title: L1829

status: Public on Aug 31 2015

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Tumor  vs normal

hyb_protocol: The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.

scan_protocol: Scanned on an Agilent G2565B scanner.

data_processing: Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).

molecule: genomic DNA

organism: Homo sapiens

source_name: TUMOR, Chronic lymphocytic leukemia sample

extract_protocol: Genomic DNA was extracted from 47 CLL samples using Qiagen extraction kits. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: gender

value: male

tag: diagnosis

value: Chronic lymphocytic leukemia

source_name: Pool normal DNA 25M/25F

value: male/female

value: Normal


title: L1104

description: Tumor  vs normal


title: L1884

description: Tumor  vs normal

value: female


title: L1059

description: Tumor  vs normal


title: D1151

description: Tumor  vs normal


title: L1882

description: Tumor  vs normal


title: L18

description: Tumor  vs normal


title: L1378

description: Tumor  vs normal


title: D1073

description: Tumor  vs normal


title: D1094

description: Tumor  vs normal


title: D1024

description: Tumor  vs normal


title: L1561

description: Tumor  vs normal


title: D1045

description: Tumor  vs normal


title: D1023

description: Tumor  vs normal


title: D1091

description: Tumor  vs normal


title: D1159

description: Tumor  vs normal


title: L1107

description: Tumor  vs normal


title: D1072

description: Tumor  vs normal


title: D1022

description: Tumor  vs normal


title: D1019

description: Tumor  vs normal


title: D1089

description: Tumor  vs normal


title: L1477

description: Tumor  vs normal


title: D1044

description: Tumor  vs normal


title: D1037

description: Tumor  vs normal


title: D1033

description: Tumor  vs normal


title: D1164

description: Tumor  vs normal


title: D1016

description: Tumor  vs normal


title: D1014

description: Tumor  vs normal


title: D990

description: Tumor  vs normal


title: D1017

description: Tumor  vs normal


title: D978

description: Tumor  vs normal


title: D986

description: Tumor  vs normal


title: D989

description: Tumor  vs normal


title: D973

description: Tumor  vs normal


title: methanol medium rep 1 dye swap

type: RNA

city: Wien

first: Alexandra

middle: Bettina

last: Graf

address: Muthgasse 18

department: Applied Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna

description: P. pastoris cells grown on methanol/glycerol medium, biological replicate 1 in dye swap

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.11.5.1.1).

data_processing: Raw data was loaded into R, the limma package was used to normalize (LOESS, Aquantile) the data, summarize, and calculate differential expression. The multiple testing adjustment method was Benjamini and Yekutieli.

molecule: total RNA

organism: Komagataella phaffii CBS 7435

source_name: Pichia pastoris CBS 7435 cells grown on Methanol/Glycerol

label_protocol: Samples were labelled with Cy3 and Cy5 according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol, version 6.5

growth_protocol: Chemostat cultivations were performed in a 1.4 L bioreactor with a working volume of 400 mL. P. pastoris CBS7435 grown in a glycerol pre-culture, before the bioreactor was inoculated. After a glycerol batch phase, the cells were grown in carbon limited chemostats either in a glucose medium or a methanol/glycerol medium.

extract_protocol: RNA was extracted using TRI reagent according to the supplier's instructions (Ambion, US).

tag: medium

value: Methanol/Glycerol

source_name: Pichia pastoris reference mix

value: various


title: methanol medium rep2

description: P. pastoris cells grown on methanol/glycerol medium, biological replicate 2


title: D981

description: Tumor  vs normal


title: D993

description: Tumor  vs normal


title: D983

description: Tumor  vs normal


title: methanol medium rep3


title: methanol medium rep3 dye swap

description: P. pastoris cells grown on methanol/glycerol medium, biological replicate 3 in dye swap


title: glucose medium rep3 dye swap

description: P. pastoris cells grown on glucose medium, biological replicate 3 in dye swap

source_name: Pichia pastoris CBS 7435 cells grown on Glucose

value: Glucose


title: D958

description: Tumor  vs normal


title: D967

description: Tumor  vs normal


title: D961

description: Tumor  vs normal


title: methanol medium rep 1

description: P. pastoris cells grown on methanol/glycerol medium, biological replicate 1


title: D964

description: Tumor  vs normal


title: D968

description: Tumor  vs normal


title: D966

description: Tumor  vs normal


title: HCV specific, NS3-1406, HCV patient 1

city: Beerse

first: Susanne

last: Johansson

address: Turnhoutseweg 30

department: Infectious Diseases and Vaccines

country: Belgium

institute: Janssen Pharmaceutica

hyb_protocol: Hybridization on the Affymetrix® Human Genome U219 array plate was done according to the protocol in the GeneTitan Instrument (Affymetrix).

scan_protocol: GeneTitan® instrument (Affymetrix) was used for scanning.

data_processing: Microarray analysis was performed using the bioconductor package version 2.12 (in R version 3.0.1). Probe annotation was done using Entrez Gene based alternative cdf version 15. RMA algorithm was used for preprocessing. Data from three different batches were combined and corrected for batch effect with the ComBat package. Limma Bioconductor package was used to identify differentially expressed  genes.

label: biotin

source_name: Blood CD8+ T cells, chronic HCV infected patient

label_protocol: The single-stranded cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN)

growth_protocol: PBMCs from human peripheral blood were isolated though Ficoll separation

extract_protocol: RNA was extracted through the RNeasy mini kit (Qiagen). From the RNA amplified cDNA was generated using the WT-Ovation Pico RNA Amplification System (NuGEN)

treatment_protocol: CD8+ T cells were surface stained with antibodies and epitope-specific tetramers and sorted through flow cytometry. Cells were frozen at -80°C in RLT buffer (Qiagen) with 1% β-mercaptoethanol.

tag: infection

value: chronic HCV infected

tag: sorting tetramer epitope

tag: cell type

value: CD8+ T cell

value: Male

tag: age

tag: alt

tag: microarray batch


title: D972

description: Tumor  vs normal


title: D1013

description: Tumor  vs normal


title: D969

description: Tumor  vs normal


title: HCV specific, NS5B-2841, HCV patient 2

value: HCV NS5B-2841


title: methanol medium rep2  dye swap

description: P. pastoris cells grown on methanol/glycerol medium, biological replicate 2 in dye swap


title: glucose medium rep3

description: P. pastoris cells grown on glucose medium, biological replicate 2


title: glucose medium rep2 dye swap

description: P. pastoris cells grown on glucose medium, biological replicate 2 in dye swap


title: HCV specific, NS3-1073, HCV patient 1


title: HCV non-specific, HCV patient 3


title: HBV specifc, HBV patient 4

source_name: Blood CD8+ T cells, chronic HBV infected patient

value: chronic HBV infected

value: HBV core 18


title: HCV specific, HCV patient 4

value: Female


title: V1041263

city: Logrono

first: Jérôme

last: Grimplet

address: C/ Madre de Dios 51

institute: Instituto de Ciencias de la Vid y del Vino

description: Sample from Vitis vinifera cv. Tempranillo collected from the clone 1041 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 3 of the 5-individual plot

hyb_protocol: If the quality control was correct, then 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent technologies).

data_processing: Scanned images (.tif) were imported into NimbleScan software (NimbleGen) where the image containing all 12 arrays on each slide was separated into 12 individual image files. An automatic alignment was performed for each individual array and X, Y, and Signal files (.xys) were generated.  Raw intensity values were processed using the R package oligo (Carvalho BS, Irizarry RA: A framework for oligonucleotide microarray preprocessing. Bioinformatics 2010, 26(19):2363-2367). Individual probes raw expression values were computed from .xys files and the in house pd info builder package pd.vitus.exp.vitnames designed to fit the 12Xv1 latest annotation nomenclature. Normalization was performed with Robust Multi-Array Average (RMA) (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264.). Resulting RMA expression values were log2-transformed. Distributions of expression values processed via RMA of all arrays were very similar with no apparent outlying arrays.

organism: Vitis vinifera

source_name: Vitis vinifera Tempranillo loose clone 1041 flowers rep 3

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

extract_protocol: Total RNA was extracted from samples using the Spectrum plant total RNA kit (Sigma, www.sigmaaldrich.com) as recommended by manufacturer. DNase I digestion was carried out with the RNase-Free DNase Set (QIAGEN). RNA integrity and quantity were assessed by a Nanodrop 2000 spectrophotometer (Thermo Scientific) and an Agilent’s Bioanalyzer 2100.

tag: tissue

value: Flowers EL-26


title: glucose medium rep 1 dye swap

description: P. pastoris cells grown on glucose medium, biological replicate 1 in dye swap


title: HBV specifc, HBV patient 9


title: HCV specific, NS3-1073, HCV patient 2


title: HCV non-specific, HCV patient 2


title: HBV specifc, HBV patient 3


title: HCV non-specific, HCV patient 1


title: V1041262

description: Sample from Vitis vinifera cv. Tempranillo collected from the clone 1041 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 2 of the 5-individual plot

source_name: Vitis vinifera Tempranillo loose clone 1041 flowers rep 2


title: glucose medium rep2


title: V1041032

source_name: Vitis vinifera Tempranillo loose clone 1041 Spring buds rep 2

value: Spring buds EL-03


title: HBV specifc, HBV patient 8

value: HBV pol 455


title: glucose medium rep 1

description: P. pastoris cells grown on glucose medium, biological replicate 1


title: HBV specific, HBV patient 5


title: HCV specific, HCV patient 3


title: HCV non-specific, HCV patient 4


title: HBV specifc, HBV patient 7


title: HBV specifc, HBV patient 6


title: V0126265

description: Sample from Vitis vinifera cv. Tempranillo collected from the clone 0126 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 5 of the 5-individual plot

source_name: Vitis vinifera Tempranillo compact clone 0126 flowers rep 5


title: V1041034

description: Sample from Vitis vinifera cv. Tempranillo collected from the clone 1041 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Tempranillo loose clone 1041 Spring buds rep 4


title: V1041264

source_name: Vitis vinifera Tempranillo loose clone 1041 flowers rep 4


title: V0126262

description: Sample from Vitis vinifera cv. Tempranillo collected from the clone 0126 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 2 of the 5-individual plot

source_name: Vitis vinifera Tempranillo compact clone 0126 flowers rep 2


title: V1041033

source_name: Vitis vinifera Tempranillo loose clone 1041 Spring buds rep 3


title: V0126032

source_name: Vitis vinifera Tempranillo compact clone 0126 Spring buds rep 2


title: V0126261

description: Sample from Vitis vinifera cv. Tempranillo collected from the clone 0126 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 1 of the 5-individual plot

source_name: Vitis vinifera Tempranillo compact clone 0126 flowers rep 1


title: HBV non-specific, HBV patient 7


title: HBV specifc, HBV patient 2


title: HBV non-specific, HBV patient 1


title: HBV non-specific, HBV patient 2


title: V0126031

source_name: Vitis vinifera Tempranillo compact clone 0126 Spring buds rep 1


title: V0906264

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0906 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 0906 flowers rep 4


title: HBV specifc, HBV patient 1


title: V0126034

description: Sample from Vitis vinifera cv. Tempranillo collected from the clone 0126 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Tempranillo compact clone 0126 Spring buds rep 4


title: V0906033

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0906 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 3 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 0906 Spring buds rep 3


title: HBV non-specific, HBV patient 5


title: CMV specific, HCV patient 1

value: CMV pp65


title: HBV non-specific, HBV patient 4


title: V1154263

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 1154 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 3 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 1154 flowers rep 3


title: V1154261

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 1154 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 1 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 1154 flowers rep 1


title: HBV non-specific, HBV patient 6

source_name: Blood CD8+ T cells, chronic HBV infected patient


title: V1154264

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 1154 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 1154 flowers rep 4


title: V0906034

source_name: Vitis vinifera Granacha tinta compact clone 0906 Spring buds rep 4


title: HBV non-specific, HBV patient 9


title: CMV specific, HBV patient 9


title: V0906031

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0906 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 1 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 0906 Spring buds rep 1


title: CMV specific, HCV patient 2

source_name: Blood CD8+ T cells, chronic HCV infected patient


title: V0906263

source_name: Vitis vinifera Granacha tinta compact clone 0906 flowers rep 3


title: D970

description: Tumor  vs normal

source_name: TUMOR, Chronic lymphocytic leukemia sample

value: male

value: Chronic lymphocytic leukemia

source_name: Pool normal DNA 25M/25F

value: male/female


title: CMV specific, HCV patient 4


title: CMV specific, healthy donor 1

source_name: Blood CD8+ T cells, healthy donor

value: healthy


title: V0906261

source_name: Vitis vinifera Granacha tinta compact clone 0906 flowers rep 1


title: V1154314

source_name: Vitis vinifera Granacha tinta loose clone 1154 Summer buds rep 4

value: Summer buds EL-31


title: V1154311

source_name: Vitis vinifera Granacha tinta loose clone 1154 Summer buds rep 1


title: V1154313

source_name: Vitis vinifera Granacha tinta loose clone 1154 Summer buds rep 3


title: CMV specific, HBV patient 5


title: CMV non-specific, HCV patient 4


title: V1154134

source_name: Vitis vinifera Granacha tinta loose clone 1154 Inflorescences rep 4

value: Inflorescences EL-13


title: V1154033

source_name: Vitis vinifera Granacha tinta loose clone 1154 Spring buds rep 3


title: CMV non-specific, HBV patient 7


title: CMV non-specific, healthy donor 1


title: CMV specific, HBV patient 1


title: V1154131

source_name: Vitis vinifera Granacha tinta loose clone 1154 Inflorescences rep 1


title: V0681133

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0681 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 3 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 0681 Inflorescences rep 3


title: V1154034

source_name: Vitis vinifera Granacha tinta loose clone 1154 Spring buds rep 4


title: CMV non-specific, HCV patient 1

value: chronic HCV infected


title: V1154133

source_name: Vitis vinifera Granacha tinta loose clone 1154 Inflorescences rep 3


title: Colonic mucosa KRCA283V

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: Validation set

data_processing:
Raw data were processed by SPSS v16 software (SPSS, Chicago, IL).
For the normalization the average of housekeeping genes was used.
Fold change reports data processed by REST 2009 software (Qiagen, Hildesheim, Germany).

label: FAM

source_name: Control

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in ViiA7 produced by Life technologies (Carlsbad, CA) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was isolated from frozen tissues using Trizol reagent according to manufacturers protocol (Invitrogen, Carlsbad, CA, USA)

value: Colonic mucosa

tag: Stage

tag: grade

tag: localization


title: V0681313

source_name: Vitis vinifera Granacha tinta loose clone 0681 Summer buds rep 3


title: V0681314

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0681 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 0681 Summer buds rep 4


title: CMV non-specific, HCV patient 2

source_name: Blood CD8+ T cells, chronic HCV infected patient

value: CD8+ T cell

value: Male


title: V0681311

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0681 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 1 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 0681 Summer buds rep 1


title: V1154031

source_name: Vitis vinifera Granacha tinta loose clone 1154 Spring buds rep 1


title: CMV non-specific, HBV patient 9

source_name: Blood CD8+ T cells, chronic HBV infected patient

value: chronic HBV infected


title: V0681034

source_name: Vitis vinifera Granacha tinta loose clone 0681 Spring buds rep 4


title: V0681131

source_name: Vitis vinifera Granacha tinta loose clone 0681 Inflorescences rep 1


title: Colonic mucosa KRCA282V

description: Validation set


title: V0681033

source_name: Vitis vinifera Granacha tinta loose clone 0681 Spring buds rep 3


title: CMV non-specific, HBV patient 5


title: V0681134

source_name: Vitis vinifera Granacha tinta loose clone 0681 Inflorescences rep 4


title: Colonic mucosa KRCA285V

description: Validation set


title: CMV non-specific, HBV patient 1


title: Colonic mucosa KRCA279V

description: Validation set


title: Colonic mucosa KRCA280V

description: Validation set


title: CMV specific, HBV patient 7


title: Colonic mucosa KRCA277V

description: Validation set


title: V1134134

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 1134 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 1134 inflorescences rep 4


title: Colonic mucosa KRCA281V

description: Validation set


title: V1134133

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 1134 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 3 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 1134 inflorescences rep 3


title: Colonic mucosa KRCA272V

description: Validation set


title: Colonic mucosa KRCA269V

description: Validation set


title: Colonic mucosa KRCA278V

description: Validation set


title: V0681031

source_name: Vitis vinifera Granacha tinta loose clone 0681 Spring buds rep 1


title: V1134135

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 1134 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 5 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 1134 inflorescences rep 5


title: V1134265

source_name: Vitis vinifera Granacha tinta compact clone 1134 flowers rep 5


title: Colonic mucosa KRCA266V

description: Validation set


title: V1134344

source_name: Vitis vinifera Granacha tinta compact clone 1134 berries rep 4

value: Berries EL-34


title: Colonic mucosa KRCA265V

description: Validation set

source_name: Control


title: Colonic mucosa KRCA274V

description: Validation set


title: V1134343

source_name: Vitis vinifera Granacha tinta compact clone 1134 berries rep 3


title: V0147134

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0147 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 0147 inflorescences rep 4


title: V0147133

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0147 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 3 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 0147 inflorescences rep 3


title: Colonic mucosa KRCA273V

description: Validation set


title: V0147131

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0147 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 1 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta compact clone 0147 inflorescences rep 1


title: Colonic mucosa KRCA263V

description: Validation set


title: Colonic mucosa KRCA267V

description: Validation set


title: V1134264

source_name: Vitis vinifera Granacha tinta compact clone 1134 flowers rep 4


title: V1134345

source_name: Vitis vinifera Granacha tinta compact clone 1134 berries rep 5


title: V0368342

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0368 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 2 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 0368 berries rep 2


title: Colonic mucosa KRCA268V

description: Validation set


title: V0368265

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0368 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 5 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 0368 flowers rep 5


title: Colonic mucosa KRCA264V

description: Validation set


title: V1134263

source_name: Vitis vinifera Granacha tinta compact clone 1134 flowers rep 3


title: Colonic mucosa KRCA262V

description: Validation set


title: Colonic mucosa KRCA249V

description: Validation set


title: Colonic mucosa KRCA251V

description: Validation set


title: Colonic mucosa KRCA261V

description: Validation set


title: Colonic mucosa KRCA260V

description: Validation set


title: V0368344

description: Sample from Vitis vinifera cv. Granacha tinta collected from the clone 0368 at the experimental vineyard of La Grajera (Logroño, La Rioja). Sampling was performed on the vine 4 of the 5-individual plot

source_name: Vitis vinifera Granacha tinta loose clone 0368 berries rep 4


title: Colonic mucosa KRCA252V

description: Validation set


title: Colonic mucosa KRCA256V

description: Validation set


title: Colonic mucosa KRCA255V

description: Validation set


title: Colonic mucosa KRCA253V

description: Validation set


title: V0368345

source_name: Vitis vinifera Granacha tinta loose clone 0368 berries rep 5


title: V0368264

source_name: Vitis vinifera Granacha tinta loose clone 0368 flowers rep 4


title: Colonic mucosa KRCA243V

description: Validation set


title: Colonic mucosa KRCA242V

description: Validation set


title: Colonic mucosa KRCA244V

description: Validation set


title: V0368262

source_name: Vitis vinifera Granacha tinta loose clone 0368 flowers rep 2


title: iPSC with a RPS19 muation, biological rep1

city: Philadelphia

first: Jingping

last: Ge

state: PA

address: 3615 CivicCenter Blvd, ARC 303

department: Pediatrics

country: USA

institute: Children's Hospital of Philadelphia

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome Arrays 2.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the RMA (Partek Genomics Suite v6.6).

source_name: iPSC with a RPS19 muation

label_protocol: 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Human iPSCs grew in the erythroid induced medium, and collected floating cells CD41+ CD235+ on day 8

extract_protocol: All RNA samples  were prepared using Trizol, and then treated with DNase.

tag: subject status

value: DBA patients carrying RPS19 mutation

value: induced pluripotent stem cells

tag: genotype/variation

value: RPS19 mutant

tag: passage

value: Passage 27


title: wild type 1 iPSC, biological rep1

source_name: wild type 1 iPSC

value: DBA patients

value: wild type


title: Colonic mucosa KRCA238V

description: Validation set


title: Colonic mucosa KRCA236V

description: Validation set


title: wild type 2 iPSC, biological rep1

source_name: wild type 2 iPSC


title: wild type 2 iPSC, biological rep2

value: Passage 28


title: Corrected RPS19 mutant iPSC, biological rep2

source_name: Corrected RPS19 mutant iPSC

value: corrected RPS19 mutant (with a wildtype cDNA of RPS19)


title: wild type 1 iPSC, biological rep2


title: Corrected RPS19 mutant iPSC, biological rep1


title: Colonic mucosa KRCA247V

description: Validation set

source_name: Control


title: Colonic mucosa KRCA246V

description: Validation set


title: Colonic mucosa KRCA240V

description: Validation set


title: Colonic mucosa KRCA239V

description: Validation set


title: Colonic mucosa KRCA241V

description: Validation set


title: Colonic mucosa KRCA235V

description: Validation set


title: Colonic mucosa KRCA229V

description: Validation set


title: Colonic mucosa KRCA228V

description: Validation set


title: Colonic mucosa KRCA226V

description: Validation set


title: Colonic mucosa KRCA234V

description: Validation set


title: Colonic mucosa KRCA221V

description: Validation set


title: Colonic mucosa KRCA223V

description: Validation set


title: Colonic mucosa KRCA224V

description: Validation set


title: Colonic mucosa KRCA225V

description: Validation set


title: Colonic mucosa KRCA233V

description: Validation set


title: iPSC with a RPS19 muation, biological rep2


title: Colonic mucosa KRCA232V

description: Validation set


title: Colonic mucosa KRCA227V

description: Validation set


title: Colonic mucosa KRCA230V

description: Validation set


title: Colonic mucosa KRCA222V

description: Validation set


title: Colonic mucosa KRCA212V

description: Validation set


title: Colonic mucosa KRCA218V

description: Validation set


title: Colonic mucosa KRCA219V

description: Validation set


title: Colonic mucosa KRCA217V

description: Validation set


title: Colonic mucosa KRCA220V

description: Validation set


title: Colonic mucosa KRCA210V

description: Validation set


title: Colonic mucosa KRCA214V

description: Validation set


title: Colonic mucosa KRCA213V

description: Validation set


title: Colonic mucosa KRCA208V

description: Validation set


title: Colonic mucosa KRCA207V

description: Validation set


title: Colonic mucosa KRCA198V

description: Validation set


title: Colonic mucosa KRCA203V

description: Validation set


title: Colonic mucosa KRCA201V

description: Validation set


title: Colonic mucosa KRCA206V

description: Validation set


title: Colorectal tumor tissue KRCA283T

description: Validation set

source_name: Tumor

value: Colorectal tumor tissue

value: female

value: colon


title: Colorectal tumor tissue KRCA278T

description: Validation set

value: sigmoideum


title: Colorectal tumor tissue KRCA279T

description: Validation set

value: male

value: rectum


title: Colorectal tumor tissue KRCA280T

description: Validation set


title: Colorectal tumor tissue KRCA284T

description: Validation set


title: Colorectal tumor tissue KRCA277T

description: Validation set


title: Colonic mucosa KRCA199V

description: Validation set

value: Colonic mucosa


title: Colorectal tumor tissue KRCA281T

description: Validation set


title: Colorectal tumor tissue KRCA282T

description: Validation set


title: Colorectal tumor tissue KRCA275T

description: Validation set


title: Colorectal tumor tissue KRCA285T

description: Validation set


title: Colorectal tumor tissue KRCA273T

description: Validation set


title: Colorectal tumor tissue KRCA274T

description: Validation set


title: Colorectal tumor tissue KRCA267T

description: Validation set


title: Colorectal tumor tissue KRCA265T

description: Validation set

value: x


title: Colorectal tumor tissue KRCA268T

description: Validation set


title: Colorectal tumor tissue KRCA263T

description: Validation set


title: Colorectal tumor tissue KRCA269T

description: Validation set


title: Colorectal tumor tissue KRCA266T

description: Validation set


title: Colorectal tumor tissue KRCA262T

description: Validation set


title: Colorectal tumor tissue KRCA261T

description: Validation set


title: Colorectal tumor tissue KRCA260T

description: Validation set


title: Colonic mucosa KRCA209V

description: Validation set


title: Colorectal tumor tissue KRCA253T

description: Validation set


title: Colorectal tumor tissue KRCA252T

description: Validation set


title: Colorectal tumor tissue KRCA256T

description: Validation set


title: Colorectal tumor tissue KRCA247T

description: Validation set


title: Colorectal tumor tissue KRCA244T

description: Validation set


title: Colorectal tumor tissue KRCA250T

description: Validation set


title: Colorectal tumor tissue KRCA245T

description: Validation set


title: Colorectal tumor tissue KRCA246T

description: Validation set


title: Colorectal tumor tissue KRCA241T

description: Validation set


title: Colorectal tumor tissue KRCA243T

description: Validation set


title: Colorectal tumor tissue KRCA240T

description: Validation set


title: Colorectal tumor tissue KRCA242T

description: Validation set


title: Colorectal tumor tissue KRCA239T

description: Validation set


title: Colorectal tumor tissue KRCA236T

description: Validation set


title: Colorectal tumor tissue KRCA238T

description: Validation set


title: Colorectal tumor tissue KRCA234T

description: Validation set


title: Colorectal tumor tissue KRCA235T

description: Validation set


title: sternal cartilage, TIMPless, biological rep 4

city: Toronto

first: Rama

last: Khokha

state: ON

address: 101 College St.

country: Canada

institute: Ontario Cancer Institute

description: gene expression data from sternal cartilage

hyb_protocol: Samples were hybridized at 45 degrees celcius for 16-18hrs.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were preprocessed with Partek Genomics Suite (v.6.6) using Affymetrix default analysis settings with robust multichip average (RMA) as normalization method.

label: biotin allonamide triphosphate

organism: Mus musculus

source_name: 4 week old TIMPless mouse sternal cartilage

label_protocol: RNA was prepared using an Affymetrix GeneChip WT Terminal Labeling kit as per the manufacturer's instructions.

growth_protocol: Mice were housed and cared for under standard conditions with food and water ad libitum, in accordance with the guidelines approved by the Canadian Council for Animal Care and the Animal Care Committee of the Ontario Cancer Institute.

extract_protocol: Sternums were dissected immediately following sacrifice and flash frozen in liquid nitrogen. Once all samples were collected, sternums were thawed in RNAlaterICE (Life Technologies).Sternal cartilge pads were dissected and homogenized in 800uL of Trizol. RNA was extracted as previously described for cartilage (Ali S.A. and Alman, B, 2012. RNA extraction from human articular cartilage by chondrocyte isolation. Anal Biochem 429:39-41.), with the addition of two extra ethanol wash steps.

treatment_protocol: Mice were not treated during the course of this experiment.

value: sternal cartilage (excluding xiphoid process)

tag: genotype

value: TIMPless

tag: strain


title: Colorectal tumor tissue KRCA233T

description: Validation set

tag: gender


title: sternal cartilage, TIMPless, biological rep 2


title: sternal cartilage, TIMPless, biological rep 6


title: Colorectal tumor tissue KRCA251T

description: Validation set


title: Colorectal tumor tissue KRCA232T

description: Validation set


title: Colorectal tumor tissue KRCA230T

description: Validation set


title: Colorectal tumor tissue KRCA228T

description: Validation set


title: sternal cartilage, TIMPless, biological rep 5


title: sternal cartilage, TIMPless, biological rep 3


title: sternal cartilage, WT, biological rep 6

source_name: 4 week old WT mouse sternal cartilage


title: sternal cartilage, WT, biological rep 3


title: Colorectal tumor tissue KRCA227T

description: Validation set


title: sternal cartilage, WT, biological rep 5


title: sternal cartilage, WT, biological rep 4


title: US 184

city: Milano

first: Elena

last: Landoni

address: Via Vanzetti 5

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: miRNA profile of archival plasma sample

hyb_protocol: Hybridization for 20 h at 55 °C on SurePrint G3 Human v16 miRNA 8x60K microarrays (G4870A) designed on miRBase 16.0 from Agilent Technologies. The arrays were washed in Agilent GE Wash Buffers, following the manufacturer’s instructions

scan_protocol: All slides were immediately scanned at 2 mm resolution using an Agilent DNA microarray scanner

data_processing: The resulting images were analyzed using Agilent’s Feature Extraction software v10.7. In the employed platform, each miRNA is targeted by one to 4 different probes and each probe is spotted 10 to 40 times on the array. Then, the total gene signal for each miRNA was obtained by summing the probe signals derived using the Agilent Feature Extraction software. Using this software, each probe is defined detected if its value is greater than 3 times its standard error, and each miRNA is defined as detected if at least one of the probes is detected. Summarized data were log2 transformed

source_name: plasma

label_protocol: 2.5 µl of total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured using 100% DMSO at 100°C for  5 min, labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 1 hour

growth_protocol: Plasma samples used in this study belong to the human plasma collection of the Fenretinide Breast Cancer Prevention Trial and RNA was extracted from 350 µl of sample.

extract_protocol: Total RNA was extracted from plasma using the commercial column-based system Qiagen miRNeasy® Mini Kit (Qiagen, Valencia, CA, USA), slightly modified by Exiqon (Vedbaek, Denmark. The eluate was digested using 1 u/µl heparinase I (Sigma-Aldrich, St. Luis, MO, USA), in the presence of an RNase inhibitor, (RNAsin; Promega, Madison, WI, USA) for 1 hour at room temperature, and RNA was stored at −80 °C.

value: plasma

tag: plasmaid

tag: er class

value: pos

tag: drawing year

tag: age at drawing

tag: time from surgery

tag: hemolysis score (hs)

tag: metastasis class

value: no metastasis


title: Colorectal tumor tissue KRCA226T

description: Validation set

tag: tissue

tag: age


title: US 188

description: miRNA profile of archival plasma sample


title: sternal cartilage, WT, biological rep 1


title: US 183

description: miRNA profile of archival plasma sample

value: metastasis


title: sternal cartilage, WT, biological rep 2

value: wild type


title: sternal cartilage, TIMPless, biological rep 1


title: US 181

description: miRNA profile of archival plasma sample


title: US 182

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA225T

description: Validation set

tag: Stage

tag: grade


title: Colorectal tumor tissue KRCA224T

description: Validation set

tag: localization


title: US 180

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA223T

description: Validation set


title: Colorectal tumor tissue KRCA220T

description: Validation set


title: Colorectal tumor tissue KRCA222T

description: Validation set


title: US 178

description: miRNA profile of archival plasma sample


title: US 170

description: miRNA profile of archival plasma sample

value: neg


title: US 176

description: miRNA profile of archival plasma sample


title: US 44b

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA219T

description: Validation set


title: Colorectal tumor tissue KRCA218T

description: Validation set


title: US 161

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA217T

description: Validation set


title: Colorectal tumor tissue KRCA213T

description: Validation set


title: US 179

description: miRNA profile of archival plasma sample


title: US 151

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA209T

description: Validation set


title: Colorectal tumor tissue KRCA207T

description: Validation set


title: US 152

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA210T

description: Validation set


title: Colorectal tumor tissue KRCA208T

description: Validation set


title: US 140

description: miRNA profile of archival plasma sample


title: US 139

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA206T

description: Validation set


title: US 131

description: miRNA profile of archival plasma sample


title: US 169

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA221T

description: Validation set


title: Colorectal tumor tissue KRCA203T

description: Validation set


title: US 162

description: miRNA profile of archival plasma sample


title: US 158

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA201T

description: Validation set


title: Colorectal tumor tissue KRCA214T

description: Validation set


title: US 157

description: miRNA profile of archival plasma sample


title: Colorectal tumor tissue KRCA212T

description: Validation set


title: Colorectal tumor tissue KRCA199T

description: Validation set


title: Colorectal tumor tissue KRCA181T

description: Validation set


title: US 124

description: miRNA profile of archival plasma sample


title: US 127

description: miRNA profile of archival plasma sample


title: US 128

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z156

description: Testing set


title: US 132

description: miRNA profile of archival plasma sample


title: US 121

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z146

description: Testing set


title: US 113

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z145

description: Testing set


title: Colonic mucosa Z144

description: Testing set


title: Colorectal tumor tissue KRCA198T

description: Validation set


title: Colonic mucosa Z143

description: Testing set


title: US 123

description: miRNA profile of archival plasma sample


title: US 81

description: miRNA profile of archival plasma sample


title: US 77

description: miRNA profile of archival plasma sample


title: US 122

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z141

description: Testing set


title: US 71

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z140

description: Testing set


title: Colonic mucosa Z139

description: Testing set


title: Colonic mucosa Z155

description: Testing set


title: Colonic mucosa Z137

description: Testing set


title: Colonic mucosa Z147

description: Testing set


title: US 96

description: miRNA profile of archival plasma sample


title: US 45

description: miRNA profile of archival plasma sample


title: US 47

description: miRNA profile of archival plasma sample


title: US 95

description: miRNA profile of archival plasma sample


title: US 24

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z135

description: Testing set


title: US 89

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z133

description: Testing set


title: Colonic mucosa Z142

description: Testing set


title: Colonic mucosa Z130

description: Testing set


title: US 18

description: miRNA profile of archival plasma sample


title: US 17

description: miRNA profile of archival plasma sample


title: US 46

description: miRNA profile of archival plasma sample


title: US 55

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z129

description: Testing set


title: US 28

description: miRNA profile of archival plasma sample


title: Colonic mucosa Z138

description: Testing set


title: Colonic mucosa Z136

description: Testing set


title: Colonic mucosa Z118

description: Testing set


title: Cell Line 4_5'aza treated

city: Singapore

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

description:
miRNA expression profiling
8226 5'azacytidine

hyb_protocol: The labeled samples were hybridized to Agilent human microRNA microarray slide for 20hrs at 55°C, 20RPM as per manufacturer's instruction.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2565CA)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09). TotalGeneSignal is set to a minimal value of 0.1 if all probes are not detected. The Feature Extraction Software obtains background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human Myeloma Cell Line

label_protocol: For each sample, 100ng of total RNA was dephosphorylated, denatured and labeled with Cy3 according to Agilent miRNA system protocol v2.4 (Agilent Technologies, Santa Clara, CA)

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1 mM L-glutamine, 100 units/ml penicillin and 100 mg/ml streptomycin. NCI-H929 was supplemented with 2-mercaptoethanol at a final concentration of 50uM. Cells were grown at 37°C in a humidified atmosphere with 5% CO2

extract_protocol: Qiagen miRNeasy Kit

treatment_protocol: Cells were treated with 5'azacytidine at the IC50 concentration, or DMSO at 0.1% v/v, for 96 hours. Fresh medium containing 5-azacytidine was replaced every 24 hours.

tag: cell line

value: 8226 myeloma cell line

tag: agent


title: Colonic mucosa Z112

description: Testing set


title: Cell Line 3_5'aza treated

description:
miRNA expression profiling
OPM2 5'azacytidine

value: OPM2 myeloma cell line


title: Cell Line 4_Control

description:
miRNA expression profiling
8226 DMSO

value: DMSO


title: Cell Line 2_5'aza treated

description:
miRNA expression profiling
MM1S 5'azacytidine

value: MM1S myeloma cell line


title: Cell Line 3_Control

description:
miRNA expression profiling
OPM2 DMSO


title: Colonic mucosa Z115

description: Testing set


title: Colonic mucosa Z103

description: Testing set


title: Colonic mucosa Z104

description: Testing set


title: Cell Line 2_Control

description:
miRNA expression profiling
MM1S DMSO


title: Cell Line 1_5'aza treated

description:
miRNA expression profiling
H929 5'azacytidine

value: H929 myeloma cell line


title: Colonic mucosa Z98

description: Testing set


title: Colonic mucosa Z101

description: Testing set


title: Colonic mucosa Z93

description: Testing set


title: Colonic mucosa Z92

description: Testing set


title: Cell Line 1_Control

description:
miRNA expression profiling
H929 DMSO


title: Colonic mucosa Z89

description: Testing set


title: Colonic mucosa Z88

description: Testing set


title: Colonic mucosa Z120

description: Testing set


title: Colonic mucosa Z85

description: Testing set


title: Colonic mucosa Z76

description: Testing set


title: Colonic mucosa Z70

description: Testing set


title: Colonic mucosa Z69

description: Testing set


title: Colonic mucosa Z65

description: Testing set


title: Colonic mucosa Z68

description: Testing set


title: Colonic mucosa Z74

description: Testing set


title: Colonic mucosa Z75

description: Testing set


title: Colonic mucosa Z63

description: Testing set


title: Colonic mucosa Z62

description: Testing set


title: Colonic mucosa Z60

description: Testing set


title: Colonic mucosa Z61

description: Testing set


title: Colonic mucosa Z64

description: Testing set


title: Colonic mucosa Z58

description: Testing set


title: Colonic mucosa Z59

description: Testing set


title: Colonic mucosa Z57

description: Testing set


title: Colonic mucosa Z19

description: Testing set


title: Colonic mucosa Z77

description: Testing set


title: Colonic mucosa Z18

description: Testing set


title: Colonic mucosa Z16

description: Testing set


title: Colonic mucosa Z5

description: Testing set


title: Colorectal tumor tissue T156

description: Testing set

value: Colorectal tumor tissue

value: male

value: colon


title: Colorectal tumor tissue T147

description: Testing set


title: Sk Mus_WY14643_10 mg/kg_Day4_Rep4

city: Dundee

first: Runxuan

last: Zhang

state: Angus

address: Errol Road, Invergowrie

department: Information and Computational Sciences

country: United Kingdom

institute: The James Hutton Institute

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_19_Sk Mus)

hyb_protocol: Following fragmentation, 3.75ug of cDNA were hybridized for 18 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multi-chip Average (RMA) normailzation method using Partek (Liver, heart, kidney, and skeletal muscle samples were each normalized independently)

source_name: Sk Mus_WY14643_10 mg/kg_Day4

label_protocol: Biotinylated cDNA were prepared according to the Nugen protocol from 100ng total RNA using Nugen WT Ovation V2 (cat. 3100-60) and Nugen Encore Biotin (cat. 4200-60)

extract_protocol: Qiagen miRNEasy was used according to maufacturers instruction including DNAse I treatment.

value: Skeletal Muscle

tag: compound

tag: dose

value: 10 mg/kg

tag: timepoint

value: 4 days


title: Colorectal tumor tissue T146

description: Testing set

tag: gender


title: Colonic mucosa Z21

description: Testing set

value: Colonic mucosa


title: Colorectal tumor tissue T145

description: Testing set

value: female


title: Sk Mus_WY14643_10 mg/kg_Day4_Rep3

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_18_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day4_Rep2

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_17_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day8_Rep4

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_59_Sk Mus)

source_name: Sk Mus_WY14643_10 mg/kg_Day8

value: 8 days


title: Sk Mus_WY14643_10 mg/kg_Day8_Rep3

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_58_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day8_Rep1

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_56_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day8_Rep5

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_60_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day4_Rep1

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_16_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day4_Rep5

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_20_Sk Mus)


title: Colorectal tumor tissue T142

description: Testing set

value: sigmoideum


title: Sk Mus_WY14643_10 mg/kg_Day15_Rep5

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_100_Sk Mus)

source_name: Sk Mus_WY14643_10 mg/kg_Day15

value: 15 days


title: Colorectal tumor tissue T143

description: Testing set


title: Colorectal tumor tissue T141

description: Testing set

value: rectum


title: Colorectal tumor tissue T144

description: Testing set


title: Sk Mus_WY14643_10 mg/kg_Day8_Rep2

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_57_Sk Mus)


title: Colorectal tumor tissue T155

description: Testing set


title: Colorectal tumor tissue T140

description: Testing set


title: Sk Mus_WY14643_10 mg/kg_Day15_Rep4

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_99_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day15_Rep3

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_98_Sk Mus)


title: Colorectal tumor tissue T139

description: Testing set


title: Sk Mus_WY14643_10 mg/kg_Day15_Rep2

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_97_Sk Mus)


title: Sk Mus_WY14643_10 mg/kg_Day15_Rep1

description: Sk Mus from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_96_Sk Mus)


title: Colorectal tumor tissue T138

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep9

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_49_Sk Mus)

source_name: Sk Mus_VEHICLE_VEHICLE_Day8

value: Vehicle

value: N / A


title: Colorectal tumor tissue T136

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep7

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_47_Sk Mus)


title: Colorectal tumor tissue T135

description: Testing set


title: Colorectal tumor tissue T133

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep6

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_46_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep8

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_48_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep4

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_44_Sk Mus)


title: Colorectal tumor tissue T120

description: Testing set


title: Colorectal tumor tissue T118

description: Testing set


title: Colorectal tumor tissue T129

description: Testing set


title: Colorectal tumor tissue T130

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep5

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_45_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep3

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_43_Sk Mus)


title: Colorectal tumor tissue T103

description: Testing set


title: Colorectal tumor tissue T112

description: Testing set


title: Colorectal tumor tissue T137

description: Testing set


title: Colorectal tumor tissue T104

description: Testing set


title: Colorectal tumor tissue T115

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep2

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_42_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep1

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_41_Sk Mus)


title: Colorectal tumor tissue T98

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day8_Rep10

description: Sk Mus from mouse treated with vehicle for 8 days (Mouse_50_Sk Mus)


title: Colorectal tumor tissue T101

description: Testing set


title: Colorectal tumor tissue T93

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep8

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_8_Sk Mus)

source_name: Sk Mus_VEHICLE_VEHICLE_Day4


title: Colorectal tumor tissue T92

description: Testing set


title: Colorectal tumor tissue T89

description: Testing set


title: Colorectal tumor tissue T85

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep6

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_6_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep5

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_5_Sk Mus)


title: Colorectal tumor tissue T77

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep7

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_7_Sk Mus)


title: Colorectal tumor tissue T88

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep10

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_10_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep9

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_9_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep2

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_2_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep4

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_4_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep1

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_1_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep7

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_87_Sk Mus)

source_name: Sk Mus_VEHICLE_VEHICLE_Day15


title: Colorectal tumor tissue T75

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep8

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_88_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day4_Rep3

description: Sk Mus from mouse treated with vehicle for 4 days (Mouse_3_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep4

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_84_Sk Mus)


title: Colorectal tumor tissue T70

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep5

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_85_Sk Mus)


title: Colorectal tumor tissue T69

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep6

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_86_Sk Mus)


title: Colorectal tumor tissue T68

description: Testing set


title: Colorectal tumor tissue T65

description: Testing set


title: Colorectal tumor tissue T64

description: Testing set


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep2

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_82_Sk Mus)


title: Colorectal tumor tissue T63

description: Testing set


title: Colorectal tumor tissue T60

description: Testing set


title: Colorectal tumor tissue T61

description: Testing set


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day8_Rep5

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_80_Sk Mus)

source_name: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day8

value: Rosiglitazone


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep3

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_83_Sk Mus)


title: Colorectal tumor tissue T58

description: Testing set


title: Colorectal tumor tissue T59

description: Testing set


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day8_Rep4

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_79_Sk Mus)


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day8_Rep1

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_76_Sk Mus)


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day8_Rep2

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_77_Sk Mus)


title: Colorectal tumor tissue T57

description: Testing set


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day8_Rep3

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_78_Sk Mus)


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day4_Rep4

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_39_Sk Mus)

source_name: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day4


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day4_Rep3

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_38_Sk Mus)


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day4_Rep5

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_40_Sk Mus)


title: Colorectal tumor tissue T76

description: Testing set


title: Colorectal tumor tissue T18

description: Testing set


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day15_Rep5

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_120_Sk Mus)

source_name: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day15


title: Colorectal tumor tissue T16

description: Testing set


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day4_Rep2

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_37_Sk Mus)


title: Colorectal tumor tissue T5

description: Testing set


title: Colorectal tumor tissue T21

description: Testing set


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day15_Rep4

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_119_Sk Mus)


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day4_Rep1

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_36_Sk Mus)


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day15_Rep2

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_117_Sk Mus)


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day15_Rep3

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_118_Sk Mus)


title: GM12878_VPA_1mM_120min_rep2

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors

hyb_protocol: Samples were hybridised using a Nimblegen Hybridisation Kit (05 583 934 001), including Sample Tracking Controls (05 223 512 001)

scan_protocol: Slides were scanned on a Nimblegen MS200 microarray scanner at a resolution of 2µm with balanced Speed/Sensitivity and 100% laser intensity using autogain

data_processing: Data were extracted using DEVA (Roche Nimblegen) and normalised by robust multichip average in R.

label_protocol: Samples were labelled with Cy3 using a Nimblegen One Colour Labeling Kit (Roche Nimblegen, 06 370 438 001)

growth_protocol: Immortalized, EBV-transformed lymphoblastoid cell lines (AH LCL) from healthy, karyotypically normal individuals were established in house. GM12878 Lymphoblastoid cells were purchased from the Coriell Institute. Both cell lines were maintained at  37°C, 5% CO2 in RPMI 1640 medium, 10% foetal bovine serum, supplemented with L-glutamine (2mM) and penicillin/streptomycin (all additives from Gibco).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was converted to double-stranded cDNA using cDNA synthesis kit (Roche Nimblegen, 11 117 831 001)

treatment_protocol: Cells were treated with 0.2mM, 1mM or 5mM valproic acid (VPA) or 0.5, 2.5 or 12.5µM suberoylanilide hydroxamic acid (SAHA) for 0, 30, 60 and 120 minutes

tag: cell  line

value: Female


title: Colorectal tumor tissue T62

description: Testing set


title: Sk Mus_GW501516_10 mg/kg_Day8_Rep5

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_70_Sk Mus)

source_name: Sk Mus_GW501516_10 mg/kg_Day8


title: Sk Mus_ROSIGLITAZONE_10 mg/kg_Day15_Rep1

description: Sk Mus from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_116_Sk Mus)


title: Sk Mus_GW501516_10 mg/kg_Day8_Rep4

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_69_Sk Mus)


title: GM12878_VPA_1mM_120min_rep3


title: Sk Mus_GW501516_10 mg/kg_Day8_Rep3

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_68_Sk Mus)


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep9

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_89_Sk Mus)


title: Sk Mus_GW501516_10 mg/kg_Day4_Rep5

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_30_Sk Mus)

source_name: Sk Mus_GW501516_10 mg/kg_Day4


title: GM12878_VPA_1mM_120min_rep1


title: GM12878_VPA_1mM_60min_rep2

source_name: GM12878, 1mM VPA, 60min


title: GM12878_VPA_1mM_30min_rep2

source_name: GM12878, 1mM VPA, 30min


title: Colorectal tumor tissue T19

description: Testing set

source_name: Tumor


title: Sk Mus_GW501516_10 mg/kg_Day8_Rep1

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_66_Sk Mus)


title: GM12878_VPA_1mM_60min_rep3


title: Sk Mus_GW501516_10 mg/kg_Day8_Rep2

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_67_Sk Mus)


title: GM12878_VPA_1mM_30min_rep3


title: Sk Mus_GW501516_10 mg/kg_Day4_Rep4

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_29_Sk Mus)


title: GM12878_VPA_1mM_0min_rep3

source_name: GM12878, 1mM VPA, 0min


title: GM12878_VPA_1mM_60min_rep1


title: Sk Mus_GW501516_10 mg/kg_Day4_Rep2

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_27_Sk Mus)


title: GM12878_VPA_1mM_30min_rep1


title: GM12878_VPA_1mM_0min_rep2


title: Sk Mus_GW501516_10 mg/kg_Day15_Rep5

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_110_Sk Mus)

source_name: Sk Mus_GW501516_10 mg/kg_Day15


title: Sk Mus_GW501516_10 mg/kg_Day15_Rep3

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_108_Sk Mus)


title: Sk Mus_GW501516_10 mg/kg_Day15_Rep2

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_107_Sk Mus)


title: AHLCL_SAHA_12.5µM_120min_rep2

source_name: AH LCL, 12.5µM SAHA, 120min

value: Male


title: Sk Mus_GW501516_10 mg/kg_Day4_Rep1

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_26_Sk Mus)


title: GM12878_VPA_1mM_0min_rep1


title: AHLCL_SAHA_12.5µM_120min_rep3


title: AHLCL_SAHA_12.5µM_120min_rep1


title: AHLCL_SAHA_12.5µM_60min_rep2

source_name: AH LCL, 12.5µM SAHA, 60min


title: AHLCL_SAHA_12.5µM_30min_rep1

source_name: AH LCL, 12.5µM SAHA, 30min


title: Kidney_WY14643_10 mg/kg_Day8_Rep4

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_59_Kidney)

source_name: Kidney_WY14643_10 mg/kg_Day8

value: Kidney


title: AHLCL_SAHA_12.5µM_60min_rep3


title: Sk Mus_GW501516_10 mg/kg_Day15_Rep1

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_106_Sk Mus)


title: Kidney_WY14643_10 mg/kg_Day8_Rep5

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_60_Kidney)


title: Sk Mus_GW501516_10 mg/kg_Day15_Rep4

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_109_Sk Mus)


title: AHLCL_SAHA_12.5µM_60min_rep1

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors


title: AHLCL_SAHA_12.5µM_30min_rep3


title: Sk Mus_GW501516_10 mg/kg_Day4_Rep3

description: Sk Mus from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_28_Sk Mus)


title: Kidney_WY14643_10 mg/kg_Day8_Rep3

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_58_Kidney)


title: AHLCL_SAHA_12.5µM_30min_rep2


title: AHLCL_SAHA_2.5µM_120min_rep3

source_name: AH LCL, 2.5µM SAHA, 120min


title: AHLCL_SAHA_12.5µM_0min_rep1

source_name: AH LCL, 12.5µM SAHA, 0min


title: Kidney_WY14643_10 mg/kg_Day8_Rep2

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_57_Kidney)


title: AHLCL_SAHA_2.5µM_60min_rep3

source_name: AH LCL, 2.5µM SAHA, 60min


title: Kidney_WY14643_10 mg/kg_Day4_Rep5

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_20_Kidney)

source_name: Kidney_WY14643_10 mg/kg_Day4


title: AHLCL_SAHA_2.5µM_120min_rep1


title: Kidney_WY14643_10 mg/kg_Day8_Rep1

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_56_Kidney)


title: AHLCL_SAHA_12.5µM_0min_rep2


title: Kidney_WY14643_10 mg/kg_Day15_Rep4

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_99_Kidney)

source_name: Kidney_WY14643_10 mg/kg_Day15


title: Kidney_WY14643_10 mg/kg_Day4_Rep4

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_19_Kidney)


title: AHLCL_SAHA_2.5µM_60min_rep2


title: Colorectal tumor tissue T74

description: Testing set

value: Colorectal tumor tissue


title: AHLCL_SAHA_2.5µM_60min_rep1


title: AHLCL_SAHA_12.5µM_0min_rep3


title: Kidney_WY14643_10 mg/kg_Day4_Rep1

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_16_Kidney)


title: Kidney_WY14643_10 mg/kg_Day15_Rep2

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_97_Kidney)


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep10

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_90_Sk Mus)

source_name: Sk Mus_VEHICLE_VEHICLE_Day15


title: Kidney_WY14643_10 mg/kg_Day4_Rep2

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_17_Kidney)


title: Sk Mus_VEHICLE_VEHICLE_Day15_Rep1

description: Sk Mus from mouse treated with vehicle for 15 days (Mouse_81_Sk Mus)


title: AHLCL_SAHA_2.5µM_30min_rep3

source_name: AH LCL, 2.5µM SAHA, 30min


title: Kidney_WY14643_10 mg/kg_Day4_Rep3

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_18_Kidney)


title: Kidney_WY14643_10 mg/kg_Day15_Rep3

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_98_Kidney)


title: AHLCL_SAHA_2.5µM_120min_rep2


title: Kidney_WY14643_10 mg/kg_Day15_Rep1

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_96_Kidney)


title: AHLCL_SAHA_2.5µM_30min_rep2


title: Kidney_WY14643_10 mg/kg_Day15_Rep5

description: Kidney from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_100_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day8_Rep9

description: Kidney from mouse treated with vehicle for 8 days (Mouse_49_Kidney)


title: AHLCL_SAHA_2.5µM_0min_rep3

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors

source_name: AH LCL, 2.5µM SAHA, 0min


title: Kidney_VEHICLE_VEHICLE_Day8_Rep8

description: Kidney from mouse treated with vehicle for 8 days (Mouse_48_Kidney)


title: AHLCL_SAHA_2.5µM_30min_rep1


title: Kidney_VEHICLE_VEHICLE_Day8_Rep7

description: Kidney from mouse treated with vehicle for 8 days (Mouse_47_Kidney)


title: AHLCL_SAHA_0.5µM_120min_rep3

source_name: AH LCL, 0.5µM SAHA, 120min


title: Kidney_VEHICLE_VEHICLE_Day8_Rep5

description: Kidney from mouse treated with vehicle for 8 days (Mouse_45_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day8_Rep4

description: Kidney from mouse treated with vehicle for 8 days (Mouse_44_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day8_Rep6

description: Kidney from mouse treated with vehicle for 8 days (Mouse_46_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day8_Rep1

description: Kidney from mouse treated with vehicle for 8 days (Mouse_41_Kidney)


title: AHLCL_SAHA_0.5µM_120min_rep2


title: AHLCL_SAHA_2.5µM_0min_rep2


title: AHLCL_SAHA_0.5µM_60min_rep2

source_name: AH LCL, 0.5µM SAHA, 60min


title: Kidney_VEHICLE_VEHICLE_Day4_Rep8

description: Kidney from mouse treated with vehicle for 4 days (Mouse_8_Kidney)


title: AHLCL_SAHA_0.5µM_60min_rep1


title: Kidney_VEHICLE_VEHICLE_Day8_Rep2

description: Kidney from mouse treated with vehicle for 8 days (Mouse_42_Kidney)


title: AHLCL_SAHA_0.5µM_30min_rep1

source_name: AH LCL, 0.5µM SAHA, 30min


title: Kidney_VEHICLE_VEHICLE_Day8_Rep10

description: Kidney from mouse treated with vehicle for 8 days (Mouse_50_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day4_Rep9

description: Kidney from mouse treated with vehicle for 4 days (Mouse_9_Kidney)


title: AHLCL_SAHA_0.5µM_0min_rep2

source_name: AH LCL, 0.5µM SAHA, 0min


title: AHLCL_SAHA_0.5µM_60min_rep3


title: AHLCL_SAHA_0.5µM_120min_rep1


title: AHLCL_SAHA_2.5µM_0min_rep1


title: AHLCL_SAHA_0.5µM_30min_rep2


title: Kidney_VEHICLE_VEHICLE_Day4_Rep6

description: Kidney from mouse treated with vehicle for 4 days (Mouse_6_Kidney)


title: AHLCL_SAHA_0.5µM_30min_rep3


title: AHLCL_SAHA_0.5µM_0min_rep3


title: Kidney_VEHICLE_VEHICLE_Day4_Rep7

description: Kidney from mouse treated with vehicle for 4 days (Mouse_7_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day8_Rep3

description: Kidney from mouse treated with vehicle for 8 days (Mouse_43_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day4_Rep4

description: Kidney from mouse treated with vehicle for 4 days (Mouse_4_Kidney)


title: AHLCL_VPA_5mM_120min_rep3

source_name: AH LCL, 5mM VPA, 120min


title: Kidney_VEHICLE_VEHICLE_Day4_Rep10

description: Kidney from mouse treated with vehicle for 4 days (Mouse_10_Kidney)


title: AHLCL_VPA_5mM_120min_rep1


title: AHLCL_VPA_5mM_60min_rep3

source_name: AH LCL, 5mM VPA, 60min


title: Kidney_VEHICLE_VEHICLE_Day4_Rep1

description: Kidney from mouse treated with vehicle for 4 days (Mouse_1_Kidney)


title: AHLCL_VPA_5mM_120min_rep2

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors


title: Kidney_VEHICLE_VEHICLE_Day15_Rep9

description: Kidney from mouse treated with vehicle for 15 days (Mouse_89_Kidney)


title: AHLCL_VPA_5mM_60min_rep2


title: AHLCL_VPA_5mM_60min_rep1


title: AHLCL_VPA_5mM_30min_rep2

source_name: AH LCL, 5mM VPA, 30min


title: Kidney_VEHICLE_VEHICLE_Day4_Rep2

description: Kidney from mouse treated with vehicle for 4 days (Mouse_2_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day4_Rep3

description: Kidney from mouse treated with vehicle for 4 days (Mouse_3_Kidney)


title: AHLCL_VPA_5mM_30min_rep3


title: AHLCL_VPA_5mM_0min_rep1

source_name: AH LCL, 5mM VPA, 0min


title: Kidney_VEHICLE_VEHICLE_Day15_Rep4

description: Kidney from mouse treated with vehicle for 15 days (Mouse_84_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day15_Rep8

description: Kidney from mouse treated with vehicle for 15 days (Mouse_88_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day15_Rep3

description: Kidney from mouse treated with vehicle for 15 days (Mouse_83_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day15_Rep2

description: Kidney from mouse treated with vehicle for 15 days (Mouse_82_Kidney)


title: AHLCL_VPA_1mM_120min_rep2

source_name: AH LCL, 1mM VPA, 120min


title: AHLCL_VPA_5mM_0min_rep3


title: Kidney_VEHICLE_VEHICLE_Day15_Rep5

description: Kidney from mouse treated with vehicle for 15 days (Mouse_85_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day15_Rep10

description: Kidney from mouse treated with vehicle for 15 days (Mouse_90_Kidney)


title: AHLCL_VPA_5mM_0min_rep2


title: Kidney_VEHICLE_VEHICLE_Day15_Rep6

description: Kidney from mouse treated with vehicle for 15 days (Mouse_86_Kidney)


title: AHLCL_VPA_1mM_120min_rep3


title: AHLCL_VPA_1mM_120min_rep1


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day8_Rep5

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_80_Kidney)

source_name: Kidney_ROSIGLITAZONE_10 mg/kg_Day8


title: Kidney_VEHICLE_VEHICLE_Day15_Rep1

description: Kidney from mouse treated with vehicle for 15 days (Mouse_81_Kidney)


title: Kidney_VEHICLE_VEHICLE_Day15_Rep7

description: Kidney from mouse treated with vehicle for 15 days (Mouse_87_Kidney)


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day8_Rep1

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_76_Kidney)


title: AHLCL_VPA_1mM_30min_rep2

source_name: AH LCL, 1mM VPA, 30min


title: AHLCL_VPA_1mM_30min_rep1


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day8_Rep2

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_77_Kidney)


title: AHLCL_VPA_1mM_60min_rep2

source_name: AH LCL, 1mM VPA, 60min


title: AHLCL_VPA_1mM_60min_rep3


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day8_Rep3

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_78_Kidney)


title: AHLCL_VPA_1mM_60min_rep1

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors


title: AHLCL_VPA_1mM_0min_rep3

source_name: AH LCL, 1mM VPA, 0min


title: AHLCL_VPA_1mM_0min_rep1


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day4_Rep4

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_39_Kidney)

source_name: Kidney_ROSIGLITAZONE_10 mg/kg_Day4


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day4_Rep5

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_40_Kidney)


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day8_Rep4

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_79_Kidney)


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day4_Rep3

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_38_Kidney)


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day15_Rep5

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_120_Kidney)

source_name: Kidney_ROSIGLITAZONE_10 mg/kg_Day15


title: AHLCL_VPA_1mM_0min_rep2


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day4_Rep2

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_37_Kidney)


title: AHLCL_VPA_0.2mM_120min_rep3

source_name: AH LCL, 0.2mM VPA, 120min


title: AHLCL_VPA_0.2mM_120min_rep2


title: AHLCL_VPA_1mM_30min_rep3


title: AHLCL_VPA_0.2mM_60min_rep2

source_name: AH LCL, 0.2mM VPA, 60min


title: AHLCL_VPA_0.2mM_120min_rep1


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day15_Rep1

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_116_Kidney)


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day4_Rep1

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_36_Kidney)


title: AHLCL_VPA_0.2mM_60min_rep3


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day15_Rep2

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_117_Kidney)


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day15_Rep4

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_119_Kidney)


title: AHLCL_VPA_0.2mM_30min_rep3

source_name: AH LCL, 0.2mM VPA, 30min


title: Kidney_ROSIGLITAZONE_10 mg/kg_Day15_Rep3

description: Kidney from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_118_Kidney)


title: AHLCL_VPA_0.2mM_60min_rep1


title: AHLCL_VPA_0.2mM_0min_rep3

source_name: AH LCL, 0.2mM VPA, 0min


title: Kidney_GW501516_10 mg/kg_Day8_Rep3

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_68_Kidney)

source_name: Kidney_GW501516_10 mg/kg_Day8


title: Kidney_GW501516_10 mg/kg_Day8_Rep4

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_69_Kidney)


title: Kidney_GW501516_10 mg/kg_Day4_Rep2

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_27_Kidney)

source_name: Kidney_GW501516_10 mg/kg_Day4


title: Kidney_GW501516_10 mg/kg_Day4_Rep1

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_26_Kidney)


title: AHLCL_VPA_0.2mM_30min_rep1


title: Kidney_GW501516_10 mg/kg_Day4_Rep5

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_30_Kidney)


title: Kidney_GW501516_10 mg/kg_Day4_Rep4

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_29_Kidney)


title: Kidney_GW501516_10 mg/kg_Day8_Rep1

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_66_Kidney)


title: Kidney_GW501516_10 mg/kg_Day15_Rep2

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_107_Kidney)

source_name: Kidney_GW501516_10 mg/kg_Day15


title: Kidney_GW501516_10 mg/kg_Day15_Rep3

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_108_Kidney)


title: Kidney_GW501516_10 mg/kg_Day8_Rep2

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_67_Kidney)


title: Kidney_GW501516_10 mg/kg_Day15_Rep5

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_110_Kidney)


title: AHLCL_VPA_0.2mM_0min_rep1

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors


title: Kidney_GW501516_10 mg/kg_Day4_Rep3

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_28_Kidney)


title: Kidney_GW501516_10 mg/kg_Day15_Rep1

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_106_Kidney)


title: Heart_WY14643_10 mg/kg_Day8_Rep5

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_60_Heart)

source_name: Heart_WY14643_10 mg/kg_Day8

value: Heart


title: Kidney_GW501516_10 mg/kg_Day15_Rep4

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_109_Kidney)


title: acetone 3

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

institute: SCK-CEN

description: induction with acetone

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit's protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices©, USA).

data_processing: Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fitted to al linear model and moderated t-statistics were calculated using empirical Bayes method. P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Cupriavidus metallidurans CH34

source_name: non-induced culture

label_protocol: For microarray analyses, 10 µg of high-quality total RNA were reverse-transcribed using random hexamer primers (Roche) and were directly labeled by incorporation of Cy3-dCTP or Cy5-dCTP nucleotides (Amersham Biosciences) according to the instructions provided by the ChipShot Direct Labeling and Clean-up System (Promega). Labeled samples for one test condition and one reference condition were dissolved in the universal hybridization buffer provided in the Pronto kit and were then mixed and added together on the spotted slide for hybridization overnight at 42°C in a TECAN HS4800 Hybridization Station (Tecan). The slides were washed according to the washing protocol supplied with the Pronto kit.

growth_protocol: C. metallidurans CH34 was grown at 30°C in the phosphate-low and Tris-buffered 284 mineral medium as described previously (Schlegel et al., 1961; Mergeay et al., 1985), supplemented with various carbon sources including sodium gluconate (Merck), acetone (Merck), isopropanol (BDH), n-propanol (UCB), hexanol (Merck), toluene (Merck), benzene (Merck) and xylene (Merck) at different concentrations. Liquid precultures (20 ml of 284 mineral medium + gluconate 55 mM of carbon) were grown overnight in hermetically closed 50 ml Falcon tubes at 30°C and shaken at 145 rpm in an orbital shaker (Aquatron, InforHT). Two milliliters of those precultures (OD600nm ± 0.8) were centrifuged at 5000 rpm, and the bacterial pellet was used to inoculate a second generation of cultures in hermetically closed 50 ml Falcon tubes containing 20 ml of medium supplemented with one of the previously cited carbon sources to test the metabolization capability of CH34.  For each culture condition, the presented data were obtained from at least 3 independent cultures.

extract_protocol: The RNA content of 20 ml of liquid bacterial cultures in the end of the exponential phase growth phase (OD600nm ± 1) was fixed with RNA Protect solution (Qiagen) directly added to the culture using a ratio of 2:1 (v/v). After an incubation of 5 min at room temperature, fixed cells were collected by centrifugation at 5000 rpm for 10 min and stored at -80°C. For cultures containing acetone in the medium, the RNA Protect fixative could not be used due to incompatibility of the organic solvents; and thus cells from these cultures were immediately processed for RNA extraction. RNA was extracted using a Promega 23100 SV Total RNA Isolation Kit (Promega) following the manufacturer’s instructions. RNA quantity was evaluated on a Nanodrop ND-1000 spectrophotometer (Peqlab). An RNA quality control was performed using the RNA 6000 NanoAssay kit with an Agilent 2100 Bioanalyzer following the manufacturer’s instructions. Only RNA of high quality, i.e. RIN values > 8, were kept to further microarray analyses. RNA samples were stored at -80°C until use for further microarray analyses.

treatment_protocol: After growth, the subculture was divided in two equal portions of 20 ml in two new falcon tubes. One tube was used as condition (i.e. challenged with the defined amount of a chemical compound – see samples) while the other flask served as control (i.e. same amount of sterile water added). Immediately after addition, the tubes were incubated at the same conditions as before for the needed duration for chemical compound challenges (i.e. 30 min). After this challenge, each 20 ml culture was immediately subdivided in 10 eppendorfs of 2 ml, and the cells were harvested by centrifugation for 1 minute at 10 000 g. Supernatans was removed and the eppendorfs containing only the centrifuged bacterial pellets (each containing ca. 109 bacterial cells) were flash frozen by immersion into liquid nitrogen. Pellets were kept frozen at -80°C at all times. Each challenge condition (i.e. each of the different tested chemical compounds) was performed in biological quadruplicate, using 4 independent bacterial cultures.

tag: treatment

value: control

source_name: induction with acetone

value: acetone


title: Heart_WY14643_10 mg/kg_Day8_Rep3

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_58_Heart)

value: 10 mg/kg


title: BLS4  WT

city: Otsu-shi

first: keiki

last: sugimoto

state: Shiga

address: 1-11-1, Karasaki

department: Fujii Memorial Research Institute

country: Japan

institute: Otsuka Pharmaceutical

hyb_protocol: Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90 ºC for 5 minutes and immediately chill on ice for 30 minutes.  Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips.  Set the shaker speed to 300 rpm and incubate slides for 18 h.  Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75× TNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75× TNT, and incubate at 46 °C for exactly 1 h.  Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir into the small reagent reservoir and incubate bioarrays at ambient temperature for 30 minutes. Wash the bioarrays four times with 1× TNT (5 minutes each wash) in large reagent reservoirs. Rinse the bioarrays in 0.1× SSC/0.05% Tween for 30 seconds. Immediately follow the rinse with centrifugation to dry bioarrays.

scan_protocol: The arrays were scanned with GenePix 4000B (Molecular Devices).

data_processing: Signal intensities were quantified with CodeLinh Expression Anlysis Software v5.0 (Applied Microarray, Inc.)

source_name: BLS4 Cell Line

label_protocol: In 25 μl total volume, add 10 μg of cRNA to 5 μl of 5× fragmentation buffer and incubate at 94 ºC for 20 minutes.

extract_protocol: none provided by the submitter

tag: Sex


title: acetone 1

description: induction with acetone


title: Kidney_GW501516_10 mg/kg_Day8_Rep5

description: Kidney from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_70_Kidney)


title: Heart_WY14643_10 mg/kg_Day8_Rep1

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_56_Heart)


title: Heart_WY14643_10 mg/kg_Day8_Rep2

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_57_Heart)


title: BLS4 PP

source_name: BLS4 cell treated by  PP


title: Heart_WY14643_10 mg/kg_Day15_Rep5

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_100_Heart)

source_name: Heart_WY14643_10 mg/kg_Day15


title: Heart_WY14643_10 mg/kg_Day4_Rep3

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_18_Heart)

source_name: Heart_WY14643_10 mg/kg_Day4

value: 4 days


title: Heart_WY14643_10 mg/kg_Day8_Rep4

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days (Mouse_59_Heart)


title: acetone 2

description: induction with acetone


title: Heart_VEHICLE_VEHICLE_Day8_Rep7

description: Heart from mouse treated with vehicle for 8 days (Mouse_47_Heart)


title: Heart_WY14643_10 mg/kg_Day15_Rep2

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_97_Heart)


title: Heart_WY14643_10 mg/kg_Day4_Rep1

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_16_Heart)


title: Heart_WY14643_10 mg/kg_Day4_Rep4

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_19_Heart)


title: Heart_WY14643_10 mg/kg_Day15_Rep4

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_99_Heart)


title: Heart_VEHICLE_VEHICLE_Day8_Rep9

description: Heart from mouse treated with vehicle for 8 days (Mouse_49_Heart)


title: Heart_WY14643_10 mg/kg_Day15_Rep3

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_98_Heart)


title: Heart_WY14643_10 mg/kg_Day4_Rep5

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_20_Heart)


title: Heart_WY14643_10 mg/kg_Day4_Rep2

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days (Mouse_17_Heart)


title: Heart_VEHICLE_VEHICLE_Day8_Rep6

description: Heart from mouse treated with vehicle for 8 days (Mouse_46_Heart)


title: Heart_VEHICLE_VEHICLE_Day8_Rep3

description: Heart from mouse treated with vehicle for 8 days (Mouse_43_Heart)


title: Heart_VEHICLE_VEHICLE_Day8_Rep4

description: Heart from mouse treated with vehicle for 8 days (Mouse_44_Heart)


title: Kidney_VEHICLE_VEHICLE_Day4_Rep5

description: Kidney from mouse treated with vehicle for 4 days (Mouse_5_Kidney)


title: Heart_VEHICLE_VEHICLE_Day8_Rep5

description: Heart from mouse treated with vehicle for 8 days (Mouse_45_Heart)


title: CLL Exosomal RNA 6

city: Liverpool

first: Mosavar

last: Farahani

address: Daulby Street

department: Molecular and Clinical Cancer Medicine

institute: University of Liverpool

description: a pool of cellular RNA from 23 CLL individuals

hyb_protocol: The Hy3-labelled exosome samples or CLL cell samples and a Hy5-labelled CLL cell samples pool (n=23; common reference sample) were hybridized to the miRCURY LNA array (Exiqon miRCURYTM LNA array v.5).  The hybridization and all steps of the image analysis and normalisation of data were carried out by Exiqon.

data_processing:
Median data for Hy3 and Hy5 was calculated from the replicated measurements on the same slide (SD-values were calculated from 4 replicate spots).
Different normalization methods such as lowess and quantile were performed to see the best method to use to compare the results between the exosomal and the cellular samples.  We were unable to find a suitable normalizing method for both exosomes and cells thus it was found that the best method was to use the raw intensity data from the arrays after background correction.  Other method skewed the data set and provided unreliable results
The supplementary file "LME_background-subtracted_Hy3.txt" contains LogMedianExpression (LME) of Hy3 background-subtracted raw values.

source_name: RNA extracted from exosomes isolated from CLL culture medium patient 6

label_protocol: We used dual colour hybridizations and we used the common reference approach which each sample whether exosomal RNA or cellular RNA was compared to common reference sample (a pool of 23 CLL cells).

growth_protocol: CLL cells were cultured for 48h and media supernatant was harvested. Exosomes were purified from this supernatant.

extract_protocol: Total RNA extractions were performed using the miRNeasy kit (Qiagen).  Briefly, the quality of the total RNA was verified by an Agilent 2100 Bioanalyzer.

tag: rna source

value: Exosomal RNA from CLL pateint 6

tag: cell type/component

value: isolated exosomes from culture medium of CLL 6

value: blood

source_name: Pooled reference sample

tag: reference type

value: a collection of 23 RNA extracted from 23 CLL cell samples


title: CLL Cellular RNA 6

scan_protocol: The hybridization and all steps of the image analysis and normalisation of data were carried out by Exiqon.

source_name: RNA extracted  from CLL cells patient 6

value: Cellular RNA from CLL patient 6

value: isolated B cells from fresh blood CLL 5

tag: tissue


title: CLL Exosomal RNA 5

source_name: RNA extracted from exosomes isolated from CLL culture medium patient 5

value: Exosomal RNA from CLL pateint 5

value: isolated exosomes from culture medium of CLL 5


title: CLL Cellular RNA 5

source_name: RNA extracted  from CLL cells patient 5

value: Cellular RNA from CLL patient 5


title: CLL Exosomal RNA 4

source_name: RNA extracted from exosomes isolated from CLL culture medium patient 4

value: Exosomal RNA from CLL pateint 4

value: isolated exosomes from culture medium of CLL 4


title: Heart_WY14643_10 mg/kg_Day15_Rep1

description: Heart from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days (Mouse_96_Heart)

value: 15 days


title: Heart_VEHICLE_VEHICLE_Day8_Rep1

description: Heart from mouse treated with vehicle for 8 days (Mouse_41_Heart)

value: Heart

value: Vehicle

value: N / A

value: 8 days


title: Heart_VEHICLE_VEHICLE_Day4_Rep9

description: Heart from mouse treated with vehicle for 4 days (Mouse_9_Heart)

value: 4 days


title: Heart_VEHICLE_VEHICLE_Day8_Rep2

description: Heart from mouse treated with vehicle for 8 days (Mouse_42_Heart)


title: CLL Cellular RNA 4

source_name: RNA extracted  from CLL cells patient 4

value: Cellular RNA from CLL patient 4

value: isolated B cells from fresh blood CLL 4


title: Heart_VEHICLE_VEHICLE_Day4_Rep8

description: Heart from mouse treated with vehicle for 4 days (Mouse_8_Heart)