title: Yer184c_ungapped_8mers

type: protein

city: Boston

first: Kevin

middle: F

last: Murphy

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) under LifterSlip cover slips (Erie Scientific) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 100 nM (unless otherwise specified) in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at 20°C. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. Slides were spun dry by centrifugation at 40 g for 5 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars at 20°C on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Separately, slides were scanned after primer extension to quantify the amount of incorporated Cy3-conjugated dUTP (543 nm ex, 570 nm em). Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: First, we normalize Alexa 488 signal by the Cy3 signal for each spot to account for differences in the total amount of double-stranded DNA. Because Cy3-dUTP incorporation is influenced both by the total number of adenines and the sequence context of each adenine, we perform a linear regression over all 41,944 variable spots to compute the relative contributions to the total signal of all trinucleotide combinations (followed by adenine). Using these regression coefficients, we calculate the ratio of observed-to-expected Cy3 intensity and use that as a normalization factor. Second, to correct for any possible non-uniformities in protein binding, we further adjust the Cy3-normalized Alexa 488 signals according to their positions on the microarray. We calculate the median normalized intensity of the 15 x 15 block centered on each spot and divide the spot’s signal by the ratio of the median within the block to the median over the entire chamber. Every non-palindromic 8-mer occurs on at least 32 spots in each chamber of our universal PBM and we provide several scores for each 8-mer in each experiment: (1) Median Intensity, (2) Z-Score, and (3) Enrichment Score (E-Score).

label: Alexa 488

molecule: protein

organism: Saccharomyces cerevisiae

source_name: Yeast Yer184c

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen).

extract_protocol: Full-length open reading frames and/or DNA binding domains were either cloned into the Gateway pDEST15 (N-terminal GST-tag) expression vector by recombinational cloning from previously created pENTR clones or were cloned by PCR amplification from genomic DNA and Gateway cloning into pDONR221. All proteins were produced from purified plasmids by in vitro transcription and translation using the PURExpress® In Vitro Protein Synthesis Kit according to manufacturer’s instructions. Glycerol was added to a final concentration of 38%, and proteins were stored at -20°C until further use. Western blots were performed for each protein to assess quality and to approximate protein concentration by visual inspection relative to a dilution series of recombinant GST standards.

tag: yeast transcription factor


title: Vhr1_ungapped_8mers

status: Public on Dec 10 2011

country: USA

source_name: Yeast Vhr1


title: Yap3_ungapped_8mers

source_name: Yeast Yap3


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT738_06_25_07]

type: RNA

city: Stanford

first: Maarten

last: Naesens

address: Pasteur Drive

institute: Stanford University

hyb_protocol: The cDNA fragments of all 120 biopsies were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays comprising more than 54,000 probe sets, covering more than 47,000 transcripts and variants, including 38,500 well-characterized human genes (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: The microarrays were scanned using GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing: For processing and normalization of the scanned images, dChip 2006 software was used, with perfect match [PM]/mismatch [MM] difference modeling and invariant set normalization

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Kidney transplant biopsy

label_protocol: biotin labeling using the OvationTM Biotin System (NuGEN Technologies, San Carlos, CA, USA)

extract_protocol: each kidney allograft biopsy (n=120), a separate biopsy core was placed in RNAlater (Ambion Inc, Austin, TX, USA) and stored at –20°C until RNA extraction. Total RNA was extracted from each biopsy using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Tacrolimus-Mycophenolate mofetil

tag: tissue

value: Kidney transplant biopsy

tag: i-ifta grade

tag: total i score

tag: cadi score

tag: time point

value: 00 months


title: Ylr278c_ungapped_8mers

source_name: Yeast Ylr278c


title: Ybr033w_ungapped_8mers

source_name: Yeast Ybr033w


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1238_2_18_09]

value: 24 months


title: Zap1_ungapped_8mers

source_name: Yeast Zap1


title: Upc2_ungapped_8mers

source_name: Yeast Upc2


title: Vhr2_ungapped_8mers

source_name: Yeast Vhr2


title: Yap2_ungapped_8mers

source_name: Yeast Yap2


title: Sut1_ungapped_8mers

source_name: Yeast Sut1


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT839_06_25_07]

value: 06 months


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT616_06_25_07]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1336_2_20_09]


title: Yap4_ungapped_8mers

source_name: Yeast Yap4


title: Ste12_ungapped_8mers

source_name: Yeast Ste12


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT1026_2_18_09_2]


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT1042_2_18_09]


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT861_2_6_09]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1098_2_18_09]


title: prostate cancer tissues

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

department: Pathology

institute: Wayne State University School of Medicine

hyb_protocol: Hybridization was performed overnight on a µparaflo microfluidic chip using a micro-circulation pump.

scan_protocol: hybridization images were collected  using a laser scaner (GenePix 40000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybemetics).

data_processing: data were analyzed by first substracting the backgound and then normaling the signals using a LOWESS filter 10.

source_name: prostate cancer tissue

label_protocol: 5 ug total RNA was size  frationated using a YM-100 Micocon centrifugal filter and small RNA (,300nt) isolated were 3'-extended with a polyA tail using polyA polymerase. An oligonucleotide tag specific-Cy3 was then ligated to the polyA tail.

growth_protocol: Retrospective archival pre-treatment prostate cancer patient tissues and matched adjacent normal prostate tissues were obtained

extract_protocol: Total RNA was isolated from formalin-fixed paraffin-embedded (FFPE) prostate tissues using miReasy FFPE kit (Qiagen)

treatment_protocol: These patients underwent radical prostatectomy

value: prostate tumor

tag: disease state

value: prostate cancer


title: matched normal prostate

source_name: Normal prostate tissue

value: prostate


title: Stp1_ungapped_8mers

source_name: Yeast Stp1


title: Stb5_ungapped_8mers

source_name: Yeast Stb5


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT897_2_16_09]


title: Stb4_ungapped_8mers

source_name: Yeast Stb4


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT702_06_25_07]


title: Mot3_ungapped_8mers

source_name: Yeast Mot3


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1374_2_20_09]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1349_2_6_09]


title: Sko1_ungapped_8mers

source_name: Yeast Sko1


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT977_06_28_07]

source_name: Kidney transplant biopsy


title: Nrg2_ungapped_8mers

source_name: Yeast Nrg2


title: Pdr3_ungapped_8mers

source_name: Yeast Pdr3


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT903_2_16_09]


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT819_06_25_07]


title: Msn1_ungapped_8mers

source_name: Yeast Msn1


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT790_2_16_09]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1289_2_18_09]


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT973_2_18_09]


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT814_05_25_07]


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT944_2_16_09]


title: Hap1_ungapped_8mers

source_name: Yeast Hap1


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1314_2_20_09]


title: Ecm22_ungapped_8mers

source_name: Yeast Ecm22


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT1018_B_2_24_09]


title: Hac1_ungapped_8mers

source_name: Yeast Hac1


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1385_2_20_09]


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT1118_2_6_09]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1207_2_18_09]


title: Hmlalpha2_ungapped_8mers

source_name: Yeast Hmlalpha2


title: Gcr1_ungapped_8mers

source_name: Yeast Gcr1


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT820_2_6_09]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1383_2_20_09]


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT707_1_2_16_09]


title: Abf1_ungapped_8mers

source_name: Yeast Abf1


title: Post-transplant rejection (Project 4) [KT1029_08_05_06]

description: Post-transplant rejection (Project 4)

value: Indication


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT1113_2_18_09]


title: Cst6_ungapped_8mers

source_name: Yeast Cst6


title: Post-transplant rejection (Project 4) [KT499_09_11_06]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT682]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT811]

description: Post-transplant rejection (Project 4)


title: dex24hr_2

city: Denver

first: Anthony

last: Gerber

state: CO

address: 1400 Jackson St

department: Medicine

institute: National Jewish Health

description: human airway smooth muscle gene expression, 24 hours dexamethasone

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays for 14 hours

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: raw signal intensities were extracted with Feature Extraction v9.1 software

source_name: cultured human airway smooth muscle, 24 hour dex treatment, replicate 2

label_protocol: RNA was labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol

growth_protocol: Primary cultured human airway smoothmuscle were grown in Hams/F12 with 10% FBS

extract_protocol: RNA was extracted using Trizol frolloed by purification with Invitrogne midilink columns

treatment_protocol: Cells were treated for 4 hours or 24 hours with 1 micromnolar dexamethasone dissolved in ethanol

tag: sample type

value: no history of asthma

value: smooth muscle cells

tag: treatment

value: dexamethasone for 24 hr


title: dex4hr_4

description: human airway smooth muscle gene expression, 4 hours dexamethasone

source_name: cultured human airway smooth muscle, 4 hour dex treatment, replicate 3

value: dexamethasone for 4 hr


title: Post-transplant rejection (Project 4) [KT777]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT821]

description: Post-transplant rejection (Project 4)


title: dex24hr_1

source_name: cultured human airway smooth muscle, 24 hour dex treatment, replicate 1


title: Post-transplant rejection (Project 4) [KT554]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT697]

description: Post-transplant rejection (Project 4)


title: dex24hr_3

source_name: cultured human airway smooth muscle, 24 hour dex treatment, replicate 3


title: dex4hr_3

source_name: cultured human airway smooth muscle, 4 hour dex treatment, replicate 2


title: Post-transplant rejection (Project 4) [KT610]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT592]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT941_09_12_06]

description: Post-transplant rejection (Project 4)


title: nodex_3

description: baseline human airway smooth muscle gene expression

source_name: cultured human airway smooth muscle, no treatment, replicate 3


title: Post-transplant rejection (Project 4) [KT628_09_11_06]

description: Post-transplant rejection (Project 4)

source_name: Kidney transplant biopsy


title: Post-transplant rejection (Project 4) [KT871_09_11_06]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT522]

description: Post-transplant rejection (Project 4)


title: dex4hr_2

source_name: cultured human airway smooth muscle, 4 hour dex treatment, replicate 1


title: Post-transplant rejection (Project 4) [KT1030_08_05_06]

description: Post-transplant rejection (Project 4)


title: nodex_4

source_name: cultured human airway smooth muscle, no treatment, replicate 4


title: Post-transplant rejection (Project 4) [KT688]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT881_09_11_06]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT659_09_11_06]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT867_09_11_06]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT1012_08_05_06]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT954]

description: Post-transplant rejection (Project 4)


title: arf6 arf8 stage 13 rep B

city: Chapel Hill

first: Jason

last: Reed

state: NC

address: CB #3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description: arf6 arf8 stage 13 rep B

hyb_protocol: Fragmented aRNA (15 µg) was then added to a hybridization cocktail (0.05 µg/µl fragmented aRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20).  aRNA (10 µg) was used for hybridization in a volume of 200 µl per slide.  ATH1 arrays (Redman et al., 2004)(Affymetrix, Santa Clara, CA) were hybridized for 16 hours at 45°C in the GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 450 (Affymetrix) using wash protocol EukGE-WS2v4, and arrays were scanned with the GeneChip Scanner 3000 7G Plus with autoloader.

data_processing: Affymetrix MAS 5.0 GeneChip Operating Software was used for washing, scanning and basic analysis.  Data were analyzed using Genespring GX 10.0.1 software.  Raw data were background corrected and normalized using the RMA algorithm with no baseline correction.

organism: Arabidopsis thaliana

source_name: arf6 arf8, stage 13 flowers

label_protocol: Total RNA (1000ng) was used to synthesize cDNA followed by aRNA.  The MessageAmp™ II-Biotin Enhanced Kit (Ambion) was used to generate biotinylated aRNA from the cDNA reaction.  The aRNA was then fragmented in fragmentation buffer from the Ambion kit at 94°C for 35 minutes before the chip hybridization.

growth_protocol: Wild-type plants were grown in 16 hour days/8 hour nights in a controlled environment growth chamber.  Light intensity was approximately 100 micromoles/m2sec.  Flowers were harvested in the morning between 2 and 4 hours after subjective dawn and frozen directly in liquid nitrogen.

extract_protocol: Frozen tissue was ground in a mortar and pestle.  RNA was isolated with Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA) or with RNeasy plant mini kits (Qiagen) according to manufacturer's instructions.

tag: ecotype

value: columbia

tag: genotype

value: arf6-2 arf8-3

tag: flower stage


title: nodex_1

source_name: cultured human airway smooth muscle, no treatment, replicate 1


title: Discovery set high CADI score (Project 1 + Project 4) [KT581_01_25_07]


title: nodex_2

source_name: cultured human airway smooth muscle, no treatment, replicate 2


title: experiment 2, control 3

city: London

first: Morgan

middle: L

last: Kleiber

state: Ontario

address: Biological and Geological Sciences Building

country: Canada

institute: University of Western Ontario

hyb_protocol: 5.5 ug of single-stranded cDNA was hybridized for 16 hours at 45 degrees C to the array.  Liquid handling steps were performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 using Command Console v1.1

data_processing: The data were analyzed with Partek Genomics Suite software v6.6.  Probes  were quantile-normalized using the GeneChip-Robust Multiarray Averaging and log2 transformed. All other settings were left as default.

organism: Mus musculus

source_name: brain, control (water-treated), P70 male

label_protocol: Single-stranded cDNA was synthesized using 200 ng of total RNA using Ambion WE Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and labelled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Mice were raised in standard same-sex housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature).  Mice were sacrificed at postnatal day 70.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and cleaned using Rneasy Mini kit (QIAGEN).

treatment_protocol: At postnatal day 70, mice were sacrificed by CO2 asphyxiation and whole brain tissue were dissected using RNAse-free tools.  Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.

value: control


title: Post-transplant rejection (Project 4) [KT948]

description: Post-transplant rejection (Project 4)


title: Post-transplant rejection (Project 4) [KT1009_09_12_06]

description: Post-transplant rejection (Project 4)


title: experiment 2, ethanol-treated 3

source_name: brain, ethanol-treated P70  male

value: ethanol


title: experiment 2, control 1


title: Discovery set low CADI score (Project 1 + Project 4) [KT477_02_07_07]

value: 03 months


title: Post-transplant rejection (Project 4) [KT966_09_11_06]

description: Post-transplant rejection (Project 4)

value: Kidney transplant biopsy


title: experiment 2, control 2


title: Wild type stage 13 rep B

description: Wild type stage 13 rep B

source_name: Wild type, stage 13 open flowers

value: Wild type


title: Discovery set high CADI score (Project 1 + Project 4) [KT331_02_07_07]

value: 12 months


title: experiment 1, control 2


title: experiment 1, ethanol-treated 1


title: Discovery set low CADI score (Project 1 + Project 4) [KT555_01_31_07]

value: 24 months


title: experiment 2, ethanol-treated 2


title: Discovery set high CADI score (Project 1 + Project 4) [KT422_01_31_07]


title: arf6 arf8 stage 12 rep B

description: arf6 arf8 stage 12 rep B

source_name: arf6 arf8, stage 12 buds


title: experiment 1, control 1


title: Discovery set high CADI score (Project 1 + Project 4) [KT691_01_24_07]


title: Discovery set low CADI score (Project 1 + Project 4) [KT952_02_08_07]


title: Discovery set low CADI score (Project 1 + Project 4) [KT614_02_06_07]


title: Discovery set high CADI score (Project 1 + Project 4) [KT1007_02_01_07]


title: Discovery set low CADI score (Project 1 + Project 4) [KT563_02_08_07]


title: Discovery set high CADI score (Project 1 + Project 4) [KT878_01_25_07]

value: 06 months


title: experiment 2, ethanol-treated 1


title: Discovery set low CADI score (Project 1 + Project 4) [KT474_01_31_07]


title: Discovery set high CADI score (Project 1 + Project 4) [KT703_01_26_07]


title: Discovery set high CADI score (Project 1 + Project 4) [KT296_02_07_07]


title: Discovery set low CADI score (Project 1 + Project 4) [KT519_01_26_07]


title: Discovery set high CADI score (Project 1 + Project 4) [KT409_01_31_07]


title: Discovery set high CADI score (Project 1 + Project 4) [KT646_01_31_07]


title: Discovery set low CADI score (Project 1 + Project 4) [KT418_02_07_07]


title: myb21 myb24 stage 12 rep B

description: myb21 myb24 stage 12 rep B

source_name: myb21 myb24, stage 12 buds


title: experiment 1, ethanol-treated 2


title: Mouse Cumulus_8hours_FSH/EGF-treated+293Hcontrol_rep4

city: Adelaide

first: Maxime

last: Sasseville

state: SA

address: Level 6, Medical school, Frome Road

country: Australia

institute: The Robinson Institute, University of Adelaide

description: expression data from mouse cumulus cells from cultured cumulus-oocyte complexes, follicle stimulating hormone/epidermal growth factor-treated with 293H control, 8 hours.

hyb_protocol: A total of 5ug of labelled cDNA was then hybridised to the Mouse Gene 1.0 ST Array GeneChip (Millenium Sciences) by preparing a cocktail probe (labelled cDNA at 0.025 μg/ul) that includes 1x hybridisation buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01 %(v/v) Tween-20), 0.1 mg/ml herring sperm DNA, 0.5 mg/ml BSA and 7% DMSO. A total hybridisation volume of 220 μl was prepared for each sample and 200 μl loaded into a Mouse Gene 1.0 ST Array GeneChip (Affimetrix).

scan_protocol: GeneChips were washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450 and then scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which is then used for generating the subsequent CEL file for analysis. The initial results were imported into Partek software (St. Louis, MO, USA), and were normalized using the Robust Multichip Average (RMA) method.

source_name: Mouse cumulus cells from cultured cumulus-oocyte complexes, follicle stimulating hormone/epidermal growth factor-treated with 293H control, 8 hours.

label_protocol: The fragmented single stranded cDNA was end-labelled using terminal deoxynucleotidyl transferase enzyme and the WT Terminal Labelling kit (Millenium Sciences).

growth_protocol: After recovery, ovaries were rinsed in Hepes-buffered tissue culture medium 199 (TCM199; MP Biomedicals, Ohio, USA) with 0.03% (w/v) polyvinyl alcohol and cilostamide (1 μM). Ovarian follicles were punctured with two syringes with 21 gauge needles and COC collected using a flame-pulled borosilicate Pasteur pipette under a 15X magnification. 20 COCs were cultured in 50 μL media drops under mineral oil overlay. COC culture media was bicarbonate-buffered α-Minimal Essential Medium with 0.03% polyvinyl alcohol, 11 mM glucose, 100 μM cysteamine, 100 IU/mL penicillin and 100 μg/mL streptomycin sulfate.

extract_protocol: RNA extraction of cumulus cells was performed with the “RNeasy Mini Kit” from Qiagen (Doncaster, Victoria, Australia) according to the manufacturer’s protocol. For microarray analysis, 8 biological replicates of the experimental conditions described above were performed and RNA extracted independently. Samples were pooled in pairs to generate four replicates with enough RNA for analysis.

treatment_protocol: whole COCs were treated with 20 ng/ml GDF9 or 293H control medium (0.125% v/v), with or without a combination of 50 mIU/ml FSH and 10 ng/ml EGF. After 8 hours of in vitro maturation, COCs were denuded by gentle pipetting, the oocytes were removed and the cumulus cells centrifuged at 16,000g for 1 minute and snap-frozen in liquid nitrogen until further analysis.

tag: gender

value: female

tag: strain

tag: age

value: 21 to 26 day old

tag: gonadotropin priming regimen

value: 44 hours post equine chorionic gonadotropin treatment (eCG (5 IU))

tag: cell type

value: cumulus cells

tag: agent


title: Discovery set low CADI score (Project 1 + Project 4) [KT664_02_01_07]

tag: tissue


title: Mouse Cumulus_8hours_FSH/EGF-treated+293Hcontrol_rep1


title: Mouse Cumulus_8hours_FSH/EGF-treated+293Hcontrol_rep2


title: Discovery set low CADI score (Project 1 + Project 4) [KT955_01_26_07]

tag: i-ifta grade


title: Mouse Cumulus_8hours_FSH/EGF-treated+293Hcontrol_rep3


title: Mouse Cumulus_8hours_GDF9-treated_rep4

description: expression data from mouse cumulus cells from cultured cumulus-oocyte complexes, growth differentiation factor 9-treated, 8 hours.

source_name: Mouse cumulus cells from cultured cumulus-oocyte complexes, growth differentiation factor 9-treated, 8 hours.


title: Healthy 0 h Control (Cy3)_O3 72 h (Cy5)_Pooled 1

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: GenePix 4000B

data_processing: Genepix ver. 4.0 quantitative microarray analysis application program

organism: Oryza sativa

source_name: Ozone Control 0 h

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Plants were grown in growth chamber in soil for 14 days

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: control, filtered

tag: cultivar

value: Nipponbare

value: 2 wk

tag: time

source_name: Ozone fumigated 72 h

value: ozone


title: Mouse Cumulus_8hours_GDF9-treated_rep3


title: Mouse Cumulus_8hours_GDF9-treated_rep2


title: Healthy 0 h Control (Cy3)_O3 48 h (Cy5)_Pooled 1

treatment_protocol: control, filtered air

source_name: Ozone fumigated 48 h


title: Healthy 0 h Control (Cy5)_O3 48 h (Cy3)_Pooled 2


title: Healthy 0 h Control (Cy5)_O3 72 h (Cy3)_Pooled 2


title: Discovery set high CADI score (Project 1 + Project 4) [KT466_02_01_07]

tag: total i score

tag: cadi score

tag: time point


title: Mouse Cumulus_8hours_293Hcontrol_rep3

description: expression data from mouse cumulus cells from cultured cumulus-oocyte complexes, 293H control-treated, 8 hours.

source_name: Mouse cumulus cells from cultured cumulus-oocyte complexes, 293H control-treated, 8 hours.


title: Discovery set low CADI score (Project 1 + Project 4) [KT1125_02_08_07]

source_name: Kidney transplant biopsy


title: Mouse Cumulus_8hours_293Hcontrol_rep2


title: Mouse Cumulus_8hours_293Hcontrol_rep4


title: neural cell_virus control_Rep1

city: Mashhad

first: Hamid

middle: Reza

last: Pourianfar

state: Khorasan Razavi

address: Azadi Square

country: Iran

institute: Current Address: Iranian Academic Centre for Education, Culture and Research, Mashhad Branch

description: Gene expression data from EV71-infected cells not treated with Hep at 72 hours post infection

hyb_protocol: Hybridization was performed into hybridization oven at 45±C, 60 rpm for 17 ± 1 hour followed by washing and scanning the arrays

scan_protocol: 1. Clean glass from chip, put tape on septa and place chip in the autoloader  2. Start Scanner  3. After Scan, check controls at corners and grid alignment  4. Transfer data out of AGCC as .DTT files  5. Run .CEL files through Expression Console to generate .CHP files for QC  6. Backup all data to DVD, including flat files and DTT for archiving

data_processing: Since Affymetrix does not put mismatch probes in the newer arrays such as GeneChip Human Gene 1.0 ST array, background noise was handled by a background-correction step during the normalization.  Partek Genomics Suite version 6.5 was utilized to import and analyze raw data from the array cells and also import latest version of annotation from Affymetrix website (as of 8/8/2011).  Using one-step Tukey’s bi-weight, normalized values of multiple probes for the same gene (at each replication) were summarized into a single value representing consensus level of expression for that gene.  Then, the following five contrasts were made: Hep vs. CC; VC vs. CC; Cyto vs CC; Hep vs. VC; and Hep vs. Cyto.  For each contrast, only samples from the two target groups were included.  A single factor ANOVA inside Partek was applied to generate P values for each gene.  Then, these P values were adjusted by Benjamini and Hochberg’s Multiple testing correction to reduce false discovery rate (FDR).

source_name: EV71-infected cells without treatment with Hep

label_protocol: The Affymetrix GeneChip WT Terminal Labeling Kit (PN 900671 or equivalent) is used for the fragmentation and labeling of the cDNA

growth_protocol: SK-N-SH cells were maintained in Dulbecco’s Modified Eagle’s Medium with high glucose supplemented with 10% heat inactivated Fetal Bovine Serum.  The cells were not passaged more than 20 times after reviving from the original stock.  A low passage clinical isolate of EV71 (the isolate number 99018233, from Victorian Infectious Disease Reference Laboratories) was propagated in 80% confluent monolayers of Vero cells using serum-free DMEM

extract_protocol: total RNA was isolated and purified from SK-N-SH cells of each of the four conditions using the RNeasy Mini Kit of Qiagene,

treatment_protocol: SK-N-SH cells were seeded at 1.3 × 105 cells/1600 in 12-well plates and incubated at 37ºC/5% CO2 for two days.  After reaching 80% cell confluency, the media was aspirated followed by addition of 1600 ul of each of the following conditions: cell control, virus control at 100 TCID50, compound control, and treatment (Hep-treated cells infected with 100 TCID50 of EV71), each in three wells (two wells for antiviral or cytotoxicity assays, one well for RNA isolation).  Each experiment was independently replicated three times.  Following incubation at 37ºC/5% CO2 for a further 48 hours, antiviral and cytotoxicity assays were quantified by MTT.  At the same time, total RNA was isolated from allocated wells.

tag: cell line

value: SK-N-SH

value: Human Caucasian neuroblastoma

tag: morphology

value: Epithelial


title: Mouse Cumulus_8hours_GDF9-treated_rep1


title: EB31 90d LPL

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: Lamina-Propria Lymphocytes Gene Expression Data from EB31 animal at day 90 (post SIV infection)

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

scan_protocol: GeneChips were scanned using a GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Macaca mulatta

source_name: intestine

label_protocol: 1 ug total RNA from all samples was used for RNA amplification; Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug aRNA

growth_protocol: Samples were extracted from live, anesthetized animals via resection surgery

extract_protocol: Tissues from pinch biopsies were ground in a pessel/mortar and RNA isolated using the RNAeasy kit. Samples were then treated with Ambion DNAfree in order to remove residual DNA

treatment_protocol: The complexity of the intestinal sample was reduced by fractionating it into LPL, IEL, stroma/matrix and the epithelium

value: Lamina-Propria Lymphocytes

tag: infection

value: SIV

tag: subject


title: ED13 21d LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from ED13 animal at day 21 (post SIV infection)


title: EB31 Pre LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from EB31 animal at day 0 (prior to SIV infection)

value: baseline

value: 0 d


title: neural cell_treatment_Rep3

description: Gene expression data from EV71-infected cells treated with Hep at 72 hours post infection

source_name: EV71-infected cells treated with Hep


title: MCF7-I0 weakly invasive cells

city: Coleraine

last: Bjourson

state: Northern Ireland

address: Cromore Road

department: School of Biomedical Sciences

country: United Kingdom

institute: University of Ulster

description: Gene expression data from parental MCF7 breast cancer cell line (3 replicates).

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data normalization was performed using GeneSpring software. All 3 unscaled CHP files were used for the analysis. Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. A per-gene normalization to specific samples (control samples) was applied. The control value was the mean of the three control replicates. The Cross Gene Error Model (CGEM) was established based on replicates.

source_name: Weakly invasive parental MCF7 breast cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneCHip Expression Analysis, Technical Manual, 701021 Rev. 5).

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

treatment_protocol: MCF-7 cell lines were obtained from the European Collection of Cell Cultures (ECACC) and maintained at 37°C in a 5% CO2, 95% air humidified atmosphere temperature controlled incubator (RS Biotech, Galaxy S). Cell lines were maintained in Dulbecos Modified Eagles Medium (DMEM) containing 1g/L D-glucose, L-glutamine, pyruvate and supplemented with 10% foetal bovine serum (FBS), 1% penicillin/streptomycin and 1% non-essential amino acids (all Gibco).

value: breast cancer

tag: subclone


title: Discovery set high CADI score (Project 1 + Project 4) [KT596_01_25_07]

value: Kidney transplant biopsy

value: 12 months


title: neural cell_treatment_Rep2


title: neural cell_treatment_Rep1


title: EB31 21d LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from EB31 animal at day 21 (post SIV infection)


title: DN85 90d LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from DN85 animal at day 90 (post SIV infection)


title: neural cell_compound control_Rep2

description: Gene expression data from cells only treated with Hep at 72 hours post infection

source_name: cells treated only with Hep


title: neural cell_virus control_Rep2


title: Mouse Cumulus_8hours_293Hcontrol_rep1

tag: gender

value: female

tag: strain


title: neural cell_compound control_Rep3


title: ED13 90d LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from ED13 animal at day 90 (post SIV infection)


title: neural cell_virus control_Rep3


title: ED13 Pre LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from ED13 animal at day 0 (prior to SIV infection)


title: DN85 Pre LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from DN85 animal at day 0 (prior to SIV infection)


title: DN85 21d LPL

description: Lamina-Propria Lymphocytes Gene Expression Data from DN85 animal at day 21 (post SIV infection)


title: neural cell_compound control_Rep1


title: neural cell_cell control_Rep2

description: Gene expression data from cells not infected or treated at 72 hours post infection

source_name: not infected or treated cells


title: S. mutans UA159 mono-species biofilm 3

status: Public on Dec 09 2011

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

country: Germany

institute: hospital university rostock

description: This sample is of wild-type S. mutans UA159 biofilm.

hyb_protocol: Hybridization was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)

scan_protocol: Scanning was performed with the DNA Microarray Scanner (Agilent) at a resolution of 5 µm and NimbleScanTM version 2.4 software

data_processing: The raw data (.pair file) were checked for inhomogenous hybridization. Probes with a high intensity caused by wash artefacts were deleted. In the case of GSM714207-GSM714212, remaining technical replicates were averaged. In the case of GSM714213-GSM714218, probes not belonging to S. mutans or RANDOM were excluded from analysis. Additionally, probes identified as interspecies cross-hybridizing biological false positive probes, identified on GSM714212, were also excluded from analysis. The remaining probes were quantile normalized, background corrected and sumarized with NimbleScan Software RMA, and subsequently analysed with GeneSpring GX 11.0, Agilent Technologies.

organism: Streptococcus mutans UA159

source_name: S. mutans UA159

label_protocol: Labeling with Cy3 was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)

growth_protocol: Bacterial cells were cultured under anaerobic conditions (10% CO2; 10% H2; 80% N2) at 37°C in chemical defined medium supplemented with 50 mM sucrose or in artificial saliva supplemented with 50 mM galactose for 24 h.

extract_protocol: RNA was extracted out of 100 mg harvested cells using the Fast RNA Pro Blue Kit (MP Biomedicals, Solon, Ohio, USA) following manufacturers instructions. Removal of DNA was performed by DNase digenstion for 1 hour at 37 °C.

value: S. mutans UA159

tag: genotype

value: wt

tag: single species biofilm / culture

value: yes

tag: two-species biofilm

value: no


title: S. mutans UA159 mono-species biofilm 2


title: S. mutans UA159 mono-species biofilm 1


title: S. mutans UA159 two-species biofilm with S. mitis ATCC 11843 1

description: This sample is of wild-type S. mutans UA159 / S. mitis ATCC 11843 co-culture biofilm.

organism:
Streptococcus mitis
Streptococcus mutans UA159

source_name: S. mutans UA159 / S.mitis ATCC 11843

value: S. mutans UA159 / S.mitis ATCC 11843


title: neural cells_cell control_Rep 2

tag: tissue


title: S. mutans UA159 two-species biofilm with S. mitis ATCC 11843 2


title: neural cells_cell control_Rep 1


title: S. mutans UA159 two-species biofilm with S. mitis ATCC 11843 3


title: Chimpanzee - cerebellar cortex - 45 days old

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 45 days old Chimpanzee individual
Ptr_45days_batch1

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols. The RNA extraction and hybridization was carried out in two batches for human and macaque samples. Batches were relatively balanced with respect to age.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. To identify array probes that contain mismatches among species, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the human (hg18), chimpanzee (panTro2), and rhesus macaque (rheMac2) genomes using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included probes which matched all three genomes perfectly and at a single location (27% of the original array probes). Intensities of probes that passed this mask were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. We considered a transcript as “expressed” if it was detected in >70% of human, chimpanzee or macaque individuals.

organism: Pan troglodytes

source_name: Dissected Chimpanzee post-mortem cerebellar cortex

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions. RNA integrity number (RIN) was measured by the Agilent® 2100 Bioanalyzer.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland). Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cerebellar cortex.

tag: age

value: 45 days

value: f

value: cerebellar cortex of the brain

tag: post-mortem interval (hours)

tag: rna integrity number (rin)

tag: batch


title: Chimpanzee - cerebellar cortex - 1 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 1 days old Chimpanzee individual
Ptr_1days_batch1

value: 1 days


title: Chimpanzee - cerebellar cortex - 525 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 525 days old Chimpanzee individual
Ptr_525days_batch1

value: 525 days


title: Chimpanzee - cerebellar cortex - 2313 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 2313 days old Chimpanzee individual
Ptr_2313days_batch1

value: 2313 days


title: Chimpanzee - cerebellar cortex - 8 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 8 days old Chimpanzee individual
Ptr_8days_batch1

value: 8 days

value: m


title: Chimpanzee - cerebellar cortex - 7 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 7 days old Chimpanzee individual
Ptr_7days_batch1

value: 7 days


title: Chimpanzee - cerebellar cortex - 39 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 39 days old Chimpanzee individual
Ptr_39days_batch1

value: 39 days


title: 14228075 - col0 Stressed 1 vs col0 Acclimated 1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant

hyb_protocol: col0 Acclimated 1 Cy5 / col0 Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

source_name: col0 Acclimated 1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 4 weeks under control conditions. Plants were then transfered for two days in a chamber at 450 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 16°C/19°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Acclimated conditions : Media=compost hygrometry=70-80 % Temperature=16°C/19°C Light=450 µmol m-2s-1

extract_protocol: col0 Acclimated 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: Name:Acclimated - environmental treatment - light,light:time 2day . Plants of Arabidopsis thaliana were grown for 4 or 8 weeks for respectively the Col0 and the ch1 mutant, under control conditions. Plants were then transfered for two days in a chamber at 450 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 16°C/19°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light.

tag: ecotype

value: columbia (col0)

tag: genotype/variation

value: wild type

tag: boyes leaf development stage (boyes et al. plant cell 2001)

source_name: col0 Stressed 1

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 4 weeks under control conditions. Plants were then transfered for two days in a chamber at 900 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 10°C/14°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Stress conditions : Media=compost hygrometry=70-80% Temperature=10°C/14°C Light=900 µmol m-2s-1

extract_protocol: col0 Stressed 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: Name:Stressed - environmental treatment - light,light:time 2day .  Plants of Arabidopsis thaliana were grown for 4 or 8 weeks for respectively the Col0 and the ch1 mutant, under control conditions. Plants were then transfered for two days in a chamber at 900 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 10°C/14°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light.


title: 14228089 - col0 Stressed 3 vs col0 Acclimated-Stressed 3

hyb_protocol: col0 Acclimated-Stressed 3 Cy5 / col0 Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Acclimated-Stressed 3

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 4 weeks for respectively under control conditions. Plants were then transfered for two days under acclimation conditions and two days under stress conditions. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Acclimation conditions: Media=compost hygrometry=70-80 % Temperature=16°C/19°C Ligh=450 µmol m-2s-1 Stress conditions : Media=compost hygrometry=70-80% Temperature=10°C/14°C Light=900 µmol m-2s-1

extract_protocol: col0 Acclimated-Stressed 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: Name:Acclimated-Stressed - environmental treatment - light,light:time 2day . Plants of Arabidopsis thaliana were grown for 4 or 8 weeks for respectively the Col0 and the ch1 mutant, under control conditions. Plants were then transfered for two days under acclimation conditions and two days under stress conditions. Plants were harvested at 11 am after two hours of light.

source_name: col0 Stressed 3

extract_protocol: col0 Stressed 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: Chimpanzee - cerebellar cortex - 4415 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 4415 days old Chimpanzee individual
Ptr_4415days_batch1

value: 4415 days


title: 14228074 - col0 Acclimated 1 vs col0 Stressed 1

hyb_protocol: col0 Stressed 1 Cy5 / col0 Acclimated 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Chimpanzee - cerebellar cortex - 4361 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 4361 days old Chimpanzee individual
Ptr_4361days_batch1

value: 4361 days


title: Chimpanzee - cerebellar cortex - 16131 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 16131 days old Chimpanzee individual
Ptr_16131days_batch1


title: 14228092 - col0 Stressed 2 vs col0 Acclimated 2

hyb_protocol: col0 Acclimated 2 Cy5 / col0 Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Acclimated 2

extract_protocol: col0 Acclimated 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

source_name: col0 Stressed 2

extract_protocol: col0 Stressed 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: 14228090 - col0 Acclimated-Stressed 3 vs col0 Stressed 3

hyb_protocol: col0 Stressed 3 Cy5 / col0 Acclimated-Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14227576 - col0 Acclimated-Stressed 1 vs col0 Stressed 1

hyb_protocol: col0 Stressed 1 Cy5 / col0 Acclimated-Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Acclimated-Stressed 1

extract_protocol: col0 Acclimated-Stressed 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: Chimpanzee - cerebellar cortex - 0 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 0 days old Chimpanzee individual
Ptr_0days_batch1

value: 0 days


title: Chimpanzee - cerebellar cortex - 12784 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 12784 days old Chimpanzee individual
Ptr_12784days_batch1


title: Rhesus macaque - cerebellar cortex - 9518 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 9518 days old Rhesus macaque individual
Mml_9518days_batch1

source_name: Dissected Rhesus macaque post-mortem cerebellar cortex

value: 9518 days


title: 14228091 - col0 Acclimated 2 vs col0 Stressed 2

hyb_protocol: col0 Stressed 2 Cy5 / col0 Acclimated 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228087 - col0 Acclimated 3 vs col0 Stressed 3

hyb_protocol: col0 Stressed 3 Cy5 / col0 Acclimated 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Acclimated 3

extract_protocol: col0 Acclimated 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: 14227577 - col0 Stressed 1 vs col0 Acclimated-Stressed 1

hyb_protocol: col0 Acclimated-Stressed 1 Cy5 / col0 Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228086 - col0 Stressed 3 vs col0 Control 3

hyb_protocol: col0 Control 3 Cy5 / col0 Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Control 3

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 4 weeks under controlled conditions : 250 µmol m-2 s-1, photoperiod of 8h/16h, temperature of 22°C/18°C and 55% of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1

extract_protocol: col0 Control 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: no treatment


title: Rhesus macaque - cerebellar cortex - 9291 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 9291 days old Rhesus macaque individual
Mml_9291days_batch2

value: 9291 days


title: 14228088 - col0 Stressed 3 vs col0 Acclimated 3

hyb_protocol: col0 Acclimated 3 Cy5 / col0 Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228085 - col0 Control 3 vs col0 Stressed 3

hyb_protocol: col0 Stressed 3 Cy5 / col0 Control 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rhesus macaque - cerebellar cortex - 7391 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 7391 days old Rhesus macaque individual
Mml_7391days_batch1

value: 7391 days


title: Rhesus macaque - cerebellar cortex - 8104 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 8104 days old Rhesus macaque individual
Mml_8104days_batch1

value: 8104 days


title: Rhesus macaque - cerebellar cortex - 739 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 739 days old Rhesus macaque individual
Mml_739days_batch1

value: 739 days

value: cerebellar cortex of the brain


title: Rhesus macaque - cerebellar cortex - 607 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 607 days old Rhesus macaque individual
Mml_607days_batch2

value: 607 days


title: 14228083 - col0 Control 3 vs col0 Acclimated 3

hyb_protocol: col0 Acclimated 3 Cy5 / col0 Control 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rhesus macaque - cerebellar cortex - 449 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 449 days old Rhesus macaque individual
Mml_449days_batch2

value: 449 days


title: Rhesus macaque - cerebellar cortex - 237 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 237 days old Rhesus macaque individual
Mml_237days_batch2

value: 237 days


title: 14228073 - col0 Stressed 1 vs col0 Control 1

hyb_protocol: col0 Control 1 Cy5 / col0 Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Control 1

extract_protocol: col0 Control 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: 14228071 - col0 Acclimated 1 vs col0 Control 1

hyb_protocol: col0 Control 1 Cy5 / col0 Acclimated 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rhesus macaque - cerebellar cortex - 3389 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 3389 days old Rhesus macaque individual
Mml_3389days_batch1

value: 3389 days

value: m


title: 14228084 - col0 Acclimated 3 vs col0 Control 3

hyb_protocol: col0 Control 3 Cy5 / col0 Acclimated 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228072 - col0 Control 1 vs col0 Stressed 1

hyb_protocol: col0 Stressed 1 Cy5 / col0 Control 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228070 - col0 Control 1 vs col0 Acclimated 1

hyb_protocol: col0 Acclimated 1 Cy5 / col0 Control 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rhesus macaque - cerebellar cortex - 7 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 7 days old Rhesus macaque individual
Mml_7days_batch2

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols. The RNA extraction and hybridization was carried out in two batches for human and macaque samples. Batches were relatively balanced with respect to age.

value: 7 days


title: Rhesus macaque - cerebellar cortex - 2936 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 2936 days old Rhesus macaque individual
Mml_2936days_batch2

value: 2936 days


title: Rhesus macaque - cerebellar cortex - 5478 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 5478 days old Rhesus macaque individual
Mml_5478days_batch2

value: 5478 days


title: S. sanguinis SK36 mono-species biofilm

description: This sample is of wild-type S. sanguinis SK36 biofilm.

hyb_protocol: Hybridization was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)

organism: Streptococcus sanguinis SK36

source_name: S. sanguinis SK36

value: S. sanguinis SK36

value: wt

value: yes

value: no


title: 14228081 - col0 Stressed 2 vs col0 Acclimated-Stressed 2

description: To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant

hyb_protocol: col0 Acclimated-Stressed 2 Cy5 / col0 Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Acclimated-Stressed 2

extract_protocol: col0 Acclimated-Stressed 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

value: columbia (col0)

value: wild type


title: Rhesus macaque - cerebellar cortex - 310 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 310 days old Rhesus macaque individual
Mml_310days_batch1

value: 310 days


title: 14228080 - col0 Acclimated-Stressed 2 vs col0 Stressed 2

hyb_protocol: col0 Stressed 2 Cy5 / col0 Acclimated-Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rhesus macaque - cerebellar cortex - -30 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a -30 days old Rhesus macaque individual
Mml_-30days_batch2

value: -30 days (prenatal individual; predicted to be ~15 days before birth)


title: P. gingivalis W83 monolayer

description: This sample is of wild-type P. gingivalis W83 adherent cells/monolayer.

organism: Porphyromonas gingivalis W83

source_name: P. gingivalis W83

value: P. gingivalis W83


title: S. mitis ATCC 11843 monospecies culture

description: This sample is of wild-type S. mitis ATCC 11843.

organism: Streptococcus mitis

source_name: S. mitis ATCC 11843

value: S. mitis ATCC 11843


title: S. mutans UA159 mono-species biofilm

description: This sample is of wild-type S. mutans UA159 biofilm.

source_name: S. mutans UA159

value: S. mutans UA159


title: Rhesus macaque - cerebellar cortex - 22 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 22 days old Rhesus macaque individual
Mml_22days_batch2

value: 22 days

value: cerebellar cortex of the brain


title: Discovery set low CADI score (Project 1 + Project 4) [KT387_02_07_07]

hyb_protocol: The cDNA fragments of all 120 biopsies were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays comprising more than 54,000 probe sets, covering more than 47,000 transcripts and variants, including 38,500 well-characterized human genes (Affymetrix Inc., Santa Clara, CA, USA).

source_name: Kidney transplant biopsy

extract_protocol: each kidney allograft biopsy (n=120), a separate biopsy core was placed in RNAlater (Ambion Inc, Austin, TX, USA) and stored at –20°C until RNA extraction. Total RNA was extracted from each biopsy using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).

value: Kidney transplant biopsy

tag: i-ifta grade

tag: total i score

tag: cadi score

tag: time point

value: 24 months


title: Rhesus macaque - cerebellar cortex - 20 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 20 days old Rhesus macaque individual
Mml_20days_batch1

value: 20 days

tag: gender

value: m


title: Rhesus macaque - cerebellar cortex - 207 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 207 days old Rhesus macaque individual
Mml_207days_batch1

value: 207 days


title: Rhesus macaque - cerebellar cortex - 179 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 179 days old Rhesus macaque individual
Mml_179days_batch2

value: 179 days


title: ∆relA,∆spoT, rep3

type: mixed

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

description: JH3370 3

hyb_protocol: Slides were blocked with DCE according to protocol at PMID 11266573. For hybridization and washing protocols, see  http://www.ifr.ac.uk/safety/Microarrays/protocols.html

scan_protocol: Axon GenePix4000A 10 µm resolution scan. See http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated using BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using block median normalization.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium JH3370 (SL1344 ∆relA,∆spoT)

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: Cultures were grown aerobically in LB to early stationary phase (OD 600=2.3).

extract_protocol: Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: strain

value: ∆relA,∆spoT

tag: growth phase

value: early stationary

molecule: genomic DNA

source_name: S. Typhimurium genomic DNA


title: ∆relA,∆spoT, rep4

description: JH3370 4

tag: genotype


title: Rhesus macaque - cerebellar cortex - -15 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a -15 days old Rhesus macaque individual
Mml_-15days_batch2

value: -15 days (prenatal individual; predicted to be ~15 days before birth)


title: ∆relA,∆spoT, rep2

description: JH3370 2

value: wild type


title: ∆relA,∆spoT, rep1

description: JH3370 1