title: HRSV at 12H, biological rep2

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: Divison of Molecular and Cell Biology

country: Singapore

institute: Nanyang Technological University

description:
Gene expression data from HRSV infected Hep2 12 hpi rep 2
Hep2_HRSV_12H-2

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.

source_name: HRSV infected Hep2 12 hpi

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM L929 (30%) cell condition media (Gibco) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 33˚C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C

treatment_protocol: The cells were infected with HRSV MOI=3 in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

value: Hep2 cells

tag: infected with

value: Human respiratory syncytial virus (HRSV)

value: 12 hr post infection


title: HRSV at 15H, biological rep1

status: Public on Dec 31 2016

type: RNA

description:
Gene expression data from HRSV infected Hep2 15 hpi rep 1
Hep2_HRSV_15H-1

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HRSV infected Hep2 15 hpi

tag: tissue

tag: time point

value: 15 hr post infection


title: HumanTumor_FreshFrozen_MET_CRC015

city: Durham

first: David

last: Hsu

state: NC

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

country: USA

institute: Duke University

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed using the R statistical platform with the Bioconductor affymetrix package [R version 2.13.1 (2011-07-08) and Bioconductor version 2.9].

source_name: human tumor, colorectal primary, metastasis, fresh frozen tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Human tumors were flash frozen in OCT at time of surgical resection. An initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca).

tag: primary tumor site

value: colorectal

tag: metastatic tumor site

value: Liver

tag: molecular subgroup

value: MSCC 6


title: HRSV at 12H, biological rep3

description:
Gene expression data from HRSV infected Hep2 12 hpi rep 3
Hep2_HRSV_12H-3


title: HRSV at 8H, biological rep2

description:
Gene expression data from HRSV infected Hep2 8 hpi rep 2
Hep2_HRSV_8H-2

source_name: HRSV infected Hep2 8 hpi

value: 8 hr post infection


title: HRSV at 15H, biological rep3

description:
Gene expression data from HRSV infected Hep2 15 hpi rep 3
Hep2_HRSV_15H-3


title: het-nox-rep.1

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) and analyzed with GenePix software V5.2 (MDS).

data_processing: Raw data was further processed using R (http://www.R-project.org)

organism: Mus musculus

source_name: lung homogenate

label_protocol: Purified total RNA was amplified and Cy-labeled using the single-color QuickAmp kit (Agilent Technologies, Palo Alto, CA) following the kit instructions.

growth_protocol: Mice were grown under standard conditions with unlimited supply of food and water.

extract_protocol: RNA was isolated by using miRNeasy Mini Kit (Qiagen, Cat. No. 217004), RNA was eluted with RNAse-free water at the last step of the protocol, concentration was measured by nanodrop, RNA was stored at -80°C.

treatment_protocol: WT vs Fgf10+/- pups of the hyperoxia group were treated from P0-P3 with 85% oxygen in a chamber

tag: age

tag: genotype/variation


title: HRSV at 12H, biological rep1

description:
Gene expression data from HRSV infected Hep2 12 hpi rep 1
Hep2_HRSV_12H-1


title: wt-hyx-repl.6

source_name: alveolar epithelial type II cells

value: wild-type


title: het-hyx-rep.2


title: HumanTumor_FreshFrozen_MET_CRC002D


title: het-hyx-rep.3


title: het-hyx-repl.2


title: het-hyx-rep.1


title: wt-hyx-rep.2


title: wt-hyx-repl.3


title: wt-hyx-repl.4


title: wt-hyx-repl.5


title: wt-hyx-repl.2


title: het-hyx-repl.1


title: wt-hyx-rep.3


title: HRSV at 15H, biological rep2

description:
Gene expression data from HRSV infected Hep2 15 hpi rep 2
Hep2_HRSV_15H-2


title: HRSV at 4H, biological rep2

description:
Gene expression data from HRSV infected Hep2 4 hpi rep 2
Hep2_HRSV_4H-2

source_name: HRSV infected Hep2 4 hpi

value: 4 hr post infection


title: het-nox-repl.4


title: HumanTumor_FreshFrozen_MET_CRC007A

value: MSCC 4


title: wt-nox-repl.4


title: wt-hyx-rep.1


title: shiyan20

city: beijing

first: zhang

last: suwei

address: changping

country: China

institute: capitalbio

description: RNA from tumor tissues of patients with  metastatic TSCC

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

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

treatment_protocol: Paired primary tumor tissues were obtained from patients with metastatic and non-metastatic TSCC. The tumor tissues were obtained from surgical excision. All tissues were snap-frozen in liquid  nitrogenat at -80C until use.

value: metastatic tumor tissue


title: HRSV at 8H, biological rep3

description:
Gene expression data from HRSV infected Hep2 8 hpi rep 3
Hep2_HRSV_8H-3


title: HRSV at 8H, biological rep1

description:
Gene expression data from HRSV infected Hep2 8 hpi rep 1
Hep2_HRSV_8H-1


title: HRSV at 4H, biological rep3

description:
Gene expression data from HRSV infected Hep2 4 hpi rep 3
Hep2_HRSV_4H-3


title: HRSV at 4H, biological rep1

description:
Gene expression data from HRSV infected Hep2 4 hpi rep 1
Hep2_HRSV_4H-1


title: HRSV at 0H, biological rep3

description:
Gene expression data from mock infected Hep2 rep 3
Hep2_HRSV_0H-3

source_name: Mock infected Hep2


title: wt-nox-repl.3


title: wt-hyx-repl.1


title: HRSV at 0H, biological rep2

description:
Gene expression data from mock infected Hep2 rep 2
Hep2_HRSV_0H-2


title: het-nox-repl.3


title: het-nox-repl.2


title: 6h_plus_TGF_B

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

description:
CD34+CD45Rahi cells cultured for 48 with GM-CSF, FL, SCF and TNFa before addition of TGFbeta at timepoint 0h
Gene expression data from human Langerhans cell progenitors

hyb_protocol: 5 µg of biotinylated DNA were hybridized to U133 Plus 2.0 GeneChips overnight, followed by washing and staining procedures, and scanning, following Affymetrix protocols.

data_processing: For generation of probe set expression values, CEL files containing probe level data were normalized using RMA (Affymetrix Expression Console).

label_protocol: RNA samples were processed and hybridised to Affymetrix U133 Plus 2.0 GeneChips according to the manufacturer's protocols.

growth_protocol: Human CD34+CD45Rahi hematopoietic progenitor cells were cultured for 2 days in GM-CSF, FLT3L, SCF and TNFa before TGFbeta was added or not

extract_protocol: Total RNA was extracted with RNeasy micro kit (Qiagen) according to the manufacturer’s instruction. Concentration and integrity of total RNA were determined by spectrophotometry (Nanodrop) and Experion automated electrophoresis system (Biorad, Munich, Germany).

treatment_protocol: TGFbeta was added for 6h and 24h

tag: tissue origin

value: human cord blood

tag: cell type

value: CD34+ progenitors


title: MB231-Control-1

city: Yilan

first: Chen-Hung

last: Ting

state: Taiwan

address: 23-10 Dawen Rd., Jiaoxi

department: Marine research station, Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression after 6hr in mock-treated control cells

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: Malignant breast cancer cell MDA-MB-231, mock treatment, 6h, exp1

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: MDA-MB-231 cells were maintained in Leibovitz’s L-15 medium supplemented with 2mM L-glutamine, 10% FBS, and antibiotics (100U/mL penicillin G and 100 g/mL streptomycin) at 37°C with 0% CO2 in a humidified incubator. HDFs were cultured in fibroblast growth medium (medium 106 wit hgrowth supplement) at 37°C with 5% CO2 in a humidified incubator.

extract_protocol: RNA was extracted by using the WelPrep cell/tissue RNA lit (WelGene biotech) following the manufacturer's standard protocol.  Total RNA was quantified by a specterophotometer (NanoDrop ND-1000, Thermo Scientific) and  quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies). The RIN values for all RNA samples were between 9.0-10.0.

treatment_protocol: TP4 was dissolved in ddH2O at a stock concentration for 1mg/mL. The cells were plated 1 day before treatment with TP4 (14 ug/mL) and harvested after 6 hours.

tag: cell line

value: mammary gland

tag: gender

value: female


title: wt-nox-repl.1


title: MB231-Control-2

source_name: Malignant breast cancer cell MDA-MB-231, mock treatment, 6h, exp2


title: e19_expression

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

country: Poland

institute: Gdansk University of Technology

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of skins collected from embryos at day 19 of the C57BL/6J mouse

hyb_protocol: Probe labeling and hybridization was performed with Roche NimbleGen kit using the standard protocol for eukaryotic RNA samples and NimbleGen mouse gene expression 12x135K array (Roche, cat. no. 05543797001). The cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit (Roche, cat. no. 06370411001), and hybridized to slides using a NimbleGen hybridization system (Roche, cat. no. 05583683001).

scan_protocol: The slides were scanned using MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.

data_processing: The data from scanned images were processed and normalized using a robust multi-chip average (RMA) algorithm using DEVA 1.0.2 software with default settings (Roche)

source_name: Transcriptomic profiling in the dorsal skin tissue of embryos at day 19 of the C57BL/6J mouse

label_protocol: First strand cDNA synthesis was performed with Maxima Reverse Transcriptase (ThermoScientificBio. cat. no. EP0742) using 3 µg of total RNA, 400 U of the Maxima Reverse Transcriptase (200 U/ul), 5 x reaction buffer (250 mM Tris-HCl, 375 mM KCl, 15 mM MgCl, 50 mM DTT) and oligo dT15.(200 pmoles) in a total volume of 40 µl. Second strand cDNA was synthesized using cDNA Synthesis System (Roche, cat. no. 11 117 831 001) according to the second strand synthesis manufacturer's protocol.

extract_protocol: Total RNAs was purified using the RNeasy Mini Kit (QIAGEN. cat. no. 74104) coupled with on-column DNA digestion following the manufacturer’s protocols.

treatment_protocol: Dorsal skin tissue samples from C57BL/6J mouse strain at different stages of development were prepared in the Tri-City's Academic Animal Experiment Centre of the Medical University of Gdańsk. All tissues were collected in RNAlater stabilization reagent (QIAGEN. cat. no. 76104), transported on dry ice and stored at -80o C.

tag: strain

value: dorsal skin

tag: developmental stage

value: embryo

value: day 19


title: het-nox-repl.1


title: wt-nox-repl.2


title: 6h_minus_TGF_A

scan_protocol: 5 µg of biotinylated DNA were hybridized to U133 Plus 2.0 GeneChips overnight, followed by washing and staining procedures, and scanning, following Affymetrix protocols.


title: 24h_minus_TGF_B


title: HRSV at 0H, biological rep1

description:
Gene expression data from mock infected Hep2 rep 1
Hep2_HRSV_0H-1

value: Hep2 cells


title: MB231-TP4-2

description: Gene expression after 6hr in TP4-treated cells

source_name: Malignant breast cancer cell MDA-MB-231, 14ug/mL TP4, 6h, exp2


title: Fibroblast-Control-2

source_name: Human dermal fibroblast (HDF), mock treatment, 6h, exp2

value: HDF

value: skin


title: 24h_plus_TGF_A


title: 6h_minus_TGF_B


title: 0h_B


title: e16_expression

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of skins collected from embryos at day 16 of the C57BL/6J mouse

source_name: Transcriptomic profiling in the dorsal skin tissue of embryos at day 16 of the C57BL/6J mouse

value: day 16


title: e18_expression

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of skins collected from embryos at day 18 of the C57BL/6J mouse

source_name: Transcriptomic profiling in the dorsal skin tissue of embryos at day 18 of the C57BL/6J mouse

value: day 18


title: 0h_A


title: 6h_plus_TGF_A


title: 24h_minus_TGF_A


title: Cross_5_leaf_multiple

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

description: HB vs LB - leaf+1 - 7 months (Progenies from the cross T3)

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: standard Agilent Feature Extraction protocol

organism: Saccharum hybrid cultivar (mixed)

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

growth_protocol: CCA/UFSCar - Araras

extract_protocol: Trizol Invitrogen

treatment_protocol: CRT3: cross T3; C1: collection 1 (7 months of growth); L1: leaf +1; R1: biological replicate 1; HB: high brix. Leaf +1 pool from 5 progenies in T3 phase (7 months old) with the highest brix values among the population.

tag: phenotype

value: high brix

value: leaves

tag: variety

value: progenies from the T3 phase

tag: collect

treatment_protocol: NO

value: low brix


title: 24h_plus_TGF_B


title: Cross_5_leaf_714vs710

description: HPvsLP-Leaf+1-7 months (Genotypes Cross T3: 710vs714)

extract_protocol: trizol invitrogen

treatment_protocol: CR2: cross 2; C2: collection 2 (photosynthesis-7 months of growth); L1: leaf +1; R1: biological replicate 1; R2: biological replicate 2; HP: high photosynthesis. eaf +1 from genotypes 714 (LP)vs Leaf +1 from genotypes 710 (HP)

value: high photosynthesis

value: Genotypes 714 (LP) and 710 (HP) from Cross T3 (multiple crossing

value: low photosynthesis


title: MB231-TP4-1

source_name: Malignant breast cancer cell MDA-MB-231, 14ug/mL TP4, 6h, exp1

value: mammary gland


title: Cross_5_internode_multiple_sw

description: HB vs LB - Internode 1 - 7 months (Progenies from the cross T3) - biological replicate

treatment_protocol: CRT3: cross T3; C1: collection 1 (7 months of growth); In1: internode 1; R2: biological replicate 2; HB: high brix. Internode 1 pool from 5 progenies in T3 phase (7 months old) with the highest brix values among the population

value: internodes


title: adult_expression

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of skins collected from 3-months old mice of the C57BL/6J strain

source_name: Transcriptomic profiling in the dorsal skin tissue of  the C57BL/6J 3 months old mouse

value: dorsal skin

value: adult

value: 3 months


title: Cross_5_leaf_714vs710_sw


title: Fibroblast-Control-1

source_name: Human dermal fibroblast (HDF), mock treatment, 6h, exp1

value: female


title: Cross_5_leaf_multiple_sw

description: HB vs LB - leaf+1 - 7 months (Progenies from the cross T3) - biological replicate

treatment_protocol: CRT3: cross T3; C1: collection 1 (7 months of growth); L1: leaf +1; R2: biological replicate 2; HB: high brix. Leaf +1 pool from 5 progenies in T3 phase (7 months old) with the highest brix values among the population.


title: Heat stress treatment for 6h, biological rep2 [sad1 2R]

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 6h

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 6h, biological rep3 [sad1 3R]

source_name: Arabidopsis sad1 seedling after heat stress for 6h

tag: tissue


title: Heat stress treatment for 6h, biological rep1 [sad1 1R]


title: Heat stress treatment for 2h, biological rep3 [sad1 3R]

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


title: e15_expression

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of skins collected from embryos at day 15 of the C57BL/6J mouse

source_name: Transcriptomic profiling in the dorsal skin tissue of embryos at day 15 of the C57BL/6J mouse

value: embryo

value: day 15


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

source_name: Arabidopsis sad1 seedling after heat stress for 2h


title: Cross_5_internode_mutiple

description: HB vs LB - Internode 1 - 7 months (Progenies from the cross T3)

treatment_protocol: CRT3: cross T3; C1: collection 1 (7 months of growth); In1: internode 1; R1: biological replicate 1; HB: high brix. Internode 1 pool from 5 progenies in T3 phase (7 months old) with the highest brix values among the population

value: high brix


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


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

description: Gene expression data from Arabidopsis sad1 seedling

source_name: Arabidopsis sad1 seedling

value: Control


title: Cross_4_leaf_553vs669_sw

description: LPxHP -Leaf+1-7 months - genotypes from crossing 4

treatment_protocol: CR4: cross 4; C2: collection 2 (7 months of growth); L1: leaf +1; R1: biological replicate 1; R2: biological replicate 2; R3: biological replicate 3; R4: biological replicate 4; LP: low photosynthesis; HP:high photosynthesis. Leaf +1 from genotype 669(7 m

value: Genotypes F1 from the cross4:RB855002 x RB855035.


title: Gastric tumor tissue KS_293_T

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

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: M

tag: location

value: body

tag: lauren classification

value: intestinal

tag: ajcc stage

value: Gastric tumor tissue


title: Gastric tumor tissue KS_289_T

value: F

tag: age

value: antrum


title: Cross_4_leaf_553vs669

value: high photosynthesis

value: low photosynthesis


title: Gastric tumor tissue KS_255_T

tag: gender


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


title: Fibroblast-TP4-2

source_name: Human dermal fibroblast (HDF), 14ug/mL TP4, 6h, exp2

tag: cell line

value: HDF

value: skin

value: female


title: Cross_4_leaf_RB855002 x RB855035_sw

description: HB vs LB - Leaf+1 - 7 months (Progenies from the cross 4, RB855002 x RB855035) - biological replicate

treatment_protocol: CR4: cross 4; C1: collection 1 (7 months of growth); L1: leaf +1; R2: biological replicate 2; HB: high brix. Leaf +1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population

value: leaves

value: progenies F1 from the cross RB855002 x RB855035

value: low brix


title: Cros_4_internode_RB855002 x RB855035_sw

description: HB vs LB - Internode 1 - 7 months (Progenies from the cross 4, RB855002 x RB855035) - biological replicate

treatment_protocol: CR4: cross 4; C1: collection 1 (7 months of growth); In1: Internode 1; R2: biological replicate 2; HB: high brix. Internode 1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population

value: high brix

value: internodes

value: progenies F1 from the cross 4 (RB855002 x RB855035)


title: Cross_4_leaf_RB855002 x RB855035

description: HB vs LB - Leaf+1 - 7 months (Progenies from the cross 4, RB855002 x RB855035)

treatment_protocol: CR4: cross 4; C1: collection 1 (7 months of growth); L1: leaf +1; R1: biological replicate 1; HB: high brix. Leaf +1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population


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

value: Ten-day-old seedling

value: Control


title: Fibroblast-TP4-1

description: Gene expression after 6hr in TP4-treated cells

source_name: Human dermal fibroblast (HDF), 14ug/mL TP4, 6h, exp1


title: Gastric tumor tissue KS_225_T

value: GC

value: M

value: mixed


title: Gastric tumor tissue KS_259_T

value: body

value: Gastric tumor tissue


title: Gastric tumor tissue KS_285_T

value: F

value: fundus


title: Cross_3_321vs318_sw

description: LP x HP

extract_protocol: trizol

treatment_protocol: CR3: cross 3; C2: collection 2 (7 months of growth); L1: leaf +1; R1: biological replicate 1; R2: biological replicate 2;R3: biological replicate 3; R4: biological replicate 4; HP: photosynthesis. Leaf +1 from genotype 127(7 months old) with the highest p

value: high photosynthesis

value: genotype 321x318, progenies F1 from the cross SP80-3280 x RB8551

value: low photosynthesis


title: PC-9

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

description: Gene expression in

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565CA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (ｖ10.7.3.1) was used for background subtraction.

label_protocol: Cy3 label: Total RNA (50 ng) was labeled with Cy3 using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: PC-9 cells were grown in RPMI-1640 medium (Wako) supplemented with 10% fetal bovine serum (Invitrogen), 100 units/ml penicillin, and 100 μg/ml streptomycin (Wako) at 37C in a 5% CO2 humidified chamber.

extract_protocol: Total RNA was extracted from cells using a TRI Reagent (MRC) according to the manufacturer’s instructions

treatment_protocol: PC-9 cells were subjected to a long-term exposure of gefitinib, whose dosage was increased in a stepwise manner; i.e., cells were treated in 0.01, 0.1, and 1µM of gefitinib for each one month. The resultant (surviving) cells after 1µM-gefitinib treatment were used as gefitinib-resistant cells.

tag: cell type

value: non-small cell lung cancer

value: Gefitinib sensitive


title: PC-9GR

description: Gene expression in

tag: phenotype

value: Gefitinib resistant


title: Gastric tumor tissue KS_287_T

value: antrum

value: diffuse


title: Gastric tumor tissue KS_297_T


title: SLCs replicate 3

city: Barcelone

first: Carolina

middle: Mercedes

last: Barra

address: Aiguader 88

country: Spain

institute: IMIM

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent). The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Sinusoid lining cells (SLCs)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit version 6.5 – Agilent 5190-2305 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.

extract_protocol: High Pure RNA Isolation Kit (Roche)

value: Sinusoid lining cells (SLCs)


title: Gastric tumor tissue KS_281_T


title: SLCs replicate 4


title: Cross_4_internode_RB855002 x RB855035

description: HB vs LB - Internode 1 - 7 months (Progenies from the cross 4, RB855002 x RB855035)

treatment_protocol: CR4: cross 4; C1: collection 1 (7 months of growth); In1: Internode 1; R1: biological replicate 1; HB: high brix. Internode 1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population

value: high brix

value: internodes

tag: variety

value: progenies F1 from the cross 4 (RB855002 x RB855035)

value: low brix


title: SLCs replicate 1


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

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

value: Ten-day-old seedling

value: heat stress


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

source_name: Arabidopsis WT seedling after heat stress for 6h


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


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

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


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

source_name: Arabidopsis WT seedling after heat stress for 2h


title: SLCs replicate 2


title: Cross_3_leaf_321vs318

description: LP vs HP

value: leaves

tag: collect


title: Macrophages replicate 3

source_name: Splenic macrophages

value: Splenic macrophages


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

description: Gene expression data from Arabidopsis WT seedling

source_name: Arabidopsis WT seedling

tag: ecotype

value: Control


title: Gastric tumor tissue KS_275_T

value: GC

value: M

value: body

value: intestinal

value: Gastric tumor tissue


title: Macrophages replicate 4


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

tag: protocol


title: Macrophages replicate 2


title: Macrophages replicate 1


title: Cross_3_leaf_SP80-3280 x RB855156_sw

description: HB vs LB - Leaf+1 - 7 months (Progenies from the cross 3, SP80-3280 x RB855156) - biological replicate

treatment_protocol: CR3: cross 3; C1: collection 1 (7 months of growth); L1: leaf +1; R2: biological replicate 2; HB: high brix. Leaf +1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population

value: progenies F1 from the cross SP80-3280 x RB855156


title: HUVECs replicate 3

source_name: HUVECs

value: HUVECs


title: Cross_3_leaf_SP80-3280 x RB855156

description: HB vs LB - Leaf+1 - 7 months (Progenies from the cross 3, SP80-3280 x RB855156)

extract_protocol: Trizol-Invitrogen

treatment_protocol: CR3: cross 3; C1: collection 1 (7 months of growth); L1: leaf +1; R1: biological replicate 1; HB: high brix. Leaf +1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population


title: Gastric tumor tissue KS_267_T


title: HUVECs replicate 1


title: HUVECs replicate 4


title: Gastric tumor tissue KS_231_T

value: fundus


title: Cross_3_internode_SP80-3280 x RB855156_sw

description: HB vs LB - Internode 1 - 7 months (Progenies from the cross 3, SP80-3280 x RB855156) - biological replicate

treatment_protocol: CR3: cross 3; C1: collection 1 (7 months of growth); In1: internode 1; R2: biological replicate 2; HB: high brix. Internode 1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population

value: high brix


title: Cross_2_leaf_153vs238

description: HP vs LH

treatment_protocol: CR2: cross 2; C2: collection 2 (photosynthesis-7 months of growth); L1: leaf +1; R1: biological replicate 1; R2: biological replicate 2; HP: high photosynthesis. Leaf +1 from genotypes 238 (HP)

value: high photosynthesis

value: Genotypes 153 (LP) and 238 (HP) from Cross 2 (SP70-1143 x RB9252

value: low photosynthesis


title: Cross_2_238vs153_sw

description: LP vs HP


title: Gastric tumor tissue KS_253_T


title: HUVECs replicate 2


title: Gastric tumor tissue KS_265_T

value: antrum


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

value: Ten-day-old seedling

tag: timpe point


title: Cross_3_internode_SP80-3280 x RB855156

description: HB vs LB - Internode 1 - 7 months (Progenies from the cross 3, SP80-3280 x RB855156)

treatment_protocol: CR3: cross 3; C1: collection 1 (7 months of growth); In1: internode 1; R1: biological replicate 1; HB: high brix. Internode 1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population

tag: tissue

value: internodes

value: low brix


title: Gastric tumor tissue KS_271_T

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


title: Cross_2_leaf_SP70-1143 x RB925211

description: HB vs LB - Leaf +1 - 7 months (Progenies from the cross 2, SP70-1143 x RB925211)

treatment_protocol: CR2: cross 2; C1: collection 1 (7 months of growth); L1: leaf +1; R1: biological replicate 1; HB: high brix. Leaf +1 pool from 10 genotypes (7 months old) with the highest brix values among the population.

value: leaves

value: progenies Cross 2

treatment_protocol: NO


title: Gastric tumor tissue KS_163_T

tag: patient

value: GC

value: F


title: Cross_2_leaf_sw_SP70-1143 x RB925211

description: HB vs LB - Leaf +1 - 7 months (Progenies from the cross 2, SP70-1143 x RB925211) - biological replicate

treatment_protocol: CR2: cross 2; C1: collection 1 (7 months of growth); L1: leaf +1; R2: biological replicate 2; HB: high brix. Leaf +1 pool from 10 genotypes (7 months old) with the highest brix values among the population.


title: R_GPRC5A_si_45min_rep1_array7

city: Helsinki

first: Daria

last: Bulanova

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

description:
GPRC5A; RNAi by siRNA, 45 min of adhesion, replica 1/2
si_Control_45_1+si_GPRC5A_25_45_1.txt: Cy5

hyb_protocol: Combined control and GPRC5A-depleted samples were mixed with blocking agent, fragmentation- and hybridization buffer, and were hybridized to Agilent SurePrint G3 Human GE 8 x 60K Microarrays for 17 hours at 65°C. Microarrays were washed

scan_protocol: Scanned with Agilent Scanner G2505C

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for image analysis.

source_name: HeLa cells, GPRC5A, 45 min

label_protocol: 100 ng of total RNA was primed using oligo-dT(T7) promoter primers and converted to cDNA with  AffinityScript RNase Block (mix of enzymes, Agilent). Primed cDNA was amplified and labeled using fluorescently labeled dNTP-nucleotides (Cy3 and Cy5) and T7 RNA Polymerase.  Clean-up of labeled and amplified samples was performed by using Qiagen´s RNeasy mini spin columns. RNA Spike-In Kit was used to monitor the success of the labeling.

growth_protocol: HeLa cells were cultured in standard conditions after RNAi. Cells were staved in serum-free DMEM overnight prior to experiment.

extract_protocol: Total RNA was extracted using NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) following manufacturer's instructions

treatment_protocol: After starvation, cells were trypsinized, suspended in serum-free DMEM, washed in serum-free DMEM twice, and 2E106 cells in 10 ml of serum-free DMEM were plated on top of 10% Matrigel-coated dishes for indicated time.

value: HeLa

tag: RNAi construct

value: GPRC5A siRNA


title: Cross_2_Internode_SP70-1143 x RB925211_sw

description: HB vs LB - Internode 1 - 7 months (Progenies from cross 2 SP70-1143 x RB925211) - biological replicate

treatment_protocol: CR2: cross 2; C1: collection 1 (7 months of growth); In1: internode 1; R2: biological replicate 2; HB: high brix. Internode 1 pool from 10 genotypes (7 months old) with the highest brix values among the population


title: Gastric tumor tissue KS_157_T

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: tumor type

value: M

tag: location

value: Gastric tumor tissue


title: R_GPRC5A_si_45min_rep2_array8

description:
GPRC5A; RNAi by siRNA, 45 min of adhesion, replica 2/2
si_Control_45_2+si_GPRC5A_25_45_2.txt: Cy5


title: HCC patient 99

first: Yu

last: Wang

address: 11 Hospital Drive

institute: National University of Singapore

description:
Two-color Tumor versus non-tumor,
ch1 raw data file: *_1b.txt, ch2 raw data file: *_2b.txt

hyb_protocol: Sample labeling was performed according to the undisclosed miRXploreTM user manual. Subsequently, the fluorescently labeled samples were hybridized overnight to miRXploreTM Microarrays using the a-HybTM Hybridization Station.

scan_protocol: Fluorescence signals of the hybridized miRXploreTM Microarrays were detected using a laser scanner from Agilent (Agilent Technologies).

data_processing: Mean signal and mean local background intensities were obtained for each spot of the microarray images using the ImaGeneâ software (Biodiscovery). Low-quality spots were flagged and excluded from data analysis. Unflagged spots were analysed with the PIQORTM Analyzer software. The PIQOR Analyzer allows automated data processing of the raw data text files derived from the ImaGene software. This includes background subtraction to obtain the net signal intensity, data normalization, and calculation of the Hy5/Hy3 ratios for the species of interest. As an additional quality filtering step, only spots/genes are taken into account for the calculation of the Hy5/Hy3 ratio that have a signal that is equal or higher than the 50% percentile of the background signal intensities.

source_name: Non-tumorous tissue from HCC patient 99

label_protocol: Non-tumor samples were labelled Hy-3 and Tumor samples were labelled Hy-5

extract_protocol: The microRNA microarray profiling were performed by certified Miltenyi Biotec microarray servicing facility in Germany and normalized ratios of tumor vs paired adjacent non-tumor samples were returned to us for further analysis.Total RNA were extracted from HCC patient tissues and assess for quality using Agilent  2100 Bioanalyzer. RNA from paired samples with RIN>6 were subjected for microarray profiling

tag: tissue type

value: Non-tumor

source_name: Tumor tissue from HCC patient 99

value: Tumor


title: HCC patient 100

source_name: Non-tumorous tissue from HCC patient 100

source_name: Tumor tissue from HCC patient 100


title: HCC patient 98

source_name: Non-tumorous tissue from HCC patient 98

source_name: Tumor tissue from HCC patient 98


title: Cross_2_internode_SP70-1143 x RB925211

description: HB vs LB - Internode 1 - 7 months (Progenies from cross 2 SP70-1143 x RB925211)

treatment_protocol: CR2: cross 2; C1: collection 1 (7 months of growth); In1: internode 1; R1: biological replicate 1; HB: high brix. Internode 1 pool from 10 genotypes (7 months old) with the highest brix values among the population

value: high brix


title: Cross_1_leaf_127vs128_sw

description: LP x HP

treatment_protocol: CR1: cross 1; C1: collection 1 (7 months of growth); L1: leaf +1; R1: biological replicate 1; R2: biological replicate 2;4: biological replicate 4; HP: photosynthesis. Leaf +1 from genotype 127(7 months old) with the highest photosynthesis value.128: geno

value: high photosynthesis

value: progenies F1 from the cross SP83-2847 x TUC71-7.

extract_protocol: trizol sugarcane


title: HCC patient 97

source_name: Non-tumorous tissue from HCC patient 97

source_name: Tumor tissue from HCC patient 97


title: Gastric tumor tissue KS_135_T

source_name: Gastric tumor tissue

tag: age

value: body

tag: lauren classification

value: intestinal

tag: ajcc stage


title: R_GPRC5A_si_6h_rep2_array6

description:
GPRC5A; RNAi by siRNA, 6 h of adhesion, replica 2/2
si_Control_6h_2+si_GPRC5A_25_6h_2.txt: Cy5

source_name: HeLa cells, GPRC5A, 6 h

tag: cell line


title: R_GPRC5A_sh_6h_rep2_array4

description:
GPRC5A; RNAi by shRNA, 6 h of adhesion, replica 2/2
sh_Control_6h_2+sh_GPRC5A_628_6h_2.txt: Cy5

value: GPRC5A shRNA


title: R_GPRC5A_si_6h_rep1_array5

description:
GPRC5A; RNAi by siRNA, 6 h of adhesion, replica 1/2
si_Control_6h_1+si_GPRC5A_25_6h_1.txt: Cy5


title: R_GPRC5A_sh_6h_rep1_array3

description:
GPRC5A; RNAi by shRNA, 6 h of adhesion, replica 1/2
sh_Control_6h_1+sh_GPRC5A_628_6h_1.txt: Cy5


title: Gastric tumor tissue KS_139_T

tag: gender

value: antrum

value: diffuse


title: Cross_1_leaf_127vs128

description: LP vs HP

tag: phenotype

value: leaves

tag: variety

value: low photosynthesis


title: R_GPRC5A_sh_45min_rep2_array2

description:
GPRC5A; RNAi by shRNA, 45 min of adhesion, replica 2/2
sh_Control_45_2+sh_GPRC5A_628_45_2.txt: Cy5


title: Gastric tumor tissue KS_203_T

value: GC

value: F


title: HCC patient 96

source_name: Non-tumorous tissue from HCC patient 96

source_name: Tumor tissue from HCC patient 96


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

description: Gene expression data from Arabidopsis WT seedling

tag: ecotype

value: Ten-day-old seedling

value: Control


title: Cross_1_internode_SP83-2847 x TUC71-7_sw

description: HB vs LB - Internode 1 - 7 months (Progenies from cross 1 SP83-2847 x TUC71-7) - biological replicate

treatment_protocol: CR1: cross 1; C1: collection 1 (7 months of growth); In1: internode 1; R2: biological replicate 2; HB: high brix. Internode 1 pool from 10 genotypes (7 months old) with the highest brix values among the population

value: internodes

value: progenies Cross 1

tag: collect

value: low brix

value: internodes 1


title: Gastric tumor tissue KS_091_T

value: M

value: Gastric tumor tissue


title: Gastric tumor tissue KS_173_T


title: HCC patient 95

source_name: Non-tumorous tissue from HCC patient 95

value: Non-tumor

source_name: Tumor tissue from HCC patient 95

value: Tumor


title: HCC patient 92

source_name: Non-tumorous tissue from HCC patient 92

source_name: Tumor tissue from HCC patient 92


title: HCC patient 94

source_name: Non-tumorous tissue from HCC patient 94

source_name: Tumor tissue from HCC patient 94


title: HCC patient 91

source_name: Non-tumorous tissue from HCC patient 91

source_name: Tumor tissue from HCC patient 91


title: HCC patient 93

source_name: Non-tumorous tissue from HCC patient 93

source_name: Tumor tissue from HCC patient 93


title: Cross_1_leaf_SP83-2847 x TUC71-7_sw

description: HB vs LB - Leaf+1 - 7 months (Progenies from the cross 1, SP83-2847 x TUC71-7) - biological replicate

treatment_protocol: CR1: cross 1; C1: collection 1 (7 months of growth); L1: leaf +1; R2: biological replicate 2; HB: high brix. Leaf +1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population

value: high brix

value: progenies F1 from the cross SP83-2847 x TUC71-7


title: Cross_1_leaf_SP83-2847 x TUC71-7

description: HB vs LB - Leaf+1 - 7 months (Progenies from the cross 1, SP83-2847 x TUC71-7)

treatment_protocol: CR1: cross 1; C1: collection 1 (7 months of growth); L1: leaf +1; R1: biological replicate 1; HB: high brix. Leaf +1 pool from 10 progenies F1 (7 months old) with the highest brix values among the population


title: HCC patient 89

source_name: Non-tumorous tissue from HCC patient 89

source_name: Tumor tissue from HCC patient 89


title: R_GPRC5A_sh_45min_rep1_array1

description:
GPRC5A; RNAi by shRNA, 45 min of adhesion, replica 1/2
sh_Control_45_1+sh_GPRC5A_628_45_1.txt: Cy5

source_name: HeLa cells, GPRC5A, 45 min

value: HeLa

value: GPRC5A shRNA


title: HCC patient 88

source_name: Non-tumorous tissue from HCC patient 88

source_name: Tumor tissue from HCC patient 88


title: Gastric tumor tissue KS_155_T

source_name: Gastric tumor tissue

value: antrum


title: Gastric tumor tissue KS_115_T

value: GC

value: fundus

value: intestinal


title: G_Control_si_6h_rep2_array6

description:
Control; RNAi by siRNA, 6 h of adhesion, replica 2/2
si_Control_6h_2+si_GPRC5A_25_6h_2.txt: Cy3

source_name: HeLa cells, Control, 6 h

value: non-targeting siRNA


title: Gastric tumor tissue KS_049_T


title: HCC patient 90

source_name: Non-tumorous tissue from HCC patient 90

source_name: Tumor tissue from HCC patient 90


title: G_Control_si_45min_rep1_array7

description:
Control; RNAi by siRNA, 45 min of adhesion, replica 1/2
si_Control_45_1+si_GPRC5A_25_45_1.txt: Cy3

source_name: HeLa cells, Control, 45 min


title: Gastric tumor tissue KS_123_T


title: G_Control_si_6h_rep1_array5

description:
Control; RNAi by siRNA, 6 h of adhesion, replica 1/2
si_Control_6h_1+si_GPRC5A_25_6h_1.txt: Cy3


title: induced sputum_healthy control_rep20

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_healthy control

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.

source_name: induced sputum_healthy control

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

value: male

tag: oral corticosteroid use

value: no


title: Cross_1_internode_SP83-2847  x TUC71-7

description: HB vs LB - Internode 1 - 7 months (Progenies from cross 1 SP83-2847  x TUC71-7)

treatment_protocol: CR1: cross 1; C1: collection 1 (7 months of growth); In1: internode 1; R1: biological replicate 1; HB: high brix. Internode 1 pool from 10 genotypes (7 months old) with the highest brix values among the population

tag: tissue

value: internodes

value: progenies Cross 1

value: low brix


title: induced sputum_healthy control_rep21

description: induced sputum_healthy control

value: female


title: induced sputum_healthy control_rep16

description: induced sputum_healthy control


title: Gastric tumor tissue KS_047_T

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

value: M

value: Gastric tumor tissue


title: induced sputum_healthy control_rep19

description: induced sputum_healthy control


title: Gastric tumor tissue KS_167_T

tag: patient

value: F

value: entire

value: diffuse


title: G_Control_si_45min_rep2_array8

description:
Control; RNAi by siRNA, 45 min of adhesion, replica 2/2
si_Control_45_2+si_GPRC5A_25_45_2.txt: Cy3

value: HeLa

tag: RNAi construct


title: MeDIP_Heart, C57BL/6J, 8 week old

type: genomic

description: Genomic DNA methylation profile in the heart tissue of the C57BL/6J mouse

hyb_protocol: The combined test and input DNA samples were suspended in hybridization buffer (Roche, cat. no. 05583683001) cohybridized onto Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays for 20 hr at 42°C, following washing with Nimblegen Wash Kit (Roche cat. no. 05584507001).

scan_protocol: The image was acquisited with MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.

data_processing: The data from scanned images were extracted and processed with NimbleScan (2.6.0.0) (Roche, Nimblegen) using default parameters. Data processing included quantile normalization of each chanel separately, obtaining log2 ratios, P-scores and peak identification. Log2 ratios represent the ratios of the immunoprecipitated DNA signal to the input DNA signal. The mean log2 ratios were calculated using a Tukey biweight mean. P-scores were calculated from log2 ratios by performing sliding-window (750 bp) Kolmogorov-Smirnov (KS) test around each probe applied to determine -log10 p-value from the windowed KS test around that probe. The methylation peaks were obtained by merging consecutive probes with P scores over the assumed cut-off (default 2.0) with maximum 500 bp spacing and minimum of two probes per peak.

molecule: genomic DNA

source_name: MeDIP enriched genomic DNA

label_protocol: DNA labeling and hybridization was performed according to NimbleGen’s protocol with our modifications. The immunoprecipitated CpG methylated DNA (test) and the untreated, sonicated DNA (input control) were labeled by using the random priming with the Nimblegen Dual-Color DNA Labeling kit (Roche-Nimblegen, cat. No. 06370250001) with fluorescent dyes Cy3 and Cy5, respectively.

extract_protocol: Hearts from 1-day, 7-day, 2-week old mice of C57BL6/J murine strain were purchased from  the Tri-City Academic Laboratory Animal Centre - Research and Services Centre, Medical University of Gdańsk. Hearts for 8-week-old mice of C57BL/6J murine strain were purchased form the Jackson Laboratories. Genomic DNA was isolated using DNeasy Blood&Tissue Kit (QIAGEN).

tag: strain

value: heart

value: 8 week

source_name: input DNA


title: induced sputum_healthy control_rep17

description: induced sputum_healthy control


title: Gastric tumor tissue KS_269_T

tag: tumor type

value: GC

tag: location

value: body


title: induced sputum_healthy control_rep15

description: induced sputum_healthy control

tag: age


title: induced sputum_healthy control_rep18

description: induced sputum_healthy control


title: G_Control_sh_6h_rep2_array4

description:
Control; RNAi by shRNA, 6 h of adhesion, replica 2/2
sh_Control_6h_2+sh_GPRC5A_628_6h_2.txt: Cy3

value: non-targeting shRNA


title: Gastric tumor tissue KS_149_T

value: antrum

tag: lauren classification

value: intestinal


title: G_Control_sh_45min_rep2_array2

description:
Control; RNAi by shRNA, 45 min of adhesion, replica 2/2
sh_Control_45_2+sh_GPRC5A_628_45_2.txt: Cy3


title: MeDIP_Heart, C57BL/6J, 2 week old

description: Genomic DNA methylation profile in the spleen tissue of the MRL/MpJ mouse

value: 2 week


title: MeDIP_Heart, C57BL/6J, 7 day old

description: Genomic DNA methylation profile in the liver tissue of the MRL/MpJ mouse

value: 7 day


title: G_Control_sh_45min_rep1_array1

description:
Control; RNAi by shRNA, 45 min of adhesion, replica 1/2
sh_Control_45_1+sh_GPRC5A_628_45_1.txt: Cy3


title: Gastric tumor tissue KS_247_T

tag: ajcc stage


title: HCC patient 85

description:
Two-color Tumor versus non-tumor,
ch1 raw data file: *_1b.txt, ch2 raw data file: *_2b.txt

source_name: Non-tumorous tissue from HCC patient 85

tag: tissue type

value: Non-tumor

source_name: Tumor tissue from HCC patient 85

value: Tumor


title: HCC patient 87

source_name: Non-tumorous tissue from HCC patient 87

source_name: Tumor tissue from HCC patient 87


title: HCC patient 86

source_name: Non-tumorous tissue from HCC patient 86

source_name: Tumor tissue from HCC patient 86


title: MeDIP_Heart, C57BL/6J, 1 day old

description: Genomic DNA methylation profile in the heart tissue of the MRL/MpJ mouse

value: 1 day


title: HCC patient 84

source_name: Non-tumorous tissue from HCC patient 84

source_name: Tumor tissue from HCC patient 84


title: HCC patient 83

source_name: Non-tumorous tissue from HCC patient 83

source_name: Tumor tissue from HCC patient 83


title: induced sputum_healthy control_rep13

description: induced sputum_healthy control

tag: gender

value: male

value: no


title: G_Control_sh_6h_rep1_array3

description:
Control; RNAi by shRNA, 6 h of adhesion, replica 1/2
sh_Control_6h_1+sh_GPRC5A_628_6h_1.txt: Cy3

source_name: HeLa cells, Control, 6 h

tag: cell line


title: Gastric tumor tissue KS_119_T

source_name: Gastric tumor tissue

value: M

value: Gastric tumor tissue


title: HCC patient 82

source_name: Non-tumorous tissue from HCC patient 82

source_name: Tumor tissue from HCC patient 82


title: Gastric tumor tissue KS_113_T

value: Body


title: HCC patient 81

source_name: Non-tumorous tissue from HCC patient 81

source_name: Tumor tissue from HCC patient 81


title: induced sputum_healthy control_rep14

description: induced sputum_healthy control

source_name: induced sputum_healthy control


title: HCC patient 80

source_name: Non-tumorous tissue from HCC patient 80

source_name: Tumor tissue from HCC patient 80


title: induced sputum_healthy control_rep11

description: induced sputum_healthy control


title: Gastric tumor tissue KS_101_T


title: Gastric tumor tissue KS_105_T


title: induced sputum_healthy control_rep12

description: induced sputum_healthy control


title: HCC patient 79

source_name: Non-tumorous tissue from HCC patient 79

source_name: Tumor tissue from HCC patient 79


title: Gastric tumor tissue KS_095_T


title: induced sputum_healthy control_rep10

description: induced sputum_healthy control


title: induced sputum_healthy control_rep9

description: induced sputum_healthy control


title: Gastric tumor tissue KS_111_T

value: F


title: induced sputum_healthy control_rep8

description: induced sputum_healthy control


title: Gastric tumor tissue KS_031_T


title: Gastric tumor tissue KS_041_T


title: induced sputum_healthy control_rep7

description: induced sputum_healthy control


title: induced sputum_healthy control_rep6

description: induced sputum_healthy control


title: Gastric tumor tissue KS_051_T


title: Gastric tumor tissue KS_021_T

value: fundus


title: HCC patient 78

source_name: Non-tumorous tissue from HCC patient 78

source_name: Tumor tissue from HCC patient 78


title: HCC patient 75

source_name: Non-tumorous tissue from HCC patient 75

source_name: Tumor tissue from HCC patient 75


title: Chicken Mature Breast sample C13_83

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

description:
ChiMaBrC13_83
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 Mature Breast sample C13

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

tag: incubated sample

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

value: pectoralis major muscle


title: HCC patient 76

source_name: Non-tumorous tissue from HCC patient 76

source_name: Tumor tissue from HCC patient 76


title: Gastric tumor tissue KS_211_T

source_name: Gastric tumor tissue

value: GC

value: antrum

tag: tissue


title: e16_meDIP

description: Genomic DNA methylation profile in the skin tissue of the mouse embryos at day 16

data_processing: The data from scanned images were extracted and processed with DEVA v. 1.0.2 (Roche, Nimblegen) using default parameters. Data processing included obtaining log2 ratios, P-scores and peak identification. Log2 ratios represent the ratios of the immunoprecipitated DNA signal to the input DNA signal. The mean log2 ratios were calculated using a Tukey biweight mean. P-scores were calculated from log2 ratios by performing sliding-window (750 bp) Kolmogorov-Smirnov (KS) test around each probe applied to determine -log10 p-value from the windowed KS test around that probe.

source_name: MeDIP enriched genomic DNA

extract_protocol: Dorsal skin tissue samples from C57BL/6J mouse strain at different stages of development were prepared in the Tri-City's Academic Animal Experiment Centre of the Medical University of Gdańsk. Genomic DNA was isolated using DNeasy Blood&Tissue Kit (QIAGEN).

value: dorsal skin

value: female

tag: developmental stage

value: embryo

value: day 16

source_name: input DNA


title: Gastric tumor tissue KS_207_T

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

tag: patient

value: entire

value: intestinal


title: HCC patient 77

source_name: Non-tumorous tissue from HCC patient 77

value: Non-tumor

source_name: Tumor tissue from HCC patient 77

value: Tumor


title: induced sputum_healthy control_rep5

description: induced sputum_healthy control

source_name: induced sputum_healthy control

tag: oral corticosteroid use

value: no


title: induced sputum_healthy control_rep3

description: induced sputum_healthy control


title: induced sputum_healthy control_rep4

description: induced sputum_healthy control

value: male


title: HCC patient 74

source_name: Non-tumorous tissue from HCC patient 74

source_name: Tumor tissue from HCC patient 74


title: Chicken Mature Breast sample L13_91

description:
ChiMaBrL13_91
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample L13

value: Low 36.8°C


title: HCC patient 73

source_name: Non-tumorous tissue from HCC patient 73

source_name: Tumor tissue from HCC patient 73


title: Chicken Mature Breast sample L10_76

description:
ChiMaBrL10_76
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample L10


title: e18_meDIP

description: Genomic DNA methylation profile in the skin tissue of the mouse embryos at day 18

tag: strain

value: day 17


title: e19_meDIP

description: Genomic DNA methylation profile in the heart tissue of the mouse embryos at day 19

value: day 18


title: induced sputum_healthy control_rep1

description: induced sputum_healthy control


title: HCC patient 72

source_name: Non-tumorous tissue from HCC patient 72

source_name: Tumor tissue from HCC patient 72


title: Chicken Mature Breast sample C13_81

description:
ChiMaBrC13_81
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample C13

value: Broiler eggs

value: Control 37.8°C


title: induced sputum_moderate_rep25

description: induced sputum_moderate asthma

source_name: induced sputum_moderate asthma


title: Gastric tumor tissue KS_195_T

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: tumor type

value: GC

value: M

tag: location

value: body

value: Gastric tumor tissue


title: Gastric tumor tissue KS_001_T

tag: age

tag: lauren classification


title: Chicken Mature Breast sample C13_70

description:
ChiMaBrC13_70
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: pectoralis major muscle


title: Gastric tumor tissue KS_191_T

value: antrum

tag: ajcc stage


title: induced sputum_healthy control_rep2

description: induced sputum_healthy control

tag: gender


title: induced sputum_moderate_rep24

description: induced sputum_moderate asthma


title: Gastric tumor tissue KS_185_T


title: e15_meDIP

description: Genomic DNA methylation profile in the skin tissue of the mouse embryos at day 15

value: dorsal skin

value: female

value: embryo

value: day 15


title: adult_meDIP

description: Genomic DNA methylation profile in the skin tissue of the 3 months old mice

value: adult

value: 3 months


title: HCC patient 70

source_name: Non-tumorous tissue from HCC patient 70

tag: tissue type

value: Non-tumor

source_name: Tumor tissue from HCC patient 70

value: Tumor


title: HCC patient 71

source_name: Non-tumorous tissue from HCC patient 71

source_name: Tumor tissue from HCC patient 71


title: HCC patient 68

source_name: Non-tumorous tissue from HCC patient 68

source_name: Tumor tissue from HCC patient 68


title: HCC patient 69

source_name: Non-tumorous tissue from HCC patient 69

source_name: Tumor tissue from HCC patient 69


title: HCC patient 67

source_name: Non-tumorous tissue from HCC patient 67

source_name: Tumor tissue from HCC patient 67


title: Gastric tumor tissue KS_169_T

source_name: Gastric tumor tissue

value: intestinal


title: Chicken Mature Breast sample L10_51

description:
ChiMaBrL10_51
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

tag: incubated sample

value: Broiler eggs

value: Low 36.8°C


title: Chicken Mature Breast sample L13_179

description:
ChiMaBrL13_179
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample L13

tag: incubation temperature in treatment interval


title: Gastric tumor tissue KS_069_T

value: GC


title: Gastric tumor tissue KS_145_T

value: M


title: Chicken Mature Breast sample L10_64

description:
ChiMaBrL10_64
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample L10

tag: developmental interval of incubation temperature


title: Gastric tumor tissue KS_107_T


title: HCC patient 66

description:
Two-color Tumor versus non-tumor,
ch1 raw data file: *_1b.txt, ch2 raw data file: *_2b.txt

source_name: Non-tumorous tissue from HCC patient 66

source_name: Tumor tissue from HCC patient 66


title: induced sputum_moderate_rep23

description: induced sputum_moderate asthma

value: no


title: induced sputum_moderate_rep20

description: induced sputum_moderate asthma

value: male


title: induced sputum_moderate_rep18

description: induced sputum_moderate asthma


title: induced sputum_moderate_rep21

description: induced sputum_moderate asthma


title: Chicken Mature Breast sample L10_170

description:
ChiMaBrL10_170
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

tag: stage/age of sampling

value: pectoralis major muscle


title: Gastric tumor tissue KS_015_T

value: F

value: antrum

tag: tissue

value: Gastric tumor tissue


title: Chicken Mature Breast sample L13_163

description:
ChiMaBrL13_163
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_moderate_rep19

description: induced sputum_moderate asthma


title: Chicken Mature Breast sample L13_178

description:
ChiMaBrL13_178
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_005_T

value: body


title: induced sputum_moderate_rep22

description: induced sputum_moderate asthma

value: female


title: Gastric tumor tissue KS_013_T


title: induced sputum_moderate_rep17

description: induced sputum_moderate asthma


title: Chicken Mature Breast sample L13_161

description:
ChiMaBrL13_161
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_moderate_rep16

description: induced sputum_moderate asthma


title: HCC patient 63

source_name: Non-tumorous tissue from HCC patient 63

source_name: Tumor tissue from HCC patient 63


title: HCC patient 64

source_name: Non-tumorous tissue from HCC patient 64

source_name: Tumor tissue from HCC patient 64


title: HCC patient 65

source_name: Non-tumorous tissue from HCC patient 65

source_name: Tumor tissue from HCC patient 65


title: HCC patient 61

source_name: Non-tumorous tissue from HCC patient 61

source_name: Tumor tissue from HCC patient 61


title: HCC patient 60

source_name: Non-tumorous tissue from HCC patient 60

source_name: Tumor tissue from HCC patient 60


title: HCC patient 62

source_name: Non-tumorous tissue from HCC patient 62

source_name: Tumor tissue from HCC patient 62


title: Chicken Mature Breast sample L10_153

description:
ChiMaBrL10_153
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 59

source_name: Non-tumorous tissue from HCC patient 59

source_name: Tumor tissue from HCC patient 59


title: Chicken Mature Breast sample L13_127

description:
ChiMaBrL13_127
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample L13


title: induced sputum_moderate_rep12

description: induced sputum_moderate asthma

source_name: induced sputum_moderate asthma


title: Gastric tumor tissue KS_205_T

source_name: Gastric tumor tissue


title: Gastric tumor tissue KS_217_T


title: induced sputum_moderate_rep14

description: induced sputum_moderate asthma


title: HCC patient 58

source_name: Non-tumorous tissue from HCC patient 58

source_name: Tumor tissue from HCC patient 58


title: induced sputum_moderate_rep15

description: induced sputum_moderate asthma


title: Chicken Mature Breast sample L10_155

description:
ChiMaBrL10_155
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample L10


title: Chicken Mature Breast sample L10_145

description:
ChiMaBrL10_145
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_199_T


title: Gastric tumor tissue KS_197_T


title: induced sputum_moderate_rep13

description: induced sputum_moderate asthma


title: Chicken Mature Breast sample L13_6

description:
ChiMaBrL13_6
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 57

source_name: Non-tumorous tissue from HCC patient 57

source_name: Tumor tissue from HCC patient 57


title: Gastric tumor tissue KS_193_T

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: fundus


title: Chicken Mature Breast sample L13_122

description:
ChiMaBrL13_122
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_moderate_rep11

description: induced sputum_moderate asthma


title: Gastric tumor tissue KS_035_T


title: induced sputum_moderate_rep10

description: induced sputum_moderate asthma


title: HCC patient 56

source_name: Non-tumorous tissue from HCC patient 56

source_name: Tumor tissue from HCC patient 56


title: Chicken Mature Breast sample C10_90

description:
ChiMaBrC10_90
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample C10

value: Control 37.8°C


title: HCC patient 55

source_name: Non-tumorous tissue from HCC patient 55

value: Non-tumor

source_name: Tumor tissue from HCC patient 55


title: HCC patient 54

source_name: Non-tumorous tissue from HCC patient 54

source_name: Tumor tissue from HCC patient 54

value: Tumor


title: induced sputum_moderate_rep9

description: induced sputum_moderate asthma


title: HCC patient 53

source_name: Non-tumorous tissue from HCC patient 53

source_name: Tumor tissue from HCC patient 53


title: Chicken Mature Breast sample L10_116

description:
ChiMaBrL10_116
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Mature Breast sample C13_77

description:
ChiMaBrC13_77
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample C13


title: Gastric tumor tissue KS_025_T

value: intestinal


title: induced sputum_moderate_rep8

description: induced sputum_moderate asthma

source_name: induced sputum_moderate asthma


title: Gastric tumor tissue KS_017_T

source_name: Gastric tumor tissue

value: entire


title: Chicken Mature Breast sample H10_74

description:
ChiMaBrH10_74
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample H10

value: Broiler eggs

value: High 38.8°C


title: Gastric tumor tissue KS_099_T

value: GC

value: M


title: HCC patient 52

source_name: Non-tumorous tissue from HCC patient 52

source_name: Tumor tissue from HCC patient 52


title: Gastric tumor tissue KS_171_T


title: induced sputum_moderate_rep7

description: induced sputum_moderate asthma

value: male

value: no


title: Chicken Mature Breast sample H10_67

description:
ChiMaBrH10_67
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: pectoralis major muscle


title: Chicken Mature Breast sample H10_72

description:
ChiMaBrH10_72
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_007_T

value: F

value: antrum

value: mixed


title: Gastric tumor tissue KS_093_T

value: body

value: Gastric tumor tissue


title: induced sputum_moderate_rep5

description: induced sputum_moderate asthma


title: Gastric tumor tissue KS_165_T


title: induced sputum_moderate_rep4

description: induced sputum_moderate asthma

value: female


title: induced sputum_moderate_rep6

description: induced sputum_moderate asthma


title: Chicken Mature Breast sample H13_60

description:
ChiMaBrH13_60
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample H13


title: Gastric tumor tissue KS_087_T


title: induced sputum_moderate_rep3

description: induced sputum_moderate asthma


title: HCC patient 51

description:
Two-color Tumor versus non-tumor,
ch1 raw data file: *_1b.txt, ch2 raw data file: *_2b.txt

source_name: Non-tumorous tissue from HCC patient 51

value: Non-tumor

source_name: Tumor tissue from HCC patient 51


title: Chicken Mature Breast sample H13_58

description:
ChiMaBrH13_58
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 50

source_name: Non-tumorous tissue from HCC patient 50

source_name: Tumor tissue from HCC patient 50

value: Tumor


title: HCC patient 49

source_name: Non-tumorous tissue from HCC patient 49

source_name: Tumor tissue from HCC patient 49


title: induced sputum_moderate_rep2

description: induced sputum_moderate asthma


title: Gastric tumor tissue KS_085_T

value: diffuse


title: HCC patient 48

source_name: Non-tumorous tissue from HCC patient 48

source_name: Tumor tissue from HCC patient 48


title: HCC patient 47

source_name: Non-tumorous tissue from HCC patient 47

source_name: Tumor tissue from HCC patient 47


title: HCC patient 46

source_name: Non-tumorous tissue from HCC patient 46

source_name: Tumor tissue from HCC patient 46


title: Chicken Mature Breast sample H10_66

description:
ChiMaBrH10_66
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 45

source_name: Non-tumorous tissue from HCC patient 45

source_name: Tumor tissue from HCC patient 45


title: Gastric tumor tissue KS_033_T

source_name: Gastric tumor tissue

value: intestinal


title: Chicken Mature Breast sample H13_50

description:
ChiMaBrH13_50
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: Broiler eggs


title: induced sputum_severe_rep93

description: induced sputum_severe asthma

source_name: induced sputum_severe asthma

value: yes


title: Chicken Mature Breast sample H13_39

description:
ChiMaBrH13_39
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample H13

value: High 38.8°C


title: Chicken Mature Breast sample H13_43

description:
ChiMaBrH13_43
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Mature Breast sample H13_53

description:
ChiMaBrH13_53
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 44

source_name: Non-tumorous tissue from HCC patient 44

source_name: Tumor tissue from HCC patient 44


title: Gastric tumor tissue KS_043_T

value: GC

value: M


title: Gastric tumor tissue KS_039_T


title: Chicken Mature Breast sample H13_31

description:
ChiMaBrH13_31
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Mature Breast sample H13_34

description:
ChiMaBrH13_34
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_059_T

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.


title: induced sputum_severe_rep92

description: induced sputum_severe asthma

value: male


title: induced sputum_moderate_rep1

description: induced sputum_moderate asthma

source_name: induced sputum_moderate asthma

value: no


title: Gastric tumor tissue KS_063_T


title: induced sputum_severe_rep89

description: induced sputum_severe asthma


title: induced sputum_severe_rep91

description: induced sputum_severe asthma


title: HCC patient 42

source_name: Non-tumorous tissue from HCC patient 42

source_name: Tumor tissue from HCC patient 42


title: HCC patient 43

source_name: Non-tumorous tissue from HCC patient 43

source_name: Tumor tissue from HCC patient 43


title: Chicken Mature Breast sample C13_29

description:
ChiMaBrC13_29
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: Gastric tumor tissue KS_027_T

value: F


title: Chicken Mature Breast sample C10_30

description:
ChiMaBrC10_30
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample C10


title: induced sputum_severe_rep90

description: induced sputum_severe asthma


title: Gastric tumor tissue KS_299_T

value: body


title: Gastric tumor tissue KS_055_T

value: Gastric tumor tissue


title: HCC patient 40

source_name: Non-tumorous tissue from HCC patient 40

source_name: Tumor tissue from HCC patient 40


title: HCC patient 41

source_name: Non-tumorous tissue from HCC patient 41

source_name: Tumor tissue from HCC patient 41


title: Chicken Mature Breast sample H10_13

description:
ChiMaBrH10_13
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Mature Breast sample H10


title: Chicken Mature Breast sample H10_11

description:
ChiMaBrH10_11
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_229_T

source_name: Gastric tumor tissue

value: antrum


title: induced sputum_severe_rep87

description: induced sputum_severe asthma

source_name: induced sputum_severe asthma

value: female


title: HCC patient 39

source_name: Non-tumorous tissue from HCC patient 39

value: Non-tumor

source_name: Tumor tissue from HCC patient 39

value: Tumor


title: HCC patient 38

source_name: Non-tumorous tissue from HCC patient 38

source_name: Tumor tissue from HCC patient 38


title: Gastric tumor tissue KS_227_T

value: intestinal


title: induced sputum_severe_rep85

description: induced sputum_severe asthma


title: HCC patient 37

source_name: Non-tumorous tissue from HCC patient 37

source_name: Tumor tissue from HCC patient 37


title: Gastric tumor tissue KS_221_T

value: fundus

value: diffuse


title: Chicken Mature Breast sample H10_15

description:
ChiMaBrH10_15
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: Broiler eggs

value: High 38.8°C


title: induced sputum_severe_rep88

description: induced sputum_severe asthma

value: yes


title: Gastric tumor tissue KS_213_T

value: GC

value: M

value: Gastric cancer tissue


title: induced sputum_severe_rep86

description: induced sputum_severe asthma


title: Chicken Mature Breast sample H10_3

description:
ChiMaBrH10_3
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: pectoralis major muscle


title: HCC patient 36

source_name: Non-tumorous tissue from HCC patient 36

source_name: Tumor tissue from HCC patient 36


title: induced sputum_severe_rep84

description: induced sputum_severe asthma

value: male


title: Chicken Embryo Breast sample C13_91

description:
ChiEmBrC13_91
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample C13

value: Control 37.8°C


title: Chicken Embryo Breast sample C13_89

description:
ChiEmBrC13_89
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_187_T

value: F

value: body

value: Gastric tumor tissue


title: induced sputum_severe_rep83

description: induced sputum_severe asthma

value: female


title: induced sputum_severe_rep82

description: induced sputum_severe asthma


title: HCC patient 35

description:
Two-color Tumor versus non-tumor,
ch1 raw data file: *_1b.txt, ch2 raw data file: *_2b.txt

source_name: Non-tumorous tissue from HCC patient 35

value: Non-tumor

source_name: Tumor tissue from HCC patient 35

value: Tumor


title: Gastric tumor tissue KS_121_T

value: antrum

value: intestinal


title: HCC patient 34

source_name: Non-tumorous tissue from HCC patient 34

source_name: Tumor tissue from HCC patient 34


title: induced sputum_severe_rep80

description: induced sputum_severe asthma


title: HCC patient 33

source_name: Non-tumorous tissue from HCC patient 33

source_name: Tumor tissue from HCC patient 33


title: HCC patient 32

source_name: Non-tumorous tissue from HCC patient 32

source_name: Tumor tissue from HCC patient 32


title: Chicken Embryo Breast sample C13_87

description:
ChiEmBrC13_87
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: Broiler eggs


title: Gastric tumor tissue KS_161_T

source_name: Gastric tumor tissue


title: induced sputum_severe_rep81

description: induced sputum_severe asthma

source_name: induced sputum_severe asthma


title: HCC patient 30

source_name: Non-tumorous tissue from HCC patient 30

source_name: Tumor tissue from HCC patient 30


title: Chicken Embryo Breast sample L13_83

description:
ChiEmBrL13_83
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample L13

value: Low 36.8°C


title: HCC patient 29

source_name: Non-tumorous tissue from HCC patient 29

source_name: Tumor tissue from HCC patient 29


title: HCC patient 31

source_name: Non-tumorous tissue from HCC patient 31

source_name: Tumor tissue from HCC patient 31


title: Gastric tumor tissue KS_103_T


title: Gastric tumor tissue KS_109_T


title: induced sputum_severe_rep79

description: induced sputum_severe asthma

value: yes


title: induced sputum_severe_rep75

description: induced sputum_severe asthma

value: no


title: Gastric tumor tissue KS_065_T

value: GC

value: M


title: Chicken Embryo Breast sample L13_77

description:
ChiEmBrL13_77
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: pectoralis major muscle


title: induced sputum_severe_rep78

description: induced sputum_severe asthma

value: male


title: Gastric tumor tissue KS_009_T


title: Chicken Embryo Breast sample C13_88

description:
ChiEmBrC13_88
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample C13

value: Control 37.8°C


title: Gastric tumor tissue KS_053_T

value: F


title: HCC patient 28

source_name: Non-tumorous tissue from HCC patient 28

source_name: Tumor tissue from HCC patient 28


title: Chicken Embryo Breast sample L13_76

description:
ChiEmBrL13_76
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_severe_rep76

description: induced sputum_severe asthma


title: Gastric tumor tissue KS_081_T


title: Chicken Embryo Breast sample L13_75

description:
ChiEmBrL13_75
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Embryo Breast sample L13_74

description:
ChiEmBrL13_74
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_011_T

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.


title: induced sputum_severe_rep74

description: induced sputum_severe asthma


title: HCC patient 27

source_name: Non-tumorous tissue from HCC patient 27

source_name: Tumor tissue from HCC patient 27


title: HCC patient 26

source_name: Non-tumorous tissue from HCC patient 26

source_name: Tumor tissue from HCC patient 26


title: Gastric tumor tissue KS_401_T

value: body


title: induced sputum_severe_rep72

description: induced sputum_severe asthma


title: HCC patient 25

source_name: Non-tumorous tissue from HCC patient 25

source_name: Tumor tissue from HCC patient 25


title: Chicken Embryo Breast sample L13_73

description:
ChiEmBrL13_73
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 23

source_name: Non-tumorous tissue from HCC patient 23

source_name: Tumor tissue from HCC patient 23


title: Chicken Embryo Breast sample L13_72

description:
ChiEmBrL13_72
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 24

source_name: Non-tumorous tissue from HCC patient 24

source_name: Tumor tissue from HCC patient 24


title: Chicken Embryo Breast sample C10_70

description:
ChiEmBrC10_70
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample C10


title: HCC patient 22

source_name: Non-tumorous tissue from HCC patient 22

source_name: Tumor tissue from HCC patient 22


title: Gastric tumor tissue KS_263_T

source_name: Gastric tumor tissue

value: Gastric tumor tissue


title: induced sputum_severe_rep73

description: induced sputum_severe asthma

source_name: induced sputum_severe asthma


title: Chicken Embryo Breast sample C10_65

description:
ChiEmBrC10_65
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_233_T

value: mixed


title: HCC patient 21

source_name: Non-tumorous tissue from HCC patient 21

value: Non-tumor

source_name: Tumor tissue from HCC patient 21


title: induced sputum_severe_rep70

description: induced sputum_severe asthma

value: female


title: Gastric tumor tissue KS_243_T

value: antrum


title: Gastric tumor tissue KS_279_T

value: intestinal


title: induced sputum_severe_rep71

description: induced sputum_severe asthma


title: Gastric tumor tissue KS_219_T


title: Chicken Embryo Breast sample C10_64

description:
ChiEmBrC10_64
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: Broiler eggs


title: Chicken Embryo Breast sample L10_61

description:
ChiEmBrL10_61
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample L10

value: Low 36.8°C


title: HCC patient 19

source_name: Non-tumorous tissue from HCC patient 19

source_name: Tumor tissue from HCC patient 19

value: Tumor


title: induced sputum_severe_rep69

description: induced sputum_severe asthma

value: no


title: induced sputum_severe_rep77

description: induced sputum_severe asthma


title: Chicken Embryo Breast sample L10_60

description:
ChiEmBrL10_60
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Embryo Breast sample C10_63

description:
ChiEmBrC10_63
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_severe_rep68

description: induced sputum_severe asthma

value: yes


title: induced sputum_severe_rep67

description: induced sputum_severe asthma


title: HCC patient 18

description:
Two-color Tumor versus non-tumor,
ch1 raw data file: *_1b.txt, ch2 raw data file: *_2b.txt

source_name: Non-tumorous tissue from HCC patient 18

source_name: Tumor tissue from HCC patient 18


title: Chicken Embryo Breast sample L10_59

description:
ChiEmBrL10_59
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_severe_rep65

description: induced sputum_severe asthma


title: HCC patient 20

source_name: Non-tumorous tissue from HCC patient 20

source_name: Tumor tissue from HCC patient 20


title: Gastric tumor tissue KS_249_T

value: GC


title: induced sputum_severe_rep66

description: induced sputum_severe asthma


title: Chicken Embryo Breast sample L10_56

description:
ChiEmBrL10_56
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: pectoralis major muscle


title: HCC patient 17

source_name: Non-tumorous tissue from HCC patient 17

source_name: Tumor tissue from HCC patient 17


title: Gastric tumor tissue KS_183_T


title: Gastric tumor tissue KS_209_T

value: M

value: fundus


title: induced sputum_severe_rep63

description: induced sputum_severe asthma


title: Chicken Embryo Breast sample L10_57

description:
ChiEmBrL10_57
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 16

source_name: Non-tumorous tissue from HCC patient 16

source_name: Tumor tissue from HCC patient 16


title: induced sputum_severe_rep64

description: induced sputum_severe asthma

value: male


title: Chicken Embryo Breast sample L13_79

description:
ChiEmBrL13_79
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample L13


title: Chicken Embryo Breast sample L10_55

description:
ChiEmBrL10_55
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_181_T

value: F


title: induced sputum_severe_rep62

description: induced sputum_severe asthma


title: HCC patient 14

source_name: Non-tumorous tissue from HCC patient 14

source_name: Tumor tissue from HCC patient 14


title: Gastric tumor tissue KS_201_T

source_name: Gastric tumor tissue

value: diffuse

value: Gastric tumor tissue


title: HCC patient 13

source_name: Non-tumorous tissue from HCC patient 13

value: Non-tumor

source_name: Tumor tissue from HCC patient 13


title: Chicken Embryo Breast sample C13_42

description:
ChiEmBrC13_42
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample C13

value: Control 37.8°C


title: induced sputum_severe_rep60

description: induced sputum_severe asthma

source_name: induced sputum_severe asthma


title: Gastric tumor tissue KS_175_T

value: body


title: Gastric tumor tissue KS_179_T

value: mixed


title: HCC patient 12

source_name: Non-tumorous tissue from HCC patient 12

source_name: Tumor tissue from HCC patient 12


title: Gastric tumor tissue KS_147_T

value: antrum

value: intestinal


title: induced sputum_severe_rep61

description: induced sputum_severe asthma

value: female


title: HCC patient 11

source_name: Non-tumorous tissue from HCC patient 11

source_name: Tumor tissue from HCC patient 11

value: Tumor


title: Gastric tumor tissue KS_151_T


title: induced sputum_severe_rep58

description: induced sputum_severe asthma

value: yes


title: Chicken Embryo Breast sample C13_41

description:
ChiEmBrC13_41
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

value: Broiler eggs


title: Chicken Embryo Breast sample L10_54

description:
ChiEmBrL10_54
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample L10

value: Low 36.8°C

value: pectoralis major muscle


title: HCC patient 10

source_name: Non-tumorous tissue from HCC patient 10

source_name: Tumor tissue from HCC patient 10


title: Gastric tumor tissue KS_133_T

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: M


title: Chicken Embryo Breast sample C13_40

description:
ChiEmBrC13_40
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: HCC patient 15

source_name: Non-tumorous tissue from HCC patient 15

source_name: Tumor tissue from HCC patient 15


title: Chicken Embryo Breast sample L10_51

description:
ChiEmBrL10_51
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Embryo Breast sample C13_39

description:
ChiEmBrC13_39
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KS_071_T


title: Chicken Embryo Breast sample H13_36

description:
ChiEmBrH13_36
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample H13

value: High 38.8°C


title: HCC patient 9

source_name: Non-tumorous tissue from HCC patient 9

source_name: Tumor tissue from HCC patient 9


title: induced sputum_severe_rep56

description: induced sputum_severe asthma

value: male


title: HCC patient 8

source_name: Non-tumorous tissue from HCC patient 8

source_name: Tumor tissue from HCC patient 8


title: Gastric tumor tissue KS_127_T

source_name: Gastric tumor tissue

value: Gastric tumor tissue


title: induced sputum_severe_rep59

description: induced sputum_severe asthma


title: HCC patient 6

source_name: Non-tumorous tissue from HCC patient 6

value: Non-tumor

source_name: Tumor tissue from HCC patient 6


title: HCC patient 5

source_name: Non-tumorous tissue from HCC patient 5

source_name: Tumor tissue from HCC patient 5


title: Gastric tumor tissue KG117C

value: Body

value: Diffuse


title: induced sputum_severe_rep54

description: induced sputum_severe asthma

source_name: induced sputum_severe asthma


title: Gastric tumor tissue KG116C

value: Antrum

value: Intestinal


title: Chicken Embryo Breast sample H13_30

description:
ChiEmBrH13_30
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Gastric tumor tissue KG115C


title: induced sputum_severe_rep57

description: induced sputum_severe asthma


title: Chicken Embryo Breast sample H13_28

description:
ChiEmBrH13_28
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Embryo Breast sample H13_27

description:
ChiEmBrH13_27
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: induced sputum_severe_rep52

description: induced sputum_severe asthma


title: induced sputum_severe_rep51

description: induced sputum_severe asthma


title: Gastric tumor tissue KG113C


title: induced sputum_severe_rep55

description: induced sputum_severe asthma


title: Gastric tumor tissue KG112C


title: HCC patient 4

description:
Two-color Tumor versus non-tumor,
ch1 raw data file: *_1b.txt, ch2 raw data file: *_2b.txt

source_name: Non-tumorous tissue from HCC patient 4

source_name: Tumor tissue from HCC patient 4


title: HCC patient 3

source_name: Non-tumorous tissue from HCC patient 3

source_name: Tumor tissue from HCC patient 3


title: HCC patient 7

source_name: Non-tumorous tissue from HCC patient 7

source_name: Tumor tissue from HCC patient 7


title: induced sputum_severe_rep50

description: induced sputum_severe asthma


title: induced sputum_severe_rep49

description: induced sputum_severe asthma


title: Chicken Embryo Breast sample H13_29

description:
ChiEmBrH13_29
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample H13


title: induced sputum_severe_rep53

description: induced sputum_severe asthma


title: Chicken Embryo Breast sample H13_32

description:
ChiEmBrH13_32
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Chicken Embryo Breast sample H13_26

description:
ChiEmBrH13_26
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Heat stress treatment for 6h, biological rep3 [sad1 3F]

description: Gene expression data from Arabidopsis sad1 seedling after heat stress for 6h

tag: ecotype

value: Ten-day-old seedling

tag: protocol

value: heat stress

tag: timpe point


title: HCC patient 2

source_name: Non-tumorous tissue from HCC patient 2

source_name: Tumor tissue from HCC patient 2

value: Tumor


title: HCC patient 1

source_name: Non-tumorous tissue from HCC patient 1

source_name: Tumor tissue from HCC patient 1


title: Gastric tumor tissue KG111C

source_name: Gastric tumor tissue

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

tag: patient


title: Chicken Embryo Breast sample H13_25

description:
ChiEmBrH13_25
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature


title: Heat stress treatment for 6h, biological rep2 [sad1 2F]

source_name: Arabidopsis sad1 seedling after heat stress for 6h


title: Gastric tumor tissue KG114C

tag: tumor type

value: F


title: Heat stress treatment for 6h, biological rep1 [sad1 1F]


title: Chicken Embryo Breast sample C10_21

description:
ChiEmBrC10_21
gene level expression of broiler Musculus pectoralis major after variation of incubation temperature

source_name: Chicken Embryo Breast sample C10

value: Broiler eggs

value: Control 37.8°C


title: Gastric tumor tissue KG110C

tag: location


title: Heat stress treatment for 2h, biological rep3 [sad1 3F]

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


title: induced sputum_severe_rep47

description: induced sputum_severe asthma

tag: age

tag: oral corticosteroid use

value: yes


title: induced sputum_severe_rep48

description: induced sputum_severe asthma

value: female


title: Gastric tumor tissue KG109C

value: GC

tag: lauren classification

tag: ajcc stage


title: Gastric tumor tissue KG108C

tag: gender