title: Col_8hrAR_Re1_rep1

description:
AR_013
Gene expression at reoxygenation 1hr in Col-0 (8hr-anoxia)


title: Col_8hrAR_Re1_rep4

status: Public on Feb 18 2014

type: RNA

city: Taipei

first: Kuen-Jin

last: Tsai

address: 128 Academia Road, Section 2, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica, Taiwan

description:
AR_016
Gene expression at reoxygenation 1hr in Col-0 (8hr-anoxia)

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Arabidopsis V4 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing the microarrays are scanned with an Agilent microarray scanner G2565CA (Agilent Technologies, USA) at 535 nm for Cy3. The array image was analyzed by the Feature Extraction software version 10.7.1.1 using the default setting.

data_processing:
The raw data of hybridization was imported into the analysis software GeneSpring 11.5 (Agilent Technologies), and the data of normaxia of Col-0 was used as control to normalize all the samples.
threshold raw signals to: 1.0; normalization algorithm: Percentile Shift; Percentile target: 75; no baseline transformation or filtering

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 1hr

label_protocol: Cy3 labeling (CyDye, Agilent Technologies, USA) was performed  during the in vitro transcription process. 1.65 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes.

growth_protocol: Seeds were sterilized by 0.5% sodium hypochlorite for 20 min and then sown on the plates containing 1/2 Murashige and Skoog (MS) medium (Duchefa Biochemie BV, Haarlem, Netherlands) with 0.55% phytagel and 0.5% sucrose. The plates were further stored at 4°C in the dark for 3 d. After cold stratification, the plates were incubated at 22°C and placed in a vertical position in a growth chamber under long photoperiod with 16 h of light and 8 h of darkness for 5 d. 5-day-old seedlings were then transplanted onto fresh plates for another 2 d before anoxia treatment.

extract_protocol: Total RNA were extracted from treated Arabidopsis seedlings by TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). Based on the manufacturer’s instruction, a 1:2 ratio of sample:TRIZOL reagent was applied to reach higher extraction efficiency. Extracted total RNA were further treated with DNase by using TURBO RNA free kit (Ambion) to remove genomic DNA contamination. For quality control, the integrity of total RNA was determined by Agilent Bioanalyzer 2100. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA)

treatment_protocol: For anoxic treatment, 7-day-old Arabidopsis seedlings were placed into a chamber that was filled with pure nitrogen (100% N2) to replace the air in chamber. To prevent remnant oxygen in the system, anaerobic bags were placed in the chamber to ensure anoxic environment. For re-aeration, air was pumped into the chamber to replace the content in it.  Both anoxic and reoxygenation treatment were carried out in dark condition.

tag: ecotype

value: Columbia

tag: genotype/variation

value: wild type

tag: age

value: 7 days

tag: tissue

value: whole seedling


title: Col_8hrAR_Re3_rep3

description:
AR_019
Gene expression at reoxygenation 3hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 3hr


title: Col_8hrAR_Re6_rep2

description:
AR_022
Gene expression at reoxygenation 6hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 6hr


title: BC24_ADN0154_s1h1

type: genomic

city: Paris

first: Jaydutt

middle: D

last: Bhalshankar

address: 26 rue d'Ulm

department: INSERM UNIT 830

country: France

institute: Institut CURIE

description: Hybridized to SNP6.154

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 to generate .CEL files for downstream analysis.

data_processing: CEL files and TXT files (generated by Affymetrix Genotyping Console 3.0.1) were processed by GAP (Popova T et al, Genome Biol, 2009) and Partek® GS software version 6.5 build 6.10.1020

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast tumoral sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tumor fragments using a standard phenol/chloroform procedure. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: group

value: validation set

value: breast cancer tissue


title: BC24_ADN0161_s1h1

description: Hybridized to SNP6.161


title: Col_8hrAR_Re3_rep1

description:
AR_017
Gene expression at reoxygenation 3hr in Col-0 (8hr-anoxia)


title: Col_8hrAR_Re0.5_rep3

description:
AR_011
Gene expression at reoxygenation 0.5hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 0.5hr


title: BC24_ADN0153_s1h1

description: Hybridized to SNP6.153


title: BC24_ADN0152_s1h1

description: Hybridized to SNP6.152


title: BC24_ADN0151_s1h1

description: Hybridized to SNP6.151


title: BC24_ADN0091_s1h1

description: Hybridized to SNP6.091

value: training set


title: BC24_ADN0096_s1h1

description: Hybridized to SNP6.096


title: Col_8hrAR_Re0.5_rep2

description:
AR_010
Gene expression at reoxygenation 0.5hr in Col-0 (8hr-anoxia)


title: Col_8hrAR_Re0.5_rep1

description:
AR_009
Gene expression at reoxygenation 0.5hr in Col-0 (8hr-anoxia)


title: BC24_ADN0085_s1h1

description: Hybridized to SNP6.085


title: BC24_ADN0083_s1h1

description: Hybridized to SNP6.083


title: BC24_ADN0087_s1h1

description: Hybridized to SNP6.087


title: BC24_ADN0150_s1h1

description: Hybridized to SNP6.150


title: BC24_ADN0149_s1h1

description: Hybridized to SNP6.149


title: BC24_ADN0088_s1h1

description: Hybridized to SNP6.088


title: BC24_ADN0082_s1h1

description: Hybridized to SNP6.082


title: Col_8hrAR_Re0_rep4

description:
AR_008
Gene expression at reoxygenation 0hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 0hr


title: BC24_ADN0081_s2h1

description: Hybridized to SNP6.081


title: Col_8hrAR_Re0_rep1

description:
AR_005
Gene expression at reoxygenation 0hr in Col-0 (8hr-anoxia)


title: Col_8hrAR_Re0_rep3

description:
AR_007
Gene expression at reoxygenation 0hr in Col-0 (8hr-anoxia)


title: BC24_ADN0086_s1h1

description: Hybridized to SNP6.086


title: BC24_ADN0080_s1h1

description: Hybridized to SNP6.080


title: Col_8hrAR_Re0_rep2

description:
AR_006
Gene expression at reoxygenation 0hr in Col-0 (8hr-anoxia)


title: BC24_ADN0077_s1h1

description: Hybridized to SNP6.077


title: BC24_ADN0079_s1h1

description: Hybridized to SNP6.079


title: BC24_ADN0078_s1h1

description: Hybridized to SNP6.078


title: Col_8hrAR_Nor_rep1

description:
AR_001
Gene expression under normal condition in Col-0 (8hr-anoxia)

source_name: WT_normal condition_before 8hr anoxia


title: BC24_ADN0076_s1h1

description: Hybridized to SNP6.076


title: Col_8hrAR_Nor_rep4

description:
AR_004
Gene expression under normal condition in Col-0 (8hr-anoxia)


title: BC24_ADN0075_s1h1

description: Hybridized to SNP6.075


title: Col_8hrAR_Nor_rep2

description:
AR_002
Gene expression under normal condition in Col-0 (8hr-anoxia)


title: Col_8hrAR_Nor_rep3

description:
AR_003
Gene expression under normal condition in Col-0 (8hr-anoxia)


title: BC24_ADN0074_s1h1

description: Hybridized to SNP6.074


title: Col_8hrAR_Re1_rep2

description:
AR_014
Gene expression at reoxygenation 1hr in Col-0 (8hr-anoxia)


title: SKMEL-28 G replicate 2

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: University of Alabama at Birmingham

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities of probes were log2-transformed and Quantile normalized (lumi package, R/Bioconductor)

source_name: SKMEL-28 cell line with pre-miR-146a with G SNP expression

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

growth_protocol: SKMEL28 FG12 or SKMEL28 C or SKMEL G cells were grown in RPMI-1640 media with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instruction

treatment_protocol: SKMEL28 melanoma cell line stably expressing either an empty vector or  pre-miR146a with either C or G SNP (SKMEL28-FG12, SKMEL28-miR-146a/C and SKMEL28-miR-146a/G) were used to prepare total RNA.

tag: cell line

value: SKMEL28 melanoma cell line

value: pre-miR-146a with G SNP expression


title: SKMEL-28 C replicate 2

description: SAMPLE 4

source_name: SKMEL-28 cell line with pre-miR-146a with C SNP expression

value: pre-miR-146a with C SNP expression


title: SKMEL-28 G replicate 1

description: SAMPLE 5


title: BC24_ADN0072_s1h2

description: Hybridized to SNP6.072


title: BC24_ADN0071_s1h1

description: Hybridized to SNP6.071


title: BC24_ADN0068_s1h1

description: Hybridized to SNP6.068


title: BC24_ADN0070_s1h1

description: Hybridized to SNP6.070


title: BC24_ADN0067_s1h1

description: Hybridized to SNP6.067


title: BC24_ADN0066_s1h1

description: Hybridized to SNP6.066


title: SKMEL-28 FG12 replicate 2

description: SAMPLE 2

source_name: SKMEL-28 cell line with FG12 vector expression

value: control


title: Region III_Aerated vs Stagnant_Replicate 3

city: Chikusa

first: Takaki

last: Yamauchi

address: Furo-cho

country: Japan

institute: Nagoya University

description: Biological Replicate 3 of 3.

hyb_protocol: Gene Expression Hybridization kit part No. 5188-5242

scan_protocol: Agilent scanner model G2505C

data_processing: Data was analyzed by Feature Extraction Software (Version 10.5.1.1, Agilent)

organism: Oryza sativa

source_name: Root 20-30 mm, Aerated

label_protocol: Total RNAs (400 ng) were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (825 ng each) were used for hybridization in a rice 44K oligo-DNA microarray (Agilent Technologies).

growth_protocol: Seeds of rice (Oryza sativa, cv. Nipponbare) were surfacely sterilized with 70% ethanol for 1 min followed by sterilization with NaClO solution (2.5% available chlorine) for 30 min and were washed with deionized water several times. The sterilized seeds were germinated in the darkness at 28OC for 2 d. Seedlings were transferred to hydroponic container with quarter- strength aerated nutrient solution [23 °C, light conditions, photosynthetically active radiation (PAR), 200–250 μmol m–2 s–1] for 4 d. Composition of the nutrient solution was described by Colmer et al. (2006). After 4 d, the seedlings were transferred to aerated full-strength nutrient solution.

extract_protocol: Total RNA was extracted from frozen fixed tissues from four sequential regions of the adventitious using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. The quality of total RNA was assessed using a RNA 6000 Pico kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Nine days after germination, the seedlings were transferred to well aerated nutrient solution or stagnant deoxygenated nutrient solution and grown for 14 days. Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen, <0.5 mg l–1) prior to use by flushing with N2 gas.

tag: cultivar

value: Nipponbare

tag: treatment

value: Aerated treatment for 14 days

source_name: Root 20-30 mm, Stagnant

value: Stagnant treatment for 14 days


title: Region III_Aerated vs Stagnant_Replicate 1

description: Biological Replicate 1 of 3.


title: Region III_Aerated vs Stagnant_Replicate 2

description: Biological Replicate 2 of 3.


title: Region II_Aerated vs Stagnant_Replicate 2

description: Biological Replicate 2 of 3.

source_name: Root 10-20 mm, Aerated

source_name: Root 10-20 mm, Stagnant


title: SKMEL-28 C replicate 1

description: SAMPLE 3


title: BC24_ADN0065_s1h1

description: Hybridized to SNP6.065


title: Region II_Aerated vs Stagnant_Replicate 1

description: Biological Replicate 1 of 3.


title: SKMEL-28 FG12 replicate 1

description: SAMPLE 1


title: Region I_Aerated vs Stagnant_Replicate 3

description: Biological Replicate 3 of 3.

source_name: Root 0-10 mm, Aerated

source_name: Root 0-10 mm, Stagnant


title: Region I_Aerated vs Stagnant_Replicate 2

description: Biological Replicate 2 of 3.


title: BC24_ADN0061_s1h1

description: Hybridized to SNP6.061


title: BC24_ADN0060_s1h1

description: Hybridized to SNP6.060


title: Region I_Aerated vs Stagnant_Replicate 1

description: Biological Replicate 1 of 3.


title: GATA1+LSK rep4

city: Fukuoka

first: Kohta

last: Miyawaki

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

data_processing: The data were normalized using quantile normalization with Illumina BeadStudio.

organism: Mus musculus

source_name: Mouse bone marrow

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit.

tag: strain

value: GATA1-GFP transgenic

value: 8 weeks

value: bone marrow

tag: cell type


title: BC24_ADN0063_s1h1

description: Hybridized to SNP6.063


title: TotRNA_oldMice_1

city: Pittsburgh

first: Maria

last: Kapetanaki

state: PA

address: 200 Lothrop Str, BSTW 1200

institute: University of Pittsburgh

description: old mice

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65 C on Agilent-28005 Human gene expression microarray  G4852A. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K (SurePrint) array slides

data_processing: Agilent Feature Extraction v10.5.1.1 default parameters

label_protocol: pCp-Cy3  labeled RNA was prepared according to the standard Agilent protocol from 50 ng total RNA

extract_protocol: Total RNA extracted using Trizol according to the manufacturer's instructions.

value: Bone  marrow mesenchymal stem cells

value: 24 months


title: TotRNA_oldMice_2

description: old mice


title: TotRNA_oldMice_3

description: old mice


title: Region II_Aerated vs Stagnant_Replicate 3

description: Biological Replicate 3 of 3.


title: BC24_ADN0058_s1h1

description: Hybridized to SNP6.058


title: TotRNA_youngMice_3

description: young mice

value: 3 months


title: TotRNA_youngMice_2

description: young mice


title: CMP rep3

value: CMP


title: TotRNA_youngMice_1

description: young mice


title: LMPP rep4

value: LMPP


title: Rat 1-3, mixed serum mRNA

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

institute: Morinaga Milk Industry Co., Ltd.

description: Total RNA were purified from rat 1-3 serum and were mixed

hyb_protocol: Cy3 labelled RNA samples were hybridized to the Whole Rat Genome Oligo Microarrays (4X44K) (Agilent Technologies) at 65 ºC for 17 hr with a Gene Expression Hybridyzation Kit (Agilent Technologies). After hybridyzation, the microarray slides were washed and dried according to the manufacture's instruction.

scan_protocol: The microarray slides were scanned on an Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: Fluorescent signal intensities were extracted from the images with the Feature Extraction Software (v.9.5.3.1) (Agilent Technologies). The raw signal values were normalized to Quantile when importing the Feature Extraction files into GeneSpring GX 11.5.1.

organism: Rattus norvegicus

source_name: Rat 1-3, mixed serum mRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low RNA Input Linear Amplification kit (Agilent) according to the manufacture's instruction, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified using an miRNeasy Mini Kit (Qiagen, Hilden, Germany). Briefly, milk whey and serum samples were diluted with five volumes of QIAzol Lysis Reagent, mixed thoroughly by vortexing and incubated for 5 min. Then chloroform (equal volume to sample) was added to homogenate, mixed thoroughly by vortexingand incubated for 3 min. The homogenate were centrifuged (12,000 x g, 4 ºC, 15 min). The resulting aqueous phase was mixed thoroughly with 1.5 volumes of 100 % ethanol and passed through an miRNeasy column. The column was washed according to the manufacture's protocol, and RNA was eluted in nuclease free water. The quanity and integrity of the RNA were assessed using RNA 6000 Pico Kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

tag: sample

value: serum

tag: time

value: 21 d post partum


title: BC24_ADN0057_s1h1

description: Hybridized to SNP6.057

value: validation set

value: breast cancer tissue


title: Rat 3, d 16 milk mRNA

source_name: Rat 3, d 16 milk mRNA

value: milk

value: 16 d post-partum


title: BC24_ADN0157_s1h1

description: Hybridized to SNP6.157


title: GATA1-LSK rep4


title: LT-HSC rep5

value: LT-HSC


title: LT-HSC rep6


title: GATA1+LSK rep3


title: Rat 2, d 16 milk mRNA

source_name: Rat 2, d 16 milk mRNA


title: BC24_ADN0056_s1h1

description: Hybridized to SNP6.056

source_name: Breast tumoral sample


title: Rat 2, d 9 milk mRNA

source_name: Rat 2, d 9 milk mRNA

value: 9 d post-partum


title: BC24_ADN0055_s1h1

description: Hybridized to SNP6.055


title: BC24_ADN0158_s1h1

description: Hybridized to SNP6.158


title: BC24_ADN0054_s1h1

description: Hybridized to SNP6.054


title: Rat 3, d 9 milk mRNA

source_name: Rat 3, d 9 milk mRNA


title: Rat 1, d 16 milk mRNA

source_name: Rat 1, d 16 milk mRNA


title: CMP rep4


title: Rat 3, d 2 milk mRNA

source_name: Rat 3, d 2 milk mRNA

value: 2 d post-partum


title: Rat 1, d 2 milk mRNA

source_name: Rat 1, d 2 milk mRNA


title: BC24_ADN0050_s1h1

description: Hybridized to SNP6.050


title: LT-HSC rep4

value: GATA1-GFP transgenic


title: BC24_ADN0051_s1h1

description: Hybridized to SNP6.051


title: Rat 2, d 2 milk mRNA

source_name: Rat 2, d 2 milk mRNA


title: Col_8hrAR_Re0.5_rep4

description:
AR_012
Gene expression at reoxygenation 0.5hr in Col-0 (8hr-anoxia)

source_name: 8hr anoxia-reoxygenated WT_reoxygenation 0.5hr

value: Columbia

value: wild type

value: 7 days

value: whole seedling


title: BC_RPPA_JS_2_RPS6

type: protein

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

country: Germany

institute: German Cancer Research Center

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 3

hyb_protocol: Slides were blocked with 50% blocking buffer for fluorescent applications (Rockland) in TBS containing 5 mM NaF and 1 mM Na3VO4 for 2h at RT, prior to incubation with target specific primary antibodies at 4°C over night. Detection of the primary antibodies was done with Alexa Fluor® 680 F(ab')2 fragments of goat anti-mouse IgG or anti-rabbit IgG in 1:8000 dilution (Life Technologies).

scan_protocol: Images of all slides were obtained at an excitation wavelength of 685 nm and a resolution of 21 µm using the Odyssey Scanner (LI-COR). These 16-bit TIFF-files where then used to quantify the signal intensities for each individual spot with the software GenePixPro 5.0 (Molecular Devices).

data_processing: Representative slides were stained for total protein quantification using the protein dye Fast Green FCF. To account for variation in total protein amount, a normalization factor for each spot was calculated using information obtained form these FCF slides and antibody signals of each spot were normalized accordingly. Each sample was printed in technical replicate on the slide and the median was used for further analyses.

label: Alexa Fluor® 680

molecule: protein

label_protocol: Alexa Fluor® 680

extract_protocol: Frozen tumor samples were homogenized using a bead mill (TissueLyser, Qiagen) and tissue protein extraction reagent (T-PER, Thermo Scientific) supplemented with 1 mM EDTA, 5 mM NaF, 2 μM staurosporine, PhosSTOP Phosphatase Inhibitor Cocktail (Roche Applied Science), and Complete Mini Protease Inhibitor Cocktail (Roche Applied Science). Total protein concentration was determined by bicinchoninic acid assay (Pierce). Prior to spotting, tumor lysates were mixed with 4x SDS sample buffer (10% Glycerol, 4% SDS, 10 mM DTT, 125 mM Tris-HCl, pH 6.8), adjusted to 2 µg/µl total protein, and boiled for 5 min at 95°C.

tag: target protein

tag: antibody id

tag: antibody manufacturer

value: CST


title: BC24_ADN0053_s1h1

description: Hybridized to SNP6.053


title: LT-HSC rep3

value: 8 weeks

value: bone marrow


title: BC_RPPA_JS_2_Ki67

description:
mouse IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 4

value: DAKO


title: BC_RPPA_JS_2_NDKA

description:
rabbit IgG
corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 2

value: NDKA


title: GATA1+LSK rep2


title: Rat 1, d 9 milk mRNA

source_name: Rat 1, d 9 milk mRNA


title: Liver_Nrf2 null_Rep3 (2)

city: Baltimore

first: Thomas

last: Kensler

state: MD

address: 615 N. Wolfe St.

institute: The Johns Hopkins University

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package

label: Biotin

source_name: Nrf2 null mouse, liver

label_protocol: Standard Affymetrix procedures

extract_protocol: Total RNA was extracted and transcribed to cDNA

tag: genotype

value: Nrf2 knockout

value: Liver

tag: Sex

value: Male

tag: compound

value: Vehicle

tag: route

value: Gavage

tag: dose

value: 0 uM/kg, 6 hours


title: LT-HSC rep2

tag: genotype/variation

tag: age

tag: tissue

value: LT-HSC


title: Liver_Nrf2 null_Rep2 (2)


title: Liver_Nrf2 null_CDDO-Im_Rep3

source_name: Nrf2 null mouse, CDDO-Im, liver

value: CDDO-Im

value: 30 uM/kg, 6 hours


title: Liver_Nrf2 null_CDDO-Im_Rep2


title: Liver_Widltype_CDDO-Im_Rep3

source_name: Wildtype mouse, CDDO-Im, liver

value: Wildtype


title: LT-HSC rep1

value: GATA1-GFP transgenic


title: GATA1+LSK rep1


title: BC24_ADN0048_s1h1

description: Hybridized to SNP6.048

tag: group

value: validation set

value: breast cancer tissue


title: Liver_Nrf2 null_CDDO-Im_Rep1


title: Liver_Nrf2 null_Rep1 (2)


title: Liver_Widltype_CDDO-Im_Rep2


title: CMP rep2

value: 8 weeks

value: CMP


title: BC24_ADN0046_s1h1

description: Hybridized to SNP6.046


title: BC_RPPA_JS_2_caveolin_1

value: SantaCruz


title: GATA1-LSK rep3

value: bone marrow


title: BC24_ADN0045_s1h1

description: Hybridized to SNP6.045


title: BC24_ADN0044_s1h1

description: Hybridized to SNP6.044


title: Liver_Widltype_CDDO-Im_Rep1


title: BC24_ADN0042_s1h1

description: Hybridized to SNP6.042


title: Rat 1, serum microRNA

hyb_protocol: Cy3 labelled RNA samples were hybridized to rat miRNA microarrays (Release 14.0) (Agilent Technologies) at 55 ºC for 20 hr. After hybridyzation, the microarray slides were washed and dried according to the manufacture's instruction.

source_name: Rat 1, serum microRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 70 ng RNA using the miRNA Complete Labeling Reagent and Hyb kit (Agilent) according to the manufacture's instruction, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

value: serum

value: 21 d post partum


title: BC24_ADN0043_s1h1

description: Hybridized to SNP6.043


title: Rat 2, serum microRNA

source_name: Rat 2, serum microRNA


title: Liver_Wildtype_Rep3 (2)

source_name: Wildtype mouse, liver

value: Liver

value: Male


title: Rat 3, d 16 milk microRNA

source_name: Rat 3, d 16 milk microRNA

value: milk

value: 16 d post-partum


title: Rat 3, serum microRNA

source_name: Rat 3, serum microRNA


title: BC24_ADN0041_s1h1

description: Hybridized to SNP6.041

source_name: Breast tumoral sample


title: GATA1-LSK rep2

source_name: Mouse bone marrow


title: BC24_ADN0038_s1h1

description: Hybridized to SNP6.038


title: Rat 2, d 16 milk microRNA

source_name: Rat 2, d 16 milk microRNA


title: BC24_ADN0040_s1h1

description: Hybridized to SNP6.040


title: Liver_Wildtype_Rep2 (2)

value: Vehicle

value: Gavage

value: 0 uM/kg, 6 hours


title: Liver_C57BL/6_Wildtype_Rep3

city: Kansas City

first: Curtis

last: Klaassen

state: KS

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

hyb_protocol: Affymetrix standard procedure for Mouse Genome 430 2.0 array; GeneChip Hybridization, Wash and stain kit - Affymetrix 900720, 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan; scanning hardware: Affymetrix GeneChip Scanner 3000 7G with Autoloader; scanning software: Affymetrix GeneChip Command Console (AGCC) ver. 1.1

data_processing: Raw data CEL files were imported into the ‘‘R’’ program using the ‘‘affy’’ package, normalized by the Robust Multichip Averaging (gcRMA) package, and log2 transformed. The probes with intensities lower than log2(100) in all groups were excluded in analysis. Only the probes with intensities higher than log2(100) were kept in the matrix file.

label_protocol: Biotinylated cRNA were prepared using One-cycle target labeling kit according to the standard Affymetrix protocol. 100ng nucleic acid waas used. Label incorporation method: In-vitro Transcription using the GeneChip 3’ IVT Express Kit - Affymetrix 901228;

growth_protocol: Animals were housed in a temperature-, light-, and humidity- controlled environment and had access to Teklad Rodent Diet #8604 (Harlan Laboratories, Madison, WI) and water ad libitum.  The housing facility is an American Animal Associations Laboratory Animal Care-accredited facility at the University of Kansas Medical Center, and all procedures were approved in accordance with the Institutional Animal Care and Use Committee guidelines.

extract_protocol: Total RNA was isolated using RNAzol B reagent (Tel Test, Inc., Friendswood, TX) according to the manufacturer’s protocol. The concentration of total RNA in each sample was quantified spectrophotometrically at 260 nm. The integrity of each RNA sample was evaluated by formaldehyde-agarose gel electrophoresis before analysis.

treatment_protocol: Naïve mice with genetic modification: Nrf2-null, wild type, Keap1-knockdown, and Keap1-hepatocyte knockout

value: Wildtype


title: CMP rep1

value: GATA1-GFP transgenic


title: GATA1-LSK rep1


title: LMPP rep3

value: LMPP


title: Liver_Wildtype_Rep1 (2)


title: Rat 1, d 16 milk microRNA

source_name: Rat 1, d 16 milk microRNA


title: BC24_ADN0036_s1h1

description: Hybridized to SNP6.036

value: validation set

value: breast cancer tissue


title: Rat 2, d 9 milk microRNA

source_name: Rat 2, d 9 milk microRNA

value: 9 d post-partum


title: Rat 3, d 9 milk microRNA

source_name: Rat 3, d 9 milk microRNA


title: Liver_C57BL/6_Wildtype_Rep1

value: 8 weeks


title: LMPP rep2

value: bone marrow


title: LMPP rep1


title: BC24_ADN0035_s1h1

description: Hybridized to SNP6.035


title: BC24_ADN0034_s1h1

description: Hybridized to SNP6.034


title: Rat 3, d 2 milk microRNA

source_name: Rat 3, d 2 milk microRNA

value: 2 d post-partum


title: Rat 1, d 9 milk microRNA

source_name: Rat 1, d 9 milk microRNA


title: BC24_ADN0033_s1h1

description: Hybridized to SNP6.033


title: BC24_ADN0031_s1h1

description: Hybridized to SNP6.031


title: Liver_Nrf2 null_Rep3

description: Nrf2-null and Keap1-KD mice (in which Keap1 was decreased throughout the body) were backcrossed onto the C57BL/6 background, and 99% congenicity was confirmed by the speed congenics group at Jackson Laboratories (Bar Harbor, ME).

value: Nrf2 null


title: Liver_Nrf2 null_Rep2

value: Liver


title: Rat 2, d 2 milk microRNA

source_name: Rat 2, d 2 milk microRNA


title: BC24_ADN0030_s1h1

description: Hybridized to SNP6.030


title: BC24_ADN0029_s1h1

description: Hybridized to SNP6.029


title: Rat 1, d 2 milk microRNA

source_name: Rat 1, d 2 milk microRNA


title: BC24_ADN0032_s1h1

description: Hybridized to SNP6.032


title: Liver_C57BL/6_Wildtype_Rep2

value: Male


title: Liver_Keap1 Knockdown_Rep2

source_name: Keap1 KD mouse liver

value: Keap1 knockdown


title: Liver_Nrf2 null_Rep1

source_name: Nrf2 null mouse, liver


title: BC24_ADN0027_s1h1

description: Hybridized to SNP6.027


title: Liver_Keap1 Knockdown_Rep1


title: primary rat islets, NR4A3_biological rep5

city: Durham

first: Larry

middle: Gene

last: Moss

state: NC

address: 4321 Medical Park Drive S200

department: Duke Molecular Physiology Institute

institute: Duke University School of Medicine

description:
NR4A3_5
Gene expression data from AdNr4a3 treated primary rat islets cultured for 48 hours

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Rat Genome 230 2.0 Arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara,CA).

scan_protocol: Targets were scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix protocols (Affymetrix, Santa Clara,CA).

data_processing: RMA using ExpressionFileCreator of GenePattern, Broad Institute. Data was quantile normalized and background corrected.

source_name: primary rat islets, AdNr4a3 treated

label_protocol: Biotin labeling was performed using the Encore Biotin Module (Nugen, San Carlos, CA).

growth_protocol: After isolation, rat islets were cultured in RPMI medium containing 10% FBS and 8 mM glucose.

extract_protocol: Total RNA was isolated using Qiagen microRNA kits. Total RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

treatment_protocol: Rat islets were left untreated or treated with adenoviruses expressising either βgal or Nkx6.1 at an approximate concentration of 2x10^9 particles/ml medium for 18 h and then cultured in virus-free medium until the islets were collected 48 h after addition of adenovirus. Five replicates for each condition were used.

tag: gender

value: male

value: Wistar

value: pancreatic islet

tag: treatment


title: primary rat islets, NR4A1_biological rep5

description:
NR4A1_5
Gene expression data from AdNr4a1 treated primary rat islets cultured for 48 hours

source_name: primary rat islets, AdNr4a1 treated

tag: strain


title: Liver_Keap1 Hepatocyte Knockout_Rep3

description: Keap1-HKO mice were generated by crossing Keap1-KD mice and AlbCre+ mice which express Cre only in hepatocytes.

source_name: Keap1 hepatocyte KO mouse, liver

value: Keap1-hepatocyte knockout


title: Liver_Keap1 Knockdown_Rep3


title: Liver_Keap1 Hepatocyte Knockout_Rep2


title: primary rat islets, NR4A3_biological rep4

description:
NR4A3_4
Gene expression data from AdNr4a3 treated primary rat islets cultured for 48 hours


title: BC24_ADN0026_s1h1

description: Hybridized to SNP6.026


title: primary rat islets, untreated_biological rep5

description:
Untreated_5
Gene expression data from untreated primary rat islets cultured for 48 hours

source_name: primary rat islets, untreated

value: untreated


title: BC24_ADN0024_s1h1

description: Hybridized to SNP6.024


title: BC24_ADN0025_s1h1

description: Hybridized to SNP6.025


title: Mammospheres-PHA+ICG-rep3 [JHO-5-06-6]

city: Berlin

first: Jane

last: Holland

address: Robert-Roessle-Str. 10

department: Signal Transduction, Invasion and Metastasis of Epithelial Cells

institute: Max Delbrück Center for Molecular Medicine

description: Gene expression from mammospheres grown 7 days and treated with PHA+ICG for 24h

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

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

data_processing: The microarrays were MAS 5.0 and RMA normalized in the R statistical environment (http://www.R-project.org) using the Bioconductor packages Affymetrix and Biobase (http://www.bioconductor.org).

source_name: Mammospheres

label_protocol: Biotinylated aRNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA

growth_protocol: Single cell suspensions were obtained from mouse mammary gland primary tumors and grown in non-adherent and non-differentiating conditions for 7 days and then treated for further 24h as described in the sample section

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA samples were further purified with Rnaesy Minikit

treatment_protocol: Mammospheres were recovered by centrifugation and resuspended in the Trizol solution

value: FVB/N

value: mammary gland

value: WAPCre-DNbcatn;HGF

value: PHA+ICG for 24h


title: Submergence, 5 d; biological replicate 2

city: Blacksburg

first: Takeshi

last: Fukao

state: VA

address: 1880 Pratt Drive

institute: Virginia Tech

hyb_protocol: Labeled DNA (5.2 µg) was hybridized for 16 h at 45 degree C on Soybean Gene 1.0 ST GeneChips. The GeneChips were stained and washed on the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned on the GeneChip Scanner 3000 7G

data_processing: The data were analyzed by use of the R program and Bioconductor packages. We used the RMA method for normalization.

organism: Glycine max

source_name: Submergence, 5 d

label_protocol: Sense-strand cDNA was synthesized from 500 ng of total RNA using Ambion WT Expression kit (PN 4411973). The Sense-strand cDNA (5.5 µg ) generated was fragmentated and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (PN 900671).

growth_protocol: Sterilized seeds were placed on wet paper towels for 4 d in the light at 25 degree C.

extract_protocol: Total RNA was extracted by using QIAGEN RNasy Plant Mini kit according to the manufacture's protocol. Genomic DNA was eliminated by on-column DNase treatment.

treatment_protocol: Four-d-old were completely submerged in deionized water at noon. Upon 1 d (24 h) or 5 d (120 h) of treatment, aerial tissue was harvested and immediately frozen in liquid nitrogen.

tag: cultivar

value: Williams 82

value: aerial tissue of seedlings

value: exposed to 5 d of submergence


title: Submergence, 5 d; reoxygenation , 1 d; biological replicate 1

source_name: Submergence, 5 d; reoxygenation , 1 d

value: exposed to 1 d of reoxygenation following 5 d of submergence


title: primary rat islets, GFP_biological rep5

description:
GFP_5
Gene expression data from AdGFP treated primary rat islets cultured for 48 hours

source_name: primary rat islets, AdGFP treated

value: 8 weeks

value: AdGFP


title: BC24_ADN0023_s1h1

description: Hybridized to SNP6.023

source_name: Breast tumoral sample

value: validation set

value: breast cancer tissue


title: Submergence, 5 d; reoxygenation , 1 d; biological replicate 2


title: Mammospheres-PHA+ICG-rep2 [JHO-5-05-5]


title: BC24_ADN0022_s1h1

description: Hybridized to SNP6.022


title: BC24_ADN0021_s1h1

description: Hybridized to SNP6.021


title: Submergence, 1 d; biological replicate 2

source_name: Submergence, 1 d

value: exposed to 1 d of submergence


title: Mammospheres-PHA+ICG-rep1 [JHO-5-04-4]


title: BC24_ADN0019_s1h1

description: Hybridized to SNP6.019


title: primary rat islets, untreated_biological rep4

description:
Untreated_4
Gene expression data from untreated primary rat islets cultured for 48 hours

value: male

value: Wistar


title: BC24_ADN0018_s1h1

description: Hybridized to SNP6.018


title: BC24_ADN0020_s1h1

description: Hybridized to SNP6.020


title: primary rat islets, NR4A3_biological rep3

description:
NR4A3_3
Gene expression data from AdNr4a3 treated primary rat islets cultured for 48 hours

value: pancreatic islet


title: primary rat islets, GFP_biological rep4

description:
GFP_4
Gene expression data from AdGFP treated primary rat islets cultured for 48 hours


title: primary rat islets, GFP_biological rep3

description:
GFP_3
Gene expression data from AdGFP treated primary rat islets cultured for 48 hours


title: Submergence, 5 d; biological replicate 1


title: primary rat islets, NR4A1_biological rep4

description:
NR4A1_4
Gene expression data from AdNr4a1 treated primary rat islets cultured for 48 hours


title: primary rat islets, untreated_biological rep3

description:
Untreated_3
Gene expression data from untreated primary rat islets cultured for 48 hours

value: untreated


title: primary rat islets, NR4A1_biological rep3

description:
NR4A1_3
Gene expression data from AdNr4a1 treated primary rat islets cultured for 48 hours


title: primary rat islets, NR4A3_biological rep2

description:
NR4A3_2
Gene expression data from AdNr4a3 treated primary rat islets cultured for 48 hours


title: Mammospheres-DMSO-rep1 [JHO-5-01-1]

description: Gene expression from mammospheres grown 7 days and treated with DMSO for 24h

value: FVB/N

value: DMSO for 24h


title: primary rat islets, NR4A1_biological rep2

description:
NR4A1_2
Gene expression data from AdNr4a1 treated primary rat islets cultured for 48 hours


title: BC24_ADN0017_s1h1

description: Hybridized to SNP6.017


title: Mammospheres-ICG-rep2 [JAH--08-S11]

description: Gene expression from mammospheres grown 7 days and treated with ICG for 24h

value: mammary gland

value: WAPCre-DNbcatn;HGF

value: ICG for 24h


title: Submergence, 1 d; biological replicate 1

value: Williams 82

value: aerial tissue of seedlings


title: Liver_Keap1 Hepatocyte Knockout_Rep1

value: Keap1-hepatocyte knockout

value: Liver

value: Male


title: Mammospheres-DMSO-rep2 [JHO-5-02-2]


title: Mammospheres-PHA-rep3 [JAH--06-S08]

description: Gene expression from mammospheres grown 7 days and treated with PHA for 24h

value: PHA for 24h


title: Submergence, 0 d; biological replicate 2

source_name: Submergence, 0 d

value: non-submerged


title: Submergence, 0 d; biological replicate 1


title: Mammospheres-ICG-rep3 [JAH--09-S12]


title: BC24_ADN0016_s1h1

description: Hybridized to SNP6.016

value: validation set

value: breast cancer tissue


title: Mammospheres-DMSO-rep3 [JHO-5-03-3]


title: Mammospheres-ICG-rep1 [JAH--07-S10]


title: BC24_ADN0014_s1h1

description: Hybridized to SNP6.014


title: Mammospheres-PHA-rep2 [JAH--05-S07]


title: BC24_ADN0012_s1h1

description: Hybridized to SNP6.012


title: BC24_ADN0015_s1h1

description: Hybridized to SNP6.015


title: primary rat islets, GFP_biological rep2

description:
GFP_2
Gene expression data from AdGFP treated primary rat islets cultured for 48 hours

value: male

value: Wistar

value: 8 weeks

value: AdGFP


title: primary rat islets, NR4A1_biological rep1

description:
NR4A1_1
Gene expression data from AdNr4a1 treated primary rat islets cultured for 48 hours

value: pancreatic islet


title: Mammospheres-PHA-rep1 [JAH--04-S06]

value: FVB/N

value: mammary gland


title: Mammospheres-DMSO-rep3 [JAH--03-S04]

value: WAPCre-DNbcatn;HGF

value: DMSO for 24h


title: BC24_ADN0010_s1h1

description: Hybridized to SNP6.010


title: primary rat islets, NR4A3_biological rep1

description:
NR4A3_1
Gene expression data from AdNr4a3 treated primary rat islets cultured for 48 hours


title: primary rat islets, untreated_biological rep2

description:
Untreated_2
Gene expression data from untreated primary rat islets cultured for 48 hours

value: untreated


title: primary rat islets, GFP_biological rep1

description:
GFP_1
Gene expression data from AdGFP treated primary rat islets cultured for 48 hours


title: BC24_ADN0009_s1h1

description: Hybridized to SNP6.009


title: BC24_ADN0008_s1h1

description: Hybridized to SNP6.008


title: BC24_ADN0007_s1h1

description: Hybridized to SNP6.007


title: Mammospheres-DMSO-rep1 [JAH--01-S02]


title: BC24_ADN0006_s1h1

description: Hybridized to SNP6.006


title: BC24_ADN0005_s1h1

description: Hybridized to SNP6.005


title: primary rat islets, untreated_biological rep1

description:
Untreated_1
Gene expression data from untreated primary rat islets cultured for 48 hours


title: primary rat islets, Nkx6.1 treated, biological rep5

description:
Nkx6.1_5
Gene expression data from AdNkx6.1 treated primary rat islets cultured for 48 hours

source_name: primary rat islets, Nkx6.1 treated


title: primary rat islets, untreated, biological rep5

description:
Untreated_5
Gene expression data from untreated primary rat islets cultured for 48 hours


title: primary rat islets, βgal treated, biological rep5

description:
BGAL_5
Gene expression data from Adβgal treated primary rat islets cultured for 48 hours

source_name: primary rat islets, βgal treated

value: βgal


title: primary rat islets, Nkx6.1 treated, biological rep4

description:
Nkx6.1_4
Gene expression data from AdNkx6.1 treated primary rat islets cultured for 48 hours


title: primary rat islets, βgal treated, biological rep6

description:
BGAL_6
Gene expression data from Adβgal treated primary rat islets cultured for 48 hours


title: Mammospheres-DMSO-rep2 [JAH--02-S03]


title: BC24_ADN0004_s1h1

description: Hybridized to SNP6.004


title: RAW_media_t22

city: Cambridge

first: Xinming

last: Cai

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

hyb_protocol: Affymetrix Target hybridization on Affymetrix 3' Expression Arrays

data_processing: R/Bioconductor LIMMA package

label: Biotin/SAPE

source_name: RAW cells in DMEM

label_protocol: NuGEN Ovation RNA Amplification System V2

growth_protocol: RAW cells were maintained under standard conditions described in the ATCC instructions

extract_protocol: RNAs were extracted using Qiagen RNeasy plus Mini kit (cat#74134) according to the manufacturer's instructions..

treatment_protocol: RAW cells were challenged with R848 (0.1mM) in the presence of indicated compound (1 uM) for the indicated time.

tag: cell type

value: macrophage cell line


title: RAW_R848+API09_t22

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of API09 for 22h


title: LNCaP_Bag1NMut_ETOH_rep1

city: Boston

first: Laura

last: Cato

address: 450 Brookline Ave., D728

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: LNCaP, Bag-1L GARRPR mutant, 4 h ETOH-treated, Rep 1

hyb_protocol: The fragmented cRNA was hybridized to a HG U133 Plus 2.0 array at 45°C, overnight, in the presence of several biotinylated control oligonucleotides (for quality control).

scan_protocol: After hybridization, bound cRNA was fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA was excited using a confocal laser scanner, according the Affymetrix protocol.

data_processing: All gene expression data was normalized and log-scaled using the RMA algorithm (RMAExpress) and the RefSeq probe definition.

label_protocol: Isolated total RNA was processed by the Dana-Farber Cancer Institute (DFCI) Microarray Core Facility (Boston, MA) according to the standard Affymetrix protocol. In short, cDNA was synthesized using T7 Oligo (dT) primers. Using the double stranded cDNA as a template, biotinylated cRNA was then generated in an in vitro transcription reaction.

growth_protocol: Routinely, LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 μg/ml), streptomycin (100 units/ml) and L-glutamine (2 mM), at 37 °C with an atmosphere of 5% CO2. For experimental conditions, cells were grown for 72 h under hormone-starvation conditions using the media conditions described above but subsituting FBS for charcoal/dextran-treated FBS (CDT). Cells were then treated with vehicle (ETOH) or 10 nM DHT for 4 h.

extract_protocol: Total RNA was isolated using a combination of Trizol (Invitrogen) and the RNAeasy Mini purification kit procedure (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: LNCaP cells were infected with retroviral constructs for wild-type or GARRPR-mutant Bag-1L, or as a control, the retroviral vector construct alone. Selection was carried out using magnetic beads (M-450 Dynabeads) coupled with IL-2-antibody. LNCaP cells stably expressing the wild-type or N-terminal mutant Bag-1L, or the empty vector construct, were then cultured under hormone-starvation conditions for 72 h and treated with vehicle or 10 nM DHT for 4 h.

value: LNCaP

tag: transfection

value: Bag-1L GARRPR mutant (poZC-Bag1LNmut)

value: ETOH


title: LNCaP_Bag1NMut_DHT_rep2

description: LNCaP, Bag-1L GARRPR mutant, 4 h DHT-treated, Rep 2

value: DHT


title: LNCaP_Bag1NMut_DHT_rep1

description: LNCaP, Bag-1L GARRPR mutant, 4 h DHT-treated, Rep 1


title: RAW_R848+apilimod_t7

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of apilimod for 7h


title: primary rat islets, βgal treated, biological rep4

description:
BGAL_4
Gene expression data from Adβgal treated primary rat islets cultured for 48 hours


title: primary rat islets, untreated, biological rep4

description:
Untreated_4
Gene expression data from untreated primary rat islets cultured for 48 hours


title: BC24_ADN0003_s1h1

description: Hybridized to SNP6.003

value: validation set

value: breast cancer tissue


title: RAW_R848_t22

source_name: RAW cells in DMEM were stimulatate with R848 for 22h


title: RAW_R848+API09_t7

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of API09 for 7h


title: RAW_R848+apilimod_t22

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of apilimod for 22h


title: LNCaP_Bag1WT_DHT_rep3

description: LNCaP, Bag-1L wild-type, 4 h DHT-treated, Rep 3

value: Bag-1L wild-type (poZC-Bag1Lwt)


title: LNCaP_Bag1NMut_DHT_rep3

description: LNCaP, Bag-1L GARRPR mutant, 4 h DHT-treated, Rep 3


title: RAW_R848_t7

source_name: RAW cells in DMEM were stimulatate with R848 for 7h


title: BC24_ADN0002_s1h1

description: Hybridized to SNP6.002


title: LNCaP_Bag1NMut_ETOH_rep3

description: LNCaP, Bag-1L GARRPR mutant, 4 h ETOH-treated, Rep 3


title: RAW_media_t7


title: primary rat islets, Nkx6.1 treated, biological rep3

description:
Nkx6.1_3
Gene expression data from AdNkx6.1 treated primary rat islets cultured for 48 hours

value: male

value: Wistar

value: 8 weeks


title: LNCaP_Bag1NMut_ETOH_rep2

description: LNCaP, Bag-1L GARRPR mutant, 4 h ETOH-treated, Rep 2


title: LNCaP_Bag1WT_DHT_rep2

description: LNCaP, Bag-1L wild-type, 4 h DHT-treated, Rep 2


title: LNCaP_Bag1WT_DHT_rep1

description: LNCaP, Bag-1L wild-type, 4 h DHT-treated, Rep 1


title: primary rat islets, untreated, biological rep3

description:
Untreated_3
Gene expression data from untreated primary rat islets cultured for 48 hours

source_name: primary rat islets, untreated

value: pancreatic islet


title: primary rat islets, βgal treated, biological rep3

description:
BGAL_3
Gene expression data from Adβgal treated primary rat islets cultured for 48 hours


title: primary rat islets, Nkx6.1 treated, biological rep2

description:
Nkx6.1_2
Gene expression data from AdNkx6.1 treated primary rat islets cultured for 48 hours


title: LNCaP_Bag1WT_ETOH_rep2

description: LNCaP, Bag-1L wild-type, 4 h ETOH-treated, Rep 2


title: Lim3 replicate 3

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: Dam-Lim3 / Dam-control in stage 17 embryos

hyb_protocol: Hybridisation has been done with HX1 mixer following Nimblegen's procedures

scan_protocol: Arrays were scanned by Nimblegen

data_processing: The  Dam-fusion/Dam log2 ratios were median normalised

organism: Drosophila melanogaster

source_name: Dam-Lim3 processed DNA from stage 17 embryos

label_protocol: Labeling has been done using the Nimbelgen Dual-Color Labeling Kit based on a Klenow enzymatic reaction following manufacturer's protocol

growth_protocol: Embryos were collected for 6 hours and allowed to develop for a further 16 hours (at 25oC).

extract_protocol: Tissues were dissected and placed n 180ul of PBS with 100mM EDTA before samples were processed as previously described (Choksi et al., 2006)

treatment_protocol: Embryos were collected, washed and frozen on dry ice.

value: w-; + ; UAS-Dam-Lim3

value: stage 17 embryos

source_name: Dam processed DNA from stage 17 embryos

value: w-; + ; UAS-Dam


title: LNCaP_Bag1WT_ETOH_rep1

description: LNCaP, Bag-1L wild-type, 4 h ETOH-treated, Rep 1


title: LNCaP_Bag1WT_ETOH_rep3

description: LNCaP, Bag-1L wild-type, 4 h ETOH-treated, Rep 3


title: primary rat islets, βgal treated, biological rep2

description:
BGAL_2
Gene expression data from Adβgal treated primary rat islets cultured for 48 hours


title: RAW_media_t3


title: RAW_R848+apilimod_t3

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of apilimod for 3h


title: RAW_R848+API09_t3

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of API09 for 3h


title: primary rat islets, untreated, biological rep2

description:
Untreated_2
Gene expression data from untreated primary rat islets cultured for 48 hours

value: untreated


title: LNCAP_Vec_DHT_rep3

description: LNCaP, Vector control, 4 h DHT-treated, Rep 3

source_name: LNCaP, Vector control, 4 h DHT-treated

value: empty vector control (poZC)


title: LNCAP_Vec_DHT_rep2

description: LNCaP, Vector control, 4 h DHT-treated, Rep 2


title: MARCO_LPS

first: M. Simo

last: Arredouani

address: 330 Brookline Ave.

department: Surgery

institute: Beth Israel Deaconess Medical Center

description: MARCO DC + LPS

hyb_protocol: cRNA (15 μg) was fragmented and hybridized to arrays according to the manufacturer's (Ambion® | Life Technologies) protocols.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 and GeneChip Operating Software acquired raw fluorescence signal.

data_processing: Scanned array images and CEL file data were analyzed and normalized  using RMAexpress.

label_protocol: Biotin-UTP was incorporated during the overnight in vitro transcription step according to the manufacturer's (Ambion® | Life Technologies) protocol.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Pure dendritic cells from the spleens of WT and MARCO KO mice were cultured overnight in PBS or Lipopolysaccharide (LPS).

value: LPS

value: MARCO-/-

tag: genetic background

value: Spleen dendritic cells


title: RAW_R848+API09_t1

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of API09 for 1h

value: macrophage cell line


title: primary rat islets, Nkx6.1 treated, biological rep1

description:
Nkx6.1_1
Gene expression data from AdNkx6.1 treated primary rat islets cultured for 48 hours


title: RAW_R848+apilimod_t1

source_name: RAW cells in DMEM were stimulatate with R848 in the presence of apilimod for 1h


title: LNCAP_Vec_DHT_rep1

description: LNCaP, Vector control, 4 h DHT-treated, Rep 1

value: LNCaP

value: DHT


title: WT

description: WT DC + Buffer

value: PBS

value: wild type


title: WT_LPS

description: WT DC + LPS


title: Hb9 replicate 2

description: Dam-Hb9 / Dam-control in stage 17 embryos

source_name: Dam-Hb9 processed DNA from stage 17 embryos

value: w-; + ; UAS-Dam-Hb9


title: RAW_R848_t1

source_name: RAW cells in DMEM were stimulatate with R848 for 1h


title: primary rat islets, βgal treated, biological rep1

description:
BGAL_1
Gene expression data from Adβgal treated primary rat islets cultured for 48 hours

source_name: primary rat islets, βgal treated

value: male

value: Wistar

value: βgal


title: LNCaP_Vec_ETOH_rep3

description: LNCaP, Vector control, 4 h ETOH-treated, Rep 3

source_name: LNCaP, Vector control, 4 h ETOH-treated

value: ETOH


title: BC24_ADN0001_s1h1

description: Hybridized to SNP6.001

source_name: Breast tumoral sample

value: validation set

value: breast cancer tissue


title: RAW_media_t1

source_name: RAW cells in DMEM


title: primary rat islets, untreated, biological rep1

description:
Untreated_1
Gene expression data from untreated primary rat islets cultured for 48 hours

value: 8 weeks

value: pancreatic islet

value: untreated


title: LNCaP_Vec_ETOH_rep2

description: LNCaP, Vector control, 4 h ETOH-treated, Rep 2

value: empty vector control (poZC)


title: Lim3 replicate 2

value: w-; + ; UAS-Dam-Lim3

value: stage 17 embryos

value: w-; + ; UAS-Dam


title: RAW_media_t0_rep2

value: macrophage cell line


title: Hb9 replicate 1


title: RAW_media_t0_rep1


title: RAW_R848_t3

source_name: RAW cells in DMEM were stimulatate with R848 for 3h


title: Islet replicate 1

description: Dam-Islet / Dam-control in stage 17 embryos

source_name: Dam-Islet processed DNA from stage 17 embryos

value: w-; + ; UAS-Dam-Islet


title: MARCO

description: MARCO DC + Buffer

value: PBS

value: MARCO-/-

value: Spleen dendritic cells


title: B cell leukemic spleen biological rep1

status: Public on Feb 17 2014

city: Charlottesville

first: R. Ariel

last: Gomez

department: Pediatrics

institute: University of Virginia

description:
X2.ll1.CEL
Gene expression data from leukemic spleen

hyb_protocol: 2 μg of fragmented and labeled DNA target were hybridized for 16 hr at 45°C on Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. GeneChips were washed and stained in the Affymetrix Fluidics Station.

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

data_processing:
All preprocessing and analysis were done using R version 2.15.0.  CEL files were imported using the Affymetrix package, version 1.34.0.  Expression intensities were summarized, normalized, and transformed using Robust Multiarray Average algorithm.
Probesets were annotated using the BioConductor annotation package mogene10sttranscriptcluster.db version 8.0.1, annotate package, version 1.34.0.  Linear models with empirical Bayes moderated standard errors were fit using the BioConductor limma package version 3.12.1.
False discovery rate was used to correct for multiple testing, RMA for probeset summarization, and ID_REFs that were not associated with an Entrez Gene ID were removed.

source_name: B cell leukemic spleen

label_protocol: Biotinylated cDNA was prepared from 500ng total RNA using the Ambion® WT Expression Kit for Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays and the GeneChip® WT Terminal Labeling and Hybridization kit for use with the Ambion® WT Expression Kit according to the manufacturer's protocols.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Microarray Tissue mini kit (73304).

tag: strain background

value: RBP-J flox/flox;Ren1dcre/cre

value: 107 days

value: female

value: spleen

tag: spleen weight


title: LNCaP_Vec_ETOH_rep1

description: LNCaP, Vector control, 4 h ETOH-treated, Rep 1

value: LNCaP

value: ETOH


title: Hb9 replicate 3

tag: genotype

value: w-; + ; UAS-Dam-Hb9


title: wild type spleen biological rep2

description:
X1.wt2.CEL
Gene expression data from control spleen

source_name: wild type spleen

value: RBP-J flox/flox;Ren1d+/+

value: 81 days


title: Islet replicate 3


title: B cell leukemic spleen biological rep2

description:
X2.ll2.CEL
Gene expression data from leukemic spleen

value: 93 days

value: male


title: Cells treated with M-CSF and sRANKL, Experiment 1

city: Toronto

first: Yongqiang

last: Wang

state: ON

address: 150 College St

department: Faculty of Dentistry

country: Canada

institute: University of Toronto

description:
Gene expression in the early stage of osteoclastogenesis in vitro
WT m +r April_8

hyb_protocol: Fragmented labelled cDNA 27ul. Hyb cocktail: For one reaction (73 ul): control Oligo B 1.7 ul , 20x Hybridization Controls 5 ul, BSA 1 ul, Herring Sperm DNA 1 ul,  2XHyb mix 50 ul, DMSO 7 ul, Nuclease free water 7.3 ul. Wash protocol FS0007.

scan_protocol: Scanner: GeneChip Scanner 3000 7G

data_processing: The cel files and library files were loaded into R (version 2.71) with package xps. RMA normalized values produced by the R package xps version 1.0.1. The intensities were exported into file 'rma_all.txt'. Mas5 present/absent calls were calculated and the result was exported into file 'mas5Call_call.txt' (not shown). Probes which were all being absent in all samples were eliminated. Genes with mad (median absolute deviation) <0.5 were eliminated. Genes with 90% log2 intensities less than 7 were eliminated.   There were 2890 genes left, and the intensities for these genes is storied in 'rma_prefilter.csv'  Both gene tree and sample tree were created using unsupervised Hierarchical clustering with Euclidean Distance as distance metric and Average linkage clustering as linkage method, and the result is the file 'HCL.png' (not shown).  T-test was done with Benjamini & Hochberg false discovery rate correction, confidence level 0.95, cutoffs: fold change 2, p-value 0.05.   There were 656 genes left. file:  'Test41_genelist_precall_mad0.5_low7_0.02_fold2_p0.05.txt'. Volcano graph for the genes is 'Test41_volcano_precall_mad0.5_low7_0.02_fold2_p0.05.png'. Unsupervised Hierarchical clustering tree is 'Test41_HCL_precall_mad0.5_low7_0.02_fold2_p0.05.png'.

source_name: Bone marrow monocytes treated with M-CSF and sRANKL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The Guide for the Human Use and Care of Laboratory Animals was followed in all the experimental procedures. All cell incubations were performed at 37°C in 5% CO2 in humidified air.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Isolation of mononucleated OC precursors (MOPs): Bone marrow (BM) cells were harvested from three SV129/BL6 mice per genotype, centrifuged at 2,500× rpm for 5 min at 4oC. The cells were re-suspended and washed with Eagle’s minimum essential medium (MEM; Life Technologies AG, Basel, Switzerland). The cells were cultured overnight (O/N) in complete α-MEM containing 10% fetal bovine serum (FBS; Seromed, Biochrom KG, Berlin, Germany), 164 IU/ml penicillin G, 50 µg/ml gentamicin, and 0.25 µg/ml fungizone. The next day, the cells were collected and centrifuged at 350× g, 22oC for 30 minutes. An enriched population of MOPs (~30%) at the interface layer was obtained. Microarray Analysis:Isolated MOPs were stimulated for 48 hr in complete α-MEM with 10 ng/ml M-CSF. Floating cells were collected, and split into two dishes each containing a cell density of 8×10^5 cells/cm2. Both dishes were subjected to two different conditions: one dish was stimulated with 20 ng/ml M-CSF (Sigma, St Louis, MO, USA) plus 200 ng/ml sRANKL (expressed and purified from pGEX-4T-1-murine sRANKL construct, provided by Dr. Morris F. Manolson, Faculty of Dentistry, University of Toronto), and the other was stimulated with 20 ng/ml M-CSF alone. After two days, the cells were washed with prewarmed α-MEM and total RNA was extracted using RNeasy Mini Kit (Qiagen); total RNA was stored at -80oC. The quality of total RNA was determined using Agilent BioAnalyser. Microarray was performed using Affymetrix GeneChip® Mouse Gene 1.0 ST array.

value: bone marrow

value: monocytes


title: Cells treated with M-CSF alone, Experiment 3

description:
Gene expression in monocytes
WT m alone May_11

source_name: Bone marrow monocytes treated with M-CSF alone


title: Cells treated with M-CSF alone, Experiment 1

description:
Gene expression in monocytes
WT m alone April_7


title: ESO1644_muscle_mutation

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

hyb_protocol: Fragmented aRNA was hybridized to Affymetrix HG-U133A 2.0 chips

scan_protocol: standard Affymetrix protocol

data_processing: Data were analyzed in R and analyzed using variance stabilizing normalization and model based index calculation (MBEI)

label_protocol: total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

extract_protocol: Total RNA was extracted from muscle biopsies using the TRIzol protocol including an extra phenol-chloroform step

tag: tissue source

value: patients with a mutation (Arg1174Gln) in the tyrosine kinase domain of the insulin receptor gene (INSR)

value: Vastus lateralis muscle

tag: tissue state

value: basal state


title: Cells treated with M-CSF and sRANKL, Experiment 3

description:
Gene expression in the early stage of osteoclastogenesis in vitro
WT m +r May_12


title: JJ1717_muscle_mutation


title: Cells treated with M-CSF and sRANKL, Experiment 2

description:
Gene expression in the early stage of osteoclastogenesis in vitro
WT m +r March_4


title: Eve replicate 2

description: Dam-Eve / Dam-control in stage 17 embryos

source_name: Dam-Eve processed DNA from stage 17 embryos

value: w-; + ; UAS-Dam-Eve

value: stage 17 embryos

source_name: Dam processed DNA from stage 17 embryos

value: w-; + ; UAS-Dam


title: Eve replicate 1


title: SA2117_muscle_mutation


title: Islet replicate 2

value: w-; + ; UAS-Dam-Islet


title: Cells treated with M-CSF alone, Experiment 2

description:
Gene expression in monocytes
WT m alone March_3


title: Lim3 replicate 1

description: Dam-Lim3 / Dam-control in stage 17 embryos

source_name: Dam-Lim3 processed DNA from stage 17 embryos

value: w-; + ; UAS-Dam-Lim3


title: EO1389_muscle_mutation


title: Mic34_muscle_control

value: matched healthy control


title: Mic33_muscle_control


title: AJ3251_muscle_mutation


title: DE1483_muscle_mutation


title: KL6_muscle_control


title: KL5_muscle_control


title: Mic26_muscle_control


title: KL3_muscle_control


title: KL1_muscle_control


title: wild type spleen biological rep1

description:
X1.wt1.CEL
Gene expression data from control spleen

value: 80 days

value: female

value: spleen


title: UM-UC14NTA

first: Tiewei

last: Cheng

state: United States

address: 7777 Knight Rd.

institute: UT MD Anderson Cancer Center

description:
SAMPLE 7
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: urothelial cancer cell line

label_protocol: Biotinylated cRNA were prepared with Illumina RNA amplification kit

growth_protocol: Cell lines were cultured in 10% FBS modified Eagle's MEM with standard supplements at 37 °C in 5% CO2 incubator

extract_protocol: Total RNA was extracted by mirVANA miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer.

tag: cell line

value: urothelial cancer cell line UM-UC14

value: Non-targeting shRNA


title: Mic29_muscle_control


title: UM-UC14NTB

description:
SAMPLE 8
replicate 2


title: UM-UC14FABP4KDC

description:
SAMPLE 12
replicate 3

value: FABP4 shRNA


title: UM-UC14FABP4KDA

description:
SAMPLE 10
replicate 1


title: KL2_muscle_control


title: UM-UC14NTC

description:
SAMPLE 9
replicate 3


title: UM-UC14FABP4KDB

description:
SAMPLE 11
replicate 2


title: Multicellular HCT116 spheroids control

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description:
HCT116 cells grown as spheroids, untreated.
Gene expression data from HCT116 spheroids without treatment

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed. and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

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

source_name: Colon cancer cell line HCT116

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression. Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

growth_protocol: HCT116 cells grown as spheroids

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

treatment_protocol: No treratment.

value: wild type

value: control


title: UM-UC9ROSIGB

description:
SAMPLE 5
replicate 2

scan_protocol: Standard Illumina scanning protocol

value: urothelial cancer cell line UM-UC9

value: rosiglitazone treated (1μM, 24hours)


title: UM-UC9CONTC

description:
SAMPLE 3
replicate 3


title: monolayer1

description: Gene expression data from HCT116 cells grown as monolayer.

growth_protocol: HCT116 cells grown as monolayer.

treatment_protocol: No treatment.

value: HCT116 cells

tag: growth protocol

value: grown as monolayer


title: Multicellular HCT116HIF1a knock-out spheroids treated with VLX600

description:
Multicellular HCT116HIF1? knock-out spheroids treated with VLX600
Gene expression data from HCT116HIF1? knock-out cells grown as spheroids and treated with VLX600.

source_name: Colon cancer cell line HCT116HIF1? knock-out

growth_protocol: HCT116HIF1? knock-out grown as spheroids

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions

treatment_protocol: Multicellular HCT116HIF1? knock-out spheroids treated with 6µM VLX600 for six hours

value: HIF1alpha KO


title: KL4_muscle_control

value: Vastus lateralis muscle

value: basal state


title: UM-UC9ROSIGC

description:
SAMPLE 6
replicate 3


title: UM-UC9ROSIGA

description:
SAMPLE 4
replicate 1


title: UM-UC9CONTA

description:
SAMPLE 1
replicate 1


title: spheroids1

description: Gene expression data from HCT116 cells grown as spheroids.

growth_protocol: HCT116 grown as spheroids

value: grown as spheroids


title: UM-UC9CONTB

description:
SAMPLE 2
replicate 2


title: Bone marrow sorted cells biological rep2

city: St. Catharines

first: Ping

last: Liang

state: Ontario

address: 500 Glenridge Ave

department: Department of Biological Sciences

institute: Brock University

description: mouse bone marrow cells expressing renin driven expression of green fluorescent protein

hyb_protocol: he labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray raw data in CEL format were processed using RMA and quantile normalization methods via locally installed Bioconductor R packages obtained from http://www.bioconductor.org

source_name: Mouse bone marrow cells sorted for renin-expression

label_protocol: The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.

growth_protocol: Freshly harvested bone marrow cells from adult femurs held on ice.

extract_protocol: Total RNA was prepared from the sorted cells using TRIzol® reagent (Invitrogen, Carlsbad,CA, USA) on non-sorted and sorted cells and stored at –70C.

treatment_protocol: For each biological replicate, 4-5 male and female adult hemizygous mice (3-6 months old) from MGI line Tg(Ren1-GFP)2Kwg were sacrificed. Bone marrow was collected by flushing femurs. Renin-expressing cells were analyzed and sorted in the RPCI Flow Cytometry Core Facility with a Becton-Dickinson Aria 2 cell sorter using an Argon ion laser at 488nm. GFP fluorescence was detected with a 530/30 bandpass filter. GFP sorting gates were established as follows: the primary gate was established on forward and side scatter to eliminate erythrocytes and subcellular sized debris, then through a secondary sort gate to discriminate single cells and lastly through a side scatter verses green fluorescence gate. Autofluorescence was analyzed on transgene negative samples to establish limits of background fluorescence. The lower limit of the GFP positive sort region was set to include 0.1% of the autofluorescent sample.  with Hanks Balanced Salt Solution (HBSS) and pooled. This material was filtered through a 70 um nylon mesh cell strainer and washed once with HBSS. Bone marrow was kept on ice or at 4C throughout the collecting and sorting process.

value: renin-expression

value: Bone marrow

tag: age

value: 3-6 months old

value: hemizygous mice from MGI line Tg(Ren1-GFP)2Kwg


title: Bone marrow presort cells biological rep2

source_name: Mouse bone marrow cells no sorting

tag: tissue


title: Bone marrow sorted cells biological rep1


title: monolayer2


title: Bone marrow presort cells biological rep1


title: spheroids2


title: Bone marrow presort cells biological rep3


title: Bone marrow sorted cells biological rep3


title: Multicellular HCT116HIF1a knock-out spheroids control

description:
HCT116HIF1? knock-out cells grown as spheroids, untreated.
Gene expression data from HCT116HIF1? knock-out spheroids without treatment


description:
Multicellular HCT116 spheroids treated with VLX600
Gene expression data from HCT116 cells grown as spheroids and treated with VLX600.

treatment_protocol: Multicellular HCT116 spheroids treated with 6µM VLX600 for six hours


title: IFN-beta induced FoxA1Treg rep3

status: Public on Feb 16 2014

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

institute: Lund University

hyb_protocol: Fifteen micrograms of the biotin labeled cRNA was fragmented to strands between 35 and 200 bases in length, 10 micrograms of which was hybridised onto the GeneChip® Mouse genome 430 2.0 array (Affymetrix, Inc, Santa Clara, CA, USA) overnight in the GeneChip® Hybridisation oven 6400 using standard procedures.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing: Affymetrix analysis and data sets were quantile normalized and processed by the PLIER (Affymetrix) algorithm in Arraystar 3.0

label_protocol: RNA quality and concentration was measured using an Agilent 2100 bioanalyzer and Nanodrop ND-1000 respectively. Total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following manufacturer’s specifications.

extract_protocol: Trizol with DNAse cleanup

tag: surface markers

value: induced FoxA1Treg


title: genomic DNA from control 4

city: Kiel

first: Susanne

last: Bens

address: Arnold-Heller-Str.3 (Haus 10)

department: Institute of Human Genetics

institute: Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein

description: conceived at least one child

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using the Illumina iScan

data_processing: GenomeStudio software (version 2011.1, Methylation module version 1.9.0)

label: Cy5 and Cy3

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: NucleoSpin 96 Blood kit (Macherey-Nagel, Düren, Germany) and Gentra Puregene Blood Kit (Qiagen, Hilden, Germany)

value: peripheral blood

tag: gender

value: male

tag: phenotype

value: fertile control


title: genomic DNA from control 8

description: conceived at least one child


title: genomic DNA from patient 31

description: normal CFTR and AZF testing, normal karyotype

value: infertile


title: genomic DNA from control 5

description: conceived at least one child


title: genomic DNA from patient 23


title: genomic DNA from patient 28


title: genomic DNA from patient 20


title: genomic DNA from patient 35


title: genomic DNA from patient 27


title: genomic DNA from patient 26


title: genomic DNA from control 2

description: conceived at least one child


title: genomic DNA from control 3

description: conceived at least one child


title: genomic DNA from patient 15


title: IFN-beta induced FoxA1Treg rep2


title: genomic DNA from control 7

description: conceived at least one child


title: genomic DNA from control 9

description: conceived at least one child


title: genomic DNA from patient 30


title: genomic DNA from patient 34


title: genomic DNA from patient 24


title: genomic DNA from control 10

description: conceived at least one child


title: genomic DNA from patient 14


title: IFN-beta induced FoxA1Treg rep1


title: Treg rep3

value: Treg


title: genomic DNA from patient 25


title: Treg rep1


title: genomic DNA from patient 19


title: neuron induced FoxA1Treg rep3

value: natural FoxA1Treg


title: genomic DNA from control 1

description: conceived at least one child


title: genomic DNA from patient 18


title: genomic DNA from control 6

description: conceived at least one child


title: genomic DNA from patient 29


title: Treg rep2


title: genomic DNA from patient 21


title: neuron induced FoxA1Treg rep1


title: neuron induced FoxA1Treg rep2


title: genomic DNA from patient 33


title: Encephalitogenic Tcells rep3

value: Encephalitogenic Tcells


title: Encephalitogenic Tcells rep2


title: genomic DNA from patient 17


title: Encephalitogenic Tcells rep1


title: genomic DNA from patient 16


title: genomic DNA from patient 13


title: Hepatocellular carcinoma [S146]

status: Public on Feb 15 2014

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

hyb_protocol: The hybridization was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA).

scan_protocol: The arrays were scanned by ScanArray scanner (Perkin-Elmer)

data_processing: Primary signal intensities were obtained using ImaGene 6.0 software (Bio-discovery, Marina del Rey, CA) and normalized using lowess and quantile method to eliminate intensity bias.

source_name: Normal liver tissue

label_protocol: The probe preparation was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA) with 20mg of total RNA.

extract_protocol: Total RNA was isolated from frozen tissue according to the manufacturer’s instructions (Qiagen), and quality of the total RNA was judged based on the ratio of 28S/18S RNA after agarose gel electrophoresis.

value: normal liver

source_name: Hepatocellular carcinoma

value: hepatocellular carcinoma


title: Hepatocellular carcinoma [S170]


title: Hepatocellular carcinoma [S161]


title: Hepatocellular carcinoma [S150]


title: Hepatocellular carcinoma [S169]


title: Hepatocellular carcinoma [S158]


title: Hepatocellular carcinoma [S135]


title: Hepatocellular carcinoma [S174]


title: Hepatocellular carcinoma [S140]


title: Hepatocellular carcinoma [S137]


title: Hepatocellular carcinoma [S145]


title: Hepatocellular carcinoma [S141]


title: Hepatocellular carcinoma [S134]


title: genomic DNA from patient 10


title: Hepatocellular carcinoma [S131]


title: Hepatocellular carcinoma [S129]


title: Hepatocellular carcinoma [S136]


title: genomic DNA from patient 11


title: Hepatocellular carcinoma [S128]


title: genomic DNA from patient 5


title: Hepatocellular carcinoma [S130]


title: genomic DNA from patient 12


title: genomic DNA from patient 8


title: genomic DNA from patient 9


title: Hepatocellular carcinoma [S126]


title: Hepatocellular carcinoma [S127]


title: genomic DNA from patient 1


title: genomic DNA from patient 7


title: Hepatocellular carcinoma [S124]


title: Hepatocellular carcinoma [S113]


title: Hepatocellular carcinoma [S125]


title: Hepatocellular carcinoma [S110]


title: Hepatocellular carcinoma [S107]


title: Hepatocellular carcinoma [S111]


title: Hepatocellular carcinoma [S122]


title: Hepatocellular carcinoma [S123]


title: Hepatocellular carcinoma [S97]


title: Hepatocellular carcinoma [S101]


title: Hepatocellular carcinoma [S98]


title: Hepatocellular carcinoma [S100]


title: Hepatocellular carcinoma [S94]


title: Hepatocellular carcinoma [S99]


title: Hepatocellular carcinoma [S87]


title: Hepatocellular carcinoma [S102]


title: genomic DNA from patient 6


title: Hepatocellular carcinoma [S92]


title: Hepatocellular carcinoma [S103]


title: Hepatocellular carcinoma [S84]


title: Hepatocellular carcinoma [S79]


title: Hepatocellular carcinoma [S132]


title: Hepatocellular carcinoma [S91]


title: microRNA_Monocytes_after exercise_15

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

institute: University of California, Irvine

description:
Mono15-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise

hyb_protocol: Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray.

scan_protocol: The hybridized array was then washed and scanned according to Agilent specifications and data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: The results were analyzed using GeneSpring GX 12.1 Software (Agilent Technologies, Inc).

source_name: monocytes after 20 min bout of exercise

label_protocol: One hundred ng of total RNA was labeled with the fluorescent dye Cyanine 3-pCp (Cy3) using the microRNA Labeling Reagent and Hybridization Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

extract_protocol: Monocytes were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Monocyte Isolation Kit II, human  #130-091-153 and the autoMACS® Pro Separator).

treatment_protocol: Blood sample was drawn before and immediately after 20 min of exercise.

value: 22-30 yr old

value: monocytes isolated from PBMC

tag: time point

value: after 20 min bout of exercise


title: Hepatocellular carcinoma [S70]


title: microRNA_Monocytes_before exercise_15

description:
Mono15-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise

source_name: monocytes before exercise

value: before exercise


title: Hepatocellular carcinoma [S74]


title: microRNA_Monocytes_after exercise_13

description:
Mono13-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: microRNA_Monocytes_before exercise_14

description:
Mono14-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: microRNA_Monocytes_before exercise_13

description:
Mono13-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: microRNA_Monocytes_after exercise_12

description:
Mono12-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: Hepatocellular carcinoma [S76]


title: Hepatocellular carcinoma [S69]


title: Hepatocellular carcinoma [S75]


title: Hepatocellular carcinoma [S62]


title: microRNA_Monocytes_before exercise_12

description:
Mono12-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: Hepatocellular carcinoma [S66]


title: Hepatocellular carcinoma [S60]


title: microRNA_Monocytes_after exercise_11

description:
Mono11-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: Hepatocellular carcinoma [H135]


title: Hepatocellular carcinoma [S64]


title: Hepatocellular carcinoma [H159]


title: Hepatocellular carcinoma [S67]


title: Hepatocellular carcinoma [H190]


title: Hepatocellular carcinoma [H152]


title: Hepatocellular carcinoma [S16]


title: Hepatocellular carcinoma [S68]


title: microRNA_Monocytes_after exercise_10

description:
Mono10-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: microRNA_Monocytes_before exercise_11

description:
Mono11-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: Hepatocellular carcinoma [S2]


title: Hepatocellular carcinoma [H133]


title: Hepatocellular carcinoma [H127]


title: microRNA_Monocytes_after exercise_09

description:
Mono09-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: microRNA_Monocytes_before exercise_09

description:
Mono09-miRNA-pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: microRNA_Monocytes_after exercise_08

description:
Mono08-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: Hepatocellular carcinoma [H129]


title: microRNA_Monocytes_before exercise_08

description:
Mono08-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: Hepatocellular carcinoma [H130]


title: microRNA_Monocytes_after exercise_05

description:
Mono05-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: microRNA_Monocytes_before exercise_05

description:
Mono05-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: microRNA_Monocytes_before exercise_10

description:
Mono10-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: Hepatocellular carcinoma [H132]


title: microRNA_Monocytes_before exercise_04

description:
Mono04-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: Hepatocellular carcinoma [H124]


title: Hepatocellular carcinoma [H116]


title: microRNA_Monocytes_after exercise_03

description:
Mono03-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: Hepatocellular carcinoma [H125]


title: Hepatocellular carcinoma [H120]


title: Hepatocellular carcinoma [H115]


title: Hepatocellular carcinoma [H117]


title: microRNA_Monocytes_before exercise_03

description:
Mono03-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: microRNA_Monocytes_after exercise_02

description:
Mono02-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: microRNA_Monocytes_after exercise_04

description:
Mono04-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise


title: microRNA_Monocytes_before exercise_02

description:
Mono02-miRNA-Pre.txt:gTotalProbeSignal(normalized)
microRNA expression before-exercise


title: Hepatocellular carcinoma [H112]


title: Hepatocellular carcinoma [S90]


title: Hepatocellular carcinoma [H105]


title: Hepatocellular carcinoma [H104]


title: Hepatocellular carcinoma [H107]


title: Hepatocellular carcinoma [H99]


title: Hepatocellular carcinoma [H113]


title: Hepatocellular carcinoma [H100]


title: Hepatocellular carcinoma [H97]


title: Hepatocellular carcinoma [H95]


title: Hepatocellular carcinoma [H106]


title: Hepatocellular carcinoma [H94]


title: Hepatocellular carcinoma [H103]


title: Hepatocellular carcinoma [H98]


title: Hepatocellular carcinoma [H92]


title: Hepatocellular carcinoma [H87]


title: Hepatocellular carcinoma [H90]


title: 20 mM 2-oxoglutarate 3

city: Syracuse

first: Christopher

last: Nomura

state: NY

address: 1 Forestry Dr.

department: Chemistry

institute: SUNY-ESF

description: Gene expression from cells grown in rich media induced with 20 mM 2-oxoglutarate

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 50C 60 rpm on GeneChip P. aeruginosa Genome Array with rotation at 60 rpm. GeneChips were processed with an Affymetrix Fluidics Station 450 using the modified Flex FS450_0002 P. aeruginosa array protocol (as specified in the Affymetrix GeneChip Expression Analysis Technical Manual), using stains from the Affymetrix Hybridization, Wash, and Stain Kit.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 7G Plus

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

organism: Pseudomonas aeruginosa PAO1

source_name: Cells harvested at 30 min post induction

label_protocol: Samples were processed according to the Prokaryotic Target Preparation Protocol in Affymetrix GeneChip Expression Analysis Technical Manual.  Briefly, 10 ug of RNA was used to synthesize cDNA via random primers and SuperScript II reverse transcriptase.  cDNA was purified using Qiagen MinElute PCR purification columns.  The resulting cDNA was fragmented and labeled with biotin.

growth_protocol: P. aeruginosa PAO1 was grown in 1 mL of nutrient broth (Oxoid number 2) at 37 C, 200 rpm, until an OD 600 of 0.3 was reached.  Cells were induced with either 0 or 20 mM 2-oxoglutarate.

extract_protocol: RNA was isolated using the enzymatic lysis and proteinase K digestion method of Qiagen Rneasy with on-column DNA digestion.

treatment_protocol: At 30 min post induction with 2-oxoglutarate, 0.5 mL of culture was treated with 1.0 mL of RNAprotect Bacterial reagent (Qiagen).

tag: sub-strain

value: wild-type


title: Bat Hindlimb developmental stage CS16  (Biological Repeat 1)

city: Rondebosch

first: Nicola

last: Illing

state: Western Cape

address: Chemistry Rd

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

description: Biological repeat 1 of 4. Gene expression levels in the CS16 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate

hyb_protocol: The Mus musculus (mouse) OpArray™  platform consists of activated epoxide coated slides printed with version 4.0 of the Mus musculus (mouse) Array Ready Oligo Set (AROS), which contains over 36 000 cDNA probes (OPERON Biotechnologies, Inc., Huntsville, AL, USA).  These Operon OpArray™ slides were printed by Operon and were treated according to the OpArray™ Protocol. Slides were prehybridised in OpArray Pre-Hyb Solution for 1 hr at 42 ºC then washed in a premixed OPERON wash solution for 5 min and rinsed in MilliQ water three times for 30 s each and dried by centrifugation. Pre-hybridised slides were placed on a solid heating block set at 50ºC and a hybridisation chamber created over the array using a LifterSlip™. The hybridisation solution consisted of 45 μL of OpArray Hyb Buffer, 250ng of Cy3-labelled target aRNA sample combined with 250ng of Cy5-labelled reference aRNA sample. This sample was denatured at 65 ºC for 5 min, centrifuged and loaded onto the array by pipetting the solution along the bottom edge of the LifterSlip™ allowing it to be evenly wicked over the array by capillary action. The slide was placed in hydrated hybridisation cassettes, which were sealed and incubated in the dark in a water bath at 42 ºC for 19 hrs. After hybridisation the slides were washed in three successive premixed wash solutions of increasing stringency (Wash1: 2X SSC and 0.1% SDS preheated to 42 ºC; Wash 2: 1X SSC; Wash 3: 0.2X SSC). The slides were transferred to a slide rack and gently agitated in Wash1 for 10 min. They were transferred to a clean slide rack and agitated in the Wash2 and then Wash 3 for 5 min each. Slides were immediately transferred to a dry slide rack and dried by centrifugation. They were kept in the sealed centrifuge until scanning which was performed within 6 hrs. After scanning, slides were placed in sealed, light free slide holders.

scan_protocol: Slides were scanned using the Genepix® 4000A scanner (Axon Instruments Inc., Molecular Devices, Sunnyvale, CA, USA). A low-resolution (40 µm/pixel) preview scan was performed to optimise the scanner settings. The gain of the Photomultiplier Tubes (PMT) for each wavelength of light emitted was adjusted to balance the signal from each channel. The signals from each channel were standardised by adjusting the PMTs until the count ratio was a value between 0.95 and 1.05 and the histogram of both channels had similar (overlapping) intensity profiles. Saturation thresholds were adjusted to ensure that the majority of the feature signals were below saturation level. The slides were then scanned with the optimised PMT gain settings. Data was captured and flagged using GenePix™ Pro (ver. 6.0) microarray analysis software (Amersham Biosciences, Piscataway, NJ, USA). A feature-indicator grid was aligned over the scanned array image capturing data associated with each feature and linking this to the Operon oligo identity number (using the Mus musculus OpArray Gal file). Each spot image was discriminated from the background and several measurements are taken. Spots were captured automatically as irregular features and were allowed to be resized from a maximum of 300% to a minimum of 33% of their original size (±100 µm). Background signal was calculated using the method of morphological closing followed by opening.

data_processing:
Features that could not be discriminated from the background, that were smaller than six pixels or that fell outside of the feature resizing threshold were automatically flagged as “Not Found” (given a flag value of -50). Found features were given a flagging value of 0. Features that had been captured automatically were checked manually and any automatic capture errors were corrected. During this time anomalous features were manually flagged as “Bad” (given a flag value of -100). These included spots that were discolored (over green) due to obvious wash effects; spots that were marked by the fluorescence of dust particles, hair or a scratch; and spots that had merged due to printing errors. Dye marker spots that occurred at the top, left-hand corner of each block were also marked “Bad”. Features were then automatically flagged as bad using the ‘Flag Features’ function. Spots were automatically flagged as “Bad” if they were: over saturated (greater than or equal to 10% saturated in either channel); misshapen (circularity of less than 35); very small (diameter of less than 80 or a number of pixels less than 40); or had an inconsistent spot signal (coefficient of variation of the pixels in either channel exceeded 99). These threshold parameters were determined by visual inspection of the scatter plots of these variables for each array in Genepix™ Pro. The latter three parameters exclude spots based on their morphology and the consistency of the signal across the spot. The raw data was then exported from Genepix™ Pro as Genepix results (.gpr) files.
Raw expression data were corrected for background effects, normalised and processed using the R programming language (ver. 2.6.0.) and associated R Bioconductor (ver. 2.1.) packages. The median foreground signal intensity of each spot for each of the channels, Cy5 (red) and Cy3 (green) as well as the median background intensity of each spot for each channel was imported into R. In addition to annotation, information weights matrix was generated, with all spots flagged as “Bad” (< -75) being weighted as 1. The 48 tiling spots (dye markers) were removed prior to normalization. The normexp background correction method was used with an offset of 32 to correct for any spatial artifacts that were present on the array. Data were adjusted within each array using a robust-spline normalisation function that was modified to accept an increased number of iterations. Data were adjusted between arrays using R-quantile normalisation which did not exclude weighted values. An estimated A value threshold for low signal (A = 7.1) was calculated using the distribution of the normalised values for the “null”, “buffer” and “negative control” spots. Genes that fell below this threshold across all arrays (“low intensity”) or that were weighted as “Bad” more than four times across all arrays were removed (values replaced with NA and then removed). Probe replicates were averaged Missing values were imputed using KNN imputation. Batch effects were corrected for using the R script COMBAT. Variance filtering (genes below the average standard deviation of all genes was classified as “Flat”) was performed to reduce the number of genes tested for differential expression. Features that did not contain mouse probe information (“Null”, “Dye”, “Buffer”, “alien spikes”) were removed. These steps reduced the dataset from 37 440 to 12 792 features (rows).
Matrix_B: Background corrected (normexp), normalised (within arrays using robust-spline, between arrays using Rquantile) log2 average signal (intensity) data (A values). Values weighted as “Bad” or filtered as “low intensity” have been replaced with “NA”.
Matrix_C: Background corrected (normexp), normalised (within arrays using robust-spline, between arrays using Rquantile) single channel data. Ch1 samples represent the signal from channel 1 (mouse reference samples) on each array while ch2 data represent the signal from ch2 (bat test samples). Values weighted as “Bad” or filtered as “low intensity” have been replaced with “NA”.

source_name: Common Reference: E13.5 mouse hand plate

label_protocol: These RNA samples were amplified and labelled using the Amino Allyl MessageAmp™ II Cy3 aRNA Amplification Kit (Ambion, Austin, TX, USA) as per manufacturer’s instructions. A fixed amount of 0.5 µg of input RNA was used in all experiments. Experiments were done in 4 batches with each biological repeat (1, 2, 3, 4) of the test conditions corresponding to an independent batch and being labelled with Cy3. In each batch the common reference was independently amplified and labelled with Cy5.

extract_protocol: Whole embryos were stored in RNAlater® (QIAGEN, Valancia, CA, USA) according to the manufacturer’s instructions. The autopods (distinguished as being the area of dorso-ventrally flattened tissue on the distal portion of the limb) were dissected off along the point of constriction of the presumptive wrist or ankle. This excluded the tissue associated with the stylopod and the zeugopod in addition to the tissue associated with the proto- and plagiopatagium of the bat. Total RNAs from these autopod tissues were extracted using QIAzol Lysis Reagent and purified using the RNeasy® Lipid Tissue Mini Kit (QIAGEN, Valancia, CA, USA). The quality of the RNA from the mouse hand plate pooled reference and ten randomly chosen bat limb samples was determined by the Centre for Proteomic and Genomic Research (CPGR, Cape Town, South Africa) using an Agilent 2100 Bioanalyser (Agilent Technologies, Stockport, UK). The RNA integrity of all samples was checked by visualization of 1 µg of RNA on a formaldehyde denaturing gel. The concentration and condition of each sample was determined using the Nanodrop® ND-1000 Uv-Vis Spectrophotometer (Nanodrop Technologies, Inc., Wilmington, DE, USA) prior to the experiment. These measurements were repeated three times and the average calculated.

value: 24 Pooled left and right embryonic handplates

tag: developmental stage

organism: Miniopterus natalensis

source_name: CS16 bat footplate

value: Left and right embryonic footplate


title: Hepatocellular carcinoma [H93]


title: Hepatocellular carcinoma [H88]


title: no substrate 3

description: Gene expression from cells grown in rich media and induced with no substrate