title: BCells_Transgenic_day2_REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Gene expression data from stimulated, transgenic B cells

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: B cells, transgenic, stimulated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: B cells from spleen were isolated by negative selection using CD43 microbeads (MACS; Milteny). The purity of the different subpopulations was above 98% as assayed by flow cytometry.B cells were grown in RPMI with Glutamax containing 10% FCS (Invitrogene), nonessential amino acids (0.1 mM), sodium pyruvate (1 mM), penicillin (100 U/ml)/streptomycin (100 µg/ml) and 50 µM b-mercaptoethanol and were maintained at 37 ºC in an atmosphere at 5% CO2.

extract_protocol: RNA was prepared using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies

treatment_protocol: For stimulation, B cells (0.4 x 106) were cultured in 24-well plates and stimulated with LPS (20 µg/ml; Sigma) and mouse recombinant IL-4 (10 ng/ml; Pharmingen) for 2 days.

value: EFLmDREAM

tag: stimulation

value: stimulated with LPS and mouse recombinant IL-4 (day 2)

tag: cell type

value: B cells


title: Burkitt MPI-079_nsp

status: Public on Dec 07 2010

type: genomic

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

country: Germany

institute: University Hospital Essen

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 washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The CEL-Files were analyzed using the BRLMM-algorithm to produce genotype calls, stored in the corresponding CHP-Files.
CEL- and CHP-Format by Affymetrix

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole tissue of tumor biopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: QiaAmp DNA Blood Kit

tag: sample type

value: tumor

tag: tissue

tag: disease state

value: Burkitt lymphoma


title: Burkitt MPI-080_nsp

description: Hybridized to 250K_Nsp


title: Burkitt MPI-082_nsp

description: Hybridized to 250K_Nsp


title: CC2_rpoNNBrich_1_vs_wtNBrich_1_7DE1577

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

country: USA

institute: University of California, Irvine

description: biological replicate, Date of Scan Tue May 26 09:10:18 2009

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv5_SP040504_adapforsmallpins_040817

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: RpoN-specific pulldown from rpoN mutant strain grown in NBrich medium

label_protocol: amplification of purified immunoprecipitated DNA followed by purification and labeling using Cy3-dCTP with Klenow and random hexamers

extract_protocol: chromatin immunoprecipitation using the ChIP assay kit (USB)

tag: antibody

value: RpoN-specific pulldown

tag: genotype/variation

value: rpoN mutant

tag: growth phase

value: late log in NBrich medium

source_name: RpoN-specific pulldown from wt strain grown in NBrich medium

label_protocol: amplification of purified immunoprecipitated DNA followed by purification and labeling using Cy5-dCTP with Klenow and random hexamers

value: wt


title: BCells_Transgenic_day2_REP1

type: RNA

label: biotin

molecule: total RNA

organism: Mus musculus

tag: genotype


title: Burkitt MPI-077_nsp

description: Hybridized to 250K_Nsp


title: Uncoated cellulose implant, 1 day, rat 2

city: Turku

first: Miretta

last: Tommila

address: Kiinamyllynkatu 10

department: Lääketieteellisen biokemian ja genetiikan laitos

country: Finland

institute: Turun yliopisto

description: no additional information

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with limma in R

organism: Rattus norvegicus

source_name: subcutaneous implantation of uncoated cellulose, 1 day, rat 2

label_protocol: For the Illumina gene expression analysis, 100 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

growth_protocol: Subcutaneous implantation into rat

extract_protocol: Total RNA from implants was isolated with RNeasy midi kit according to manufacturer´s instructions, followed by the Dnase I treatment (Promega) as recommended by manufacturer.

tag: strain

value: Sprague-Dawley

tag: age

value: 10 weeks

value: Granulation tissue

tag: time

value: 1 day


title: Hydroxyapatite-coated cellulose, 3 days, rat 4

description: no additional information

source_name: subcutaneous implantation of hydroxyapatite-coated cellulose, 3 days, rat 4

value: 3 days


title: rosettes_drought_rep3

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Soil water deficit stress was imposed on four week old plants by withholding water until plants reached a relative water content (RWC) of 65%.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using Rosetta Resolver 6.0, creating ratio-experiments  using control reps as one pool, and treatment reps as the other pool.  Resulting log ratios and p-values are calculated using Rosetta's proprietary ratio error model.

organism: Arabidopsis thaliana

source_name: vegetative rosettes, water deficit

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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


title: BCells_WildType_day2_REP1

description: Gene expression data from stimulated, wild type B cells

source_name: B cells, wild type, stimulated

value: Wild Type


title: BCells_WildType_day2_REP3


title: BCells_WildType_day2_REP2


title: Hydroxyapatite-coated cellulose, 3 days, rat 7

description: no additional information

source_name: subcutaneous implantation of hydroxyapatite-coated cellulose, 3 days, rat 7


title: CC2_wt_vs_rpoN_7DE1399

description: biological replicate, Date of Scan Tue Mar 17 11:47:41 2009

source_name: RpoN-specific pulldown from wt

value: late log

source_name: RpoN-specific pulldown from rpoN mutant strain


title: CC2_wtpPBHP92_vs_rpoNpPBHP92_7DE1400

description: biological replicate, Date of Scan Mon Mar 16 09:01:56 2009

source_name: RpoN-specific pulldown from wt grown with pPBHP92

tag: agent

source_name: RpoN-specific pulldown from rpoN mutant strain grown with pPBHP92


title: BCells_Transgenic_day2_REP3


title: Burkitt MPI-048_nsp

description: Hybridized to 250K_Nsp


title: CC2_wtpPBHP92rif_vs_wtrif_7DE1398

description: biological replicate, Date of Scan Mon Mar 16 08:42:35 2009

source_name: RpoN-specific pulldown from wt grown with pBHP92 and rifampicin

value: pPBHP92 and rifampicin

source_name: RpoN-specific pulldown from wt grown with rifampicin

value: rifampicin


title: rosettes_drought_rep1


title: BCells_Transgenic_day0_REP3

description: Gene expression data from unstimulated, transgenic B cells

source_name: B cells, transgenic, unstimulated

value: EFLmDREAM

value: non stimulated


title: Hydroxyapatite-coated cellulose, 3 days, rat 6

description: no additional information

source_name: subcutaneous implantation of hydroxyapatite-coated cellulose, 3 days, rat 6


title: CC2_rpoNNBrich_2_vs_wtNBrich_2_7DE1578

description: biological replicate, Date of Scan Tue May 26 09:18:45 2009


title: CC2_wtdctDAAArif_vs_rpoNdctDAAArif_7DE1397

description: biological replicate, Date of Scan Fri Mar 06 13:43:00 2009

source_name: RpoN-specific pulldown from wt grown with dctDAAA and rifampicin

value: dctDAAA and rifampicin

source_name: RpoN-specific pulldown from rpoN mutant strain grown with dctDAAA and rifampicin


title: Burkitt MPI-071_nsp

description: Hybridized to 250K_Nsp

source_name: Whole tissue of tumor biopsy

value: tumor

value: Burkitt lymphoma


title: rosettes_drought_rep2


title: Uncoated cellulose implant, 1 day, rat 1

description: no additional information

source_name: subcutaneous implantation of uncoated cellulose, 1 day, rat 1


title: rosettes_watered_rep2

description: Four week old plants were continued to be watered.

source_name: vegetative rosettes, watered


title: rosettes_watered_rep3


title: 252978410007_B7A_CY5_BCE002_MS12_CY3.mev.refIsIB.out

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

organism: Escherichia coli

source_name: Genomic DNA purified from wild type bacteria

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: cells were grown in LB overnight at 37 degrees celcius.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.


title: Burkitt MPI-032_nsp

description: Hybridized to 250K_Nsp


title: Burkitt MPI-018_nsp

description: Hybridized to 250K_Nsp


title: Burkitt MPI-043_nsp

description: Hybridized to 250K_Nsp


title: BCells_WildType_day0_REP3

description: Gene expression data from unstimulated, wild type B cells

source_name: B cells, wild type, unstimulated

value: B cells


title: Burkitt MPI-033_nsp

description: Hybridized to 250K_Nsp


title: BCells_WildType_day0_REP2


title: Burkitt MPI-044_nsp

description: Hybridized to 250K_Nsp


title: fetal liver-derived megakaryocytes B2

city: Philadelphia

first: Mitchell

middle: J

last: Weiss

state: PA

address: 3615 Civic Center Blvd

institute: The Children's Hospital of Philadelphia

description: Geometric average of normalized 532 and 635 measurements for Sample B2.

hyb_protocol: Hybridized to the miRCURY locked nucleic acid (LNA) array. Automated microarray hybridizations and washes were performed on a Tecan HS4800 station with 20 hr hybridization at 56ºC.

scan_protocol: Axon GenePix 400b.

data_processing: Normalize background-subtracted data of individual channels by loess method, truncate values less than 1 to 1.0, take geometric average of Hy3 and Hy5 measurements of each sample. The affy package R/BioConductor version 1.24.2 was used to normalize the data.

source_name: BSA gradient-purified megakaryocytes

label_protocol: 0.5 ug RNA was labeled using the miRCURY LNA Hy3/Hy5 labeling kit (Exiqon).

growth_protocol: Day13.5-14.5 murine fetal livers were depleted of erythroid cells and cultured with murine thrombopoietin in StemSpan SFEM medium (StemCell Technologies, Vancouver, Canada) to generate megakaryocytes.

extract_protocol: Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: Megakaryocytes were purified on a bovine serum albumin gradient.

value: fetal liver

value: megakaryocyte


title: fetal liver-derived megakaryocytes B3

description: Geometric average of normalized 532 and 635 measurements for Sample B3.


title: fetal liver-derived megakaryocytes B1

description: Geometric average of normalized 532 and 635 measurements for Sample B1.


title: Brain CD8 T cells that are IL-10+ rep3

city: Iowa City

first: Stanley

last: Perlman

state: IA

address: 51 Newton Road

department: Department of Microbiology

institute: University of Iowa

description: Gene expression data from IL-10+CD8 T cells in a J2.2-V-1-infected mouse

hyb_protocol: 2.5 ug of labeld cDNA were hybridized on mouse GENE 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 complete with a 7G upgrade.

data_processing: The data were analyzed with Partek GS v 6.4 using default RMA as normalization method.

source_name: Directly ex vivo brain CD8 T cells

label_protocol: Biotinylated cDNA were prepared using NuGEN WT-Ovation PicoRNA amplification system, starting from 800 pg to 50 ng of total RNA.

growth_protocol: C57Bl/6 Vert-X (IL-10-eGFP) mice were infected intracranially with 500 PFU J2.2-V-1 virus and seven days later their brain lymphocytes were isolated and negatively selected for CD8 T cells. The CD8 brain lymphocytes were then sorted for IL-10+ and IL-10- CD8 T lymphocytes using GFP as a marker.

extract_protocol: Extraction of total RNA was achieved by purification on RNeasy columns.

treatment_protocol: These CD8 T lymphocytes are naturally IL-10+ and IL-10-.

value: brain

value: C57/BL6 Vert-X

value: 6-8 weeks

value: CD8 T cells that are IL-10+


title: Burkitt MPI-017_nsp

description: Hybridized to 250K_Nsp


title: Hydroxyapatite-coated cellulose, 1 day, rat 1

description: no additional information

source_name: subcutaneous implantation of hydroxyapatite-coated cellulose, 1 day, rat 1

value: Sprague-Dawley

value: 10 weeks

value: Granulation tissue

value: 1 day


title: Brain CD8 T cells that are IL-10- rep3

description: Gene expression data from IL-10-CD8 T cells in a J2.2-V-1-infected mouse

value: CD8 T cells that are IL-10-


title: Ter119- fetal liver progenitors A2

description: Geometric average of normalized 532 and 635 measurements for Sample A2.

source_name: Ter119– fetal liver cells

value: Ter119- progenitor


title: BCells_WildType_day0_REP1

value: Wild Type

value: non stimulated


title: rosettes_watered_rep1


title: Infected HFF cells (t=120h) vs. Uninfected HFF cells (t=0h)

city: Saint Nazaire

first: goncalves

last: olivier

address: 37, boulevard de l'Université

country: France

institute: CNRS

description:
t0-t120
IHFF cells vs. UHFF, 120 hours post infection.

hyb_protocol: Hybridization reactions were performed using Agilent’s two-colour microarray-based gene expression kit in Agilent hybridization chambers at 65°C for 17 hours. Slides were washed according to manufacturer’s instructions, and allowed to dry.

scan_protocol: Data were scanned at a resolution of 10μm using a High-Resolution Microarray Scanner (G2565CA, Agilent Technologies®) at a sensitivity setting of the photomultiplier of 100%. Images were quantified using Genepix Pro6® Software (Axon Instruments, Union City CA).

data_processing: Acuity® (Axon Instruments, Union City CA) Software was used for background substraction and LOWESS normalization.

source_name: uninfected human foreskin fibroblasts (UHFF)

label_protocol: 750ng of aRNAs were labelled using the Kreatech ULS aRNA Labeling Kit, following manufacturer’s recommendations.

growth_protocol: An E.cuniculi isolate from a mouse (strain I, karyotype form A) was kindly provided by Prof. E.U.Canning (Imperial College of Science, Technology and Medicine, London, UK). Human foreskin fibroblasts (HFFs) were grown in Minimum Essential Medium (MEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% fongizone, 1% glutamine, 1% penicillin-streptomycin, 10-3 % ampicillin, and 0.04% gentamicin. Cells were seeded in 80 cm2 cell culture flasks. For infection experiments, 4 x 10^8 spores produced in MDCK cells (Beauvais et al. 1994)  were used to infect confluent host cells (2 x 10^7) cultured in MEM supplemented with 5% FBS. The cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated from uninfected (0 h) and infected cells (4, 16, 48, 72 and 120 hours after infection). The cells were washed twice in 2 mL of ice-cold PBS, and 2 mL of RNAlater (Ambion, Inc) were added. Then, the cells were scraped in PBS and collected by centrifugation and total RNA was isolated using the “RNeasy mini kit” from Qiagen (Valencia, CA, USA) according to manufacturer’s recommendations. Total RNA was quantified and the quality was evaluated using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies®, USA). RNA was stored at -80°C until use.

Reverse transcription using an oligodT probe (Ambion) was made using the Superscript III reverse transcriptase (Invitrogen) according to manufacturer’s instructions. The whole reverse transcription product is used to synthesize the second cDNA strand; dNTP (0.28μM), ribonuclease H (2U), DNA polymerase 1 from E.coli (20 U) and ligase from E.coli (10 U) are added and incubated for 2 hours at 42°C. Double strand cDNA was purified and concentrated on a MiniElute PCR purification column (Qiagen), according to manufacturer’s instructions. cDNA was then quantified using the Agilent 2100 Bioanalyzer and the RNA 7500 DNA kit (Agilent Technologies®, USA). Antisense RNAs (aRNAs) were obtained by in vitro transcription using the MEGAscript kit (Ambion) according to the manufacturer’s recommendations.

tag: cell line

value: ATCC SCRC-1041

value: foreskin fibroblasts

tag: infection

tag: infection time

value: hour 0

source_name: HFF infected with E. cuniculi isolated from mouse (GB-M1), 120 hrs

value: Encephalitozoon cuniculi strain I, karyotype form A (GB-M1)

value: hour 120


title: Infected HFF cells (t=48h) vs. Uninfected HFF cells (t=0h)

description:
t0-t48
IHFF cells vs. UHFF, 48 hours post infection.

source_name: HFF infected with E. cuniculi isolated from mouse (GB-M1), 48 hrs

value: hour 48


title: Ter119- fetal liver progenitors A1

description: Geometric average of normalized 532 and 635 measurements for Sample A1.

value: fetal liver


title: Burkitt MPI-001_nsp

description: Hybridized to 250K_Nsp

value: tumor

value: Burkitt lymphoma


title: Infected HFF cells (t=72h) vs. Uninfected HFF cells (t=0h)

description:
t0-t72
IHFF cells vs. UHFF, 72 hours post infection.

source_name: HFF infected with E. cuniculi isolated from mouse (GB-M1), 72 hrs

value: hour 72


title: Brain CD8 T cells that are IL-10+ rep2

value: brain

value: C57/BL6 Vert-X

value: 6-8 weeks

value: CD8 T cells that are IL-10+


title: Infected HFF cells (t=4h) vs. Uninfected HFF cells (t=0h)

description:
t0-t4
IHFF cells vs. UHFF, 4 hours post infection.

source_name: HFF infected with E. cuniculi isolated from mouse (GB-M1), 4 hrs

value: hour 4


title: Infected HFF cells (t=16h) vs. Uninfected HFF cells (t=0h)

description:
t0-t16
IHFF cells vs. UHFF, 16 hours post infection.

source_name: HFF infected with E. cuniculi isolated from mouse (GB-M1), 16 hrs

value: hour 16


title: Brain CD8 T cells that are IL-10- rep2

value: CD8 T cells that are IL-10-


title: BCells_Transgenic_day0_REP2

description: Gene expression data from unstimulated, transgenic B cells

source_name: B cells, transgenic, unstimulated

value: EFLmDREAM

value: non stimulated

value: B cells


title: Burkitt MPI-003_nsp

description: Hybridized to 250K_Nsp


title: Brain CD8 T cells that are IL-10+ rep1


title: Ter119- fetal liver progenitors A3

description: Geometric average of normalized 532 and 635 measurements for Sample A3.

value: Ter119- progenitor


title: UGS at P0 from BPA exposed fetus

status: Public on Dec 06 2010

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

country: Japan

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

description: Gene expression data from BPA exposed fetus UGS at P0

hyb_protocol: Fragmented cRNAs were hybridized with the GeneChip Mouse Genome 430 ver. 2.0 (Affymetrix Inc., Santa Clara, CA, USA) at 45C for 18 h. GeneChips were stained in the Affymetrix Fluidics Station 450.

scan_protocol: Stained GeneChips were scanned using the Affymetrix 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 500.

source_name: BPA-exposed, Mouse fetus UGS region at P0

label_protocol: During the in vitro transcription using Bioarray kit (Enzo Biochem., Farmingdale, NY, USA), generated cRNAs were labeled with biotin-16-UTP and biotin-11-CTP.

growth_protocol: Pregnant female C57BL/6 mice were exposed with BPA (20 μg/kg/day) or synthetic estrogen Diethylstilbestrol (DES: 0.2 μg/kg/day), which were dissolved in tocopherol-stripped corn oil on embryonic day 13 (E13) to E16. Fetuses were collected at E17, E18, P0, and P1 to sample UGS region.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA).

treatment_protocol: The bladder and urethra were removed and dissected to isolate UGS. To purify UGS, other tissues such as the bladder, urethra, Wolffian duct (WD), seminal vesicle (SV), and Mullerian duct (MD) were removed from both the male and female urogenital tracts.

value: BPA

value: urogenital sinus


title: Zfp295 ES clone at T0, biological rep1

city: Napoli

first: Mario

last: Lauria

address: via P. Castellino 111

country: Italy

institute: TIGEM

description: Gene expression data from ES clone before induction of gene overexpression.

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430_2 Array (430A_2 in case of Runx1).

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

data_processing: The data were analyzed using the RMA function of the Affy package of the Bioconductor tool. RMA analysis was performed separately on each set of six arrays relative to a same gene overexpression experiment.

source_name: inducible ES cell clone

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: ES cells were grown in mES media + LIF and supplemented with 1ug/ml tetracycline (Tc) at 37°C in an atmosphere of 5% CO2.

extract_protocol: Total RNA samples at various times of induction were purified by QIAshredder and extracted with RNeasy Protect Mini Kit using standard conditions. Total RNA were reverse transcribed to single stranded cDNA with a special oligo (dT)24 primer containing a T7 RNA promoter site prior to second strand synthesis (One cycle cDNA synthesis kit by Affymetrix).

treatment_protocol: Clones were grown in medium deprived of Tc to perform a time course of induction (24, 39 or 48hrs depending on experiment). In presence of Tc (0 hrs), the expression of each mRNA was indicative of the basal expression level in mES cells.

tag: inducible gene

value: ES cell


title: UGS at E18 from vehicle exposed fetus

description: Gene expression data from vehicle exposed fetus UGS at E18

source_name: Control, Mouse fetus UGS region at E18

value: Control


title: Hydroxyapatite-coated cellulose, 1 day, rat 2

description: no additional information

source_name: subcutaneous implantation of hydroxyapatite-coated cellulose, 1 day, rat 2

value: Sprague-Dawley

value: 10 weeks

value: Granulation tissue

value: 1 day


title: UGS at E18 from BPA exposed fetus

description: Gene expression data from BPA exposed fetus UGS at E18

source_name: BPA-exposed, Mouse fetus UGS region at E18


title: Zfp295 ES clone at T0, biological rep3


title: UGS at P0 from DES exposed fetus

description: Gene expression data from DES exposed fetus UGS at P0

source_name: DES-exposed, Mouse fetus UGS region at P0

value: DES


title: Brain CD8 T cells that are IL-10- rep1

value: brain

value: C57/BL6 Vert-X

value: 6-8 weeks


title: UGS at E17 from BPA exposed fetus

description: Gene expression data from BPA exposed fetus UGS at E17

source_name: BPA-exposed, Mouse fetus UGS region at E17


title: Hydroxyapatite-coated cellulose, 1 day, rat 3

description: no additional information

source_name: subcutaneous implantation of hydroxyapatite-coated cellulose, 1 day, rat 3


title: UGS at E18 from DES exposed fetus

description: Gene expression data from DES exposed fetus UGS at E18

source_name: DES-exposed, Mouse fetus UGS region at E18


title: Zfp295 ES clone at T24, biological rep1

description: Gene expression data from ES clone 24h after induction of gene overexpression.


title: UGS at E17 from DES exposed fetus

description: Gene expression data from DES exposed fetus UGS at E17

source_name: DES-exposed, Mouse fetus UGS region at E17


title: UGS at P0 from vehicle exposed fetus

description: Gene expression data from vehicle exposed fetus UGS at P0

source_name: Control, Mouse fetus UGS region at P0


title: Zfp295 ES clone at T24, biological rep3


title: Zfp295 ES clone at T0, biological rep2


title: Sim2 ES clone at T39, biological rep3

description: Gene expression data from ES clone 39h after induction of gene overexpression.


title: Zfp295 ES clone at T24, biological rep2


title: Sim2 ES clone at T39, biological rep2


title: Sim2 ES clone at T0, biological rep1


title: Sim2 ES clone at T39, biological rep1


title: Olig2 ES clone at T24, biological rep3


title: Sim2 ES clone at T0, biological rep2


title: Olig2 ES clone at T0, biological rep2


title: Olig2 ES clone at T24, biological rep2


title: Olig2 ES clone at T24, biological rep1


title: Olig2 ES clone at T0, biological rep3


title: BCells_Transgenic_day0_REP1

tag: stimulation


title: Ripk4 ES clone at T39, biological rep2

tag: cell type


title: Pdxk ES clone at T48, biological rep3

description: Gene expression data from ES clone 48h after induction of gene overexpression.

value: Pdxk


title: Pfkl ES clone at T24, biological rep1

value: Pfkl


title: Pfkl ES clone at T0, biological rep3


title: Snf1lk ES clone at T24, biological rep2


title: Ripk4 ES clone at T39, biological rep3


title: Pdxk ES clone at T0, biological rep3


title: Pfkl ES clone at T24, biological rep3


title: Pdxk ES clone at T0, biological rep1


title: Ripk4 ES clone at T0, biological rep3


title: Pfkl ES clone at T24, biological rep2


title: Snf1lk ES clone at T24, biological rep1


title: Snf1lk ES clone at T24, biological rep3


title: UGS at E17 from vehicle exposed fetus

description: Gene expression data from vehicle exposed fetus UGS at E17

source_name: Control, Mouse fetus UGS region at E17


title: Pfkl ES clone at T0, biological rep1


title: Ripk4 ES clone at T0, biological rep2


title: Pfkl ES clone at T0, biological rep2


title: Sim2 ES clone at T0, biological rep3


title: Pdxk ES clone at T48, biological rep2


title: Ripk4 ES clone at T39, biological rep1


title: Pdxk ES clone at T48, biological rep1


title: Pdxk ES clone at T0, biological rep2


title: Ripk4 ES clone at T0, biological rep1


title: Snf1lk ES clone at T0, biological rep3


title: Snf1lk ES clone at T0, biological rep1


title: Dyrk1a ES clone at T24, biological rep2


title: Snf1lk ES clone at T0, biological rep2


title: Dyrk1a ES clone at T0, biological rep2


title: Dyrk1a ES clone at T0, biological rep3


title: Hunk ES clone at T39, biological rep2

value: Hunk


title: RIKEN-1810007M14 ES clone at T24, biological rep3


title: Dyrk1a ES clone at T24, biological rep3


title: Hunk ES clone at T0, biological rep3


title: RIKEN-1810007M14 ES clone at T0, biological rep3


title: Dyrk1a ES clone at T0, biological rep1


title: Hunk ES clone at T39, biological rep3


title: Dyrk1a ES clone at T24, biological rep1


title: Pknox1 ES clone at T24, biological rep2


title: Pknox1 ES clone at T0, biological rep1


title: RIKEN-1810007M14 ES clone at T24, biological rep1


title: RIKEN-1810007M14 ES clone at T0, biological rep1


title: Pknox1 ES clone at T24, biological rep3


title: Hunk ES clone at T39, biological rep1


title: Pknox1 ES clone at T24, biological rep1


title: Pknox1 ES clone at T0, biological rep3


title: Hunk ES clone at T0, biological rep2


title: Olig1 ES clone at T24, biological rep3


title: Olig1 ES clone at T24, biological rep2


title: Hunk ES clone at T0, biological rep1


title: Pknox1 ES clone at T0, biological rep2


title: RIKEN-1810007M14 ES clone at T0, biological rep2


title: RIKEN-1810007M14 ES clone at T24, biological rep2


title: Nrip1 ES clone at T24, biological rep2


title: Olig2 ES clone at T0, biological rep1


title: Olig1 ES clone at T0, biological rep3


title: Olig1 ES clone at T0, biological rep2


title: Olig1 ES clone at T0, biological rep1


title: Gabpa ES clone at T24, biological rep3

value: Gabpa


title: Olig1 ES clone at T24, biological rep1


title: Nrip1 ES clone at T0, biological rep1


title: Ets2 ES clone at T24, biological rep3


title: E3-xGem injected st.12

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description: xGem st.12-set 3.CEL

hyb_protocol: Performed by the Washington University Genome Technololgy Access Center

scan_protocol: Affymetrix  Genechip 3000 used by the Washington University Genome Technololgy Access Center

data_processing: To define microarray target genes, raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(Li and Hung Wong, 2001) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 2-fold in treated versus untreated samples (E/B >2.0) groups, ii) MBEI differences were larger than 70 (E-B > 70), iii) expression was claimed as “present (P)” in at least one sample in each experiment.   Probesets were considered putatively Geminin-regulated if they met microarray cutoff values in at least 2 of the 3 experiments. A subset of these genes was then further validated.

organism: Xenopus laevis

source_name: embryonic ectoderm

label_protocol: biotin

growth_protocol: Xenopus laevis embryos were obtained by in vitro fertilization

extract_protocol: When sibling embryos reached stage 10.5 or 12, total RNA (20 μg/sample) was isolated using Trizol (Invitrogen).

treatment_protocol: xGemininΔcoil RNA/300 pg was injected into both blastomeres of two-cell stage pigmented Xenopus laevis embryos (animal hemisphere). Injected embryos were raised until stage 8-9 and 80 ectodermal (animal cap) explants/sample were isolated and incubated in 0.7X MMR/25ºC.

tag: developmental stage

tag: manipulation

value: xGem injected


title: Nrip1 ES clone at T24, biological rep1


title: E2-xGem injected st. st.12

description: xGem st.12-set 2.CEL


title: Gabpa ES clone at T24, biological rep1


title: Ets2 ES clone at T24, biological rep2


title: Nrip1 ES clone at T0, biological rep3


title: Gabpa ES clone at T24, biological rep2


title: Gabpa ES clone at T0, biological rep1


title: Ets2 ES clone at T0, biological rep3


title: Gabpa ES clone at T0, biological rep2


title: E3-uninjected st.12

description: uninjected st.12-set 3.CEL

value: uninjected


title: Ets2 ES clone at T24, biological rep1


title: Nrip1 ES clone at T0, biological rep2


title: E1-uninjected st. st.12

description: uninjected st.12-set 1.CEL


title: Gabpa ES clone at T0, biological rep3


title: Ets2 ES clone at T0, biological rep2


title: E2-uninjected st.12

description: uninjected st.10.5-set 2.CEL


title: E1-xGem injected st.12

description: xGem st.12-set 1.CEL


title: E2-uninjected st.10.5

description: uninjected st.10.5-set 2.CEL


title: Ets2 ES clone at T0, biological rep1


title: E3-uninjected st.10.5

description: uninjected st.10.5-set 3.CEL


title: E3-xGem injected st.10.5

description: xGem St.10.5-set 3.CEL


title: Erg ES clone at T24, biological rep3

value: Erg


title: Erg ES clone at T24, biological rep1

value: ES cell


title: E1-xGem injected st.10.5

description: xGem st.10.5-set 1.CEL


title: E1-uninjected st.10.5

description: uninjected st.10.5-set 1.CEL


title: Erg ES clone at T24, biological rep2


title: E2-xGem injected st.10.5

description: xGem st.10.5-set 2.CEL


title: Gene expression_sex_1337UT

city: Ann Arbor

first: GORDON

last: PAUL

state: MI

address: 325 E Eisenhower

institute: University of Michigan

hyb_protocol: Hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays (Santa Clara, CA) according to the manufacturer’s instructions.

scan_protocol: The intensity of bound dye was measured with an argon laser confocal scanner (GeneArray Scanner, Agilent).

data_processing: The probe arrays were scanned twice and the stored images were analyzed using the Expression Console (Affymetrix, Santa Clara, CA). RMA data was derived by using Bioconductor.

source_name: Biceps Brachii

label_protocol: Total RNA was used as a template for double-stranded cDNA synthesis (Superscript Double-Stranded cDNA synthesis kit, Invitrogen, Carlsbad, CA). Biotin-labelled cRNA was synthesized by using Enzo Bioarray High Yield RNA transcription Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted from frozen tissue with a polytron homogenizer (Brinkman, Westbury, NY) and Trizol reagent (Invitrogen, Rockville, MD) and purified with an RNAse kit (Qiagen, Santa Clara, CA).

tag: gender

value: female

value: young

tag: condition

value: resting


title: Gene expression_sex_1339T

value: 24h post acute resistance exercise following 12-week resistance training


title: Erg ES clone at T0, biological rep2


title: Erg ES clone at T0, biological rep3


title: Gene expression_sex_1337T


title: Gene expression_sex_1328T


title: Gene expression_sex_1339UT


title: Gene expression_sex_1334T


title: Gene expression_sex_1315UT


title: Gene expression_sex_1334UT


title: Dscr1 ES clone at T24, biological rep2


title: Gene expression_sex_1328UT


title: Dscr1 ES clone at T24, biological rep1


title: Dscr1 ES clone at T0, biological rep1


title: Gene expression_sex_1322UT


title: Dscr1 ES clone at T24, biological rep3


title: Bach1 ES clone at T24, biological rep3


title: Gene expression_sex_1336T

value: 4h post acute resistance exercise following 12-week resistance training


title: Bach1 ES clone at T24, biological rep2


title: Gene expression_sex_1322T


title: Dscr1 ES clone at T0, biological rep3


title: Bach1 ES clone at T0, biological rep3


title: Bach1 ES clone at T24, biological rep1


title: Bach1 ES clone at T0, biological rep2


title: Gene expression_sex_1315T


title: Aire ES clone at T48, biological rep3

value: Aire


title: Gene expression_sex_1332T

value: male


title: Gene expression_sex_1331UT


title: Gene expression_sex_1331T


title: Bach1 ES clone at T0, biological rep1


title: Gene expression_sex_1314T


title: Gene expression_sex_1332UT


title: Gene expression_sex_1326UT


title: gpa1 +ABA GC repl1

city: State College

first: Sarah

last: Assmann

address: 210 Mueller Laboratory, University Park

department: Biology

institute: Pennsylvania State University

description: Gene expression data from gpa1 mutant guard cells treated with ABA (50 μM) for 3 hrs

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The RMA method implemented in the affy package in the bioconductor project (http://bioconductor.org/packages/release/bioc/html/affy.html) was used to normalize the data for the entire probe sets using default parameters (PMID: 14960456).

source_name: gpa1 mutant guard cells, abscisic acid treatment

label_protocol: RNA samples exhibiting a 25S/18S ratio >1.4 and no significant degradation in Bioanalyzer profiles (Agilent Technology, Palo Alto, CA) were used for cDNA and then cRNA synthesis.

growth_protocol: Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark, 20oC/18oC cycle, with light intensity of 120 µmol m-2s-1.

extract_protocol: Three hundred Arabidopsis leaves excised from 60-70 five-week-old plants were used as the starting material for each guard cell microarray. Ten mature leaves taken from 3-4 plants grown side-by side with the plants for guard cell isolation were used for each leaf sample. Total RNA was isolated from each sample using Trizol reagent (Invitrogen). Trizol-isolated RNA was further purified using the Plant RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Leaves were incubated in ddH2O containing 50 micromolar ABA for 3 hours

tag: ecotype

value: Columbia (Col-0)

value: gpa1-4 mutant

tag: tissue

value: Guard cells taken for mature leaves of five week-old plants


title: Aire ES clone at T0, biological rep3


title: Aire ES clone at T48, biological rep2


title: Aire ES clone at T48, biological rep1


title: Dscr1 ES clone at T0, biological rep2


title: Aire ES clone at T0, biological rep2


title: Runx1 ES clone at T24, biological rep3


title: Gene expression_sex_1326T


title: Runx1 ES clone at T24, biological rep1


title: Runx1 ES clone at T0, biological rep1


title: Gene expression_sex_1321UT


title: Aire ES clone at T0, biological rep1


title: Gene expression_sex_1313UT


title: Runx1 ES clone at T0, biological rep3


title: Runx1 ES clone at T0, biological rep2


title: Gene expression_sex_1338T


title: Gene expression_sex_1338UT


title: Gene expression_sex_1321T


title: Sti1 IP (2b, oligo)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70321.gif

hyb_protocol: not provided

scan_protocol: GenePix 4200A

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

organism: Saccharomyces cerevisiae

source_name: tot. RNA extract (2)

label_protocol: not provided

growth_protocol: yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation.

extract_protocol: not provided

tag: experiment

value: tot. RNA extract (2)

source_name: RNA TEV eluate (Sti, 2)

value: RNA TEV eluate (Sti, 2)


title: Runx1 ES clone at T24, biological rep2


title: Gene expression_sex_1313T

source_name: Biceps Brachii muscle


title: Nrip1 ES clone at T24, biological rep3

source_name: inducible ES cell clone


title: Dfr1 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70647.gif

source_name: Extract tot. RNA Dfr1-TAP (3)

value: Extract tot. RNA Dfr1-TAP (3)

source_name: Affinity isolated RNA, Dfr1-TAP (3)

value: Affinity isolated RNA, Dfr1-TAP (3)


title: Mdh3 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70646.gif

source_name: Extract tot. RNA Mdh3-TAP (3)

value: Extract tot. RNA Mdh3-TAP (3)

source_name: Affinity isolated RNA, Mdh3-TAP (3)

value: Affinity isolated RNA, Mdh3-TAP (3)


title: Map1 Overexpression (3)

description:
Simple annotation: Mutant vs Wild-type, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81692.gif
allele name: MAP1

hyb_protocol: competitively hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer

scan_protocol: GenePix 4200A 01

source_name: BY4741 pBG1805 empty vector

growth_protocol: 100 ml of BY4741 cells bearing plasmid pBG1805-Map1 (MAP1 with a galactose inducible promotor) or the empty plasmid pBG1805 (=control) were grown in synthetic medium lacking uracil (SC-Ura) at 30C to an OD600 of 0.45- 0.5. Expression was induced with 2% galactose for 1.5 h

extract_protocol: cells were harvested by centrifugation, washed twice with 800 ul of ice-cold sterile water and frozen in liquid nitrogen. RNA was isolated by hot-phenol extraction for further microarray analysis. Therefore, total RNA isolated from the control (empty plasmid) and from MAP1 overexpressing cells was reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture, and cDNAs were fluorescently labeled with Cy3 and Cy5 dyes, respectively

tag: plasmid

value: pBG1805 empty vector


title: Pfk2 IP (1) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72827.gif

source_name: Extract tot. RNA Pfk2 (1)

value: Extract tot. RNA Pfk2 (1)

source_name: Affinity isolated RNA,  Pfk2 (1)

value: Affinity isolated RNA,  Pfk2 (1)


title: Ymr1 IP (3)B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73886.gif

source_name: Extract tot. RNA Ymr1-TAP (3)

value: Extract tot. RNA Ymr1-TAP (3)

source_name: Affinity isolated RNA, Ymr1-TAP (3)

value: Affinity isolated RNA, Ymr1-TAP (3)


title: 13

city: New York

first: Nicholas

middle: D

last: Socci

state: NY

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: According to Illumina mRNA microarray RNA hybridization system specifications

scan_protocol: According to Illumina mRNA microarray scanning system specifications

data_processing: Quantized Illumina BeadStudio; Normalized and log2 (log BASE 2) transformed using the LUMI package from Bioconductor

source_name: Control cells

label_protocol: Labelling protocol is carried out by following Illumina TotalPrep RNA Amplification kit accodring to Illumina specifications.

growth_protocol: The orthotopically grown human prostate xenograft CWR22 tumor was dissociated in collagen based single cell extraction medium as described in the methods. The single cells were processed for prospective isolation with different antibodies by FACS. Unsorted total single cells of the tumor form the control.

extract_protocol: RNA is extracted using trizol reagent according to Invitrogen specifications.

treatment_protocol: The prospectively sorted cells or the unsorted control cells were flash frozen in liquid N2 and stored at -80C till RNA extraction.

tag: sphere and tumor forming efficiency

value: No S/TFE


title: Map1 IP (2) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73675.gif

source_name: Extract tot. RNA Map1-TAP (2)

value: Extract tot. RNA Map1-TAP (2)

source_name: Affinity isolated RNA, Map1-TAP (2)

value: Affinity isolated RNA, Map1-TAP (2)


title: 13

hyb_protocol: Labelling protocol is carried out by following Agilent miRNA labeling reagent and hybridization system.

scan_protocol: Labelling protocol is carried out by following Agilent miRNA microarray system and manufacturer's protocol.

data_processing: Quantized with Agilent Feature Extractor; Quantile normalized and glog2 (generalized log; BASE 2) transformed.

label: Cyanine 3-Cytidine bisphosphate

label_protocol: Labelling protocol is carried out by following Agilent miRNA labeling reagent with 100ng of starting material.

extract_protocol: RNA is extracted using Trizol reagent according to Invitrogen specifications


title: Mdh1 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-01/72126.gif

source_name: Extract tot. RNA Mdh1-TAP (3)

value: Extract tot. RNA Mdh1-TAP (3)

source_name: Affinity isolated RNA, Mdh1-TAP (3)

value: Affinity isolated RNA, Mdh1-TAP (3)


title: 12


title: Gene expression_sex_1336UT

source_name: Biceps Brachii

value: female

tag: age

value: young

value: resting


title: 21

source_name: Cell type-60

value: Moderate S/TFE


title: Map1 Overexpression (1)

description:
Simple annotation: Mutant vs Wild-type, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81690.gif
allele name: MAP1


title: Sti1 IP (3, oligo)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70017.gif

source_name: total RNA extract Sti1 (3)

value: total RNA extract Sti1 (3)

source_name: RNA from affinity-purified Sti (3)

value: RNA from affinity-purified Sti (3)


title: Map1 Overexpression (2)

description:
Simple annotation: Mutant vs Wild-type, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81691.gif
allele name: MAP1


title: 11


title: 12


title: Phr1 IP (2)B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73884.gif

source_name: Extract tot. RNA Phr1-TAP (2)

value: Extract tot. RNA Phr1-TAP (2)

source_name: Affinity isolated RNA, Phr1-TAP (2)

value: Affinity isolated RNA, Phr1-TAP (2)


title: Gre3 IP (2) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-01/72125.gif

source_name: Extract tot. RNA Gre3-TAP (2)

value: Extract tot. RNA Gre3-TAP (2)

source_name: Affinity isolated RNA, Pot1-TAP (2)

value: Affinity isolated RNA, Pot1-TAP (2)


title: Ymr1 IP (2) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73669.gif

source_name: Extract tot. RNA Ymr1-TAP (2)

value: Extract tot. RNA Ymr1-TAP (2)

source_name: Affinity isolated RNA, Ymr1-TAP (2)

value: Affinity isolated RNA, Ymr1-TAP (2)


title: 11

value: No S/TFE


title: Phr1  IP (1) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73436.gif

source_name: Extract tot. RNA Phr1 (1)

value: Extract tot. RNA Phr1 (1)

source_name: Affinity isolated RNA,  Phr1 (1)

value: Affinity isolated RNA,  Phr1 (1)


title: Pfk2 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73891.gif

source_name: Extract tot. RNA Pfk2-TAP (3)

value: Extract tot. RNA Pfk2-TAP (3)

source_name: Affinity isolated RNA, Pfk2-TAP (3)

value: Affinity isolated RNA, Pfk2-TAP (3)


title: 10

source_name: Control cells


title: 9

source_name: Cell type-A6


title: Gene expression_sex_1314UT

value: female


title: Pot1 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-01/72124.gif

source_name: Extract tot. RNA Pot1-TAP (3)

value: Extract tot. RNA Pot1-TAP (3)

source_name: Affinity isolated RNA, Pot1-TAP (3)

value: Affinity isolated RNA, Pot1-TAP (3)


title: 41

source_name: Cell type-51

value: Moderate S/TFE


title: 40

source_name: Cell type-60


title: 42

source_name: Cell type-66


title: Mdh1 IP (1) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73671.gif

source_name: Extract tot. RNA Mdh1-TAP (1)

value: Extract tot. RNA Mdh1-TAP (1)

source_name: Affinity isolated RNA, Mdh1-TAP (1)

value: Affinity isolated RNA, Mdh1-TAP (1)


title: Phr1  IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73439.gif

source_name: Extract tot. RNA Phr1 (2)

value: Extract tot. RNA Phr1 (2)

source_name: Affinity isolated RNA,  Phr1 (2)

value: Affinity isolated RNA,  Phr1 (2)


title: 39

source_name: Triple+ cell type

value: High S/TFE


title: 8

source_name: Cell type-B4


title: 9


title: 6

source_name: Cell type-EP

value: Low S/TFE


title: Mock IP (3) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72573.gif

source_name: Extract tot. RNA BY4741

tag: test

value: Extract total RNA BY4741

source_name: Affinity isolated RNA, BY4741

tag: control

value: Affinity isolated RNA, BY4741


title: 7

source_name: Cell type-44

tag: cell line


title: Mock IP (7) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74288.gif

source_name: Extract tot. RNA BY4741 (7)

value: Extract total RNA BY4741 (7)

source_name: Affinity isolated RNA, BY4741 (7)

value: Affinity isolated RNA, BY4741 (7)


title: 10

source_name: Control cells

value: No S/TFE


title: Meu1  IP (3)B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73885.gif

source_name: Extract tot. RNA Meu1-TAP (3)

value: Extract tot. RNA Meu1-TAP (3)

source_name: Affinity isolated RNA, Meu1-TAP (3)

value: Affinity isolated RNA, Meu1-TAP (3)


title: 4


title: Mdh3 IP (3)B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73888.gif

source_name: Extract tot. RNA Mdh3-TAP (3)

value: Extract tot. RNA Mdh3-TAP (3)

source_name: Affinity isolated RNA, Mdh3-TAP (3)

value: Affinity isolated RNA, Mdh3-TAP (3)


title: Mock IP (6) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74287.gif

source_name: Extract tot. RNA BY4741 (6)

value: Extract total RNA BY4741 (6)

source_name: Affinity isolated RNA, BY4741 (6)

value: Affinity isolated RNA, BY4741 (6)


title: 5

source_name: Cell type-A2


title: Ymr1  IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72322.gif

source_name: Extract tot. RNA Ymr1-TAP (3)

value: Extract tot. RNA Ymr1-TAP (3)

source_name: Affinity isolated RNA, Ymr1-TAP (3)

value: Affinity isolated RNA, Ymr1-TAP (3)


title: Pot1 IP (3) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73674.gif

source_name: Extract tot. RNA Pot1-TAP (3)

value: Extract tot. RNA Pot1-TAP (3)

source_name: Affinity isolated RNA, Pot1-TAP (3)

value: Affinity isolated RNA, Pot1-TAP (3)


title: Gre3 IP (2) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73673.gif

source_name: Extract tot. RNA Gre3-TAP (2)

value: Extract tot. RNA Gre3-TAP (2)

source_name: Affinity isolated RNA, Gre3-TAP (2)

value: Affinity isolated RNA, Gre3-TAP (2)


title: 38

source_name: Triple+ cell type

value: High S/TFE


title: Mock IP (4) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72829.gif

source_name: Extract tot. RNA BY4741 (4)

value: Extract total RNA BY4741 (4)

source_name: Affinity isolated RNA, BY4741 (4)

value: Affinity isolated RNA, BY4741 (4)


title: Dfr1 IP (4) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73437.gif

source_name: Extract tot. RNA Dfr1 (4)

value: Extract tot. RNA Dfr1 (4)

source_name: Affinity isolated RNA,  Dfr1 (4)

value: Affinity isolated RNA,  Dfr1 (4)


title: 37


title: 8

source_name: Cell type-B4

value: No S/TFE


title: 32

source_name: Control cells


title: 31


title: Meu1  IP (1) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72323.gif

source_name: Extract tot. RNA Meu1-TAP (1)

value: Extract tot. RNA Meu1-TAP (1)

source_name: Affinity isolated RNA, Meu1-TAP (1)

value: Affinity isolated RNA, Meu1-TAP (1)


title: Dfr1 IP (2) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73670.gif

source_name: Extract tot. RNA Dfr1-TAP (2)

value: Extract tot. RNA Dfr1-TAP (2)

source_name: Affinity isolated RNA, Dfr1-TAP (2)

value: Affinity isolated RNA, Dfr1-TAP (2)


title: 5

source_name: Cell type-A2

value: Low S/TFE


title: 3

source_name: Cell type-51

value: Moderate S/TFE


title: Lap3 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72828.gif

source_name: Extract tot. RNA Lap3 (3)

value: Extract tot. RNA Lap3 (3)

source_name: Affinity isolated RNA,  Lap3 (3)

value: Affinity isolated RNA,  Lap3 (3)


title: Pfk2 IP (2) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73433.gif

source_name: Extract tot. RNA Pfk2 (2)

value: Extract tot. RNA Pfk2 (2)

source_name: Affinity isolated RNA, Pfk2 (2)

value: Affinity isolated RNA, Pfk2 (2)


title: 2

source_name: Cell type-60


title: 1


title: Lap3 IP (2) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73890.gif

source_name: Extract tot. RNA Lap3-TAP (2)

value: Extract tot. RNA Lap3-TAP (2)

source_name: Affinity isolated RNA, Lap3-TAP (2)

value: Affinity isolated RNA, Lap3-TAP (2)


title: Mdh3 IP (2) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73668.gif

source_name: Extract tot. RNA Mdh3-TAP (2)

value: Extract tot. RNA Mdh3-TAP (2)

source_name: Affinity isolated RNA, Mdh3-TAP (2)

value: Affinity isolated RNA, Mdh3-TAP (2)


title: Gre3 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73440.gif

source_name: Extract tot. RNA Gre3-TAP (3)

value: Extract tot. RNA Gre3-TAP (3)

source_name: Affinity isolated RNA, Gre3-TAP (3)

value: Affinity isolated RNA, Gre3-TAP (3)


title: Pot1 IP (2) B

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73672.gif

source_name: Extract tot. RNA Pot1-TAP (2)

value: Extract tot. RNA Pot1-TAP (2)

source_name: Affinity isolated RNA, Pot1-TAP (2)

value: Affinity isolated RNA, Pot1-TAP (2)


title: 39

source_name: Triple+ cell type

value: High S/TFE


title: 42

source_name: Cell type-66


title: Meu1 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73434.gif

source_name: Extract tot. RNA Meu1 (3)

value: Extract tot. RNA Meu1 (3)

source_name: Affinity isolated RNA,  Meu1 (3)

value: Affinity isolated RNA,  Meu1 (3)


title: 40


title: LSD1 Lox/Δ3_C 3

city: Leicester

first: Jinli

last: Luo

address: Lancaster Road

department: University of Leicester

country: United Kingdom

institute: Department of Biochemistry,

description: replicate 3

data_processing: The data were normalised using meadian scaling normalisation with ArrayTrack software (version 3.4.5).

source_name: mouse embryonic stem cell

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA  Amplification Kit.

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

tag: strain

value: E14 ES cell

tag: genotype/variation

value: LSD1 Lox/Δ3


title: Map1 IP (1) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72826.gif

source_name: Extract tot. RNA Map1 (1)

value: Extract tot. RNA Map1 (1)

source_name: Affinity isolated RNA, Map1 (1)

value: Affinity isolated RNA, Map1 (1)


title: 7

source_name: Cell type-44

value: Low S/TFE


title: Sti1  IP (4) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72574.gif

source_name: Extract tot. RNA Sti1-TAP (4)

value: Extract tot. RNA Sti1-TAP (4)

source_name: Affinity isolated RNA, Sti1-TAP (4)

value: Affinity isolated RNA, Sti1-TAP (4)


title: Pre10 IP (2) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73889.gif

source_name: Extract tot. RNA Pre10-TAP (2)

value: Extract tot. RNA Pre10-TAP (2)

source_name: Affinity isolated RNA, Pre10-TAP (2)

value: Affinity isolated RNA, Pre10-TAP (2)


title: 6

source_name: Cell type-EP


title: Erg ES clone at T0, biological rep1

description: Gene expression data from ES clone before induction of gene overexpression.

source_name: inducible ES cell clone

tag: inducible gene

value: Erg

value: ES cell


title: Lap3 IP (2) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72834.gif

source_name: Extract tot. RNA Lap3 (2)

value: Extract tot. RNA Lap3 (2)

source_name: Affinity isolated RNA,  Lap3 (2)

value: Affinity isolated RNA,  Lap3 (2)


title: 4

value: Moderate S/TFE


title: 3

source_name: Cell type-51


title: 41


title: 1

source_name: Cell type-60


title: Mdh1 IP (4) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73435.gif

source_name: Extract tot. RNA Mdh1 (4)

value: Extract tot. RNA Mdh1 (4)

source_name: Affinity isolated RNA, Mdh1 (4)

value: Affinity isolated RNA, Mdh1 (4)


title: LSD1 Lox/Δ3_B 2

description: replicate 2

tag: cell type


title: WT_rep2

status: Public on Dec 04 2010

city: Hamilton

first: Herb

middle: E

last: Schellhorn

state: ON

address: 1280 Main St. W.,

country: Canada

institute: McMaster University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GCRMA method

organism: Escherichia coli K-12

source_name: Exponential phase culture of MG1655 wild type in M9 at OD600 of 0.3

label_protocol: Affymetrix protocol

growth_protocol: Cultures were grown in M9 minimal media (0.2% glucose) at 37C at 200 rpm. Overnight cultures were inoculated with single, independent colonies in triplicate, incubated aerobically overnight at 37oC, and sub-cultured to a starting OD600 of 0.0001. Cultures were harvested at OD600 = 0.3 in exponential phase.

extract_protocol: Acidic Hot Phenol

tag: substrain


title: 37

source_name: Triple+ cell type

value: High S/TFE


title: rpoN_rep1

source_name: Exponential phase culture of MG1655 rpoN mutants in M9 at OD600 of 0.3


title: rpoN_rep3


title: rpoS_rep1

source_name: Exponential phase culture of MG1655 rpoS mutants in M9 at OD600 of 0.3


title: 38


title: Pre10 IP (1) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72321.gif

source_name: Extract tot. RNA Pre10-TAP (1)

value: Extract tot. RNA Pre10-TAP (1)

source_name: Affinity isolated RNA, Pre10-TAP (1)

value: Affinity isolated RNA, Pre10-TAP (1)


title: rpoS_rep3


title: WT_rep1


title: Mock IP (5) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73438.gif

source_name: Extract tot. RNA BY4741 (5)

value: Extract total RNA BY4741 (5)

source_name: Affinity isolated RNA, BY4741 (5)

value: Affinity isolated RNA, BY4741 (5)


title: WT_rep3


title: Map1 IP (2) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72833.gif

source_name: Extract tot. RNA Map1 (2)

value: Extract tot. RNA Map1 (2)

source_name: Affinity isolated RNA,  Map1 (2)

value: Affinity isolated RNA,  Map1 (2)


title: Pre10 IP (3) A

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73887.gif

source_name: Extract tot. RNA Pre10-TAP (3)

value: Extract tot. RNA Pre10-TAP (3)

source_name: Affinity isolated RNA, Pre10-TAP (3)

value: Affinity isolated RNA, Pre10-TAP (3)


title: 33

source_name: Control cells

value: No S/TFE


title: LSD1 Δ3/Δ3_A 1

description: replicate 1

source_name: mouse embryonic stem cell

value: E14 ES cell

value: LSD1 Δ3/Δ3


title: 31


title: LSD1 Δ3/Δ3_C 3

description: replicate 3


title: rpoS_rep2


title: 2

source_name: Cell type-60


title: LSD1 Lox/Δ3_A 1

description: replicate 1

value: LSD1 Lox/Δ3


title: Dshibae_4h_dark_rep1

status: Public on Dec 03 2010

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

hyb_protocol: 600 ng of Cy3-labeled RNA was fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned using the GenePixPro 4001 scanner, data extraction was performed using the GenePix 4.0 software

data_processing: Data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org). Batch specific effects of different slides were eliminated using the R script Combat (http://jlab.byu.edu/ComBat/Abstract.html)

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: Dshibae,4h dark

label_protocol: RNA samples were labelled with Cy3 using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: cell were grown in artificial salt water medium supplemented with 5mM Succinate as carbon source at 30°C, pH 8 and 85% oxygen saturation in a Biostat B bioreactor (Sartorius)

extract_protocol: RNA was extracted from RNAprotect (Qiagen) treated cells with the Rneasy mini (Qiagen) RNA extraction kit

treatment_protocol: cells illuminated with 100 µmol photons/(m2*s) using a 35W halogen bulb (Osram) were set to darkness

tag: protocol

value: light to dark

tag: dark timepoint

value: 4 h


title: rpoN_rep2


title: Dshibae_4h_dark_rep2


title: Dshibae_15min_dark_rep1

source_name: Dshibae,15min dark

value: 15 min


title: Dshibae_8h_dark_rep1

source_name: Dshibae,8h dark

value: 8 h


title: Dshibae_30min_dark_rep2

source_name: Dshibae,30min dark

value: 30 min


title: Dshibae_2h_dark_rep1

source_name: Dshibae,2h dark

value: 2 h


title: D.shibae_light_rep2

value: light

value: control


title: Dshibae_15min_dark_rep2


title: Dshibae_8h_dark_rep2


title: D.shibae_light_rep1


title: Dshibae_1h_dark_rep1

source_name: Dshibae,1h dark

value: 1 h


title: Dshibae_30min_dark_rep1


title: Dshibae_8h_light_rep4

data_processing: Data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

source_name: Dshibae,8h light

treatment_protocol: dark grown cells were illuminated with 100 µmol photons/(m2*s) using a 35W halogen bulb (Osram)

value: dark to light

tag: light timepoint


title: Dshibae_4h_light_rep4

source_name: Dshibae,4h light


title: Dshibae_1h_dark_rep2


title: Unfetilized eggs (Cy5) vs 32-cell stage embryos (Cy3) Replicate1

city: Okinawa

first: Takeshi

last: Noda

address: Tancha

institute: Okinawa Institute of Science and Technology

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.

organism: Ciona intestinalis

source_name: Unfetilized eggs

label_protocol: Total RNA was labeled with Cy3 or Cy5 using an Agilent Quick-Amp Labeling Kit (Agilent Technologies). The protocols were according to the manufacturer's instructions.

extract_protocol: Total RNA from dechorionated unfertilized eggs or 32-cell stage embryos of Ciona intestinalis was extracted by acid guanidium thiocyanate-phenol-chloroform extraction method.

tag: Stage

value: Unfetilized eggs

source_name: 32-cell stage embryos

value: 32-cell stage embryos


title: Dshibae_2h_light_rep4

source_name: Dshibae,2h light


title: Unfetilized eggs (Cy5) vs 32-cell stage embryos (Cy3) Replicate2


title: Unfetilized eggs (Cy3) vs 32-cell stage embryos (Cy5) Replicate2


title: Dshibae_8h_light_rep3


title: Dshibae_8h_light_rep1


title: Dshibae_8h_light_rep2


title: Unfetilized eggs (Cy3) vs 32-cell stage embryos (Cy5) Replicate1


title: Dshibae_4h_light_rep3


title: Dshibae_4h_light_rep1


title: Dshibae_30min_light_rep4

source_name: Dshibae,30min light


title: Dshibae_2h_light_rep2


title: Dshibae_2h_light_rep3


title: Dshibae_1h_light_rep1

source_name: Dshibae,1h light


title: Dshibae_2h_light_rep1


title: Dshibae_15min_light_rep4

source_name: Dshibae,15min light


title: Dshibae_1h_light_rep4


title: LSD1 Δ3/Δ3_B 2

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol


title: Dshibae_30min_light_rep2


title: Dshibae_1h_light_rep2


title: Dshibae_30min_light_rep1


title: Dshibae_30min_light_rep3


title: Dshibae_15min_light_rep3


title: Dshibae_1h_light_rep3


title: Dshibae_2h_dark_rep2


title: D.shibae_dark_rep3

value: dark


title: D.shibae_dark_rep4


title: D.shibae_dark_rep1


title: CTLs after CD3 mAb stimulation for 24h: replicate 1

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

hyb_protocol: Slides were hybridized with probes according to the standard hybridization.

scan_protocol: Scanned on a GenePix 4000B scanner Images were quantified using GenePix Pro 4.1 software.

data_processing: Raw data (gpr file) and images were uploaded to the mAdb microarray Database (NCBI/NIH) for normalization. Median normalized log2 ratio Cy5/Cy3 data sets were extracted from mAdb.

source_name: CTL-unstimulated

label_protocol: Ten µg of total RNA were used for cDNA synthesis, probe preparation and labeling using the FairPlay DNA Microarray Labeling Kit (Strategene). Monoreactive Cy3 and Cy5 were obtained from GE HealthCare. All reactions were carried out following the manufacturer's instructions.

growth_protocol: Tumor-specific CTLs were maintained by weekly stimulation with irradiated tumor cells (as Ag) and irradiated spleen cells (as feeder cells) plus 10 IU/ml recombinant IL-2. For treatment, CTLs were purified with a lymphocyte separation medium (LSM) and cultured in the presence of irradiated tumor cells (Ag) or CD3 and CD28 mAbs for the indicated time.

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

value: BALB/c

value: Tumor-specific cytotoxic T cells

source_name: CD3-stimulated CTLs: 24h


title: D.shibae_dark_rep2


title: CTLs after Ag stimulation for 24h: replicate 3

source_name: Ag-stimulated CTLs: 24h


title: CTLs after Ag stimulation for 3h: replicate 2

source_name: Ag-stimulated CTLs: 3h


title: CTLs after Ag stimulation for 3h: replicate 3


title: CTLs after Ag stimulation for 3h: replicate 1


title: CTLs after CD3 mAb stimulation for 3h: replicate 1

source_name: CD3-stimulated CTLs: 3h


title: CTLs after CD3 mAb stimulation for 3h: replicate 3


title: CTLs after Ag stimulation for 24h: replicate 2


title: CTLs after CD3 mAb stimulation for 24h: replicate 3


title: CTLs after CD3 mAb stimulation for 3h: replicate 2


title: 9.3_IRR_2_24

city: Oslo

first: Erta

last: kalanxhi

address: Montebello 0310

country: Norway

institute: Oslo University Hospital

description: replicate 3

data_processing: performed with Illumina BeadStudio 3.1.3.0 Gene Expression Module 3.4.0

label: biotin, Cy3

source_name: irradiated fibroblasts 24 h

label_protocol: Performed with Illumina® TotalPrep RNA Amplification Kit

growth_protocol: The cells were grown in DMEM supplied with 1% L-Glutamine and Penicillin/ Streptomycin and 20% FBS and kept at 37°C and 5% CO2.

extract_protocol: Total RNA from 4 independent experiments was isolated from cells irradiated with 2.0 Gy and bystander fibroblasts 4, 8 and 26 h after irradiation using Pure Link RNA mini kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Irradiated cells were irradiated with 2.0 Gy of gamma radiation. Control cells were incubated in medium from non-irraidated cells 2 h after irradiation. Bystander cells were incubated with medium from cells irradiated with 2.0 Gy, 2 h after irradiation. Extraction of RNA was done 4, 6 and 8 h after irradiation.

value: immortalized hTERT

value: irradiated fibroblast

tag: time point


title: CTLs after Ag stimulation for 24h: replicate 1


title: 9.4_IRR_2_24

description: replicate 4


title: 7.3_IRR_2_2

description: replicate 3

source_name: irradiated fibroblasts 4 h


title: 9.1_IRR_2_24

description: replicate 1


title: 8.1_IRR_2_6

description: replicate 1

source_name: irradiated fibroblasts 8 h


title: 9.2_IRR_2_24

description: replicate 2


title: Dshibae_15min_light_rep2


title: 8.4_IRR_2_6

description: replicate 4


title: 7.4_IRR_2_2

description: replicate 4


title: 7.2_IRR_2_2

description: replicate 2


title: 8.2_IRR_2_6

description: replicate 2


title: 6.4_B_2_6

description: replicate 4

source_name: bystander fibroblast 24 h

value: bystander fibroblast


title: 8.3_IRR_2_6

description: replicate 3


title: 7.1_IRR_2_2

description: replicate 1

value: 4 h


title: 6.3_B_2_6

description: replicate 3


title: 5.4_B_2_6

description: replicate 4

source_name: bystander fibroblast 8 h


title: 5.2_B_2_6

description: replicate 2


title: 6.1_B_2_6

description: replicate 1


title: 6.2_B_2_6

description: replicate 2


title: 4.3_B_2_2

description: replicate 3

source_name: bystander fibroblast 4 h


title: 5.3_B_2_6

description: replicate 3


title: 4.1_B_2_2

description: replicate 1


title: 4.4_B_2_2

description: replicate 4


title: 4.2_B_2_2

description: replicate 2


title: 3.3_B_0_24

description: replicate 3

source_name: control fibroblast 24 h

value: control fibroblast


title: 2.4_B_0_6

description: replicate 4

source_name: control fibroblast 8 h

value: 8 h


title: 3.2_B_0_24

description: replicate 2


title: 3.1_B_0_24

description: replicate 1


title: 5.1_B_2_6

description: replicate 1


title: 2.2_B_0_6

description: replicate 2


title: 3.4_B_0_24

description: replicate 4


title: MgCl2-3

city: Corvallis

first: Jeff

last: Chang

state: Oregon

address: 3097 Cordley Hall

institute: Oregon State University

description: 7 hours post infiltration with 10mM MgCl2

hyb_protocol: 10 µg from each experimental sample along with Affymetrix eukaryotic hybridization controls were hybridized for 16 hours to arabidopsis genome arrays (ATH1) in an Affymetrix GeneChip® Hybridization Oven 640

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm.

data_processing:
RMA
affymetrix-algorithm-version = 1.0
program-name = Expression Console

source_name: Whole leaf

label_protocol: Biotinylated cRNA was synthesized from the double stranded cDNA using T7 RNA polymerase and a biotin-conjugated pseudouridine containing nucleotide mixture provided in the IVT Labeling Kit (Affymetrix, Santa Clara, CA)

extract_protocol: Liquid N2, phenol:chloroform, Qiagen RNAeasy, DNAse

tag: hpi

tag: treatment

value: 10mM MgCl2


title: MgCl2-1


title: hrcC-3

description: 7 hours post infiltration with 5x10^7 cfu/ml DC3000 hrcC mutant

value: 5x10^7 cfu/ml DC3000 hrcC mutant


title: MgCl2-2


title: M0 25__Q521A5

city: Hamburg

first: Simon

middle: A

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.

label_protocol: According to the manufacturer's instructions (Kreatech Biotechnology, Amsterdam).

extract_protocol:
As decribed in:
Joosse SA, et al. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat. 2008 Aug 14

tag: tissue

value: colon

tag: disease state

value: carcinoma

tag: metastasis

value: metastasis-free

source_name: Women reference pool

tag: sample type

value: A pool of DNA from peripheral blood lymphocytes, from 7 apperently healty women.


title: 2.3_B_0_6

description: replicate 3

tag: cell line


title: 2.1_B_0_6

description: replicate 1


title: M0 21__Q515E3

scan_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.


title: 1.3_B_0_2

description: replicate 3

source_name: control fibroblast 4 h


title: 1.2_B_0_2

description: replicate 2


title: M0 23__Q521A1

data_processing:
As described in:
Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.


title: M0 19__Q515E1


title: hrcC-1


title: M0 22__Q515E4


title: M0 18__Q515E0


title: M0 16__Q515D8


title: M0 17__Q515D9


title: 1.1_B_0_2

description: replicate 1


title: 1.4_B_0_2

description: replicate 4


title: M0 20__Q515E2


title: M0 11__Q515B8


title: M0 15__Q515D7


title: M0 10__Q515B7


title: M0 12__Q515D4


title: M0 14__Q515D6


title: M0 09__Q515B6


title: M0 24__Q521A4


title: M0 02__Q511D7


title: M0 03__Q515B0


title: M0 07__Q515B4


title: M0 08__Q515B5


title: M0 06__Q515B3


title: M0 04__Q515B1


title: M0 05__Q515B2


title: PM31__Q515C5

value: peritoneum


title: PM34__Q515C8


title: PM37__Q515D2


title: PM35__Q515C9


title: M0 01__Q511D3


title: PM36__Q515D0


title: CTLs after CD3 mAb stimulation for 24h: replicate 2

tag: strain


title: PM32__Q515C6


title: hrcC-2


title: PM33__Q515C7


title: PM30__Q515C4


title: PM29__Q515C3


title: PM28__Q511B2


title: PM24__Q511A7


title: PM25__Q511A9


title: PM27__Q511B1


title: PM17__Q503D7


title: PM23__Q511A6


title: PM15__Q503D3


title: PM22__Q511A4


title: PM18__Q503E0


title: PM13__Q503D1


title: PM11__Q503C6


title: PM21__Q503E6


title: PM20__Q503E4


title: PM12__Q503D0


title: PM10__Q503C5


title: PM26__Q511B0


title: PM06__Q500D2


title: PM19__Q503E2


title: PM09__Q503C4


title: PM16__Q503D4


title: PM08__Q500D4


title: PM05__Q500D1


title: PM14__Q503D2


title: EGFP-1

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: 3.75 micrograms cDNA hybridized overnight with Affymetrix M430 2.0 array per Affymetrix eukaryotic array protocol except cDNA used instead of cRNA

scan_protocol: Biotinylated cDNA labeled with phycoerythrin-streptavidin per Affymetrix staining protocol; Fluorescence detected with Affymetrix Scanner 3000

data_processing: GCOS software (Affymetrix) generated cel files from scans; cel files were analyzed by GCRMA normalization and background subtraction with Bioconductor gcrma package

label: biotin-phycoerythrin-streptavidin

source_name: EGFP expressing mouse lung type II cells

label_protocol: Total RNA was converted to biotinylated cDNA with kits purchased from NuGEN as recommended by NuGEN

extract_protocol: Total RNA was extracted with Qiagen RNeasy kits according to the vendor's recommended protocol

tag: age

value: 8 weeks old

value: pulmonary epithelial type II

tag: cell surface marker

value: EGFP-positive


title: EGFP-3

tag: cell type


title: nonEGFP-1

source_name: mouse lung type II cells - no EGFP

value: EGFP-negative


title: nonEGFP-3


title: nonEGFP-2


title: EGFP-2


title: PM03__Q500A5


title: PM01__Q500A2


title: LM73__Q509A7

value: liver

tag: tag


title: PM02__Q500A4


title: LM70__Q509A6


title: LM67__Q509A5


title: LM57__Q505C4


title: LM60__Q509A0


title: LM53__Q505C3


title: PM04__Q500D0


title: LM50__Q505C0


title: LM51__Q505C1


title: LM63__Q509A2


title: LM44__Q505B1


title: LM45__Q505B2


title: PM07__Q500D3


title: LM49__Q505B9


title: LM47__Q505B4


title: LM52__Q505C2


title: LM48__Q505B5


title: Heart-apoE-deficient-age 5 months-rep2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

description: Gene expression data of apoE-deficient heart, age 5 months

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

source_name: Heart, apoE-deficient, age 5 months

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: The study was performed with 5 month-old apolipoprotein E- (apoE)- deficient mice treated for 1 month with the mild thiol-blocking agent cystamine to inhibit cellular respiration. Control groups consisted of age-matched untreated apoE-deficient mice and non-transgenic B6 mice. All mice had free access to food and water. Mice were fed a rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). At an age of 4 months, the treatment group of apoE-deficient mice received cystamine (300 mg/kg in drinking water) for 1 month. At an age of 5 months, cardiac function of all study groups was determined by echocardiography and hearts were isolated.

extract_protocol: Total RNA was isolated from heart tissue with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: For the microarray study hearts were isolated from three study groups: (i) failing hearts from 5 month-old apoE-deficient mice with 1 month of cystamine treatment (300 mg/kg in drinking water), (ii) hearts from 5 month-old untreated apoE-deficient mice, and (iii) hearts from 5 month-old untreated B6 controls.

tag: genotype/variation

value: apoE-deficient

value: 5 months

value: heart

tag: disease status

value: control

value: untreated


title: Heart-apoE-deficient-age 5 months-rep1


title: Ranolazine-treated heart-age 18 months-apoE-deficient-rep1

description: Gene expression data of apoE-deficient heart-age 18 months-2 months of ranolazine treatment

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.

source_name: Heart, apoE-deficient, 2 months of ranolazine treatment, age 18 months

growth_protocol: The study was performed with 18 month-old apoE-deficient mice on a C57BL/6J (B6) background as a model of atherosclerosis-induced heart failure and non-transgenic B6 mice. All mice had free access to food and water. ApoE-deficient mice and B6 controls were fed a rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). At an age of 16 months, a group of apoE-deficient mice with symptoms of heart failure (ejection fraction <35%) received ranolazine (200 mg/kg in drinking water) for two months. At an age of 18 months, cardiac function of all study groups was determined by echocardiography and hearts were isolated.

treatment_protocol: For the microarray study hearts were isolated from three study groups: (i) failing hearts from 18 month-old apoE-deficient mice, (ii) hearts from 18 month-old apoE-deficient mice treated for two months with 200 mg/kg ranolazine, and (iii) 18 month-old untreated B6 controls.

value: 18 months

value: atherosclerosis

value: 2 months of ranolazine treatment


title: Failing heart-apoE-deficient-1 month of cystamine-age 5 months-rep2

description: Gene expression data of failing apoE-deficient heart with 1 month of cystamine-age 5 months

source_name: Failing heart, apoE-deficient, 1 month of cystamine, age 5 months

value: failing

value: 1 month of cystamine


title: Failing heart-apoE-deficient-1 month of cystamine-age 5 months-rep1


title: Control heart-age 5 months-BSIX-rep2

description: Gene expression data of control B6 heart-age 5 months

source_name: Control heart, B6, age 5 months

growth_protocol: The study was performed with 18 month-old apoE-deficient mice on a C57BL/6J (B6) background as a model of atherosclerosis-induced heart failure. Pressure overload-induced heart failure was induced in non-transgenic B6 mice and apoE-deficient mice by abdominal aortic constriction (AAC). All mice had free access to food and water. To induce atherosclerosis-dependent heart failure apoE-deficient mice were fed a rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). All other mice were fed a standard rodent chow containing 4.5 % fat. At an age of 18 months, hearts were isolated from apoE-deficient mice with symptoms of heart failure (ejection fraction ≤33% as determined by echocardiography) and age-matched B6 controls. Failing hearts from aortic constricted mice were isolated from (i) 6 month-old apoE-deficient mice with 2 months of AAC, and from (ii) 10 month-old B6 mice with 6 months of AAC (ejection fraction ≤33 %). As controls, heart tissue from age-matched, sham-operated apoE-deficient and non-transgenic B6 mice were used. Hearts from 5 month-old B6 mice with 1 month of AAC were also included in the study displaying cardiac hypertrophy without failure (ejection fraction ≥50 %).

treatment_protocol: For the microarray study hearts were isolated from four study groups and their respective controls: (i) failing hearts from 18 month-old apoE-deficient mice and age-matched B6 controls; (ii) failing hearts from 6 month-old apoE-deficient mice with 2 months of AAC, and age-matched, sham-operated apoE-deficient and non-transgenic B6 controls, respectively; (iii) failing hearts from 10 month-old B6 mice with 6 months of AAC and age-matched sham-operated B6 controls; (iv) hearts with cardiac hypertrophy isolated from 5 month-old B6 mice with 1 month of AAC and age-matched B6 controls.

value: wild type


title: Ranolazine-treated heart-age 18 months-apoE-deficient-rep2


title: LM41__Q505B0

value: colon

value: carcinoma

value: A pool of DNA from peripheral blood lymphocytes, from 7 apperently healty women.


title: LM39__Q505A8


title: LM40__Q505A9


title: LM37__Q505A6


title: LM35__Q505A3


title: LM31__Q504E3


title: LM32__Q505A0


title: LM34__Q505A2


title: LM25__Q504E0


title: LM24__Q504D9


title: Control heart-age 5 months-BSIX-rep1


title: LungcancerCellLine_unirradiated_siRNA_neg.control_rep2

city: Stockholm

first: Markus

last: Selenius

address: Karolinska University Hospital, Huddinge F46

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary ssDNA to Rat Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median

source_name: Lung cancer cell line, unirradiated, scrambled siRNA

label_protocol: Total RNA were amplified and converted to cDNA and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37 °C and 5% CO2.

extract_protocol: Total RNA was extracted from cells stored in RNA later using Rneasy (QIAGEN, Valencia, CA, USA)

treatment_protocol: Approximately 500,000 cells were seeded in 25 cm2 flasks and incubated for 24 hours. Medium was then exchanged for either fresh medium or medium prepared with 2,5 µM [Au(SCN)(PEt3)]  and incubated for 24 hours prior to radiation treatment. Cells were further incubated for 24 hours immediately after irradiation and then medium was exchanged. For the purpose of gene expression analysis, cells were harvested 96 hours after subjection to ionizing radiation and stored in RNAlater (Qiagen, Valencia, CA) at -70 °C prior to RNA purification.

value: lung cancer


title: Hypertrophic heart-1 month AAC-age 5 months-BSIX-rep1

description: Gene expression data of hypertrophic B6 heart with 1 month of AAC-age 5 months

source_name: Hypertrophic heart, B6, 1 month of AAC, age 5 months

value: hypertrophic, 1 month of AAC


title: Control heart-sham-age 10 months-BSIX-rep2

description: Gene expression data of control B6 heart-age 10 months

source_name: Control heart, B6, age 10 months

value: 10 months


title: LM20__Q504D5

value: liver


title: Hypertrophic heart-1 month AAC-age 5 months-BSIX-rep2

value: 5 months


title: Ranolazine-treated heart-6 months of AAC-age 10 months-BSIX-rep2

description: Gene expression data of B6 heart with 6 months of AAC-age 10 months-2 months of ranolazine treatment

source_name: Heart, B6, 6 months of AAC, 2 months of ranolazine treatment, age 10 months

growth_protocol: The study was performed with 10 month-old C57BL/6J (B6) mice with 6 months of abdominal aortic constriction (AAC) as a model of pressure overload-induced heart failure, and sham-operated control mice. All mice had free access to food and water. Mice were fed a standard rodent chow containing 4.5 % fat. At an age of 8 months, a group of aortic constricted B6 mice (4 months of AAC) with symptoms of heart failure (ejection fraction <35%) received ranolazine (200 mg/kg in drinking water) for two months. At an age of 10 months, cardiac function of all study groups was determined by echocardiography and hearts were isolated.

treatment_protocol: For the microarray study hearts were isolated from three study groups: (i) failing hearts from 10 month-old B6 mice with 6 months of AAC, (ii) hearts from 10 month-old B6 mice with 6 months of AAC treated for two months with 200 mg/kg ranolazine, and (iii) 10 month-old untreated, sham-operated B6 controls.

value: heart

value: 6 months of AAC


title: LungcancerCellLine_irradiated_TrxRinhibited_rep2

source_name: Lung cancer cell line, irradiated, TrxR-inhibitor


title: LungcancerCellLine_irradiated_TrxRinhibited_rep3


title: Ranolazine-treated heart-6 months of AAC-age 10 months-BSIX-rep1


title: Control heart-sham-age 10 months-BSIX-rep1

value: control


title: Failing heart-6 months AAC-age 10 months-BSIX-rep2

description: Gene expression data of failing B6 heart with 6 months of AAC-age 10 months

source_name: Failing heart, B6, 6 months of AAC, age 10 months

value: failing, 6 months of AAC


title: LungcancerCellLine_unirradiated_siRNA_TrxR1_rep1

source_name: Lung cancer cell line, unirradiated, TrxR1 siRNA


title: Failing heart-6 months AAC-age 10 months-BSIX-rep1


title: M0 13__Q515D5

value: metastasis-free


title: Control heart-age 6 months-BSIX-rep1

description: Gene expression data of control B6 heart-age 6 months

source_name: Control heart, B6, age 6 months

value: 6 months


title: LungcancerCellLine_irradiated_TrxRinhibited_rep1


title: LM19__Q504D4


title: LM12__Q504D1


title: LM18__Q504D3


title: LM16__Q504D2


title: Control heart-age 6 months-BSIX-rep2


title: LungcancerCellLine_unirradiated_TrxRinhibited_rep3

source_name: Lung cancer cell line, unirradiated, TrxR inhibitor


title: LungcancerCellLine_unirradiated_TrxRinhibited_rep2


title: second_trimester_amniotic_fluid_trisomy18_female_5_trisomy18study

city: Medford

first: Donna

middle: K

last: Slonim

state: MA

address: 161 College Ave.

department: Computer Science

institute: Tufts University

description: gene expression data from second trimester fetus with trisomy 18

hyb_protocol: A minimum of 5ug of cDNA from each sample was hybridized to Affymetrix U133 Plus 2.0 microarrays.  Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  Identification of individual differentially-expressed genes was performed via two-sided t-tests using the multtest package in BioConductor, with the Benjamini-Hochberg false-discovery rate adjustment for multiple testing.

source_name: cell free mRNA from second trimester amniotic fluid, trisomy 22

label_protocol: Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

extract_protocol: RNA was extracted from 10 mL amniotic fluid supernatant with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA).  RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).

tag: rna source

tag: karyotype


title: Sham control heart-age 6 months-apoE-deficient-rep1

description: Gene expression data of control apoE-deficient heart-age 6 months

source_name: Control heart, apoE-deficient, age 6 months

value: apoE-deficient

value: control, atherosclerosis


title: Sham control heart-age 6 months-apoE-deficient-rep2


title: LungcancerCellLine_unirradiated_TrxRinhibited_rep1


title: second_trimester_amniotic_fluid_trisomy18_female_3_trisomy18study

source_name: cell free mRNA from second trimester amniotic fluid, trisomy 20


title: LM11__Q504D0

source_name: Women reference pool


title: LungcancerCellLine_irradiated_uninhibited_rep3

source_name: Lung cancer cell line, irradiated, no inhibitor


title: LM10__Q504C9


title: second_trimester_amniotic_fluid_trisomy18_female_4_trisomy18study

source_name: cell free mRNA from second trimester amniotic fluid, trisomy 21


title: LungcancerCellLine_irradiated_uninhibited_rep2


title: Failing heart-2mo AAC-age 6 months-apoE-deficient-rep2

description: Gene expression data of failing apoE-deficient heart with 2 months of AAC-age 6 months

source_name: Failing heart, apoE-deficient, 2 months of AAC, age 6 months

value: failing, 2 months of AAC and atherosclerosis


title: Failing heart-2mo AAC-age 6 months-apoE-deficient-rep1


title: second_trimester_amniotic_fluid_trisomy18_female_1_trisomy18study

source_name: cell free mRNA from second trimester amniotic fluid, trisomy 18


title: LM05__Q505B8

value: colon


title: second_trimester_amniotic_fluid_euploid_female5_trisomy18study

description:
gene expression data from normal second trimester fetus
raw data is the same as for GEO sample GSM406288 - second_trimester_amniotic_fluid_euploid_female2

source_name: cell free mRNA from second trimester amniotic fluid, euploid control


title: second_trimester_amniotic_fluid_trisomy18_female_2_trisomy18study

source_name: cell free mRNA from second trimester amniotic fluid, trisomy 19


title: LungcancerCellLine_unirradiated_uninhibited_rep3

source_name: Lung cancer cell line, unirradiated, no inhibitor


title: LungcancerCellLine_irradiated_uninhibited_rep1


title: second_trimester_amniotic_fluid_euploid_female3_trisomy18study

description:
gene expression data from normal second trimester fetus
raw data is the same as for GEO sample GSM406286 - second_trimester_amniotic_fluid_euploid_female1

value: cell free mRNA from second trimester amniotic fluid


title: LungcancerCellLine_unirradiated_uninhibited_rep1


title: Control heart-age 18 months-BSIX-rep1

description: Gene expression data of control B6 heart-age 18 months

source_name: Control heart, B6, age 18 months

value: wild type

value: 18 months


title: Control heart-age 18 months-BSIX-rep2


title: Failing heart-age 18 months-apoE-deficient-rep1

description: Gene expression data of failing apoE-deficient heart-age 18 months

source_name: Failing heart, apoE-deficient, age 18 months

value: failing, atherosclerosis


title: LungcancerCellLine_unirradiated_uninhibited_rep2

value: lung cancer


title: Failing heart-age 18 months-apoE-deficient-rep2


title: LM04__Q504C7

value: carcinoma

value: liver

value: A pool of DNA from peripheral blood lymphocytes, from 7 apperently healty women.


title: LM02__Q504C6


title: ZFA169_HK_9mer

status: Public on Dec 02 2010

type: protein

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: platform design file: GPL11261

hyb_protocol: 12.5 μl of the in vitro translation mix was added to 137.5 μl of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween 20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween 20 and once with PBS/0.01% Triton X 100. After a one-hour incubation at room temperature, the array was washed once with PBS/0.5% Tween 20/50 μM zinc acetate and once with PBS/0.01% Triton X 100/50 μM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 μM zinc acetate. After a one-hour incubation at room temperature, the array was washed three times with PBS/0.05% Tween 20/50 μM zinc acetate and once with PBS/50 μM zinc acetate.

scan_protocol: Protein-bound microarrays were scanned using an Agilent microarray scanner at 2 μM resolution to detect Cy5-conjugated antibody.

data_processing:
Microarray TIF images were analyzed using ImaGene version 7.5 software (BioDiscovery)
We provide several scores for each 8-mer or 9-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.
Please see the supplementary files on the platform record (GPL11261) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: Artificial zinc finger array 169, HK design

label_protocol: T7-GST tagged proteins were not labelled after purification

extract_protocol: The zinc finger arrays were cloned as SacI-BamHI fragments into pTH5352, a modified T7-driven GST expression vector (see http://hugheslab.ccbr.utoronto.ca/supplementary-data/C2H2_modularity/ for a vector map). We expressed proteins using a PURExpress in vitro protein synthesis kit (New England BioLabs), supplemented with RNase inhibitor and 50 μM zinc acetate.

tag: zn finger

tag: platform_id design

value: HK


title: ZFA188_HK_9mer

description: platform design file: GPL11261

source_name: Artificial zinc finger array 188, HK design