title: H3S10phK14ac, rep1

description: Chip-chip S2 cells H3S10phK14ac


title: JIL-1, rep3

status: Public on Feb 01 2011

type: genomic

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: Chip-chip S2 cells JIL-1

hyb_protocol: performed by imaGenes (www.imagenes-bio.de)

data_processing: raw signals of all channels in all replicate arrays were log2 transformed and quantile normalized in R/Bioconductor (normalize.quantiles in preprocessCore package).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Input DNA

growth_protocol: Cells were grown in Schneider Medium supplemented with 10% FCS, penicillin and streptomycin.

extract_protocol: ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma). Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).

treatment_protocol: no treatment

tag: cell type

value: Schneider line2 (S2) cells

tag: chip antibody

value: none, input DNA

source_name: JIL1 IP DNA

value: JIL1, R70 (custom rabbit anti JIL-1 antibody)


title: Patient 24, before first IFN-beta injection_chipA

status: Public on Sep 29 2010

type: RNA

city: Rostock

first: Robert

last: Goertsches

address: Gehlsheimer Strasse 20

department: Neurology

institute: University

description: Gene expression data from a multiple sclerosis patient treated with IFN-beta

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133A and B arrays, respectively. Microarrays 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 raw probe-level signals were converted to expression values using the MAS5.0 algorithm. Accordingly, probeset specific detection calls (Absent/Present) and changes with respect to baseline (Increase/Decrease/NoChange) were ascertained.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 µg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Patient blood samples were drawn immediately before first IFN-beta injection as well as two days, one, twelve and twenty-four months post therapy initiation.

extract_protocol: Blood was separated using isopycnic centrifugation (Ficoll), and peripheral blood mononuclear cells were lysed using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocol.

treatment_protocol: Patients were treated with subcutaneous IFN-beta-1b (Betaferon, Bayer Healthcare) at standard dose (250 µg every other day).

tag: gender

value: female

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up

tag: number of relapses during 2-year follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ifn-beta therapy


title: Patient 22, before second IFN-beta injection_chipB


title: Patient 24, before second IFN-beta injection_chipA


title: Patient 21, before month1 IFN-beta injection_chipB


title: Patient 21, before month24 IFN-beta injection_chipB


title: Patient 21, before month12 IFN-beta injection_chipB


title: Patient 23, before month24 IFN-beta injection_chipA

value: male


title: Patient 21, before second IFN-beta injection_chipB


title: Patient 23, before month1 IFN-beta injection_chipA


title: Patient 20, before month24 IFN-beta injection_chipB


title: Patient 23, before month12 IFN-beta injection_chipA


title: Patient 20, before month1 IFN-beta injection_chipB


title: Patient 20, before second IFN-beta injection_chipB


title: Patient 23, before first IFN-beta injection_chipA


title: Patient 20, before first IFN-beta injection_chipB


title: Patient 22, before month12 IFN-beta injection_chipA


title: Patient 22, before first IFN-beta injection_chipA


title: Patient 19, before month24 IFN-beta injection_chipB


title: Patient 22, before month24 IFN-beta injection_chipA


title: Patient 19, before month12 IFN-beta injection_chipB


title: Patient 22, before second IFN-beta injection_chipA


title: Patient 19, before first IFN-beta injection_chipB


title: Patient 21, before month24 IFN-beta injection_chipA


title: Patient 20, before month12 IFN-beta injection_chipB


title: Patient 22, before month1 IFN-beta injection_chipA


title: Patient 21, before first IFN-beta injection_chipA


title: Patient 21, before month12 IFN-beta injection_chipA


title: Patient 19, before month1 IFN-beta injection_chipB


title: Patient 21, before month1 IFN-beta injection_chipA


title: Patient 20, before second IFN-beta injection_chipA


title: Patient 21, before second IFN-beta injection_chipA


title: Patient 17, before month12 IFN-beta injection_chipB


title: Patient 20, before month12 IFN-beta injection_chipA


title: Patient 20, before month1 IFN-beta injection_chipA


title: Patient 20, before month24 IFN-beta injection_chipA


title: Patient 19, before second IFN-beta injection_chipB


title: Patient 17, before month24 IFN-beta injection_chipB


title: Patient 17, before month1 IFN-beta injection_chipB


title: Patient 19, before month12 IFN-beta injection_chipA


title: Patient 19, before month24 IFN-beta injection_chipA


title: Patient 17, before first IFN-beta injection_chipB


title: Patient 19, before month1 IFN-beta injection_chipA


title: Patient 17, before second IFN-beta injection_chipB


title: Patient 16, before second IFN-beta injection_chipB


title: Patient 19, before first IFN-beta injection_chipA


title: Patient 16, before month24 IFN-beta injection_chipB


title: Patient 20, before first IFN-beta injection_chipA


title: Patient 16, before first IFN-beta injection_chipB


title: Patient 16, before month12 IFN-beta injection_chipB


title: Patient 15, before month1 IFN-beta injection_chipB


title: Patient 15, before month24 IFN-beta injection_chipB


title: Patient 15, before month12 IFN-beta injection_chipB


title: Patient 16, before month1 IFN-beta injection_chipB


title: Patient 15, before second IFN-beta injection_chipB


title: Patient 17, before month24 IFN-beta injection_chipA


title: Patient 17, before month12 IFN-beta injection_chipA


title: Patient 19, before second IFN-beta injection_chipA


title: Patient 15, before first IFN-beta injection_chipB


title: Patient 23, before second IFN-beta injection_chipA


title: Patient 14, before month24 IFN-beta injection_chipB


title: Patient 25, before second IFN-beta injection_chipA


title: Patient 17, before month1 IFN-beta injection_chipA


title: Patient 17, before second IFN-beta injection_chipA


title: Patient 16, before month12 IFN-beta injection_chipA


title: Patient 16, before month1 IFN-beta injection_chipA


title: Patient 17, before first IFN-beta injection_chipA


title: Patient 15, before month24 IFN-beta injection_chipA


title: Patient 13, before month1 IFN-beta injection_chipB


title: Patient 14, before month12 IFN-beta injection_chipB


title: Patient 13, before month24 IFN-beta injection_chipB


title: Patient 14, before month1 IFN-beta injection_chipB


title: Patient 13, before month12 IFN-beta injection_chipB


title: Patient 13, before first IFN-beta injection_chipB


title: Patient 14, before first IFN-beta injection_chipB


title: Patient 15, before month12 IFN-beta injection_chipA


title: Patient 15, before month1 IFN-beta injection_chipA


title: Patient 12, before month24 IFN-beta injection_chipB


title: Patient 13, before second IFN-beta injection_chipB


title: Patient 16, before first IFN-beta injection_chipA


title: Patient 16, before month24 IFN-beta injection_chipA


title: Patient 15, before first IFN-beta injection_chipA


title: Patient 15, before second IFN-beta injection_chipA


title: Patient 16, before second IFN-beta injection_chipA


title: Patient 14, before second IFN-beta injection_chipB


title: Patient 14, before month1 IFN-beta injection_chipA


title: Patient 11, before month24 IFN-beta injection_chipB


title: Patient 14, before second IFN-beta injection_chipA


title: Patient 14, before first IFN-beta injection_chipA


title: Patient 11, before first IFN-beta injection_chipB


title: Patient 11, before month12 IFN-beta injection_chipB


title: Patient 14, before month24 IFN-beta injection_chipA


title: Patient 13, before month24 IFN-beta injection_chipA


title: Patient 11, before month1 IFN-beta injection_chipB


title: Patient 12, before second IFN-beta injection_chipB


title: Patient 13, before first IFN-beta injection_chipA


title: Patient 11, before second IFN-beta injection_chipB


title: Patient 13, before second IFN-beta injection_chipA


title: Patient 14, before month12 IFN-beta injection_chipA


title: Patient 21, before first IFN-beta injection_chipB


title: Patient 13, before month12 IFN-beta injection_chipA


title: Patient 12, before first IFN-beta injection_chipB


title: Patient 12, before month12 IFN-beta injection_chipB


title: Patient 12, before month24 IFN-beta injection_chipA


title: Patient 9, before month24 IFN-beta injection_chipB


title: Patient 9, before month12 IFN-beta injection_chipB


title: Patient 12, before month1 IFN-beta injection_chipB


title: Patient 12, before first IFN-beta injection_chipA


title: Patient 13, before month1 IFN-beta injection_chipA


title: Patient 12, before month12 IFN-beta injection_chipA


title: Patient 9, before month1 IFN-beta injection_chipB


title: Patient 11, before month12 IFN-beta injection_chipA


title: Patient 12, before second IFN-beta injection_chipA


title: Patient 12, before month1 IFN-beta injection_chipA


title: Patient 9, before second IFN-beta injection_chipB


title: Patient 11, before first IFN-beta injection_chipA


title: Patient 9, before first IFN-beta injection_chipB


title: Patient 11, before month1 IFN-beta injection_chipA


title: Patient 11, before month24 IFN-beta injection_chipA


title: Patient 8, before month1 IFN-beta injection_chipB


title: Patient 11, before second IFN-beta injection_chipA


title: Patient 8, before month24 IFN-beta injection_chipB


title: Patient 8, before second IFN-beta injection_chipB


title: Patient 7, before month1 IFN-beta injection_chipB


title: Patient 8, before first IFN-beta injection_chipB


title: Patient 7, before first IFN-beta injection_chipB


title: Patient 7, before second IFN-beta injection_chipB


title: Patient 8, before month12 IFN-beta injection_chipB


title: Patient 7, before month12 IFN-beta injection_chipB


title: Patient 9, before first IFN-beta injection_chipA


title: Patient 6, before month12 IFN-beta injection_chipB


title: Patient 9, before month1 IFN-beta injection_chipA


title: Patient 6, before month24 IFN-beta injection_chipB


title: Patient 9, before second IFN-beta injection_chipA


title: Patient 6, before second IFN-beta injection_chipB


title: Patient 7, before month24 IFN-beta injection_chipB


title: Patient 5, before month24 IFN-beta injection_chipB


title: Patient 5, before month12 IFN-beta injection_chipB


title: Patient 9, before month24 IFN-beta injection_chipA


title: Patient 8, before month24 IFN-beta injection_chipA


title: Patient 8, before month12 IFN-beta injection_chipA


title: Patient 8, before month1 IFN-beta injection_chipA


title: Patient 5, before first IFN-beta injection_chipB


title: Patient 9, before month12 IFN-beta injection_chipA


title: Patient 5, before second IFN-beta injection_chipB


title: Patient 6, before month1 IFN-beta injection_chipB


title: Patient 8, before first IFN-beta injection_chipA


title: Patient 4, before month24 IFN-beta injection_chipB


title: Patient 7, before month24 IFN-beta injection_chipA


title: Patient 6, before first IFN-beta injection_chipB


title: Patient 7, before second IFN-beta injection_chipA


title: Patient 6, before month24 IFN-beta injection_chipA


title: Patient 5, before month1 IFN-beta injection_chipB


title: Patient 4, before month1 IFN-beta injection_chipB


title: Patient 4, before second IFN-beta injection_chipB


title: Patient 3, before month24 IFN-beta injection_chipB


title: Patient 6, before month12 IFN-beta injection_chipA


title: Patient 4, before first IFN-beta injection_chipB


title: Patient 3, before month12 IFN-beta injection_chipB


title: Patient 2, before month24 IFN-beta injection_chipB


title: Patient 6, before first IFN-beta injection_chipA


title: Patient 3, before second IFN-beta injection_chipB


title: Patient 7, before month12 IFN-beta injection_chipA


title: Patient 7, before month1 IFN-beta injection_chipA


title: Patient 3, before first IFN-beta injection_chipB


title: Patient 6, before month1 IFN-beta injection_chipA


title: Patient 5, before first IFN-beta injection_chipA


title: Patient 6, before second IFN-beta injection_chipA


title: Patient 5, before month24 IFN-beta injection_chipA


title: Patient 2, before month12 IFN-beta injection_chipB


title: Patient 5, before second IFN-beta injection_chipA


title: Patient 5, before month1 IFN-beta injection_chipA


title: Patient 2, before month1 IFN-beta injection_chipB


title: Patient 2, before first IFN-beta injection_chipB


title: Patient 4, before month24 IFN-beta injection_chipA


title: Patient 2, before second IFN-beta injection_chipB


title: Patient 1, before month24 IFN-beta injection_chipB


title: Patient 4, before month12 IFN-beta injection_chipA


title: Patient 1, before month12 IFN-beta injection_chipB


title: Patient 4, before second IFN-beta injection_chipA


title: Patient 4, before month1 IFN-beta injection_chipA


title: Patient 1, before month1 IFN-beta injection_chipB


title: Patient 4, before first IFN-beta injection_chipA


title: Patient 3, before month24 IFN-beta injection_chipA


title: Patient 3, before first IFN-beta injection_chipA


title: Patient 1, before second IFN-beta injection_chipB


title: Patient 3, before month1 IFN-beta injection_chipA


title: Patient 2, before month24 IFN-beta injection_chipA


title: Patient 3, before month12 IFN-beta injection_chipA


title: Patient 2, before first IFN-beta injection_chipA


title: Patient 1, before month24 IFN-beta injection_chipA


title: Patient 2, before month12 IFN-beta injection_chipA


title: Patient 3, before second IFN-beta injection_chipA


title: Patient 1, before first IFN-beta injection_chipA


title: Patient 2, before second IFN-beta injection_chipA


title: Patient 1, before month12 IFN-beta injection_chipA


title: Patient 2, before month1 IFN-beta injection_chipA


title: Patient 1, before month1 IFN-beta injection_chipA


title: Patient 1, before first IFN-beta injection_chipB


title: Masseter muscle_AQM_Treatment, rep1

status: Public on Sep 21 2010

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

country: Sweden

institute: uppsala university

description:
PA079_P13D5_090128_(porcine).
Masseter muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA), corticosteroids(CS) and sepsis.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were normalized using RMA.

label: biotin

organism: Sus scrofa

source_name: masseter muscle, treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: All piglets originated from the same farm (Vallrums Lantbruk, Ransta, Sweden).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup.

treatment_protocol: Five female domestic piglets (Sus scrofa, average body weight 26.9 kg) were used in this study. Piglets were immobilized by anesthesia and mechanically ventilated via a tracheotomy for a period of five days. During this study period, the animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 – 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed.  Core body temperature (blood) was maintained in the range of 38.5 – 40°C by a servo controlled heating pad.  The animals received intravenous crystalloid fluid (Ringeracetat) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 – 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and bensylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period. A neuromuscular blocking agent (NMBA) was administered as a continuous infusion of pancuronium bromide 0.1mg/kg/h (Pavolun; Organon, Boxtel, The Netherlands) for 5 days while a corticosteroid (CS) was given as bolus doses of betamethasone 0.1 mg/kg (Betapred; GSK, Slona, Sweden) twice daily for 5 days. Endotoxemia was induced by a continuous infusion of Escherichia coli endotoxin, serotype O26:B6 (Sigma Labkemi, Stockholm, Sweden) at 36 µg/kg/h for 1h.

tag: breed

value: Eurasian wild boar

tag: tissue

value: masseter muscle

tag: disease

value: acute quadriplegic myopathy (AQM)

tag: treatment

value: non-depolarizing neuromuscular blocking agents (NMBA), corticosteroids (CS) and sepsis

tag: time

value: 5 days


title: Masseter muscle_AQM_Treatment, rep5

description:
PA079_P18D5_090128_(porcine).
Masseter muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA), corticosteroids(CS) and sepsis.

tag: gender


title: Masseter muscle_AQM_Treatment, rep4

description:
PA079_P17D5_090128_(porcine).
Masseter muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA), corticosteroids(CS) and sepsis.


title: Masseter muscle_AQM_Treatment, rep3

description:
PA079_P16D5_090128_(porcine).
Masseter muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA), corticosteroids(CS) and sepsis.


title: Masseter muscle_AQM_Control, rep3

source_name: masseter muscle, untreated

value: untreated

value: 1 day


title: Patient 1, before second IFN-beta injection_chipA

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)


title: Masseter muscle_AQM_Control, rep5


title: Trioleate with nitrogen 3

status: Public on Aug 27 2010

city: Cambridge

first: Christopher

middle: John

last: Brigham

state: MA

address: 31 Ames Street

department: Biology

country: USA

institute: Massachusetts Institute of Technology

description: Gene expression interogated with 15 perfect match and 15 mismatch probes = 183480 probes. The 37784 remaining probe positions were used for tiling array.

hyb_protocol: Samples were hybridized to the arrays at 45C for 16h Arrays were washed using Affymtrix Genechip Fluidics Station 450 and Affymetrix washing kit (900720)

scan_protocol: Arrays were scaned using Affymtrix Genechip scanner 7G

data_processing: Expression data was examined using ArrayStar software by DNAStar, with RMA normailzation, and Student's t test and ANOVA statistical method

organism: Cupriavidus necator H16

source_name: R. eutropha H16

label_protocol: RNA samples were quanitified using the Agilent Bioanalyzer 2100. 100ng of total RNA was labelled using the Ambion MessageAmpII-Bacteria prokaryotic RNA Kit (Ambion-AM1790)

growth_protocol: Cells were grown initially in tryptic soy broth at 30C overnight, then transferred to PHB production medium with 0.1% ammonium chloride and a.) fructose or b.) trioleate (emulsified with gum arabic) to an initial OD600 = 0.1, and grown at 30C for 24h.  Cells were subcultured into PHB production medium with 0.05% ammonium chloride, with the same carbon sources, to an initial OD600 = 0.05 and grown for 12h at 30C.  Cells were subcultured again to an initial OD = 0.05 and grown until nitrogen was depleted.  Cells were harvested at 50% nitrogen depletion and 2h after total nitrogen depletion.

extract_protocol: Total cellular RNA was extracted using the QIAgen RNEasy Mini RNA isolation kit, following the manufacturer's instructions.

treatment_protocol: Cells were treated with QIAgen RNA Protect reagent before freezing in a dry ice/ethanol slurry, then frozen at -80C.

tag: strain

tag: agent (carbon source)

value: Trioleate

tag: growth protocol

value: with nitrogen

tag: phase in pha production cycle

value: Cell growth, mid log phase


title: Masseter muscle_AQM_Control, rep2


title: Masseter muscle_AQM_Treatment, rep2

description:
PA079_P14D5_090128_(porcine).
Masseter muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA), corticosteroids(CS) and sepsis.


title: Trioleate with nitrogen 2


title: Fructose no nitrogen 3

value: Fructose

value: no nitrogen

value: PHA production, 2 h after nitrogen depletion


title: Trioleate no nitrogen 1


title: Fructose no nitrogen 2


title: Trioleate no nitrogen 2


title: Trioleate with nitrogen 1


title: Fructose with nitrogen 3


title: Patient 5, before month12 IFN-beta injection_chipA

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up


title: Fructose no nitrogen 1


title: Fructose with nitrogen 2


title: Fructose with nitrogen 1


title: Patient 8, before second IFN-beta injection_chipA

tag: number of relapses during 2-year follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ifn-beta therapy


title: Masseter muscle_AQM_Control, rep1

tag: breed

tag: gender

tag: tissue

tag: disease

tag: treatment

tag: time


title: Patient 4, before month12 IFN-beta injection_chipB

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)


title: Patient 7, before first IFN-beta injection_chipA

tag: edss at baseline

tag: edss after 1 year


title: Masseter muscle_AQM_Control, rep4


title: Stationary phase_biological replicate_3_technical replicate_1

status: Public on May 07 2010

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

description: This sample is of stationary phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the third of three biological replicates used in this experiment and it is the first technical replicate

hyb_protocol: 2 µg of labeled cDNA was applied in duplicate to 4x72K custom design NimbleGen arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

scan_protocol: Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.

data_processing: The raw data (.pair) images were processed with NimbleScan software using the RMA algorithm. Background correction was used as implemented in the NimbleScan software package (Roche NimbleGen, Inc.)

label: 5'Cy3-labeled random nonamers

organism: Moraxella catarrhalis RH4

source_name: Moraxella catarrhalis RH4, BHI growth, stationary phase

label_protocol: Total RNA was labeled essentially as described by Ouellet et al. 2009 BMC Biotechnology (available from http://www.biomedcentral.com/1472-6750/9/97). Briefly, 10 µg of RNA was incubated for three hours with 7 µg of 5'Cy3-labeled random nonamers (TriLink Biotechnologies) and Superscript III reverse transcriptase (800 U, Invitrogen) in appropriate reaction conditions (1x First-Strand buffer, 5 mM DTT, 0.33 mM dNTPs, 21 mM actinomycin D (Sigma Aldrich), and 40 U RNaseOut). After first strand synthesis, RNA was degraded by incubating with sodium hydroxide, followed by reaction neutralization with hydrochloric acid. Labeled cDNA was purified and concentrated with CyScribe columns (GE Healthcare Life Sciences) followed by Micron-30 columns (Millipore).

growth_protocol: Moraxella catarrhalis RH4 was grown overnight on brain heart infusion (BHI) agar plates at 37°C in the presence of 5% CO2. BHI broth cultures were grown at 37°C and 200 rpm till lag phase (OD620 = 0.2-0.3), exponential phase (OD620 = 1.2-1.4), and stationary phase (OD620 = 2.0-2.2).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by DNase digestion with the DNAfree kit (Ambion).

treatment_protocol: Bacteria treated with 2 volumes of RNAprotect bacteria reagent (Qiagen).

tag: genotype

value: wild-type

tag: genbank accession


title: Stationary phase_biological replicate_2_technical replicate_2

description: This sample is of stationary phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the second of three biological replicates used in this experiment and it is the second technical replicate


title: Stationary phase_biological replicate_2_technical replicate_1

description: This sample is of stationary phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the second of three biological replicates used in this experiment and it is the first technical replicate


title: Patient 3, before month1 IFN-beta injection_chipB

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up


title: Stationary phase_biological replicate_1_technical replicate_2

description: This sample is of stationary phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the first of three biological replicates used in this experiment and it is the second technical replicate


title: Stationary phase_biological replicate_3_technical replicate_2

description: This sample is of stationary phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the third of three biological replicates used in this experiment and it is the second technical replicate


title: Exponential phase_biological replicate_2_technical replicate_2

description: This sample is of exponential phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the second of three biological replicates used in this experiment and it is the second technical replicate

source_name: Moraxella catarrhalis RH4, BHI growth, exponential phase


title: Stationary phase_biological replicate_1_technical replicate_1

description: This sample is of stationary phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the first of three biological replicates used in this experiment and it is the first technical replicate


title: Exponential phase_biological replicate_1_technical replicate_1

description: This sample is of exponential phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the first of three biological replicates used in this experiment and it is the first technical replicate


title: Lag phase_biological replicate_2_technical replicate_1

description: This sample is of lag phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the second of three biological replicates used in this experiment and it is the first technical replicate

source_name: Moraxella catarrhalis RH4, BHI growth, lag phase


title: Lag phase_biological replicate_3_technical replicate_2

description: This sample is of lag phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the third of three biological replicates used in this experiment and it is the second technical replicate


title: Exponential phase_biological replicate_1_technical replicate_2

description: This sample is of exponential phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the first of three biological replicates used in this experiment and it is the second technical replicate


title: Exponential phase_biological replicate_3_technical replicate_1

description: This sample is of exponential phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the third of three biological replicates used in this experiment and it is the first technical replicate


title: Trioleate no nitrogen 3

tag: strain

tag: agent (carbon source)

tag: growth protocol

tag: phase in pha production cycle


title: Exponential phase_biological replicate_2_technical replicate_1

description: This sample is of exponential phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the second of three biological replicates used in this experiment and it is the first technical replicate


title: Lag phase_biological replicate_2_technical replicate_2

description: This sample is of lag phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the second of three biological replicates used in this experiment and it is the second technical replicate


title: Exponential phase_biological replicate_3_technical replicate_2

description: This sample is of exponential phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the third of three biological replicates used in this experiment and it is the second technical replicate


title: Lag phase_biological replicate_3_technical replicate_1

description: This sample is of lag phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the third of three biological replicates used in this experiment and it is the first technical replicate


title: Lag phase_biological replicate_1_technical replicate_1

description: This sample is of lag phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the first of three biological replicates used in this experiment and it is the first technical replicate


title: Lag phase_biological replicate_1_technical replicate_2

description: This sample is of lag phase wild-type Moraxella catarrhalis RH4 grown in BHI medium. This is the first of three biological replicates used in this experiment and it is the second technical replicate


title: 257_RDb (HG_U95A)

status: Public on Apr 15 2010

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

description: anthracycline resistant derivative of the parental cancer cell line

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing:
Affymetrix Microarray Suite version 5.0
The raw data files that are labeled as '.txt' files cannot be read by Affymetrix sotware. However, they can be loaded, normalized, processed and exported by dChip (http://biosun1.harvard.edu/complab/dchip/). The most current version of dChip can be directly downloaded using following link: http://www.biostat.harvard.edu/~cli/dchip_2010_01.exe

label: standard Affymetrix procedure

source_name: cancer cell line

label_protocol: standard Affymetrix procedure

extract_protocol: Qiagen Rneasy

tag: gastric


title: 181_RDb (HG_U95A)

tag: pancreatic


title: 257_par (HG_U95A)

description: untreated parental cancer cell line


title: MCF7_par_treatDb (HG-U133A)

description: anthracycline-treated parental cancer cell line

tag: breast


title: HT29_par (HG_U95A)

description: untreated parental cancer cell line

tag: colon


title: 181_par (HG_U95A)

description: untreated parental cancer cell line


title: 257_RDb (HG-U133A)


title: HT29_RDb (HG_U95A)


title: HT29_par_treatDb (HG-U133A)


title: HT29_par (HG-U133A)

description: untreated parental cancer cell line


title: HT29_RDb (HG-U133A)


title: 257_par_treatDb (HG-U133A)


title: MCF7_par (HG-U133A)

description: untreated parental cancer cell line


title: MCF7_par (HG_U95A)

description: untreated parental cancer cell line


title: 181_RDb (HG-U133A)


title: coli_lactose_timepoint6_rep3

status: Public on Feb 13 2010

city: Potsdam

first: Szymon

last: Jozefczuk

address: Am Mühlenberg 1

institute: Max Planck Institute

description: US45103052_251684410010_S01_GE1-v5_95_Feb07_1_4_lac3_6.txt

hyb_protocol: The labelling and hybridisation of cDNA microarrays was performed by the out-sourced service provider imaGene GmbH (Berlin, Germany) and was based on Agilent technology.

scan_protocol: The scanning of cDNA microarrays was performed by the out-sourced service provider imaGene GmbH (Berlin, Germany) and was based on Agilent technology.

data_processing: For further analyses the processed signal intensities of all coding regions and RNA genes were extracted and used. Variance stabilization and normalization of the extracted intensities were performed with the vsn packages of the R software environment (R Development Core Team, 2007) and back-transformed to normal intensity scale. For each probeset, e.g. all probes representing for example, a single coding gene, outliers were removed by boxplot statistics and the outlier-removed probe intensities were averaged in a robust way by computing the Tukey biweight.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli_stress experiment

growth_protocol: All cultures were grown aerobically in a thermostatically controlled 37oC culture room. Cultures (150ml culture volume) were stirred by magnetic stirrers at 330 rpm (Thermo Scientific Variomag Multipoint 6in) 1000ml Erlenmeyer flask. Starting cultures were inoculated from a single colony and grown overnight. Each experimental culture was then inoculated from such an overnight culture at a dilution of 1:20 into 150 ml fresh MOPS minimal medium in a 1000 ml flask. The minimal medium used for all experiments was a modification of MOPS (morpholinopropane sulfonate) minimal medium obtained from Teknova, CA (product number M2006) which contains 86 mM NaCl, 9.5 mM NH4Cl, 5 mM K2HPO4 and 0.2% glucose.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit (74104) and mechanical cell disruption with glass beads but without enzymatic lysis. This was carried out in the Qiagen RNeasy kit lysis RLT buffer with beta-mercaptethanol, according to the manufacturer’s recommendations. Mechanical cell disruption was completed through shaking for five min using a Retsch mill (Retsch MM200) on maximum speed. RNA was subsequently cleaned on-column with an additional DNase treatment (Qiagen 79254). The quality of extracted RNA was determined with an Agilent 2100 bioanalyzer having used an Agilent RNA 6000 Nano Kit according to the manufacturer’s recommendations.

treatment_protocol: Oxidative stress 200 ug/ml of 30% pre-warmed hydrogen peroxide (Fluka) was added to 150 ml constantly stirred (330 rpm) cultures kept in 1000 ml flasks. Cold stress Cultures were transferred from 37oC into an ice cold water bath in order to lower the temperature, while stirring, to 16oC in less than 2 min, heat stress Cultures were transferred from 37oC to a 50oC water bath. While stirring, the temperature of each culture was raised to 45oC in less than 2 min. The constantly stirring (330rpm) cultures were then transferred to a 45oC water bath to maintain this temperature glucose lactose shift Carbon source concentrations of 0.15% lactose and 0.05% glucose were used (150 ml culture in 1000 ml flasks, 330 rpm stirring).

tag: treatment group

value: lactose shift

tag: treatment time

value: T6:30 min after growth lag


title: MCF7_RDb (HG-U133A)


title: MCF7_RDb (HG_U95A)


title: 181_par_treatDb (HG-U133A)


title: 181_par (HG-U133A)

description: untreated parental cancer cell line


title: 257_par (HG-U133A)

description: untreated parental cancer cell line


title: coli_lactose_timepoint5_rep3

description: US45103052_251684410013_S01_GE1-v5_95_Feb07_1_2_lac3_5.txt

label_protocol: The labelling and hybridisation of cDNA microarrays was performed by the out-sourced service provider imaGene GmbH (Berlin, Germany) and was based on Agilent technology.

value: T5:20 min after growth lag


title: coli_lactose_timepoint4_rep2

description: US45103052_251684410010_S01_GE1-v5_95_Feb07_1_3_lac2_4.txt

value: T4:10 min after growth lag


title: coli_lactose_timepoint5_rep2

description: US45103052_251684410009_S01_GE1-v5_95_Feb07_1_2_lac2_5.txt


title: coli_lactose_timepoint2_rep2

description: US45103052_251684410011_S01_GE1-v5_95_Feb07_1_4_lac2_2.txt


title: coli_lactose_timepoint4_rep3

description: US45103052_251684410010_S01_GE1-v5_95_Feb07_1_1_lac3_4.txt


title: coli_lactose_timepoint6_rep2

description: US45103052_251684410012_S01_GE1-v5_95_Feb07_1_4_lac2_6.txt


title: coli_lactose_timepoint3_rep3

description: US45103052_251684410011_S01_GE1-v5_95_Feb07_1_1_lac3_3.txt


title: coli_lactose_timepoint6_rep1

description: US45103052_251684410012_S01_GE1-v5_95_Feb07_1_1_lac1_6.txt


title: coli_oxidativestress_timepoint7_rep4

description: US45103052_251684410008_S01_GE1-v5_95_Feb07_1_1_oxd4_7c.txt

value: oxidative stress

value: T7:40 min after stress


title: coli_lactose_timepoint7_rep1

description: US45103052_251684410010_S01_GE1-v5_95_Feb07_1_2_lac1_7.txt

value: T7:40 min after growth lag


title: coli_lactose_timepoint7_rep2

description: US45103052_251684410011_S01_GE1-v5_95_Feb07_1_3_lac2_7.txt


title: coli_lactose_timepoint3_rep1

description: US45103052_251684410011_S01_GE1-v5_95_Feb07_1_2_lac1_3.txt


title: coli_oxidativestress_timepoint8_rep4

description: US45103052_251684410007_S02_GE1-v5_95_Feb07_1_4_oxd4_8b.txt

value: T8:90 min after stress


title: coli_lactose_timepoint4_rep1

description: US45103052_251684410013_S01_GE1-v5_95_Feb07_1_1_lac1_4.txt


title: coli_oxidativestress_timepoint11_rep4

description: US45103052_251684410008_S01_GE1-v5_95_Feb07_1_3_oxd4_11c.txt

value: T11:235 min after stress


title: coli_lactose_timepoint2_rep1

description: US45103052_251684410012_S01_GE1-v5_95_Feb07_1_2_lac1_2.txt


title: coli_oxidativestress_timepoint9_rep4

description: US45103052_251684410008_S01_GE1-v5_95_Feb07_1_4_oxd4_9c.txt

value: T9:150 min after stress


title: coli_oxidativestress_timepoint10_rep4

description: US45103052_251684410004_S01_GE1-v5_95_Feb07_1_4_oxd4_10a.txt

value: T10:210 min after stress


title: coli_lactose_timepoint5_rep1

description: US45103052_251684410012_S01_GE1-v5_95_Feb07_1_3_lac1_5.txt


title: coli_lactose_timepoint2_rep3

description: US45103052_251684410013_S01_GE1-v5_95_Feb07_1_4_lac3_2.txt


title: coli_oxidativestress_timepoint3_rep4

description: US45103052_251684410004_S01_GE1-v5_95_Feb07_1_3_oxd4_3b.txt


title: coli_oxidativestress_timepoint5_rep4

description: US45103052_251684410007_S02_GE1-v5_95_Feb07_1_2_oxd4_5a.txt

value: T5:20 min after stress


title: coli_oxidativestress_timepoint6_rep4

description: US45103052_251684410005_S01_GE1-v5_95_Feb07_1_4_oxd4_6a.txt

value: T6:30 min after stress


title: coli_oxidativestress_timepoint2_rep4

description: US45103052_251684410006_S01_GE1-v5_95_Feb07_1_2_oxd4_2c.txt


title: coli_oxidativestress_timepoint4_rep4

description: US45103052_251684410005_S01_GE1-v5_95_Feb07_1_2_oxd4_4b.txt

value: T4:10 min after stress


title: coli_oxidativestress_timepoint12_rep2

description: US22502595_251684410003_S01_GE1-v5_95_Feb07_1_1_oxd3_12acb.txt

value: T12:260 min after stress


title: coli_oxidativestress_timepoint11_rep2

description: US45103052_251684410006_S01_GE1-v5_95_Feb07_1_1_oxd3_11a.txt


title: coli_oxidativestress_timepoint10_rep2

description: US45103052_251684410004_S01_GE1-v5_95_Feb07_1_1_oxd3_10.txt


title: coli_oxidativestress_timepoint9_rep2

description: US45103052_251684410005_S01_GE1-v5_95_Feb07_1_3_oxd3_9b.txt


title: coli_oxidativestress_timepoint8_rep2

description: US45103052_251684410005_S01_GE1-v5_95_Feb07_1_1_oxd3_8b.txt


title: coli_oxidativestress_timepoint11_rep1

description: US22502595_251684410001_S01_GE1-v5_95_Feb07_1_1_oxd1_11abc.txt


title: coli_oxidativestress_timepoint2_rep2

description: US45103052_251684410004_S01_GE1-v5_95_Feb07_1_3 4 smaples_oxd3_2a.txt


title: coli_oxidativestress_timepoint1_rep2

description: US45103052_251684410006_S01_GE1-v5_95_Feb07_1_3_oxd3_1b.txt


title: coli_oxidativestress_timepoint7_rep2

description: US45103052_251684410007_S02_GE1-v5_95_Feb07_1_3_oxd3_7a.txt


title: coli_oxidativestress_timepoint6_rep2

description: US45103052_251684410006_S01_GE1-v5_95_Feb07_1_4_oxd3_6a.txt


title: coli_oxidativestress_timepoint3_rep2

description: US45103052_251684410004_S01_GE1-v5_95_Feb07_1_1 4samples_oxd3_3a.txt


title: coli_oxidativestress_timepoint5_rep2

description: US45103052_251684410008_S01_GE1-v5_95_Feb07_1_2_oxd3_5a.txt


title: coli_oxidativestress_timepoint4_rep2

description: US45103052_251684410004_S01_GE1-v5_95_Feb07_1_2_oxd3_4b.txt


title: Ovarian cancer cell line PEA2

status: Public on Jun 28 2010

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Genomic DNA extracted from PEA2 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Data was processed in BeadStudio using the standard Illumina protocol. Log R Ratio and B Allele Frequency values were produced by tQN (Staaf et al 2008)

label: C-Bio and A-DNP

source_name: Ovarian cancer cell line PEA2

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

tag: patient number

tag: disease stage

value: Relapse


title: Ovarian cancer cell line PEO4

description: Genomic DNA extracted from PEO4 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer cell line PEO4


title: coli_oxidativestress_timepoint10_rep1

description: US22502595_251684410003_S01_GE1-v5_95_Feb07_1_2_oxd1_10ab.txt


title: coli_oxidativestress_timepoint9_rep1

description: US22502595_251684410002_S01_GE1-v5_95_Feb07_1_1_oxd1_9abc.txt


title: coli_oxidativestress_timepoint8_rep1

description: US22502595_251684410001_S01_GE1-v5_95_Feb07_1_2_oxd1_8abc.txt


title: Ovarian cancer cell line PEO6

description: Genomic DNA extracted from PEO6 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer cell line PEO6


title: coli_oxidativestress_timepoint1_rep4

description: US45103052_251684410007_S02_GE1-v5_95_Feb07_1_1_oxd4_1.txt


title: coli_oxidativestress_timepoint4_rep1

description: US22502595_251684410001_S01_GE1-v5_95_Feb07_1_3_oxd1_4ab.txt


title: coli_oxidativestress_timepoint5_rep1

description: US22502595_251684410002_S01_GE1-v5_95_Feb07_1_3_oxd1_5abc.txt


title: coli_oxidativestress_timepoint6_rep1

description: US22502595_251684410003_S01_GE1-v5_95_Feb07_1_3_oxd1_6abc.txt


title: coli_oxidativestress_timepoint2_rep1

description: US22502595_251684410002_S01_GE1-v5_95_Feb07_1_4_oxd1_2abc.txt


title: coli_oxidativestress_timepoint3_rep1

description: US22502595_251684410003_S01_GE1-v5_95_Feb07_1_4_oxd1_3abc.txt


title: Ovarian cancer cell line PEO23

description: Genomic DNA extracted from PEO23 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer cell line PEO23


title: Ovarian cancer cell line PEO14

description: Genomic DNA extracted from PEO14 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer cell line PEO14

value: Pre-treatment


title: Ovarian cancer cell line PEO1

description: Genomic DNA extracted from PEO1 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer cell line PEO1

value: Post-treatment


title: Ovarian cancer cell line PEA1

description: Genomic DNA extracted from PEA1 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer cell line PEA1


title: coli_heatstress_timepoint4_rep3

description: US45103052_251684410030_S01_GE1-v5_95_Feb07_1_2_heat3_4c.txt

value: heat stress

value: T4:20 min after stress


title: coli_heatstress_timepoint2_rep1

description: US45103052_251684410024_S01_GE1-v5_95_Feb07_1_3_heat1_2a.txt


title: coli_heatstress_timepoint8_rep1

description: US45103052_251684410020_S01_GE1-v5_95_Feb07_1_3_heat1_8c.txt


title: coli_oxidativestress_timepoint1_rep1

description: US22502595_251684410001_S01_GE1-v5_95_Feb07_1_4_oxd1_1ab.txt


title: coli_heatstress_timepoint6_rep3

description: US45103052_251684410032_S01_GE1-v5_95_Feb07_1_2_heat3_6c.txt

value: T6:40 min after stress


title: coli_heatstress_timepoint4_rep1

description: US45103052_251684410024_S01_GE1-v5_95_Feb07_1_1_heat1_4a.txt


title: coli_heatstress_timepoint3_rep3

description: US45103052_251684410031_S01_GE1-v5_95_Feb07_1_1_heat3_3a.txt

value: T3:10 min after stress


title: coli_heatstress_timepoint1_rep3

description: US45103052_251684410032_S01_GE1-v5_95_Feb07_1_3_heat3_1a.txt


title: coli_heatstress_timepoint2_rep3

description: US45103052_251684410031_S01_GE1-v5_95_Feb07_1_2_heat3_2a.txt


title: coli_heatstress_timepoint6_rep1

description: US45103052_251684410025_S01_GE1-v5_95_Feb07_1_1_heat1_6c.txt


title: coli_heatstress_timepoint7_rep1

description: US45103052_251684410029_S01_GE1-v5_95_Feb07_1_2_heat1_7a.txt

value: T7:50 min after stress


title: coli_heatstress_timepoint3_rep1

description: US45103052_251684410028_S01_GE1-v5_95_Feb07_1_4_heat1_3c.txt


title: coli_heatstress_timepoint7_rep3

description: US45103052_251684410031_S01_GE1-v5_95_Feb07_1_4_heat3_7c.txt


title: coli_heatstress_timepoint1_rep1

description: US45103052_251684410019_S01_GE1-v5_95_Feb07_1_4_heat1_1c.txt


title: coli_heatstress_timepoint4_rep2

description: US45103052_251684410018_S01_GE1-v5_95_Feb07_1_1_heat2_4c.txt


title: coli_heatstress_timepoint3_rep2

description: US45103052_251684410028_S01_GE1-v5_95_Feb07_1_2_heat2_3a.txt


title: coli_heatstress_timepoint1_rep2

description: US45103052_251684410016_S01_GE1-v5_95_Feb07_1_2_heat2_1c.txt


title: coli_heatstress_timepoint5_rep3

description: US45103052_251684410032_S01_GE1-v5_95_Feb07_1_4_heat3_5c.txt

value: T5:30 min after stress


title: coli_heatstress_timepoint2_rep2

description: US45103052_251684410016_S01_GE1-v5_95_Feb07_1_4_heat2_2c.txt


title: coli_heatstress_timepoint6_rep2

description: US45103052_251684410030_S01_GE1-v5_95_Feb07_1_3_heat2_6c.txt


title: coli_heatstress_timepoint7_rep2

description: US45103052_251684410030_S01_GE1-v5_95_Feb07_1_1_heat2_7a.txt


title: coli_heatstress_timepoint8_rep2

description: US45103052_251684410031_S01_GE1-v5_95_Feb07_1_3_heat2_8c.txt

value: T8:90 min after stress


title: coli_heatstress_timepoint8_rep3

description: US45103052_251684410030_S01_GE1-v5_95_Feb07_1_4_heat3_8c.txt


title: coli_heatstress_timepoint5_rep2

description: US45103052_251684410032_S01_GE1-v5_95_Feb07_1_1_heat2_5c.txt


title: coli_control_timepoint6_rep3

description: US45103052_251684410027_S01_GE1-v5_95_Feb07_1_2_control3_6a.txt

value: control

value: T6:40 min after reaching OD 0.6


title: coli_control_timepoint7_rep3

description: US45103052_251684410015_S01_GE1-v5_95_Feb07_1_4_control3_7c.txt

value: T7:50 min after reaching OD 0.6


title: coli_control_timepoint5_rep3

description: US45103052_251684410019_S01_GE1-v5_95_Feb07_1_1_control3_5a.txt

value: T5:30 min after reaching OD 0.6


title: coli_control_timepoint8_rep3

description: US45103052_251684410027_S01_GE1-v5_95_Feb07_1_1_control3_8c.txt

value: T8:90 min after reaching OD 0.6


title: coli_control_timepoint4_rep3

description: US45103052_251684410016_S01_GE1-v5_95_Feb07_1_1_control3_4a.txt

value: T4:20 min after reaching OD 0.6


title: coli_heatstress_timepoint5_rep1

description: US45103052_251684410015_S01_GE1-v5_95_Feb07_1_3_heat1_5a.txt


title: coli_control_timepoint3_rep2

description: US45103052_251684410021_S01_GE1-v5_95_Feb07_1_1_control2_3c.txt

value: T3:10 min after reaching OD 0.6


title: coli_control_timepoint4_rep2

description: US45103052_251684410026_S01_GE1-v5_95_Feb07_1_4_control2_4c.txt


title: coli_control_timepoint5_rep1

description: US45103052_251684410015_S01_GE1-v5_95_Feb07_1_2_control1_5a.txt


title: coli_control_timepoint4_rep1

description: US45103052_251684410027_S01_GE1-v5_95_Feb07_1_3_control1_4a.txt


title: coli_control_timepoint5_rep2

description: US45103052_251684410020_S01_GE1-v5_95_Feb07_1_2_control2_5a.txt


title: coli_control_timepoint2_rep2

description: US45103052_251684410022_S01_GE1-v5_95_Feb07_1_1_control2_2a.txt


title: coli_control_timepoint3_rep1

description: US45103052_251684410023_S01_GE1-v5_95_Feb07_1_2_control1_3a.txt


title: coli_control_timepoint8_rep1

description: US45103052_251684410026_S01_GE1-v5_95_Feb07_1_2_control1_8a.txt


title: coli_control_timepoint6_rep1

description: US45103052_251684410020_S01_GE1-v5_95_Feb07_1_1_control1_6a.txt


title: coli_control_timepoint7_rep1

description: US45103052_251684410024_S01_GE1-v5_95_Feb07_1_4_control1_7a.txt


title: coli_control_timepoint7_rep2

description: US45103052_251684410018_S01_GE1-v5_95_Feb07_1_2_control2_7c.txt


title: coli_coldstress_timepoint6_rep3

description: US45103052_251684410017_S01_GE1-v5_95_Feb07_1_2_cold3_6c.txt

value: cold stress


title: coli_control_timepoint8_rep2

description: US45103052_251684410029_S01_GE1-v5_95_Feb07_1_1_control2_8a.txt


title: coli_control_timepoint2_rep3

description: US45103052_251684410028_S01_GE1-v5_95_Feb07_1_3_control3_2a.txt


title: coli_control_timepoint1_rep2

description: US45103052_251684410020_S01_GE1-v5_95_Feb07_1_4_control2_1c.txt


title: coli_control_timepoint1_rep1

description: US45103052_251684410025_S01_GE1-v5_95_Feb07_1_2_control1_1a.txt


title: coli_coldstress_timepoint8_rep3

description: US45103052_251684410022_S01_GE1-v5_95_Feb07_1_4_cold3_8a.txt


title: coli_coldstress_timepoint4_rep3

description: US45103052_251684410018_S01_GE1-v5_95_Feb07_1_4_cold3_4a.txt


title: coli_coldstress_timepoint7_rep3

description: US45103052_251684410026_S01_GE1-v5_95_Feb07_1_3_cold3_7c.txt


title: coli_control_timepoint1_rep3

description: US45103052_251684410019_S01_GE1-v5_95_Feb07_1_2_control3_1c.txt


title: coli_coldstress_timepoint5_rep3

description: US45103052_251684410025_S01_GE1-v5_95_Feb07_1_3_cold3_5c.txt


title: coli_control_timepoint2_rep1

description: US45103052_251684410022_S01_GE1-v5_95_Feb07_1_3_control1_2c.txt


title: coli_coldstress_timepoint2_rep3

description: US45103052_251684410024_S01_GE1-v5_95_Feb07_1_2_cold3_2a.txt


title: coli_coldstress_timepoint3_rep3

description: US45103052_251684410021_S01_GE1-v5_95_Feb07_1_4_cold3_3c.txt


title: coli_coldstress_timepoint7_rep2

description: US45103052_251684410017_S01_GE1-v5_95_Feb07_1_4_cold2_7c.txt


title: coli_coldstress_timepoint1_rep3

description: US45103052_251684410029_S01_GE1-v5_95_Feb07_1_4_cold3_1c.txt


title: coli_coldstress_timepoint5_rep2

description: US45103052_251684410022_S01_GE1-v5_95_Feb07_1_2_cold2_5a.txt


title: coli_coldstress_timepoint4_rep2

description: US45103052_251684410015_S01_GE1-v5_95_Feb07_1_1_cold2_4c.txt


title: coli_coldstress_timepoint3_rep2

description: US45103052_251684410021_S01_GE1-v5_95_Feb07_1_3_cold2_3c.txt


title: coli_coldstress_timepoint2_rep2

description: US45103052_251684410025_S01_GE1-v5_95_Feb07_1_4_cold2_2a.txt


title: coli_coldstress_timepoint6_rep2

description: US45103052_251684410023_S01_GE1-v5_95_Feb07_1_1_cold2_6c.txt


title: coli_coldstress_timepoint4_rep1

description: US45103052_251684410026_S01_GE1-v5_95_Feb07_1_1_cold1_4c.txt


title: coli_control_timepoint6_rep2

description: US45103052_251684410028_S01_GE1-v5_95_Feb07_1_1_control2_6a.txt


title: coli_coldstress_timepoint7_rep1

description: US45103052_251684410023_S01_GE1-v5_95_Feb07_1_4_cold1_7c.txt


title: coli_coldstress_timepoint5_rep1

description: US45103052_251684410017_S01_GE1-v5_95_Feb07_1_3_cold1_5c.txt


title: coli_coldstress_timepoint6_rep1

description: US45103052_251684410029_S01_GE1-v5_95_Feb07_1_3_cold1_6c.txt


title: coli_coldstress_timepoint3_rep1

description: US45103052_251684410019_S01_GE1-v5_95_Feb07_1_3_cold1_3c.txt


title: coli_coldstress_timepoint2_rep1

description: US45103052_251684410021_S01_GE1-v5_95_Feb07_1_2_cold1_2c.txt


title: coli_coldstress_timepoint1_rep1

description: US45103052_251684410017_S01_GE1-v5_95_Feb07_1_1_cold1_1c.txt


title: coli_coldstress_timepoint1_rep2

description: US45103052_251684410027_S01_GE1-v5_95_Feb07_1_4_cold2_1a.txt


title: coli_coldstress_timepoint8_rep1

description: US45103052_251684410016_S01_GE1-v5_95_Feb07_1_3_cold1_8a.txt


title: coli_coldstress_timepoint8_rep2

description: US45103052_251684410023_S01_GE1-v5_95_Feb07_1_3_cold2_8c.txt


title: A/J Hippocampus (1855537001_H)

status: Public on Jan 28 2010

city: Utrecht

first: Simone

last: de Jong

address: Universiteitsweg 100

department: Medical Genetics

institute: UMC Utrecht

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were backgroundcorrected in Beadstudio and transformed (vst) and normalised (rsn) in Lumi (R package)

organism: Mus musculus

source_name: Mouse Hippocampus

label_protocol: RNA samples were prepared with the Illumina TotalPrep kit amplification and labeling protocol. Amplified and biotinylated CRNA was measured with a ribogreen assay

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. Concentrations were det

tag: age

value: 3-4 months

tag: gender

value: M

value: A/J

tag: brain region

value: Hippocampus


title: A/J Amygdala (1855537013_B)

source_name: Mouse Amygdala

value: Amygdala


title: C57BL/6J Amygdala (1855537001_B)


title: C57BL/6J Hippocampus (1855537013_A)


title: A/J Hippocampus (1855537001_G)


title: C57BL/6J Hippocampus (1855537037_F)


title: C57BL/6J Hippocampus (1855537005_G)


title: C57BL/6J Hippocampus (1855537075_A)


title: C57BL/6J Amygdala (1855537037_A)


title: A/J Amygdala (1855537005_E)


title: A/J Hippocampus (1855537001_F)


title: C57BL/6J Amygdala (1855537083_G)


title: C57BL/6J Amygdala (1855537005_B)


title: A/J Amygdala (1855537075_F)


title: A/J Hippocampus (1901214046_G)


title: C57BL/6J Amygdala (1855537084_D)


title: A/J Amygdala (1901214046_A)


title: A/J Hippocampus (1855537083_H)


title: C57BL/6J Amygdala (1855537084_A)


title: C57BL/6J Amygdala (1855537083_F)


title: A/J Hippocampus (1901214046_D)


title: A/J Amygdala (1855537075_G)


title: A/J Amygdala (1901214052_G)


title: C57BL/6J Hippocampus (1855537083_E)


title: C57BL/6J Amygdala (1901214046_F)


title: C57BL/6J Hippocampus (1855537084_B)


title: coli_oxidativestress_timepoint7_rep1

description: US22502595_251684410002_S01_GE1-v5_95_Feb07_1_2_oxd1_7abc.txt

value: oxidative stress

value: T7:40 min after stress


title: A/J Hippocampus (1901214052_F)


title: C57BL/6J Amygdala (1901214052_H)


title: C57BL/6J Hippocampus (1901214046_E)


title: Patient 22, before fifth IFN-beta injection U133B

status: Public on Dec 03 2009

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: Gene expression data from a multiple sclerosis patient treated with IFN-beta

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133B arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 1.5.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each B-chip yielded mRNA abundances of 6,771 human genes.

source_name: Peripheral blood mononuclear cells

growth_protocol: Patient blood samples were taken immediately before first IFN-beta injection as well as one and four weeks post therapy initiation.

extract_protocol: Blood was separated using isopycnic centrifugation (Ficoll), and peripheral blood mononuclear cells were lysated using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocol.

treatment_protocol: Patients were treated with intramuscular IFN-beta-1a (Avonex, Biogen Idec) at standard dose.

value: female

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 2-year follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ifn-beta therapy


title: Patient 23, before second IFN-beta injection U133B

value: male

tag: number of relapses during 1-year follow-up


title: C57BL/6J Hippocampus (1901214052_E)

tag: strain


title: A/J Amygdala (1901214093_B)


title: Patient 23, before first IFN-beta injection U133B


title: Patient 24, before first IFN-beta injection U133B


title: Patient 24, before second IFN-beta injection U133B


title: A/J Amygdala (1901214055_C)


title: C57BL/6J Hippocampus (1901214052_A)


title: A/J Hippocampus (1901214093_A)


title: Patient 23, before fifth IFN-beta injection U133B


title: Patient 24, before fifth IFN-beta injection U133B


title: Patient 19, before first IFN-beta injection U133B


title: Patient 22, before first IFN-beta injection U133B


title: Patient 22, before second IFN-beta injection U133B


title: Patient 20, before first IFN-beta injection U133B


title: Patient 20, before fifth IFN-beta injection U133B


title: Patient 21, before first IFN-beta injection U133B


title: Patient 19, before fifth IFN-beta injection U133B


title: Patient 18, before second IFN-beta injection U133B


title: Patient 19, before second IFN-beta injection U133B


title: Patient 20, before second IFN-beta injection U133B


title: Patient 21, before second IFN-beta injection U133B


title: Patient 18, before first IFN-beta injection U133B


title: A/J Hippocampus (1901214093_C)


title: Patient 17, before fifth IFN-beta injection U133B


title: Patient 18, before fifth IFN-beta injection U133B


title: Patient 14, before second IFN-beta injection U133B


title: Patient 21, before fifth IFN-beta injection U133B


title: Patient 14, before fifth IFN-beta injection U133B


title: Patient 11, before fifth IFN-beta injection U133B


title: Patient 13, before first IFN-beta injection U133B


title: Patient 12, before first IFN-beta injection U133B


title: Patient 12, before second IFN-beta injection U133B


title: Patient 14, before first IFN-beta injection U133B


title: Patient 17, before second IFN-beta injection U133B


title: Patient 13, before fifth IFN-beta injection U133B


title: Patient 17, before first IFN-beta injection U133B


title: Patient 11, before second IFN-beta injection U133B


title: Patient 13, before second IFN-beta injection U133B


title: coli_control_timepoint3_rep3

description: US45103052_251684410018_S01_GE1-v5_95_Feb07_1_3_control3_3c.txt

tag: treatment group

value: control

tag: treatment time


title: Patient 12, before fifth IFN-beta injection U133B

tag: gender


title: Patient 11, before first IFN-beta injection U133B


title: Patient 7, before second IFN-beta injection U133B


title: Patient 8, before first IFN-beta injection U133B


title: Patient 7, before first IFN-beta injection U133B


title: Patient 8, before second IFN-beta injection U133B


title: Patient 9, before fifth IFN-beta injection U133B


title: Patient 7, before fifth IFN-beta injection U133B


title: Patient 6, before fifth IFN-beta injection U133B


title: Patient 8, before fifth IFN-beta injection U133B


title: Patient 9, before first IFN-beta injection U133B


title: Patient 9, before second IFN-beta injection U133B


title: Patient 10, before fifth IFN-beta injection U133B


title: Patient 10, before second IFN-beta injection U133B


title: Patient 10, before first IFN-beta injection U133B


title: Patient 6, before second IFN-beta injection U133B


title: Patient 6, before first IFN-beta injection U133B


title: Patient 3, before second IFN-beta injection U133B


title: Patient 3, before fifth IFN-beta injection U133B


title: Patient 4, before first IFN-beta injection U133B


title: Patient 5, before fifth IFN-beta injection U133B


title: Patient 4, before fifth IFN-beta injection U133B


title: Patient 5, before first IFN-beta injection U133B


title: Patient 4, before second IFN-beta injection U133B


title: Patient 1, before first IFN-beta injection U133B


title: Patient 2, before second IFN-beta injection U133B


title: Patient 5, before second IFN-beta injection U133B


title: Patient 2, before first IFN-beta injection U133B


title: Patient 1, before fifth IFN-beta injection U133B


title: Patient 2, before fifth IFN-beta injection U133B


title: Patient 1, before second IFN-beta injection U133B


title: Patient 3, before first IFN-beta injection U133B


title: Patient 22, before fifth IFN-beta injection U133A

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133A arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 1.5.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each A-chip yielded mRNA abundances of 11,220 human genes.


title: Patient 21, before second IFN-beta injection U133A


title: Patient 24, before first IFN-beta injection U133A


title: Patient 23, before first IFN-beta injection U133A


title: Patient 23, before fifth IFN-beta injection U133A


title: Patient 24, before second IFN-beta injection U133A


title: Patient 23, before second IFN-beta injection U133A


title: Patient 20, before second IFN-beta injection U133A


title: Patient 21, before first IFN-beta injection U133A


title: Patient 24, before fifth IFN-beta injection U133A


title: Patient 20, before first IFN-beta injection U133A


title: Patient 21, before fifth IFN-beta injection U133A


title: Patient 22, before second IFN-beta injection U133A

description: Gene expression data from a multiple sclerosis patient treated with IFN-beta; in comparison to all the other microarrays in the data set, this array was scanned with a GeneChip Scanner 3000 (Affymetrix) at 1.56 micron resolution


title: Patient 22, before first IFN-beta injection U133A


title: Patient 18, before first IFN-beta injection U133A


title: Patient 17, before second IFN-beta injection U133A


title: Patient 18, before second IFN-beta injection U133A


title: Patient 20, before fifth IFN-beta injection U133A


title: Patient 18, before fifth IFN-beta injection U133A


title: Patient 19, before second IFN-beta injection U133A


title: Patient 14, before second IFN-beta injection U133A


title: Patient 19, before fifth IFN-beta injection U133A


title: Patient 14, before first IFN-beta injection U133A


title: Patient 13, before second IFN-beta injection U133A


title: Patient 13, before fifth IFN-beta injection U133A


title: Patient 14, before fifth IFN-beta injection U133A


title: Patient 19, before first IFN-beta injection U133A


title: Patient 17, before first IFN-beta injection U133A


title: Patient 11, before first IFN-beta injection U133A


title: Patient 12, before second IFN-beta injection U133A


title: Patient 12, before fifth IFN-beta injection U133A


title: Patient 12, before first IFN-beta injection U133A


title: Patient 11, before fifth IFN-beta injection U133A


title: Patient 10, before fifth IFN-beta injection U133A


title: Patient 10, before first IFN-beta injection U133A


title: Patient 10, before second IFN-beta injection U133A


title: Patient 13, before first IFN-beta injection U133A


title: Patient 8, before second IFN-beta injection U133A


title: Patient 11, before second IFN-beta injection U133A


title: Patient 8, before fifth IFN-beta injection U133A


title: Patient 9, before fifth IFN-beta injection U133A


title: Patient 6, before fifth IFN-beta injection U133A


title: Patient 7, before fifth IFN-beta injection U133A


title: Patient 9, before first IFN-beta injection U133A


title: Patient 6, before second IFN-beta injection U133A


title: Patient 7, before second IFN-beta injection U133A


title: Patient 6, before first IFN-beta injection U133A


title: Patient 7, before first IFN-beta injection U133A


title: Patient 4, before fifth IFN-beta injection U133A


title: Patient 5, before second IFN-beta injection U133A


title: Patient 5, before first IFN-beta injection U133A


title: Patient 9, before second IFN-beta injection U133A


title: Patient 5, before fifth IFN-beta injection U133A


title: Patient 17, before fifth IFN-beta injection U133A


title: Patient 8, before first IFN-beta injection U133A


title: Patient 3, before fifth IFN-beta injection U133A


title: Patient 4, before first IFN-beta injection U133A


title: Patient 4, before second IFN-beta injection U133A


title: Patient 2, before fifth IFN-beta injection U133A


title: Patient 1, before fifth IFN-beta injection U133A


title: Patient 2, before first IFN-beta injection U133A


title: Patient 3, before first IFN-beta injection U133A


title: Patient 1, before second IFN-beta injection U133A


title: Patient 1, before first IFN-beta injection U133A


title: Patient 2, before second IFN-beta injection U133A


title: Patient 3, before second IFN-beta injection U133A


title: Col-0_C2H4_24hr_1

status: Public on Dec 01 2009

city: La Jolla

first: Joseph

middle: R.

last: Ecker

state: CA

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

hyb_protocol: Performed according to manufacturer’s recommendations

scan_protocol: After hybridization, the arrays were scanned and the.CEL files were used for further analysis.

data_processing: All normalization and quality controls were performed using the packages from the remote analysis computation for gene expression data (RACE, http://race.unil.ch) (Psarros et al. 2005). After normalization, present, marginal, and absent flags, together with the intensity values converted from logarithmic to linear scales, were exported to GeneSpring GX (Aligent). Ethylene- and auxin-regulated genes were selected using a linear model approach (Smyth 2004) implemented in the limma package from BioConductor (Smyth 2004) . This analysis was done using the Remote Analysis Computation for Gene Expression (Psarros et al. 2005). Genes that had a P value of <0.05 and a fold change between control and treatment or control and mutants experiments greater than 1.5 were selected. To account for the multiple testing, a highly sensitive low-stringency false discovery rate (q-value) of 0.15 was used. Finally, only genes that were present or marginal in both replicates in the treated (when selecting upregulated genes) or in the untreated (when selecting for down regulated genes) samples were further considered.

organism: Arabidopsis thaliana

source_name: ethylene treated

label_protocol: cRNA synthesis, labeling, and hybridization to Arabidopsis  ATH1 gene expression arrays (Affymetrix inc) were performed according to manufacturer’s recommendations  except that the labeling reactions were scaled down by 50%.

growth_protocol: The Columbia ecotype (Col-0) was the parent strain for all mutant and transgenic lines used in this study. Arabidopsis seeds were surface-sterilized and plate on the MS medium (4.3g MS salt, 10g sucrose pH 5.7, 8g bactoagar per liter).  After 3-4 days cold (4ºC) treatment, the plates were wrapped in foil and kept in a 24ºC incubator before the phenotypes of seedlings were analyzed. For propagation, seedlings were transferred from plates to soil (Pro-mix-HP) and grown to maturity at 22ºC under a 16 hr light/8 hr dark cycles.

extract_protocol: All RNA extractions were performed using the RNeasy Kit (Qiagen) per manufacturers instructions.

treatment_protocol: Ethylene treatment of Arabidopsis seedlings grown on plates was performed in air-tight containers (AirGas) by flowing hydrocarbon-free air supplied with 10 parts per million (ppm) ethylene or treated with hydrocarbon-free air alone (Kieber et al. 1993).

tag: age

value: 3 week old plants

tag: treatment

value: 4 hour ethylene gas (10 ppm)

tag: cultivar


title: Col-0_C2H4_24hr_2


title: amiR-ETP1/2_2

source_name: microRNA knockdown mutant (amiR-ETP1/2)


title: amiR-ETP1/2_1


title: MCC Patient 174

status: Public on Nov 14 2009

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

description: Gene expression

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: Bioconductor's affy package was used for RMA normalization and raw data processing using default settings for background correction and normalization. Cox regression hazards model was applied to the processed data using the survival package. All analyses were performed using R software.

source_name: Moffitt Cancer Center

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

tag: ethnicity

value: caucasian

tag: grade

value: 3 - Poorly differentiated (PD)

tag: overall_event (death from any cause)

value: no death

tag: dss_event (disease specific survival; death from cancer)

tag: dfs_event (disease free survival; cancer recurrence)

value: recurrence

tag: overall survival follow-up time


title: Col-0_air_1

source_name: air control


title: MCC Patient 173

description: Gene expression

value: 2 - Moderately differentiated (MD)

value: death

value: no recurrence


title: MCC Patient 160

description: Gene expression


title: Col-0_air_2


title: MCC Patient 161

description: Gene expression


title: MCC Patient 170

description: Gene expression


title: MCC Patient 172

description: Gene expression


title: MCC Patient 163

description: Gene expression

value: other (not caucasian, black, or hispanic)


title: MCC Patient 167

description: Gene expression


title: MCC Patient 177

description: Gene expression


title: MCC Patient 171

description: Gene expression


title: MCC Patient 148

description: Gene expression


title: MCC Patient 169

description: Gene expression


title: MCC Patient 147

description: Gene expression


title: MCC Patient 146

description: Gene expression


title: MCC Patient 119

description: Gene expression


title: MCC Patient 139

description: Gene expression


title: MCC Patient 121

description: Gene expression


title: MCC Patient 154

description: Gene expression


title: MCC Patient 145

description: Gene expression


title: MCC Patient 144

description: Gene expression


title: MCC Patient 117

description: Gene expression


title: MCC Patient 116

description: Gene expression


title: MCC Patient 114

description: Gene expression


title: MCC Patient 113

description: Gene expression


title: MCC Patient 118

description: Gene expression


title: MCC Patient 104

description: Gene expression


title: MCC Patient 103

description: Gene expression


title: MCC Patient 99

description: Gene expression


title: MCC Patient 81

description: Gene expression

value: black


title: MCC Patient 68

description: Gene expression


title: MCC Patient 78

description: Gene expression


title: MCC Patient 93

description: Gene expression

value: 1 - Well differentiated (WD)


title: MCC Patient 83

description: Gene expression


title: MCC Patient 77

description: Gene expression


title: MCC Patient 92

description: Gene expression


title: MCC Patient 84

description: Gene expression


title: MCC Patient 107

description: Gene expression


title: MCC Patient 94

description: Gene expression


title: MCC Patient 69

description: Gene expression


title: MCC Patient 60

description: Gene expression


title: MCC Patient 63

description: Gene expression


title: MCC Patient 59

description: Gene expression


title: MCC Patient 66

description: Gene expression


title: MCC Patient 67

description: Gene expression


title: MCC Patient 55

description: Gene expression


title: MCC Patient 37

description: Gene expression


title: MCC Patient 54

description: Gene expression


title: MCC Patient 52

description: Gene expression


title: MCC Patient 58

description: Gene expression


title: MCC Patient 56

description: Gene expression


title: MCC Patient 36

description: Gene expression


title: MCC Patient 26

description: Gene expression


title: MCC Patient 15

description: Gene expression


title: MCC Patient 14

description: Gene expression


title: MCC Patient 23

description: Gene expression


title: MCC Patient 34

description: Gene expression


title: MCC Patient 17

description: Gene expression


title: MCC Patient 29

description: Gene expression


title: MCC Patient 22

description: Gene expression


title: MCC Patient 100

description: Gene expression


title: MCC Patient 9

description: Gene expression


title: MCC Patient 5

description: Gene expression


title: Δrsf1 YPG biological-rep1

status: Public on May 29 2009

city: Detroit

first: George

middle: Gordon

last: Roberts III

address: 540 E. Canfield

department: Immunology/Microbiology

institute: Wayne State University

description: Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S cerevisiae (submitted)

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hours at 37ºC. Fragmentation and hybridization were performed at the MSU Research Technology Support Facility

scan_protocol: Gene Chips were scanned in a high density GC3000 scanner using GCOS operating software

data_processing: The data were pre-analyzed with Microarray Suite version 5.0 (MAS 5.0). Median of each chip scaled to 500, values less than 0.01 set to 0.01 at the MSU Research Technology Support Facility

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: isogenic Δrsf1 mutant yeast grown to A600=0.6 in YPG

label_protocol: 1 µg ds cDNA was labeled according to Affymetrix manual specifications.

growth_protocol: Cells grown to A600 = 0.6 in 50 ml of rich medium containing dextrose, glycerol or ethanol as sole carbon source

extract_protocol: total nucleic acids were extracted using the "hot phenol extraction" method (McEntee and Hudson, Anal Biochem. 1989 176(2):303-6.) PolyA mRNA was prepared according to oligotex manual specifications.

treatment_protocol: Cells grown to A600 = 0.6 in 50 ml of rich medium containing dextrose as sole carbon source were collected by centrifugation, washed 2x in YPG and resupended in YPG prewarmed to 30ºC and incubated for the specified number of minutes

value: isogenic Δrsf1 mutant


title: Δrsf1 YPE biological-rep1

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hours at 37ºC. Fragmentation and hybridization were performed at the MSU Research Tecnhology Support

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). Median of each chip scaled to 500, values less than 0.01 set to 0.01. MSU Research Tecnhology

source_name: isogenic Δrsf1 mutant yeast grown to A600=0.6 in YPE


title: Δrsf2 YPG biological-rep2

description:
PMID: 16208474
Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S cerevisiae (submitted)

source_name: isogenic Δrsf2 mutant yeast grown to A600=0.6 in YPG

value: isogenic Δrsf2 mutant


title: Δrsf1 YPG biological-rep2

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). Median of each chip scaled to 500, values less than 0.01 set to 0.01 at the MSU Research Technology Support Facility


title: Δrsf2 YPG biological-rep1


title: BY4741 YPG biological-rep3

description:
PMID: 16741729
PMID: 16208474
Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S cerevisiae (submitted)

source_name: wild type yeast grown to A600=0.6 in YPG

value: wild type parent BY4741


title: Δrsf1 YPG biological-rep3


title: Δrsf1 YPD biological-rep1

source_name: isogenic Δrsf1 mutant yeast grown to A600=0.6 in YPD


title: Δrsf1 YPG15 biological-rep1

source_name: isogenic Δrsf1 mutant  yeast grown to A600=0.6 in YPD then switched to YPG for 15 minutes


title: BY4741 YPE biological-rep1

description:
PMID: 16741729
Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S cerevisiae (submitted)

source_name: wild type yeast grown to A600=0.6 in YPE


title: BY4741 YPG biological-rep1


title: Δrsf1 YPG30min biological-rep2

source_name: isogenic Δrsf1 mutant  yeast grown to A600=0.6 in YPD then switched to YPG for 30 minutes


title: Δrsf1 YPG30min biological-rep1

source_name: isogenic Δrsf1 mutant   yeast grown to A600=0.6 in YPD then switched to YPG for 30 minutes


title: Δrsf1 YPG30min biological-rep3


title: BY4741 YPG biological-rep2

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). Median of each chip scaled to 500, values less than 0.01 set to 0.01.


title: BY4741 YPG60min biological-rep1

source_name: wild type yeast grown to A600=0.6 in YPD then switched to YPG for 60 minutes


title: Δrsf1 YPG60 biological-rep1

source_name: isogenic Δrsf1 mutant  yeast grown to A600=0.6 in YPD then switched to YPG for 60 minutes


title: BY4741 YPG30min biological-rep1

source_name: wild type yeast grown to A600=0.6 in YPD then switched to YPG for 30 minutes


title: BY4741 YPG30min biological-rep3


title: BY4741 YPD biological-rep1

source_name: wild type yeast grown to A600=0.6 in YPD


title: BY4741 YPG15min biological-rep1

source_name: wild type yeast grown to A600=0.6 in YPD then switched to YPG for 15 minutes


title: PCL-004_GWP

status: Public on May 16 2009

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human plasma cell leukemia patient PCL-004

hyb_protocol: Following fragmentation, 40 micrograms of biotin-labeled DNA were hybridized for 16 hr at 48°C on GeneChip Human Mapping 50K XbaI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Mapping 50K XbaI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. FBN procedure was finally applied to infer exact local copy number as described in the mentioned Reference.

source_name: Human multiple myeloma patient PCL-004

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 nanograms of genomic DNA.

extract_protocol: Genomic DNA extraction was performed using Wizard® Genomic DNA Purification kit according to the manufacturer's instructions (Promega).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: tc classification

value: PCL


title: MM-254_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-254

source_name: Human multiple myeloma patient MM-254


title: PCL-005_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human plasma cell leukemia patient PCL-005

source_name: Human multiple myeloma patient PCL-005


title: PCL-011

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human plasma cell leukemia patient PCL-011

source_name: Human multiple myeloma patient PCL-011


title: BY4741 YPG30min biological-rep2


title: MM-253_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-253

source_name: Human multiple myeloma patient MM-253


title: MM-239_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-239

source_name: Human multiple myeloma patient MM-239


title: PCL-012

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human plasma cell leukemia patient PCL-012

source_name: Human multiple myeloma patient PCL-012


title: MM-251_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-251

source_name: Human multiple myeloma patient MM-251


title: MM-250_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-250

source_name: Human multiple myeloma patient MM-250


title: MM-238_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-238

source_name: Human multiple myeloma patient MM-238


title: MM-242_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-242

source_name: Human multiple myeloma patient MM-242


title: MM-246_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-246

source_name: Human multiple myeloma patient MM-246


title: MM-240_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-240

source_name: Human multiple myeloma patient MM-240


title: MM-257_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-257

source_name: Human multiple myeloma patient MM-257


title: MM-236_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-236

source_name: Human multiple myeloma patient MM-236


title: MM-237_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-237

source_name: Human multiple myeloma patient MM-237


title: MM-229_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-229

source_name: Human multiple myeloma patient MM-229


title: MM-210_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-210

source_name: Human multiple myeloma patient MM-210


title: MM-225_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-225

source_name: Human multiple myeloma patient MM-225


title: MM-208_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-208

source_name: Human multiple myeloma patient MM-208


title: MM-209_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-209

source_name: Human multiple myeloma patient MM-209


title: MM-233_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-233

source_name: Human multiple myeloma patient MM-233


title: MM-154_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-154

source_name: Human multiple myeloma patient MM-154


title: MM-194_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-194

source_name: Human multiple myeloma patient MM-194


title: MM-179_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-179

source_name: Human multiple myeloma patient MM-179


title: MM-174_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-174

source_name: Human multiple myeloma patient MM-174


title: MM-206_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-206

source_name: Human multiple myeloma patient MM-206


title: MM-212_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-212

source_name: Human multiple myeloma patient MM-212


title: MM-228_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-228

source_name: Human multiple myeloma patient MM-228


title: MM-177_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-177

source_name: Human multiple myeloma patient MM-177


title: MM-195_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-195

source_name: Human multiple myeloma patient MM-195


title: MM-151_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-151

source_name: Human multiple myeloma patient MM-151


title: MM-131_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-131

source_name: Human multiple myeloma patient MM-131


title: MM-150_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-150

source_name: Human multiple myeloma patient MM-150


title: MM-149_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-149

source_name: Human multiple myeloma patient MM-149


title: MM-030_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-030

source_name: Human multiple myeloma patient MM-030


title: MM-042_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-042

source_name: Human multiple myeloma patient MM-042


title: MM-016_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-016

source_name: Human multiple myeloma patient MM-016


title: MM-015_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-015

source_name: Human multiple myeloma patient MM-015


title: MM-079_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-079

source_name: Human multiple myeloma patient MM-079


title: MM-043_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-043

source_name: Human multiple myeloma patient MM-043


title: MM-031_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-031

source_name: Human multiple myeloma patient MM-031


title: MM-038_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-038

source_name: Human multiple myeloma patient MM-038


title: MM-037_GWP

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-037

source_name: Human multiple myeloma patient MM-037


title: WT vs ade16 ade17 knock-out mutant (dye swap)

status: Public on May 15 2009

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

description: Technical replicate 2 of 2 (dye swap).

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dried and ready for scanning.

scan_protocol: Scanned on a genepix 4000B scanner (Axon)

data_processing:
Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method.

source_name: Total RNA extracted from WT strain labeled with Cyanine-5 (red).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Cell growth 24 hours at 30°C in SD medium (Casaminoacid 0.2%, Adenin 300µM, Uracil 200µM, Tryptophan 200µM) to an OD = 0.5

extract_protocol: Hot phenol extract procedure followed by RNEasy Mini Kit purification step (Quiagen)

tag: WT Mat alpha his3D1 leu2D0 ura3D0 strain

source_name: Total RNA extracted from ade16 ade17 knock-out mutant strain labeled with Cyanine-3 (green).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

tag: ade16 ade17 knock-out mat alpha ade16

value: :KanMX4 ade17::KanMX4 his3D1 leu2D0 ura3D0 strain


title: PCL-008_5

status: Public on Apr 14 2009

description: Gene expression profiling data from human plasma cell leukemia patient PCL-008

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.

source_name: Human multiple myeloma patient PCL-008

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

tag: legend

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); N:Normal donor sample; MGUS:Monoclonal Gammopathy of Undetermined Significance sample; PCL:Plasma Cell Leukemia sample.

tag: cell type

value: purified plasma cells (PCs)

tag: sample type


title: PCL-002_5

description: Gene expression profiling data from human plasma cell leukemia patient PCL-002

source_name: Human multiple myeloma patient PCL-002