title: K (H7)


title: SK-NEP-1_2uM SKI-5C

city: suzhou

first: Jian

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

institute: Children's Hospital of Soochow University

description: [SKI](normalized)

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

source_name: SK-NEP-1_2uM SKI-5C

growth_protocol: SK-NEP-1  Human kidney (Wilm's Tumor) cell line obtained from the American Type Culture Collection (ATCC) was maintained in the Maccyo’5 (Life Technologies Inc., Gaithersburg, MD, USA) supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen Co., NY, USA) in a humidified incubator with 5% CO2 at 37℃. LBH589 (Cat: S1030 Selleck Chemicals, West Paterson, NJ, USA) was dissolved in DMSO (Cat: D4540 Sigma–Aldrich, St. Louis, MO, USA)

extract_protocol: Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v3.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

treatment_protocol: SK-NEP-1 cells were treated with 2uM SKI-5C and control group cells were treated with the same volume of DMSO 24 hours later.

value: human kidney (Wilm's Tumor) cell line

tag: treated with

value: 2uM SKI-5C


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Li_D5_3


title: syncytiotrophoblast (ST) Replicate 1

description:
Biological replicate 1 of 5. Syncytiotrophoblast vs placenta
amplfied RNA

source_name: term placenta 1


title: syncytiotrophoblast (ST) Replicate 3

description:
Biological replicate 3 of 5. Syncytiotrophoblast vs placenta
amplfied RNA

source_name: term placenta 3


title: syncytiotrophoblast (ST) Replicate 2

description:
Biological replicate 2 of 5. Syncytiotrophoblast vs placenta
amplfied RNA

source_name: term placenta 2


title: J (H1)


title: AW (L4)


title: SK-NEP-1_DMSO

description: [Blank](normalized)

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

value: DMSO


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Li_D3_1


title: AU (L6)


title: HT1080 MMC 0.1uM  r1

description: HT 1080 Human Fibrosarcoma Cell Line

source_name: ATCC CCL121 (HT-1080 Cells)

value: Fibrosarcoma


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Sp_D3_3


title: cytotrophoblast (VCT) Replicate 5

description:
Biological replicate 5 of 6. Cytotrophoblast vs placenta
amplfied RNA

value: primary-cultured mononucleated villous cytotrophoblast


title: cytotrophoblast (VCT) Replicate 4

description:
Biological replicate 4 of 6. Cytotrophoblast vs placenta
amplfied RNA


title: cytotrophoblast (VCT) Replicate 6

description:
Biological replicate 6 of 6. Cytotrophoblast vs placenta
amplfied RNA

source_name: term placenta 6


title: EBV_M_2015_1_MAVSKO_Mu_Mock_Sp_D5_1


title: AM (L3)


title: EBV_M_2015_1_MAVSKO_Mu_WTZEBOV_Li_D5_1


title: L (H6)


title: cytotrophoblast (VCT) Replicate 3

description:
Biological replicate 3 of 6. Cytotrophoblast vs placenta
amplfied RNA


title: cytotrophoblast (VCT) Replicate 2

description:
Biological replicate 2 of 6. Cytotrophoblast vs placenta
amplfied RNA


title: W1 (L2)


title: cytotrophoblast (VCT) Replicate 1

description:
Biological replicate 1 of 6. Cytotrophoblast vs placenta
amplfied RNA