title: Yap cKO 1

city: Boston

first: Fernando

last: Camargo

address: 1 Blackfan Circle

institute: Children's Hospital Boston

description: gene expression of mouse intestine

hyb_protocol: Samples were hybridized onto arrays for approximately 18 hours. The arrays were washed and stained with streptavidin phycoerythrin.

scan_protocol: Scanned in array reader. Standard Affymetix protocol.

data_processing: Affymetrix Expression Console software 1.1, affymetrix-algorithm-name = rma-gene-default.

source_name: Mouse intestinal epithelium cKO 1

label_protocol: Total RNA was reverse transcribed  to generate double-stranded cDNA. The cDNA then underwent an in-vitro transcription reaction in which biotin-labeled cRNA was created.

extract_protocol: Tissue was lysed and RNA was isolated using RNEasy kit from Qiagen

treatment_protocol: Intestine epithelium was isolated using EDTA/PBS incubation

value: whole intestinal epithelium

tag: genotype/variation

value: Yap cKO

value: RSpondin1 adenovirus


title: N_H14_I7_P_P14_F_82-04_F

status: Public on Nov 29 2012

type: RNA

city: Bethesda

first: Luis Fernando

last: Menezes

state: MD

address: Room 8D12A, Building 10, 10 Center Dr

department: NIDDK

country: USA

institute: National Institutes of Health

description:
Array name: X82.04_LM8.031
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

hyb_protocol: 0.75 ugs of biotin-labeled cRNA was hybridized according to standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: The data were normalized using VST transformation with lummi in R.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Kidney

label_protocol: cRNA was generated and labeled by incorporating biotin-16-UTP.

extract_protocol: RNA was isolated using Trizol (Invitrogen), followed by RNeasy plus kit (Qiagen)

tag: genotype (n

value: Control; P:Mutant):N

tag: age induced (days)

tag: age harvested (days)

tag: gender (m

value: Male; F:Female; U:Unknown):F

tag: litter

tag: batch


title: Control Mouse 3 [Yap cKO_Rspondin study]

description: gene expression of mouse intestine

label: Biotin

source_name: Mouse intestinal epithelium Control 3

tag: tissue

value: Yap control

tag: treatment


title: H9-derived neural rosettes biological rep 1-1

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
Gene expression data from neural rosettes
B1

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX ref8 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina BeadArray Reader scanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. Quantile normalization is performed.

organism: Homo sapiens

source_name: neural rosettes manually purified

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

tag: cell line

tag: cell type

value: neural rosettes


title: P_H12_I7_N_P12_M_41-02_M

description:
Array name: X41.02_LM8.032
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

value: Control; P:Mutant):P

value: Male; F:Female; U:Unknown):M


title: N_H12_I7_N_P12_M_41-04_M

description:
Array name: X41.04_LM8.030
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: HFB1 10Gy 0 days

type: genomic

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: 5mC profile in HFB1 sample

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Loess normalization was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio

molecule: genomic DNA

source_name: HFB1 10Gy-0days 5mC (MIRA) enriched samples

label_protocol: According to standard NimbleGen Protocol

extract_protocol: MinElute PCR Purification Kit (Qiagen; Valencia, CA). Genomic DNA was fragmented by sonication to an average size of ~400 bp using a Sonifier cell disruptor 350 (Branson; Danbury, CT).

treatment_protocol: 10 Gy; no recovery time before harvest

value: Normal human diploid fibroblasts

tag: enrichment procedure

value: 5mC (MIRA)

tag: antibody

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: 10 Gy; no recovery time before harvest

source_name: HFB1 input DNA

tag: sample type

value: input DNA


title: ALI+12

city: Stanford

first: Tim

last: Stearns

address: Lorry Lokey Chem/Bio, 337 Campus Drive

department: Biology

institute: Stanford University

description: Analysis used total Reference RNA as a control for comparison to experimental samples taken from ciliated cells (timepoints ALI+4 and ALI+12) and non-ciliated cells from in vitro differentiated cultures of mouse tracheal epithelial cells.

hyb_protocol: Hybridization was done on MEEBO oligonucleotide arrays printed at the Stanford Functional Genomics Facility. MEEBO slides were post-processed the same day of hybridization. Fluorescently labeled amplified RNA samples from MTECs were hybridized to the array with an amplified reference RNA sample for 16 hours at 65°C.

scan_protocol: Arrays were scanned on an Agilent G2565AA scanner.

data_processing: Data processing was carried out using LIMMA.  The mean values from each channel were log2 transformed and normalized using print-tip LOESS to minimize printing effects.

source_name: FOXJ1:GFP+ sorted ciliated cells from MTEC cultures 12 days after air-liquid interface.

label_protocol: Total RNA was amplified and coupled to Cy3/Cy5 using amino allyl MessageAmp II aRNA amplification kit (Ambion) according to the manufacturer’s protocols.  Labeled RNA was then fragmented using RNA Fragmentation Reagent (Ambion)

growth_protocol: Mouse tracheal epithelial cells (MTECs) dissociated from the tracheas of approximately 12-15 wild type (control) or FoxJ1/EGFP mice were seeded on 6-well plates containing Transwell-Clear permeable membrane supports. MTECs were cultured under immersion until confluence, at which point an air-liquid interface was established by removing media from the top of the filter. FOXJ1/GFP transgenic mice were a gift from Larry Ostrowski (Ostrowski et al., 2003). FOXJ1/GFP mice were mixed background C3H x C57Bl/6J F1 hybrids.

extract_protocol: Total RNA was extracted from FACS sorted cells using Rneasy mini kits (Qiagen) according to manufacturer's protocols.

treatment_protocol: Differentiation of ciliated cells was intiiated by establishment of an air-liquid interface.  Experimental samples were obtained by FACS.

value: tracheal epithelium

tag: strain

value: C3H x C57Bl/6J F1 hybrids

source_name: Universal Reference RNA

tag: cell lines

value: embryo, embryonic fibroblast, kidney, liver hepatocyte, lung alveolar macrophage, B-lymphocyte, T-lymphocyte, mammary gland, muscle myoblast, skin, testis

tag: vendor

value: Stratagene (now Agilent #740100)


title: GFP-

source_name: FOXJ1:GFP- sorted non-ciliated cells from MTEC cultures.

tag: genotype/variation

value: non-ciliated cells from MTEC cultures


title: Yap cKO 3

description: gene expression of mouse intestine

source_name: Mouse intestinal epithelium cKO 3

value: whole intestinal epithelium

value: Yap cKO

value: RSpondin1 adenovirus


title: ALI+4

source_name: FOXJ1:GFP+ sorted ciliated cells from MTEC cultures 4 days after air-liquid interface.


title: H9 hESCs biological rep 1-2

description:
Gene expression data from H9 hESC line
A2

source_name: hESCs

value: undifferentiated hESC


title: Monoculture C24L_mono

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

description: Monoculture C24L_mono

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: quantile normalized the probe intensities to match the G20 mono culture  sample and averaged the log2 values for each gene and set the median log2 expression level in each sample to zero

label: Alexa fluor 555

organism: Oleidesulfovibrio alaskensis G20

source_name: Desulfovibrio alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.047h-1)

label_protocol: prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen)

growth_protocol: We collected expression data for 2 growth conditions: syntrophic or respiratory growth of Desulfovibrio alaskensis str. G20 on lactate. Desulfovibrio alaskensis str. G20 was grown in monoculture under sulfate-limited conditions and in syntrophic coculture with the methanogen Methanococcus maripaludis. The basal salt solution of the media is described in Walker et. al. (2009) and contained 30 mM sodium DL-lactate or sodium pyruvate, resazurin as redox indicator, and 10 mM Na2SO4 (chemostat monoculture media) or 30 mM Na2SO4 (batch monoculture media). The media were prepared in bioreactor glass vessels (2 liters), medium reservoir bottles (10 liters) and Widdel flasks (1 and 2 liters) anoxically under a N2-CO2 (80:20, v/ v) gas atmosphere according to Widdel and Bak (1992). The media were buffered using 1.1 mM KH2PO4 and 30 mM NaHCO3. Nonchelated trace element mixture 1 and selenite-tungstate solution as well as vitamin mixture, riboflavin, vitamin B1 and B12 solutions and [1M] Na2S solution (79) were added aseptically in 1 ml aliquots per liter of medium. All stock solutions were prepared under anoxic conditions. For batch culture cultivation, the media were dispensed anoxically in sterile N2-CO2 (80:20, v/ v) pre-gassed 250 ml serum bottles or 25 ml Balch tubes in 130 and 13 ml aliquots, repectively. After preparation, the bioreactor and medium reservoir bottles were connected to a N2-CO2 (90:10, v/ v) gas mixture tank.  Cells were harvested from triplicate mono- and coculture chemostat runs after at least 3 volume turnovers at steady state in the chemostat at constant dilution rate of 0.047h-1.  The effect of time for harvesting on transcription results was examined for two reactor studies by collecting biomass at two time points separated by 15 min. at the end of the chemostat run (named E as early harvest  and L as late harvest) giving a total of five coculture and three monoculture gene expression data set.

extract_protocol: Isolated total RNA with RNAeasy mini kit (Qiagen)

treatment_protocol: Varying growth conditions: syntrophy versus sulfate respiration on substrate lactate

tag: carbon source

value: lactate (30 mM)

tag: electron acceptor

value: sulfate (10 mM)

tag: stressor

value: growth rate 0.047h-1 (chemostat growth)


title: Yap cKO 2

description: gene expression of mouse intestine

source_name: Mouse intestinal epithelium cKO 2


title: H9-derived oligodendrocytes biological rep 1-1

description:
Gene expression data from H9 oligos
M1

source_name: Oligos O4+ from H9

value: oligodendrocytes


title: P_H12_I7_P_P12_M_82-02_M

description:
Array name: X82.02_LM8.029
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

tag: genotype (n

value: Control; P:Mutant):P

tag: age induced (days)

tag: age harvested (days)

tag: gender (m

value: Male; F:Female; U:Unknown):M


title: Control Mouse 2 [Yap cKO_Rspondin study]

description: gene expression of mouse intestine

source_name: Mouse intestinal epithelium Control 2

tag: tissue

value: Yap control

tag: treatment


title: Control Mouse 1 [Yap cKO_Rspondin study]

description: gene expression of mouse intestine

source_name: Mouse intestinal epithelium Control 1


title: Mycobacterium smegmatis-Spheroplast induced

city: Amherst

first: Andrea

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

description: 3 Technical (spot) replicates. Mycobacterium smegmatis, spheroplast induced.

hyb_protocol: Hybridization was performed following the Recommended Sample Preparation and Hybridization Protocol drawn-up by the MYcroarrays® Company (Biodiscovery LLC) with some modifications. 220µl of hybridization solution (66µl of 20X SSPE (3M NaCl, 20mM EDTA, 118.2mM NaH2PO4, 81.8mM Na2HPO4), 10% formamide, 0.01mg/ml BSA, 0.01% Tween-20, 1mM DTT, 1% manufacturer control oligos, 10µg of each target coupled-aRNA, RNAse-free water to final volume) was prepared and pre-warmed at 56°C. Hybridizations were carried out in a water bath at 55°C for 18h with OneArray Sealed Hybridization Chambers (PhalanxBio Inc., Palo Alto, CA, USA). After incubation, slides were washed twice with SSPE 1X- 0.1mM DTT for 2 min followed by a 30 sec final wash with 0.25 X SSPE – 0.1mM DTT, dried with air-spray and immediately scanned.

scan_protocol: Scans were carried out with the Gene Pix AXON 4200A instrument (Axon Instruments) at 5-um resolution with full dynamic range of signal intensities at 1 – 65.000 in two-colour red/green mode (635nm and 532 nm filters).

data_processing:
The intensities of the two dyes for each spot were quantified using the Gene Pix 6.0 Software and calculated as the mean of median intensity of each replicate spot for each gene. Total array intensity was used to normalize spot signal intensities with the ratio-mean based algorithm option. Subtraction of local feature background median was achieved as default. Negative corrected intensities were set to 10 .
A change of 2-fold in the intensities with a p-value < 0.05 was considered significant for a differential gene expression. Data were trasnformed in normalized log2 ratio (Alexa Fluor dye 555/647) representing MSMEG-exp/MSMEGk-.

label: Alexa Fluor 555

organism: Mycolicibacterium smegmatis MC2 155

source_name: M. smegmatis spheroplast induced

label_protocol: Forty µg samples of amplified RNA (aRNA)  were labelled with either Alexa Fluor dye 647 or 555  purchased from Invitrogen, USA, following manufacturer's protocol. Purification of coupled aRNA was performed by RNeasy purification system (Qiagen) and incorporation of dye was evaluated using the Nanodrop spectrophotometer. Before hybridization, coupled aRNA was fragmented using the RNA fragmentation reagents (Ambion, Inc) following the manufacturer's protocol.

growth_protocol: MSMEG MC2155 (ATCC 700084 ) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C before lysozyme treatement.

extract_protocol: total RNA extracted with the RiboPure-Bacteria Kit (Ambion, Inc). Mycobacterial cells were re-suspended in 350µl of RNAwiz solution and transferred to a 0.5ml RNAse-free skirted screw-cap microcentrifuge tube containing 250µl of 0.1mm ice-cold Zirconia Beads. Tubes were immediately processed in the RiboLyser RNA Lysing Machine (RiboLyser FP120-HY-230, Hybaid) for 2 cycles (30s at speed 6.5 with 1 min of cooling interval between each bead beating step). Remaining steps were performed according to the manufacturer’s instructions. All RNA samples were treated with Dnase I (Ambion, Inc)  and  purified by RNeasy column (Qiagen). RNA yield and purity was evaluated with the Nanodrop spectrophotometer (NanoDrop1000, Thermo Scientific) and RNA quality was examined by Denaturing Gel Electrophoresis. We carried out three independent experiments on three different flasks. Good quality RNA samples obtained from each pellet were then pooled together and used for microarray experiments to get an average of three separate experiments. mRNA was obtained by using the MICROBExpress Bacterial mRNA Purification Kit (Ambion) and was lineary amplified bu using the MessageAmp II Bacterial Kit (Ambion, Inc)

treatment_protocol: Mid log-phase cells were treated with a 1% glycine solution in 7H9/ADC/Tw80 medium for 18h at 37°C. Pre-spheroplasts were harvested by centrifugation at 5800 x g for 15min at RTand washed 2 times with a sucrose – MgCl2 (SM) solution (0.5M sucrose, 20mM MgCl2). The cell pellet was re-suspended in the original volume of 7H9/ADC/Tw80-SM (60:40) solution supplemented with 25μg/ml lysozyme (Sigma-Aldrich, MO, USA) and 1.2% glycine. Conversion from the bacillary form to the CWD state was completed after 48h incubation at 37°C.

tag: bacterial cells

value: Mycobacterium smegmatis

label: Alexa Fluor 647

source_name: M. smegmatis control untreated

growth_protocol: MSMEG MC2155 (ATCC 700084 ) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C until mid-log phase.

treatment_protocol: Mid log-phase cells were grown in 7H9/ADC/Tw80 medium for 18h at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at RTand washed 2 times with PBS/Tw80. The cell pellet was re-suspended in the original volume of 7H9/ADC/Tw80 and incubated  48h at 37°C.


title: YAP Tg 3

description: Gene expression data from Tg crypts

source_name: Tg Crypts 3

growth_protocol: Crypts were not cultured

extract_protocol: Intestine was washed in PBS and crypts were isolated using standard procedures using 4mM EDTA/PBS solution. Tissue was then processed for total RNA using Qiagen RNEasy kit.

value: Intestinal crypts

value: YAP Tg


title: YAP Tg 1

description: Gene expression data from Tg crypts

source_name: Tg Crypts 1


title: N_H12_I7_N_P12_M_82-01_M

description:
Array name: X82.01_LM8.026
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

source_name: Kidney

value: Control; P:Mutant):N

tag: litter

tag: batch


title: P_H12_I7_P_P12_M_29-101_M

description:
Array name: X29.101_LM8.025
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: P_H14_I7_P_P14_M_41-07_M

description:
Array name: X41.07_LM8.027
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: N_H14_I7_N_P14_M_81-20_M

description:
Array name: X81.20_LM8.024
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: YAP Tg 2

description: Gene expression data from Tg crypts

source_name: Tg Crypts 2


title: N_H14_I7_N_P14_F_29-110_F

description:
Array name: X29.110_LM8.028
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

value: Male; F:Female; U:Unknown):F


title: P_H14_I7_P_P14_F_82-07_F

description:
Array name: X82.07_LM8.023
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Control mouse 1 [YAP Tg study]

description: Gene expression data from control crypts

source_name: Control Crypts 1

value: Control


title: P_H12_I7_P_P12_F_80-02_F

description:
Array name: X80.02_LM8.021
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: P_H14_I7_P_P14_M_29-102_M

description:
Array name: X29.102_LM8.019
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Day 29 S1 Replicate 3

city: Miami

first: Anthony

middle: John

last: Bellantuono

state: FL

department: Biological Sciences

institute: Florida International University

description: The reference sample consisted of pooled RNA from all treatments and time points.

hyb_protocol: Static hybridizations were performed using formamide-based hybribization buffer (Genisphere).  Prehybridization used 1 μg Human Cot-1 DNA for 90 minutes. Hybridization with cDNA was performed for 16 hours at 47°C. Arrays were washed in 65°C 2x SSC/0.2% SDS for 15 minutes, 2x SSC at room temperature for 15 minutes, and 0.2x SSC at room temperature for 15 minutes. Dye capture with Array 900 3DNA capture reagents (Genisphere) was performed at 50°C for 4 hours, followed by washing. Arrays were dipped in DyeSaver II (Genisphere).

scan_protocol: Scanning was performed on a GenePix Personal 4100A (Axon Instruments) microarray scanner using GenePix Pro 4.1.

data_processing: Following gridding and quality control using GenePix Pro 4.1 (Axon Instruments), background-subtracted mean intensity values were log- and lowess-transformed using R/Maanova version 1.18 (Wu and Churchill 2008). A fixed-effect ANOVA model was fit to the normalized data. Empirical-Bayes Fs statistic was used to test for differentially expressed genes at each sampling time. P-values for each clone were calculated from 500 permutations of residual shuffling. False discovery rate adjustments were implemented using jsFDR (Storey 2002, J Roy Stat Soc B), using an adjusted p-value threshold of less than 0.05.

organism: Acropora millepora

source_name: S1 Treatment, Day 29 (31°C for 4 days following 10 days preconditioning)

label_protocol: Complementary DNA was synthesized from 650 ng total RNA per channel, following the Array 900 kit protocol (Genisphere) with SuperScript III reverse transcriptase (Invitrogen). RNA from individual coral fragments under comparison was used to synthesize cDNA using primers for downstream capture by Cy5. Reference cDNA (Channel 2) was synthesized using primers for downstream capture by Cy3.

extract_protocol: Coral fragments were immediately frozen in liquid nitrogen at sampling times. Frozen coral fragments were crushed and then homogenized in Trizol Reagent (Invitrogen). Trizol RNA extraction protocol was followed as per manufacturer’s protocol through phase separation, after which  the aqueous phase was recovered, mixed with an equal volume of absolute ethanol, and processed with an RNeasy Mini kit (QIAGEN). RNA integrity was assessed by electrophoresis on MOPS denaturing gels; only high integrity RNA was used for cDNA synthesis and subsequent hybridization.

tag: day

tag: replicate

tag: sample type

value: reference (consisting of pooled RNA from all sampling times and treatments)


title: Day 29 NPC Replicate 2

source_name: Non-Preconditioned Treatment, Day 29 (31°C for 4 days)

value: Non-Preconditioned

value: 29 (31°C for 4 days)

source_name: pooled RNA from all treatments and time points


title: Day 29 NPC Replicate 1


title: Day 29 S1 Replicate 2

value: 29 (31°C for 4 days following 10 days preconditioning)


title: Day 29 NPC Replicate 3


title: Day 29 Control Replicate 3

source_name: Control Treatment, Day 29 (ambient temperature)

value: 29 (ambient temperature)


title: HFB3 0.1Gy 7 days

description: 5mC profile in HFB3 sample

source_name: HFB3 0.1Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 0.1 Gy; 7 days recovery time before harvest

tag: cell type

value: Normal human diploid fibroblasts

tag: enrichment procedure

value: 5mC (MIRA)

tag: antibody

value: In Lab purified His-MBD3L1 & GST-MBD2b

source_name: HFB3 input DNA

value: input DNA


title: Control mouse 2 [YAP Tg study]

source_name: Control Crypts 2

tag: genotype/variation


title: Day 29 Control Replicate 2


title: Day 29 S1 Replicate 1


title: Control mouse 3 [YAP Tg study]

source_name: Control Crypts 3


title: Day 25 S1 Replicate 3

source_name: S1 Treatment, Day 25 (31°C for 4 days following 10 days preconditioning)


title: Day 29 Control Replicate 1


title: N_H14_I7_N_P14_M_81-02_M

description:
Array name: X81.02_LM8.020
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

value: Male; F:Female; U:Unknown):M


title: N_H12_I7_N_P12_F_29-107_F

description:
Array name: X29.107_LM8.022
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Day 25 S1 Replicate 2

value: 25 (31°C for 4 days following 10 days preconditioning)


title: Day 25 NPC Replicate 1

source_name: Non-Preconditioned Treatment, Day 25 (31°C for 4 days)

value: 25 (31°C for 4 days)


title: Day 25 NPC Replicate 2


title: P_H12_I7_P_P12_M_40-40_M

description:
Array name: X40.40_LM8.017
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

value: Control; P:Mutant):P


title: Day 25 S1 Replicate 1


title: Dox 2

description: Gene Expression from SubQ tumor

source_name: SubQ Tumor 5

growth_protocol: Cells were transplanted SubQ in matrigel and mice were either given Dox water or no dox water for 21 days.

extract_protocol: Tumors were excised from the flanks of nude mice and tumor tissue was grinded using mortar and pestle cooled with liquid nitrogen on dry ice.

treatment_protocol: Dox or no dox for 21 days

tag: cells

value: DLD1 SubQ Tumor

value: Dox


title: Day 25 NPC Replicate 3


title: Dox 3

description: Gene Expression from SubQ tumor

source_name: SubQ Tumor 6


title: N_H12_I7_N_P12_M_80-01_M

description:
Array name: X80.01_LM8.018
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

tag: genotype (n

value: Control; P:Mutant):N


title: Day 25 Control Replicate 1

source_name: Control Treatment, Day 25 (ambient temperature)

value: Control

value: 25 (ambient temperature)


title: Dox 1

description: Gene Expression from SubQ tumor

source_name: SubQ Tumor 4


title: P_H14_I7_P_P14_M_81-10_M

description:
Array name: X81.10_LM8.015
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

source_name: Kidney

tag: age induced (days)


title: No Dox 3

description: Gene Expression from SubQ tumor

source_name: SubQ Tumor 3

value: No Dox


title: Day 25 Control Replicate 3

value: reference (consisting of pooled RNA from all sampling times and treatments)


title: Day 23 S1 Replicate 2

source_name: S1 Treatment, Day 23 (31°C for 2 days following 10 days preconditioning)


title: No Dox 2

description: Gene Expression from SubQ tumor

source_name: SubQ Tumor 2


title: Day 25 Control Replicate 2


title: Day 23 S1 Replicate 1

value: 23 (31°C for 2 days following 10 days preconditioning)


title: Day 23 NPC Replicate 3

source_name: Non-Preconditioned Treatment, Day 23 (31°C for 2 days)

value: Non-Preconditioned

value: 23 (31°C for 2 days)


title: Day 23 S1 Replicate 3

source_name: pooled RNA from all treatments and time points


title: No Dox 1

description: Gene Expression from SubQ tumor

source_name: SubQ Tumor 1


title: N_H12_I7_N_P12_F_40-07_F

description:
Array name: X40.07_LM8.014
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

tag: age harvested (days)

value: Male; F:Female; U:Unknown):F


title: Day 23 NPC Replicate 2


title: P_H12_I7_P_P12_M_27-01_M

description:
Array name: X27.01_LM8.013
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

tag: gender (m


title: Expression data of V44

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Robust Multichip Analysis (RMA) using Genespring GX (Agilent Technologies, Santa Clara, CA). Log2 RMA signal is the value after baseline transformation using the median value of all samples.

source_name: Patient V44

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

tag: tissue

value: Colorectal Cancer

tag: chromosome instability (cin) phenotype

value: CIN-low


title: N_H14_I7_N_P14_F_56-01_F

description:
Array name: X56.01_LM8.016
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Day 23 NPC Replicate 1

tag: treatment


title: Expression data of V48

source_name: Patient V48

value: CIN-high


title: N_H14_I7_N_P14_F_40-04_F

description:
Array name: X40.04_LM8.012
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

tag: litter


title: N_H12_I7_N_P12_M_27-02_M

description:
Array name: X27.02_LM8.010
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

value: Male; F:Female; U:Unknown):M

tag: batch


title: Expression data of V49

source_name: Patient V49


title: Day 23 Control Replicate 3

source_name: Control Treatment, Day 23 (ambient temperature)

tag: day

value: 23 (ambient temperature)


title: Expression data of V42

source_name: Patient V42


title: Day 23 Control Replicate 1

tag: replicate


title: Day 23 Control Replicate 2

tag: sample type


title: P_H12_I7_P_P12_F_16-07_F

description:
Array name: X16.07_LM8.009
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

value: Control; P:Mutant):P


title: N_H14_I7_N_P14_M_27-20_M

description:
Array name: X27.20_LM8.008
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Day 20 S1 Replicate 3

source_name: S1 Treatment, Day 20 (28°C for 10 days)

value: 20 (28°C for 10 days)


title: Expression data of V38

source_name: Patient V38


title: N_H12_I7_N_P12_M_16-10_M

description:
Array name: X16.10_LM8.006
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Expression data of V39

source_name: Patient V39


title: P_H14_I7_P_P14_F_56-02_F

description:
Array name: X56.02_LM8.011
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Day 20 S1 Replicate 2


title: P_H14_I7_P_P14_F_40-20_F

description:
Array name: X40.20_LM8.007
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Expression data of V36

source_name: Patient V36


title: Expression data of V41

source_name: Patient V41


title: Day 20 S1 Replicate 1


title: P_H12_I7_P_P12_M_16-02+04_M

description:
Array name: X16.02.and.04_LM8.005
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

source_name: Kidney


title: Day 20 NPC Replicate 3

description: The reference sample consisted of pooled RNA from all treatments and time points.

source_name: Non-Preconditioned Treatment, Day 20 (28°C for 1 day)

value: 20 (28°C for 1 day)


title: N_H14_I7_N_P14_M_27-10_M

description:
Array name: X27.10_LM8.004
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8

value: Control; P:Mutant):N


title: Day 20 NPC Replicate 2


title: Expression data of V32

source_name: Patient V32


title: Day 20 NPC Replicate 1


title: Expression data of V31

source_name: Patient V31


title: Expression data of V34

source_name: Patient V34


title: Expression data of V33

source_name: Patient V33


title: Day 20 Control Replicate 3

source_name: Control Treatment, Day 20 (ambient temperature)

value: Control

value: 20 (ambient temperature)

source_name: pooled RNA from all treatments and time points


title: P_H14_I7_P_P14_M_27-07_M

description:
Array name: X27.07_LM8.003
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: N_H12_I7_N_P12_F_29-02_F

description:
Array name: X29.02_LM8.002
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Expression data of V30

source_name: Patient V30


title: Expression data of V29

source_name: Patient V29


title: P_H12_I7_P_P12_M_29-10_M

description:
Array name: X29.10_LM8.001
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM8


title: Day 20 Control Replicate 2


title: Expression data of V28

source_name: Patient V28


title: P_H14_I7_10P14_U

description:
Array name: X4592728005_H
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

value: Male; F:Female; U:Unknown):U


title: Expression data of V27

source_name: Patient V27


title: N_H14_I7_7P14_U

description:
Array name: X4592728005_G
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6


title: Day 20 Control Replicate 1

value: reference (consisting of pooled RNA from all sampling times and treatments)


title: Day 4 S1 Replicate 2

source_name: S1 Treatment, Day 4 (ambient temperature)

value: 4 (ambient temperature)


title: Day 4 S1 Replicate 3


title: P_H12_I8_9P8_U

description:
Array name: X4592728005_D
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6


title: 312_MIRA

description: DNA methylation profile in 312

data_processing: Loess normalization was applied exclusing top 5% probes with the largest original Cy5/Cy3 log2 ratio

source_name: MIRA enriched samples

growth_protocol: Modified 3T3 protocol

extract_protocol: Genomic DNA was isolated using standard phenol/chloroform extraction and ethanol precipitation method.

tag: strain

value: Big Blue® mouse

value: Tumor on SV from mice injected with chronic doses of B(a)P

value: MIRA

tag: antibodies/kit  information

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: B(a)P

source_name: Genomic Input DNA

value: Tumor on GU apparatus from mice injected with chronic doses of B(a)P


title: N_H14_I8_8P8_M

description:
Array name: X4592728005_E
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

value: Male; F:Female; U:Unknown):M


title: 314_MIRA

description: DNA methylation profile in 314

tag: enrichment procedure


title: P_H14_I8_14P8_M

description:
Array name: X4592728005_F
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6


title: 310_MIRA

description: DNA methylation profile in 310


title: Expression data of V26

source_name: Patient V26

value: Colorectal Cancer

value: CIN-low


title: Expression data of V25

source_name: Patient V25


title: Expression data of V24

source_name: Patient V24

value: CIN-high


title: Day 4 S1 Replicate 1


title: 210_MIRA

description: DNA methylation profile in 210

value: Seminal vesicles  (SV) from mice injected with chronic doses of DMSO (~6 month-old

value: DMSO

value: Seminal vesicles from mice injected with chronic doses of DMSO (~6 month-old


title: 309_MIRA

description: DNA methylation profile in 309


title: 211_MIRA

description: DNA methylation profile in 211

value: Seminal vesicles (SV) from mice injected with chronic doses of DMSO (~6 month-old


title: Day 4 NPC Replicate 2

source_name: Non-Preconditioned Treatment, Day 4 (ambient temperature)

value: Non-Preconditioned


title: Lu.94_MIRA

description: DNA methylation profile in Lu.94

value: Lung from mice exposed to SHS for 4 months  + 7 months recovery(~13 month-old)

value: SHS


title: Day 4 NPC Replicate 3

value: 4 (ambient temperature)

value: reference (consisting of pooled RNA from all sampling times and treatments)


title: Expression data of V23

source_name: Patient V23


title: N_H12_I8_10P8_U

description:
Array name: X4592728005_B
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

source_name: Kidney

value: Control; P:Mutant):N

value: Male; F:Female; U:Unknown):U


title: Expression data of V21

source_name: Patient V21


title: Day 4 NPC Replicate 1


title: N_H12_I8_4P8_U

description:
Array name: X4592728005_A
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6


title: Day 4 Control Replicate 3

source_name: Control Treatment, Day 4 (ambient temperature)

value: Control


title: N_H11_I7_4P11_U

description:
Array name: X4592728004_H
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6


title: Lu.86_MIRA

description: DNA methylation profile in Lu.86

value: Big Blue® mouse

value: MIRA

value: In Lab purified His-MBD3L1 & GST-MBD2b


title: Expression data of V17

source_name: Patient V17

value: Colorectal Cancer


title: Day 4 Control Replicate 2

source_name: pooled RNA from all treatments and time points


title: P_H11_I7_2P11_U

description:
Array name: X4592728004_G
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

value: Control; P:Mutant):P


title: Lu.208_MIRA

description: DNA methylation profile in Lu.208

value: Lung from mice exposed to clean air for 4 months  + 7 months recovery(~13 month-old)

value: clean air


title: Lu.89_MIRA

description: DNA methylation profile in Lu.89


title: Expression data of V15

source_name: Patient V15

value: CIN-high


title: Day 4 Control Replicate 1


title: P_H12_I8_5P8_U

description:
Array name: X4592728005_C
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6


title: P_H14_I8_11P8_M

description:
Array name: X4592728004_E
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

value: Male; F:Female; U:Unknown):M


title: Expression data of V16

source_name: Patient V16


title: P_H14_I8_15P8_M

description:
Array name: X4592728004_F
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6


title: Lu.88_MIRA

description: DNA methylation profile in Lu.88


title: Expression data of V20

source_name: Patient V20

value: CIN-low


title: Lu.212_MIRA

description: DNA methylation profile in Lu.212


title: 7dpf.b_sib.cy5_mut.cy3

city: Utrecht

first: Leonie

last: Huitema

state: Utrecht

address: Uppsalalaan 8

department: Schulte-Merker group

country: Netherlands

institute: Hubrecht Institute

description:
Samples were run in dye swap
Sample 4

hyb_protocol: Labeled samples were hybridized for 17 hours at 60 degrees Celcius to a 4x44K zebrafish expression array using the Gene Expression Hybrdization Kit (Agilent technologies). Arrays were washed according to the manufactures protocol.

scan_protocol: The microarray was scanned using the G2505C Agilent DNA microarray scanner using default parameters.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Danio rerio

label_protocol: cDNA synthesis and labeling were performed using the two color Low Input  Quick-Amp labeling kit (5190-2306, Agilent Technologies) and samples were purified using the Rneasy Mini kit (Qiagen). Concentration and cy3 and cy5 incorporation were determined using a nanodrop spectrophotometer.

growth_protocol: Embryos were raised in standard E3 medium at 28 degrees Celcius. At 6 dpf  mutant were separated from siblings by an in vivo skeletal staining as mutants fail to mineralize their skeleton. At 7 dpf,  embryos were sacrificed by an overdosis of ms222 and frozen in liquid nitrogen

extract_protocol: Total RNA from (n=30) entpd5 mutants versus siblings was isolated using the Rnaesy mini kit (Qiagen) according to the manufactures protocol.

tag: genotype/variation

value: wild type

value: whole embryos at 7 dpf

value: entpd5 mutant

tag: phenotype/selection

value: failure to mineralize their skeleton at 7 dpf


title: Expression data of V08

source_name: Patient V08


title: N_H14_I8_6P8_F

description:
Array name: X4592728004_C
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

tag: genotype (n

value: Control; P:Mutant):N

value: Male; F:Female; U:Unknown):F


title: Lu.87_MIRA

description: DNA methylation profile in Lu.87

value: Lung from mice exposed to SHS for 4 months  + 7 months recovery(~13 month-old)

value: SHS


title: Lu.206_MIRA

description: DNA methylation profile in Lu.206

value: Big Blue® mouse

value: MIRA


title: N_H14_I8_12P8_M

description:
Array name: X4592728004_D
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

tag: age induced (days)


title: 7dpf.b_sib.cy3_mut.cy5

description:
Samples were run in dye swap
Sample 3


title: Expression data of V09

source_name: Patient V09

value: Colorectal Cancer


title: Lu.207_MIRA

description: DNA methylation profile in Lu.207

source_name: MIRA enriched samples

value: In Lab purified His-MBD3L1 & GST-MBD2b


title: P_H12_I8_1P8_U

description:
Array name: X4592728004_B
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

value: Control; P:Mutant):P

tag: age harvested (days)

value: Male; F:Female; U:Unknown):U


title: Expression data of V07

source_name: Patient V07

value: CIN-high


title: Lu.73_MIRA

description: DNA methylation profile in Lu.73

value: Lung from mice exposed to SHS for 4 months + 1 month recovery (~7 month-old)

source_name: Genomic Input DNA

value: Lung from mice exposed to SHS for 4 months + 1 month recovery (~6 month-old)


title: N_H12_I8_2P8_U

description:
Array name: X4592728004_A
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM6

tag: gender (m


title: P_H14_I7_a1481_M

description:
Array name: X4443087015_H
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5

value: Male; F:Female; U:Unknown):M


title: Expression data of V05

source_name: Patient V05

tag: tissue


title: Expression data of V03

source_name: Patient V03

tag: chromosome instability (cin) phenotype


title: Mouse embryonic fibroblasts, immortalized, passage # >10 Mo.29 (expression)

description: Mouse embryonic fibroblasts. Set 3, immortalized, passage # >10

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Mouse Genome 430 2.0 arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: Immortalized; Set 3

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

growth_protocol: Cells were harvested at different passages before-, during- and after-crisis.

extract_protocol: Genomic DNA- and RNA were isolated using standard phenol/chloroform extraction and ethanol precipitation method, and the RNeasy kit (Qiagen, Valencia, CA), respectively.

tag: cell type

tag: total RNA


title: 7dpf.a_sib.cy5_mut.cy3

description:
Samples were run in dye swap
Sample 2

value: wild type

value: whole embryos at 7 dpf


title: Mouse embryonic fibroblasts, senescent, passage # 6-10 Mo.28 (expression)

description: Mouse embryonic fibroblasts. Set 3, senescent, passage # 6-10

source_name: Senescent; Set 3


title: Expression data of V06

source_name: Patient V06

value: CIN-low


title: Lu.72_MIRA

description: DNA methylation profile in Lu.72

tag: treatment


title: N_H14_I7_a1479_F

description:
Array name: X4443087015_F
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5

source_name: Kidney

value: Control; P:Mutant):N

tag: litter

tag: batch


title: Expression data of V02

source_name: Patient V02


title: Mouse embryonic fibroblasts, primary, passage # <6 Mo.27 (expression)

description: Mouse embryonic fibroblasts. Set 3, primary, passage # <6

source_name: Primary; Set 3


title: Lu.70_MIRA

description: DNA methylation profile in Lu.70


title: P_H16_I9_a1476_M

description:
Array name: X4443087015_E
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5


title: P_H14_I7_a1480_F

description:
Array name: X4443087015_G
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5

value: Male; F:Female; U:Unknown):F


title: 7dpf.a_sib.cy3_mut.cy5

description:
Samples were run in dye swap
Sample 1

value: entpd5 mutant

value: failure to mineralize their skeleton at 7 dpf


title: Uranyl acetate reducing conditions with pyruvate versus pyruvate fermenting conditions (control)

city: East Lansing

first: Christina

last: Harzman

state: MI

address: Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: Analysis used anaerobic mid-log phase RNA extracted in an anaerobic environment for comparison of control samples fermenting pyruvate to experimental conditions of inorganic ion reduction (Fe(+3), Se(+6), U(+6), or NO3(-).

hyb_protocol: Hybridization mixtures were incubated at 70°C, and applied to the array using capillary action.  Microarray slides were then sealed in a hybridization chamber (CMT Hybridization Chamber; Corning Incorporated, Corning, NY) and incubated for 18 h in a 49°C shaking water bath (30 rpm).  LifterSlips® were removed from hybridized microarray slides carefully in a wash of 1× SSC buffer and 0.1% SDS at 49°C.  Slides were then washed in a shaking water bath (50 rpm) for 5 min in 1× SSC buffer and 0.1% SDS at 49°C, twice for 5 min in 0.1× SSC buffer and 0.1% SDS at room temperature, four times for 1 min in 0.1× SSC buffer at room temperature, and once for 10 s in 0.01× SSC buffer.  Washed slides were spun dry at 1800 rpm for 2 min prior to scanning.

scan_protocol: Slides were immediately scanned on an Axon 4000B laser scanner (Axon Laboratories, Molecular Devices, Sunnyvale, CA) using histogram verification in GenPix Pro 5.1 (Axon Laboratories) for raw data production followed by gene identifier alignment.

data_processing:
Following background correction by background subtraction of the median value, median signal intensities for each channel (Cy5 and Cy3) were imported into GeneSpring 6.0 (Silicon Genetics, Redwood City, CA)
Normalized by dye swapping and (per chip and per gene) using Lowess intensity-dependent normalization, reporting (test/control) fold-change

organism: Desulfitobacterium hafniense DCB-2

source_name: [experimental] Log phase cultures grown with uranyl acetate and pyruvate in anaerobic modified DCB-1 medium

label_protocol: Dyes were incorporated at 25°C for 1.5 h with 4.5 µl amino-allyl labeled cDNA in 0.1 M sodium carbonate (pH 9) and 4.5 µl reactive Cy5 and Cy3 N-hydroxysuccinamide ester fluorophores (Amersham, Piscataway, NJ) in dimethyl sulfoxide (GE Biosciences, Piscataway, NJ).  Amino-allyl labeled cDNA quantity and fluorophore incorporation efficiency were determined using UV-visible spectrophotometry.

growth_protocol: Desulfitobacterium hafniense DCB-2 was grown in modified anaerobic DCB-1 medium with 20 mM pyruvate and 1x Wolin vitamins to which all cultures were compared during hybridization and microarray analyses.

extract_protocol: In triplicate, cell cultures were harvested at mid-log phase by centrifugation under anaerobic conditions with the pellet suspended in room temperature RNA Protect (QIAGEN, Valencia, CA) with a 45 min lysozyme digestion.  RNA was extracted from the cell pellet using an RNeasy RNA extraction kit (QIAGEN) according to the manufacturer's instructions with the DNase digestion step included.

treatment_protocol: Iron reduction studies used Desulfitobacterium hafniense DCB-2 grown in modified anaerobic ferric citrate medium containing 50 mM ferric citrate with 20 mM lactate added.  Modified anaerobic DCB-1 medium was used for selenium and uranium studies with 1 mM sodium selenate, and 500 µM uranyl acetate, added with vitamins and a sole carbon source of 20 mM pyruvate.  Nitrate reduction studies used anaerobic carbonate-buffered freshwater medium with 10 mM nitrate, Wolin vitamins, and 20 mM lactate as the sole carbon source.

tag: growth protocol

source_name: [control] Log phase cultures grown with pyruvate in modified DCB-1 medium


title: Mouse embryonic fibroblasts, immortalized, passage # >10 Mo.26 (expression)

description: Mouse embryonic fibroblasts. Set 2, immortalized, passage # >10

source_name: Immortalized; Set 2


title: Lu.205_MIRA

description: DNA methylation profile in Lu.205

tag: strain

value: Big Blue® mouse

value: Lung from mice exposed to clean air for 4 months  + 7 months recovery(~13 month-old)

value: clean air


title: N_H16_I9_a1475_M

description:
Array name: X4443087015_D
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5


title: P_H16_I9_a1474_M

description:
Array name: X4443087015_C
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5


title: Mouse embryonic fibroblasts, primary, passage # <6 Mo.24 (expression)

description: Mouse embryonic fibroblasts. Set 2, primary, passage # <6

source_name: Primary; Set 2


title: Lu.67_MIRA

description: DNA methylation profile in Lu.67

value: Lung from mice exposed to SHS for 4 months (~6 month-old)

value: MIRA

tag: antibodies/kit  information

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: SHS


title: Mouse embryonic fibroblasts, senescent, passage # 6-10 Mo.25 (expression)

description: Mouse embryonic fibroblasts. Set 2, senescent, passage # 6-10

source_name: Senescent; Set 2


title: Selenate reducing conditions with pyruvate (experiment) versus pyruvate fermenting conditions (control)

source_name: [experimental] Log phase cultures grown with selenate and pyruvate in anaerobic modified DCB-1 medium

value: grown with pyruvate in modified DCB-1 medium


title: Lu.69_MIRA

description: DNA methylation profile in Lu.69

source_name: MIRA enriched samples

tag: enrichment procedure


title: Nitrate reducing conditions with lactate versus pyruvate fermenting conditions (control)

source_name: [experimental] Log phase cultures grown in anaerobic carbonate-buffered freshwater medium with nitrate and lactate


title: Lu.71_MIRA

description: DNA methylation profile in Lu.71

value: Lung from mice exposed to SHS for 4 months + 1 month recovery (~7 month-old)

source_name: Genomic Input DNA

value: Lung from mice exposed to SHS for 4 months + 1 month recovery (~6 month-old)


title: Lu.66_MIRA

description: DNA methylation profile in Lu.66


title: Lu.68_MIRA

description: DNA methylation profile in Lu.68


title: Lu.4_MIRA

description: DNA methylation profile in Lu.4

value: Lung from mice exposed to clean air for 4 months (~6 month-old)


title: Ferric citrate reducing conditions with lactate (experiment) versus pyruvate fermenting conditions (control)

source_name: [experimental] Log phase cultures grown in anaerobic ferric citrate medium with lactate


title: N_H19_I9_a1471_M

description:
Array name: X4443087015_B
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5

value: Male; F:Female; U:Unknown):M


title: Lu.3_MIRA

description: DNA methylation profile in Lu.3


title: Lu.2_MIRA

description: DNA methylation profile in Lu.2


title: Mouse embryonic fibroblasts, immortalized, passage # >10 Mo.23 (expression)

description: Mouse embryonic fibroblasts. Set 1, immortalized, passage # >10

source_name: Immortalized; Set 1


title: Mycobacterium avium subspecies paratuberculosis-Spheroplast induced

description: 4 Technical (spot) replicates. Mycobacterium avium subspecies paratuberculosis, spheroplast induced.

data_processing:
The intensities of the two dyes for each spot were quantified using the Gene Pix 6.0 Software and calculated as the mean of median intensity of each replicate spot for each gene. Total array intensity was used to normalize spot signal intensities with the ratio-mean based algorithm option. Subtraction of local feature background median was achieved as default. Negative corrected intensities were set to 10.
A change of 2-fold in the intensities with a p-value < 0.05 was considered significant for a differential gene expression. Data were trasnformed in normalized log2 ratio (Alexa Fluor dye 555/647) representing MAP exp/MAP k-.

organism: Mycobacterium avium subsp. paratuberculosis

source_name: M. avium subspecies paratuberculosis spheroplast induced

growth_protocol: MAP1515 (ATCC 43015)  was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA), 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) and 2 mg/L of Mycobactin J (MicJ, Allied Monitors, Fayette, MO, USA)  in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C before lysozyme treatement.

extract_protocol: tot-RNA extracted with the RiboPure-Bacteria Kit (Ambion, Inc). Mycobacterial cells were re-suspended in 350µl of RNAwiz solution and transferred to a 0.5ml RNAse-free skirted screw-cap microcentrifuge tube containing 250µl of 0.1mm ice-cold Zirconia Beads. Tubes were immediately processed in the RiboLyser RNA Lysing Machine (RiboLyser FP120-HY-230, Hybaid) for 3 cycles (30s at speed 6.5 with 1 min of cooling interval between each bead beating step). Remaining steps were performed according to the manufacturer’s instructions. All RNA samples were treated with Dnase I (Ambion, Inc)  and  purified by RNeasy column (Qiagen). RNA yield and purity was evaluated with the Nanodrop spectrophotometer (NanoDrop1000, Thermo Scientific) and RNA quality was examined by Denaturing Gel Electrophoresis. We carried out three independent experiments on three different flasks. Good quality RNA samples obtained from each pellet were then pooled together and used for microarray experiments to get an average of three separate experiments. mRNA was obtained by using the MICROBExpress Bacterial mRNA Purification Kit (Ambion) and was lineary amplified bu using the MessageAmp II Bacterial Kit (Ambion, Inc)

treatment_protocol: Mid log-phase cells were treated with a 1% glycine solution in 7H9/ADC/Tw80/MicJ medium for 92h at 37°C. Pre-spheroplasts were harvested by centrifugation at 5800 x g for 15min at RTand washed 2 times with a sucrose – MgCl2 (SM) solution (0.5M sucrose, 20mM MgCl2). The cell pellet was re-suspended in the original volume of 7H9/ADC/Tw80/MicJ-SM (60:40) solution supplemented with 25μg/ml lysozyme (Sigma-Aldrich, MO, USA) and 1.2% glycine. Conversion from the bacillary form to the CWD state was completed after 5 days at 37°C.

tag: bacterial cells

source_name: M. avium subspecies paratuberculosis control untreated

growth_protocol: MAP1515 (ATCC 43015)  was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA), 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA)and  2 mg/L of Mycobactin J (MicJ, Allied Monitors, Fayette, MO, USA)  in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C.

treatment_protocol: Mid log-phase cells were grown in 7H9/ADC/Tw80/MicJ  medium for 92h at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at RTand washed 2 times with PBS/Tw80. The cell pellet was re-suspended in the original volume of 7H9/ADC/Tw80/MicJ  and incubated 5 days at 37°C.


title: Mouse embryonic fibroblasts, primary, passage # <6 Mo.21 (expression)

description: Mouse embryonic fibroblasts. Set 1, primary, passage # <6

source_name: Primary; Set 1


title: P_H19_I9_a1470_M

description:
Array name: X4443087015_A
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM5

source_name: Kidney

value: Control; P:Mutant):P


title: mercury_control_expose-8h_rep3

status: Public on Nov 28 2012

city: Ft. Detrick

first: John

middle: A.

last: Lewis

address: 568 Doughten Drive

department: Biomarkers Program

institute: U.S. Army Center for Environmental Health Research

description:
gene expression data from L4 larvae
556-009-006

hyb_protocol: Biotin labeled cRNA was fragmented and hybridized to Affymetrix C. elegans whole genome GeneChips as recommended by Affymetrix.

scan_protocol: Hybridized Affymetrix C. elegans whole genome GeneChips were then scanned as recommended by Affymetrix.

data_processing: The data were analyzed with MAS 5.0 using Affymetrix default analysis settings.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

label_protocol: cDNA was synthesized using SuperScript Choice kit and a T24T7 primer following the manufacturer's protocol. Biotin labeled cRNA was synthesized using the Enzo BioArray High Yield Kit following the manufacturer's protocol. cRNA was purified from unincorporated nucleotides and other reaction components using the RNeasy Mini Kit (Qiagen).

growth_protocol: C. elegans cultures were grown in CeHR medium at 22.5 °C in T-75 tissue culture flasks with shaking at 70 rpm.

extract_protocol: Flash frozen worms were pulverized under liquid nitrogen in a Spex 6750 Freezer Mill. RNA was extracted from pulverized worms with Trizol followed by an additional purification step using RNeasy Midi columns. PolyA RNA was then isolated using OligoTex. All steps were performed following manufacturers recommendations.

treatment_protocol: Nematode populations were synchrnoized to the same developmental stage by treating the gravid adults with bleach and sodium hydroxide. This dissolves the adults, but allows the less sensitive embryos to remain viable. Following bleaching, embryos were maintained in an aqueous salt solution to allow larval nematodes to emerge and proceed into the first larval stage. Development is arrested at this time until the larvae are supplied with an adequate source of nutrition to support further development. Synchronized nematodes were then transferred to CeHR medium and allowed to proceed to mid L4 larval stage before the study compound was added. The study compounds were incorporated into the CeHR medium. Incubation under exposure conditions was at  22.5 °C for 4 and 8 hours. A single flasks of worms was harvested prior to beginning the exposure as the 0 h control.

tag: developmental stage

value: L4 larvae

tag: exposure chemical

value: Mercury

tag: exposure concentration (mg/l)

tag: exposure length (hours)


title: Mouse embryonic fibroblasts. Set 3, senescent, passage # 6-10 (methylation)

description: DNA Methylation Profile in Mo27

value: Mouse embryonic fibroblasts, senescent, passage # 6-10

tag: antibody

tag: genetic background

value: 129/sv (93%) with residual C57BL/6

value: input DNA


title: mercury_high_expose-8h_rep3

description:
gene expression data from L4 larvae
556-009-009


title: mercury_mid_expose-8h_rep3

description:
gene expression data from L4 larvae
556-009-008


title: Mouse embryonic fibroblasts, senescent, passage # 6-10 Mo.22 (expression)

description: Mouse embryonic fibroblasts. Set 1, senescent, passage # 6-10

source_name: Senescent; Set1


title: mercury_high_expose-4h_rep3

description:
gene expression data from L4 larvae
556-009-005


title: mercury_mid_expose-4h_rep3

description:
gene expression data from L4 larvae
556-009-004


title: mercury_high_expose-8h_rep2

description:
gene expression data from L4 larvae
556-008-009


title: mercury_low_expose-4h_rep3

description:
gene expression data from L4 larvae
556-009-003


title: Lu.1_MIRA

description: DNA methylation profile in Lu.1

value: Big Blue® mouse

tag: tissue


title: mercury_control_expose-4h_rep3

description:
gene expression data from L4 larvae
556-009-002


title: mercury_mid_expose-8h_rep2

description:
gene expression data from L4 larvae
556-008-008


title: Expression data of V01

source_name: Patient V01

value: Colorectal Cancer

tag: chromosome instability (cin) phenotype

value: CIN-low


title: mercury_control_expose-0h_rep3

description:
gene expression data from L4 larvae
556-009-001


title: Mouse embryonic fibroblasts. Set 2, immortalized, passage # >10 (methylation)

description: DNA Methylation Profile in Mo26

value: MIRA

tag: cell type

value: Mouse embryonic fibroblasts, immortalized, passage # >10


title: Mouse embryonic fibroblasts. Set 3, primary, passage # <6 (methylation)

description: DNA Methylation Profile in Mo26

value: Mouse embryonic fibroblasts, primary, passage # <6

value: In Lab purified His-MBD3L1 & GST-MBD2b


title: Mouse embryonic fibroblasts. Set 3, immortalized, passage # >10 (methylation)

description: DNA Methylation Profile in Mo28


title: mercury_low_expose-8h_rep2

description:
gene expression data from L4 larvae
556-008-007


title: mercury_control_expose-4h_rep2

description:
gene expression data from L4 larvae
556-008-002


title: mercury_high_expose-8h_rep1

description:
gene expression data from L4 larvae
556-007-009


title: mercury_control_expose-4h_rep1

description:
gene expression data from L4 larvae
556-007-002


title: mercury_control_expose-0h_rep2

description:
gene expression data from L4 larvae
556-008-001


title: mercury_high_expose-4h_rep2

description:
gene expression data from L4 larvae
556-008-005


title: mercury_mid_expose-4h_rep2

description:
gene expression data from L4 larvae
556-008-004


title: mercury_low_expose-8h_rep3

description:
gene expression data from L4 larvae
556-009-007


title: Mouse embryonic fibroblasts. Set 2, primary, passage # <6 (methylation)

description: DNA Methylation Profile in Mo24


title: mercury_mid_expose-8h_rep1

description:
gene expression data from L4 larvae
556-007-008


title: mercury_low_expose-4h_rep1

description:
gene expression data from L4 larvae
556-007-003


title: mercury_control_expose-8h_rep2

description:
gene expression data from L4 larvae
556-008-006r


title: mercury_low_expose-8h_rep1

description:
gene expression data from L4 larvae
556-007-007


title: mercury_high_expose-4h_rep1

description:
gene expression data from L4 larvae
556-007-005


title: mercury_mid_expose-4h_rep1

description:
gene expression data from L4 larvae
556-007-004


title: cadmium_control_expose-8h_rep3

description:
gene expression data from L4 larvae
552-006-006

value: Cadmium


title: mercury_low_expose-4h_rep2

description:
gene expression data from L4 larvae
556-008-003


title: cadmium_low_expose-8h_rep3

description:
gene expression data from L4 larvae
552-006-007


title: mercury_control_expose-0h_rep1

description:
gene expression data from L4 larvae
556-007-001


title: cadmium_low_expose-4h_rep3

description:
gene expression data from L4 larvae
552-006-003


title: cadmium_high_expose-8h_rep2

description:
gene expression data from L4 larvae
552-005-009


title: cadmium_high_expose-8h_rep3

description:
gene expression data from L4 larvae
552-006-009


title: cadmium_mid_expose-8h_rep3

description:
gene expression data from L4 larvae
552-006-008


title: cadmium_control_expose-4h_rep3

description:
gene expression data from L4 larvae
552-006-002


title: cadmium_high_expose-4h_rep3

description:
gene expression data from L4 larvae
552-006-005


title: cadmium_mid_expose-8h_rep2

description:
gene expression data from L4 larvae
552-005-008


title: cadmium_control_expose-0h_rep3

description:
gene expression data from L4 larvae
552-006-001


title: Mouse embryonic fibroblasts. Set 1, immortalized, passage # >10 (methylation)

description: DNA Methylation Profile in Mo23


title: Mouse embryonic fibroblasts. Set 2, senescent, passage # 6-10 (methylation)

description: DNA Methylation Profile in Mo25


title: cadmium_mid_expose-8h_rep1

description:
gene expression data from L4 larvae
552-004-008


title: cadmium_mid_expose-4h_rep1

description:
gene expression data from L4 larvae
552-004-012


title: cadmium_control_expose-0h_rep2

description:
gene expression data from L4 larvae
552-005-001


title: cadmium_low_expose-4h_rep2

description:
gene expression data from L4 larvae
552-005-003


title: cadmium_control_expose-4h_rep2

description:
gene expression data from L4 larvae
552-005-002


title: acrylamide_mid_expose-8h_rep3

description:
gene expression data from L4 larvae
551-007-008

value: Acrylamide


title: cadmium_high_expose-8h_rep1

description:
gene expression data from L4 larvae
552-004-009


title: acrylamide_high_expose-8h_rep2

description:
gene expression data from L4 larvae
551-006-009


title: cadmium_low_expose-8h_rep2

description:
gene expression data from L4 larvae
552-005-007


title: acrylamide_control_expose-8h_rep3

description:
gene expression data from L4 larvae
551-007-006


title: cadmium_high_expose-4h_rep2

description:
gene expression data from L4 larvae
552-005-005


title: cadmium_low_expose-4h_rep1

description:
gene expression data from L4 larvae
552-004-003


title: cadmium_low_expose-8h_rep1

description:
gene expression data from L4 larvae
552-004-007


title: acrylamide_high_expose-8h_rep3

description:
gene expression data from L4 larvae
551-007-009


title: acrylamide_mid_expose-4h_rep3

description:
gene expression data from L4 larvae
551-007-004


title: cadmium_control_expose-4h_rep1

description:
gene expression data from L4 larvae
552-004-002


title: acrylamide_control_expose-4h_rep3

description:
gene expression data from L4 larvae
551-007-002


title: cadmium_mid_expose-4h_rep2

description:
gene expression data from L4 larvae
552-005-004


title: acrylamide_low_expose-8h_rep3

description:
gene expression data from L4 larvae
551-007-007


title: acrylamide_control_expose-0h_rep3

description:
gene expression data from L4 larvae
551-007-001


title: cadmium_control_expose-8h_rep2

description:
gene expression data from L4 larvae
552-005-006


title: cadmium_control_expose-0h_rep1

description:
gene expression data from L4 larvae
552-004-011


title: acrylamide_mid_expose-8h_rep2

description:
gene expression data from L4 larvae
551-006-008


title: cadmium_control_expose-8h_rep1

description:
gene expression data from L4 larvae
552-004-010


title: acrylamide_low_expose-4h_rep3

description:
gene expression data from L4 larvae
551-007-003


title: acrylamide_high_expose-4h_rep3

description:
gene expression data from L4 larvae
551-007-005


title: mercury_control_expose-8h_rep1

description:
gene expression data from L4 larvae
556-007-006r


title: acrylamide_low_expose-8h_rep2

description:
gene expression data from L4 larvae
551-006-007


title: acrylamide_control_expose-8h_rep2

description:
gene expression data from L4 larvae
551-006-006


title: acrylamide_control_expose-0h_rep2

description:
gene expression data from L4 larvae
551-006-001


title: acrylamide_high_expose-4h_rep2

description:
gene expression data from L4 larvae
551-006-005


title: acrylamide_mid_expose-8h_rep1

description:
gene expression data from L4 larvae
551-005-008


title: acrylamide_control_expose-4h_rep2

description:
gene expression data from L4 larvae
551-006-002


title: acrylamide_mid_expose-4h_rep2

description:
gene expression data from L4 larvae
551-006-004


title: acrylamide_low_expose-4h_rep2

description:
gene expression data from L4 larvae
551-006-003


title: acrylamide_control_expose-8h_rep1

description:
gene expression data from L4 larvae
551-005-006


title: acrylamide_high_expose-8h_rep1

description:
gene expression data from L4 larvae
551-005-009


title: acrylamide_high_expose-4h_rep1

description:
gene expression data from L4 larvae
551-005-005


title: Ps_un_2hr_C

city: Richland

first: Katrina

middle: M

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description: Gene expression data from control JB6 cells

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

source_name: Ps vector, untreated, 2hr, replicate3

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Maintained in MEM + 5% fetal bovine serum + antibiotics and glutamax at preconfluence and passaged by trypsonation.  Stable shRNA transfection was achieved using Phoenix retroviral packing cell system and puromycin selection.  Western blot and in situ hybridization used to confirm >95% knockdown of AnxA2 RNA.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Normal growth media, cells were exposed to 10 and 100cGy using a Therapax X-RAD 320 system (6.5 cGy/min) equipped with 320 kV high stability X-ray generator, metal ceramic X-ray tube, variable X-ray beam collimator and no. 8 filter (Precision X-ray Incorporated, East Haven, CT).  Sham controls were also collected at 2hr and 24hr.

tag: cells

value: JB6 progenitor cells

tag: transfection

value: Ps vector

tag: treatment

value: untreated control

tag: time


title: acrylamide_low_expose-4h_rep1

description:
gene expression data from L4 larvae
551-005-003

value: L4 larvae


title: Ps_un_24hr_B

source_name: Ps vector, untreated, 24hr, replicate2


title: Ps_10_2hr_B

description: Gene expression data from JB6 cells exposed to ionizing radiation

source_name: Ps vector, 10cGy radiation, 2hr, replicate2

value: 10cGy radiation


title: acrylamide_control_expose-4h_rep1

description:
gene expression data from L4 larvae
551-005-002


title: Ps_un_24hr_A

source_name: Ps vector, untreated, 24hr, replicate1


title: acrylamide_control_expose-0h_rep1

description:
gene expression data from L4 larvae
551-005-001


title: Ps_un_2hr_B

source_name: Ps vector, untreated, 2hr, replicate2


title: Ps_10_24hr_A

source_name: Ps vector, 10cGy radiation, 24hr, replicate1


title: Ps_un_24hr_C

source_name: Ps vector, untreated, 24hr, replicate3


title: acrylamide_mid_expose-4h_rep1

description:
gene expression data from L4 larvae
551-005-004


title: Ps_10_2hr_C

source_name: Ps vector, 10cGy radiation, 2hr, replicate3


title: Ps_10_6hr_A

source_name: Ps vector, 10cGy radiation, 6hr, replicate1


title: Ps_10_6hr_C

source_name: Ps vector, 10cGy radiation, 6hr, replicate3


title: acrylamide_low_expose-8h_rep1

description:
gene expression data from L4 larvae
551-005-007


title: Ps_10_6hr_B

source_name: Ps vector, 10cGy radiation, 6hr, replicate2


title: Ps_10_24hr_C

source_name: Ps vector, 10cGy radiation, 24hr, replicate3


title: Ps_100_24hr_C

source_name: Ps vector, 100cGy radiation, 24hr, replicate3

value: 100cGy radiation


title: Ps_10_2hr_A

source_name: Ps vector, 10cGy radiation, 2hr, replicate1


title: Ps_100_24hr_A

source_name: Ps vector, 100cGy radiation, 24hr, replicate1


title: Ps_100_6hr_B

source_name: Ps vector, 100cGy radiation, 6hr, replicate2


title: Ps_100_24hr_B

source_name: Ps vector, 100cGy radiation, 24hr, replicate2


title: Ps_100_6hr_C

source_name: Ps vector, 100cGy radiation, 6hr, replicate3


title: Mouse embryonic fibroblasts. Set 1, primary, passage # <6 (methylation)

description: DNA Methylation Profile in Mo21

source_name: MIRA enriched samples

value: 129/sv (93%) with residual C57BL/6

source_name: Genomic Input DNA


title: Ps_100_6hr_A

source_name: Ps vector, 100cGy radiation, 6hr, replicate1


title: A2_un_24hr_C

source_name: AnxA2 shRNA, untreated, 24hr, replicate3

value: AnxA2 shRNA


title: A2_un_2hr_B

source_name: AnxA2 shRNA, untreated, 2hr, replicate2


title: Ps_100_2hr_B

source_name: Ps vector, 100cGy radiation, 2hr, replicate2


title: A2_10_24hr_A

source_name: AnxA2 shRNA, 10cGy radiation, 24hr, replicate1


title: A2_un_2hr_C

source_name: AnxA2 shRNA, untreated, 2hr, replicate3


title: A2_10_24hr_C

source_name: AnxA2 shRNA, 10cGy radiation, 24hr, replicate3


title: A2_un_2hr_A

source_name: AnxA2 shRNA, untreated, 2hr, replicate1


title: A2_10_2hr_C

source_name: AnxA2 shRNA, 10cGy radiation, 2hr, replicate3


title: A2_10_2hr_A

source_name: AnxA2 shRNA, 10cGy radiation, 2hr, replicate1


title: Ps_100_2hr_A

source_name: Ps vector, 100cGy radiation, 2hr, replicate1


title: A2_10_6hr_B

source_name: AnxA2 shRNA, 10cGy radiation, 6hr, replicate2


title: A2_100_24hr_C

source_name: AnxA2 shRNA, 100cGy radiation, 24hr, replicate3


title: Ps_100_2hr_C

source_name: Ps vector, 100cGy radiation, 2hr, replicate3


title: A2_100_2hr_C

source_name: AnxA2 shRNA, 100cGy radiation, 2hr, replicate3


title: A2_un_24hr_A

source_name: AnxA2 shRNA, untreated, 24hr, replicate1


title: A2_un_24hr_B

source_name: AnxA2 shRNA, untreated, 24hr, replicate2


title: A2_100_2hr_B

source_name: AnxA2 shRNA, 100cGy radiation, 2hr, replicate2


title: A2_100_6hr_A

source_name: AnxA2 shRNA, 100cGy radiation, 6hr, replicate1


title: A2_10_24hr_B

source_name: AnxA2 shRNA, 10cGy radiation, 24hr, replicate2


title: A2_100_24hr_A

source_name: AnxA2 shRNA, 100cGy radiation, 24hr, replicate1


title: A2_10_6hr_A

source_name: AnxA2 shRNA, 10cGy radiation, 6hr, replicate1


title: A2_10_6hr_C

source_name: AnxA2 shRNA, 10cGy radiation, 6hr, replicate3


title: A2_10_2hr_B

source_name: AnxA2 shRNA, 10cGy radiation, 2hr, replicate2


title: A2_100_6hr_B

source_name: AnxA2 shRNA, 100cGy radiation, 6hr, replicate2


title: A2_100_24hr_B

source_name: AnxA2 shRNA, 100cGy radiation, 24hr, replicate2


title: A2_100_6hr_C

source_name: AnxA2 shRNA, 100cGy radiation, 6hr, replicate3


title: A2_100_2hr_A

source_name: AnxA2 shRNA, 100cGy radiation, 2hr, replicate1


title: Lymph node patient 178

city: Darlinghurst

first: David

last: Ma

state: NSW

address: L8 Lowy Packer Building, 405 Liverpool St

department: Haematology research

country: Australia

institute: St Vincent's Hospital

hyb_protocol: Tagged probes in hybridisation buffer (3DNA 900MPX kit) were hybridised to a microarray overnight in a humidified slide chamber box After hybridization, slides were washed sequentially and hybridisation repeated using tagged Cy3 or Cy5 3DNA capture reagents

scan_protocol: Scanned on a GenePix 4000A scanner; fluorescent signals were quantified using GenePix Pro 3.0

data_processing: Data from GenePix result files were pre-processed by within-array print-tip Lowess normalisation using R.

source_name: Lymph node patient 178

label_protocol: Probe (with capture sequences) synthesis was carried out on 2ug of patient (Cy5) and reference (Cy3) total RNA using the 3DNA 900MPX kit (Genisphere) following manufacturer's instructions.

extract_protocol: Total RNA extracted using Trizol and RNeasy columns following manufacturer's instructions

tag: gender

value: Male

tag: age at diagnosis

tag: hospital

value: St Vincent's Hospital

tag: array batch

tag: diagnosis

value: FL

tag: subtype/fl grade

value: Grade 1

tag: nhl or chl

value: NHL

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects

value: PBMSC


title: Lymph node patient 172

source_name: Lymph node patient 172

value: cHL

value: Nodular sclerosing


title: Lymph node patient 180

source_name: Lymph node patient 180

value: Female

value: Grade 3


title: Lymph node patient 179

source_name: Lymph node patient 179

value: Grade 2


title: Lymph node patient 168

source_name: Lymph node patient 168

value: DLBCL

value: Non-GCB (BCL6 +,NUM-1 +)


title: Lymph node patient 164

source_name: Lymph node patient 164


title: Lymph node patient 175

source_name: Lymph node patient 175

value: Reactive


title: Lymph node patient 181

source_name: Lymph node patient 181


title: Lymph node patient 170

source_name: Lymph node patient 170

value: Non-GCB (NUM-1 +)


title: Lymph node patient 166

source_name: Lymph node patient 166


title: Lymph node patient 169

source_name: Lymph node patient 169


title: Lymph node patient 173

source_name: Lymph node patient 173


title: Lymph node patient 183

source_name: Lymph node patient 183


title: Lymph node patient 112

source_name: Lymph node patient 112

value: Mixed cellularity


title: Lymph node patient 118

source_name: Lymph node patient 118

value: block missing


title: Lymph node patient 150

source_name: Lymph node patient 150

value: Non-GCB


title: Lymph node patient 165

source_name: Lymph node patient 165

value: Male

value: St Vincent's Hospital


title: Lymph node patient 100

source_name: Lymph node patient 100

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects


title: Lymph node patient 182

source_name: Lymph node patient 182


title: Lymph node patient 177

source_name: Lymph node patient 177

value: FL

value: Grade 1


title: Lymph node patient 176

source_name: Lymph node patient 176

value: NHL

value: PBMSC


title: Lymph node patient 127

source_name: Lymph node patient 127


title: Lymph node patient 125

source_name: Lymph node patient 125


title: Lymph node patient 77

source_name: Lymph node patient 77


title: cadmium_high_expose-4h_rep1

description:
gene expression data from L4 larvae
552-004-005

source_name: whole organism

tag: developmental stage

value: L4 larvae

tag: exposure chemical

value: Cadmium

tag: exposure concentration (mg/l)

tag: exposure length (hours)


title: Lymph node patient 163

source_name: Lymph node patient 163

value: cHL

value: Lymphocyte depleted

tag: tissue


title: Lymph node patient 55

source_name: Lymph node patient 55

value: Female


title: Lymph node patient 47

source_name: Lymph node patient 47


title: Lymph node patient 151

source_name: Lymph node patient 151


title: Lymph node patient 27

source_name: Lymph node patient 27

value: Grade 3


title: Lymph node patient 39

source_name: Lymph node patient 39

value: DLBCL

value: GCB (CD10 +, BCL6 +)


title: Lymph node patient 155

source_name: Lymph node patient 155

value: Reactive


title: Lymph node patient 5

source_name: Lymph node patient 5


title: Lymph node patient 135

source_name: Lymph node patient 135

value: Newcastle Mater Misericordiae Hospital

value: Nodular sclerosing


title: Lymph node patient 132

source_name: Lymph node patient 132

value: Grade 2

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects


title: Lymph node patient 137

source_name: Lymph node patient 137

value: Male

value: not tested


title: Lymph node patient 113

source_name: Lymph node patient 113

value: St Vincent's Hospital

value: T cell lymphoma


title: Lymph node patient 161

source_name: Lymph node patient 161

value: FL

value: Grade 1

value: NHL

value: PBMSC


title: Lymph node patient 154

source_name: Lymph node patient 154

value: Small lymphocytic lymphoma


title: Lymph node patient 4

source_name: Lymph node patient 4

value: Female


title: Ps_un_2hr_A

source_name: Ps vector, untreated, 2hr, replicate1

value: JB6 progenitor cells

value: Ps vector

value: untreated control


title: Lymph node patient 111

source_name: Lymph node patient 111

value: Burkitt-like lymphoma


title: Lymph node patient 147

source_name: Lymph node patient 147


title: Lymph node patient 126

source_name: Lymph node patient 126

value: Reactive


title: Lymph node patient 121

source_name: Lymph node patient 121

value: cHL

value: Nodular sclerosing


title: Lymph node patient 116

source_name: Lymph node patient 116

value: Male


title: Lymph node patient 120

source_name: Lymph node patient 120

value: MALT


title: Lymph node patient 131

source_name: Lymph node patient 131

value: Newcastle Mater Misericordiae Hospital

value: DLBCL

value: not tested


title: Lymph node patient 157

source_name: Lymph node patient 157

value: St Vincent's Hospital


title: Lymph node patient 156

source_name: Lymph node patient 156

value: FL

value: Grade 1

value: NHL


title: Lymph node patient 160

source_name: Lymph node patient 160

value: PBMSC


title: Lymph node patient 110

source_name: Lymph node patient 110

value: Anaplastic lymphoma

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects


title: Lymph node patient 128

source_name: Lymph node patient 128


title: Lymph node patient 2

source_name: Lymph node patient 2

value: Non-GCB (BCL6 +, NUM-1 +)


title: Lymph node patient 3

source_name: Lymph node patient 3

value: Female

value: GCB (CD10 +, BCL6 +)


title: Lymph node patient 162

source_name: Lymph node patient 162

value: Burkitt-like lymphoma


title: Lymph node patient 158

source_name: Lymph node patient 158

value: Reactive


title: Lymph node patient 34

source_name: Lymph node patient 34


title: Lymph node patient 138

source_name: Lymph node patient 138


title: Lymph node patient 108

source_name: Lymph node patient 108


title: Lymph node patient 109

source_name: Lymph node patient 109

value: Grade 3


title: Lymph node patient 99

source_name: Lymph node patient 99


title: Lymph node patient 94

source_name: Lymph node patient 94

value: cHL

value: Nodular sclerosing


title: Lymph node patient 88

source_name: Lymph node patient 88

value: Male


title: Lymph node patient 89

source_name: Lymph node patient 89


title: Wt glucose 24h x ΔgprD glucose 48h Replicate 2

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

description:
Biological replicate 2 of 2
log2 Cy5/Cy3  gprD 48h Replicate 2

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

source_name: Wt_glucose 1%_48hr_Cy3

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40C.

growth_protocol: A. nidulans strains (Wt and ΔgprB and ΔgprD) were grown on minimal medium with glucose 1%  during  24 or 48 hours at 37 oC.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

tag: genotype/variation

value: wild type

tag: grown in

value: minimal media with glucose 1% for 48h

source_name: ΔgprD_glucose 1%_48hr_Cy5

value: ΔgprD


title: Lymph node patient 104

source_name: Lymph node patient 104

value: St Vincent's Hospital

value: not tested


title: Wt glucose 24h x ΔgprB glucose 24h Replicate 2

description:
Biological replicate 2 of 2
log2 Cy5/Cy3  gprB 24h Replicate2

source_name: Wt_glucose 1%_24hr_Cy3

value: minimal media with glucose 1% for 24h

source_name: ΔgprB_glucose 1%_24hr_Cy5

value: ΔgprB


title: Lymph node patient 91

source_name: Lymph node patient 91

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects

value: PBMSC


title: Wt glucose 24h x ΔgprB glucose 24h Replicate 1

description:
Biological replicate 1 of 2
log2 Cy5/Cy3  gprB 24h Replicate 1


title: Lymph node patient 106

source_name: Lymph node patient 106

value: FL

value: Grade 2

value: NHL


title: Lymph node patient 93

source_name: Lymph node patient 93

value: Female

value: T cell lymphoma


title: Wt glucose 24h x ΔgprD glucose 24h Replicate 1

description:
Biological replicate 1 of 2
log2 Cy5/Cy3  gprD 24h Replicate 1

source_name: ΔgprD_glucose 1%_24hr_Cy5


title: Lymph node patient 90

source_name: Lymph node patient 90

value: NK cell


title: Lymph node patient 101

source_name: Lymph node patient 101

value: Mantle cell


title: Wt glucose 24h x ΔgprD glucose 48h Replicate 1

description:
Biological replicate 1 of 2
log2 Cy5/Cy3  gprD 48h Replicate 1


title: Lymph node patient 102

source_name: Lymph node patient 102

value: Small lymphocytic lymphoma


title: Lymph node patient 84

source_name: Lymph node patient 84

value: Male

value: Reactive


title: Wt glucose 48h x ΔgprB glucose 48h Replicate 1

description:
Biological replicate 1 of 2
log2 Cy5/Cy3  gprB 48h Replicate 1

value: wild type

value: minimal media with glucose 1% for 48h

source_name: ΔgprB_glucose 1%_48hr_Cy5


title: DC_unstimulated_3_rep3_gene

city: Lisbon

first: Raquel

middle: Ferreira

last: Rodrigues

address: Av. Prof. Egas Moniz, Edifício Egas Moniz - Sala P3-A-16

country: Portugal

institute: Molecular Medicine Institute

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) using Affymetrix hybridization kit materials

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Microarray data pre-processing and summarization was performed using AltAnalyze application, which includes several rigorous statistical methods for data filtering, summarization and determination of differential splicing. Briefly, low quality probesets were removed according to detection above background (DABG) p-value and absolute expression values. Next, probesets were summarized with RMA algorithm and using the AltAnalyze annotations, derived from Ensembl and UCSC databases. Gene expression levels were determined using only probesets targeting constitutive exons.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.clf
Determination of overall gene level variation was assessed using linear models and empirical Bayes methods as implemented in ‘limma’ package. The B-statistics gives the log odds of differential expression and it requires an ‘a priori’ value for the estimated proportion of differentially expressed genes. To determine this value, we visually inspected the volcano plot, which compares biological significance (represented by fold-changes) with statistical significance (B-values), finding the value which enabled genes to be distinguished from the majority (logFC≤~1.585). Additionally, we verified the P-values corresponding to moderated F-statistics. Using the Benjamini and Hochberg method, all genes selected as differentially expressed had adjusted P-values<0.05.  Detection of alternative splicing variations were determined using splicing-index and FIRMA approache, calculating MiDAS and normalized intensity p-values (p-value <0.05).

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Elutriated human monocytes (Advanced Biotechnology Inc., Columbia, MD) were grown in RPMI with 10% fetal bovine serum (Life Technologies, Paisley, UK) supplemented with 1000 U/ml GM-CSF (R&D Systems, Minneapolis, MN) and 1000 U/ml IL-4 (R&D Systems Minneapolis, MN) for 7 days in 24 well plates (106 cells in 1 ml medium/well), and fed every 2 days after plating

extract_protocol: At each timepoint control and stimulated DCs were harvested and lysed using TRIzol® (Molecular Research Center Inc., Cincinnati, OH).

treatment_protocol: On day 7, DCs were harvested and aliquoted into 100mm plates at 107 cells/plate/timepoint and incubated at 37°C for 60 min. E.coli SD54 (ATCC, Middlesex, UK) [multiplicity of infection (MOI) 5:1] was then added to the DCs and cultured for 4 hours (timepoint 1 – T1), 8 hours (timepoint 2 – T2) and 18 hours (timepoint 3 – T3). Control DCs (non-stimulated cells) were collected at equivalent timepoints.

tag: cell type

value: Dendritic cells

value: not stimulated


title: Lymph node patient 76

source_name: Lymph node patient 76

value: St Vincent's Hospital

value: Anaplastic lymphoma


title: Wt glucose 24h x ΔgprD glucose 24h Replicate 2

description:
Biological replicate 2 of 2
log2 Cy5/Cy3  gprD 24h Replicate 2

value: minimal media with glucose 1% for 24h

value: ΔgprD


title: DC_stimulated_18h_gene

tag: treatment

value: stimulated with E.coli


title: DC_unstimulated_2_rep2_gene


title: Lymph node patient 82

source_name: Lymph node patient 82

value: FL

value: Grade 3

value: NHL

value: PBMSC


title: DC_unstimulated_1_rep1_gene


title: Wt glucose 48h x ΔgprB glucose 48h Replicate 2

description:
Biological replicate 2 of 2
log2 Cy5/Cy3  gprB 48h Replicate 2

source_name: Wt_glucose 1%_48hr_Cy3

value: ΔgprB


title: DC_stimulated_4h_gene


title: DC_stimulated_8h_gene


title: Lymph node patient 75

source_name: Lymph node patient 75

value: Female


title: Lymph node patient 74

source_name: Lymph node patient 74

value: Male


title: Lymph node patient 69

source_name: Lymph node patient 69

value: DLBCL

value: GCB (CD10 +, BCL6 +)


title: Lymph node patient 71

source_name: Lymph node patient 71

value: Reactive


title: Lymph node patient 73

source_name: Lymph node patient 73


title: Lepmyo/Lepmkyo rats, Leptin

city: Kyoto

first: MEGUMI

last: AIZAWA-ABE

address: Shokogin Kawahara-cho

department: Translational Research Center

institute: Kyoto University Hospital

description: Gene expression data from Lepmkyo/Lepmkyo rats with leptin administration intraperitonealy

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

organism: Rattus norvegicus

source_name: Lepob/Lepob rats with leptin administration intraperitonealy

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

value: male

tag: age

value: 20 weeks-old

tag: genetic background

value: liver

tag: genotype

value: Lepmyo/Lepmkyo

value: leptin


title: Lymph node patient 57

source_name: Lymph node patient 57

tag: gender

tag: age at diagnosis

tag: hospital

value: St Vincent's Hospital

value: cHL

value: Mixed cellularity

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects


title: Lymph node patient 60

source_name: Lymph node patient 60

tag: array batch

tag: diagnosis

tag: subtype/fl grade


title: 996-P-8hr-1

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road, Furong District

country: China

institute: Hunan Agricultural University

description:
Gene expression of rice spikelets of developmental stage7-9,8hr after 40 degree centigrade
rice spikelets of developmental stage7-9 at the middle of main panicle

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rice Genome Oligo Microarrays (015241) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, respectively), and the scan data with 100% and 10% PMT were merged automatically.

data_processing: The above hybridization signal data files in text format from the Feature Extraction Software were imported into GeneSpring GX (Agilent Technologies). The data were marked with specific flag such as P, A, M (representing detected, not detected and compromised, respectively) using the default parameter and algorithm, and then normalized by Quantile algorithm followed by the process of baseline to median of all samples. The normalized data from two replicates of each sample were log2 transformed, and the correlation coefficient of replicates was determined through hierarchical clustering using complete linkage algorithm as implemented TIGR MeV version 4.0.

organism: Oryza sativa

source_name: rice spikelets of developmental stage7-9,8hr after 40 degree centigrade,replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by QIAGEN RNeasy Mini Kit (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Heat-tolerant rice cultivar 996 was cultivated in the field until phase 7-9 of panicle development with half length of mature spikelets.

extract_protocol: Young spikelets with the phase 7-9 at the middle of main panicles were collected at the time point of 0min (as control), 20min, 1hr, 2hr, 4hr, and 8hr, respectively, after heat treatment, and frozen in liquid nitrogen immediately, and stored at -80°C for microarray hybridization.

treatment_protocol: The proper rice plants transplanted into pots were moved in a growth chamber (Binder, Tuttlingen, Germany) under the condition of 32°C with 80% humidity at day, and 28°C with 80% relative humidity at night for one day, and then at 40°C with 80% relative humidity and 600 μmol m-2 s-1 of photosynthetically active radiation for 8hr.

tag: cultivar

value: Heat-tolerant rice cultivar 996

tag: developmental stage

tag: stress

value: heat shock

tag: time


title: 996-P-2hr-2

description:
Gene expression of rice spikelets of developmental stage7-9,2hr after 40 degree centigrade
rice spikelets of developmental stage7-9 at the middle of main panicle

source_name: rice spikelets of developmental stage7-9,2hr after 40 degree centigrade,replicate 2

value: phase 7-9 of panicle development with half length of mature spikelets

tag: tissue

value: Young spikelets with the phase 7-9 at the middle of main panicles


title: Lymph node patient 64

source_name: Lymph node patient 64

value: Female

value: FL

value: Grade 1

tag: nhl or chl

value: NHL

value: PBMSC


title: 996-P-4hr-2

description:
Gene expression of rice spikelets of developmental stage7-9,4hr after 40 degree centigrade
rice spikelets of developmental stage7-9 at the middle of main panicle

source_name: rice spikelets of developmental stage7-9,4hr after 40 degree centigrade,replicate 2


title: Lymph node patient 58

source_name: Lymph node patient 58

value: Male

value: Grade 2


title: Lymph node patient 59

source_name: Lymph node patient 59


title: 996-P-8hr-2

source_name: rice spikelets of developmental stage7-9,8hr after 40 degree centigrade,replicate 2


title: Lymph node patient 63

source_name: Lymph node patient 63

value: Anaplastic lymphoma


title: WT rats, Saline

description: Gene expression data from WT rats with saline administration intraperitonealy

value: male

value: 20 weeks-old

value: liver

value: WT

value: saline


title: 996-P-4hr-1

source_name: rice spikelets of developmental stage7-9,4hr after 40 degree centigrade,replicate 1

value: Heat-tolerant rice cultivar 996


title: Lepmyo/Lepmkyo rats, Saline

description: Gene expression data from Lepmkyo/Lepmkyo rats with saline administration intraperitonealy

source_name: Lepob/Lepob rats with saline administration intraperitonealy

value: Lepmyo/Lepmkyo


title: Lymph node patient 56

source_name: Lymph node patient 56

value: St Vincent's Hospital

value: Marginal zone lymphoma


title: Lymph node patient 61

source_name: Lymph node patient 61


title: Lymph node patient 54

source_name: Lymph node patient 54


title: 996-P-2hr-1

source_name: rice spikelets of developmental stage7-9,2hr after 40 degree centigrade,replicate 1

value: phase 7-9 of panicle development with half length of mature spikelets

value: Young spikelets with the phase 7-9 at the middle of main panicles

value: heat shock


title: Lymph node patient 66

source_name: Lymph node patient 66

value: Female

value: cHL

value: Nodular sclerosing


title: Lymph node patient 70

source_name: Lymph node patient 70

value: Male

value: FL

value: Grade 3

value: NHL

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects

value: PBMSC


title: 996-P-1hr-2

description:
Gene expression of rice spikelets of developmental stage7-9,1hr after 40 degree centigrade
rice spikelets of developmental stage7-9 at the middle of main panicle

source_name: rice spikelets of developmental stage7-9,1hr after 40 degree centigrade,replicate 2


title: 996-P-20min-2

description:
Gene expression of rice spikelets of developmental stage7-9,20min after 40 degree centigrade
rice spikelets of developmental stage7-9 at the middle of main panicle

source_name: rice spikelets of developmental stage7-9,20min after 40 degree centigrade,replicate 2


title: Lymph node patient 53

source_name: Lymph node patient 53

value: Mantle cell


title: 996-P-1hr-1

source_name: rice spikelets of developmental stage7-9,1hr after 40 degree centigrade,replicate 1


title: 996-P-20min-1

source_name: rice spikelets of developmental stage7-9,20min after 40 degree centigrade,replicate 1


title: 996-P-ck-2

description:
Gene expression of rice spikelets of developmental stage7-9,0min after 40 degree centigrade
rice spikelets of developmental stage7-9 at the middle of main panicle

source_name: rice spikelets of developmental stage7-9,0min after 40 degree centigrade,replicate 2

value: control


title: Lymph node patient 50

source_name: Lymph node patient 50

value: Grade 2