title: mesenteric arterial tree, WT mouse, replicate 3, female young

status: Public on Sep 01 2010

type: RNA

city: Montreal

first: Stefania

last: Simeone

state: Quebec

address: 3755 Côte Ste-Catherine Road

department: Hypertension and Vascular Research Unit

country: Canada

institute: Lady Davis Institute for Medical Research

description: FEMALE YOUNG 7

hyb_protocol: standard Illumina hybridization protocol

scan_protocol: standard Illumina scanning protocol

data_processing: The data was normalised using the lumi algorithm in FlexArray analysis software (RMA background adjustment, variance stabililizing tranformation, robust splin normalization)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mesenteric arterial tree, WT mouse

label_protocol: Biotinylated cRNA were prepared with the Illumina Total Prep RNA amplification kit for Illumina arrays

extract_protocol: Tissue was collected and stored in RNAlater overnight at 4°C with gentle agitation. Fat was removed from tissue in RNA later. RNA was extracted from cleaned arteries with Trizol reagent and chlorofom, followed by Qiagen RNeasy MinElute Cleanup Kit spin columns in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: strain

tag: genome/variation

value: wild type

tag: gender

value: female

tag: age

value: 7 weeks

tag: tissue

value: mesenteric arterial tree


title: mesenteric arterial tree, WT mouse, replicate 3, male mature

description: MALE MATURE 7

value: male

value: 7.7 months


title: mesenteric arterial tree, eET-1 mouse, replicate 1, male mature

description: MALE MATURE 1

source_name: mesenteric arterial tree, eET-1 mouse

value: 6.7 months


title: mesenteric arterial tree, WT mouse, replicate 4, female young

description: FEMALE YOUNG 8

value: 6 weeks


title: mesenteric arterial tree, eET-1 mouse, replicate 1, female young

description: FEMALE YOUNG 1


title: Leaf Biological Replicate 2

status: Public on Dec 01 2010

city: Nanjing

first: miao

last: weiguo

address: Weigang

country: China

institute: Nanjing Agricultural Uiversity

description: Leaf Biological replicate 2 of 3,T34(transgenic) vs Z35(control)

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

organism: Gossypium hirsutum

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP,ambion) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction.  We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: All plants were cultured in a sterile incubator at 28˚C

extract_protocol: Total RNA samples were extracted from 1 g of cotton true leaves and roots from Z35 and T-34 using the Plant Total RNA Extract Kit (Autolab Biotech, Beijing, China) according to the manufacturer’s instructions.

treatment_protocol: Before microarray analysis of transgenic T-34, homozygous plants were further confirmed by kanamycin-resistance screening, PCR analysis, and Southern and western blot analyses.

tag: gentype/variation

tag: tissue type

value: leaf

tag: genotype/variation


title: Leaf Biological Replicate 1

description: Leaf Biological replicate 1 of 3,T34(transgenic) vs Z35(control)


title: mesenteric arterial tree, eET-1 mouse, replicate 3, female young

description: FEMALE YOUNG 3


title: Root Biological Replicate 1

description: Root Biological replicate 1 of 3,T34(transgenic) vs Z35(control)

value: root


title: mesenteric arterial tree, WT mouse, replicate 1, female young

description: FEMALE YOUNG 5


title: Root Biological Replicate 3

description: Root Biological replicate 3 of 3,T34(transgenic) vs Z35(control)


title: Root Biological Replicate 2

description: Root Biological replicate 2 of 3,T34(transgenic) vs Z35(control)


title: Leaf Biological Replicate 3

description: Leaf Biological replicate 3 of 3,T34(transgenic) vs Z35(control)


title: mesenteric arterial tree, eET-1 mouse, replicate 4, female young

description: FEMALE YOUNG 4


title: mesenteric arterial tree, eET-1 mouse, replicate 2, female young

description: FEMALE YOUNG 2


title: mesenteric arterial tree, WT mouse, replicate 1, male young

description: MALE YOUNG 5


title: mesenteric arterial tree, WT mouse, replicate 4, male mature

description: MALE MATURE 8

value: 7.1 months


title: mesenteric arterial tree, WT mouse, replicate 3, male young

description: MALE YOUNG 7


title: mesenteric arterial tree, eET-1 mouse, replicate 4, male mature

description: MALE MATURE 4

value: 6.4 months


title: mesenteric arterial tree, WT mouse, replicate 1, male mature

description: MALE MATURE 5

value: 7 months


title: mesenteric arterial tree, eET-1 mouse, replicate 2, male mature

description: MALE MATURE 2


title: mesenteric arterial tree, eET-1 mouse, replicate 3, male young

description: MALE YOUNG 3


title: mesenteric arterial tree, WT mouse, replicate 2, female young

description: FEMALE YOUNG 6


title: mesenteric arterial tree, eET-1 mouse, replicate 3, male mature

description: MALE MATURE 3


title: mesenteric arterial tree, eET-1 mouse, replicate 2, male young

description: MALE YOUNG 2


title: mesenteric arterial tree, WT mouse, replicate 2, male young

description: MALE YOUNG 6


title: mesenteric arterial tree, WT mouse, replicate 4, female mature

description: FEMALE MATURE 8

value: 6.6 months


title: mesenteric arterial tree, eET-1 mouse, replicate 4, male young

description: MALE YOUNG 4


title: mesenteric arterial tree, eET-1 mouse, replicate 2, female mature

description: FEMALE MATURE 2

value: 6.8 months


title: mesenteric arterial tree, eET-1 mouse, replicate 4, female mature

description: FEMALE MATURE 4


title: mesenteric arterial tree, eET-1 mouse, replicate 1, male young

description: MALE YOUNG 1


title: mesenteric arterial tree, WT mouse, replicate 4, male young

description: MALE YOUNG 8


title: mesenteric arterial tree, WT mouse, replicate 1, female mature

description: FEMALE MATURE 5


title: mesenteric arterial tree, eET-1 mouse, replicate 3, female mature

description: FEMALE MATURE 3


title: mesenteric arterial tree, WT mouse, replicate 3, female mature

description: FEMALE MATURE 7


title: mesenteric arterial tree, WT mouse, replicate 2, female mature

description: FEMALE MATURE 6


title: mesenteric arterial tree, eET-1 mouse, replicate 1, female mature

description: FEMALE MATURE 1


title: mesenteric arterial tree, WT mouse, replicate 2, male mature

description: MALE MATURE 6


title: Vector-MRK003-2

status: Public on Aug 15 2010

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

country: USA

institute: Princeton University

hyb_protocol: Labeled cRNA (mixed Cy5-labeled and Cy3-labeled) was incubated with Blocking agent and Fragmentation buffer (Agilent Gene Expression Hybridization Kit) for 30min at 60°C. GEx Hybridization Buffer HI-RPM was then added to the mixture. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16h. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.Images were quantified using Agilent Feature Extraction Software (version 9.1.3).

data_processing: The data were analyzed with Genespring GX 7.3 Expression Analysis using Per Spot (divide by control channel), Per Chip (normalize to 50th percentile) and Per Gene (normalize to median) normalization methods.

source_name: MC3T3-E1 osteoblasts cocultured with Vector control tumor cells and treated with MRK-003, repeated

label_protocol: 175 ng of total RNA were primed with T7 promoter primer at 65°C for 10 min, then reversed transcribed to cDNA at 40°C for 2h with MMLV RT, and transcribed to cRNA with T7 RNA polymerase with dATP, dTTP, dGTP and Cy5-CTP or Cy3-CTP at 40°C for 2. Labeled cRNA was purified with Qiagen RNeasy mini kit.

growth_protocol: The cocultures were maintained in alpha MEM with 10% FBS and antibiotics (MC3T3-E1 media)

extract_protocol: Total RNA was extracted using RNAeasy Qiagen kit according to the manufacturer's instructions

tag: cell line

source_name: Universal Mouse Reference RNA (Stratagene)

tag: sample type


title: mES-Dgcr8

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Both alleles of the Dgcr8 locus of vdR2-4 ES cells were mutagenized with a molony murine leukemia virus-based gene trap vector, resulting in K16C06-1.

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

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: mouse ES cells

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: ES cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 20% fetal bovine serum, non-essential amino acids, sodium pyruvate, 0.1 mM 2-mercaptoethanol and 1,000 U/ml leukemia inhibitory factor on mouse embryonic fibroblast feeder cells. Feeder cells were removed prior to microarray analysis.

extract_protocol: RNA samples were extracted from cells using Trizol (Invitrogen).

tag: genoytpe

value: Dgcr8-homozygous mutant

tag: cell type

value: embryonic stem cell


title: mES-Wt

description: The parental ES cells of vdR2-4 is V6.5 ES cells derived from C57BL/6 x 129S4/SvJae F1 mice (PNAS 98, 6209-6214, 2001). vdR2-4 was generated by engineering V6.5 ES cells as follows: Both alleles of the Bloom's syndrome gene were modified for tetracycline-dependent regulation (Nature 429, 896-899, 2004), and tamoxifen-inducible Cre recombinase was inserted into the Rosa26 locus (Genesis 34, 208-214 (2002)). vdR2-4 ES cells were used as wild-type control for the analysis of Dgcr8-homozygous mutant ES cells (K16C06-1).

value: wild type


title: Vector-MRK003-1

source_name: MC3T3-E1 osteoblasts cocultured with Vector control tumor cells and treated with MRK-003

value: Universal Mouse Reference RNA (Stratagene)


title: Jagged1-MRK003-1

source_name: MC3T3-E1 osteoblasts cocultured with Jagged1-overexpressing tumor cells and treated with MRK-003


title: MCF7 day 90

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

description: Gene expression data from MCF7 cell line after 90 days of estrogen deprivation

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Homo sapiens

label_protocol: FL-Ovation cDNA Biotin Module V2 from NuGen Technologies Inc

growth_protocol: MCF7 cells were grown in phenol red-free RPMI medium containing 10% dextran-coated charcoal-stripped FBS (DCC-FBS) during 6 months

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

value: breast cancer


title: MCF7 day 150

description: Gene expression data from MCF7 cell line after 150 days of estrogen deprivation

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2)


title: MCF7 day 180

description: Gene expression data from MCF7 cell line after 180 days of estrogen deprivation


title: Vector-DMSO-2

source_name: MC3T3-E1 osteoblasts cocultured with Vector control tumor cells and treated with DMSO, repeated


title: MCF7 day 120

description: Gene expression data from MCF7 cell line after 120 days of estrogen deprivation


title: MCF7 day 0

description: Gene expression data from MCF7 cell line

source_name: MCF7 cell line


title: Jagged1-MRK003-2

source_name: MC3T3-E1 osteoblasts cocultured with Jagged1-overexpressing tumor cells and treated with MRK-003, repeated


title: MCF7 day 3

description: Gene expression data from MCF7 cell line after 3 days of estrogen deprivation


title: Vector-DMSO-1

source_name: MC3T3-E1 osteoblasts cocultured with Vector control tumor cells and treated with DMSO


title: Jagged1-DMSO-2

source_name: MC3T3-E1 osteoblasts cocultured with Jagged1-overexpressing tumor cells and treated with DMSO, repeated


title: MCF7 day 30

description: Gene expression data from MCF7 cell line after 30 days of estrogen deprivation


title: MCF7 day 15

description: Gene expression data from MCF7 cell line after 15 days of estrogen deprivation


title: colon_old_PPB_3

status: Public on Aug 01 2010

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

description:
Gene expression data from colon tissue of 12-yr-old dogs after 1 yr on PPB diet.
colon_old_PPB_3

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Canine Genome Array (version 1) using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages.

organism: Canis lupus familiaris

source_name: Colon tissue at 12 yrs, after 1 year on PPB diet

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Young dogs (mean age = 8 wk at baseline) were fed ad libitum throughout the study to allow for adequate growth; old dogs (mean age = 11.1 yr at baseline) were fed to maintain baseline BW.

extract_protocol: Total RNA from epithelial scrapings was extracted using Trizol as suggested by the manufacturer.

treatment_protocol: Dogs were allotted to 1 of 2 diets and fed for 12 months: 1) animal protein-based (APB) diet primarily composed of highly digestible, animal-derived ingredients and formulated to exceed protein and fat recommendations provided by the Association of American Feed Control Officials (AAFCO) for growth and reproduction; or 2) plant protein-based (PPB) diet primarily composed of moderately digestible, plant-derived ingredients and formulated to meet protein and fat recommendations for growth and reproduction by AAFCO.  The exception was 10% meat and bone meal in the diet.  All samples were collected after an overnight food-restricted period.

value: colon

value: 12 yrs

tag: diet

value: plant protein-based

tag: breed

value: beagle

value: female


title: colon_young_PPB_2

description:
Gene expression data from colon tissue of 1-yr-old dogs after 1 yr on PPB diet.
colon_you_PPB_2

source_name: Colon tissue at 1 yr, after 1 year on PPB diet

value: 1 yr


title: colon_young_PPB_1

description:
Gene expression data from colon tissue of 1-yr-old dogs after 1 yr on PPB diet.
colon_you_PPB_1


title: Jagged1-DMSO-1

source_name: MC3T3-E1 osteoblasts cocultured with Jagged1-overexpressing tumor cells and treated with DMSO


title: colon_old_APB_3

description:
Gene expression data from colon tissue of 12-yr-old dogs after 1 yr on APB diet.
colon_old_APB_3

source_name: Colon tissue at 12 yrs, after 1 year on APB diet

value: animal protein-based


title: colon_young_APB_2

description:
Gene expression data from colon tissue of 1-yr-old dogs after 1 yr on APB diet.
colon_you_APB_2

source_name: Colon tissue at 1 yr, after 1 year on APB diet


title: colon_young_APB_3

description:
Gene expression data from colon tissue of 1-yr-old dogs after 1 yr on APB diet.
colon_you_APB_3


title: colon_young_PPB_3

description:
Gene expression data from colon tissue of 1-yr-old dogs after 1 yr on PPB diet.
colon_you_PPB_3


title: colon_old_APB_2

description:
Gene expression data from colon tissue of 12-yr-old dogs after 1 yr on APB diet.
colon_old_APB_2


title: colon_young_APB_1

description:
Gene expression data from colon tissue of 1-yr-old dogs after 1 yr on APB diet.
colon_you_APB_1


title: D.rerio_embryo_CR_rep2_2

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

country: Netherlands

institute: University of Amsterdam

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_2: Cy5

hyb_protocol: 825 ng for each channel were combined and made to 55 μl with 10x Blocking Agent and 25x Fragmentation Buffer. 55 μl of 2x Hi-RPM Hybridization Buffer was added (Gene Expression Hybridization Kit, Agilent Technologies). 100 μl of hybridization mixture was loaded onto each array and allowed to hybridize at 65°C (10 RPM) for 17h. The slides were washed  with Gene Expression Wash Buffers I and II (Gene Expression Wash Buffer Kit, Agilent Technologies).

scan_protocol: Slides were scanned on an Agilent G2505B scanner at 5 μm resolution and data was extracted with Feature Extraction version 9.3.1.1. (Protocol GE2-v5_95).

data_processing: LOWESS NORMALIZED using R maanova package

organism: Danio rerio

label_protocol: 1 μg of total RNA was amplified with the Amino-Allyl MessageAmp II kit (Ambion) according to manufacturer’s instruction. After aRNA synthesis, samples were labeled with Cy3-NHS mono-reactive dye (GE Healthcare) for the test samples and Cy5-NHS (GE Healthcare) mono-reactive dye for the common reference (pooled aRNA).

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5-30°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Embryos were injected either with a translation blocking morpholino or a 5bp mismatch morpholino directed against traf6 at the 1 cell stage. Subsequently these embryos were injected with either Salmonella typhimurium strain SL1027 or with PBS at 27 hours post fertilization (hpf). Samples were collected at 8 hours post injection (hpi) and immediately quenched in liquid nitrogen and stored at -80˚C prior to RNA extraction. This sample is a mixture of all cRNA samples used in this study.

tag: treatment

value: The  CR (common reference) was composed by combining 1 ug of cRNA from each sample


title: Embryo_Control morpholino.Injected_Infected_rep2

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_3: Cy3

treatment_protocol: Embryos were injected with a 5bp mismatch morpholino (mm) directed against traf6 at the 1 cell stage. Subsequently these embryos were injected with Salmonella typhimurium strain SL1027 at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

value: Traf6 mismatch morpholino and Salmonella typhimurium injected zebrafish embryos


title: Embryo_Control morpholino.Injected_Not.Infected_rep2

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_4: Cy3

treatment_protocol: Embryos were injected with a 5bp mismatch morpholino (mm) directed against traf6 at the 1 cell stage. Subsequently these embryos were injected with PBS at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

value: Traf6 mismatch morpholino and PBS injected zebrafish embryos


title: Embryo_Control morpholino.Injected_Not.Infected_rep3

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_4: Cy3


title: D.rerio_embryo_CR_rep3_3

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_3: Cy5


title: colon_old_PPB_2

description:
Gene expression data from colon tissue of 12-yr-old dogs after 1 yr on PPB diet.
colon_old_PPB_2


title: colon_old_PPB_1

description:
Gene expression data from colon tissue of 12-yr-old dogs after 1 yr on PPB diet.
colon_old_PPB_1


title: Embryo_Control morpholino.Injected_Infected_rep3

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_3: Cy3


title: D.rerio_embryo_CR_rep3_4

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_4: Cy5


title: D.rerio_embryo_CR_rep3_2

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_2: Cy5


title: Embryo_Morpholino.Injected_Infected_rep2

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_1: Cy3

treatment_protocol: Embryos were injected with an translation blocking morpholino directed against traf6 (traf6 mo) at the 1 cell stage. Subsequently these embryos were injected with Salmonella typhimurium strain SL1027 at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

value: Traf6 morpholino and Salmonella typhimurium injected zebrafish embryos


title: D.rerio_embryo_CR_rep1_3

description: MAD_252162610006_S02_GE2-v5_95_Feb07_1_3: Cy5


title: Embryo_Morpholino.Injected_Not.Infected_rep3

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_2: Cy3

treatment_protocol: Embryos were injected with a translation blocking morpholino directed against traf6 (traf6 mo) at the 1 cell stage. Subsequently these embryos were injected with PBS at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

value: Traf6 morpholino and PBS injected zebrafish embryos


title: colon_old_APB_1

description:
Gene expression data from colon tissue of 12-yr-old dogs after 1 yr on APB diet.
colon_old_APB_1


title: D.rerio_embryo_CR_rep3_1

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_1: Cy5


title: D.rerio_embryo_CR_rep1_2

description: MAD_252162610006_S02_GE2-v5_95_Feb07_1_2: Cy5


title: Embryo_Morpholino.Injected_Not.Infected_rep2

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_2: Cy3


title: D.rerio_embryo_CR_rep2_4

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_4: Cy5


title: 62 h vs 44 h replicate a

status: Public on Jul 04 2010

city: Bremen

first: Patricia

last: Wecker

address: Celsiusstr, 1

department: Molecular Ecology

country: Germany

institute: Max Planck Institut for Marine Microbiology

hyb_protocol: Blocking, denaturing, hybridization, washing and drying of the slides with N2 were carried out in an automated hybridization station HS400 (Tecan, Crailsheim, Germany). The spotted arrays were blocked in prehybridization solution containing 250 mM NaCl, 5 mM Tris/HCl at pH 8.0, 50% formamide, 0.5x SSC, 0.05% BSA, and 1% blocking reagent from Roche Diagnostics, Mannheim, Germany for 45 min at 52°C. For hybridisation at least 2 μg of Alexa 546 dye-labeled and 2 μg of Alexa 647 dye-labeled total cDNA were combined and taken up in a final volume of 100 µl DIG Easy Hyb hybridization solution (Roche Diagnostics, Mannheim, Germany). After the blocking step the sample solution was applied to the arrays, denaturized at 95°C for 3 min and hybridized under stringent conditions at 52°C for over 12 hours. After hybridization slides were washed at RT in ULTRArray Low Stringency Wash Buffer (Ambion, Austin, USA) and dried by N2.

scan_protocol: Slides were scanned at a resolution of 5 μm using a ScanArray Express Microarray scanner (Perkin Elmer, Wellesley, USA) with varied laser power and sensitivity level of the photomultiplier tube (PMT) for each slide. The provided image analysis software ScanArray Express Version 4.0 was used for automatic spot detection and signal quantification of both fluorophores.

data_processing: Raw data were automatically processed using the in-house developed microarray data analysis software tool MADA (www.megx.net/mada). First of all the spot intensities were local background corrected (spot intensity minus spot background intensity). Then signals were only assessed as positive if mean spot pixel intensity was higher than the mean local background intensity plus 2 times the standard deviation of the mean local background pixel intensity. Each gene is spotted in 3 replicates. Spot replicates with poor quality were removed from the data set according to the outlier test of MADA. For this test, first the standard deviation of all replicates is computed. Second, one replicate is omitted and the standard deviation is recalculated, if the deviation differs more than 50% from the previous deviation, the omitted replicate is regarded as outlier. This procedure is alternately repeated for all replicates  The expression is described through the ratio and intensity, where R is the fluorescence log ratio of the experiment time point relative to the control condition (e.g. R = log2 (result of channel 44 h / result of channel 62 h)) and I is the log mean fluorescence intensity (e.g. I = log10 (result of channel 44 h * result of channel 62 h)).  Each data point represents a regulation factor (ratio) in a logarithmic scale for one gene calculated from the positive replicates for a particular probe coming from two RNA pools. Normalization was carried out by LOWESS fitting on an R-versus-I plot with a smoothing factor of 0.05. Each time point of the growth curve  experiment was hybridized. The expression data (ratio) of more than one hybridization were combined to one expression data point (ratio) by average and the standard deviation was calculated.  Differentially expressed genes are determinate by a fixed threshold cut off method (i.e. a two-fold increase or decrease) based on the self-self hybridization.

organism: Rhodopirellula baltica

source_name: R. baltica cells 44 h

label_protocol: cDNA was directly labeled using the PlatinumBrightTM nucleic acid labeling kit based on KREATECH´s patented Universal Linkage System (ULS) (Biocat, Heidelberg, Germany) according to the manufacturer's protocol

growth_protocol: Cells of R. baltica were grown in batch culture (500ml) with mineral medium. The cultures were incubated at 28°C on a rotary shaker

extract_protocol: The culture pellets were re-suspended in 0.1 M Tris-HCL and then re-centrifuged to cell pellets that were shock-frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using the proposed protocol of the TRI Reagent® Kit by Ambion (Austin, USA).  cDNA synthesis was performed using the SuperScript direct cDNA labeling system kit by Invitrogen (Karlsruhe, DE) according to the manufacturer's instructions with random hexamers and unlabeled dCTP/dUTP.

treatment_protocol: Cultures were harvested by centrifugation (Beckman CoulterTM AvantiTM J-20XP, JA10 Rotor, 20 min, 6000 rpm, 4°C), after different incubation times (44, 62, 82, 96 and 240 h). The culture broth was collected in 500 ml tubes and swirled briefly in an ethanol/dry ice bath to rapidly cool down the cultures and freeze the RNA profile. Subsequently, the broth was centrifuged at 6000 rpm for 20 min at 4°C (Beckman CoulterTM AvantiTM J-20XP, JA10 Rotor). The pellets were re-suspended in 0.1 M Tris-HCl and then re-centrifuged to obtain cell pellets that were subsequently shock-frozen in liquid nitrogen and stored at -80°C

tag: time point

value: Cells harvested after 44 h of growth

source_name: R. baltica cells 62 h

value: Cells harvested after 62 h of growth


title: D.rerio_embryo_CR_rep1_1

description: MAD_252162610006_S02_GE2-v5_95_Feb07_1_1: Cy5


title: D.rerio_embryo_CR_rep2_3

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_3: Cy5


title: D.rerio_embryo_CR_rep1_4

description: MAD_252162610009_S01_GE2-v5_95_Feb07_1_1: Cy5


title: 96 h vs 82 h replicate b

source_name: R. baltica cells 82 h

value: Cells harvested after 82 h of growth

source_name: R. baltica cells 96 h

value: Cells harvested after 96 h of growth


title: Embryo_Morpholino.Injected_Infected_rep3

description: MAD_252162610008_S01_GE2-v5_95_Feb07_1_1: Cy3


title: Embryo_Control morpholino.Injected_Infected_rep1

description: MAD_252162610006_S02_GE2-v5_95_Feb07_1_3: Cy3


title: 62 h vs 44 h replicate b


title: Embryo_Control morpholino.Injected_Not.Infected_rep1

description: MAD_252162610009_S01_GE2-v5_95_Feb07_1_1: Cy3


title: HEK293T-4ug miR cluster-rep2

status: Public on Jul 02 2010

city: Delhi

first: Neeru

last: Saini

address: Mall Road

department: FGU

country: India

institute: IGIB

description: This  sample is hybridized to  4090082069_B array

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Average Normalization using Illumina Beadstudio

label: Streptavidin Cy3

source_name: HEK293T + 4 micrograms of cloned miR-23a~27a~24-2

label_protocol: As described in the illumina Human-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

extract_protocol: The total RNA was extracted using TRIzol reagent (Invitrogen Corporation) according to the manufacturer's protocol.The RNA was resuspended in diethyl pyrocarbonate-treated water, quantified by UV absorbance at 260/280 nm and immediately used for RNA amplification and labeling by Illumina TotalPrep RNA amplification kit

treatment_protocol: HEK293T transfected with 4 micrograms of cloned miR-23a~27a~24-2 in 1 well of 6-well plate

value: Human embryonic kidney (HEK293T)


title: Embryo_Morpholino.Injected_Infected_rep1

description: MAD_252162610006_S02_GE2-v5_95_Feb07_1_1: Cy3


title: 240 h vs 82 h replicate a

source_name: R. baltica cells 240 h

value: Cells harvested after 240 h of growth


title: Embryo_Morpholino.Injected_Not.Infected_rep1

description: MAD_252162610006_S02_GE2-v5_95_Feb07_1_2: Cy3


title: 96 h vs 82 h replicate a


title: Biofilm 48h Replicate 1 vs Submers 48h Replicate 1

status: Public on Jul 01 2010

city: Jena

first: Daniela

last: Albrecht

address: Wildenbruchstr. 15

institute: BioControl Jena GmbH

description: no additional information

hyb_protocol: The hybridization of the arrays was performed according to the protocol of TIGR (SOP#M008 http://pga.tigr.org).

scan_protocol: The chips were scanned and analyzed using an Axon GenePix 4000B scanner and the GenePix4 software.

data_processing:
Only those spots were used for analysis that were similar regulated double on each array in both dye swap conditions. Median values of replicate spots of the same gene were used. Normalization used vsn and loess, filtering used robust Z-Scores and ANOVA.
VALUE = normalized log2 ratios of biofilm vs non-biofilm

organism: Aspergillus fumigatus

source_name: Submers 48h Replicate 1

label_protocol: 20µg pure RNA of each condition was synthesized using the LabelStar Array Kit (Qiagen, Hilden, Germany) with aadUTP (Sigma, Munich, Germany) instead of aadTTP. As washing buffer, a TRIS-free buffer containing 84.25ml 95% (v/v) ethanol, 15.25ml H2O and 0.5ml 1M KHPO4 was used. The dried pellets were resuspended in 4.5µl 0.1M NaHCO3. Then, 4.5µl Cy-dye esters (Cy3 and Cy5 from GE Healthcare, Munich, Germany) in DMSO were added. After 1h of incubation at RT, the probes were neutralized with 35 µl 100mM NaOAc pH 5.1 and incubated for 15min with 4.5µl hydroxylamine at RT. The clean-up was performed using the Qiaquick PCR Purification Kit (Qiagen, Hilden, Germany) with standard buffer PB and PE (Qiagen, Hilden, Germany). For stabilization, 5µg poly(A)-DNA (MWG Biotech, Ebersberg, Germany), 10µg Cot1 DNA (Roche, Mannheim, Germany) and 20µg yeast tRNA (Sigma-Aldrich, Taufkirchen, Germany) were added and the pellets dried in a SpeedVac.

growth_protocol: Aspergillus fumigatus strain ATCC #46645 was grown on fresh potato dextrose agar plates until sporulation. The plates were overlaid with 0.1% (v/v) Tween 20 and the conidia were gently removed. The suspension of conidia was harvested with a syringe and passed through a 5.0µm syringe-driven filter (Millipore GmbH, Schwalbach, Germany) to remove hyphae. Conidia were washed and the conidial pellet was resuspended in PBS (PAA, Cölbe, Germany), adjusted to a final concentration of 10^6 conidia/ml MEM media (C.c.pro, Oberdola, Germany) and left to grow in fibronectin-coated cell culture flasks at 35 °C for 24h and 48h, respectively.

extract_protocol: Total RNA was isolated from biofilm-like and planktonic grown mycelium in three independent experiments using TRI Reagent (Sigma-Aldrich, Taufkirchen, Germany) according to the manufacture's instructions. Isolated RNA was treated with Dnase I (Invitrogen, Karlsruhe, Germany) and further purification was achieved with RNeasy Clean up columns (Qiagen, Hilden, Germany) according to the manufactures' instructions. The RNA quality and quantity was checked using Agilent Total RNA Nano 6000 chips (Agilent, Böblingen, Germany). cDNA was synthesized from 1.5µg of total RNA using the First strand cDNA kit (Roche, Mannheim, Germany). Additionally, we analyzed two types of controls. Instead of culturing in an incubator with CO2, we incubated 48h biofilm in normal air under the same conditions to see a possible influence of CO2. The second control was performed using vigorous shaking at 220 rpm using the same conditions of 48 h biofilm-like growth to avoid the production of a biofilm due to lack of attachment.

treatment_protocol: 5% (v/v) FCS (PAA, Cölbe, Germany) were added to induce biofilm-like growth.

tag: culture

value: submers

tag: time

source_name: Biofilm 48h Replicate 1

value: biofilm


title: Fusobacterium nucleatum stimulated neutrophils, 2

status: Public on Jul 20 2010

city: Birmingham

first: Helen

middle: Joan

last: Wright

state: West Midlands

address: St Chads Queensway

department: Oral Biology

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133Aa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: peripheral blood neutrophils after 3hrs of stimulation with fusobacterium nucleatum

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

extract_protocol:
Neutrophils were extracted using a percoll density gradient followed by eytherocyte lysis
Neutrophils were extracted using phenol choloroform extraction followed by Dnase treatment on a Quiagen spin column.

treatment_protocol: Neutrophils were incubated with or without Fusobaterium nucleatum (10953, MOI 1:300) for 3hrs

value: stimulated neutrophil


title: D.rerio_embryo_CR_rep2_1

description: MAD_252162610007_S01_GE2-v5_95_Feb07_1_1: Cy5


title: 82 h vs 62 h replicate b


title: Fusobacterium nucleatum stimulated neutrophils, 1


title: 82 h vs 62 h replicate a


title: C12-N1

first: Garabet

last: Yeretssian

state: QC

address: 3649 Promenade Sir-William Osler

department: Medicine

institute: McGill

description: Replicate of sample 4

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
The raw data (see Supplementary file 'GSE20407_matrix_non-normalized.txt' on Series record) were obtained from Beadstudio version 3.2.7.
The raw data were normalized using Genesifter software. Specifically, the raw intensity of each gene on the Illumina microarray was log transformed and normalized according to the total mean of the whole microarray (hence, normalized "all mean" values).

source_name: C12 normal colon tissue

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: caspase-12 deficient

value: colon

tag: disease state

value: normal


title: Biofilm 24h Replicate 1 vs Submers 24h Replicate 1

description: no additional information

source_name: Submers 24h Replicate 1

source_name: Biofilm 24h Replicate 1


title: C12-T2

description: Replicate of sample 7

source_name: C12 colon tumor tissue

value: tumor


title: C12-N2

description: Replicate of sample 3


title: WT-T2

description: Replicate of sample 5

source_name: WT colon tumor tissue

value: wild type


title: 62 h vs 62 h

description: self-self hybridization


title: HEK293T-2ug miR cluster-rep2

description: This  sample is hybridized to  4090082069_D array

scan_protocol: Refer to the Illumina Gene Expression System Manual

source_name: HEK293T + 2 micrograms of cloned miR-23a~27a~24-2

treatment_protocol: HEK293T transfected with 2 micrograms of cloned miR-23a~27a~24-2 in 1 well of 6-well plate


title: Biofilm 24h Replicate 2 vs Submers 24h Replicate 2

description: no additional information

source_name: Biofilm 24h Replicate 2

source_name: Submers 24h Replicate 2


title: Biofilm 48h Replicate 2 vs Submers 48h Replicate 2

description: no additional information

source_name: Biofilm 48h Replicate 2

source_name: Submers 48h Replicate 2


title: pooled normals vs 67 number sample

status: Public on Jun 30 2010

city: Bangalore

first: Paturu

last: Kondaiah

state: Karnataka

address: CV Raman Avenue

department: MRDG

institute: IISc

description: Contains all the biological replicates 7 to 10, pooled normals, OSMF tissues

hyb_protocol: 825ng of labeled cRNA of the respective sample was used for hybridization in following combinations - Pooled Normal (Cy3) and OSMF sample (Cy5). Hybridization was performed for 17 hrs, 10 rpm at 65⁰C.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization was done using Genespring (GX v 10.0).

source_name: Oral cavity

label_protocol: 500ng of RNA from OSMF tissue and Pooled normal was used. Labeling was done using Quick Amp labeling kit (Agilent) as per the manufacturer’s protocol. Breifly, using T7 promoter element coupled oligodT primer cDNA was generated and using T7 polymerase and from cDNA, labeled cRNA was generated via an in vitro transcription reaction using T7 RNA polymerase and Cy3 (for LEC and MC-L) or Cy5 (MC-L and MSC-BM) CTP.

extract_protocol:
Tissues were obtained from patients suffering form oral submucous fibrosis (OSMF), and normal tissue biopsies were obtained from Gingiva of patients referred for third molar excision.
Total RNA extracted using Trizol following manufacturer's instructions.

value: Gingival tissue

value: Oral submucous fibrosis


title: HEK293T-4ug miR cluster-rep1

description: This  sample is hybridized to  4090082069_A array


title: pooled normals vs 65 number sample

description: Contains all the biological replicates 5 to 10, pooled normals, OSMF tissues


title: WT-T1

description: Replicate of sample 6


title: HEK293T-control-rep1

description: This  sample is hybridized to  4090082069_E array

source_name: HEK293T - control

treatment_protocol: HEK293T - untransfected


title: HEK293T-2ug miR cluster-rep1

description: This  sample is hybridized to  4090082069_C array


title: HEK293T-control-rep2

description: This  sample is hybridized to  4090082069_F array


title: HEK 5uM CDDP, Day 1, #3

status: Public on Jun 26 2010

city: Woolloongabba

first: Kim

last: Poth

state: Qld

address: Ipswich Rd

country: Australia

institute: Diamantina Institute

description:
Replicate 3 of 3.
KH24

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalized using robust spline normalization with Illumina lumi in R.

Non-normalized data is available in 'GSE20185_non-normalized.txt', which is linked to the Series GSE20185 record as a supplementary file.

source_name: Neonatal foreskin epidermis, cisplatin, 24hr

label_protocol: Biotinylated cRNAs were prepared using the Illumina TotalPrep kit.

growth_protocol: Cell lines were grown at 37°C / 5% CO2 in medium consisting of 50% DMEM, 50% Ham's F12, 5% Fetal calf serum, 1% Penicillin/Streptomycin/Glutamine, 10 μg per mL Gentamycin and 0.43 μg per mL Hydrocortisone.

extract_protocol: Total RNA was extracted with TRIzol reagent and subsequently cleaned up with QIAGEN RNeasy micro kits in accordance with the protocols provided by the manufacturers. Quality control was performed using an Agilent BioAnalyzer.

treatment_protocol: Cells were treated with 5 μM cisplatin for 48 hours at 37°C, then harvested after a further 24 hours and either 96 hours (FaDu and HEK) or 120 hours (Detroit-562). The FaDu and Detroit-562  cell lines were then sorted using a MoFlo flow cytometer to obtain the smallest 10-20% of cells and RNA was extracted from these. HEKs were not sorted.

value: HEK

value: Neonatal foreskin epidermis

value: 5 μM cisplatin (CDDP) for 48 hours

tag: post-treatment processing

value: Harvest 24 hours after drug treatment


title: HEK 5uM CDDP, Day 4, #3

description:
Replicate 3 of 3.
KH27

source_name: Neonatal foreskin epidermis, cisplatin, 96hr

value: Harvest 96 hours after drug treatment


title: WT-N1

description: Replicate of sample 2

source_name: WT normal colon tissue

tag: tissue


title: pooled normals vs 125 number sample

description: Contains all the biological replicates 9 to 10, pooled normals, OSMF tissues


title: WT-N2

description: Replicate of sample 1


title: pooled normals vs 78 number sample

description: Contains all the biological replicates 8 to 10, pooled normals, OSMF tissues


title: pooled normals vs 130 number sample

description: Contains all the biological replicates 10 to 10, pooled normals, OSMF tissues


title: pooled normals vs 66 number sample

description: Contains all the biological replicates 6 to 10, pooled normals, OSMF tissues


title: pooled normals vs 63 number sample

description: Contains all the biological replicates 4 to 10, pooled normals, OSMF tissues


title: pooled normals vs 62 number sample

description: Contains all the biological replicates 3 to 10, pooled normals, OSMF tissues


title: FaDu, 5uM CDDP, Day 1, #1

description:
Replicate 1 of 3.
KH13

source_name: FaDu cell line, cisplatin, 24hr

value: FaDu

value: Hypopharyngeal squamous cell carcinoma

value: 24 hours after drug treatment, sort to obtain smallest sized cell fraction


title: FaDu, 5uM CDDP, Day 1, #3

description:
Replicate 3 of 3.
KH15


title: FaDu, 5uM CDDP, Day 1, #2

description:
Replicate 2 of 3.
KH14


title: FaDu, Untreated, #1

description:
Replicate 1 of 3.
KH10

source_name: FaDu cell line, untreated

value: No drug treatment


title: FaDu, Untreated, #2

description:
Replicate 2 of 3.
KH11


title: Detroit-562, 5uM CDDP, Day 5, #3

description:
Replicate 3 of 3.
KH9

source_name: Detroit-562 cell line, cisplatin, 120hr

value: Plural effusion derived from laryngeal carcinoma

value: 120 hours after drug treatment, sort to obtain smallest sized cell fraction


title: pooled normals vs 58 number sample

description: Contains all the biological replicates 1 to 10, pooled normals, OSMF tissues


title: HEK 5uM CDDP, Day 4, #1

description:
Replicate 1 of 3.
KH25


title: HEK 5uM CDDP, Day 4, #2

description:
Replicate 2 of 3.
KH26


title: HEK 5uM CDDP, Day 1, #2

description:
Replicate 2 of 3.
KH23


title: HEK 5uM CDDP, Day 1, #1

description:
Replicate 1 of 3.
KH22


title: pooled normals vs 61 number sample

description: Contains all the biological replicates 2 to 10, pooled normals, OSMF tissues


title: HEK, Untreated, #3

description:
Replicate 3 of 3.
KH21

source_name: Neonatal foreskin epidermis, untreated


title: HEK, Untreated, #2

description:
Replicate 2 of 3.
KH20


title: Detroit-562, 5uM CDDP, Day 1, #2

description:
Replicate 2 of 3.
KH5

source_name: Detroit-562 cell line, cisplatin, 24hr


title: FaDu, 5uM CDDP, Day 4, #3

description:
Replicate 3 of 3.
KH18

source_name: FaDu cell line, cisplatin, 96hr

value: 96 hours after drug treatment, sort to obtain smallest sized cell fraction


title: HEK, Untreated, #1

description:
Replicate 1 of 3.
KH19


title: P4_Ovary_PDGFab_biological rep1_9GF

status: Public on Jun 13 2010

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml PDGF alfa beta heterodimer for 48 hours

hyb_protocol: Following fragmentation, ssDNA were hybridized on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the  Affymetrix Fluidics Station 4500.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quantile normalization, median polish methos for probesets summarization, and log values of probes signals using base 2.  These VALUES were then unlogged for network analysis; the unlogged data are retained in the PRE-VALUE column below.

organism: Rattus norvegicus

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously [Dole, G., et al., 2008].

extract_protocol: RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: For each ovary sample from which RNA was collected for microarrays, 2-3 ovaries per well were cultured with media changes every 24 hours for two days in the absence (controls) or presence (treated) of either Amh (human Anti-Mülerian hormone)(50ng/mL, R&D Systems Inc., USA), Fgf2 (rat Fibroblast growth factor 2)(50ng/mL, R&D Systems Inc., USA), Bmp4 (human Bone morphogenetic protein 4)(50ng/mL, R&D Systems Inc., USA), Gdnf (rat Glial derived neurotrophic factor)(50ng/mL, Calbiochem, USA), Fgf7 (human fibroblast growth factor 7/keratinocyte growth factor)(50ng/mL, R&D Systems Inc., USA), Kitlg (mouse Kit ligand)(50ng/mL, R&D Systems Inc., USA), Lif (rat leukemia inhibitory factor)(50ng/mL, Chemicon/Millipore, USA), Pdgf-ab (rat platelet derived growth factor AB heterodimer)(50ng/mL, R&D Systems Inc., USA), Tgfb1 (human transforming growth factor beta 1)(50ng/mL, R&D Systems Inc., USA).  Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together. On any given day a culture experiment was performed, the treatment groups included untreated control ovaries and one to three different growth factor treatments.

value: Sprague-Dawley

tag: gender

value: Female

value: ovary

tag: developmental stage

value: day P4 incubated for 2 more days

tag: treatment group


title: FaDu, 5uM CDDP, Day 4, #1

description:
Replicate 1 of 3.
KH16

tag: cell line


title: P4_Ovary_KITLG_biological rep3_9GF

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml KITLG for 48 hours

value: 50 ng/ml KITLG for 48 hours


title: FaDu, 5uM CDDP, Day 4, #2

description:
Replicate 2 of 3.
KH17


title: FaDu, Untreated, #3

description:
Replicate 3 of 3.
KH12


title: P4_Ovary_LIF_biological rep2_9GF

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml LIF for 48 hours

value: 50 ng/ml LIF for 48 hours


title: Detroit-562, 5uM CDDP, Day 1, #1

description:
Replicate 1 of 3.
KH4


title: Detroit-562, Untreated, #2

description:
Replicate 2 of 3.
KH2

source_name: Detroit-562 cell line, untreated


title: Detroit-562, 5uM CDDP, Day 5, #1

description:
Replicate 1 of 3.
KH7


title: Detroit-562, 5uM CDDP, Day 5, #2

description:
Replicate 2 of 3.
KH8


title: P4_Ovary_FGF7_biological rep3_9GF

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml FGF7 for 48 hours

value: 50 ng/ml FGF7 for 48 hours


title: Detroit-562, Untreated, #1

description:
Replicate 1 of 3.
KH1


title: P4_Ovary_FGF7_biological rep1_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml FGF7 for 48 hours


title: Detroit-562, 5uM CDDP, Day 1, #3

description:
Replicate 3 of 3.
KH6

value: 5 μM cisplatin (CDDP) for 48 hours


title: P4_Ovary_FGF7_biological rep2_9GF


title: Detroit-562, Untreated, #3

description:
Replicate 3 of 3.
KH3


title: P4_Ovary_FGF2_biological rep2_9GF

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml FGF2 for 48 hours

value: 50 ng/ml FGF2 for 48 hours


title: P4_Ovary_FGF2_biological rep3_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml FGF2 for 48 hours


title: P4_Ovary_FGF2_biological rep1_9GF


title: P4_Ovary_PDGFab_biological rep3_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml PDGF alfa beta heterodimer for 48 hours


title: P4_Ovary_LIF_biological rep1_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml LIF for 48 hours


title: P4_Ovary_PDGFab_biological rep2_9GF

value: 50 ng/ml PDGF alfa beta heterodimer for 48 hours


title: P4_Ovary_BMP4_biological rep1_9GF

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml BMP4 for 48 hours

value: 50 ng/ml BMP4 for 48 hours


title: P4_Ovary_AMH_biological rep1_9GF

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml AMH for 48 hours

value: 50 ng/ml AMH for 48 hours


title: P4_Ovary_GDNF_biological rep2_9GF

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml GDNF for 48 hours

value: 50 ng/ml GDNF for 48 hours


title: P4_Ovary_Control_biological rep13_9GF

description: Gene expression data from rat P4 Ovary incubated for 48 hours with no treatment

value: no treatment


title: P4_Ovary_Control_biological rep14_9GF

source_name: P4 Ovary incubated for 48 hours with no treatment


title: P4_Ovary_GDNF_biological rep3_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml GDNF for 48 hours


title: P4_Ovary_AMH_biological rep3_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml AMH for 48 hours


title: C12-T1

description: Replicate of sample 8

source_name: C12 colon tumor tissue

tag: genotype/variation

value: caspase-12 deficient

value: colon

value: tumor


title: P4_Ovary_KITLG_biological rep1_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml KITLG for 48 hours

value: Sprague-Dawley


title: P4_Ovary_BMP4_biological rep3_9GF

source_name: P4 Ovary incubated in the presence of 50 ng/ml BMP4 for 48 hours

value: Female


title: P4_Ovary_AMH_biological rep2_9GF

value: ovary


title: P4_Ovary_GDNF_biological rep1_9GF

value: day P4 incubated for 2 more days


title: P4_Ovary_LIF_biological rep3_9GF


title: P4_Ovary_KITLG_biological rep2_9GF

value: 50 ng/ml KITLG for 48 hours


title: P4_Ovary_Control_biological rep11_9GF


title: P4_Ovary_BMP4_biological rep2_9GF


title: P4_Ovary_Control_biological rep10_9GF


title: P4_Ovary_Control_biological rep4_9GF


title: P4_Ovary_Control_biological rep1_9GF


title: P4_Ovary_Control_biological rep2_9GF


title: P4_Ovary_Control_biological rep6_9GF


title: P4_Ovary_Control_biological rep12_9GF


title: P4_Ovary_Control_biological rep8_9GF


title: P4_Ovary_Control_biological rep5_9GF


title: P4_Ovary_Control_biological rep3_9GF


title: P4_Ovary_CTGF_biological rep1

description: Gene expression data from rat P4 Ovary incubated in the presence of 50 ng/ml CTGF for 48 hours

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.

treatment_protocol: For each ovary sample from which RNA was collected for microarrays, 2-3 ovaries per well were cultured with media changes every 24 hours for two days in the absence (controls) or presence (treated) CTGF (human connective tissue growth factor)(50ng/mL, PeproTech Inc., NJ USA).  Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together.


title: P4_Ovary_CTGF_biological rep2

source_name: P4 Ovary incubated in the presence of 50 ng/ml CTGF for 48 hours


title: P4_Ovary_Control_biological rep9_9GF


title: P4_Ovary_Control_biological rep7_9GF


title: P4_Ovary_Control_biological rep2


title: P4_Ovary_Control_biological rep3


title: WT 3-2

status: Public on May 14 2010

type: genomic

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

hyb_protocol: Using an in-house humidity chamber for 45 hours at 45 °C

scan_protocol: ProScan Array HT scanner (Perkin Elmer) using a laser power of 90% and 10 µm resolution.

data_processing: BlueFuse software package v3.3 (BlueGnome).Four replicate spots combined and no background subtractions.Normalised by Global Lowess (f = 1/4, iter = 3).

molecule: genomic DNA

label_protocol: 100 ng input (micrococcal nuclease-digested chromatin) and 50-100 ng immuno-enriched material were labelled with Alexa3 and Alexa 5 (and dye swap) using Bioprime Kit according to manufacturers instructions (Invitrogen)

growth_protocol: Grown on mitomycin C-treated primary embryonic fibroblasts (PEFs) derived from E12.5 mouse embryos, in DMEM supplemented with 15% fetal calf serum (FCS), 1000 units/ml LIF, non-essential amino acids, sodium pyruvate, 2-mecaptoethanol, L-glutamine, and Penicillin/Streptomycin. For analysis of chromatin,ES cells were trypsinized and the PEFs allowed reattaching 2x 30 min. (Ref cells: J Cell Biol. 2007 Jul 16;178(2):219-29:PMID: 17620408 )

extract_protocol: RNase A and ProteinaseK digestion. Purified using Qiagen PCR purification kit (Qiagen).

treatment_protocol: Nuclei micrococcal nuclease digested and chromatin released. ChIP for H3K27me3 (ab6002).

tag: antibody

tag: genotype

value: WT

source_name: Input

tag: type

value: Input


title: WT 2-2


title: P4_Ovary_Control_biological rep1


title: WT 3-1


title: P4_Ovary_CTGF_biological rep3


title: IRL

status: Public on Jun 01 2010

city: Farmington

first: Leo

last: Lefrancois

state: CT

address: 263 Farmington Ave.

institute: UCONN Health Center

description: Two arrays were performed for each sample for a total of 8 arrays.  RAW data file (supplementary file on the Series record) contains raw data for each array individually.

hyb_protocol: Hyb at 58C 16hrs according to standard protocols

scan_protocol: Illumina Bead array reader

data_processing: Quantile normalization was performed using Illumina Bead studio; Multiexperiment Viewer

source_name: OT-I transfer, IRL

label_protocol: Eberwine protocol was used

growth_protocol: 2 biological replicates per group

extract_protocol: Qiagen RNeasy

tag: cell type

value: CD8 T cells

tag: vaccine strain

value: Irradiated Listeria monocytogenes (LM)


title: Naïve control

source_name: OT-I transfer, naïve

value: control (naïve)


title: RPE-chor replicate 3

status: Public on May 30 2010

first: arthur

last: bergen

address: Meibergdreef 47

institute: NIN

description: Biological replicate 3 of 3

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5).

data_processing: Agilent Feature Extraction Software (v 8.5) was used for background subtraction and LOWESS normalization.

source_name: RPE cells

label_protocol: aRNA samples were labeled with either a Cy3 or a Cy5 fluorescent probe

extract_protocol: Total RNA was isolated and the mRNA component was amplified (van Soest 2007). Amplified RNA (aRNA) was quantified with a nanodrop (Isogen Life Science B.V., The Netherlands) and the quality was checked on a BioAnalyzer (Agilent Technologies, Amstelveen, The Netherlands)

value: Retinal pigment epithelial cells

source_name: choroid cells

value: choroid cells


title: HKL

source_name: OT-I transfer, HKL

value: Heat killed Listeria monocytogenes (LM)


title: WT 1-1


title: WT 2-1


title: T6SS mutant H. hepaticus

city: Pasadena

first: Janet

last: Chow

state: CA

address: 1200 E. California Blvd

institute: Caltech

hyb_protocol: Microarray hybridizations (65ºC, 16h) and washes were performed with Agilent reagents and following standard protocols.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner G2565CA

data_processing: Data were acquired using Agilent's Feature Extraction Software version 10.1.1.1.

source_name: Intestinal epithelial cells with T6SS mutant bacteria

label_protocol: RNA samples were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent).

growth_protocol: MODE-K cells were cultured in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50U/ml penicillin, 50μg/ml streptomycin, and 10mM hepes at 37°C in 5% CO2 incubator. Cells were passaged using trypsin-EDTA. For bacterial incubations, media were changed to UltraDOMA-PF media (Lonza) supplemented with 10% FBS, 2mM L-glutamine, 10mM hepes, non-essential amino acids, 1mM sodium pyruvate, and 0.5mM β-mercaptoethanol. Bacteria were added at a multiplicity of infection (MOI) of 100.

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

treatment_protocol: Co-cultures of bacteria and MODE-K intestinal epithelial cells were incubated at 37°C for 6hr under microaerophilic conditions (1% O2).

value: epithelial cells

source_name: Intestinal epithelial cells with no bacteria


title: Live LM

source_name: OT-I transfer, live LM

value: live actA- Listeria monocytogenes (LM)


title: RPE-phot replicate 1

description: Biological replicate 1 of 3

source_name: photoreceptor cells

value: photoreceptor cells


title: Ring1B KO 2-1


title: WT H. hepaticus

source_name: Intestinal epithelial cells with wild-type bacteria


title: RPE-chor replicate 1

description: Biological replicate 1 of 3


title: RPE-phot replicate 3

description: Biological replicate 3 of 3


title: RPE-phot replicate 2

description: Biological replicate 2 of 3


title: Ring1B KO 2-2


title: Ring1B KO 3-1


title: Ring1B KO 1-2


title: igo12 180min [100 nM rapamycin]

first: Soyeon

last: Lippman

address: 301 Lewis Thomas Lab

institute: Princeton University

description: igo1Δigo2Δ 180 minutes after addition of 100nM rapamycin

hyb_protocol: 500ng of fluorescence-incoporated amplified RNA per reference and sample was added with Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus). Combined reference and sample RNA was loaded to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Arrays were hybridized for 17 hours at 10rpm at 65C in ozone free room. After hybridization, slides were washed and scanned.

scan_protocol: Scanned on an Agilent G2505B scanner using software ChipScan A.6.3.1 Images were quantified using Agilent Feature Extraction Software (version A.7.5.1).

data_processing: Agilent Feature Extraction Software (A.7.5.1) was used for background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae

source_name: igo1Δigo2Δ untreated

label_protocol: 325ng of total RNA was used for Agilent Linear Amplification Protocol. The reference and sample RNA were processed in parallel and combined immediately before framentation and hybridization.

growth_protocol: All strains were freshly streaked onto YEPD plates from frozen stock at -80C before the experiment. Strains were inoculated to SC 2% glucose medium and grown to saturation overnight. The strains were then diluted next day in fresh prewarmed SC 2% glucose medium to a OD600 of 0.05. Strains were grown in water bath at 30C with shaking 160rpm and allowed to go through at least 2 generations to OD of ~0.3. Rapamycin (reconstituted to 1mg/ml in DMSO) was added to the culture (100 nM final concentration), and 5ml samples were collected at indicated timepoints via rapid vacuum filtration then immediately frozen in liquid nitrogen, then stored in -80C. Cells for reference RNA for channel 1 was collected immediately before rapamycin addition.

extract_protocol: Total RNA extracted using Qiagen RNeasy kit following manufacturer's instructions via mechanical lysis using BeadBeater.

tag: treatment

value: Immediately before rapamycin addition

source_name: igo1Δigo2Δ 180 minutes after rapamycin addition

value: 180 minutes after rapamycin addition


title: igo12 120min [100 nM rapamycin]

description: igo1Δigo2Δ 120 minutes after addition of 100nM rapamycin

source_name: igo1Δigo2Δ 120 minutes after rapamycin addition

value: 120 minutes after rapamycin addition


title: RPE-chor replicate 2

description: Biological replicate 2 of 3


title: igo12 20min [100 nM rapamycin]

description: igo1Δigo2Δ 20 minutes after addition of 100nM rapamycin

source_name: igo1Δigo2Δ 20 minutes after rapamycin addition

value: 20 minutes after rapamycin addition


title: Ring1B KO 1-1


title: igo12 60min [100 nM rapamycin]

description: igo1Δigo2Δ 60 minutes after addition of 100nM rapamycin

source_name: igo1Δigo2Δ 60 minutes after rapamycin addition

value: 60 minutes after rapamycin addition


title: rim15 180min [100 nM rapamycin]

description: rim15Δ 180 minutes after addition of 100nM rapamycin

source_name: rim15Δ untreated

source_name: rim15Δ 180 minutes after rapamycin addition


title: rim15 120min [100 nM rapamycin]

description: rim15Δ 120 minutes after addition of 100nM rapamycin

source_name: rim15Δ 120 minutes after rapamycin addition


title: Day 3 differentiated ES cells Rep 3-2

data_processing: BlueFuse software package v3.2 (BlueGnome).Four replicate spots combined and no background subtractions.Normalised by Global Lowess (f = 1/4, iter = 3).

source_name: H3K27me3 D3 Differentiated ES Cells

growth_protocol: OS25 cells grown on 0.1% gelatin-coated dishes in Glasgow’s minimal Eagle’s medium supplemented with 10% fetal calf serum, nonessential amino acids, 1 mmol/l sodium pyruvate, 0.3 mg/ml L-glutamine, .1 mmol/l 2-mercaptoethanol, 1000 U/ml human recombinant leukaemia inhibitory factor (LIF) and 0.1 mg/ml hygromycin. Differentiation was induced by plating the cells at low density without LIF or hygromycin for 1 day. Retinoic acid (RA) 5x10–6 M was then added and cells collected on day 3.

treatment_protocol: Cells harvested, nuclei micrococcal nuclease digested and chromatin released. ChIP for H3K27me3 (ab6002).

tag: cell stage

value: Day 3 Differentiated

source_name: Input D3 ES Cells

growth_protocol: OS25 cells grown on 0.1% gelatin-coated dishes in Glasgow?s minimal Eagle?s medium supplemented with 10% fetal calf serum, nonessential amino acids, 1 mmol/l sodium pyruvate, 0.3 mg/ml L-glutamine, .1 mmol/l 2-mercaptoethanol, 1000 U/ml human recombinant leukaemia inhibitory factor (LIF) and 0.1 mg/ml hygromycin. Differentiation was induced by plating the cells at low density without LIF or hygromycin for 1 day. Retinoic acid (RA) 5x10?6 M was then added and cells collected on day 3.


title: Undifferentiated ES Cells Rep 3-2

source_name: Input UD ES Cells

source_name: H3K27me3 UD ES Cells

value: Undifferentiated


title: rim15 20min [100 nM rapamycin]

description: rim15Δ 20 minutes after addition of 100nM rapamycin

source_name: rim15Δ 20 minutes after rapamycin addition


title: Undifferentiated ES Cells Rep 3-1

value: Input


title: Day 3 differentiated ES cells Rep 1-1


title: rim15 60min [100 nM rapamycin]

description: rim15Δ 60 minutes after addition of 100nM rapamycin

source_name: rim15Δ 60 minutes after rapamycin addition


title: Day 3 differentiated ES cells Rep 2-2


title: Y2092 20min [100 nM rapamycin]

description: Y2092 20 minutes after addition of 100nM rapamycin

source_name: Y2092 untreated

source_name: Y2092 20 minutes after rapamycin addition


title: Undifferentiated ES Cells Rep 1-2


title: Undifferentiated ES Cells Rep 2-1

source_name: UD ES Cells Input


title: Y2092 180min [100 nM rapamycin]

description: Y2092 180 minutes after addition of 100nM rapamycin

source_name: Y2092 180 minutes after rapamycin addition


title: Undifferentiated ES Cells Rep 2-2


title: Day 3 differentiated ES cells Rep 1-2


title: Y2092 60min [100 nM rapamycin]

description: Y2092 60 minutes after addition of 100nM rapamycin

source_name: Y2092 60 minutes after rapamycin addition


title: Day 3 differentiated ES cells Rep 2-1


title: Day 3 differentiated ES cells Rep 3-1


title: Y2092 120min [100 nM rapamycin]

description: Y2092 120 minutes after addition of 100nM rapamycin

source_name: Y2092 120 minutes after rapamycin addition


title: Rim15 vs W303

description: W303 vs rim15Δ at early log phase in SC 2% glucose

source_name: W303 untreated


title: igo12 vs W303

description: W303 vs igo1Δigo2Δ at early log phase in SC 2% glucose

source_name: igo1Δigo2Δ untreated


title: Undifferentiated ES Cells Rep 1-1


title: ReCFN42_WTvsNifA_rep1

status: Public on May 10 2010

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

description: Transcriptional profiling in Minimal Medium 1% O2 was compared between wild type strain and nifA mutant.

hyb_protocol: Both Cy3 and Cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 45 ul of hybridization buffer UniHyb (TeleChem International INC). The mixture was hybridized at 42 C for 14 to 16 h. Hybridized arrays were washed with 2X SSC, 0.1% SDS at 42 C for 2 min, and, subsequently, with 0.1X SSC at room temperature for 2 min, and twice with 0.1X SSC at room temperature for 2 min.

scan_protocol: The array was scanned using a pixel size of 10 um with a Scan Array Lite microarray scanner (Perkin-Elmer, Boston, MA).

data_processing: Spot detection, mean signals, mean local background intensities, image segmentation, and signal quantification were determined for the microarray images using the Array-Pro Analyzer 4.0 software (Media Cybernetics, L.P). Microarray data analysis was performed with genArise software, developed in the Computing Unit of the Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico (http://www.ifc.unam.mx/genarise/). The Lowess normalization was applied using the genArise software. This software identifies differentially expressed genes by calculating an intensity-dependent z-score. It uses a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point and defines a z-score where z measures the number of standard deviations that a data point is from the mean: zi = [Ri•mean(R)]/sd(R), where zi is the z-score for each element; mean (R) is the mean log ratio; Ri is the log ratio for each element; and sd(R) is the standard deviation of the log ratio.

organism: Rhizobium etli CFN 42

source_name: Minimal medium 1% O2

label_protocol: 10 ug of RNA was labeled with Cy3-dUTP using a CyScribe First-Strand cDNA labeling kit (Amersham Biosciences).

extract_protocol: Total RNA isolated using a RNeasy Mini Kit (QIAGEN, Hilden, Germany)

tag: growth conditions

value: minimal medium during 12 hrs with 1% O2

tag: genome/variation

value: wild type

label_protocol: 10 ug of RNA was labeled with Cy5-dUTP using a CyScribe First-Strand cDNA labeling kit (Amersham Biosciences).

value: nifA mutant


title: ReCFN42_WTvsNifA_rep2

description: Transcriptional profiling in Minimal Medium 1% O2 was compared between wild type strain and nifA mutant strain.

tag: strain


title: ReCFN42_WTvsNifA_rep3


title: polysomal RNA, untreated, 0 min, biological replicate #1

status: Public on May 09 2010

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: Polysomal RNA sample extracted from serum starved HeLa cells.

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/).  Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: Hela cells, untreated, 0 min, polysomal RNA, biological replicate #1

growth_protocol: HeLa cells were  cultured in Dulbecco Modified Eagle Medium (DMEM)  supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: Cells were washed once with phosphate buffer saline (PBS) and treated directly on the plate with 300 µl lysis buffer [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/µl RNase inhibitor (Fermentas) and 1 mM dithiothreitol] and transferred to an Eppendorf tube. After a few minute incubation on ice with occasional vortexing, the extracts were centrifuged for 10 min at 12000 g at 4°C. The supernatant was stored at –80°C or loaded directly onto a 15–50% linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged in an Sorvall rotor for 120 min at 40000 rpm. Polysomal fractions were collected monitoring the absorbance at 254 nm and treated directly with proteinase K. After phenol–chloroform extraction and isopropanol precipitation, polysomal RNA was resuspended in 30 µl of water and then repurified with RNeasy kit (Qiagen, Hilden, Germany). RNA quality was assessed by agarose gel electrophoresis and the Agilent 2100 Bioanalyzer platform.

treatment_protocol: HeLa cells were seeded on adherent plates and serum starved for 12h with DMEM, 0.5% FBS, 2mM glutamine.

value: Hela cells, CCL-2

tag: agent

tag: time point

value: 0 min

tag: population

value: polysomal RNA

tag: biological replicate


title: total RNA, untreated, 0 min, biological replicate #3

description: Total RNA sample extracted from serum starved HeLa cells.

source_name: Hela cells, untreated, 0 min, total RNA, biological replicate #3

extract_protocol: Total RNA was extracted using TRIZOL reagent according to the manufacturer's protocol. Briefly, the aqueous phase was used for RNA precipitation with an equal volume of isopropanol. The RNA pellet was washed once with 75% ethanol, then air-dried and re-dissolved in 20 μl of RNase-free water. RNA was quantified using a spectrophotometer and its quality was checked by agarose gel electrophoresis and by Agilent 2100 Bioanalyzer platform, following the manifacturer’s guidelines for sample preparation and analysis of data (Agilent 2100 Bioanalyzer 2100 Expert User's Guide, http://www.agilent.com).

value: total RNA


title: polysomal RNA, untreated, 0 min, biological replicate #3

source_name: Hela cells, untreated, 0 min, polysomal RNA, biological replicate #3


title: total RNA, untreated, 0 min, biological replicate #2

source_name: Hela cells, untreated, 0 min, total RNA, biological replicate #2


title: polysomal RNA, EGF treated, 40 min, biological replicate #3

description: Polysomal RNA sample extracted from serum starved HeLa cells treated with hEGF (1 μg/ml final concentration)  for 40 minutes.

source_name: Hela cells, EGF treated, 40 min, polysomal RNA, biological replicate #3

treatment_protocol: HeLa cells were seeded on adherent plates and serum starved for 12h with DMEM, 0.5% FBS, 2mM glutamine. Cells were treated for 40 minutes with recombinant human epidermal growth factor (hEGF) at final concentration of 1 μg/ml.

value: EGF

value: 40 min


title: subpolysomal RNA, EGF treated, 40 min, biological replicate #2

description: Subpolysomal RNA sample extracted from serum starved HeLa cells treated with hEGF (1 μg/ml final concentration)  for 40 minutes.

source_name: Hela cells, EGF treated, 40 min, subpolysomal RNA, biological replicate #2

extract_protocol: Cells were washed once with phosphate buffer saline (PBS) and treated directly on the plate with 300 µl lysis buffer [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/µl RNase inhibitor (Fermentas) and 1 mM dithiothreitol] and transferred to an Eppendorf tube. After a few minute incubation on ice with occasional vortexing, the extracts were centrifuged for 10 min at 12000 g at 4°C. The supernatant was stored at –80°C or loaded directly onto a 15–50% linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged in an Sorvall rotor for 120 min at 40000 rpm. Subpolysomal fractions were collected monitoring the absorbance at 254 nm and treated directly with proteinase K. After phenol–chloroform extraction and isopropanol precipitation, subpolysomal RNA was resuspended in 30 µl of water and then repurified with RNeasy kit (Qiagen, Hilden, Germany). RNA quality was assessed by agarose gel electrophoresis and the Agilent 2100 Bioanalyzer platform.

value: subpolysomal RNA


title: subpolysomal RNA, untreated, 0 min, biological replicate #1

description: Subpolysomal RNA sample extracted from serum starved HeLa cells.

source_name: Hela cells, untreated, 0 min, subpolysomal RNA, biological replicate #1


title: subpolysomal RNA, untreated, 0 min, biological replicate #3

source_name: Hela cells, untreated, 0 min, subpolysomal RNA, biological replicate #3


title: total RNA, untreated, 0 min, biological replicate #1

source_name: Hela cells, untreated, 0 min, total RNA, biological replicate #1


title: subpolysomal RNA, EGF treated, 40 min, biological replicate #3

source_name: Hela cells, EGF treated, 40 min, subpolysomal RNA, biological replicate #3


title: Young Fat #1

status: Public on May 01 2010

city: Bronx

first: Reid

middle: F

last: Thompson

state: NY

address: 1301 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

description: no additional information

hyb_protocol: See Roche NimbleGen website and R.R. Selzer et al., PMID: 16075461, for details.

scan_protocol: Scanned using a GenePix 4000B scanner (Axon Instruments) (See R.R. Selzer et al., PMID: 16075461)

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (See R.F. Thompson et al., PMID: 18353789, for more details).  Robust multichip average (RMA) was then applied to each group independently (See R.A. Irizarry et al., PMID: 12925520).

source_name: visceral adipose tissue (young)

label_protocol: Random 9-mers pre-labeled with Cy3 or Cy5, for MspI or HpaII, respectively. (See R.R. Selzer et al., PMID: 16075461)

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al., PMID:16809668)

tag: gender

value: male

tag: age

value: 3 months

tag: tissue

value: perinephric visceral adipose tissue

tag: restriction enzyme

value: MspI

tag: genome representation

value: HpaII

value: methylation-sensitive representation


title: Old Fat #1

description: no additional information

source_name: visceral adipose tissue (old)

value: 18 months


title: Old Fat #3

description: no additional information


title: subpolysomal RNA, EGF treated, 40 min, biological replicate #1

source_name: Hela cells, EGF treated, 40 min, subpolysomal RNA, biological replicate #1

tag: cell line


title: Young Fat #4

description: no additional information


title: Young Fat #3

description: no additional information


title: polysomal RNA, EGF treated, 40 min, biological replicate #1

source_name: Hela cells, EGF treated, 40 min, polysomal RNA, biological replicate #1


title: total RNA, EGF treated, 40 min, biological replicate #2

description: Total RNA sample extracted from serum starved HeLa cells treated with hEGF (1 μg/ml final concentration)  for 40 minutes.

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

source_name: Hela cells, EGF treated, 40 min, total RNA, biological replicate #2


title: Young Fat #2

description: no additional information


title: Old Fat #2

description: no additional information


title: polysomal RNA, untreated, 0 min, biological replicate #2

source_name: Hela cells, untreated, 0 min, polysomal RNA, biological replicate #2


title: subpolysomal RNA, untreated, 0 min, biological replicate #2

source_name: Hela cells, untreated, 0 min, subpolysomal RNA, biological replicate #2


title: Old Liver #4

description: no additional information

source_name: liver (old)

value: liver


title: polysomal RNA, EGF treated, 40 min, biological replicate #2

source_name: Hela cells, EGF treated, 40 min, polysomal RNA, biological replicate #2


title: Old Liver #5

description: no additional information


title: Old Liver #3

description: no additional information


title: Young Liver #1

description: no additional information

source_name: liver (young)


title: Old Liver #1

description: no additional information


title: Old Liver #2

description: no additional information


title: total RNA, EGF treated, 40 min, biological replicate #3

source_name: Hela cells, EGF treated, 40 min, total RNA, biological replicate #3


title: Young Liver #6

description: no additional information


title: Young Liver #5

description: no additional information


title: Young Liver #4

description: no additional information


title: total RNA, EGF treated, 40 min, biological replicate #1

source_name: Hela cells, EGF treated, 40 min, total RNA, biological replicate #1


title: Young Liver #2

description: no additional information


title: Young Liver #3

description: no additional information


title: 36a

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

description: raw data file: toka_3.gpr

hyb_protocol: Agilent (Agilent, Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2

data_processing:
Image analysis with GenePix Pro 6.0, bad spots were manually flagged (flag-value -100). Data preprocessing in R with limma package: background subtraction with normexp and offset 50. Log-ratio was calculated between each hybridization and reference (ATCC49173). Normalization was based on setting main peak of log-ratio distribution to zero. Value of reference intensity was added to the normalized log-ratio resulting in the normalized log2-intensity. Bad spots are left blank.
Each channel of a two-channel hybridization was analyzed independently, so each raw data file is associated with two Samples.

organism: Streptomyces turgidiscabies

source_name: potato scab lesion

label_protocol: Invitrogen, BioPrime Array CGH genomic Labeling System

growth_protocol: Streptomyces strains were grown on YME agar plates at 28 °C for 6-8 days

extract_protocol: Bacterial growth was scraped into a mortar and grinded in liquid nitrogen. DNA was extracted from the bacteria using DNeasy Plant Mini Kit (Qiagen GmpH, Germany) according to the manufacturer’s instructions.


title: 22b

description: raw data file: eka_3.gpr


title: 43a

description: raw data file: 251958510007_3.gpr


title: 48a

description: raw data file: 251958510007_5.gpr


title: 48b

description: raw data file: toka_8.gpr


title: 46a

description: raw data file: 251958510007_6.gpr


title: 39a

description: raw data file: toka_7.gpr


title: 37a

description: raw data file: toka_5.gpr


title: 46b

description: raw data file: toka_6.gpr


title: 36b

description: raw data file: 251958510007_3.gpr


title: 37b

description: raw data file: 251958510007_5.gpr


title: 43b

description: raw data file: toka_4.gpr


title: 39b

description: raw data file: 251958510007_7.gpr


title: 22a

description: raw data file: 006_2.gpr


title: 44a

description: raw data file: eka_7.gpr


title: 19a

description: raw data file: 006_5.gpr


title: 19b

description: raw data file: eka_1.gpr


title: 8b

description: raw data file: 006_1.gpr


title: 8a

description: raw data file: eka_1.gpr


title: 7b

description: raw data file: 006_8.gpr


title: 5b

description: raw data file: 006_4.gpr


title: 6b

description: raw data file: 006_6.gpr


title: 6a

description: raw data file: eka_6.gpr


title: St32d

description: raw data file: toka_5.gpr


title: 3a

description: raw data file: eka_2.gpr


title: 3b

description: raw data file: 006_2.gpr


title: St32c

description: raw data file: toka_3.gpr


title: St32a

description: raw data file: 006_4.gpr


title: 31b

description: raw data file: 251958510007_4.gpr

organism: Streptomyces europaeiscabiei


title: 35b

description: raw data file: 251958510007_1.gpr


title: 32a

description: raw data file: toka_6.gpr


title: 35a

description: raw data file: toka_1.gpr


title: 32b

description: raw data file: 251958510007_6.gpr


title: St32b

description: raw data file: 251958510007_1.gpr


title: 31a

description: raw data file: toka_4.gpr


title: 50b

description: raw data file: toka_2.gpr


title: 21a

description: raw data file: 006_7.gpr


title: 26b

description: raw data file: 251958510007_2.gpr


title: 40a

description: raw data file: 251958510007_2.gpr


title: 7a

description: raw data file: eka_8.gpr


title: 5a

description: raw data file: eka_4.gpr


title: 26a

description: raw data file: toka_2.gpr


title: 40b

description: raw data file: eka_5.gpr


title: 21b

description: raw data file: toka_7.gpr


title: 33a

description: raw data file: toka_8.gpr


title: 50a

description: raw data file: 251958510007_7.gpr


title: 18b

description: raw data file: eka_8.gpr


title: 17b

description: raw data file: eka_2.gpr


title: 15a

description: raw data file: 006_1.gpr


title: 14b

description: raw data file: 006_7.gpr


title: 15b

description: raw data file: toka_1.gpr


title: 18a

description: raw data file: 006_3.gpr


title: 17a

description: raw data file: 006_6.gpr


title: 14a

description: raw data file: eka_7.gpr


title: ATCC49173c

description: raw data file: eka_4.gpr

organism: Streptomyces scabiei


title: ATCC49173a

description: raw data file: 006_8.gpr


title: ATCC49173d

description: raw data file: eka_6.gpr


title: 9a

description: raw data file: eka_3.gpr


title: 10b

description: raw data file: 006_5.gpr


title: 9b

description: raw data file: 006_3.gpr


title: ATCC49173b

description: raw data file: 251958510007_4.gpr


title: 10a

description: raw data file: eka_5.gpr


title: Aft1del_Untreated_rep2

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

description: Gene expression in untreated Aft1-deletion yeast

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custom Yeast Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Robbins Model 400 hybridization oven (Robbins Scientific) and an Agilent Rotator Rack.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then a 10 seconds Acetonitrile Wash (Agilent) followed by a 30 seconds Stabilization and Drying Solution wash (Agilent).

scan_protocol: Slides were scanned immediately after washing using a GenePix 4200A (Molecular Devices) using only the cy3 channel, scanning each each array individually (scan area 2088 x 3112 pixels). Scan resolution 10 µm, lines to average= 1, focus position 0µm. Laser set at 100% and PMT between 330 and 370 according to strength of the individual array.

data_processing: The scanned images were analyzed with GenePix 6.0 (Molecular Devices) using default parameters to obtain background subtracted. Features flagged in GenePix as absent or non-uniform outliers were excluded.

source_name: Aft1 delete, no treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Protocol version 5.7 (Agilent) according to the manufacturer's instructions, except using half of the reagents amount in step 2, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Overnight YPD cultures were diluted to 0.05 at OD 600nm in fresh YPD and incubated at 30ºC to an optical density of 0.4 (OD600nm). Untreated samples were removed and flash frozen.

extract_protocol: Total RNA was extracted from yeast cells using TRI reagent (Sigma) as per the manufacturers protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). The RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Once the untreated samples were removed, 120μl of benomyl (final concentration 20μg/ml) was added to each flask. Cells were incubated at 30ºC for 20minutes and 10ml aliquots were removed and flash frozen. Three biological replicates were collected for each sample treatment.

tag: development stage

value: log


title: Aft1del_20minBenomyl_rep1

description: Gene expression in Aft1-deletion yeast after 20 minutes Benomyl treatment

source_name: Aft1 delete, 20 minutes Benomyl treatment


title: Aft1del_Untreated_rep3


title: WT_Untreated_rep1

description: Gene expression in untreated wild-type yeast

source_name: wild type yeast, no treatment


title: WT_Untreated_rep2


title: WT_20minBenomyl_rep1

description: Gene expression in wild-type yeast after 20 minutes Benomyl treatment

source_name: wild type yeast, 20 minutes Benomyl treatment


title: WT_20minBenomyl_rep3


title: Aft1del_20minBenomyl_rep3


title: Aft1del_Untreated_rep1


title: Aft1del_20minBenomyl_rep2


title: WT_Untreated_rep3


title: WT_20minBenomyl_rep2


title: Primary culture of human airway epithelia submerged in growth media, biological replicate 6

status: Public on Apr 15 2010

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

description: Gene expression data from airway epithelia

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix HsAirway array. The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station.

scan_protocol: The arrays were scanned using the Affymetrix Model 3000 scanner

data_processing: Raw data .cel files were imported into Partek Genomics Suite v 6.4 and normalized using the RMA algorithm.

source_name: Primary culture of human airway epithelia, submerged in nutrient media

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen)

tag: condition

value: In vitro

tag: surface

value: Submerged

tag: localization

value: Other

tag: sample date


title: Primary culture of human airway epithelia submerged in growth media, biological replicate 5


title: Primary culture of human airway epithelia submerged in growth media, biological replicate 2


title: Primary culture of human airway epithelia submerged in growth media, biological replicate 1


title: Primary culture of human airway epithelia submerged in growth media, biological replicate 4


title: Primary culture of human airway epithelia submerged in growth media, biological replicate 3


title: In vivo human airway epithelia from brush biopsy, biological replicate 16

source_name: Human airway epithelia in vivo from brush biopsy, trachea

value: In vivo

value: Air-liquid interface

value: Trachea


title: In vivo human airway epithelia from brush biopsy, biological replicate 14


title: In vivo human airway epithelia from brush biopsy, biological replicate 15

source_name: Human airway epithelia in vivo from brush biopsy, bronchus

value: Bronchus


title: In vivo human airway epithelia from brush biopsy, biological replicate 13


title: In vivo human airway epithelia from brush biopsy, biological replicate 11


title: In vivo human airway epithelia from brush biopsy, biological replicate 5


title: In vivo human airway epithelia from brush biopsy, biological replicate 9


title: In vivo human airway epithelia from brush biopsy, biological replicate 8


title: In vivo human airway epithelia from brush biopsy, biological replicate 6


title: In vivo human airway epithelia from brush biopsy, biological replicate 7


title: In vivo human airway epithelia from brush biopsy, biological replicate 12


title: In vivo human airway epithelia from brush biopsy, biological replicate 10


title: In vivo human airway epithelia from brush biopsy, biological replicate 2


title: In vivo human airway epithelia from brush biopsy, biological replicate 1


title: Differentiated primary culture of human airway epithelia, biological replicate 11

source_name: Differentiated primary culture of human airway epithelia, air-liquid interface,trachea


title: In vivo human airway epithelia from brush biopsy, biological replicate 4


title: Differentiated primary culture of human airway epithelia, biological replicate 12


title: Differentiated primary culture of human airway epithelia, biological replicate 13


title: In vivo human airway epithelia from brush biopsy, biological replicate 3


title: Differentiated primary culture of human airway epithelia, biological replicate 6

source_name: Differentiated primary culture of human airway epithelia, air-liquid interface,bronchus


title: Differentiated primary culture of human airway epithelia, biological replicate 10


title: Differentiated primary culture of human airway epithelia, biological replicate 1


title: Differentiated primary culture of human airway epithelia, biological replicate 14


title: Differentiated primary culture of human airway epithelia, biological replicate 5


title: Calu3, replicate 12

source_name: Calu3, air-liquid interface


title: Calu3, replicate 11


title: Differentiated primary culture of human airway epithelia, biological replicate 7


title: Differentiated primary culture of human airway epithelia, biological replicate 9


title: Differentiated primary culture of human airway epithelia, biological replicate 3


title: Differentiated primary culture of human airway epithelia, biological replicate 8


title: Differentiated primary culture of human airway epithelia, biological replicate 15


title: Calu3, replicate 10


title: Differentiated primary culture of human airway epithelia, biological replicate 2


title: Calu3, replicate 5


title: Calu3, replicate 6


title: Calu3, replicate 9


title: Calu3, replicate 7


title: Calu3, replicate 8


title: Calu3, replicate 4


title: Calu3, replicate 2


title: Calu3, replicate 3


title: KO vs WT

status: Public on Apr 01 2010

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). No interslide scaling was performed

organism: Lactiplantibacillus plantarum WCFS1

source_name: L. plantarum delta lp_2991

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Non-pH controlled Batch cultivation MRS-broth. Sampled at OD 1.

extract_protocol: Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µl TE buffer  1.For each sample prepare a tube with Extraction Mixture  2.Harvest cells and quench them immediately in Quenching Buffer. Add 4 volumes of Quenching Buffer ( 40°C) to 1 volume of cell culture  3.Mix and store the sample at -40°C  4.Centrifuge cells at -20°C at 9000 rpm for 10 minutes (Centrifuge RC5B)  5.Discard the supernatant; keep the cell pellet cooled and work quickly to prevent condensation of water. Transfer the pellet with a pre-cooled spatula to a screw-crap tube with Extraction Mixture  6.Mix the cell pellet thoroughly with Extraction Mixture by shaking by hand  7.Freeze the tube immediately in liquid nitrogen  8.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary)  9.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm  10.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C)  11.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C)  12.Continue with the High Pure RNA Isolation Kit from Roche (order # 1 828 665)  13.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer   14.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.

value: delta lp_2991

source_name: L. plantarum WCFS1 Wildtype

value: wildtype


title: WT vs KO


title: Calu3, replicate 1