title: 3812_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3812


title: 3815_Stom_Tum_U133A

status: Public on Oct 06 2009

type: RNA

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

description: Series of 31 primary gastric tumors

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Array Set HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary gastric tumor, 3815

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: RNeasy mini spin columns (Qiagen) were used according to the manufacturer's instructions.

tag: tissue

value: gastric tumor


title: 3811_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3811


title: 3809_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3809


title: 3810_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3810


title: Molly 3 days, replicate 2

city: Manhattan

first: Ming

last: Chen

state: KS

address: Kansas State University, 123 Waters Hall

department: Entomology

country: USA

institute: Kansas State University

description: Abundance of transcripts in salivary glands.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC following standard procedure (www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: GeneChips were scanned using the genechip scanner 3000-7G.

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

organism: Mayetiola destructor

source_name: Molly Day3 old larvae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3.75 µg total RNA using Biotin module V2 kit (NuGEN technologies, Inc).

growth_protocol: One and half leaf stage of wheat seedlings were infested with Hessian fly eggs with average density of 8 eggs per plant. The plants were maintained in growth chambers at 20oC. Three days after larval hatching, the plants were peered off and larvae were obtained for dissection.

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

treatment_protocol: 200 larvae were collected for RNA extraction

value: Whole larvae

tag: genotype

value: Kansas population (Biotype GP)

tag: age

value: 3day old larvae


title: 3798_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3798


title: Molly 1 day, replicate 2

source_name: Molly Day1 old larvae

value: 1day old larvae


title: Molly 5 days, replicate 2

source_name: Molly Day5 old larvae

value: 5day old larvae


title: Tumour Low Hypoxia L1

status: Public on Oct 07 2009

city: Manchester

first: Carla

middle: Sofia

last: Moller-Levet

address: Wilmslow Road

department: Paterson Insitute for Cancer Research

country: United Kingdom

institute: The University of Manchester

description: Tumour Low Hypoxia L1

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChip scanner 3000 7G

data_processing:
Exon array analysis was performed using the Bioconductor package Exonmap and Matlab. Data were  first summarised using RMA (affy package in Bioconductor)  and then filltered to include only exon targeting probesets, predicted to hybridize to a single locus within the genome.
probe group file: HuEx-1_0-st-v2.pgf

source_name: HNSCC low HS

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

extract_protocol: Samples were treated with the RiboMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: hypoxia score

value: Low


title: Newton 5 days, replicate 2

source_name: Newton Day5 old larvae


title: Molly 12 hrs, replicate 2

source_name: Molly 12 hrs old larvae

value: 12hrs old larvae


title: Newton 3 days, replicate 2

source_name: Newton Day3 old larvae


title: 3803_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3803


title: Newton 12 hrs, replicate 2

source_name: Newton 12 hrs old larvae


title: Newton 1 day, replicate 2

source_name: Newton Day1 old larvae


title: 3793_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3793


title: 3792_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3792


title: 3794_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3794


title: Sample_MIRG3

city: Chicago

first: monika

last: stankiewicz

state: IL

address: 303 E. Superior St. Lurie Bldg 5-250

department: Hematology/Oncology

institute: Northwestern University

description: Serial replated GFP + lineage negative cells from Gata1neoHS fetal liver hematopoietic progenitors for 4 generations in methocult M3234 under megakaryocyte promoting conditions, IL3,TPO, IL6, and IL11. Cells were subject to retro-viral infection with MIGR1GFP, MIGR1ETS2, MIGR1ERG, and MIGR1FLI1. Used Qiagen Rneasy plus mini kit.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.7.18). It was vst transformed and quantile normalized.

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: ETS2 and ERG promote megakaryopoiesis and synergize with alterations in GATA1 to immortalize hematopoietic progenitor cells Sample MIRG3


title: Newton 5 days, replicate 1


title: Molly 5 days, replicate 1


title: Sample_MIRG1

tag: ETS2 and ERG promote megakaryopoiesis and synergize with alterations in GATA1 to immortalize hematopoietic progenitor cells Sample MIRG1


title: Sample_MIRG4

tag: ETS2 and ERG promote megakaryopoiesis and synergize with alterations in GATA1 to immortalize hematopoietic progenitor cells Sample MIRG4


title: Molly 3 days, replicate 1


title: Molly 12 hrs, replicate 1


title: Sample_MIRG2

tag: ETS2 and ERG promote megakaryopoiesis and synergize with alterations in GATA1 to immortalize hematopoietic progenitor cells Sample MIRG2


title: Molly 1 day, replicate 1


title: 3796_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3796


title: Cascade replicate 2

source_name: The remaining cascade collected after removing salivary glands, gut, and Malpighian tubules

treatment_protocol: Dissected tissues were immediately socked into Trizol for RNA isolation.

value: Three day old larvae


title: Newton 12 hrs, replicate 1


title: Cascade replicate 1

value: The remaining cascade collected after removing salivary glands, gut, and Malpighian tubules


title: Gut replicate 3

source_name: Gut dissected from Hessian fly larvae

value: Gut


title: Newton 1 day, replicate 1


title: Salivary gland replicate 3

source_name: Salivary glands dissected from Hessian fly larvae

value: Salivary glands


title: Gut replicate 2


title: Malpighian tubule replicate 1

source_name: Malpighian tubule dissected from Hessian fly larvae

value: Malpighian tubule


title: Gut replicate 1


title: Newton 3 days, replicate 1


title: Salivary gland replicate 2


title: Salivary gland replicate 1


title: 3859_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3859


title: Myeloid progenitors Dnmt1 hypomorph rep.2 (RMA set 2)

city: Berlin

first: Frank

last: Rosenbauer

state: Berlin

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

description: gene expression data of myeloid progenitors from Dnmt1 hypomorph mice

hyb_protocol: Hybridization was performed by ImaGenes (Germany, Berlin) according to standard Affymetrix protocols

scan_protocol: Scanning was performed by ImaGenes (Germany, Berlin)

data_processing: The data were analyzed using R/Bioconductor and the RMA normalization method. The B cell progenitor arrays were not used in the initial analysis but were added later as an out group for hierarchical clustering and principal components analysis. Therefore two matrix tables are provided, one with the B cell progenitor arrays included in the normalization and one without them.

organism: Mus musculus

source_name: mouse bone marrow

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocols (including small sample protocol) from 35000 to 100000 sorted cells

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Micro Kit

tag: cell type

value: Myeloid progenitor

value: 129ola Dnmt1-/chip

value: 8-12 weeks


title: Myeloid progenitors wildtype rep.3 (RMA set 2)

description: gene expression data of myeloid progenitors from Dnmt1 wildtype mice

value: 129ola Dnmt1+/+


title: Malpighian tubule replicate 2


title: Hematopoietic stem cells Dnmt1 hypomorph rep.3 (RMA set 2)

description: gene expression data of hematopoietic stem cells from Dnmt1 hypomorph mice

value: Hematopoietic stem cell


title: Myeloid progenitors wildtype rep.2 (RMA set 2)


title: Hematopoietic stem cells wildtype rep.2 (RMA set 2)

description: gene expression data of hematopoietic stem cells from Dnmt1 wildtype mice


title: Hematopoietic stem cells Dnmt1 hypomorph rep.2 (RMA set 2)


title: Hematopoietic stem cells wildtype rep.1 (RMA set 2)


title: Myeloid progenitors wildtype rep.1 (RMA set 2)


title: Myeloid progenitors Dnmt1 hypomorph rep.1 (RMA set 2)


title: B cell progenitors wildtype rep.1 (RMA set 1)

description: gene expression data of B cell progenitors from Dnmt1 wildtype mice

value: B cell progenitor


title: Myeloid progenitors wildtype rep.2 (RMA set 1)


title: Hematopoietic stem cells Dnmt1 hypomorph rep.1 (RMA set 2)


title: psj39st

status: Public on Oct 05 2009

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

institute: University Hospital Essen

description: no additional information

hyb_protocol: According the manufacturers recommendations (Affymetrix).

data_processing: Signal intensities were determined using GeneChip Microarray Suite (MAS) 5.0.

source_name: neurotrophin-receptor null cell line SY5Y transfected with Trk, +/- activation

extract_protocol: Following neurotrophin treatment, the cells were harvested and lysed using Trizol, followed by QIAGEN Rneasy mini kit.

treatment_protocol: SY5Y cells and TrkA/B expressing subclones were grown in RPMI 1640 containing 10 % FCS at 37°C in an atmosphere containing 5% CO2 to 50-75% confluency and stimulated with the respective neurotrophins for the time indicated (see Characteristics attribute)

tag: transfectants

value: trka

tag: ligand treatment

tag: time (hrs after neurotrophin ligand treatment)


title: Myeloid progenitors wildtype rep.1 (RMA set 1)


title: B cell progenitors wildtype rep.2 (RMA set 1)


title: Myeloid progenitors Dnmt1 hypomorph rep.2 (RMA set 1)


title: Hematopoietic stem cells wildtype rep.2 (RMA set 1)


title: Myeloid progenitors Dnmt1 hypomorph rep.3 (RMA set 2)


title: Hematopoietic stem cells Dnmt1 hypomorph rep.2 (RMA set 1)


title: psj37st

description: no additional information

scan_protocol: According the manufacturers recommendations (Affymetrix).


title: psj38st

description: no additional information

label_protocol: According the manufacturers recommendations (Affymetrix).


title: NSC76022

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description: Gene expression data from MCF7 cells treated with NSC76022 for 6 hours.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

source_name: Breast cancer cell line MCF7

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions

treatment_protocol: MCF7 cells treated with 10 microM NSC76022 for 6 hours.

tag: perturbagen

value: small molecule, type:treatment, name:NSC76022, concentration:.00001 M, vehicle:DMSO, duration:6 h, cell:MCF7


title: Myeloid progenitors Dnmt1 hypomorph rep.3 (RMA set 1)


title: psj17

description: no additional information

value: vec

value: ngf-bdnf


title: psj35st

description: no additional information

value: trkb


title: psj36st

description: no additional information


title: Myeloid progenitors wildtype rep.3 (RMA set 1)


title: Hematopoietic stem cells Dnmt1 hypomorph rep.3 (RMA set 1)


title: DMSO control

description: Gene expression data from MCF7 cells treated only with DMSO for 6 hours.

treatment_protocol: MCF7 control cells treated with DMSO for 6 hours.

value: small molecule, type:control, name:DMSO control, concentration:.00001 M, vehicle:DMSO, duration:6 h, cell:MCF7


title: AC31

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: The raw signal intensities were obtained with Bluefuse . The unreliable and morphologically corrupted measurement spots were removed from the data.

molecule: genomic DNA

source_name: Pulmonary adenocarcinoma of the lung

extract_protocol: Either manual dissection or LPC using the Laser Microbeam System (P.A.L.M.) was used to obtain a tumor cell content of at least 70%. DNA extraction was performed using the the QIAmp DNA Micro Kit (Qiagen).

tag: Sex=male, BM= positive, N= positieve, T=2, G=3, R=0, Age=71

source_name: female reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: Characteristics Pooled DNA from the blood of 10 normal female individuals


title: Myeloid progenitors Dnmt1 hypomorph rep.1 (RMA set 1)


title: Hematopoietic stem cells Dnmt1 hypomorph rep.1 (RMA set 1)


title: AC29

label_protocol: According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: Sex=male, BM= positive, N= positieve, T=2, G=3, R=2, Age=51


title: Yeast_20.9%oxygen_steadystate_rep3

city: VTT

first: Eija

last: Rintala

country: Finland

institute: VTT Technical Research Centre of Finland

description: Steady state sample of glucose-limited chemostat with 20.9 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 3/4.

hyb_protocol: Hybridisation was done at +45°C overnight (16 h) according to GeneChip Expression Analysis Technical Manual (Affymetrix). GeneChip Fluidics Station 450 was used to wash and stain the arrays.

scan_protocol: GeneChip Scanner 3000 with AutoLoader was used to scan the arrays.

data_processing: RMA normalised without outlier sample VTT_Ys23_13_1% and excluding S.pombe data and control probes

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, 20.9 % oxygen, steady state.

label_protocol: Approximately 2 µg of total RNA was processed to produce biotinylated cRNA targets using Affymetrix One-Cycle Target prep protocol.

growth_protocol: Cells were grown in 0.8–1 L of medium in B. Braun Biotech International (Sartorius AG, Germany) Biostat CT (2.5 Lworking volume) bioreactors. Cultures were inoculated to aninitial OD600 nm of c. 0.5, and maintained as batch culturesfor 6–9 h, after which continuous medium feed was startedwhile the cells were still growing exponentially. Chemostatcultures were maintained at D= 0.10 /h, pH 5.0, and30C, with 1.5 volume gas [volume culture]/min (vvm).For cultures that received 20.9% O2 in the gas stream, O2was replaced with the equivalent volume of N2, so that totalgas flow was kept constant for all experiments. Steady-state samples were taken after the cultures had beenin constant conditions for a minimum of four residence times (six generations). Steady states were assessed over fourto nine residence times (six to 13 generations) for constantbiomass production, carbon dioxide evolution and oxygenuptake rates (CER and OUR), alkali utilization, and extracellularmetabolites, as well as constant intracellular metabolites and gene transcription.Cultures that were fed 2.8% or 20.9% O2 were subject tooscillations. To prevent these, c. 5% of the total cellconcentration in the bioreactor was added to the culture ascells in mid-exponential to late exponential phase at thetime when continuous medium feed was started (Zamamiri et al., 2001).

extract_protocol: 15 ml of cell culture was mixed with 35 ml cold (+4C) 10mM Na-phosphate buffer on ice. After centrifugation for 5 min, 3500 rpm, +4C, cells were frozen in liquid nitrogen and stored at -80C. Total RNA was extracted using QIAGEN RNeasy Mini Kit (QIAGEN, Inc., Valencia, CA) according to the manufacturers instructions with the following modification to the cell lysis step. 5-20 mg dry mass of cells were suspended in 400µl of cold (+4°C) disruption buffer (20mM Tris-HCl, pH 7.4, 100 mM KCl, 2 mM MgCl2,  2 mM DTT). 400µl of phenol-chlorophorm (50:50), 5µl 20% SDS and 400 µl glass beads (0.5 mm diameter; Biospec Products) was added. The cells were disrupted with Fastprep machine (Q-Biogene), 2 x 20s, at speed 6. After centrifugation (14000 rpm, 15 min, +4°C), supernatant was used for total RNA extraction. RNA quality was checked with Agilent bioanalyzer (Agilent Technologies).

tag: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 20.9% oxygen provision.


title: psj15

description: no additional information


title: Yeast_20.9%oxygen_steadystate_rep4

description: Steady state sample of glucose-limited chemostat with 20.9 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 4/4.


title: Yeast_1%oxygen_steadystate_rep7

description: Steady state sample of glucose-limited chemostat with 1 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 7/7.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, 1 % oxygen, steady state.

tag: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen provision.


title: AC26

tag: Sex=female, BM= positive, N= positieve, T=2, G=3, R=0, Age=62

source_name: male reference DNA

tag: Characteristics Pooled DNA from the blood of 10 normal male individuals


title: psj12

description: no additional information

value: ngf


title: C14

tag: Sex=male, BM=negative, N= positieve , T=1, G=1, R=0, Age=58


title: AC32

tag: Sex=male, BM= positive, N= positieve, T=2, G=2, R=0, Age=64


title: AC30

tag: Sex=male, BM= positive, N= positieve, T=2, G=3, R=0, Age=60


title: psj13

description: no additional information


title: psj16

description: no additional information


title: psj10

description: no additional information


title: Yeast_1%oxygen_steadystate_rep5

description: Steady state sample of glucose-limited chemostat with 1 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 5/7.


title: psj09

description: no additional information


title: psj11

description: no additional information


title: AC25

tag: Sex=male, BM= positive, N= positieve, T=2, G=3, R=0, Age=73


title: Yeast_1%oxygen_steadystate_rep6

description: Steady state sample of glucose-limited chemostat with 1 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 6/7.


title: psj07

description: no additional information

value: bdnf


title: psj08

description: no additional information


title: Hematopoietic stem cells wildtype rep.1 (RMA set 1)

tag: genotype

tag: age


title: AC28

tag: Sex=female, BM= positive, N= positieve, T=2, G=2, R=0, Age=70


title: psj06

description: no additional information

tag: transfectants

tag: ligand treatment


title: psj05

description: no additional information

tag: time (hrs after neurotrophin ligand treatment)


title: AC27

tag: Sex=female, BM= positive, N= positieve, T=2, G=2, R=0, Age=75


title: AC22

tag: Sex=female, BM= positive, N= negative, T=2, G=2, R=0, Age=75


title: AC24

tag: Sex=male, BM= positive, N= negative, T=1, G=1, R=0, Age=52

tag: Characteristics Pooled DNA from the blood of 10 normal female individuals


title: AC21

tag: Sex=female, BM= positive, N= negative, T=1, G=2, R=0, Age=66


title: Yeast_1%oxygen_steadystate_rep4

description: Steady state sample of glucose-limited chemostat with 1 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 4/7.

tag: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen provision.


title: psj04

description: no additional information


title: AC19

tag: Sex=male, BM= positive, N= negative, T=1, G=2, R=0?, Age=72


title: Yeast_1%oxygen_steadystate_rep3

description: Steady state sample of glucose-limited chemostat with 1 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 3/7.


title: Yeast_1%oxygen_steadystate_rep2

description: Steady state sample of glucose-limited chemostat with 1 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 2/7.


title: Yeast_0%oxygen_steadystate_rep3

description: Steady state sample of glucose-limited chemostat with 0 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 3/4.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, 0 % oxygen, steady state.

tag: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 0% oxygen provision.


title: Yeast_0%oxygen_steadystate_rep4

description: Steady state sample of glucose-limited chemostat with 0 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 4/4.


title: AC20

tag: Sex=female, BM= positive, N= negative, T=1, G=2, R=0?, Age=51

tag: Characteristics Pooled DNA from the blood of 10 normal male individuals


title: js2

description: no additional information

value: anti-ngf


title: Yeast_0.5%oxygen_steadystate_rep4

description: Steady state sample of glucose-limited chemostat with 0.5 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 4/4.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, 0.5 % oxygen, steady state.

tag: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 0.5% oxygen provision.


title: psj02

description: no additional information


title: js1

description: no additional information


title: js3

description: no additional information


title: js5

description: no additional information


title: js4

description: no additional information

value: anti-bdnf


title: psj03

description: no additional information


title: AC16

tag: Sex=male, BM=negative, N=positive, T=1, G=2, R=?, Age=55


title: Yeast_0.5%oxygen_steadystate_rep2

description: Steady state sample of glucose-limited chemostat with 0.5 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 2/4.


title: Yeast_0.5%oxygen_steadystate_rep3

description: Steady state sample of glucose-limited chemostat with 0.5 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 3/4.


title: AC17

tag: Sex=male, BM=negative, N=positive, T=2, G=?, R=0, Age=49


title: js6

description: no additional information


title: Yeast_20.9%oxygen_steadystate_rep2

description: Steady state sample of glucose-limited chemostat with 20.9 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 2/4.

tag: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 20.9% oxygen provision.


title: AC15

tag: Sex=female, BM=negative, N=positive, T=3, G=3, R=?, Age=63


title: AC13

tag: Sex=female, BM=negative, N=positive, T=2, G=2, R=0, Age=54


title: AC11

tag: Sex=male, BM=negative, N=positive, T=2, G=?, R=?, Age=76


title: AC10

tag: Sex=female, BM=negative, N=positive, T=1, G=2, R=?, Age=49


title: AC8

tag: Sex=female, BM=negative, N=negative, T=2, G=2, R=0, Age=72


title: Yeast_2.8%oxygen_steadystate_rep3

description: Steady state sample of glucose-limited chemostat with 2.8 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 3/4.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, 2.8 % oxygen, steady state.

tag: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 2.8% oxygen provision.


title: Yeast_2.8%oxygen_steadystate_rep4

description: Steady state sample of glucose-limited chemostat with 2.8 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 4/4.

extract_protocol: 10 ml of cell culture was centrifuged for 5 min, 3500 rpm, +4C, cells were frozen in liquid nitrogen and stored at -80C. Total RNA was extracted using QIAGEN RNeasy Mini Kit (QIAGEN, Inc., Valencia, CA) according to the manufacturers instructions with the following modification to the cell lysis step. 5-20 mg dry mass of cells were suspended in 400µl of cold (+4°C) disruption buffer (20mM Tris-HCl, pH 7.4, 100 mM KCl, 2 mM MgCl2,  2 mM DTT). 400µl of phenol-chlorophorm (50:50), 5µl 20% SDS and 400 µl glass beads (0.5 mm diameter; Biospec Products) was added. The cells were disrupted with Fastprep machine (Q-Biogene), 2 x 20s, at speed 6. After centrifugation (14000 rpm, 15 min, +4°C), supernatant was used for total RNA extraction. RNA quality was checked with Agilent bioanalyzer (Agilent Technologies).


title: AC9

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

tag: Sex=male, BM=negative, N=positive, T=1, G=3, R=?, Age=63

tag: Characteristics Pooled DNA from the blood of 10 normal female individuals


title: Yeast_20.9%oxygen_steadystate_rep1

description: Steady state sample of glucose-limited chemostat with 20.9 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 1/4.


title: Yeast_0%oxygen_steadystate_rep2

description: Steady state sample of glucose-limited chemostat with 0 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 2/4.


title: Yeast_0.5%oxygen_steadystate_rep1

description: Steady state sample of glucose-limited chemostat with 0.5 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 1/4.


title: Yeast_0%oxygen_steadystate_rep1

description: Steady state sample of glucose-limited chemostat with 0 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 1/4.


title: Yeast_2.8%oxygen_steadystate_rep2

description: Steady state sample of glucose-limited chemostat with 2.8 % oxygen provision in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 2/4.


title: AC7

tag: Sex=female, BM=negative, N=negative, T=2, G=1, R=0, Age=61


title: AC5

tag: Sex=female, BM=negative, N=negative, T=2, G=3, R=?, Age=58


title: Yeast_2.8%oxygen_steadystate_rep1

description: Steady state sample of glucose-limited chemostat with 2.8 % oxygen provision, in a series of chemostats with oxygen provision 0,0.5,1,2.8 and 20.9 % oxygen provision. Replicate 1/4.


title: Day30

status: Public on Oct 03 2009

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: Mature adipocyte phenotype.

hyb_protocol: The slides were pretreated with 1% BSA fraction V, 5× SSC, 0.1% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight at 60°C in a cocktail containing 1.3 × Denhardt’s, 3 × SSC 0.3% SDS, 0.67 µg/µl polyadenylate and 1.4 µg/µl yeast tRNA. After hybridization, slides were washed at room temperature in 0.5 x SSC and 0.1% SDS (15 min), 0.5 x SSC and 0.01% SDS (15 min), and twice in 0.06 x SSC (2 and 1 min, respectively).

scan_protocol: Scanned with GenePix4100A.

data_processing: LOWESS normalized, median background subtracted from median signal, log2 of processed Red signal/processed Green signal.

organism: Salmo salar

source_name: Cell culture, day 30

label_protocol: 20 µg of total RNA were labled with SuperScript™ Indirect cDNA Labelling System (Invitrogen) according to the manufacturer's instructions.

growth_protocol: Adipose-derived stromal cell fraction was kept in the growth media that contained L-15, 10% fetal bovine serum, 2 mM L glutamine, 10 mM HEPES, and antibiotics until confluence. Cells were then treated with differentiation mix (growth medium supplemented with 1 µM dexamethasone, 33 µM biotin, 10 nM triiodothyronine, 17 µM panthothenate and 25 µM isobutylmethylxanthine, 20 µg/ml insulin and a lipid mixture) for 48h. After that cells were transferred to a maintenance differentiation media containing growth media only supplemented with 2 µl/ml of lipid mixture.

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions.

tag: cell type

value: primary adipose-derived stromal-vascular cells

tag: stage

value: Mature adipocytes

source_name: Cell culture, all time-points equalized

tag: description

value: Pooled equalized samples from all time-points

tag: sample type

value: reference


title: AC1

tag: Sex=male, BM=negative, N=negative, T=1, G=1, R=0 Age=78


title: Day4

description: Reduced variety of cell types.

source_name: Cell culture, day 4

value: Growth


title: AC6

tag: Sex=male, BM= negative, N= negative , T=2, G=3, R=?, Age=52


title: AC23

tag: Sex=male, BM= positive, N= negative , T=2, G=3, R=0, Age=55


title: Day9

description: Suppression of non-adipogenic lineages.

source_name: Cell culture, day 9

value: Hormones withdrawn


title: AC2

tag: Sex=female, BM=negative, N=negative,T=1, G=2, R=0, Age=73

tag: Characteristics Pooled DNA from the blood of 10 normal male individuals


title: Day7

description: Hormonal stimulation of adipogenesis.

source_name: Cell culture, day 7

value: Confluence, hormone treatment


title: Hybrid replica2

city: Moncada

first: Gema

last: Ancillo

state: Valencia

address: Ctr. Moncada-Naquera Km 4.5

department: Protección Vegetal y Biotecnología

country: Spain

institute: Instituto Valenciano de Investigaciones Agrarias (IVIA)

description: Fruits from their somatic allotetraploid hybrid field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 2

hyb_protocol: Microarray hybridisation and washing were performed as described by Martinez-Godoy et al. (2008).

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-nm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.

organism: Citrus limon x Citrus reticulata

source_name: Fruits (225 DAA) of a somatic allotetraploid between (Citrus reticulata Blanco) and (Citrus limon (L.) Burm.).

label_protocol: RNA was labelled following an indirect method (Randolph and Waggoner, 1997). Reverse transcription, cDNA purification, dye coupling and fluorescent cDNA purification was accomplished as described by Forment et al. (2005), except that total RNA (40 ug) was used instead of poly(A)+ RNA.

growth_protocol: The somatic allotetraploid and the two parents were all grafted onto Volkamer lemon rootstock (Citrus limonia Obs.) and three trees of each genotype were randomly planted in the same field at the Station de Recherche Agronomiques (INRA/CIRAD) in San Giuliano (Corsica, France).

extract_protocol: Total RNA was extracted from fruits (225 days after anthesis) according to the protocol described by Ancillo et al. (2007), except that the high pH of the lemon fruit homogenates was neutralized by adding NaOH up to pH-neutral to ensure a better stability of RNA.

tag: hybrid

organism:
Citrus x limon
Citrus reticulata
Citrus limon x Citrus reticulata

source_name: Common reference obtained by mixing equimolar amounts of all samples

tag: reference

value: Mix of equimolar amounts of all samples


title: Day15

description: Establishment of the adipocyte phenotype.

source_name: Cell culture, day 15

value: Early adipocytes


title: Hybrid replica3

description: Fruits from their somatic allotetraploid hybrid field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 3

value: somatic allotetraploid between (Citrus reticulata Blanco) and (Citrus limon (L.) Burm.)


title: Day1

description: High cellular heterogeneity.

source_name: Cell culture, day 1

value: Plating


title: Mandarin replica 3

description: Fruits from Mandarin field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 3

organism: Citrus reticulata

source_name: Fruits (225 DAA) of Willowleaf mandarin SRA 133 (Citrus reticulata Blanco.)

tag: parent

value: Willowleaf mandarin SRA (Citrus reticulata Blanco.)


title: Mandarin replica 2

description: Fruits from Mandarin field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 2


title: Mandarin replica 1

description: Fruits from Mandarin field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 1


title: Lemon replica 3

description: Fruits from Lemon field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 3

organism: Citrus x limon

source_name: Fruits (225 DAA) of Eureka lemon SRA 4 (Citrus limon (L.) Burm.)


title: Lemon replica 2

description: Fruits from Lemon field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 2

value: Eureka lemon SRA 4 (Citrus limon (L.) Burm.)


title: XFM-glucan_rep2

city: Berkeley

first: Nabil

last: Killiny

state: CA

address: University of California

department: Environmental science, policy and management

institute: UC-Berkeley

description: This sample is of Xf grown in XFM-glucan medium. It is the second of the four biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Expression analysis core facility UC-Davis, USA following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Expression analysis core facility UC-Davis, USA, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Xylella fastidiosa Temecula1

label_protocol: Labeling by us, following Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: Xylella fastidiosa was grown at 29°C in PWG, XFM, XFM-pectin or XFM-glucan solid media for 10 days.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and 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 Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: strain

value: PD Temecula


title: Hybrid replica1

description: Fruits from their somatic allotetraploid hybrid field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 1


title: XFM-glucan_rep1

description: This sample is of Xf grown in XFM-glucan medium. It is the first of the four biological replicates used in this experiment, each from separate cultures.


title: Lemon replica 1

description: Fruits from Lemon field trees, labeled with Cy3,  compared to a common reference, labeled with Cy5; replica 1


title: XFM-glucan_rep3

description: This sample is of Xf grown in XFM-glucan medium. It is the third of the four biological replicates used in this experiment, each from separate cultures.


title: XFM-pectin_rep3

description: This sample is of Xf grown in XFM-pectin medium. It is the third of the four biological replicates used in this experiment, each from separate cultures.


title: XFM-pectin_rep4

description: This sample is of Xf grown in XFM-pectin medium. It is the fourth of the four biological replicates used in this experiment, each from separate cultures.


title: XFM-pectin_rep2

description: This sample is of Xf grown in XFM-pectin medium. It is the second of the four biological replicates used in this experiment, each from separate cultures.


title: XFM-glucan_rep4

description: This sample is of Xf grown in XFM-glucan medium. It is the fourth of the four biological replicates used in this experiment, each from separate cultures.


title: XFM-pectin_rep1

description: This sample is of Xf grown in XFM-pectin medium. It is the first of the four biological replicates used in this experiment, each from separate cultures.


title: AC3

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

source_name: Pulmonary adenocarcinoma of the lung

tag: Sex=male, BM=negative, N=negative, T=2, G=3, R=0, Age=58

source_name: female reference DNA


title: PWG_rep4

description: This sample is of Xf grown in PWG medium. It is the fourth of the four biological replicates used in this experiment, each from separate cultures.


title: PWG_rep3

description: This sample is of Xf grown in PWG medium. It is the third of the four biological replicates used in this experiment, each from separate cultures.


title: XFM_rep2

description: This sample is of Xf grown in XFM medium. It is the second of the four biological replicates used in this experiment, each from separate cultures.


title: XFM_rep3

description: This sample is of Xf grown in XFM medium. It is the third of the four biological replicates used in this experiment, each from separate cultures.


title: js7

description: no additional information

source_name: neurotrophin-receptor null cell line SY5Y transfected with Trk, +/- activation

tag: transfectants

value: vec

tag: ligand treatment

value: anti-ngf-bdgf

tag: time (hrs after neurotrophin ligand treatment)


title: XFM_rep1

description: This sample is of Xf grown in XFM medium. It is the first of the four biological replicates used in this experiment, each from separate cultures.


title: PWG_rep2

description: This sample is of Xf grown in PWG medium. It is the second of the four biological replicates used in this experiment, each from separate cultures.


title: XFM_rep4

description: This sample is of Xf grown in XFM medium. It is the fourth of the four biological replicates used in this experiment, each from separate cultures.


title: PWG_rep1

description: This sample is of Xf grown in PWG medium. It is the first of the four biological replicates used in this experiment, each from separate cultures.


title: psj14

description: no additional information

value: ngf-bdnf


title: AC4

tag: Sex=male, BM=negative, N=negative, T=2, G=2, R=0, Age=60


title: CD4+GFPnegFoxP3neg

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

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

extract_protocol: Trizol

value: DEREG

tag: genetic modification

tag: tissue

value: CD4+ T-cells


title: 872-41

status: Public on Oct 02 2009

city: Houston

first: Samuel

last: Mok

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas M.D. Anderson Cancer Center

description: Microdissected ovrian cancer tissue sample

hyb_protocol: Dried DNA pallet was reconstituted in SlideHyb buffer I (Ambion) and hybridized onto a 22K 60mer oligonucleotide array platform (provided by the microarray core facility at the Advanced Technology Center, National Cancer Institute) overnight at 42°C using a GeneMachines Hyb4 slide hybridization machine (Genomic Solutions, Ann Arbor, MI).

scan_protocol: Scanning was performed on a ScanArray 4000XL Microarray Analysis System, and quantified using ScanArray Express (Perkin Elmer, Downers Grove, IL).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. ScanArray Express software (Perkin Elmer) was used.

source_name: Pooled female blood DNA

label_protocol: DNA was labeled with aminoallyl-dUTP (Ambion, Austin, TX)  by adding 1.5μl of the reagent directly to the normal GenomiPhi reaction prior to overnight incubation at 30°C.  Similar amplification and labeling was performed on a commercially available genomic female control DNA (Promega, San Luis Obispo, CA).  Amplified DNA was then digested with HaeIII digestion enzyme (N.E. Biosciences, Ipswich, MA) and quantified by PicoGreen dsDNA quantitation (Molecular Probes, Eugene, OR).  A minimum of 8.0μg DNA was then precipitated overnight at -80°C, washed with 70% ethanol, and vacuum dried. Control/tumor pairs were then resuspended in sodium bicarbonate buffer (pH 9.0), and coupled with 3.0μl Cy3/Cy5 dye (Amersham) for 1.5 hours at room temperature. After coupling, the reaction was quenched with 4M hydroxylamine, control/tumor pairs were combined into one tube, and remaining uncoupled dye was removed by passing the samples through NucAway spin columns (Ambion).  COT human DNA and yeast tRNA (Roche, Indianapolis, IN) were then added to the column flow-through and dried by vacuum centrifugation.

extract_protocol: DNA was extracted by the QIAamp DNA micro kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, and amplified by the GenomiPhi whole genome amplification system (Amersham, Piscataway, NJ).

value: normal blood

source_name: DNA from microdissected tumor tissue 872

value: high-grade late stage serous tumor


title: 860-40f

source_name: DNA from microdissected tumor tissue 860


title: 1312-42f

source_name: DNA from microdissected tumor tissue 1312


title: 1293-24f

source_name: DNA from microdissected tumor tissue 1293


title: 1109-90d

source_name: DNA from microdissected tumor tissue 1109


title: 715-11c

source_name: DNA from microdissected tumor tissue 715


title: 1316-25f

source_name: DNA from microdissected tumor tissue 1316


title: 744-15b

source_name: DNA from microdissected tumor tissue 744


title: 1064-12c

source_name: DNA from microdissected tumor tissue 1064


title: CD4+GFP+FoxP3+


title: 799-3c

source_name: DNA from microdissected tumor tissue 799


title: 1214-91d

source_name: DNA from microdissected tumor tissue 1214


title: 780-10

source_name: DNA from microdissected tumor tissue 780


title: 794-39f

source_name: DNA from microdissected tumor tissue 794


title: 934-41f

source_name: DNA from microdissected tumor tissue 934


title: 702-05

source_name: DNA from microdissected tumor tissue 702


title: 765-14c

source_name: DNA from microdissected tumor tissue 765


title: 524-20b

source_name: Pooled female blood DNA

source_name: DNA from microdissected tumor tissue 524


title: 692-34c

source_name: DNA from microdissected tumor tissue 692


title: 629-17c

source_name: DNA from microdissected tumor tissue 629


title: 467-17b

source_name: DNA from microdissected tumor tissue 467


title: 486-43c

source_name: DNA from microdissected tumor tissue 486


title: CD4 T-cell responder rep2

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

institute: Vall d'Hebron Hospital Research Institute

description:
Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning
Isolated whole blood CD4 T cells, rituximab responder

hyb_protocol: Biotin labeled cRNA was hybridized to Sentrix(r) whole genome bead chips 6 x 2 (Illumina, San Diego, CA, USA)

scan_protocol: Scanning was performed on the Illumina(r) BeadStation 500x.

data_processing: Log2 transformation of BeadStudio raw data, gene filtering of Beadchip version2 RefSeq valid probes, quantile normalization using R.

label: Biotin

label_protocol: Biotin labeled cRNA preparation for the Illumina platform was performed using the Ambion(r) Illumina RNA amplification kit (Ambion Europe, Huntington, Cambridgeshire, UK).

extract_protocol: Extraction using Rneasy Kit (Qiagen) from CD4 T cell isolates preserved in RNALater.

tag: disease state

value: Rheumatoid arthritis

tag: cell type

value: CD4 T cells

tag: phenotype

value: Rituximab responder


title: 428-7c

source_name: DNA from microdissected tumor tissue 428


title: CD4 T-cell responder rep4

source_name: Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning


title: 434-6c

source_name: DNA from microdissected tumor tissue 434


title: 443-30b

source_name: DNA from microdissected tumor tissue 443


title: 423-42c

source_name: DNA from microdissected tumor tissue 423


title: CD4 T-cell responder rep1


title: CD4 T-cell non-responder rep4

description:
Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning
Isolated whole blood CD4 T cells, rituximab Non-responder

value: Rituximab Non-responder


title: CD4 T-cell non-responder rep1


title: 410-8c

source_name: DNA from microdissected tumor tissue 410


title: B cell responder rep2

description:
Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning
Isolated whole blood B cells, rituximab responder

extract_protocol: Extraction using Rneasy Kit (Qiagen) from B cell isolates preserved in RNALater.

value: B cells


title: B cell responder rep4


title: 402-02

source_name: DNA from microdissected tumor tissue 402


title: 396-10c

source_name: DNA from microdissected tumor tissue 396


title: CD4 T-cell non-responder rep3


title: CD4 T-cell non-responder rep2


title: 389-09b

source_name: DNA from microdissected tumor tissue 393


title: 393-4c

source_name: DNA from microdissected tumor tissue 390


title: B cell non-responder rep3

description:
Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning
Isolated whole blood B cells, rituximab Non-responder


title: 412-13c

source_name: DNA from microdissected tumor tissue 412


title: 388-20b

source_name: Pooled female blood DNA

source_name: DNA from microdissected tumor tissue 388


title: B cell non-responder rep2


title: 386-36b

source_name: DNA from microdissected tumor tissue 386


title: 380-46a

source_name: DNA from microdissected tumor tissue 380


title: B cell non-responder rep4


title: B cell non-responder rep5


title: Whole blood non-responder rep5

description:
Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning
Whole blood RNA, rituximab non-responder

hyb_protocol: Biotin labeled cRNA (1.5ug) was hybridized to Sentrix(r) whole genome bead chips 6 x 2 (Illumina, San Diego, CA, USA)

extract_protocol: PaxGene RNA extraction system.

value: Whole blood RNA

value: Rituximab non-responder


title: B cell non-responder rep1


title: Whole blood responder rep4

description:
Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning
Whole blood RNA, rituximab responder


title: Whole blood responder rep1


title: 377-43b

source_name: DNA from microdissected tumor tissue 377


title: Whole blood responder rep2


title: 351-05c

source_name: DNA from microdissected tumor tissue 351


title: Whole blood responder rep3


title: 332-18b

source_name: DNA from microdissected tumor tissue 332


title: 349-19b

source_name: DNA from microdissected tumor tissue 349


title: Whole blood non-responder rep4

source_name: Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning


title: 317-46b

source_name: DNA from microdissected tumor tissue 317


title: Whole blood non-responder rep1

description:
Rheumatoid arthritis patient, whole blood, at 8:30-9:30 morning
Whole blood RNA, Rituximab Non-responder

extract_protocol: PaxGene RNA extraction system


title: 321-40c

source_name: DNA from microdissected tumor tissue 321


title: Whole blood non-responder rep3


title: 326-13b

source_name: DNA from microdissected tumor tissue 326


title: 324-9c

source_name: DNA from microdissected tumor tissue 324


title: Blood_CNT_8

city: La Jolla

last: Tsuang

address: 9500 Gilman Drive

institute: UCSD

hyb_protocol: Samples were transcribed to cDNA and hybridized to GeneChip® Human Exon 1.0 ST Arrays (Affymetrix, Inc.; Santa Clara, CA) per the “Whole Transcript (WT) Sense Target Labeling Assay protocol (Affymetrix, 2006) using 1µg of total RNA from each sample.

scan_protocol: GCOS version 1.0

data_processing: The data were analyzed with Partek Genomics Suite v6.4 using robust multichip average to analyze probe intensities and to determine differential gene expression between diagnostic and control groups

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

extract_protocol: Each blood sample was passed over a LeukoLOCK™ filter, which was flushed with PBS and then fully saturated with RNAlater®

tag: diagnosis

value: Control

tag: history of psychosis

value: No

tag: age

tag: education

tag: gender

value: Female

tag: current tobacco use

tag: ancestry

value: European-American


title: IR-Pv/Vt-3

city: Talence

first: angela

last: tingaud-sequeira

address: avenue des Facultés

country: France

institute: Université Bordeaux 1

description: Biological replicate 3 of 3

hyb_protocol: Hybridizations were carried out for 17 h at 60°C using Agilent's gaskets G2534-60002, G2534A hybridization chambers, and DNA Hybridization Oven G2545A, according to the manufacturer's instructions

scan_protocol: Microarray raw data were obtained using Agilent's DNA Microarray Scanner G2505B and Feature Extraction software (v10.1)

data_processing: The raw fluorescence intensity data were processed using the Polyphemus™ software (Oryzon Genomics), Q-Splines normalization.

organism: Solea senegalensis

label_protocol: Total RNA (0.5 μg) from each sample was amplified and labelled with fluorescent cyanine dyes, Cy3 or Cy5, using the Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems) following the manufacturer's instructions with minor modifications

growth_protocol: Females were sacrificed at different times during the annual reproductive cycle and pieces of the ovary were deep-frozen

extract_protocol: Total RNA was extracted from previtellogenic and vitellogenic ovaries using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

value: ovary pieces

tag: developmental stage

value: previtellogenic

value: vitellogenic


title: IR-Pv/Vt-1

description: Biological replicate 1 of 3


title: IR-Mt/At-3

description: Biological replicate 3 of 3

extract_protocol: Total RNA was extracted from mature and atretic ovaries using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions

treatment_protocol: To collect females with maturing and mature ovaries, fish were treated with intramuscular injection of 5 μg/kg GnRHa and killed 24-48 h later.

value: mature

value: atretic


title: Blood_CNT_7

value: Asain-PI


title: IR-Pv/Vt-2

description: Biological replicate 2 of 3


title: Blood_CNT_6

value: Male

value: African-American


title: IR-Mt/At-2

description: Biological replicate 2 of 3


title: IR-Mt/At-1

description: Biological replicate 1 of 3


title: IR-Vt/At-1

description: Biological replicate 1 of 3

extract_protocol: Total RNA was extracted from vitellogenic and atretic ovaries using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions


title: Blood_CNT_5


title: Whole blood non-responder rep2

value: Rheumatoid arthritis


title: Blood_CNT_4

value: Mexican-Hispanic


title: Blood_CNT_1


title: Blood_CNT_2


title: Blood_SCZ_13

value: Schizophrenia

value: Yes


title: Blood_SCZ_12


title: IR-Vt/At-2

description: Biological replicate 2 of 3


title: IR-Vt/Mt-2

description: Biological replicate 2 of 3

extract_protocol: Total RNA was extracted from vitellogenic and mature ovaries using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions


title: IR-Vt/Mt-1

description: Biological replicate 1 of 3


title: Blood_SCZ_9


title: Blood_CNT_3


title: IR-Vt/Mt-3

description: Biological replicate 3 of 3


title: Blood_SCZ_10


title: Blood_SCZ_8


title: IR-Vt/At-3

description: Biological replicate 3 of 3


title: Blood_SCZ_7


title: Blood_SCZ_11


title: S. mansoni cercariae replicate 2 of 2

city: Herston

first: Alex

middle: P

last: Loukas

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR

description: S. mansoni cercariae

hyb_protocol: One-color Microarray-Based gene expression version 5.5 February 2007

scan_protocol: Microarrays were scanned using the Aglient DNA microarray scanner

data_processing: Agilent Feature Extraction software version 9.5.3.1

organism: Schistosoma mansoni

source_name: S. mansoni cercariae

label_protocol: Agilent Low RNA Input linear amplification kit

extract_protocol: Trizol / QIAGEN RNeasy isolated total RNA

tag: stage

value: cercariae


title: Blood_SCZ_4


title: Blood_SCZ_5


title: S. mansoni cercariae replicate 1 of 2

description: S. mansoni cercariae


title: S. mansoni schistosomula batch 1, 3h + RBC replicate 1 of 2

description: S. mansoni schistosomula

source_name: S. mansoni schistosomula, 3h + RBC

value: schistosomula


title: Blood_BPD_9

value: Bipolar Disorder

value: No


title: Blood_SCZ_3

value: European-American


title: Blood_SCZ_6

value: Female


title: S. mansoni schistosomula batch 1, 3h + RBC replicate 2 of 2

description: S. mansoni schistosomula


title: S. mansoni schistosomula batch 1, 5d replicate 2 of 2

description: S. mansoni schistosomula

source_name: S. mansoni schistosomula, 5d


title: Blood_SCZ_1


title: Blood_BPD_8


title: E-IAA pos_A15.6

city: Paris

first: Evie

last: Melanitou

address: 25 rue du Dr Roux

department: Parasitology & Mycology

institute: Institut Pasteur

description: Gene expression data from PLN of NOD mice at 5 weeks

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MG_U74Av2_A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Raw data were preprocessed using RMA method

source_name: PLN E-IAA pos, 5 weeks old NOD mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed by using Qiagen mini- RNA kit according to the manufacturer's instructions.

treatment_protocol: NOD mice positive or negative for Insulin AutoAntibodies as tested between 3 and 5 weeks of age were used at 5 weeks to isolate pancreatic lymph nodes. Immediately after dissection PLN have been placed in RNALater (Quiagen) buffer.

tag: genotype

value: PLN E-IAA pos

value: 5 weeks old

tag: animal

value: NOD mice

tag: strain

value: Non Obese Diabetic mouse for Type 1 diabetes


title: Blood_SCZ_2

first: Ming


title: S. mansoni schistosomula batch 1, 3h replicate 2 of 2

description: S. mansoni schistosomula

source_name: S. mansoni schistosomula, 3h


title: Magnaporthe oryzae Guy11 inoculated root 4 dpi rep 2

city: Lausanne

first: Sylvain

last: Marcel

state: VD

address: Campus Dorigny

department: Department of Plant Molecular Biology

institute: University of Lausanne

description: Gene expression data from M. oryzae inoculated roots at 4 dpi

hyb_protocol: Labelled cDNA was hybridized for 16 hr at 45°C on GeneChip® Rice Genome Array. GeneChips were washed and stained in a Fluidics Station (Affymetrix).

scan_protocol: The probe arrays were scanned twice. The intensities were averaged with an Agilent  GeneArray Scanner by using MAS 5.0 (Affymetrix).

data_processing: Data was normalized using the RMA function on the affy Bioconductor package for R statistics software.

organism: Oryza sativa

source_name: In vitro grown rice seedlings

label_protocol: Biotinylated cDNA was prepared from 5 ug total RNA using NuGEN-Ovation Pico kit according to manufacturer's instructions.

growth_protocol: Rice seedlings were germinated in vitro in water agar plates. Germination was performed at 30°C in the dark for 5 days. Seedlings were then transfered in a controlled environment growth chamber with a 16h-light/8h-dark photoperiod at 28/24°C for another 6 days prior inoculation. M. oryzae mycelium was cultured at 26°C on solid agar Complete Medium with a 16h-light/8h-dark photoperiod and conidia were harvested from 8-days old cultures.

extract_protocol: Total RNA was extracted in Trizol reagent followed by nucleic acid precipitation. Extracted RNA was further precipitated with 2M lithium chloride.

treatment_protocol: Infection was conducted on roots laid on sterile filter paper prepositioned on fresh water agar. Each plate containing 4 to 6 plants, received a total of 5.104 conidia randomly distributed on top of the root system. Sterile 0.1% Tween20 and 0.01% antifoam A (Sigma) solution was used for Mock inoculation. Inoculated plants were kept horizontally at 26°C with a 16h-light/8h-dark photoperiod.

value: Roots

tag: cultivare

value: Nipponbare


title: Magnaporthe oryzae Guy11 inoculated root 6 dpi rep 1

description: Gene expression data from M. oryzae inoculated roots at 6 dpi

tag: tissue


title: Magnaporthe oryzae Guy11 inoculated root 2 dpi rep 2

description: Gene expression data from M. oryzae inoculated roots at 2 dpi


title: Magnaporthe oryzae Guy11 inoculated root 4 dpi rep 1


title: S. mansoni schistosomula batch 1, 3h replicate 1 of 2

description: S. mansoni schistosomula


title: Magnaporthe oryzae Guy11 inoculated root 2 dpi rep 1


title: Blood_BPD_7

value: Male


title: S. mansoni schistosomula batch 1, 5d + RBC replicate 2 of 2

description: S. mansoni schistosomula

source_name: S. mansoni schistosomula, 5d + RBC


title: S. mansoni schistosomula batch 1, 5d + RBC replicate 1 of 2

description: S. mansoni schistosomula


title: Magnaporthe oryzae Guy11 inoculated root 6 dpi rep 2


title: Blood_BPD_6


title: Mock inoculated root 6 dpi rep 1

description: Gene expression data from Mock inoculated roots at 6 dpi


title: ki-1122

first: julien

last: Ratelade

address: 149 rue de Sèvres

institute: INSERM U574

description: According to manufacturers instructions

hyb_protocol: According to manufacturers instructions

scan_protocol: According to manufacturers instructions

data_processing:
RMA normalization (Irizary et al., 2003) using background adjustment, quantile normalization, and median polish as the summarization method
  Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research 31(4): e15 (2003)

source_name: Isolated glomeruli from 27-day-old male knockin FVB/N (backcross N4)

label_protocol: According to manufacturers instructions

extract_protocol: RNA was extracted using the Qiagen's RNeasy Total RNA Isolation kit (Qiagen GmBH, Hilden, Germany), and quality was assessed by agarose-formaldehyde gel electrophoresis.

value: Isolated glomeruli

value: male

value: FVB/N (backcross N4)

tag: type

value: Knockin for the WT1 R394W mutation. Heterozygous for the mutation.


title: Mock inoculated root 4 dpi rep 2

description: Gene expression data from Mock inoculated roots at 4 dpi


title: Mock inoculated root 6 dpi rep 2


title: E-IAA neg_A36.4

source_name: PLN E-IAA neg, 5 weeks old NOD mice

value: PLN E-IAA neg


title: Blood_BPD_4


title: Blood_BPD_5

value: Yes


title: Mock inoculated root 4 dpi rep 1


title: Blood_BPD_3

value: Bipolar Disorder


title: ki-1067

description: According to manufacturers instructions


title: E-IAA neg_A36.1


title: Mock inoculated root 2 dpi rep 2

description: Gene expression data from Mock inoculated roots at 2 dpi


title: E-IAA neg_A37.1


title: E-IAA pos_A9.6


title: ki-1066

description: According to manufacturers instructions


title: S. mansoni schistosomula batch 1, 5d replicate 1 of 2

description: S. mansoni schistosomula

value: schistosomula


title: Blood_BPD_2

value: No

value: Asain-PI


title: E-IAA neg_A12.2


title: Mock inoculated root 2 dpi rep 1


title: E-IAA pos_A15.4

value: PLN E-IAA pos


title: Blood_BPD_1

value: European-American


title: ki-1058

description: According to manufacturers instructions


title: FEAT-20

city: Fukuoka

first: Atsushi

last: Takahashi

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description: stably transfected with pEF-DEST51-FEAT

hyb_protocol: Illumina Gene Expression System Block Buffer Illumina Gene Expression System GEX-HCB&GEX-HYB Buffers Illumina Gene Expression System Wash E1BC Buffer and Components Illumina Gene Expression System  High Temp Wash  Buffer

scan_protocol: BeadArray Reader

data_processing: average normalization, BeadStudio

label_protocol: Illumina®  TotalPrep RNA Amplification Kit

extract_protocol: RNeasy Mini

value: NIH Swiss

tag: cell

value: immortalized cell line derived from embyronic fibroblasts


title: E-IAA neg_A8.1

value: 5 weeks old

value: NOD mice

value: Non Obese Diabetic mouse for Type 1 diabetes


title: E-IAA neg_A12.1


title: ki-1065

description: According to manufacturers instructions

value: Isolated glomeruli


title: contr-1068

description: According to manufacturers instructions

source_name: Isolated glomeruli from 27-day-old male wild type FVB/N (backcross N4)

value: male

value: Wild-type mouse


title: contr-1057

description: Isolated glomeruli from 27-day-old male FVB/N (backcross N4). Wild-type mouse.

value: FVB/N (backcross N4)


title: FEAT-3

description: stably transfected with pEF-DEST51-FEAT


title: contr-1102

description: According to manufacturers instructions


title: contr-1064

description: According to manufacturers instructions


title: ΔccdB-3

description: stably transfected with pEF-DEST51 without ccdB gene


title: FEAT-15

description: stably transfected with pEF-DEST51-FEAT


title: contr-1047

source_name: Isolated glomeruli from 27-day-old male wild type FVB mouse


title: Brain Cy3 vs Control Cy5 (Batch2)

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

description: RNA quality control with Agilent Bioanalyzer 2100

hyb_protocol: Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies).  The protocols were according to the manufacturer's instructions.

scan_protocol: Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.

data_processing: The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.5 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default condition of the software. Some probes which were judged beyond analysis by Feature Extraction 10.5 software were eliminated from the following analysis.

organism: Ciona intestinalis

source_name: Brain

label_protocol: Total RNA was labeled with Cy3 using an Agilent Quick-Amp Labeling Kit (Agilent Technologies).  The protocols were according to the manufacturer's instructions.

extract_protocol: Total RNA from brain vesicle was extracted by acid guanidium thiocyanate-phenol-chloroform extraction method.

value: Brain vesicle of larva

source_name: Control

label_protocol: Total RNA was labeled with Cy5 using an Agilent Quick-Amp Labeling Kit (Agilent Technologies).  The protocols were according to the manufacturer's instructions.

extract_protocol: Total RNA from cells without brain vesicle was extracted by acid guanidium thiocyanate-phenol-chloroform extraction method.

value: Cells of larva without brain vesicles


title: liver_female AFB1-treated wild-type 11 wk

city: Taipei

first: Yi-Ming

middle: Arthur

last: Chen

state: Taiwan

address: 155, Li-Noun St., Sec. 2

department: AIDS Prevention and Research Center

country: Taiwan

institute: National Yang-Ming University

description: Gene expression data from 3 wild-type female mice liver tissues at 11 weeks old

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Liver tissue from 3 mice at 11 weeks old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

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

treatment_protocol: At 7 days of age, Gnmt-/- and wild-type mice from the same litter were intraperitoneally injected with 10 mg AFB1/kg of body weight; a second treatment of 40 µg AFB1 per mouse was given at 9 weeks of age.

value: female

value: wild-type

value: 11 weeks

value: liver

tag: agent


title: liver_female AFB1-treated Gnm-/- 11 wk

description: Gene expression data from 3 Gnmt -/- female mice liver tissues at 11 weeks old

value: Gnmt knockout


title: liver_male AFB1-treated wild-type 11 wk

description: Gene expression data from 3 wild-type male mice liver tissues at 11 weeks old


title: Conrtrol Cy3 vs Brain Cy5 (Batch1)


title: Brain Cy3 vs Control Cy5 (Batch1)


title: ΔccdB-1


title: cytosol_rep2

status: Public on Oct 01 2009

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

institute: University of Queensland

description: HES2 cells were cultured as above on 1/3 MEFs in media containing KOSR/DMEM F12.  10 µg/ml of Cycloheximide (Sigma-Aldrich, St. Louis, http://www.sigmaaldrich.com) was added to the cultures for 10 mins and these were harvested and washed twice with 10 µg/ml of Cycloheximide in PBS. The pellet was frozen in liquid nitrogen.  Membrane bound polysome and free ribosome associated RNA was separated on a sucrose gradient as described in Diehn et al., 2000. In short, 5x107 HES2 hESCs were lysed, nuclei removed and supernatant was applied to sucrose gradient as described previously (Diehn et al., 2000). RNA was further separated by ultracentrifugation at 55,000 rpm for 16 hours.  60 uL fractions were obtained from the top of the gradient, and the concentration of RNA was determined by A260 measurement.  RNA from fractions 1-16 (cytosol) and 28-37 (membrane) was isolated by the RNeasy kit (Qiagen) and hybridised to Illumina Sentrix6-V2 microarrays.

hyb_protocol: llumina Human 6V2 BeadChips were hybridized, washed, stained and scanned according to Illuminas protocol

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were first extracted with Illumina BeadStudio software without normalisation.  Data was then uploaded into R, where RMA background adjustment was performed using the BeadExplorer package

source_name: HES2+KOSR, cytosolic/free fraction, replicate 2

label_protocol: Targets were prepared from 500 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: RNA samples were prepared using Qiagen RNeasy Micro Kit (Qiagen) and then assayed using the Agilent Systems Bioanalyzer 2100 to ensure that high-quality RNA was used for the array experiments.

tag: HES2 cell line

tag: Embryonic stem cells


title: cytosol_rep3

source_name: HES2+KOSR, cytosolic/free fraction, replicate 3


title: liver_male AFB1-treated Gnm-/- 11 wk

description: Gene expression data from 3 Gnmt -/- male mice liver tissues at 11 weeks old

tag: age


title: Conrtrol Cy3 vs Brain Cy5 (Batch2)


title: H9.mTESR_p7_rep3

hyb_protocol: llumina Human 6 BeadChips were hybridized, washed, stained and scanned according to Illuminas protocol

data_processing: Data were first extracted with Illumina BeadStudio software without normalisation.  Data was then uploaded into R, where RMA background adjustment and Quantile normalisation was performed using the BeadExplorer package

source_name: Embryonic Stem Cells

label_protocol: Targets were prepared from 100 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

tag: H9 +mTESR culture, Fraction p7, Replicate 3


title: ΔccdB-2


title: H9.mTESR_p5_rep3

tag: H9 +mTESR culture, Fraction p5, Replicate 3


title: H9.mTESR_p5_rep2

tag: H9 +mTESR culture, Fraction p5, Replicate 2


title: H9.mTESR_p6_rep2

tag: H9 +mTESR culture, Fraction p6, Replicate 2


title: membrane_rep3

source_name: HES2+KOSR, membrane-polysome associated fraction, replicate 3


title: membrane_rep2

source_name: HES2+KOSR, membrane-polysome associated fraction, replicate 2


title: membrane_rep1

source_name: HES2+KOSR, membrane-polysome associated fraction, replicate 1


title: H9.mTESR_p6_rep1

tag: H9 +mTESR culture, Fraction p6, Replicate 1


title: MEL1.KOSR_p7_rep3

tag: MEL1 +KOSR culture, Fraction p7, Replicate 3


title: H9.mTESR_p4_rep1

tag: H9 +mTESR culture, Fraction p4, Replicate 1


title: H9.mTESR_p4_rep2

tag: H9 +mTESR culture, Fraction p4, Replicate 2


title: H9.mTESR_p7_rep2

tag: H9 +mTESR culture, Fraction p7, Replicate 2


title: MEL1.KOSR_p7_rep2

tag: MEL1 +KOSR culture, Fraction p7, Replicate 2


title: H9.mTESR_p5_rep1

tag: H9 +mTESR culture, Fraction p5, Replicate 1


title: MEL1.KOSR_p6_rep2

tag: MEL1 +KOSR culture, Fraction p6, Replicate 2


title: H9.mTESR_p7_rep1

tag: H9 +mTESR culture, Fraction p7, Replicate 1


title: H9.mTESR_p6_rep3

tag: H9 +mTESR culture, Fraction p6, Replicate 3


title: MEL1.KOSR_p4_rep2

tag: MEL1 +KOSR culture, Fraction p4, Replicate 2


title: MEL1.KOSR_p5_rep1

tag: MEL1 +KOSR culture, Fraction p5, Replicate 1


title: cytosol_rep1

source_name: HES2+KOSR, cytosolic/free fraction, replicate 1

tag: HES2 cell line

tag: Embryonic stem cells


title: MEL1.KOSR_p5_rep2

tag: MEL1 +KOSR culture, Fraction p5, Replicate 2


title: MEL1.KOSR_p4_rep1

tag: MEL1 +KOSR culture, Fraction p4, Replicate 1


title: MEL1.KOSR_p6_rep1

tag: MEL1 +KOSR culture, Fraction p6, Replicate 1


title: HES2.KOSR_p4_rep3

tag: HES2 +KOSR culture, Fraction p4, Replicate 3


title: p7_rep2

description:
Replicate 2 of 3
1705168082_B

hyb_protocol: Illumina Human 6 BeadChips were hybridized, washed, stained and scanned according to Illumina's protocol.

data_processing: Data were first extracted with Illumina BeadStudio software without normalisation.  Data was then uploaded into R, where RMA background adjustment and Quantile normalisation was performed using the BeadExplorer package.

source_name: Embryonic stem cells, fraction p7

label_protocol: Targets were prepared from 100 ng total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791).

growth_protocol: HES2 ESCs were grown in standard ES culture conditions.

treatment_protocol: HES2 cells were subjected to FACs sorting, and fractions p4, p5, p6, and p7 were collected.

tag: HES2 standard culture


title: HES2.KOSR_p4_rep2

tag: HES2 +KOSR culture, Fraction p4, Replicate 2


title: HES2.KOSR_p6_rep1

tag: HES2 +KOSR culture, Fraction p6, Replicate 1


title: HES2.KOSR_p6_rep2

tag: HES2 +KOSR culture, Fraction p6, Replicate 2


title: HES2.KOSR_p4_rep1

tag: HES2 +KOSR culture, Fraction p4, Replicate 1


title: MEL1.KOSR_p5_rep3

tag: MEL1 +KOSR culture, Fraction p5, Replicate 3


title: p4_rep3

description:
Replicate 3 of 3
1705168082_C

source_name: Embryonic stem cells, fraction p4


title: HES2.KOSR_p7_rep1

tag: HES2 +KOSR culture, Fraction p7, Replicate 1


title: p5_rep3

description:
Replicate 3 of 3
1705168082_D

source_name: Embryonic stem cells, fraction p5


title: p7_rep3

description:
Replicate 3 of 3
1705168082_F


title: MEL1.KOSR_p7_rep1

tag: MEL1 +KOSR culture, Fraction p7, Replicate 1


title: HES2.KOSR_p5_rep2

tag: HES2 +KOSR culture, Fraction p5, Replicate 2


title: HES2.KOSR_p5_rep3

tag: HES2 +KOSR culture, Fraction p5, Replicate 3


title: MEL1.KOSR_p4_rep3

tag: MEL1 +KOSR culture, Fraction p4, Replicate 3


title: HES2.KOSR_p7_rep2

tag: HES2 +KOSR culture, Fraction p7, Replicate 2


title: p6_rep2

description:
Replicate 2 of 3
1705168082_A

source_name: Embryonic stem cells, fraction p6


title: p5_rep2

description:
Replicate 2 of 3
1705168044_F


title: p7_rep1

description:
Replicate 1 of 3
1705168044_D


title: p4_rep1

description:
Replicate 1 of 3
1705168044_A


title: p6_rep1

description:
Replicate 1 of 3
1705168044_C


title: p4_rep2

description:
Replicate 2 of 3
1705168044_E


title: HES2.KOSR_p6_rep3

tag: HES2 +KOSR culture, Fraction p6, Replicate 3


title: HES2.KOSR_p7_rep3

tag: HES2 +KOSR culture, Fraction p7, Replicate 3


title: HES2.KOSR_p5_rep1

tag: HES2 +KOSR culture, Fraction p5, Replicate 1


title: MEL1.KOSR_p6_rep3

tag: MEL1 +KOSR culture, Fraction p6, Replicate 3


title: p6_rep3

description:
Replicate 3 of 3
1705168082_E


title: p5_rep1

description:
Replicate 1 of 3
1705168044_B


title: H9.mTESR_p4_rep3

tag: H9 +mTESR culture, Fraction p4, Replicate 3


title: Mononuclear cells Nsp29

city: Ulm

first: Frank

last: Stegelmann

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University Hospital of Ulm

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE) were processed by Copy Number Analyzer for GeneChip (CNAG) version 2.0 software. Normalization was performed against an own set of 30 Sty and 30 Nsp reference samples, respectively. In one case (UPN23) dermal cells were used for paired tumor-germline analysis (UPN23_2).

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from granulocyte preparations obtained from peripheral blood using DNAzol reagent. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: cell type

value: mononuclear cells

tag: diagnosis

value: remission


title: Mononuclear cells Nsp19

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp23

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp22

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp17

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp25

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp12

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp28

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp14

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp15

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp20

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp26

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp9

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp4

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp7

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp27

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp21

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp13

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp8

description: Hybridized to 250K_Nsp


title: Esx1+72h_rep2

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 124 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Esx1, +Dox, 72h

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: The samples were dissolved in the well with TRIzol reagent 1/2 mL. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer. ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.

treatment_protocol: Day 3: Cells were plated in regular ES medium with Doxycycline (0.2ug/ml) and Puromycin (1.5ug/ml). Approximately 18 hours after plating, the cells were rinsed once with PBS, then the medium was replaced with warmed medium with Doxycycline. Three hours after the first medium change, the medium was changed again. Finally, at three hours after the second medium change, the medium was replaced for a final time.  Thereafter, the medium was changed daily.  At 72 hours after the final wash, the cells were harvested in Trizol. There was no medium change on the day of RNA harvest.

value: Embryonic Stem Cells

tag: strain

tag: gender

tag: development stage

value: embryo

tag: individual identifier 1

value: Esx1 clone16, Dox+, 72h #3

tag: individual identifier 2

tag: individual identifier 3

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube.

tag: cell line

value: mixed


title: Mononuclear cells Nsp24

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp11

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp30

description: Hybridized to 250K_Nsp


title: Esx1-72h_rep1

source_name: Esx1, -Dox, 72h

treatment_protocol: Day 3: Cells were plated in regular ES medium with Doxycycline (0.2ug/ml) and Puromycin (1.5ug/ml). Approximately 18 hours after plating, the cells were rinsed once with PBS, then the medium was replaced with warmed medium without Doxycycline. Three hours after the first medium change, the medium was changed again. Finally, at three hours after the second medium change, the medium was replaced for a final time.  Thereafter, the medium was changed daily.  At 72 hours after the final wash, the cells were harvested in Trizol. There was no medium change on the day of RNA harvest.

value: Esx1 clone16, Dox-, 72h #1


title: Esx1+72h_rep1

value: male

value: Esx1 clone16, Dox+, 72h #1


title: Mononuclear cells Nsp2

description: Hybridized to 250K_Nsp


title: Esx1-24h_rep2

source_name: Esx1, -Dox, 24h

treatment_protocol: Day 1: Cells were plated in regular ES medium with Doxycycline (0.2ug/ml) and Puromycin (1.5ug/ml). Approximately 18 hours after plating, the cells were rinsed once with PBS, then the medium was replaced with warmed medium without Doxycycline. Three hours after the first medium change, the medium was changed again. Finally, at three hours after the second medium change, the medium was replaced for a final time. At 24 hours after the final wash, the cells were harvested in Trizol. There was no medium change on the day of RNA harvest.

value: Esx1 clone16, Dox-, 24h #2


title: Mononuclear cells Nsp10

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp16

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp3

description: Hybridized to 250K_Nsp


title: Mononuclear cells Nsp6

description: Hybridized to 250K_Nsp


title: Esx1-24h_rep1

value: Esx1 clone16, Dox-, 24h #1


title: Esx1+24h_rep2

source_name: Esx1, +Dox, 24h

treatment_protocol: Day 1: Cells were plated in regular ES medium with Doxycycline (0.2ug/ml) and Puromycin (1.5ug/ml). Approximately 18 hours after plating, the cells were rinsed once with PBS, then the medium was replaced with warmed medium with Doxycycline. Three hours after the first medium change, the medium was changed again. Finally, at three hours after the second medium change, the medium was replaced for a final time.  At 24 hours after the final wash, the cells were harvested in Trizol. There was no medium change on the day of RNA harvest.

value: Esx1 clone16, Dox+, 24h #2


title: Esx1+24h_rep1

value: Esx1 clone16, Dox+, 24h #1


title: Klf4-72h_rep2

source_name: Klf4, -Dox, 72h

value: Klf4 clone16, Dox-, 72h #3


title: Mononuclear cells Nsp5

description: Hybridized to 250K_Nsp


title: Cdx2+72h_rep2

source_name: Cdx2, +Dox, 72h

value: Cdx2 clone6, Dox+, 72h #2


title: Cdx2-24h_rep2

source_name: Cdx2, -Dox, 24h

value: Cdx2 clone6, Dox-, 24h #2


title: Mononuclear cells Nsp18

description: Hybridized to 250K_Nsp


title: Cdx2+72h_rep1

value: Cdx2 clone6, Dox+, 72h #1


title: Ascl1-72h_rep2

source_name: Ascl1, -Dox, 72h

value: Ascl1 clone12, Dox-, 72h #2


title: Cdx2+24h_rep2

source_name: Cdx2, +Dox, 24h

value: Cdx2 clone6, Dox+, 24h #2


title: Cdx2-72h_rep1

source_name: Cdx2, -Dox, 72h

value: Embryonic Stem Cells


title: Cdx2+24h_rep1

value: embryo

value: Cdx2 clone6, Dox+, 24h #1


title: Cdx2-24h_rep1

value: Cdx2 clone6, Dox-, 24h #1

value: mixed


title: Ascl1-72h_rep1

value: male

value: Ascl1 clone12, Dox-, 72h #1


title: Ascl1+72h_rep2

source_name: Ascl1, +Dox, 72h

value: Ascl1 clone12, Dox+, 72h #3


title: Ascl1-24h_rep2

source_name: Ascl1, -Dox, 24h

value: Ascl1 clone12, Dox-, 24h #3


title: Ascl1-24h_rep1

value: Ascl1 clone12, Dox-, 24h #1


title: Ascl1+24h_rep2

source_name: Ascl1, +Dox, 24h

value: Ascl1 clone12, Dox+, 24h #3


title: Mononuclear cells Nsp1

description: Hybridized to 250K_Nsp

value: mononuclear cells

value: remission


title: Ascl1+24h_rep1

value: Ascl1 clone12, Dox+, 24h #2


title: Ascl1+72h_rep1

value: Ascl1 clone12, Dox+, 72h #2


title: Granulocytes UPN199

description: Hybridized to 250K_Nsp

value: granulocytes

value: essential thrombocythemia


title: Granulocytes UPN202

description: Hybridized to 250K_Nsp


title: Ascl2-72h_rep1

source_name: Ascl2, -Dox, 72h

value: Embryonic Stem Cells

value: Ascl2 clone21, Dox-, 72h #2


title: Ascl2+72h_rep2

source_name: Ascl2, +Dox, 72h

value: embryo

value: Ascl2 clone21, Dox+, 72h #3


title: Ascl2-72h_rep2

value: Ascl2 clone21, Dox-, 72h #3

value: mixed


title: Granulocytes UPN203

description: Hybridized to 250K_Nsp

source_name: peripheral blood


title: Granulocytes UPN201

description: Hybridized to 250K_Nsp


title: Myc-72h_rep2

source_name: Myc, -Dox, 72h

value: male

value: Myc clone16, Dox-, 72h #2


title: Myc-72h_rep1

value: Myc clone16, Dox-, 72h #1

source_name: Universal Mouse Reference 129ES Cell


title: Ascl2+24h_rep2

source_name: Ascl2, +Dox, 24h

value: Ascl2 clone21, Dox+, 24h #2


title: Ascl2+72h_rep1

value: Ascl2 clone21, Dox+, 72h #2


title: Ascl2-24h_rep2

source_name: Ascl2, -Dox, 24h

value: Ascl2 clone21, Dox-, 24h #2


title: Granulocytes UPN196

description: Hybridized to 250K_Nsp


title: Granulocytes UPN194

description: Hybridized to 250K_Nsp


title: Ascl2-24h_rep1

value: Ascl2 clone21, Dox-, 24h #1


title: Myc+72h_rep1

source_name: Myc, +Dox, 72h

value: Myc clone16, Dox+, 72h #2


title: Myc+72h_rep2

value: Myc clone16, Dox+, 72h #3


title: Myc-24h_rep2

source_name: Myc, -Dox, 24h

value: Myc clone16, Dox-, 24h #3


title: Myc-24h_rep1

value: Myc clone16, Dox-, 24h #1


title: Ascl2+24h_rep1

value: Embryonic Stem Cells

value: Ascl2 clone21, Dox+, 24h #1


title: Myc+24h_rep2

source_name: Myc, +Dox, 24h

value: embryo

value: Myc clone16, Dox+, 24h #2


title: Gata3-72h_rep2

source_name: Gata3, -Dox, 72h

value: Gata3 clone14, Dox-, 72h #3


title: Gata3+72h_rep2

source_name: Gata3, +Dox, 72h

value: Gata3 clone14, Dox+, 72h #3

value: mixed


title: Granulocytes UPN198

description: Hybridized to 250K_Nsp

value: granulocytes

value: essential thrombocythemia


title: Granulocytes UPN195

description: Hybridized to 250K_Nsp


title: Gata3-72h_rep1

value: male

value: Gata3 clone14, Dox-, 72h #2


title: Myc+24h_rep1

value: Myc clone16, Dox+, 24h #1


title: Gata3-24h_rep2

source_name: Gata3, -Dox, 24h

value: Gata3 clone14, Dox-, 24h #2


title: Gata3-24h_rep1

value: Gata3 clone14, Dox-, 24h #1


title: Granulocytes UPN189

description: Hybridized to 250K_Nsp


title: Granulocytes UPN187

description: Hybridized to 250K_Nsp


title: Granulocytes UPN192

description: Hybridized to 250K_Nsp


title: Granulocytes UPN191

description: Hybridized to 250K_Nsp


title: Gata3+24h_rep2

source_name: Gata3, +Dox, 24h

value: Gata3 clone14, Dox+, 24h #2


title: Klf4-72h_rep1

source_name: Klf4, -Dox, 72h

value: Klf4 clone16, Dox-, 72h #1


title: Granulocytes UPN193

description: Hybridized to 250K_Nsp


title: Granulocytes UPN188

description: Hybridized to 250K_Nsp


title: Gata3+72h_rep1

value: Gata3 clone14, Dox+, 72h #1


title: Granulocytes UPN190

description: Hybridized to 250K_Nsp


title: Granulocytes UPN197

description: Hybridized to 250K_Nsp


title: Granulocytes UPN200

description: Hybridized to 250K_Nsp


title: Granulocytes UPN185

description: Hybridized to 250K_Nsp


title: Klf4+72h_rep1

source_name: Klf4, +Dox, 72h

value: Embryonic Stem Cells

value: Klf4 clone16, Dox+, 72h #2


title: Klf4-24h_rep1

source_name: Klf4, -Dox, 24h

value: embryo

value: Klf4 clone16, Dox-, 24h #1


title: Klf4+24h_rep1

source_name: Klf4, +Dox, 24h

value: Klf4 clone16, Dox+, 24h #1


title: Klf4+48h_rep2

source_name: Klf4, +Dox, 48h

treatment_protocol: Day 2: Cells were plated in regular ES medium with Doxycycline (0.2ug/ml) and Puromycin (1.5ug/ml). Approximately 18 hours after plating, the cells were rinsed once with PBS, then the medium was replaced with warmed medium with Doxycycline. Three hours after the first medium change, the medium was changed again. Finally, at three hours after the second medium change, the medium was replaced for a final time.  Thereafter, the medium was changed daily.  At 48 hours after the final wash, the cells were harvested in Trizol. There was no medium change on the day of RNA harvest.

value: Klf4 clone16, Dox+, 48h #2


title: Granulocytes UPN186

description: Hybridized to 250K_Nsp

source_name: peripheral blood


title: Cdx2-48h_rep1

source_name: Cdx2, -Dox, 48h

treatment_protocol: Day 2: Cells were plated in regular ES medium with Doxycycline (0.2ug/ml) and Puromycin (1.5ug/ml). Approximately 18 hours after plating, the cells were rinsed once with PBS, then the medium was replaced with warmed medium without Doxycycline. Three hours after the first medium change, the medium was changed again. Finally, at three hours after the second medium change, the medium was replaced for a final time.  Thereafter, the medium was changed daily.  At 48 hours after the final wash, the cells were harvested in Trizol. There was no medium change on the day of RNA harvest.

value: Cdx2 clone6, Dox-, 48h #3

value: mixed


title: Gata3+24h_rep1

value: Gata3 clone14, Dox+, 24h #1

source_name: Universal Mouse Reference 129ES Cell