title: HD_24_NA

status: Public on Dec 28 2015

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description: RNA from purified neutrophils

hyb_protocol: Fragmented and labeled cDNA was hybridized for 18 h at 50°C. Hybridization was performed using GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix).

scan_protocol: The microarrays were read with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Normalization processing and quality controls were performed using R/Bioconductor (R version 3.0.0 (2013-04-03)) (R Development Core Team – 2009). We performed quality controls at both probe and probeset levels). Raw expression profiles were normalized using the GC-RMA algorithm (R/Bioconductor). To reduce the number of probeset, we applied a filtering process based on the MAS5.0 p-values.

source_name: Purified neutrophils

label_protocol: Fragmented cDNA was end-labeled with a biotin-conjugated nucleotide analog (DLR-1a; Affymetrix, Santa Clara, CA) by using terminal transferase (Roche Diagnostics, Germany).

extract_protocol: RNA was isolated using Qiagen RNAeasy Plus Mini RNA isolation kit according to the manufacturer’s protocol. The integrity and quality of the total RNA was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) by means of the RNA 6000 Nano assay (Agilent). cDNA was synthesized from 50 ng total RNA using the WT-Ovation™ System (NuGEN, San Carlos, CA).

treatment_protocol: Blood samples were first diluted (1:2) with phosphate-buffered saline, layered over Ficoll-Paque (Biochrom, Germany) and centrifuged. Neutrophils were then aspirated and collected; after a washing step and red blood cell lysis (Versalyse, Beckman Coulter), viability and purity were determined by flow cytometry using LDS 751 (Life Technologies, Carlsbad, CA). Human neutrophil Enrichment Kit (Stem Cell, Canada) was used to purify neutrophils following the manufacturer’s recommendations. 5.107 cells/well (dilution in recommended buffer: PBS + 2% Fetal Bovine Serum or 0.5% BSA+ 1mM EDTA) were plated into a 96-untreated U-bottom plate (Corning, NY) and 50µl/ml of EasySep™ Human Enrichment Cocktail were added for 10 min. Incubation with 100µl/ml of EasySep™ D Magnetic Particles for 5 min preceded the action held by the EasyPlate™ magnet when placing the plate onto the magnet for 10 min. The supernatant contained the enriched neutrophils. Granulocytes were suspended in Qiagen RLT Buffer (Qiagen, the Netherlands) containing 1% B-mercaptoethanol and stored at -80°C until RNA isolation.

value: healthy control


title: HD_22_NA

type: RNA

description: RNA from purified neutrophils

label: biotin

molecule: total RNA

organism: Homo sapiens


title: HD_23_NA

description: RNA from purified neutrophils


title: HD_21_NA

description: RNA from purified neutrophils


title: HD_26_NA

description: RNA from purified neutrophils


title: Patient_20_J3

description: RNA from purified neutrophils

value: Patient


title: Fetal Liver 2

status: Public on Dec 29 2015

type: genomic

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

country: USA

institute: Rhode Island Hospital

description: Normal Fetal Liver

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 450k Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Hiscan according to manufacturer's instructions

data_processing:
GenomeStudio software
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Fetal Liver

label_protocol: Standard Illumina Protocol

growth_protocol: Normal adult liver was obtained through the The Liver Tissue Cell Distribution System is funded by NIH Contract #HHSN276201200017C.  Fetal liver was obtained from spontaneous stillbirths occuring between 20-22wk gestation

extract_protocol: Genomic DNA was extracted using the Qiagen All prep kit according to the manufacturer's instructions.

treatment_protocol: Liver was flash frozen in liquid nitrogen at the time of harvest and stored at -80 until use

tag: gender

value: Male

tag: age


title: Adult Liver 3

description: Normal Adult liver

source_name: Adult Liver

value: 65 yr


title: HD_28_NA

description: RNA from purified neutrophils


title: HD_27_NA

description: RNA from purified neutrophils


title: Fetal Liver 3

description: Normal Fetal Liver


title: Patient_19_J6

description: RNA from purified neutrophils


title: Healthy Control1

city: Athens

first: Marianthi

last: Logotheti

address: 48 Vassileos Constantinou Avenue

country: Greece

institute: National Hellenic Research Foundation

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Quantile normalisation with FlexArray software

source_name: Skin fibroblast

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Fibroblast cells were cultured from skin biopsies obtained from 10 patients (six men and four women aged 29–77 years) diagnosed with bipolar type-1, according to DSM-IV criteria [Persson et al., 2009]. Fibroblast cell lines from 5 volunteers, without a diagnosis of a psychiatric disease were used as matching controls. The fibroblast cells were cultured in plastic tissue culture flasks, contained minimal essential medium (MEM) supplemented with 10% fetal bovine serum (FBS), l-glutamine (2 mM/l), penicillin (100 mg/ml), streptomycin (100 mg/ml) and Amnio-MaxTM. The cells were maintained in a humidified atmosphere of 5% CO2 in air at 37◦C for approximately 4 weeks, until sufficient amount of cells had achieved. The cells were harvested by used EDTA and Trypsin solutions, washed and stored in -80oC until were used for RNA extraction. Cell lines between 8th and 13th passages (number of splitting) were used for the experiments. All growth media, antibiotics and fetal bovine serum (FBS) were obtained from Gibco Invitrogen cell culture (Sweden).

extract_protocol: Total RNA was extracted with using NucleoSpin® RNA ll kit. Quality control was performed with Agilent Bioanalyser.

tag: disease state

value: healthy


title: Fetal Liver 1

description: Normal Fetal Liver


title: Patient_18_J4

description: RNA from purified neutrophils


title: Differentiated hUC-MSCs, biological rep3

status: Public on Dec 30 2015

city: Chongqing

first: xiaoqin

last: zhou

address: Zhongshan Er Road

country: China

institute: Children's hospital of Chongqing medical university

description: Gene expression data from four stages of hUC-MSCs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Human umbilical cord derived mesenchymal stem cells induced differentiation for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: hUC-MSCs at passage 5 were seeded at 4x105/well in a 6-well culture plate.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Cells were pre-induced in all-trans-retinoic acid (ATRA) (1μmol/L) for 24 hours, the undifferentiated hUC-MSCs were induced using MNM for 24 hours to achieve a neuronal differentiation status (Dif). The MNM was replaced with complete culture medium (DMEM/F12 containing 10% FBS) for 24 hours following neuronal differentiation to achieve a neuronal dedifferentiation status（De-Dif）. Then, cells were transferred to MNM for another 24 hours to achieve neuronal redifferentiation status (Re-Dif).

tag: tissue

value: umbilical cord

tag: origin

value: yellow and Chongqing, China parents

tag: cell stage

value: induced differentiation for 24h


title: Healthy Control2


title: Bipolar Disorder9

value: Bipolar Disorder


title: Bipolar Disorder10


title: Adult Liver 1

description: Normal Adult liver

value: 55 yr


title: Adult Liver 2

description: Normal Adult liver

value: 56 yr


title: HD_25_NA

description: RNA from purified neutrophils


title: Patient_16_J4

description: RNA from purified neutrophils


title: Patient_17_J7

description: RNA from purified neutrophils


title: Patient_9_J3

description: RNA from purified neutrophils


title: Patient_11_J3

description: RNA from purified neutrophils


title: Bipolar Disorder7


title: Bipolar Disorder8


title: Patient_3_J7

description: RNA from purified neutrophils


title: Patient_12_J7

description: RNA from purified neutrophils


title: Patient_15_J7

description: RNA from purified neutrophils


title: BCBL1 treatment rep 1

city: Los Angeles

first: Timothy

middle: J.

last: Triche

state: CA

address: 1450 Biggy St., Harlyne Norris Research Tower 3509

department: Norris Comprehensive Cancer Center

institute: University of Southern California, Keck School of Medicine

description: BCBL1 treatment rep 1

data_processing: The data were normalised using limma::neqc() background correction and quantile normalisation in R

source_name: BCBL1 cell line

label_protocol: Standard as recommended by Illumina

growth_protocol: Identical culture media save for treatment (DMSO or lenalidomide)

extract_protocol: Standard as recommended by Illumina

treatment_protocol: DMSO or 5uM lenalidomide added to media

tag: cell line

tag: treatment

value: Lenalidomide 5uM


title: Patient_6_J8

description: RNA from purified neutrophils


title: Bipolar Disorder5


title: Patient_5_J4

description: RNA from purified neutrophils


title: Bipolar Disorder6


title: Bipolar Disorder3


title: Bipolar Disorder1


title: BCBL1 treatment rep 2

description: BCBL1 treatment rep 2


title: Bipolar Disorder4


title: m-DC_A

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: The labelled samples were hybridized to the HTA 2.0 GeneChip array (Affymetrix) for 16h at 45 C

scan_protocol: The arrays were scanned in an Affymetrix 3000 7G scanner

data_processing:
Data were normalized using Robust Multichip Average (RMA) normalization in Expression Console, build 1.3.1.187 (Affymetrix). Pelase note, that this is a GENE level analysis.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

label: Biotin

source_name: mature dendritic cells + 1mM acetate

label_protocol: WT_PLUS labeling kit (Affymetrix) according to the manufacturers´ instructions

growth_protocol: Monocytes were cultured at 37°C in 5%CO2 in media supplemented with 10% fetal bovine serum (FBS, Gibco) GM-CSF and IL-4 (50 ng/ml both, PeproTech) for 7 days to generate im-DC.

extract_protocol: RNeasy kit (Qiagen) according to the manufacturers´ instructions

treatment_protocol: The maturation of DC, via LPS (100ng/ml, E.coli 055:B5), as well as treatment with individual short-chain fatty acids took place for the last 24h of culture.

tag: cell type

value: mature dendritic cells

value: 1mM acetate

value: hematopoietic tissue


title: Bipolar Disorder2


title: m-DC_P

source_name: mature dendritic cells + 1mM propionate

value: 1mM propionate


title: Patient_14_J4

description: RNA from purified neutrophils


title: BCBL1 control rep 2

description: BCBL1 control rep 2

value: DMSO


title: Adult Liver, bio rep 2

description:
Gene expression from Affymetrix Human Gene 1.0 ST Array.
SAPE (streptavidin-conjugated Phycoerythrin)

hyb_protocol: After fragmentation, 2.475ug cRNA was hybridized for 17 h at 45 C, 60rpm, on a GeneChip Human Gene 1.0 ST Array. Then, washing and staining were done according to manufacturer's instructions using the Fluidics recommended for the arrays and Affymetrix Wash/Stain/Hyb kit.

scan_protocol: The arrays were scanned with a Affymetrix 3000 7G scanner using manufacturer's instructions.

data_processing: RMA algorithm.

source_name: Adult liver

label_protocol: Samples (100ng total RNA) were labeled with biotin using the Affymetrix WT labeling kit (Cat#900670) according to manufacturer's instructions.

growth_protocol: Normal adult liver was obtained through The Liver Tissue Cell Distribution System is funded by NIH Contract #HHSN276201200017C. Fetal liver was obtained from spontaneous stillbirths.

extract_protocol: Nucleic acids were extracted from liver using the All prep kit (Qiagen) according to the manufacturer's directions.

treatment_protocol: Samples were flash frozen in liquid nitrogen at the time of harvest and stored at -80 until use.

value: liver

value: male

value: 56 yrs


title: BCBL1 control rep 1

description: BCBL1 control rep 1


title: m-DC_B

source_name: mature dendritic cells + 1mM butyrate

value: 1mM butyrate


title: BC3 treatment rep 2

description: BC3 treatment rep 2

source_name: BC3 cell line


title: BC3 treatment rep 1

description: BC3 treatment rep 1


title: ssn6 wor1 (a/a) v. pooled reference (replicate B)

city: San Francisco

first: Matthew

last: Lohse

address: 44 Vicksburg Street

institute: BioSynesis, Inc.

description: ssn6 wor1 (a/a)_repB

hyb_protocol: 0.4 µg Cy3-labelled cDNA and 0.4 µg Cy5-labelled cDNA were hybridized onto custom Agilent 8*15k microarrays (AMADID #020166)

scan_protocol: 4000B Axon Instrument Scanner

data_processing: Arrays were gridded with Gene Pix Pro software version 7, Lowess normalization was performed using a Goulphar script for R. Following normalization, the 2 or 5 probes per feature were collapsed to their median value prior to further analysis.

organism: Candida albicans

source_name: SSN6, WOR1 homozygous double deletion (a/a)

label_protocol: cDNA was synthesized from either 8 µg (Replicate C) or 6.25 µg (Replicates A&B) total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instructions, and using a mixture of 0.5 mM 3:2 aminoallyl-dUTP (Ambion 8437):dNTPs. A pooled reference was created by taking equal mass proportions of cDNA from each experimental strain, cDNA from the experimental strain was dye coupled to Cy5 (GE Healthcare PA25001). The pooled reference was dye coupled to Cy3 (GE Healthcare PA23001).

growth_protocol: All samples were grown @ 25°C to log phase in synthetic defined (SD) media plus amino acids and uridine; samples labeled replicates A & B were further supplemented with 2.5 mg/ml of arginine to accommodate a growth defect likely associated with the arg- genotype of the WT a/α strain.

extract_protocol: Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)

tag: parental strain background

tag: source strain

tag: strain

source_name: pooled reference

tag: source strains

value: pooled reference from equal amounts of RNA from each of source strains in ch1


title: ssn6 wor1 (a/a) v. pooled reference (replicate C)

description: ssn6 wor1 (a/a)_repC

value: SSN6, WOR1 homozygous double deletion (a/a)


title: ssn6 (a/a) v. pooled reference (replicate C)

description: ssn6 (a/a)_repC

source_name: SSN6 homozygous deletion (a/a)

value: SSN6 homozygous deletion (a/a)


title: Patient_2_J4

description: RNA from purified neutrophils

value: Patient


title: MCF7, ΔNp63α induced [miRNA]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: MCF7 cells were grown in 6 well plate with RPMI medium

extract_protocol: miRNeasy mini kit (Qiagen) was used according to manufacturer's protocol

treatment_protocol: ΔNp63α was induced by treating the cells with doxycycline for 48 hours

value: Luminal breast cancer cells

tag: genotype/variation

value: inducible ΔNp63α

tag: treated with

value: doxycycline for 48 hrs


title: ssn6 (a/a) v. pooled reference (replicate B2)

description: ssn6 (a/a)_repB2


title: ssn6 (a/a) v. pooled reference (replicate A2)

description: ssn6 (a/a)_repA2


title: im-DC_P

source_name: immature dendritic cells + 1mM propionate

value: immature dendritic cells


title: ssn6 (a/a) v. pooled reference (replicate C2)

description: ssn6 (a/a)_repC2


title: ssn6 wor1 (a/a) v. pooled reference (replicate A)

description: ssn6 wor1 (a/a)_repA


title: ssn6 (a/a) v. pooled reference (replicate A)

description: ssn6 (a/a)_repA


title: BC3 control rep 2

description: BC3 control rep 2


title: WT opaque (a/a) v. pooled reference (replicate C)

description: WT opaque (a/a)_repC

source_name: WT opaque (a/a)

value: WT opaque (a/a)


title: forelimb buds Ring1b 1

city: Yokohama

first: Takaho

middle: A.

last: Endo

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

hyb_protocol: Agilent Mammalian ChIP-on-chip Version 9.0, August 2006

data_processing: Signal intensities were normalized using rank consistency filter algorithm and Ring1b-binding genes and H3K27me3-positive genes were determined using enrichment index dependent on the maximum log(fold enrichment) of 500bp window around TSS (-4kb to +4kb). Since the index had two peaks, the group having higher scores were obtained with false discovery ratio 0.05.

organism: Mus musculus

source_name: ChIP

extract_protocol: Antibodies against Ring1B (clone #3) (Atsuta et al., 2001) and H3K27me3 (07-449, Millipore) were used for immunoprecipitation. Purified immunoprecipitated and whole cell extract (input) DNA were amplified using the double-round T7 RNA polymerase-based amplification method (van Bakel et al., 2008).

treatment_protocol: Whole forelimb buds at E10.5 from wild type embryos were fixed in 1% formaldehyde/PBS for 20 min at room temperature, washed three times with cold PBS containing protease inhibitors and stored at -80°C. Pools of forelimb buds were used for ChIP and it was performed as described previously (Endoh et al., 2012).

value: forelimb buds

tag: chip antibody

source_name: input

value: input


title: im-DC_A

source_name: immature dendritic cells + 1mM acetate

value: 1mM acetate

value: hematopoietic tissue


title: ssn6 (a/a) v. pooled reference (replicate B)

description: ssn6 (a/a)_repB


title: im-DC

source_name: immature dendritic cells


title: WT opaque (a/a) v. pooled reference (replicate B)

description: WT opaque (a/a)_repB


title: MCF7, ΔNp63α not induced [miRNA]

value: none (control)


title: m-DC

source_name: mature dendritic cells

value: mature dendritic cells


title: BC3 control rep 1

description: BC3 control rep 1

value: DMSO


title: Patient_13_J3

description: RNA from purified neutrophils

source_name: Purified neutrophils


title: forelimb buds H3K27me3 1

scan_protocol: Agilent Mammalian ChIP-on-chip Version 9.0, August 2006


title: WT opaque (a/a) v. pooled reference (replicate A)

description: WT opaque (a/a)_repA


title: MCF7, ΔNp63α not induced

description:
ΔNp63α, not induced
MCF7-PTO-dNp63alpha-Dox-

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..


title: WT white (a/a) v. pooled reference (replicate C)

description: WT white (a/a)_repC

source_name: WT white (a/a)

value: WT white (a/a)


title: MCF7, ΔNp63α induced

description:
ΔNp63α, induced
MCF7-PTO-dNp63alpha-Dox+


title: Kidney-Tumor-12

city: Voronezh

first: Sergey

last: Solodskikh

address: Universitetskaya sq, 1

department: Genetics, Cytology and Bioengineering

country: Russia

institute: Voronezh State University

description: Gene expression data from renal cell carcinoma tissue

hyb_protocol: cDNA was hybridized with microarrays for 16 hours under constant temperature of 48 °С according to manufacturer protocol

scan_protocol: Microarrays were scanned and images were converted into digital data with Affymetrix® GeneAtlas™ Instrument Control Software according to manufacturer protocol

data_processing: Signal processing, normalization, noise filtering and background substraction were performed with Partek Genomics Suite (PGS) v. 6.6 using included variation of RMA algorithm with adjustment for probe GC-content and sequence allele position

source_name: Renal cell carcinoma tissue

label_protocol: Hybridization-ready cDNA was prepared using Ambion® WT Expression Kit (Life Technologies, USA, cat. #4411974)

extract_protocol: Total RNA was extracted and purified with RNeasy Mini Kit (QIAGEN, USA, cat. #74104) according to manufacturer protocol

tag: tissue type

value: Tumor (renal cell carcinoma)

tag: organ

value: Kidney


title: WT white (a/a) v. pooled reference (replicate B)

description: WT white (a/a)_repB

value: pooled reference from equal amounts of RNA from each of source strains in ch1


title: im-DC_B

source_name: immature dendritic cells + 1mM butyrate

value: 1mM butyrate


title: WT white (a/a) v. pooled reference (replicate A)

description: WT white (a/a)_repA


title: ssn6 (a/α) v. pooled reference (replicate B)

description: ssn6 (a/α)_repB

source_name: SSN6 homozygous deletion (a/α)

value: SSN6 homozygous deletion (a/alpha)


title: WT (a/α) v. pooled reference (replicate C)

description: WT (a/α)_repC

source_name: WT (a/α)

value: WT (a/alpha)


title: Kidney-Tumor-11


title: Kidney-Tumor-10


title: ssn6 (a/α) v. pooled reference (replicate A)

description: ssn6 (a/α)_repA


title: WT (a/α) v. pooled reference (replicate A)

description: WT (a/α)_repA


title: WT (a/α) v. pooled reference (replicate B)

description: WT (a/α)_repB


title: ssn6 (a/α) v. pooled reference (replicate C)

description: ssn6 (a/α)_repC


title: ProxFL_10.5_WT+RA

description: proximal, WT E10.5 (+RA)

hyb_protocol: Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.

scan_protocol: GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.

data_processing: The data were analzyed with Affymetrix MAS 5.0 algorithm using Bioconductor package.  Signal intensiy was normalized using quantilie normalization method.

source_name: Forelimb buds

label_protocol: The ds-cDNA derived from total RNA was incubated at 37℃ for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.

extract_protocol: Total RNA was extracted using the Rneasy Micro Kit (QIAGEN) following the manufacturer's protocol.

treatment_protocol: Wild type embryos received all trans Retinoic acid (100 mg/kg) at E10.25 by maternal oral gavage.

tag: genotype

value: WT

tag: tissues

value: Proximal forelimb buds

tag: age

tag: retinoic acid treatment


title: DisFL_10.5_WT+RA

description: distal, WT E10.5 (+RA)

value: Distal forelimb buds


title: Kidney-Tumor-07


title: Kidney-Tumor-06


title: Kidney-Tumor-09


title: DisFL_10.5_Ring1A/B-dKO

description: distal, Ring1A/B-dKO E10.5

value: Prx1-Cre; Ring1A-/-; Ring1Bfl/fl

value: No


title: ProxFL_10.5_Ring1A/B-dKO

description: proximal, Ring1A/B-dKO E10.5


title: Arabidopsis silique in stage17(ind-6 mutant ),biological rep2

city: Guangzhou

first: JIANG

middle: Xin

last: Shan

state: Guangdong

address: Zhongshan Road No. 55, Tianhe District

department: school of life sciences

institute: South China Normal University

description: Gene expression data from ind-6 mutant silique in stage 17  during fruit dehiscence

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned using the Affymetrix Scanner 3000

data_processing:
The normalization of raw data is needed to eliminate dye-related artifacts. Consecutive filtering procedures were performed to normalize the data(GC-RMA), and remove noise derived from absent genes, background and non-specific hybridizations.
Genes with the most significant differential expression genes between different stages were identified using the significance analysis of microarrays (SAM) algorithm

organism: Arabidopsis thaliana

source_name: Arabidopsis silique in stage17 during fruit dehiscence(dehiscence zone just completed the differentiation,ind-6 mutant)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis plants were grown in a growth room with a 16-h-light/8-h-dark cycle at 22°C. Silique for each stage 11, 15 and 17 were used for experiments

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

treatment_protocol: Arabidopsis silique immediately frozen in liquid nitrogen.

tag: tissue

value: Arabidopsis silique

value: ind-6 mutant

tag: development stage

value: stage 17  during fruit dehiscence


title: Kidney-Tumor-05


title: DisFL_10.5_control

description: distal, WT E10.5


title: ProxFL_10.5_control

description: proximal, WT E10.5


title: Kidney-Tumor-04


title: Kidney-Tumor-08


title: Arabidopsis silique in stage17(ind-6 mutant ),biological rep1


title: Arabidopsis silique in stage15(ind-6 mutant ),biological rep3

description: Gene expression data from ind-6 mutant silique in stage 15  during fruit dehiscence

source_name: Arabidopsis silique in stage15 during fruit dehiscence(fruit dehiscence zone started asymmetric cell division,ind-6 mutant)

value: stage 15  during fruit dehiscence


title: Arabidopsis silique in stage15(ind-6 mutant ),biological rep2


title: Arabidopsis silique in stage17(ind-6 mutant ),biological rep3


title: Arabidopsis silique in stage15(ind-6 mutant ),biological rep1


title: forelimb buds Ring1b 2

label_protocol: Agilent Mammalian ChIP-on-chip Version 9.0, August 2006

value: forelimb buds

value: input


title: forelimb buds H3K27me3 2


title: Kidney-Tumor-01

value: Tumor (renal cell carcinoma)


title: Arabidopsis silique in stage11(ind-6 mutant ),biological rep3

description: Gene expression data from ind-6 mutant silique in stage 11  during fruit dehiscence

source_name: Arabidopsis silique in stage11 during fruit dehiscence(dehiscence zone did not start differentiate,ind-6 mutant)

value: stage 11  during fruit dehiscence


title: Kidney-Tumor-03

value: Kidney


title: Kidney-Normal-11

description: Gene expression data from healthy human kidney tissue

source_name: Normal kidney tissue

value: Normal


title: Arabidopsis silique in stage11(ind-6 mutant ),biological rep2


title: Kidney-Tumor-02


title: Kidney-Normal-12


title: moDCs_rep3

description:
SAMPLE 8
monocyte-derived Dendritic cells

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies, G4112F) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).

data_processing: Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were done using hierarchical clustering, correspondence analysis (COA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Supervised analysis was performed using SAM. Genes were considered to be differentially expressed when the false discovery rate was below 1% and absolute fold change (FC) was above 4.

source_name: moDCs

label_protocol: In brief, 400 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: at-term placentas obtained by vaginal delivery were collected in the Gynecology-Obstetrics Department of the Hôpital de la Conception (Marseille, France) after written informed consent of healthy pregnant women. The study was approved by the Ethics Committee from Aix-Marseille University (N° 08-012). The placenta samples (approximately 150 grams) were incubated in a solution consisting of HBSS (Invitrogen, Cergy Pontoise, France), MgSO4, DNase I (Sigma-Aldrich, Saint-Quentin Fallavier, France) and 2.5% trypsin (Invitrogen) buffered with HEPES for 45 min and were then incubated for 30 min under gentle agitation at 37°C, as described previously (9). The digestion products were then filtered through 100-µm pores, incubated in 50-ml tubes containing 2 ml FCS and centrifuged at 1,000 × g for 15 min. The cells were counted, deposited on a Ficoll cushion and centrifuged at 700 × g for 20 min. Preparation of moDCs: Mononuclear cells were recovered, and macrophages were discarded using magnetic beads coated with anti-CD14 Abs (Miltenyi Biotech, Paris, France). CD14- cells were recovered and CD11c+ cells were sorted using magnetic beads (Miltenyi Biotec) coupled with anti-CD11c Abs (Beckman Coulter, Villepinte, France). The purity of CD11c+ cells was higher than 95%. Blood from healthy donors was provided by the Etablissement Français du Sang (Marseille, France). PBMCs from buffy coats were recovered from the Ficoll-Hypaque interface after a 700 × g centrifugation for 20 min. Monocytes were isolated from PBMCs using magnetic beads coupled with Abs specific for CD14, as previously described (19). Monocyte purity was higher than 98%. To obtain moDCs, monocytes were incubated in RPMI 1640 containing 20 mM HEPES, 2 mM glutamine, 10% FCS, 1 ng/ml IL-4 and 1 ng/ml GM-CSF (R&D Systems, Lille, France) for 7 d. The purity of moDCs was assessed by the absence of CD14 and the presence of CD11c and purity was higher than 98%.

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.

tag: pladcs

value: NO

tag: preparation

value: differentiated

tag: origin

value: blood

value: moDCs


title: Arabidopsis silique in stage11(ind-6 mutant ),biological rep1


title: moDCs_rep2

description:
SAMPLE 7
monocyte-derived Dendritic cells


title: Kidney-Normal-10


title: Arabidopsis silique in stage17,biological rep3

description: Gene expression data from wild silique in stage 17  during fruit dehiscence

source_name: Arabidopsis silique in stage17 during fruit dehiscence(dehiscence zone just completed the differentiation)

value: wild


title: Arabidopsis silique in stage17,biological rep2


title: Kidney-Normal-07


title: Arabidopsis silique in stage15,biological rep3

description: Gene expression data from wild silique in stage 15  during fruit dehiscence

source_name: Arabidopsis silique in stage15 during fruit dehiscence(fruit dehiscence zone started asymmetric cell division)


title: plaDCs_Placenta2_rep1

description:
SAMPLE 3
isolated CD11c+ plaDCs

source_name: plaDCs

value: YES

value: isolated

value: placenta

value: plaDCs


title: plaDCs_Placenta2_rep3

description:
SAMPLE 5
isolated CD11c+ plaDCs


title: Arabidopsis silique in stage15,biological rep2

value: Arabidopsis silique


title: Kidney-Normal-09


title: Kidney-Normal-08


title: plaDCs_Placenta1_rep3

description:
SAMPLE 2
isolated CD11c+ plaDCs


title: Arabidopsis silique in stage15,biological rep1

value: stage 15  during fruit dehiscence


title: Arabidopsis silique in stage11,biological rep1

description: Gene expression data from wild silique in stage 11  during fruit dehiscence

source_name: Arabidopsis silique in stage11 during fruit dehiscence(dehiscence zone did not start differentiate)


title: Kidney-Normal-06


title: plaDCs_Placenta2_rep2

description:
SAMPLE 4
isolated CD11c+ plaDCs


title: Arabidopsis silique in stage11,biological rep2


title: Kidney-Normal-02


title: Kidney-Normal-04


title: Kidney-Normal-03


title: plaDCs_Placenta1_rep1

description:
SAMPLE 1
isolated CD11c+ plaDCs


title: Arabidopsis silique in stage11,biological rep3


title: C2C12_Fv2E-PERK_AP_rep1

status: Public on Dec 26 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

description: Gene expression of C2C12-Fv2E-PERK stimulated with AP20187

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation buffer and 2x Agilent Blocking Agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-028005 Whole Mouse Genome Oligo Microarrays for 17.5 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. Global normalization has been conducted using Subio software. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: C2C12 Fv2E-PERK, AP20187

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: All the mouse protocols were approved by the Animal Experimentation Committee of the University of Tokushima. The mice were housed in a room maintained at 22℃ (71.6 F), with a 12:12 h light-dark cycle starting from 8:00 AM under SPF conditions. C2C12 cells were cultured in DMEM supplymented with 10% fetal bovine serum and differentiated in DMEM supplymeted with 2% horse serum for 3 days.

extract_protocol: Muscles were snap frozen in liquid nitrogen. Total RNA was extracted using the conventional acid guanidinium thiocyanate phenol-chloroform (AGPC) procedure and cleaned up using the RNeasy MinElute Cleanup Kit according to manufacturer's instructions (QIAGEN Valencia, CA).

treatment_protocol: In mice, AP20187 (1 ng/g) or vehicle (4% ethanol, 10% PEG-400, 1.75% Tween-20 in water) was intraperitoneally injected and muscles were collected after 12 h. In C2C12, AP20187 (100 nM) or vehicle (ethanol) were added and cells were harvested after 12 h.

tag: cell line

tag: treatment


title: C2C12_Fv2E-PERK_AP_rep2


title: Kidney-Normal-01


title: C2C12_Fv2E-PERK_Vehicle_rep2

description: Gene expression of C2C12-Fv2E-PERK stimulated with vehicle

source_name: C2C12 Fv2E-PERK, vehicle

value: vehicle


title: Mouse_TG_Muscle_AP_rep1

description: Gene expression of hSA::Fv2E-PERK mouse muscles injected with AP20187

source_name: Mouse TG muscle, AP20187

tag: strain/background

tag: gender

value: male

value: muscle


title: C2C12_Fv2E-PERK_Vehicle_rep1


title: Mouse_TG_Muscle_AP_rep2


title: Arabidopsis silique in stage17,biological rep1

value: stage 17  during fruit dehiscence


title: Mouse_TG_Muscle_Vehicle_rep1

description: Gene expression of hSA::Fv2E-PERK mouse muscles injected with vehicle

source_name: Mouse TG muscle, vehicle


title: Mouse_WT_Muscle_UT_rep2

description: Gene expression of WT mouse untreated muscles

source_name: Mouse WT muscle, untreated

value: WT


title: Boron deficiency_4d, Biological rep_1

status: Public on Dec 25 2015

city: Oeiras

first: Marta

last: Alves

address: Av. da República, Apartado 127

country: Portugal

institute: ITQB

description: AtH1_ B1_4D

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the ATH1 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Scanned arrays were analyzed first with GCOS 1.4 software to obtain Absent/Present calls and for subsequent analysis with DNA-Chip Analyzer.

source_name: Plants grown with B-free nutrient solution for 4 days

label_protocol: Biotinylated cRNA were prepared according to Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: Plants were grown on perlite with a complete nutrient solution in which  B concentration was 25 µM and Ca concentration 3 mM.

extract_protocol: Total RNA was extracted from the cells by using RNeasy Plant Mini kit (Qiagen).

treatment_protocol: After 17 days B was supressed for 2 and 4 days or Ca was supressed for 2 days.

value: Whole plant

value: 21 days


title: Calcium deficiency_2d, Biological rep_2

description: AtH1_ Ca2_2D

source_name: Plants grown with Ca-free nutrient solution for 2 days

value: 19 days


title: moDCs_rep1

description:
SAMPLE 6
monocyte-derived Dendritic cells

value: NO

value: differentiated

value: blood


title: Mouse_TG_Muscle_Vehicle_rep2


title: Mouse_WT_Muscle_UT_rep1


title: Control_4d, Biological rep_1

description: AtH1_ C1_4D

source_name: Plants grown with complete nutrient solution


title: Boron deficiency_4d, Biological rep_2

description: AtH1_ B2_4D


title: Control_2d, Biological rep_1

description: AtH1_ C1_2D


title: Calcium deficiency_2d, Biological rep_1

description: AtH1_ Ca1_2D


title: Boron deficiency_2d, Biological rep_1

description: AtH1_ B2_2D

source_name: Plants grown with B-free nutrient solution for 2 days


title: Boron deficiency_2d, Biological rep_2

description: AtH1_ B3_2D


title: Control_4d, Biological rep_2

description: AtH1_ C2_4D


title: Control_2d, Biological rep_2

description: AtH1_ C2_2D


title: HSCs, Dkk1 treatment

first: Hidekazu

last: Tsukamoto

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

description: Gene expression data

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol in an Affymetrix GeneChip Hybridization Oven 640. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data were analyzed with Affymetrix Expression Console using Robust Multichip Average (RMA) using Affymetrix default analysis settings.

organism: Rattus norvegicus albus

source_name: HSCs, Dkk1 treatment

label_protocol: Ambion WT Expression Kit was used to generate ssDNA targets. Fragmentation and biotin labeling were performed using the Affymetrix WT Terminal Labeling and Hybridization Kit.

extract_protocol: Total RNA was extracted from HSCs using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: cell type

value: primary hepatic stellate cells (HSCs)


title: HSCs, Control for FJ9

description: Gene expression data

source_name: HSCs, Control for FJ9


title: HSCs, Control for Dkk1

description: Gene expression data

source_name: HSCs, Control for Dkk1


title: HSCs, Control for ICG-001

description: Gene expression data

source_name: HSCs, Control for ICG-001


title: HSCs, ICG-001 treatment

description: Gene expression data

source_name: HSCs, ICG-001 treatment


title: tomato-Trichoderma harzianum amds6 interaction, biological rep 3

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

country: Spain

institute: University of Salamanca

description: 11.amds 6_(Tomato)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Digitalization of fluorescent signals emitted after the hybridization was performed with the Gene Array Reader (Affimetrix) and the GCOS and Desktop Mining Solution (Micro DB 3.0, Data MiningTool 3.0) programs

data_processing:
A Robust Multichip Average (RMA) convolution model was applied for background correction. To identify probe sets showing a significant difference in expression level, a multi-class Significance Analysis of Microarray (SAM) test was carried out on the expression values using a False Discovery Rate (FDR) of 0.10. The analysis was performed using the Gene Spring GX program through the R software.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.29167

organism: Solanum lycopersicum

source_name: aerial parts of 3-wk-old tomato plants interacting with T. harzianum amds6

label_protocol: cDNAs were synthesized from 1 μg of total RNA using the Transplex Whole Transcriptome Amplification kit (Sigma), were labeled using the GeneChip IVT Labeling kit (Affymetrix)

extract_protocol: Total RNA was obtained from aerial parts of 3-week-old tomato plants using the NucleoSpin® RNA Plant kit (Macherey-Nagel, Germany), and was purified using the RNeasy MinElute Cleanup kit (Quiagen), following to the instructions of manufacturers

treatment_protocol: Trichoderma-plant interaction protocol: Sterilized tomato seeds were coated with an aqueous suspension containing 2 x 10^7 spores/mL of T. harzianum T34 or amdS transformants and then air. Treated tomato seeds were sown in pots containing commercial loamy field soil, previously autoclaved. Pots with untreated tomato seeds were used as controls. The pots were incubated in a greenhouse at 22±4 °C, and watered as needed. Aerial parts were collected from tomato plants after three weeks, frozen, and used for microarray experiments.

value: leaves

tag: interaction with

value: Trichoderma harzianum amds6


title: tomato-Trichoderma harzianum amds122 interaction, biological rep 3

description: 12.amds 122_(Tomato)

source_name: aerial parts of 3-wk-old tomato plants interacting with T. harzianum amds122

value: Trichoderma harzianum amds122


title: tomato-Trichoderma harzianum T34 interaction, biological rep 3

source_name: aerial parts of 3-wk-old tomato plants interacting with T. harzianum T34

value: Trichoderma harzianum T34


title: HSCs, FJ9 treatment

description: Gene expression data

source_name: HSCs, FJ9 treatment


title: tomato-Trichoderma harzianum amds122 interaction, biological rep 2

description: 8.amds 122_(Tomato)


title: tomato-Trichoderma harzianum amds6 interaction, biological rep 2

description: 7.amds 6_(Tomato)


title: tomato control plants, biological rep2

source_name: aerial parts of 3-wk-old tomato plants

value: none (control)


title: tomato control plants, biological rep3


title: tomato-Trichoderma harzianum T34 interaction, biological rep 2


title: tomato-Trichoderma harzianum amds122 interaction, biological rep 1


title: tomato-Trichoderma harzianum T34 interaction, biological rep 1


title: tomato-Trichoderma harzianum amds6 interaction, biological rep 1


title: tomato control plants, biological rep1


title: genomic DNA from  B_WT.DS05

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Primary tumor: PGL

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor samples using Qiagen DNeasy Kit according to standard instructions

value: M

tag: location

value: PGL

value: tumor

tag: disease progression

value: without metastases


title: genomic DNA from  B_WT.DS21

source_name: Primary tumor: PCC

value: F

value: PCC


title: genomic DNA from  B_WT.DS18


title: genomic DNA from  B_WT.DS24


title: genomic DNA from  B_WT.DS27


title: genomic DNA from  B_WT.DS11


title: genomic DNA from  B_RET.DS24


title: genomic DNA from  B_RET.DS25


title: genomic DNA from  B_VHL.DS19


title: genomic DNA from  B_RET.DS26


title: genomic DNA from  B_WT.DS26


title: genomic DNA from  B_VHL.DS20


title: genomic DNA from  B_RET.DS16


title: genomic DNA from  B_RET.DS23


title: genomic DNA from  B_HRAS.DS02


title: genomic DNA from  B_WT.DS25


title: genomic DNA from  B_VHL.DS10


title: genomic DNA from  B_VHL.DS21


title: genomic DNA from  B_NF1.DS08


title: genomic DNA from  B_WT.DS17


title: genomic DNA from  B_VHL.DS22


title: genomic DNA from  B_NF1.DS04


title: genomic DNA from  B_RET.DS22


title: genomic DNA from  B_NF1.DS07


title: genomic DNA from  B_SDHD.DS01


title: genomic DNA from  B_RET.DS17


title: genomic DNA from  M_WT.DS44

value: with metastases


title: genomic DNA from  B_WT.DS28


title: Kidney-Normal-05

source_name: Normal kidney tissue

tag: tissue type

value: Normal

tag: organ

value: Kidney


title: genomic DNA from  M_WT.DS43

tag: age


title: genomic DNA from  B_RET.DS20


title: genomic DNA from  B_WT.DS23


title: HI4320, replicate 3

type: SRA

city: Atlanta

first: Philip

last: Rather

state: GA

address: 3001 Rollins Research Bldg

department: Microbiology

institute: Emory University

library_source: transcriptomic

data_processing:
CLC Genomics workbench was used to analyze the data. The number of reads per transcript was determined and normalized to get RPKM values. A Baggerly¹s proportion test was used to find differentially expressed transcripts over the control sample and was accounted for multiple testing.

Raw data were lost and therefore are not included in this submission

organism: Proteus mirabilis

source_name: wild-type P. mirabilis strain

growth_protocol: Cells were grown in LB broth to an optical density A600 of 1.1

extract_protocol:
RNA was extracted using  MasterPure reagent from Epicentre
RNA purity was confirmed on the Agilent 2100 Bioanalyzer (Agilent Technologies).  DNA-free samples were then enriched for mRNA using MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion). Two rounds of rRNA depletion were performed and RNA purity was confirmed on an Agilent 2100 Bioanalyzer (Agilent Technologies).  cDNA libraries were constructed from HI4320 and rcsB::strR  mRNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen).  The cDNA libraries were purified by phenol extraction and ethanol precipitation. Sequences were analyzed on an Illumina HiSeq2000 instrument with 50 bp paired end reads and matched to the HI4320 genome using CLC Genomics Workbench (CLC Bio-Qiagen, Aarhus Denmark).

treatment_protocol: RNAprotect Bacteria Reagent was used at a 1:1 ratio (Qiagen).

tag: genotype

value: HI4320 wild-type


title: genomic DNA from  B_SDHD.DS02

tag: tissue


title: rcsB, replicate 2

source_name: isogenic P. mirabilis rcsB mutant

value: HI4320 rcsB mutant


title: rcsB, replicate 3


title: genomic DNA from  B_WT.DS20


title: genomic DNA from  B_VHL.DS17


title: genomic DNA from  B_RET.DS21


title: genomic DNA from  B_WT.DS19


title: genomic DNA from  B_VHL.DS16


title: genomic DNA from  B_VHL.DS15


title: genomic DNA from  B_VHL.DS13


title: genomic DNA from  B_WT.DS16


title: genomic DNA from  B_RET.DS15


title: genomic DNA from  B_RET.DS14


title: HI4320, replicate 2


title: genomic DNA from  B_RET.DS18


title: genomic DNA from  B_WT.DS15


title: genomic DNA from  B_RET.DS13


title: genomic DNA from  B_SDHB.DS04


title: genomic DNA from  B_HRAS.DS01


title: genomic DNA from  B_RET.DS19


title: genomic DNA from  B_VHL.DS14


title: genomic DNA from  M_MAX.DS04


title: genomic DNA from  B_EPAS1.DS04


title: rcsB, replicate 1


title: HI4320, replicate 1


title: genomic DNA from  B_EPAS1.DS03


title: genomic DNA from  B_VHL.DS12


title: genomic DNA from  B_RET.DS12


title: genomic DNA from  B_RET.DS11


title: genomic DNA from  B_RET.DS10


title: genomic DNA from  B_TMEM127.DS1


title: genomic DNA from  B_VHL.DS11


title: genomic DNA from  M_SDHB.DS08


title: genomic DNA from  M_WT.DS42


title: genomic DNA from  B_NF1.DS06


title: genomic DNA from  M_WT.DS40


title: genomic DNA from  B_WT.DS13


title: genomic DNA from  B_WT.DS14


title: genomic DNA from  B_VHL.DS18


title: genomic DNA from  B_SDHB.DS03


title: genomic DNA from  B_WT.DS12


title: genomic DNA from  B_SDHB.DS02


title: genomic DNA from  B_WT.DS06


title: genomic DNA from  B_WT.DS09


title: genomic DNA from  B_MAX.DS02


title: genomic DNA from  M_WT.DS41

source_name: Primary tumor: N/A


title: genomic DNA from  M_WT.DS38


title: genomic DNA from  M_WT.DS39


title: genomic DNA from  B_WT.DS10


title: genomic DNA from  M_SDHB.DS07


title: genomic DNA from  B_NF1.DS05


title: genomic DNA from  B_WT.DS08


title: genomic DNA from  M_WT.DS37


title: genomic DNA from  B_RET.DS09


title: 3 IF 1

city: Saitama

first: Yuta

last: Muto

address: 1-847 Amanuma-cho, Omiya-ku

department: Department of Surgery

institute: Saitama Medical Center, Jichi Medical University

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented at 60 °C for 30 min. On completion of the fragmentation reaction, 25μL of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 h at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with GE Wash Buffer.

scan_protocol: Slides were scanned after washing on the Agilent Technologies Microarray Scanner.

data_processing: The fluorescence intensities on scanned images were extracted and preprocessed by Agilent Feature Extraction Software (v10.7.3.1).

source_name: Colorectal cancer tissue at invasive front

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75 ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies), followed by RNeasy Mini Kit (Qiagen, Hilden, Germany) purification. Dye incorporation and cRNA yield were checked by the NanoDrop Spectrophotometer.

extract_protocol: Total RNA was extracted from samples using the Illustra RNAspin Mini RNA Isolation Kit (GE Healthcare UK, Buckinghamshire, UK) according to the manufacturer's instructions. For assessing RNA quality and yield, A260/A280 and A260/A230 ratios for RNA preparation samples were analysed with a Nano-Drop® ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE, USA) and RNA integrity number (RIN) was calculated by an Agilent 2100 Bioanalyzer. (Agilent Technologies, Santa Clara, CA, USA) RNAs with RIN from 7 to 10 were used for experience.

tag: sample site

value: invasive front

value: Human colon

value: male


title: genomic DNA from  B_VHL.DS09


title: 4 IF 1


title: genomic DNA from  B_VHL.DS08


title: genomic DNA from  M_WT.DS36


title: 4 IF 2


title: genomic DNA from  B_WT.DS04


title: genomic DNA from  B_WT.DS22


title: genomic DNA from  B_WT.DS07


title: genomic DNA from  B_EPAS1.DS02


title: 8 PD 2

source_name: Colorectal cancer tissue in peritoneal dissemination

value: peritoneal dissemination

value: female


title: 4 TC

source_name: Colorectal cancer tissue at tumor center

value: tumor center


title: 3 IF 2


title: genomic DNA from  M_WT.DS35


title: genomic DNA from  B_RET.DS08

value: M


title: 3 TC 1


title: genomic DNA from  M_MAX.DS03


title: genomic DNA from  B_RET.DS07


title: genomic DNA from  B_VHL.DS07


title: 8 NC

source_name: Normal colon mucosa


title: genomic DNA from  M_WT.DS34


title: 8 IF 1


title: 8 IF 2


title: 8 TC 1


title: 3 TC 2


title: genomic DNA from  M_WT.DS33


title: 8 PD 1


title: 8 TC 2


title: 8 OM

source_name: Metastatic colorectal cancer tissue in ovary

value: metastaic tumors


title: genomic DNA from  B_NF1.DS03

value: tumor


title: genomic DNA from  M_WT.DS29


title: genomic DNA from  B_NF1.DS02

value: without metastases


title: genomic DNA from  M_SDHB.DS06

value: PGL


title: 6 LM2

source_name: Metastatic colorectal cancer tissue in liver


title: genomic DNA from  M_VHL.DS23

value: F

value: PCC


title: 6 IF 1


title: 6 LM 1


title: genomic DNA from  B_RET.DS06


title: genomic DNA from  M_SDHB.DS05

value: with metastases


title: 6 IF 2


title: genomic DNA from  B_RET.DS05


title: genomic DNA from  B_VHL.DS05


title: genomic DNA from  B_RET.DS04


title: 6 TC 3


title: genomic DNA from  B_VHL.DS06


title: genomic DNA from  M_WT.DS32


title: 6 TC 1


title: Sheep red blood cells, Effector T cells_003

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 1.1 ST Arrays according to manufacturer’s protocol.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing:
Data were processed using rma and limma packages in R/Bioconductor. Pairwise group comparisons were undertaken using linear modelling. Subsequently, empirical Bayesian analysis was applied, including vertical (within a given comparison) p value adjustment for multiple testing, which controls for false discovery rate, using the limma Bioconductor package
The normalised data are log2 values for the probes reliably detected on all arrays, processed using rma followed by quantile normalisation.

source_name: Mice injected with 2x10^9 sheep red blood cells i.p.

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 100-300ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol.

extract_protocol: RNA was extracted by passing TRIZOL over Qiagen Rneasy columns as per manufacturer's instructions.

treatment_protocol:
Mice were immunised with sheep red blood cells (2x10^9 i.p.) or S. enterica (10^6 colony forming units of SL3261 strain, i.v.). Mice were left untreated for 6 days, at which point spleens were harvested for analysis.
Red blood cells were lysed with RBC lysis buffer. Splenocytes were enriched in CD4+ T cells by negative selection with Dynabeads (Invitrogen). Cells were then stained for flow cytometry and sorted over BD Aria flow cytometer sorter based on the expression of surface markers as described in the table.

tag: strain

value: spleen

tag: sorting parameters

value: Effector T cells:CD19-, CD4+, CXCR5-, PD-1+


title: Sheep red blood cells, Effector T cells_002


title: 2 IF 2


title: 2 IF 1


title: Sheep red blood cells, TFH cells, PD-1_LOW_003

value: TFH cells:CD19-, CD4+, CXCR5+, PD-1LOW


title: 6 NC


title: genomic DNA from  B_VHL.DS03


title: genomic DNA from  B_VHL.DS04


title: 5 LM


title: 5 NL

source_name: Normal liver tissue

value: Human liver


title: genomic DNA from  B_SDHB.DS01


title: Sheep red blood cells, Effector T cells_001


title: 2 TC

value: Human colon


title: genomic DNA from  M_WT.DS31


title: Sheep red blood cells, TFH cells, PD-1_LOW_002


title: Sheep red blood cells, TFH cells, PD-1_HIGH_003

value: TFH cells:CD19-, CD4+, CXCR5+, PD-1HIGH


title: Sheep red blood cells, TFH cells, PD-1_LOW_001


title: 5 IF 2

value: invasive front

value: male


title: 5 TC

value: tumor center


title: genomic DNA from  M_WT.DS45

value: M


title: genomic DNA from  B_EPAS1.DS01


title: Sheep red blood cells, TFH cells, PD-1_HIGH_002

value: female


title: 5 NC


title: 5 IF 1


title: genomic DNA from  B_VHL.DS01

value: tumor


title: Sheep red blood cells, TFH cells, PD-1_HIGH_001


title: genomic DNA from  B_VHL.DS02

value: without metastases


title: S. enterica Effector T cells_003

source_name: Mice infected with 1x10^6 CFU of Salmonella enterica strain SL3261 i.v.


title: genomic DNA from  B_RET.DS02


title: genomic DNA from  B_RET.DS03


title: 7 PD

value: peritoneal dissemination


title: S. enterica Effector T cells_002


title: S. enterica Effector T cells_001


title: CDX2P-G22Cre;Apcflox/flox_2

city: Hiroshima

first: Hiroaki

last: Niitsu

address: 1-2-3 Kasumi, Minamiku

department: Department of gastroenterological surgery

institute: Hiroshima University

description: Gene expression of tumor from CDX2P-G22Cre;Apcflox/flox that were macroscopically dissected.

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner according to the manufacturer's protocols.

data_processing: The data were analyzed with GeneSpring GX version 11 (Agilent Technology, Inc., Santa Clara, CA)

source_name: Colon cancer generated in mouse

label_protocol: Biotinylated aRNA were prepared according to GeneChip 3' IVT Express Kit User Manual (2008, Affymetrix)from 50ng total RNA .

growth_protocol: A tumours were harvested from each  mouse at an age of 6-8 weeks.

extract_protocol: Total RNA was isolated using an RNeasy Kit (Qiagen, Hilden, Germany). RNA quality was determined using a 2100 Bioanalyzer (Agilent Technologies, Inc, Waldbronn, Germany).

treatment_protocol: Tumors were macroscopicly dissected and fixed in RNA-later.

value: 6-8 week-old

tag: background strain


title: genomic DNA from  M_WT.DS30

value: PCC


title: CDX2P-G22Cre;Apcflox/flox_3


title: 7 IF 2


title: CDX2P-G22Cre;Apcflox/flox; KrasG12D_2

description: Gene expression of tumor from CDX2P-G22Cre;Apcflox/flox; KrasG12D that were macroscopically dissected.

value: CDX2P-G22Cre;Apcflox/flox; KrasG12D


title: 7 TC


title: CDX2P-G22Cre;Apcflox/flox_1


title: 7 IF 1


title: S. enterica TFH cells_003

value: spleen

value: Salmonella TFH:CD19-, CD4+, CXCR5+, PD-1+


title: CDX2P-G22Cre;Apcflox/flox; KrasG12D_1


title: 1 IF


title: 1 TC


title: CDX2P-G22Cre;Apcflox/flox; KrasG12D_3


title: S. enterica TFH cells_001


title: S. enterica TFH cells_002


title: genomic DNA from  B_WT.DS03


title: genomic DNA from  B_MAX.DS01


title: genomic DNA from  B_NF1.DS01


title: genomic DNA from  B_WT.DS02

value: F


title: Naive T cells_002

source_name: Naive mouse

value: Naive T cells:CD8-, B220-, CD4+, CD44-, CD62L+


title: Naive T cells_003


title: Naive T cells_001


title: genomic DNA from  B_RET.DS01


title: control 1

source_name: Perchased Rerference RNA (Agilent)

value: Universal Human Reference RNA


title: control 2


title: P1 KO/WT

description: normalized log2 ratio (P1 KO/P1 WT)

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: P1 livers derived from WT mice

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

tag: genotype/variation

value: wild-type

source_name: P1 livers derived from MMP-14 KO mice

value: MMP-14 KO


title: E14 KO/WT

description: normalized log2 ratio (E14 KO/E14 WT)

source_name: E14 Dlk+ cells derived from WT livers

source_name: E14 Dlk+ cells derived from KO livers


title: 6 TC 2

value: Human colon


title: Embryo at D5, biological replicate 3

city: Iowa City

first: Bradley

last: Van Voorhis

state: IA

address: 200 Hawkins Drive

department: Div. of Reproductive Endocrinology

institute: Univ. of Iowa

description: Gene expression data from embryo at time of blastocyst formation i.e. immediately prior to implantation

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix Inc., USA), placed onto Affymetrix Human Exon 1.0 ST arrays, and incubated at 45°C for 18 hours with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the GeneChip operating software (GCOS) v3.1

data_processing: Gene-level and exon-level signals were generated from CEL files using the RMA algorithm. CEL file output from Affymetrix microarray processing was uploaded, normalized, and filtered for excessive missing values or outliers. Probe set summaries and annotations were abstracted from standard annotations files.  specific to Affymetrix Human Exon 1.0 ST arrays (http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st). Genes were considered to be differentially expressed when differences achieved a univariate significance level of p <0.001. To identify over-represented and significant pathways among the selected significant genes in the Kyoto Encyclopedia of Genes and Genomes (Kanehisa et al., 2014), we used MetaCore (GeneGo, Inc., USA) and clusterProfiler, an R statistical package.

source_name: Human embryo, blastocyst stage, good quality

label_protocol: The amplified product was fragmented (average fragment size = 85 bases) and biotin-labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, USA) per the manufacturer’s recommended protocol.

growth_protocol: Previously cryopreserved, thawed zygotes at the pronuclear stage zygotes were cultured in sequential culture media (IVC-One and IVC-Three; InVitroCare, Frederick, MD) supplemented with 20% Quinns Advantage Serum Protein Substitute (Cooper Surgical, Inc., USA) in 5.5-6.0% CO2 in air at 37°C

extract_protocol: RNA was isolated from each of six human embryos (three D3, three D5, processed in singleton) using the RNeasy kit (Qiagen, USA) according to manufacturer protocol.

value: preimplantation embryo

tag: Stage

value: blastocyst


title: Embryo at D5, biological replicate 2

treatment_protocol: Previously cryopreserved, thawed zygotes at the pronuclear stage zygotes were cultured in sequential culture media (IVC-One and IVC-Three; InVitroCare, Frederick, MD) supplemented with 20% Quinns Advantage Serum Protein Substitute (Cooper Surgical, Inc., USA) in 5.5-6.0% CO2 in air at 37°C


title: Embryo at D5, biological replicate 1


title: Embryo at D3, biological replicate 3

description: Gene expression data from embryo at time of embryonic gene activation

source_name: Human embryo, cleavage stage, good quality

value: cleavage


title: genomic DNA from  B_WT.DS01

source_name: Primary tumor: PGL

value: M

value: PGL

value: tumor


title: Embryo at D3, biological replicate 2


title: yrr1-del-1-d

status: Public on Dec 24 2015

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)  * Priming: 5xSSC, 0.1%SDS  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ  * Wash: 5xSSC, 0.1%SDS  * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)  * Hybridization: 16 hours at 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC at 23C  * Drying: blow with nitrogen for 3min at 30C

scan_protocol: scanning of slides using Agilent G256BA: Scanning of slides using the Agilent G2565BA scanner. Imagene feature extraction: Features were extracted using Imagene software from Biodiscovery.

data_processing:
genes, no bg corr, dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.
limma: A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth.  The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).    mRNA amplification protocol description:  * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.  * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * plate is incubated @ 70C for 10 mins, cooled to 48C.  * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well.  * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.   * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.    Labeling protocol description:   * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).    All subsequent steps are performed by the robot script :  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.0

extract_protocol: yeast HTP RNA isolation for robot v2.0

source_name: refpool

growth_protocol: yeast-deleteome[grow]

extract_protocol: yeast RNA isolation for robotic amplification v1.0

value: wild type


title: yrr1-del+met28-del-2-a


title: zap1-del-3-a


title: zap1-del-3-b


title: yrr1-del-1-b


title: yrm1-del-1-a


title: yrm1-del+yrr1-del-1-b


title: yrm1-del-1-b


title: ypr015c-del-1-a


title: ypr196w-del-1-b


title: yrr1-del+met28-del-2-b


title: ypr196w-del-1-a


title: yrm1-del+yrr1-del-1-a


title: yox1-del-1-b


title: yox1-del+yhp1-del-1-b


title: Embryo at D3, biological replicate 1


title: yml081w-del-1-a


title: yox1-del-1-a


title: yml081w-del+rsf2-del-1-d


title: ygr067c-del-1-a


title: ygr067c-del+yml081w-del-1-d


title: ygr067c-del+yml081w-del-1-a


title: yox1-del+yhp1-del-1-a


title: ygr067c-del+mig2-del-1-b


title: yhp1-del-1-b


title: yml081w-del+rsf2-del-1-c


title: yml081w-del-2-b


title: ygr067c-del+mig2-del-1-a


title: yfl052w-del-1-a


title: yfl052w-del+ypr196w-del-1-b


title: yfl052w-del+ypr196w-del-1-a


title: yfl052w-del-1-b


title: yap1-del+stb4-del-2-b


title: yer184c-del-1-b


title: upc2-del-3-a


title: yap1-del+stb4-del-2-a


title: yap1-del-2-a


title: yer184c-del+sip4-del-matA-3-b


title: upc2-del-3-b


title: ydr026c-del-1-a


title: yap6-del-1-a


title: ydr266c-del-2-b


title: yap6-del-1-d


title: yap1-del+msn2-del-1-a


title: ydr266c-del-2-a


title: upc2-del+ecm22-del-1-e


title: usv1-del-1-b


title: yer184c-del+sip4-del-matA-3-a


title: yap1-del+msn2-del-1-b


title: yap1-del-2-b


title: uga3-del+dal81-del-1-b


title: uga3-del-1-a


title: tos8-del+cup9-del-1-b


title: uga3-del+dal81-del-1-a


title: tye7-del-1-b


title: tos8-del+cup9-del-1-a


title: upc2-del+ecm22-del-1-a


title: sut2-del-2-b


title: tos8-del-1-b


title: sut2-del-2-a


title: tye7-del-1-a


title: stp3-del-1-b


title: stp4-del-1-a


title: stp3-del-1-a


title: stp3-del+stp4-del-1-b


title: stp3-del+stp4-del-1-a


title: stb5-del+gzf3-del-2-a


title: stb5-del-1-b


title: stb5-del+isw2-del-2-b


title: rhabdomyosarcoma cell line [509903A03]

city: shihezi

first: chunxia

last: liu

address: 2nd North Road

institute: Shihezi University School of Medicine

description: aCGH  RMS

hyb_protocol: The labeled genomic DNA (31μg) was dried at 45℃ and diluted in 5.6 μl Sample Tracking Control. Then hybridized in 14.4 μl Hybridization solution (containing 2X Hybridization Buffer, Hybridization Component A, Alignment Oligo). Arrays were hybridized in Maui hybridization stations for 40-72 hr at 42 °C, and then washed in 42 °C with buffer (containing VWR Water, 10X Wash Buffer (I, II or III), 1M DTT) by using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using NimbleScan 2.6 software,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal log2 ratio (EXP_NORM/REF_NORM).

source_name: genomic DNA

label_protocol: 1. Add 4μL β-mercaptoethanol to 2200μL Random Primer Buffer, Mix by pulse-vortexing. Use 1050 μL Random Primer Buffer (containing β-mercaptoethanol) to dilute cy3-Random Nonamers and cy5-Random Nonamers respectively. 2. Add 500ng genomic DNA to LHC(Labeling and Hybridization Control). Then add 2μLLCH-1 to test Sample, and 2μLLCH-2 to Reference Sample, amount to 40μL respectively. Add test Sample (containing LLCH-1) to cy3-Random Nonamers, and Reference Sample (containing LLCH-2) to cy5-Random Nonamers, amount to 80μL respectively. 98 °C for 10 min，4°C for 2min. 3. Prepare dNTP/Klenow Master Mix (20μL): 8μL Nuclease-free Water, 10μL 10mM dNTP Mix, 2μL Klenow Fragment (3’->5’ exo-)50U/μl. 4. Add dNTP/Klenow Master Mix (20μL) to Sample mixtures (80μL) respectively. 37 °C  for 2 hr. 5. Add 21.5μL Stop Solution to stop reaction. 6. Then purify the label reaction liquid.

extract_protocol: Use QIAamp DNA Blood Mini kit to extract genomic DNA. 1. Pipet 20 μl QIAGEN Protease (or proteinase K) into the bottom of a 1.5 ml microcentrifuge tube. 2. Add 200 μl whole blood in 200 μl PBS. Add 4 μl of an RNase A stock solution (100 mg/ml) to the sample. 3. Add 200 μl Buffer AL to the sample. Mix by pulse-vortexing for 15 s. 4. Incubate at 56°C for 10 min. DNA yield reaches a maximum after lysis for 10 min at 56°C. 5. Briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 6. Add 200 μl ethanol (96–100%) to the sample, and mix again by pulse-vortexing for 15 s. After mixing, briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 7. Carefully apply the mixture from step 6 to the QIAamp Mini spin column (in a 2 ml collection tube) without wetting the rim. Close the cap, and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the tube containing the filtrate. 8. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW1 without wetting the rim. Close the cap and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the collection tube containing the filtrate. 9. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW2 without wetting the rim. Close the cap and centrifuge at full speed (20,000 x g; 14,000 rpm) for 3 min. 10. Recommended: Place the QIAamp Mini spin column in a new 2 ml collection tube and discard the old collection tube with the filtrate. Centrifuge at full speed for 1 min. 11. Place the QIAamp Mini spin column in a clean 1.5 ml microcentrifuge tube, and discard the collection tube containing the filtrate. Carefully open the QIAamp Mini spin column and add 200 μl Buffer AE or distilled water. Incubate at room temperature (15–25°C) for 1 min, and then centrifuge at 6000 x g (8000 rpm) for 1 min.

value: female

tag: ethinicty

value: Caucasian

tag: cell line

value: RD

source_name: Control DNA

tag: reference

value: Promega Human Genomic DNA:Female(G1521)


title: stb5-del+gzf3-del-2-b


title: stb5-del-1-a


title: rhabdomyosarcoma cell line [509872A03]

description: aCGH  RMS

tag: gender

value: male

value: Chinese

value: Promega Human Genomic DNA:male(G1471)


title: spt2-del-3-a


title: stb5-del+isw2-del-2-a


title: spt2-del-3-b


title: Horse_4_pre_exercise

city: Seoul

first: Hang Ah

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

description: Gene expression in leukocyte before exercise in warmblood horse

hyb_protocol: Nanodrop spectrophotometer. The labeled cRNAs were subjected to the 4X44K Horse Gene Expression Microarray Kit, one-color, using the Gene Expression Hybridization Kit for 17 h at 65 ℃. The hybridized microarray chips were washed with the Gene Expression Wash Buffer Kit

scan_protocol: The microarray chip was scanned using a DNA microarray scanner, and the raw signal density was acquired by using the Feature Extraction software. The threshold raw signal values were set at 1.0, and all raw signal values were normalized using a percentile shift (75th percentile).

data_processing: The normalized expression data of the microarray were analyzed using the GeneSpring GX12 software.

organism: Equus caballus

source_name: Leukocyte, before exercise

label_protocol: A phenol-chloroform method utilizing the TRIzol reagent

extract_protocol: Immediately before and after the exercise, 6 ml of blood was sampled from the jugular vein of each horse in anti-coagulated tubes containing ethylenediaminetetraacetic acid (EDTA). The samples were centrifuged at 4℃ at 3,000 rpm for 10 min, and the subsequent leukocytes from the buffy coat area were collected using sterilized Pasteur pipettes.

value: buffy coat

value: gelding (neutered)


title: stb4-del-1-a


title: Horse_1_pre_exercise


title: rhabdomyosarcoma tissue [509858A03]

description: aCGH  RMS

value: ERMS


title: Horse_2_pre_exercise


title: Horse_1_post_exercise

description: Gene expression in leukocyte after exercise in warmblood horse

source_name: Leukocyte, after exercise, 60min


title: Horse_4_post_exercise


title: snt1-del+spt2-del-matA-1-b


title: Horse_2_post_exercise


title: stb4-del-1-b


title: snt1-del+spt2-del-matA-1-a


title: snt1-del+hac1-del-matA-1-a


title: rhabdomyosarcoma tissue [509858A01]

description: aCGH  RMS


title: rsf2-del-1-b


title: snt1-del+hac1-del-matA-1-b


title: rsf2-del-1-a


title: rpn4-del-4-a


title: smp1-del-1-a


title: sip4-del+ecm22-del-2-b


title: sip4-del+ecm22-del-2-a


title: rhabdomyosarcoma tissue [509858A02]

description: aCGH  RMS


title: rhabdomyosarcoma tissue [510541A03]

description: aCGH  RMS


title: rhabdomyosarcoma tissue [510541A02]

description: aCGH  RMS


title: rhabdomyosarcoma tissue [510541A01]

description: aCGH  RMS

value: PRMS


title: rhabdomyosarcoma tissue [509945A03]

description: aCGH  RMS

value: ARMS


title: rhabdomyosarcoma tissue [509945A02]

description: aCGH  RMS


title: rpn4-del+ydr266c-del-1-d


title: rpn4-del+ydr266c-del-1-a


title: rpn4-del+ydr026c-del-1-b


title: rhabdomyosarcoma tissue [509945A01]

description: aCGH  RMS


title: rhabdomyosarcoma tissue [509903A02]

description: aCGH  RMS


title: rpn4-del+hac1-del-1-b


title: rpn4-del+mig1-del-1-b


title: rpn4-del+snt1-del-1-a


title: rhabdomyosarcoma tissue [509903A01]

description: aCGH  RMS


title: rpn4-del+ydr026c-del-1-a


title: rpn4-del+snt1-del-1-b


title: rhabdomyosarcoma tissue [465860A03]

description: aCGH  RMS


title: rpn4-del+cup9-del-2-b


title: rpn4-del+isw2-del-1-a


title: rpn4-del+mig1-del-1-a


title: rpn4-del+hac1-del-1-a


title: rpn4-del-3-b


title: rpn4-del+isw2-del-1-b


title: rpn4-del+asg1-del-1-b


title: rpi1-del+zap1-del-1-a


title: rhabdomyosarcoma tissue [465860A01]

description: aCGH  RMS


title: rpi1-del-2-a


title: rpn4-del+asg1-del-1-a


title: rpi1-del+zap1-del-1-b


title: rpn4-del+cup9-del-2-a


title: rph1-del+gis1-del-1-b


title: rox1-del-1-b


title: rhabdomyosarcoma tissue [458643A03]

description: aCGH  RMS


title: rph1-del+gis1-del-1-a


title: rpi1-del-2-b


title: rhabdomyosarcoma tissue [458643A02]

description: aCGH  RMS


title: rhabdomyosarcoma tissue [458643A01]

description: aCGH  RMS


title: rox1-del-1-a


title: rhabdomyosarcoma tissue [458270A02]

description: aCGH  RMS


title: rlm1-del-1-a


title: rlm1-del-2-b


title: rhabdomyosarcoma tissue [458270A01]

description: aCGH  RMS


title: rhabdomyosarcoma tissue [465860A02]

description: aCGH  RMS


title: rlm1-del+smp1-del-1-a


title: rgm1-del+usv1-del-2-b


title: rim101-del-2-a


title: rim101-del-2-b


title: rlm1-del+smp1-del-1-b


title: rhabdomyosarcoma tissue [458270A03]

description: aCGH  RMS


title: rgm1-del-1-a


title: rgm1-del+usv1-del-2-a


title: ppr1-del-1-a


title: pho2-del-2-b


title: PBMC from patient with normal renal biopsy:NORMAL_45

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.13) 'rma' in R.3.0.1

source_name: PBMC from patients showing normal biopsy

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: renal biopsy group

value: NORMAL

tag: cell type

value: Peripheral blood mononuclear cells (PBMC)


title: pho2-del-1-a


title: pho2-del+yox1-del-1-d


title: pho2-del+nhp6b-del-2-b


title: PBMC from patient with normal renal biopsy:NORMAL_42


title: PBMC from patient with normal renal biopsy:NORMAL_44


title: ppr1-del-1-b


title: pho2-del+yox1-del-2-a


title: msn2-del+ppr1-del-1-b


title: pho2-del+nhp6b-del-1-a


title: nrg1-del+nrg2-del-1-a


title: nhp6a-del+nhp6b-del-1-a


title: msn2-del+msn4-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_43


title: msn2-del+ppr1-del-1-a


title: PBMC from patient with normal renal biopsy:NORMAL_40


title: PBMC from patient with normal renal biopsy:NORMAL_39


title: msn2-del+msn4-del-1-a


title: PBMC from patient with normal renal biopsy:NORMAL_41


title: mig3-del-2-b


title: nhp6a-del+nhp6b-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_37


title: mig3-del+mig2-del-1-a


title: mig2-del-4-b


title: nrg1-del+nrg2-del-1-b


title: mig3-del+mig2-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_36


title: mig2-del-4-a


title: mig3-del-2-a


title: mig1-del+ygr067c-del-1-a


title: mig1-del-3-b


title: PBMC from patient with normal renal biopsy:NORMAL_38


title: mig1-del+ygr067c-del-1-b


title: mig1-del-3-a


title: PBMC from patient with normal renal biopsy:NORMAL_35


title: mig1-del+stb5-del-1-b


title: mig1-del+stb5-del-1-a


title: mig1-del+mig2-del-2-b


title: mig1-del+mig3-del-2-d


title: mig1-del+mig2-del-2-a


title: met31-del+met32-del-2-i


title: met31-del-2-b


title: PBMC from patient with normal renal biopsy:NORMAL_31


title: mig1-del+mig3-del-2-c


title: PBMC from patient with normal renal biopsy:NORMAL_33


title: PBMC from patient with normal renal biopsy:NORMAL_29


title: PBMC from patient with normal renal biopsy:NORMAL_30


title: met31-del+met32-del-2-g


title: PBMC from patient with normal renal biopsy:NORMAL_32


title: PBMC from patient with normal renal biopsy:NORMAL_34


title: mal33-del-2-b


title: PBMC from patient with normal renal biopsy:NORMAL_28


title: met28-del-1-b


title: met31-del-1-a


title: met32-del-1-b


title: mal13-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_26


title: mal13-del-1-a


title: PBMC from patient with normal renal biopsy:NORMAL_25


title: mal13-del+mal33-del-1-a


title: S9_rep3

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

institute: NIZO food research

description: raw data: 253432210002-4_2: Cy5

hyb_protocol: Co-hybridization of Cy5- and Cy3-labeled cDNA probes was performed on these oligonucleotide arrays at 65°C and 10 rpm for 17 h using GEX HI-RPM buffer (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: The raw expression data were Lowess normalized and scaled to normalized probe expression levels using MicroPreP (van Hijum, 2003). As in general multiple probes were designed for each ORF, the ORF expression level was calculated from the median of its probe signals.

organism: Lactococcus cremoris subsp. cremoris SK11

source_name: SK11 fermentation 9

label_protocol: 5 µg of total RNA was used for cDNA synthesis and indirect labeling with cyanine 5 or cyanine 3

growth_protocol: Lactococcus lactis strain SK11 was grown in chemically defined medium

extract_protocol: Cultures were lysed by bead-beating and total RNA was isolated by subsequent phenol/chloroform extraction.

treatment_protocol: Harvested cells were resuspended in cold TE buffer with phenol/chloroform, SDS, sodium acetate and zirconia beads, frozen in liquid nitrogen and stored at -80°C.

tag: fermentation conditions

value: 0 mM NaCl, pH 6.0, 35°C, shaken


title: mal13-del+cst6-del-3-b


title: mal13-del+mal33-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_27


title: PBMC from patient with normal renal biopsy:NORMAL_24


title: lys14-del-1-a


title: mal13-del+cst6-del-3-a


title: lys14-del-1-b


title: lys14-del+rpn4-del-1-b


title: isw2-del+gln3-del-1-a


title: lys14-del+rpn4-del-2-c


title: PBMC from patient with normal renal biopsy:NORMAL_22


title: hmo1-del-2-b


title: hmo1-del-2-a


title: S13_rep4

description: raw data: 253432210002-4_2: Cy3

source_name: SK11 fermentation 13

value: 100 mM NaCl, pH 6.5, 30°C, static


title: met28-del-1-a

value: wild type


title: hmo1-del+gat4-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_23


title: hcm1-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_20


title: isw2-del+gln3-del-2-b


title: PBMC from patient with normal renal biopsy:NORMAL_21


title: hmo1-del+gat4-del-1-a


title: hmo1-del+rox1-del-1-b


title: hcm1-del-1-a


title: hmo1-del+rox1-del-1-a


title: hac1-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_18


title: S13_rep3

description: raw data: 253432210002-4_1: Cy3


title: PBMC from patient with normal renal biopsy:NORMAL_19


title: S13_rep2

description: raw data: 253432210002-3_2: Cy5


title: PBMC from patient with normal renal biopsy:NORMAL_17


title: haa1-del-1-b


title: haa1-del-1-a


title: S12_rep2

description: raw data: 253432210002-3_2: Cy3

source_name: SK11 fermentation 12

value: 100 mM NaCl, pH 6.0, 35°C, static


title: S7_rep2

description: raw data: 253432210002-4_1: Cy5

source_name: SK11 fermentation 7

value: 0 mM NaCl, pH 6.5, 30°C, shaken


title: PBMC from patient with normal renal biopsy:NORMAL_16


title: haa1-del+gln3-del-1-a


title: S12_rep1

description: raw data: 253432210002-3_1: Cy5


title: S11_rep2

description: raw data: 253432210002-3_1: Cy3

source_name: SK11 fermentation 11

value: 0 mM NaCl, pH 6.5, 35°C, static


title: S11_rep1

description: raw data: 253432210002-2_2: Cy5


title: S10_rep2

description: raw data: 253432210002-2_2: Cy3

source_name: SK11 fermentation 10

value: 100 mM NaCl, pH 6.5, 35°C, shaken


title: PBMC from patient with normal renal biopsy:NORMAL_15


title: haa1-del+cup2-del-matA-1-b


title: haa1-del+cup2-del-matA-1-a


title: PBMC from patient with normal renal biopsy:NORMAL_13


title: gzf3-del-1-a


title: gln3-del+sum1-del-2-a


title: PBMC from patient with normal renal biopsy:NORMAL_11


title: S9_rep2

description: raw data: 253432210002-2_1: Cy3


title: PBMC from patient with normal renal biopsy:NORMAL_14


title: PBMC from patient with normal renal biopsy:NORMAL_10


title: gln3-del-1-b


title: gln3-del+rim101-del-1-b


title: haa1-del+gln3-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_12


title: gln3-del+rox1-del-1-a


title: gln3-del+rim101-del-1-a


title: S10_rep1

description: raw data: 253432210002-2_1: Cy5


title: gln3-del+rox1-del-1-b


title: gln3-del-1-a


title: gln3-del+sum1-del-2-b


title: S9_rep1

description: raw data: 253432210002-1_2: Cy5


title: gzf3-del-1-b


title: gln3-del+mig1-del-1-a


title: PBMC from patient with normal renal biopsy:NORMAL_8


title: gln3-del+gzf3-del-1-b


title: gat4-del-1-d


title: gln3-del+gzf3-del-1-a


title: gln3-del+mig1-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_9


title: S8_rep1

description: raw data: 253432210002-1_1: Cy5

source_name: SK11 fermentation 8

value: 100 mM NaCl, pH 6.0, 30°C, shaken


title: gat3-del-1-a


title: S7_rep1

description: raw data: 253432210002-1_1: Cy3


title: S13_rep1

description: raw data: 253432210001-4_2: Cy5


title: S8_rep2

description: raw data: 253432210002-1_2: Cy3


title: S6_rep3

description: raw data: 253432210001-4_1: Cy5

source_name: SK11 fermentation 6


title: gat3-del-1-b


title: S3_rep3

description: raw data: 253432210001-4_1: Cy3

source_name: SK11 fermentation 3

value: 0 mM NaCl, pH 6.5, 27°C, static


title: PBMC from patient with normal renal biopsy:NORMAL_5


title: PBMC from patient with normal renal biopsy:NORMAL_2


title: gat1-del+gzf3-del-2-a


title: gat3-del+ecm23-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_3


title: gat3-del+gat4-del-1-a


title: gat3-del+ecm23-del-1-a


title: gat3-del+gat4-del-1-b


title: PBMC from patient with normal renal biopsy:NORMAL_7


title: PBMC from patient with normal renal biopsy:NORMAL_4


title: PBMC from patient with normal renal biopsy:NORMAL_6


title: S6_rep4

description: raw data: 253432210001-4_2: Cy3


title: S1_rep2

description: raw data: 253432210001-3_2: Cy5

source_name: SK11 fermentation 1

value: 0 mM NaCl, pH 6.0, 27°C, shaken


title: gat1-del-1-b


title: fkh2-del-2-b


title: gat1-del-1-a


title: gat1-del+gln3-del-2-c


title: gat1-del+gln3-del-1-b


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_14

source_name: PBMC from patients with IFTA with inflammation

value: IFTA with inflammation (i-IFTA)


title: S6_rep2

description: raw data: 253432210001-3_2: Cy3


title: fkh1-del-1-b

source_name: refpool


title: S6_rep1

description: raw data: 253432210001-3_1: Cy5


title: S5_rep2

description: raw data: 253432210001-3_1: Cy3

source_name: SK11 fermentation 5

value: 0 mM NaCl, pH 6.0, 30°C, static


title: gat1-del+gzf3-del-1-b


title: S5_rep1

description: raw data: 253432210001-2_2: Cy5


title: fkh1-del+hcm1-del-1-b


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_13


title: fkh1-del-1-a


title: fkh2-del-1-a


title: PBMC from patient with normal renal biopsy:NORMAL_1


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_12


title: fkh1-del+fkh2-del-1-a


title: ecm23-del+gat4-del-1-b


title: ecm23-del-3-a


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_10


title: ecm23-del-3-b


title: fkh1-del+fkh2-del-1-b


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_9


title: fkh1-del+hcm1-del-1-a


title: S4_rep1

description: raw data: 253432210001-2_1: Cy5

source_name: SK11 fermentation 4

value: 100 mM NaCl, pH 6.0, 27°C, static


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_8


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_11


title: ecm22-del-1-b


title: ecm23-del+gat4-del-1-a


title: S4_rep2

description: raw data: 253432210001-2_2: Cy3


title: S3_rep1

description: raw data: 253432210001-1_2: Cy5


title: S3_rep2

description: raw data: 253432210001-2_1: Cy3


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_7


title: S2_rep1

description: raw data: 253432210001-1_1: Cy5

source_name: SK11 fermentation 2

value: 100 mM NaCl, pH 6.5, 27°C, shaken


title: dal81-del-rep-100A3-b


title: dot6-del+tod6-del-1-b


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_5


title: dal81-del-1-c


title: S1_rep1

description: raw data: 253432210001-1_1: Cy3


title: I9_rep3

description: raw data: 253132410002-4_2: Cy5

organism: Lactococcus lactis subsp. lactis Il1403

source_name: IL1403 fermentation 9

growth_protocol: Lactococcus lactis strain IL1403 was grown in chemically defined medium


title: dal80-del+gzf3-del-1-a


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_6


title: dot6-del+tod6-del-1-a


title: dal80-del-1-b


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_4


title: I13_rep4

description: raw data: 253132410002-4_2: Cy3

source_name: IL1403 fermentation 13


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_3


title: dal80-del-1-d


title: dal80-del+gzf3-del-1-b


title: cup9-del-1-a


title: cst6-del-3-b


title: I7_rep2

description: raw data: 253132410002-4_1: Cy5

source_name: IL1403 fermentation 7


title: PBMC from patient showing IFTA in renal biopsy:IFTA_14

source_name: PBMC from patients with signs of tubular atrophy and interstitial fibrosis (IFTA)


title: cup9-del-1-b


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_2


title: cup2-del-1-a


title: cin5-del-2-b


title: PBMC from patient showing IFTA with inflammation in renal biopsy:i.IFTA_1

value: signs of tubular atrophy and interstitial fibrosis (IFTA)


title: cin5-del-2-a


title: cbf1-del-1-a


title: cst6-del-3-a


title: PBMC from patient showing IFTA in renal biopsy:IFTA_13


title: I13_rep2

description: raw data: 253132410002-3_2: Cy5


title: I12_rep2

description: raw data: 253132410002-3_2: Cy3

source_name: IL1403 fermentation 12


title: PBMC from patient showing IFTA in renal biopsy:IFTA_12


title: cbf1-del-1-b


title: cbf1-del+tye7-del-3-a


title: PBMC from patient showing IFTA in renal biopsy:IFTA_11


title: cbf1-del+tye7-del-3-b


title: cbf1-del+mal33-del-1-a


title: cbf1-del+sut2-del-1-a


title: I12_rep1

description: raw data: 253132410002-3_1: Cy5


title: I11_rep2

description: raw data: 253132410002-3_1: Cy3

source_name: IL1403 fermentation 11


title: I11_rep1

description: raw data: 253132410002-2_2: Cy5


title: I13_rep3

description: raw data: 253132410002-4_1: Cy3


title: cbf1-del+sut2-del-1-b


title: I10_rep1

description: raw data: 253132410002-2_1: Cy5

source_name: IL1403 fermentation 10


title: I10_rep2

description: raw data: 253132410002-2_2: Cy3


title: cbf1-del+hac1-del-3-a


title: I9_rep2

description: raw data: 253132410002-2_1: Cy3


title: PBMC from patient showing IFTA in renal biopsy:IFTA_10


title: cbf1-del+hac1-del-3-b


title: PBMC from patient showing IFTA in renal biopsy:IFTA_8


title: K9_rep3

description: raw data: 253432310002-4_2: Cy5

organism: Lactococcus lactis subsp. lactis KF147

source_name: KF147 fermentation 9

growth_protocol: Lactococcus lactis strain KF147 was grown in chemically defined medium


title: PBMC from patient showing IFTA in renal biopsy:IFTA_9


title: asg1-del-2-a


title: cad1-del+yap1-del-1-a


title: cat8-del+ypr015c-del-1-b


title: cat8-del+ypr015c-del-1-a


title: I8_rep2

description: raw data: 253132410002-1_2: Cy3

source_name: IL1403 fermentation 8


title: PBMC from patient showing IFTA in renal biopsy:IFTA_7


title: cin5-del+yap6-del-2-a


title: PBMC from patient showing IFTA in renal biopsy:IFTA_4


title: PBMC from patient showing IFTA in renal biopsy:IFTA_6


title: cad1-del+yap1-del-1-b


title: PBMC from patient showing IFTA in renal biopsy:IFTA_3


title: cbf1-del+mal33-del-1-b


title: asg1-del-1-b


title: PBMC from patient showing IFTA in renal biopsy:IFTA_5


title: PBMC from patient showing IFTA in renal biopsy:IFTA_2


title: mixed culture_ 96h_biological rep2

city: Vila Real

first: Ana

last: Mendes-Ferreira

address: Quinta de Prados

institute: Universidade de Trás-os-Montes e Alto Douro

description: Gene expression data from cells in mixed culture at 96h

hyb_protocol: 5 µg of fragmented aRNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0003; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

source_name: S. cerevisiae in mixed culture at 96h

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Yeast Genome 2.0 Arrays, according to the manufacturer's GeneChip 3' IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3' IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3' IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Exponential cell populations of both yeast strains  were used to inoculate natural grape juice (10^6 cel/ml). Paralell fermentations were conducted with S. cerevisiae pure-culture and S. cerevisiae in mxed-culture with H. guilliermondii strain

extract_protocol: Total RNA isolation was performed using the hot-phenol method (Koher & Domdey, 1991, Methods in Enzimology 194:398-405).

treatment_protocol: Natural grape juice fermentations were conducted by inoculation with with S. cerevisiae (UCD522) either in single (Control) or in mixed culture with a strain of Hanseniaspora guilliermondii (Treatment)

tag: treatment

value: mixed culture

tag: time


title: K13_rep4

description: raw data: 253432310002-4_2: Cy3

source_name: KF147 fermentation 13


title: cad1-del-1-b

tag: genotype


title: I9_rep1

description: raw data: 253132410002-1_2: Cy5


title: K7_rep2

description: raw data: 253432310002-4_1: Cy5

source_name: KF147 fermentation 7


title: I8_rep1

description: raw data: 253132410002-1_1: Cy5


title: mixed culture_ 96h_biological rep3


title: K13_rep3

description: raw data: 253432310002-4_1: Cy3


title: I7_rep1

description: raw data: 253132410002-1_1: Cy3


title: mixed culture_ 96h_biological rep1