title: IgG_Control_rep2

description: chromatin IP


title: Unfractionated, Gcn2 knockout liver, +Met, biological rep1

status: Public on Nov 10 2009

type: RNA

city: Hershey

first: An

last: Dang Do

state: PA

address: 500 University Drive

department: Cellular and Molecular Physiology

country: USA

institute: Penn State College of Medicine

description: Unfractionated sample

hyb_protocol: 15 ug of fragmented cRNA was used to prepare 300 ul of hybridization cocktail as per the manufacturer's instructions.  200 ul of that hybridization cocktail was hybridized to Mouse Genome 430_2.0 Arrays for 16 hours at 45C.  Arrays were washed and stained using a GeneChip Fluidics Station 400 as per the manufacturer's instructions.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 scanner.

data_processing: Affymetrix CHP files containing qualitative and quantitative values of each probe set on the arrays were imported into GeneSpring (Agilent Technologies, Inc., Palo Alto, CA) and sorted for raw expression values > 80 in at least 1 of 16 conditions as an initial filter to eliminate background noise.  The resulting lists were imported into Excel and analyzed using the Z-ratio method (Cheadle et al., J Mol Diagn 5:73-81; Mazan-Mamczarz et al., Biotechniques 39:61-7).  First, the data were transformed using log10.  The transformed values were used in the following calculations:  Zscore = (intensityG – mean intensityG1…Gn)/SDG1…Gn, where G = any gene on hybridization array, G1…Gn = aggregate measure of all genes.  Zratios = [(ZscoreG1ave)Exp – (ZscoreG1ave)Con]/SD of Zscore differencesG1…Gn, where G1 = average Z score for any particular gene being tested under multiple experimental conditions (experimental vs. control), G1…Gn = aggregate measure of all of the genes. Z ratio data provided as a supplementary file on the Series record.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: liver, Gcn2-/-, +Met, unfractionated

label_protocol: RNA from two perfused liver samples per condition (8 conditions:  unfractionated and polysomal fractions of treated or control wild-type or knockout) were pooled to minimize biological variations.  Twelve μg of total RNA were used in the initial cDNA conversion step.  All steps including double-strand cDNA synthesis, in vitro labeling and cRNA fragmentation were done using the Affymetrix One-Cycle Target Labeling and Control Reagents kit and protocol.

growth_protocol: All animals received water and food (Harkland, TX) ad libitum and were maintained according to the Institutional Animal Care and Use Committee-approved protocol at The Pennsylvania State University College of Medicine.  Global Gcn2-/- and wild-type littermate mice, 3-6 months old, were generated according to a previously published protocol (Zhang et al., Mol Cell Biol 22:6681-8).

extract_protocol: Total RNA was extracted from one mL of detergent-containing supernatant or from the sucrose density gradient fractions using acid phenol:chloroform (Ambion, Inc., Austin, TX).  Per mL of sample, 40 μL of 0.5 M EDTA, 25 μL of 20% SDS and one volume of acid phenol:chloroform were added.  After a 30 min centrifugation at 3, 000 x g (Beckmann GS-6KR), 4°C, the top clear layer was removed, and RNA extracted a second time with the addition of one volume acid phenol:chloroform.  Precipitation of RNA was done overnight in 2.5 volumes of 100% ethanol and 1/10 volume of 5 M NH4OAc (Ambion).  RNA was pelleted, washed twice with 75% ethanol and resuspended in RNA storage solution plus anti-RNAse (Ambion).  The concentration and purity of RNA samples were measured by the Agilent 2100 Bioanalyzer (Robert Brucklacher, Functional Genomics Core Facility, PSU-COM) prior to hybridization array and QRT-PCR applications.

treatment_protocol: We followed previously published protocols (Feldhoff et al., J Biol Chem 252:3611-6; Tolman et al., J Biol Chem 248:4552-60) for single-pass perfusion.  For perfusion of Gcn2 +/+ and -/- mice, methionine was omitted from the perfusate for the treated condition.  Discontinuous, 9-step 20% (10 mM HEPES, pH 7.4; 250 mM KCl; 5 mM MgCl2; 0.5 mM EDTA; 20% w/w sucrose) to 47% (10 mM HEPES, pH 7.4; 250 mM KCl; 5 mM MgCl2; 0.5 mM EDTA; 47% w/w sucrose) sucrose density gradients were used to separate mRNAs based on the number of bound ribosomes.  One mL of detergent-containing supernatant (from perfused liver homogenate) was loaded onto the 20-47% sucrose gradients and centrifuged at 28,000 rpm (Beckmann SW-28), 4°C, for 3 h 38 min for polysome profiles or 22,500 rpm (Beckmann JS-24.38), 4°C, for 19 h 9 min for subunit profiles.  Gradient profiles were visualized using an ISCO UV detection unit with a 254 nm filter and fractionated using an ISCO gradient pump (Teledyne Isco, Inc., Lincoln, NE).

tag: Genotype

value: Gcn2 knockout

tag: Age

value: 3-6 months


title: mgrR knockout mutation, 2

city: BETHESDA

first: Deborah

middle: M

last: Hinton

state: MD

address: 8 center Dr., Building 8, Rm 2A21

institute: NIH

description: Gene expression from mgrR mutant derived from  E. coli K12 MG1655

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip E. coli Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray software version 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Escherichia coli K-12

source_name: mgrR knockout mutation, 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: A fresh colony of each strain was innoculated in LB (with ampicilline if strains contain plasmids) and was grown at 37C with agitation. The cells were grown to OD600=0.5.

extract_protocol: Hot phenol extraction method was used for RNA purification according to the manufacturer's instructions.

treatment_protocol: To induce MgrR, IPTG was added into culture at a final concentration of 100uM for 15min.

tag: genotype/variation

value: mgrR knockout mutation


title: mgrR knockout mutation, 1

source_name: mgrR knockout mutation, 1


title: miR-124 12 hrs 10_09 (4) NO AMP

city: Stanford

first: Patrick

middle: O

last: Brown

state: CA

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85432.gif

hyb_protocol: not provided

scan_protocol: GenePix

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: universal reference AMPLIFIED

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: universal reference AMPLIFIED

source_name: miR-124 12 hrs NO AMP

tag: experiment

value: miR-124 12 hrs NO AMP


title: mock 12 hrs 10_09 (6) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85431.gif

source_name: mock 12 hrs NO AMP

value: mock 12 hrs NO AMP


title: wild type; derivative of E. coli MG 1655, 1

description: Gene expression from Wild type E. coli K12 MG1655


title: LCB-30-1

status: Public on Nov 09 2009

city: Pittsburgh

first: Xinghua

last: Lu

address: 5607 Baum Blvd

department: Dept Biomedical Informatics

institute: University of Pittsburgh

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Bioconductor robust microarray averaging (RMA)

organism: Saccharomyces cerevisiae

label_protocol: standard Affymetrix protocol

growth_protocol: YPD, log phase

extract_protocol: standard Affymetrix protocol

treatment_protocol: Heat stress at 39C

tag: strain

tag: genotype

value: MAT α leu2-3 112 ura3-52 rme1 trp1 his4 HMLa lcb4::KanMX lcb5::KanMX

tag: time

value: 30 min after heat stress


title: Unfractionated, Gcn2 wild-type liver, +Met, biological rep1

description: Unfractionated sample

source_name: liver, Gcn2+/+, +Met, unfractionated

value: Gcn2 wild-type


title: mock 12 hrs 10_09 (3) NO AMP

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85423.gif

source_name: mock 12 hrs no amp

value: mock 12 hrs no amp


title: LCB-30-2


title: wild type; derivative of E. coli MG 1655, 2


title: mir-124 12 hrs SS #2 (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80616.gif
Measurement: concentration(absolute) 60 nM

source_name: universal reference

value: universal reference

tag: cell line


title: mock 12 hrs SS #2 (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80617.gif


title: Unfractionated, Gcn2 wild-type liver, +Met, biological rep2

description: Unfractionated sample


title: Unfractionated, Gcn2 wild-type liver, -Met, biological rep1

description: Unfractionated sample

source_name: liver, Gcn2+/+, -Met, unfractionated


title: mock 12 hrs SS #2 (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80613.gif


title: LCB-25-2

value: 25 min after heat stress


title: mock 12 hrs SS #2 (5-14-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80615.gif


title: LCB-10-2

value: 10 min after heat stress


title: LCB-15-2

value: 15 min after heat stress


title: LCB-5-2

value: 5 min after heat stress


title: LCB-25-1


title: LCB-15-1


title: LCB-20-1

value: 20 min after heat stress


title: LCB-5-1


title: JK-25-2

value: MAT α leu2-3 112 ura3-52 rme1 trp1 his4 HMLa


title: LCB-0-1

value: Before heat stress


title: LCB-0-2


title: JK-20-2


title: Polysome, Gcn2 knockout liver, +Met, biological rep2

description: Polysome sample

source_name: liver, Gcn2-/-, +Met, polysome

value: Gcn2 knockout

value: 3-6 months


title: JK-25-1


title: JK-30-2


title: mir-124 12 hrs SS #2 (5-12-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80614.gif
Measurement: concentration(absolute) 60 nM


title: JK-30-1


title: mir-124 12 hrs SS #2 (5-20-08)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80618.gif
Measurement: concentration(absolute) 60 nM


title: LCB-20-2


title: JK-15-2


title: JK-20-1


title: JK-10-2


title: JK-15-1


title: JK-10-1


title: JK-0-2


title: DPL-30-1

value: MAT α leu2-3 112 ura3-52 rme1 trp1 his4 HMLa dpl1:KanMX


title: DPL-25-1


title: DPL-25-2


title: DPL-30-2


title: DPL-20-1


title: DPL-15-2


title: DPL-5-2


title: JK-5-2


title: DPL-5-1


title: LCB-10-1


title: DPL-10-2


title: DPL-0-1


title: JK-0-1


title: DPL-20-2


title: DPL-15-1


title: DPL-0-2


title: DPL-10-1


title: CD4+ T cell rep1

city: Lund

first: Joanne

last: Attema

address: Tornavagen 10

department: Immunology

country: Sweden

institute: Lund University

description: CD4+ T cell replicate 1

hyb_protocol: Hybridization was performed by Lund University and Linköping University Array facilities

scan_protocol: Scanning was performed by Lund University and Linköping University Array facilities

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and quantile normalization (Bolstad et al. Bioinformatics 19(2):185)

label: Biotin

source_name: spleen derived CD4+ T cell

label_protocol: Labeling was performed by Lund University and Linköping University Array facilities

extract_protocol: Total RNA was extracted using the RNeasy Microkit (Qiagen, USA) and genomic DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the SciBlue Facilty, Lund University.

treatment_protocol: HSCs and MPPs were FACS sorted from the bone marrow of 10-12 week old C57Bl/6 mice

tag: age

value: 10-12 week old

tag: tissue

value: spleen

tag: cell type

value: mature CD4+ T cells


title: PreMegE rep4

description: PreMegE replicate 3

source_name: bone marrow derived PreMegE

value: bone marrow


title: CD4+ T cell rep2

description: CD4+ T cell replicate 2


title: PreMegE rep2

description: PreMegE replicate 2


title: Unfractionated, Gcn2 wild-type liver, -Met, biological rep2

description: Unfractionated sample

value: Gcn2 wild-type


title: PreMegE rep3

description: PreMegE replicate 3


title: PreMegE rep1

description: PreMegE replicate 1


title: MPP rep3

description: MPP replicate 3

source_name: bone marrow derived MPP

value: multipotent progenitors (MPP)


title: pb WT 5

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

description: parasites were cultured for 12h in ookinete culture medium.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4X44k for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91_0806) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Plasmodium berghei

source_name: wildtype AP2 domain

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent)

growth_protocol: Blood stage parasites were cultured for 20h in ookinete culture medium.

extract_protocol: Total RNA was extracted from ookinetes using Total RNA Isolation System (Promega).

value: WT


title: MPP rep2

description: MPP replicate 2


title: HSC rep2

description: HSC replicate 2

source_name: bone marrow derived HSC

value: hematopoieitic stem cells (HSC)


title: XY SSCs at E12.5, pool 3

city: Fort Collins

first: Gerrit

middle: J

last: Bouma

state: CO

address: 3801 W. Rampart Road

department: Biomedical Sciences

institute: Colorado State University

description: Gene expression data from E12.5 XY isolated SSCs

hyb_protocol: 10ug of cRNA was hybridized on the Mouse Genome 430v2.0 GeneChipTM array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix) laser confocal scanner.

data_processing: Probe level data were imported into the R software environment, and R/affy software was used to normalize the data, perform background subtraction, and obtain summary expression values for each probe.

source_name: Mouse E12.5 testis

label_protocol: Total RNA was amplified and biotin-labelled using the TargetAmp 2 -Round Aminoallyl-aRNA Amplification Kit (Epicenter Biotechnologies) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated using the PicoPureTM RNA isolation kit (Arcturus) per manufacturer's instructions.

value: Embryonic day (E) 12.5

tag: gender

value: Male

value: testis

value: somatic support cells (SSC)


title: HSC rep3

description: HSC replicate 3


title: pb WT 4


title: HSC rep1

description: HSC replicate 1


title: MPP rep1

description: MPP replicate 1


title: pb WT 2


title: XY SSCs at E12.5, pool 2


title: pb WT 3


title: XY SSCs at E12.5, pool 1


title: JK-5-1

value: MAT α leu2-3 112 ura3-52 rme1 trp1 his4 HMLa

value: 5 min after heat stress


title: XX SSCs at E12.5, pool 3

description: Gene expression data from E12.5 XX isolated SSCs

source_name: Mouse E12.5 ovary

value: Female

value: ovary


title: pb AP2-O KO 4

source_name: knockout AP2 domain

value: AP2-O KO


title: pb WT 1


title: pb AP2-O KO 6


title: pb AP2-O KO 2


title: pb AP2-O KO 3


title: XX SSCs at E12.5, pool 2


title: pb AP2-O KO 1


title: XX SSCs at E12.5, pool 1


title: XY SSCs at E11.5, pool 2

description: Gene expression data from E11.5 XY isolated SSCs

source_name: Mouse E11.5 testis

value: Embryonic day (E) 11.5


title: pb AP2-O::Sp 8

source_name: AP2 domain of AP2-O was swapped with that of AP2-Sp


title: pb AP2-O::Sp 10

value: AP2 domain of AP2-O was swapped with that of AP2-Sp


title: pb AP2-O::Sp 6


title: pb AP2-O::Sp 4


title: XY SSCs at E11.5, pool 3


title: pb AP2-O::Sp 5


title: pb AP2-O::Sp 2


title: XY SSCs at E11.5, pool 1


title: pb AP2-O::Sp 7


title: pb AP2-O::Sp 3


title: pb AP2-O::Sp 9


title: pb AP2-O KO 5


title: XX SSCs at E11.5, pool 3

description: Gene expression data from E11.5 XX isolated SSCs

source_name: Mouse E11.5 ovary


title: pb AP2-O::Sp 1


title: XX SSCs at E11.5, pool 1


title: XX SSCs at E11.5, pool 2


title: BW25113 hfq mutant

status: Public on Nov 08 2009

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from planktonic cells of E. coli K-12 hfq deleted mutant, grown OD0.5, adjusted OD1.0, and then exposed to 100 ug/mL ampicillin for 2 h in LB at 37oC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: hfq deletion mutant

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation upto OD=0.5 h at 37°C with shaking (250 rpm), the adjusted OD=1.0, then exposed to 100 ug/mL ampicillin for 2 h, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: hfq deletion


title: BW25113 wild-type persister

description: RNA extracted from planktonic cells of E. coli K-12 wild type, grown OD0.5, adjusted OD1.0, and then exposed to 100 ug/mL ampicillin for 2 h in LB at 37oC

source_name: wild type

value: wild-type


title: Anterior horn, control, Patient 55

status: Public on Nov 07 2009

city: Seattle

first: John

last: Ravits

state: WA

address: 1201 Ninth Avenue

department: Translational Research

institute: Benaroya Research Institute

description:
probe_group_file: = HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: = Not applicable

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 2 minutes, then 45° for 5 minutes centrifuge at max speed for 5 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then cover holes with adhesive spots (Tough SpotsTM). • Hybridize 18 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: GeneChip 3000 scanner 3G (Affymetrix).

data_processing: Data were processed using Partek Genomics Suite version 6.4.  RMA background correction and quantile normalization were performed, and probeset summarization used the median polish method (RMA default setting in Partek).  Core probesets were used for the analysis.  For alternative splicing analysis, probe sets with maximum signal <3 and differential expression p-values > 0.5 were excluded.

source_name: Anterior horn, control

label_protocol: 5 µg of ST-cDNA was fragmented and biotin labeled using FL-Ovation™ cDNA Biotin Module v2 (NuGEN).

growth_protocol: Laser capture microdissected motor neuron enriched samples and anterior horn samples were obtained from frozen spinal cord sections.

extract_protocol: 30–40 8–10 mm cryocut frozen tissue sections stained with cresyl violet acetate were microdissected from each nervous system on a Pixcell IIe Laser Capture Microdissection (LCM) System (Arcturus Bioscience) in a 2-hour long epoch for the motor neuron enriched RNA pool. Microdissected cells were captured on CapSure™ Macro LCM Caps (Arcturus Bioscience). After completion of LCM, the surrounding remaining anterior horn region was collected to create a second parallel RNA pool. RNA isolations were based on a guanadinium isothiocyanate and 2-mercaptoethanol extraction and column purification with RNeasyÒ Micro Kit (Qiagen).  For exon profiling, total RNA was amplified to cDNA probe using random priming with WT-Ovation™ Pico RNA Amplification System (NuGEN). The antisense-sense orientation was converted to sense transcript-cDNA (ST-cDNA) using WT-Ovation™ Exon Module (NuGEN).

treatment_protocol: Spinal cord segments were embedded in cutting media, frozen on blocks of dry ice, and stored at −80˚C.

value: Spinal cord


title: Anterior horn, control, Patient 44


title: Anterior horn, control, Patient 26


title: Anterior horn, control, Patient 59


title: Anterior horn, control, Patient 67


title: Anterior horn, control, Patient 42


title: Anterior horn, ALS, Patient 60

source_name: Anterior horn, ALS


title: Anterior horn, ALS, Patient 27


title: Anterior horn, ALS, Patient 17


title: Anterior horn, control, Patient 65


title: Anterior horn, ALS, Patient 14


title: Anterior horn, ALS, Patient 34


title: Anterior horn, ALS, Patient 63


title: Anterior horn, ALS, Patient 18


title: Anterior horn, ALS, Patient 33


title: Anterior horn, ALS, Patient 35


title: Anterior horn, ALS, Patient 16


title: Motor neuron enriched, control, Patient 65

source_name: motor neurons, control


title: Anterior horn, control, Patient 10


title: Anterior horn, ALS, Patient 68


title: Anterior horn, ALS, Patient 64


title: Anterior horn, control, Patient 39


title: Motor neuron enriched, control, Patient 39


title: Motor neuron enriched, control, Patient 44


title: Motor neuron enriched, control, Patient 59


title: Motor neuron enriched, control, Patient 55


title: Motor neuron enriched, control, Patient 19


title: Motor neuron enriched, control, Patient 26


title: Motor neuron enriched, control, Patient 10


title: Motor neuron enriched, ALS, Patient 35

source_name: motor neurons, ALS


title: Motor neuron enriched, ALS, Patient 63


title: Motor neuron enriched, control, Patient 42


title: Motor neuron enriched, ALS, Patient 14


title: Motor neuron enriched, ALS, Patient 60


title: Gonocyte_Mouse_61

city: Philadelphia

first: xin

last: wu

address: 3850 baltimore Ave,

department: Animal Biology

institute: School of Veterinary Medicine, University of Pennsylvania

hyb_protocol: cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Affymetrix Human Hu133+v2 and Mouse 430 2.0 GeneChips (Affymetrix Inc., Santa Clara CA). Each sample (n=6 per species) was hybridized to its own array.

scan_protocol: According to Affymetrix protocol

data_processing: Probe level data (.cel files) were created with Affymetrix Command Console and Expression Console software. They were imported into Partek Genomics Suite (version 6.4) were RMA was applied to calculate probe set intensities.

label_protocol: Briefly, total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer. Second-strand cDNA synthesis was followed by ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) for linear amplification of each transcript, and the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated.

extract_protocol: Microarray services were provided by the Penn Microarray Facility, including quality control tests of the total RNA samples by Agilent Bioanalyzer and Nanodrop spectrophotometry, as described in the NuGEN Ovation manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Selected germ and somatic cells were placed in 25 ml Trizol reagent (Invitrogen) immediately after isolation

treatment_protocol:
After digestion, mouse and human cells were cultured overnight using MSFM or RSFM respectively in wells pre-coated with 0.1% gelatin. Media was supplemented with 20 ng/ml recombinant human GDNF, 150ng/ml recombinant rat GFR alpha 1 (R&D Systems Inc., Minneapolis, MN) and 1 ng/ml recombinant human bFGF (BD Biosciences
cells were removed from the wells using gentle pipetting, then transferred into a 15 ml conical tube and collected by centrifugation at 4°C, 600 X g for 7 min.  After washing with HBSS twice, the cell pellet was concentrated in MSFM or RSFM with GDNF, bFGF and GFR alpha 1. Cells were then placed in drops in a 10 cm culture dish and covered with silicone oil for micromanipulation.

tag: tissuet type


title: Gonocyte_Mouse_41


title: Motor neuron enriched, ALS, Patient 27


title: Motor neuron enriched, ALS, Patient 34


title: Motor neuron enriched, ALS, Patient 64


title: Somatic cell _Mouse_62


title: Motor neuron enriched, ALS, Patient 33


title: Motor neuron enriched, control, Patient 67


title: Motor neuron enriched, ALS, Patient 17


title: Motor neuron enriched, ALS, Patient 18


title: Motor neuron enriched, ALS, Patient 16


title: Somatic cell _Mouse_42


title: Maternal low protein + 1% taurine offspring muscle, biological replicate 3

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

country: Denmark

institute: University of Copenhagen

description: Hindleg skeletal muscle tissue from newborn C56BL/6 mouse

hyb_protocol: After fragmentation at 94 C for 35 min in fragmentation buffer (40 mM Tris, 30 mM MgOAc, 10 mM KOAc), the labeled cRNA was hybridized for 16 h to Affymetrix Mouse 430 2.0 arrays (Affymetrix Inc., Santa Clara, CA, USA).After hybridization the array was washed and stained with streptavidin phycoerythrin solution using the Fluidics Station 400 (Affymetrix Inc.).

scan_protocol: Finally the arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Inc.) to obtain non-normalized expression levels.

data_processing: Affymetrix CEL-files were normalized using justRMA (i.e. RMA) available in the Bioconductor package version 2.2 (http://www.bioconductor.org) for the statistical software package R version 2.7.0 (R Development Core Team, 2005). MAS5 absent/present calls were calculated using the same software.

source_name: Newborn mouse hindleg skeletal muscle, maternal low protein + 1% taurine offspring

label_protocol: Total RNA was synthesized to double-strand cDNA using Superscript Choice System (Invitrogen, Carlsbad, CA, USA) with an oligo-dT primer containing a T7 RNA polymerase promoter (GenSet, Evry, France). The cDNA was used as a template for in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (BioArray High Yield RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY, USA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by RNA cleanup using Qiagen RNEasy columns

treatment_protocol:
Pregnant mouse dams were subjected to different diet schemes from day 1 of pregnancy until birth. Pups were killed following birth and hindleg skeletal muscle taken out.
Diet schemes: Normal Protein (20% casein; NP), Normal Protein + taurine (1% taurine supplementation in water ad libitum; NP+tau), Low Protein (8% casein; LP) and LP+tau

value: Day 0 after birth

tag: Maternal diet group

value: Low protein (8% casein) + 1% taurine in drinking water


title: Somatic cell _Mouse_52


title: Maternal low protein + 1% taurine offspring muscle, biological replicate 2


title: Maternal low protein offspring muscle, biological replicate 3

source_name: Newborn mouse hindleg skeletal muscle, maternal low protein offspring

value: Low protein (8% casein)


title: Maternal low protein offspring muscle, biological replicate 2


title: Maternal low protein offspring muscle, biological replicate 1


title: Maternal normal protein offspring muscle, biological replicate 2

source_name: Newborn mouse hindleg skeletal muscle, maternal normal protein offspring

value: Normal protein (20% casein)


title: Maternal normal protein + 1% taurine offspring muscle, biological replicate 2

source_name: Newborn mouse hindleg skeletal muscle, maternal normal protein offspring + 1% taurine

value: Normal protein (20% casein) + 1% taurine in drinking water


title: Maternal normal protein + 1% taurine offspring muscle, biological replicate 3


title: Maternal low protein + 1% taurine offspring muscle, biological replicate 1


title: Maternal low protein + 1% taurine offspring liver, biological replicate 3

description: Liver tissue from newborn C56BL/6 mouse

source_name: Newborn mouse liver, maternal low protein + 1% taurine offspring

treatment_protocol:
Pregnant mouse dams were subjected to different diet schemes from day 1 of pregnancy until birth. Pups were killed following birth and liver taken out.
Diet schemes: Normal Protein (20% casein; NP), Normal Protein + taurine (1% taurine supplementation in water ad libitum; NP+tau), Low Protein (8% casein; LP) and LP+tau


title: Maternal normal protein offspring muscle, biological replicate 1


title: Maternal normal protein offspring muscle, biological replicate 3


title: Maternal low protein + 1% taurine offspring liver, biological replicate 1

description: Liver tissue from newborn C56BL/6 mouse


title: Maternal low protein offspring liver, biological replicate 3

description: Liver tissue from newborn C56BL/6 mouse

source_name: Newborn mouse liver, maternal low protein offspring


title: spermatogonia_7boy2 GDNF-SSC

description: 7boy2 GDNF-SSC

source_name: 10 years old

value: testis

value: 10 years old


title: Maternal low protein offspring liver, biological replicate 1

description: Liver tissue from newborn C56BL/6 mouse


title: Somatic cell _7boy3 GDNF-TSC

description: 7boy3 GDNF-TSC


title: Maternal low protein offspring liver, biological replicate 2

description: Liver tissue from newborn C56BL/6 mouse


title: Maternal normal protein + 1% taurine offspring liver, biological replicate 3

description: Liver tissue from newborn C56BL/6 mouse

source_name: Newborn mouse liver, maternal normal protein + 1% taurine offspring


title: Maternal low protein + 1% taurine offspring liver, biological replicate 2

description: Liver tissue from newborn C56BL/6 mouse


title: Anterior horn, control, Patient 19


title: Maternal normal protein + 1% taurine offspring liver, biological replicate 2

description: Liver tissue from newborn C56BL/6 mouse


title: Maternal normal protein + 1% taurine offspring liver, biological replicate 1

description: Liver tissue from newborn C56BL/6 mouse


title: Maternal normal protein offspring liver, biological replicate 3

description: Liver tissue from newborn C56BL/6 mouse

source_name: Newborn mouse liver, maternal normal protein offspring


title: Maternal normal protein offspring liver, biological replicate 2

description: Liver tissue from newborn C56BL/6 mouse


title: Somatic cell _5boy4 GDNF-TSC

description: 5boy4 GDNF-TSC

source_name: 2 years old

value: 2 years old


title: Maternal normal protein offspring liver, biological replicate 1

description: Liver tissue from newborn C56BL/6 mouse


title: PCL-011_GEP

status: Public on Nov 06 2009

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description:
Gene expression profiling data from human plasma cell leukemia patient PCL-011
Same raw data (CEL file) as GSM342084

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 custom GeneAnnot-based Chip Annotation Files version 2.0.1 (CDF), available at the URL http://www.xlab.unimo.it/GA_CDF, and 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-011

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).

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: sex

value: M

tag: age at diagnosis (years)

tag: stage (durie-salmon)

value: PCL

tag: monoclonal component

value: Gk

tag: tc classification


title: Somatic cell _4boy3 GDNF-TSC

description: 4boy3 GDNF-TSC

source_name: 8 years old

value: 8 years old


title: spermatogonia_5boy3 GDNF-SSC

description: 5boy3 GDNF-SSC


title: MM-253_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-253
Same raw data (CEL file) as GSM342044

source_name: Human multiple myeloma patient MM-253

value: F

value: nd

value: G


title: PCL-006_GEP

description:
Gene expression profiling data from human plasma cell leukemia patient PCL-006
Same raw data (CEL file) as GSM342080

source_name: Human multiple myeloma patient PCL-006


title: MM-243_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-243
Same raw data (CEL file) as GSM341996

source_name: Human multiple myeloma patient MM-243

value: Gl


title: MM-212_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-212
Same raw data (CEL file) as GSM341966

source_name: Human multiple myeloma patient MM-212

value: IIIA

value: Al


title: MM-246_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-246
Same raw data (CEL file) as GSM341971

source_name: Human multiple myeloma patient MM-246


title: orc2-1_mutant_normalized_log2ratios

type: genomic

city: Madison

first: Christopher

middle: Lawrence

last: Warren

state: WI

address: 1400 University Ave

institute: University of Wisconsin - Madison

description: None.

hyb_protocol: Hybridization performed by NimbleGen.

scan_protocol: Scanning performed by NimbleGen.

data_processing: The log2 ratios of IP over input were obtained from the values extracted from the S. cerevisiae tiling microarray for each feature. These log2 ratios for each experiment were plotted as a histogram and then background subtracted so that the peak of each histogram was centered over 0. The most repetitive probes (1.1%) were removed from the dataset.

molecule: genomic DNA

source_name: orc2-1 Mutant ChIP-chip IP (cy3) channel

label_protocol: Labeling performed by NimbleGen.

extract_protocol:
Cultures were grown to OD600 of 0.5 to 0.9 and ChIPs were performed as described [44] using a cocktail of monoclonal antibodies against Orc1, Orc2, Orc3, and Orc4 proteins (Gabrielse et al 2006). Average chromatin shearing size was around 0.5 Kb. IP and total DNAs were purified using a QIAquick PCR purification kit (Qiagen).
For ORC ChIP-on-chip, cells were grown at 23°C, the permissive temperature for orc2-1. Under these conditions, Orc2p levels are reduced approximately 10-fold compared to wild type Orc2p [28]. IP and total DNA were amplified using ligation-mediated PCR and mailed to Nimblegen for hybridization to high density tiled arrays (2006-10-12_Ansari_tiling_51mer).

tag: original entry

value: strains used in this study are of W303 background. For the ORC ChIP, CFY1211 (ORC2) and CFY1219 (orc2-1) strains were used. Both contain the synthetic HMR-E silencer with a high affinity binding site. YPD medium (1% yeast extract, 2% peptone, and 2% glucose) was used for liquid culture growth.

source_name: orc2-1 Mutant ChIP-chip Input (cy5) channel


title: Motor neuron enriched, ALS, Patient 68

source_name: motor neurons, ALS

value: Female

value: Spinal cord


title: orc2_WT_normalized_log2ratios

description: None.

source_name: orc2 WT ChIP-chip IP (cy3) channel

value: wild type

source_name: orc2 WT ChIP-chip Input (cy5) channel


title: MM-179_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-179
Same raw data (CEL file) as GSM341962

source_name: Human multiple myeloma patient MM-179

value: Ak


title: MM-131_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-131
Same raw data (CEL file) as GSM341986

source_name: Human multiple myeloma patient MM-131

value: IA

value: A


title: MM-143_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-143
Same raw data (CEL file) as GSM341987

source_name: Human multiple myeloma patient MM-143

value: M

value: IIA

value: l


title: MM-123_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-123
Same raw data (CEL file) as GSM342059

source_name: Human multiple myeloma patient MM-123

value: Gk


title: MM-177_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-177
Same raw data (CEL file) as GSM342029

source_name: Human multiple myeloma patient MM-177


title: MM-206_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-206
Same raw data (CEL file) as GSM342067

source_name: Human multiple myeloma patient MM-206

value: F


title: MM-087_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-087
Same raw data (CEL file) as GSM342054

source_name: Human multiple myeloma patient MM-087


title: MM-074_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-074
Same raw data (CEL file) as GSM342052

source_name: Human multiple myeloma patient MM-074


title: MM-154_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-154
Same raw data (CEL file) as GSM342074

source_name: Human multiple myeloma patient MM-154


title: MM-069_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-069
Same raw data (CEL file) as GSM342072

source_name: Human multiple myeloma patient MM-069


title: MM-067_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-067
Same raw data (CEL file) as GSM342051

source_name: Human multiple myeloma patient MM-067


title: MM-052_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-052
Same raw data (CEL file) as GSM341949

source_name: Human multiple myeloma patient MM-052

value: nd


title: MM-115_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-115
Same raw data (CEL file) as GSM341956

source_name: Human multiple myeloma patient MM-115


title: MM-104_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-104
Same raw data (CEL file) as GSM342056

source_name: Human multiple myeloma patient MM-104


title: MM-229_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-229
Same raw data (CEL file) as GSM342040

source_name: Human multiple myeloma patient MM-229


title: Phaeodactylum_HL_30min_rep3

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

hyb_protocol: Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). 825 ng cRNA from HL exposed cells were mixed with 825 ng cRNA from low light acclimated cells from the corresponding time point. The cRNA mixture was fragmented and hybridized on 4x44K Phaeodactylum tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in a rotary oven (10 rpm, 65°C, 17 h). The slides were washed with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325), Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), acetonitrile (VWR International) and Stabilization and Drying Solution (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The slides were scanned at 5 micrometer resolution on an Agilent DNA microarray scanner (Agilent Technologies). The resulting images were processed using GenePix 5.1 software (Axon Instruments, Union City, USA).

data_processing: The GenePix processed data were filtered to remove spots that had been flagged ‘Absent’, ‘Not Found’ or ‘Bad’, by the GenePix program or by manual flagging. Spots with more than 50% saturated pixels, or had median foreground intensity less than the local median background intensity were excluded from the analysis. No background subtraction was performed. For making statistical inference about differentially regulated genes the limma package and the R statistical data analysis program package (R 2.7.1) was used. The limma approach is based on fitting a linear model to the expression data of each probe on a microarray. In this experiment each time point consists of 3 sets of biological replicates (test and control samples) which are dye swapped and adjusted for probe-specific dye effects. Due to some scale differences in the responses between samples, identified as differences in spread of M-values between the arrays, scale normalization between the arrays was performed. The Benjamini and Hochberg’s method to control the false discovery rate (fdr) was used to identify differentially regulated genes. Genes with adjusted P-values less than 0.05 were regarded as statistical significantly differentially expressed. If a gene was identified by less than 3 spots it was excluded from the result tables.

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum, high light, 30 min

label_protocol: Total RNA was isolated from three biological replicas of diatoms cultured under LL and HL conditions at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h. The RNA (0.36 - 1 μg) was reverse transcribed, amplified and labelled using the Quick Amp Labelling Kit, Two-Color (Agilent p/n 5190-0444).

growth_protocol: Cultures were grown in f/2 medium made with 0.2 μm-filtered and autoclaved local seawater supplemented with f/2 vitamins and inorganic nutrients, filter sterilized and added after autoclaving. Cultures were incubated at 15°C under cool white fluorescent light at scalar irradiance (EPAR) of approximately 35 μmol m-2s-1 on a rotary table in continuous light (control conditions), and were kept in exponential growth phase under these conditions for 3 weeks to ensure that all cells were acclimated. The cells were first grown axenically in a 10-litre batch culture to reach an approximate density of 106 cells mL-1, then volumes of 250 ml were transferred to 75 cm2 sterile Falcon polystyrene flasks to reach cell densities of 0.15 - 1.0 x 106 cells mL-1 on the day of the experiment.

extract_protocol: Diatom cultures were centrifuged at 4000 g for 10 min at 15°C. The supernatant was removed and the cell pellet was resuspended in 1 ml f/2 medium. The suspension was transferred to 2 ml tubes and centrifuged at 18000 g for 1 min at 4°C. Supernatants were removed and the cell pellets were flash frozen in liquid nitrogen and stored at -80°C. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen cell pellets, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified by denaturing agarose gel electrophoresis and ethidium bromide staining following the protocol described in the RNeasy Mini handbook (QIAGEN).

treatment_protocol: The cultures were transferred to EPAR irradiance conditions of 500 μmol m-2s-1 (HL = high light) and sampled at incubation times of 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h. In addition, LL control cultures were kept for each of the HL exposures and parallels. Three biological replica and two parallels for each treatment and control culture were harvested (6 samples) to ensure statistical validation. The two parallels for each of the biological replicas destined to be used for isolation of RNA were merged during harvesting to get enough starting material for the microarray analyses.

tag: clone

source_name: Phaeodactylum, low light (reference), 30 min


title: MM-049_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-049
Same raw data (CEL file) as GSM341979

source_name: Human multiple myeloma patient MM-049

value: IIIB


title: Maternal normal protein + 1% taurine offspring muscle, biological replicate 1

description: Hindleg skeletal muscle tissue from newborn C56BL/6 mouse

source_name: Newborn mouse hindleg skeletal muscle, maternal normal protein offspring + 1% taurine

tag: Genotype

tag: Age

value: Day 0 after birth

value: Normal protein (20% casein) + 1% taurine in drinking water


title: Phaeodactylum_HL_3h_rep1

source_name: Phaeodactylum, high light, 3 h

source_name: Phaeodactylum, low light (reference), 3 h


title: MM-043_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-043
Same raw data (CEL file) as GSM341978

source_name: Human multiple myeloma patient MM-043

value: k


title: MM-042_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-042
Same raw data (CEL file) as GSM342048

source_name: Human multiple myeloma patient MM-042

value: IIIA

value: Gk + Gl


title: MM-040_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-040
Same raw data (CEL file) as GSM342000

source_name: Human multiple myeloma patient MM-040

value: Gl


title: MM-036_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-036
Same raw data (CEL file) as GSM341999

source_name: Human multiple myeloma patient MM-036


title: MM-038_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-038
Same raw data (CEL file) as GSM341976

source_name: Human multiple myeloma patient MM-038


title: Phaeodactylum_HL_24h_rep2

source_name: Phaeodactylum, low light (reference), 24 h

source_name: Phaeodactylum, high light, 24 h


title: Phaeodactylum_HL_24h_rep3


title: MM-035_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-035
Same raw data (CEL file) as GSM341975

source_name: Human multiple myeloma patient MM-035


title: Phaeodactylum_HL_48h_rep3

source_name: Phaeodactylum, low light (reference), 48 h

source_name: Phaeodactylum, high light, 48 h


title: Phaeodactylum_HL_48h_rep1


title: MM-037_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-037
Same raw data (CEL file) as GSM341948

source_name: Human multiple myeloma patient MM-037

value: II A


title: MM-039_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-039
Same raw data (CEL file) as GSM341977

source_name: Human multiple myeloma patient MM-039


title: MM-032_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-032
Same raw data (CEL file) as GSM341947

source_name: Human multiple myeloma patient MM-032


title: Phaeodactylum_HL_24h_rep1


title: MM-030_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-030
Same raw data (CEL file) as GSM341973

source_name: Human multiple myeloma patient MM-030


title: MM-034_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-034
Same raw data (CEL file) as GSM341974

source_name: Human multiple myeloma patient MM-034


title: Phaeodactylum_HL_48h_rep2


title: Phaeodactylum_HL_12h_rep1

source_name: Phaeodactylum, high light, 12 h

source_name: Phaeodactylum, low light (reference), 12 h


title: Phaeodactylum_HL_12h_rep3


title: Phaeodactylum_HL_30min_rep1

source_name: Phaeodactylum, high light, 30 min

source_name: Phaeodactylum, low light (reference), 30 min


title: Phaeodactylum_HL_12h_rep2


title: Phaeodactylum_HL_6h_rep3

source_name: Phaeodactylum, high light, 6 h

source_name: Phaeodactylum, low light (reference), 6 h


title: MM-016_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-016
Same raw data (CEL file) as GSM341997

source_name: Human multiple myeloma patient MM-016


title: MM-015_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-015
Same raw data (CEL file) as GSM341943

source_name: Human multiple myeloma patient MM-015


title: MM-027_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-027
Same raw data (CEL file) as GSM341998

source_name: Human multiple myeloma patient MM-027

value: Gl + Al


title: MM-026_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-026
Same raw data (CEL file) as GSM341945

source_name: Human multiple myeloma patient MM-026

value: Gk + Ak


title: MM-025_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-025
Same raw data (CEL file) as GSM342071

source_name: Human multiple myeloma patient MM-025

value: IA


title: Phaeodactylum_HL_6h_rep1


title: Phaeodactylum_HL_6h_rep2


title: Phaeodactylum_HL_3h_rep2

source_name: Phaeodactylum, low light (reference), 3 h

source_name: Phaeodactylum, high light, 3 h


title: knockout liver neonatal replicate3

status: Public on Nov 05 2009

city: Research Triangle Park

first: Andrew

last: Billin

state: NC

address: 5 Moore Drive

institute: GlaxoSmithKline

description: neonatal liver tissue from ERRγ null mice

hyb_protocol: After fragmentation, labeled cRNA was hybridized to Affymetrix MOE430A expression arrays using standard Affymetrix protocols.

scan_protocol: Hybridized arrays were scanned using standard Affymetrix protocols.

data_processing: Data was normalized within MAS5.0. by using the global scaling option using all probe sets.  Target intensity of each chip was set to 150 and the normalization factor for each chip was obtained as the factor required to convert the trimmed mean signal (2% trim from the top and bottom) for each chip to 150.  Then the raw signal for each gene on that chip was multiplied by the normalization factor to obtain normalized gene signals.

source_name: liver

label_protocol: cRNA labeling was carried out using standard Affymetrix protocols.

growth_protocol: Mice were maintained on standard laboratory chow and allowed food and water ad libitum.

extract_protocol: Total RNA was extracted using Trizol, per manufacturer's instructions.

treatment_protocol: Not applicable.

tag: genetic background

value: mixed SV129/C57BL/6

value: unknown

value: neonatal

value: liver

tag: genotype

value: ERRγ null


title: HONE1-LMP1 vs. HONE1-Vector

city: Guangzhou

first: Chen

last: Jing

address: 651 Dong Feng Road East

department: Dept. of Pathology

country: China

institute: Sun Yat-Sen University Cancer Center

description: compare gene expression profiles of control HONE1-Vector cells with HONE1-LMP1 cells

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were incubated in RPMI-1640 medium supplement with 10% fetal bovine serum (FBS) (Gibco, USA)，100 units of Penicillin/ml and 100μg of streptomycin/ml.

extract_protocol: Total RNA isolation was isolated by TRIZOL (Invitrogen, CA) and purified by Nucleospin RNA clean-up (MN, USA).

treatment_protocol: LMP1 stably transfectted to HONE1 cell line.

tag: cell line


title: Phaeodactylum_HL_30min_rep2


title: wildtype salivary neonatal replicate2

description: neonatal salivary tissue from wild type mice

source_name: salivary

tag: age

tag: tissue

value: salivary

value: wildtype


title: wildtype salivary neonatal replicate1

tag: gender


title: knockout salivary neonatal replicate2

description: neonatal salivary tissue from ERRγ null mice


title: Phaeodactylum_HL_3h_rep3


title: spermatogonia_4boy2 GDNF-SSC

description: 4boy2 GDNF-SSC

source_name: 8 years old

tag: tissuet type

value: testis

value: 8 years old


title: wildtype liver neonatal replicate3

description: neonatal liver tissue from wild type mice


title: knockout salivary neonatal replicate3


title: wildtype salivary neonatal replicate3


title: knockout salivary neonatal replicate1


title: wildtype stomach neonatal replicate2

description: neonatal stomach tissue from wild type mice

source_name: stomach

value: stomach


title: knockout liver neonatal replicate1


title: wildtype liver neonatal replicate1


title: knockout liver neonatal replicate2


title: knockout stomach neonatal replicate2

description: neonatal stomach tissue from ERRγ null mice


title: knockout stomach neonatal replicate3


title: MM-239_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-239
Same raw data (CEL file) as GSM342042

source_name: Human multiple myeloma patient MM-239

value: F

value: nd

value: Gk


title: knockout stomach neonatal replicate1


title: wildtype liver neonatal replicate2


title: wildtype stomach neonatal replicate1


title: knockout kidney neonatal replicate3

description: neonatal kidney tissue from ERRγ null mice

source_name: kidney

value: kidney


title: wildtype kidney neonatal replicate2

description: neonatal kidney tissue from wild type mice


title: wildtype kidney neonatal replicate3


title: knockout kidney neonatal replicate1


title: Gonocyte_Mouse_51


title: knockout kidney neonatal replicate2


title: knockout brain neonatal replicate3

description: neonatal brain tissue from ERRγ null mice

source_name: brain

value: brain


title: wildtype brain neonatal replicate1

description: neonatal brain tissue from wild type mice


title: knockout brain neonatal replicate1


title: wildtype brain neonatal replicate2


title: wildtype kidney neonatal replicate1


title: wildtype stomach neonatal replicate3


title: Cuticle_Day 8 of the pupa

city: Beibei

first: Jiubo

last: Liang

state: Chongqing

address: Tiansheng Road No. 2

department: Molecular Biology

hyb_protocol: Cy5-dCTP-labeled (test samples) and Cy3-dCTP-labeled (reference samples) double-stranded cDNA were dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from images using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing:
LOWESS-normalized, background-subtracted data obtained from log2 of processed Red signal/processed Green signal. The software from CapitalBio Crop was used. Cluster 3.0 and Mev software (version 4.2.01) were also used in further data processing.
Probes with signal intensity lower than 800 after subtracting the background were considered as unexpressed genes since signals at that detection level are not reliable.

organism: Bombyx mori

source_name: Cuticle of day 8 of the pupa

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: Silkworm larvae (p50 strain) maintained at the Institute of Sericulture and System Biology (Southwest University, China) were reared on mulberry leaves at 25°C-26°C.

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

tag: strain

value: mixed-sex

value: cuticle containing epidermis

tag: developmental stage

value: pupa

source_name: Whole body of day 3 of the fifth instar larva

value: whole body

value: larva


title: foxl2-mad transfected 3

city: Kingsville

first: Ken

last: Escudero

state: TX

address: 700 University Blvd MSC 158

department: Biological & Health Sciences

institute: Texas A&M-Kingsville

description: foxl2-mad transfected

scan_protocol: Performed by the CSU Core Facility using the Affymetrix GeneChip Scanner 3000 enabled for high resolution scanning

data_processing: Data were analyzed using Affymetrix® Microarray Suite (MAS) 5.0 statistical algorithms

label: biotinylated pseudouridine molecule

molecule: polyA RNA

source_name: foxl2-mad transfected

label_protocol: Performed by the Colorado State University (CSU) Affymetrix Core Facility using standard Affymetrix protocols.  The GeneChip® Expression 3'-Amplification Reagents for IVT Labeling (IVT Labeling Kit) utilizes a single-label formulation based on a biotinylated pseudouridine molecule.

growth_protocol: KK1 cells are grown in DMEM / F12 (50/50) containing 10% heat inactivated FBS (Gemini Bioproducts; West Sacramento, CA), 100µg/ml penicillin-streptomycin, and 0.25 µg/ml amphotericin B.  All cell culture reagents other than FBS were purchased from Mediatech; Manassas, VA.

extract_protocol: After 24 hours incubation at 37ºC the cells were harvested and polyA+ RNA was isolated using RNeasy (Qiagen Inc.; Valencia, CA) according to manufacturer’s procedures.

treatment_protocol: KK1 cells were grown in 150 mm tissue culture plates to 50% confluence.  Three plates were mock transfected with 30 μl of Fugene 6 transfection reagent (Roche Applied Science; Indianapolis, IN) and 10 µg of empty vector (pcDNA 3.1).  Three plates were transfected with 10 μg Foxl2-VP16 expression vector in 30 μl Fugene reagent and 3 plates were transfected with 10 μg Foxl2- MAD expression vector in 30 μl Fugene reagent.

tag: cell type

value: KK1 granulosa cells

tag: organ

value: ovary


title: Cuticle_Day 5 of the pupa

institute: Institute of Sericulture and System Biology

source_name: Cuticle of day 5 of the pupa


title: foxl2-vp16 transfected 3

description: foxl2-vp16 transfected

hyb_protocol: Performed by the Colorado State University (CSU) Affymetrix Core Facility using standard Affymetrix protocols.

source_name: foxl2-vp16 transfected


title: knockout brain neonatal replicate2

value: mixed SV129/C57BL/6

value: unknown

value: neonatal

value: ERRγ null


title: Cuticle_Day 7 of the pupa

source_name: Cuticle of day 7 of the pupa


title: foxl2-mad transfected 1

description: foxl2-mad transfected


title: foxl2-mad transfected 2

description: foxl2-mad transfected


title: foxl2-vp16 transfected 2

description: foxl2-vp16 transfected


title: Cuticle_Day 3 of the pupa

source_name: Cuticle of day 3 of the pupa


title: Cuticle_Day 2 of the wandering phase

source_name: Cuticle of day 2 of the wandering phase

value: wandering stage


title: Cuticle_Day 1 of the wandering phase

source_name: Cuticle of day 1 of the wandering phase


title: Cuticle_Day 3 of the wandering phase

source_name: Cuticle of day 3 of the wandering phase


title: Cuticle_Day 3 of the fifth instar larva

source_name: Cuticle of day 3 of the fifth instar larva


title: Cuticle_Day 4 of the fourth instar larva

source_name: Cuticle of day 4 of the fourth instar larva


title: Cuticle_Day 7 of the fifth instar larva

source_name: Cuticle of day 7 of the fifth instar larva


title: foxl2-vp16 transfected 1

description: foxl2-vp16 transfected


title: Cuticle_Fourth instar larval molting

source_name: Cuticle of the fourth instar larval molting


title: Whole-Body_Day 3 of the third instar larva

source_name: Whole body of day 3 of the third instar larva


title: Whole-Body_Second instar larval molting

source_name: Whole body of the second instar larval molting


title: Whole-Body_First instar larval molting

source_name: Whole body of the first instar larval molting


title: mock transfected 3

description: mock transfected

source_name: mock transfected


title: stageIII colorectal cancer patient8 with distant recurrence in validation phase

city: Suita

first: masakazu

last: miyake

state: Osaka

address: Yamadaoka 2-2

department: Gastroenterological Surgery

institute: Graduate School of Medicine, Osaka University

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -122°C until RNA extraction.

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).

data_processing: In each sample, the Cy5/Cy3 ratio values were log-transformed and global equalization to remove a deviation of the signal intensity between whole Cy3- and Cy5-fluorescence was performed by subtracting a median of all log (Cy5/Cy3) values from each log (Cy5/Cy3) value. Genes with missing values in more than 10% of samples were excluded from further analysis.

source_name: 40 Total RNAs mixture from normal colorectal mucosa labeled with Cyanine-3 (green).

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

extract_protocol: Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

treatment_protocol: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.

value: mixture of normal colorectal mucosa

source_name: Total RNA from primary colorectal cancer of stageIII patient with distant recurrence labeled with Cyanine-5 (red).

value: stageIII colorectal cancer with distant recurrence


title: mock transfected 1

description: mock transfected


title: Whole-Body_Third instar larval molting

source_name: Whole body of the third instar larval molting

source_name: Whole body of day 3 of the fifth instar larva


title: stageIII colorectal cancer patient7 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -121°C until RNA extraction.


title: stageIII colorectal cancer patient10 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -124°C until RNA extraction.


title: stageIII colorectal cancer patient9 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -123°C until RNA extraction.


title: stageIII colorectal cancer patient5 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -119°C until RNA extraction.


title: stageIII colorectal cancer patient3 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -117°C until RNA extraction.


title: stageIII colorectal cancer patient2 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -116°C until RNA extraction.


title: stageIII colorectal cancer patient28 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -114°C until RNA extraction.

source_name: Total RNA from primary colorectal cancer of stageIII patient with no recurrence labeled with Cyanine-5 (red).

value: stageIII colorectal cancer with no recurrence


title: stageIII colorectal cancer patient1 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -115°C until RNA extraction.


title: stageIII colorectal cancer patient6 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -120°C until RNA extraction.


title: MM-050_GEP

description:
Gene expression profiling data from human multiple myeloma patient MM-050
Same raw data (CEL file) as GSM341979

source_name: Human multiple myeloma patient MM-050

tag: sex

value: M

tag: age at diagnosis (years)

tag: stage (durie-salmon)

value: IA

tag: monoclonal component

value: Gk


title: stageIII colorectal cancer patient27 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -113°C until RNA extraction.


title: stageIII colorectal cancer patient25 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -111°C until RNA extraction.


title: stageIII colorectal cancer patient16 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -102°C until RNA extraction.


title: stageIII colorectal cancer patient23 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -109°C until RNA extraction.


title: stageIII colorectal cancer patient26 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -112°C until RNA extraction.


title: stageIII colorectal cancer patient20 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -106°C until RNA extraction.


title: stageIII colorectal cancer patient19 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -105°C until RNA extraction.


title: stageIII colorectal cancer patient17 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -103°C until RNA extraction.


title: stageIII colorectal cancer patient22 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -108°C until RNA extraction.


title: stageIII colorectal cancer patient24 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -110°C until RNA extraction.


title: stageIII colorectal cancer patient18 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -104°C until RNA extraction.


title: stageIII colorectal cancer patient15 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -101°C until RNA extraction.


title: stageIII colorectal cancer patient21 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -107°C until RNA extraction.


title: stageIII colorectal cancer patient14 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -100°C until RNA extraction.


title: stageIII colorectal cancer patient13 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -99°C until RNA extraction.


title: stageIII colorectal cancer patient9 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -95°C until RNA extraction.


title: stageIII colorectal cancer patient10 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -96°C until RNA extraction.


title: stageIII colorectal cancer patient8 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -94°C until RNA extraction.


title: stageIII colorectal cancer patient12 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -98°C until RNA extraction.


title: wilson

status: Public on Nov 04 2009

city: Bethesda

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: Tissue:Osteosarcoma; Type:Tumor

hyb_protocol: Per manufacturer's recommendation

scan_protocol: Per manufacturer's recommendation

data_processing: RMA as implemented in Bioconductor package affy

organism: Canis lupus familiaris

source_name: wilson

label_protocol: Per manufacturer's recommendation

extract_protocol: Per manufacturer's recommendation for trizol extraction

value: Osteosarcoma

tag: disease state

value: Tumor


title: stageIII colorectal cancer patient5 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -91°C until RNA extraction.


title: stageIII colorectal cancer patient1 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -87°C until RNA extraction.


title: stageIII colorectal cancer patient4 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -90°C until RNA extraction.


title: stageIII colorectal cancer patient7 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -93°C until RNA extraction.


title: stageIII colorectal cancer patient6 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -92°C until RNA extraction.


title: weatherwax

description: Tissue:Osteosarcoma; Type:Tumor

source_name: weatherwax


title: wible

description: Tissue:Osteosarcoma; Type:Tumor

source_name: wible


title: stageIII colorectal cancer patient3 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -89°C until RNA extraction.


title: stageIII colorectal cancer patient2 with no recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -88°C until RNA extraction.


title: stageII colorectal cancer patient8 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -86°C until RNA extraction.

source_name: Total RNA from primary colorectal cancer of stageII patient with distant recurrence labeled with Cyanine-5 (red).

value: stageII colorectal cancer with distant recurrence


title: trafton

description: Tissue:Osteosarcoma; Type:Tumor

source_name: trafton


title: wagner

description: Tissue:Osteosarcoma; Type:Tumor

source_name: wagner


title: schooley

description: Tissue:Osteosarcoma; Type:Tumor

source_name: schooley


title: LN-1

description: Tissue:Lymph Node; Type:Normal

value: Lymph Node

value: Normal


title: LIVER-2

description: Tissue:Liver; Type:Normal

value: Liver


title: paynter

description: Tissue:Osteosarcoma; Type:Tumor

source_name: paynter


title: Kidney-2

description: Tissue:Kidney; Type:Normal

value: Kidney


title: set3_cbp60g,cbp60h,pad4 triple_Psm_24h

city: St Paul

first: lin

last: wang

state: MN

address: 350 Cargill building, 1500 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: cbp60g,cbp60h,pad4 triple infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset3 experiment.

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)

scan_protocol: Slide was scaned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. set1_col_hrcC_9h, set1_col_psm_24h, set1_double_Psm_24h, set1_double_hrcC_9h, set1_pad4_Psm_24h, set1_pad4_hrcC_9h, set1_triple_Psm_24h, set1_triple_hrcC_9h, set2_col_hrcC_9h, set2_col_psm_24h, set2_double_hrcC_9h, set2_double_psm_24h, set2_pad4_Psm_24h, set2_pad4_hrcC_9h, set2_triple_Psm_24h, set2_triple_hrcC_9h, set3_col_Psm_24h, set3_col_hrcC_24h, set3_double_Psm_24h, set3_double_hrcC_24h, set3_pad4_Psm_24h, set3_pad4_hrcC_24h, set3_triple_Psm_24h, set3_triple_hrcC_24h, set1_052422_hrcC_9h, set2_052422_hrcC_9h, and set3_052422_hrcC_9h were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana cbp60g,cbp60h,pad4 triple, leaves, 1x10E8 Pseudomonas syringae ES4326-infiltrated, 24h

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and75% humidity with a 12 hour day length.

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

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 Pseudomonas syringae ES4326 and harvested 24h later.

value: cbp60g,cbp60h,pad4 triple

value: leaves

value: 4 week-old

tag: treatment

value: 1x10E8 Pseudomonas syringae ES4326

tag: time point


title: lyngar

description: Tissue:Osteosarcoma; Type:Tumor

source_name: lyngar


title: LN-2

description: Tissue:Lymph Node; Type:Normal


title: set3_cbp60g,cbp60h,pad4 triple_hrcC_24h

description: cbp60g,cbp60h,pad4 triple infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 24h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana cbp60g,cbp60h,pad4 triple, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 24h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 24h later.

tag: genotype


title: D1-012706

description: Tissue:Osteosarcoma; Type:CellLine

tag: cell line


title: warner

description: Tissue:Osteosarcoma; Type:Tumor

source_name: warner


title: armstrong

description: Tissue:Osteosarcoma; Type:Tumor

source_name: armstrong


title: bennett

description: Tissue:Osteosarcoma; Type:Tumor

source_name: bennett


title: LIVER-1

description: Tissue:Liver; Type:Normal


title: set3_pad4-1_Psm_24h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae ES4326-infiltrated, 24h

tag: age


title: Kidney-1

description: Tissue:Kidney; Type:Normal

tag: tissue


title: set3_cbp60g,cbp60h double_hrcC_24h

description: cbp60g,cbp60h double infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 24h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana cbp60g,cbp60h double, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 24h

value: cbp60g,cbp60h double


title: lane

description: Tissue:Osteosarcoma; Type:Tumor

source_name: lane


title: set3_pad4-1_hrcC_24h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 24h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 24h


title: godbold

description: Tissue:Osteosarcoma; Type:Tumor

source_name: godbold


title: set3_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae ES4326-infiltrated, 24h


title: jimmerson

description: Tissue:Osteosarcoma; Type:Tumor

source_name: jimmerson


title: D2-012706

description: Tissue:Osteosarcoma; Type:CellLine


title: set3_cbp60h_hrcC_9h

description: cbp60h infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana cbp60h, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 9h later.


title: set3_cbp60g,cbp60h double_Psm_24h

description: cbp60g,cbp60h double infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana cbp60g,cbp60h double, leaves, 1x10E8 Pseudomonas syringae ES4326-infiltrated, 24h


title: set3_Col-0_hrcC_24h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 24h after infiltration in setset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 24h


title: alvaney

description: Tissue:Osteosarcoma; Type:Tumor

source_name: alvaney


title: set2_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: set2_cbp60h_hrcC_9h

description: cbp60h infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset2 experiment.


title: set1_cbp60g,cbp60h,pad4 triple_Psm_24h

description: cbp60g,cbp60h,pad4 triple infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset1 experiment.

source_name: Arabidopsis thaliana cbp60g,cbp60h,pad4 triple, leaves, 1x10E8 Pseudomonas syringae ES4326-infiltrated, 24h


title: set2_pad4-1_Psm_24h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset2 experiment.


title: set2_cbp60g,cbp60h,pad4 triple_Psm_24h

description: cbp60g,cbp60h,pad4 triple infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset2 experiment.


title: set2_pad4-1_hrcC_9h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset2 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: set2_cbp60g,cbp60h,pad4 triple_hrcC_9h

description: cbp60g,cbp60h,pad4 triple infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset2 experiment.

source_name: Arabidopsis thaliana cbp60g,cbp60h,pad4 triple, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: set2_cbp60g,cbp60h double_hrcC_9h

description: cbp60g,cbp60h double infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset2 experiment.

source_name: Arabidopsis thaliana cbp60g,cbp60h double, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: set2_cbp60g,cbp60h double_psm_24h

description: cbp60g,cbp60h double infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset2 experiment.

source_name: Arabidopsis thaliana cbp60g,cbp60h double, leaves, 1x10E8 -infiltrated, 24h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8  and harvested 24h later.


title: set2_Col-0_psm_24h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 -infiltrated, 24h


title: wildtype brain neonatal replicate3

description: neonatal brain tissue from wild type mice

source_name: brain

tag: genetic background

value: mixed SV129/C57BL/6

tag: gender

value: unknown

value: neonatal

value: brain

value: wildtype


title: set1_cbp60g,cbp60h double_hrcC_9h

description: cbp60g,cbp60h double infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset1 experiment.


title: set1_pad4-1_Psm_24h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset1 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 Pseudomonas syringae ES4326-infiltrated, 24h


title: set1_cbp60g,cbp60h,pad4 triple_hrcC_9h

description: cbp60g,cbp60h,pad4 triple infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset1 experiment.


title: set1_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset1 experiment.


title: set1_pad4-1_hrcC_9h

description: pad4-1 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset1 experiment.


title: set1_cbp60g,cbp60h double_Psm_24h

description: cbp60g,cbp60h double infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset1 experiment.


title: set1_Col-0_psm_24h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae ES4326, harvested 24h after infiltration in setset1 experiment.


title: set1_cbp60h_hrcC_9h

description: cbp60h infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setset1 experiment.


title: D197

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 703

source_name: Human Osteosarcoma; D197

tag: alive-or-dead

value: D

tag: days-followup


title: D195

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 3753

source_name: Human Osteosarcoma; D195


title: D171

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 25

source_name: Human Osteosarcoma; D171


title: D169

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 2835

source_name: Human Osteosarcoma; D169

value: A


title: D184

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 1008

source_name: Human Osteosarcoma; D184


title: D173

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 225

source_name: Human Osteosarcoma; D173


title: D202

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 1206

source_name: Human Osteosarcoma; D202


title: D201

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 4836

source_name: Human Osteosarcoma; D201


title: D6 embryoid body (EB) cells

city: shanghai

first: Huang

last: Chengyang

address: Yue Yang Road 320

institute: Institute of biochemistry and cell biology

description: neural precusor cells (D6)

hyb_protocol: Standard manufacturer protocol (www.agilent.com)

data_processing: Raw data was extracted from scan image by FeatrueExtract software(Agilent). Data normaliztion and further data analysis were carried out by using GeneSpring software (Agilent).

source_name: D6 embryoid body (EB) cells

extract_protocol: Cell total RNA was extracted by using trizol reagent. The total RNA was then purified by using Qiagen Rnaesy mini Kit

tag: cell type

value: D6 embryoid body (EB)


title: D185

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 4747

source_name: Human Osteosarcoma; D185


title: D0 embryonic stem (ES) cells

description: ES cells (D0)

scan_protocol: Standard manufacturer protocol (www.agilent.com)

source_name: D0 embryonic stem (ES) cells

value: D0 embryonic stem (ES)


title: D081

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 43

source_name: Human Osteosarcoma; D081


title: D158

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 4158

source_name: Human Osteosarcoma; D158


title: D162

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 3574

source_name: Human Osteosarcoma; D162


title: D208

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 4537

source_name: Human Osteosarcoma; D208


title: D080

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 3200

source_name: Human Osteosarcoma; D080


title: mock transfected 2

description: mock transfected

source_name: mock transfected

value: KK1 granulosa cells

tag: organ

value: ovary


title: stageIII colorectal cancer patient4 with distant recurrence in validation phase

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -118°C until RNA extraction.

source_name: 40 Total RNAs mixture from normal colorectal mucosa labeled with Cyanine-3 (green).

value: mixture of normal colorectal mucosa

source_name: Total RNA from primary colorectal cancer of stageIII patient with distant recurrence labeled with Cyanine-5 (red).

value: stageIII colorectal cancer with distant recurrence


title: pCMX_20% O2 vs. pCMX-hRORa1_20% O2, H6

city: Grenoble

first: Gaelle

last: Saint-Auret

address: 17 rue des martyrs

country: France

institute: CEA

description:
Simultaneous hybridization of Hep-5 and Hep-9 on H6 array.
Hep-5 is a technical replicate.

hyb_protocol: The Whole Human Genome Oligonucleotides Microarray 4x44K (G4112F) were purchased from Agilent technology. The hybridizations on these slides were performed using Gene expression Hybridization kit (Agilent technology).

scan_protocol: The hybridized microarrays were scanned with an Agilent G2505B scanner using PMT Cy3 XDR High 100% low 10% and PMT Cy5 XDR 100%, low 10% adjustments and 5µm resolution.

data_processing: Raw data were extracted using Agilent Feature Extraction 9.1.3 (Agilent technology) with GE2-v5_91_806 protocol and the grid 014850_D_20060807. The data are analyzed using the following parameters: correct background and signal biases (spatial detrend). The correction of dye biases was processed by Linear lowess.

source_name: HepG2 cells transfected by pCMX, 20% oxygen

label_protocol: Within each RNA preparation prepared as above, the target poly(A) mRNAs were labelled as follows : 500 nanogrammes of total RNAs were labelled using the Low RNA input linear amplification (Agilent Technologies). These RNAs were labelled by incorporation of cyanine 3- or cyanine 5- CTP. The reactions were purified using Rneasy Mini Kit from QIAgen. These labelled cRNA were quantified using Bioanalyzer 2100 (Agilent technology) and broken up into 50-200 mer nucleotides.

growth_protocol: HepG2 human hepatoma cells (American Type Culture Collection HB-8065) were cultured as monolayers at 37°C in a humidified 95% air/5% CO2 incubator. The culture medium used was a 1:1 mixture of DMEM and Ham-F12 media with Glutamax-I, supplemented with 10%(v/v) fetal bovine serum, 100µg/ml gentamycine and 2,5µg/ml fungizone (all from Invitrogen, San Diego, CA).

extract_protocol: Total RNA was isolated using TRIZOLTM LS reagent (Invitrogen).

treatment_protocol: Engineered HepG2 cells were 70-80% confluent before use. Hypoxic treatment was performed for 24h in sealed chambers, exactly as described in Chauvet et al BJ 2002, 364, 449-456.

tag: transfection

value: pCMX (empty vector)

tag: culture oxygen

tag: culture time

tag: sample name

tag: sample type

value: control

source_name: HepG2 cells transfected by pCMX-hRORa1 clone 18, 20% oxygen

value: pCMX-hRORa1 clone 18


title: D166

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 205

source_name: Human Osteosarcoma; D166


title: D188

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 4577

source_name: Human Osteosarcoma; D188


title: pCMX_20% O2 vs. pCMX-hRORa1_20% O2, H5

description:
Simultaneous hybridization of Hep-3 and Hep-8 on H5 array.
Hep-3 is a technical replicate.

source_name: HepG2 cells transfected by pCMX-hRORa1 clone 17, 20% oxygen

value: pCMX-hRORa1 clone 17


title: D072

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 1436

source_name: Human Osteosarcoma; D072


title: pCMX_20% O2 vs. pCMX_2% O2, H3

description:
Simultaneous hybridization of Hep-5 and Hep-6 on H3 array.
Hep-5 is a technical replicate.

source_name: HepG2 cells transfected by pCMX, 2% oxygen

treatment_protocol: Engineered HepG2 cells were 70-80% confluent before use. Hypoxic treatment was performed for 24h in sealed chambers, exactly as described in Chauvet et al BJ 2002, 364, 449-456. Final oxygen concentration of 2% was used.

value: 2% (hypoxic)


title: pCMX_20% O2 vs. pCMX-hRORa1_20% O2, H4

description:
Simultaneous hybridization of Hep-1 and Hep-7 on H4 array.
Hep-1 is a technical replicate.

source_name: HepG2 cells transfected by pCMX-hRORa1 clone 16, 20% oxygen

value: pCMX-hRORa1 clone 16


title: B804

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 927

source_name: Human Osteosarcoma; B804