title: HeJ, air, biological rep 3

status: Public on Feb 29 2012

type: RNA

city: Aurora

first: Alison

middle: Kendall

last: Bauer

state: CO

address: 12850 E. Montview Blvd.; Rm 3125

department: Environmental and Occupational Health

country: USA

institute: University of Colorado Denver

description: 3SRK 3-23

hyb_protocol: 10ug fragmented, biotinylated cRNA was hybridized to MOE430A GeneChips for 16hours at 45oC and 60rpm. The signal amplification protocol for washing/staining was performed in a FS450 automated fluidics station according to Affymetrix protocol.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

data_processing: The data were analyzed with GCOS 1.4 software. All probe sets scaling was performed with a target signal value of 500. No normalization was performed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: left lung lobe

label_protocol: 7.5 ug total RNA was processed according to the Affymetrix Technical manual Rev3 protocol. Biotinylated cRNA was prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit.

extract_protocol: Total RNA was extracted from individual lungs homogenized in TRIZOL. RNA was column-purified using the Qiagen RNeasy Mini Kit.

treatment_protocol: Animals were exposed to air or ozone, for 6, 24, 48 or 72 hours.

tag: treatment group

value: air

tag: tissue

value: left lung lobe

tag: gender

value: Male

tag: strain


title: HeJ, 6 hr Ozone, biological rep 1

description: 3SRK 3-31

value: 6 hr Ozone


title: HeJ, 24 hr Ozone, biological rep 3

description: 3SRK 13-3b

value: 24 hr Ozone


title: HeJ, 48 hr Ozone, biological rep 2

description: 3SRK 13-12

value: 48 hr Ozone


title: HeJ, 6 hr Ozone, biological rep 3

description: 3SRK 3-34


title: HeJ, 24 hr Ozone, biological rep 2

description: 3SRK 13-2


title: HeJ, 24 hr Ozone, biological rep 1

description: 3SRK 13-1b


title: HeJ, 48 hr Ozone, biological rep 3

description: 3SRK 13-14


title: HeJ, air, biological rep 2

description: 3SRK 3-22 star


title: RBP2

city: Gothenburg

first: Kuk-Ki

last: Hong

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description:
Sample 12
rep2

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

label: Biotin

organism: Saccharomyces cerevisiae

label_protocol: Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated from ground frozen mycelium using the Qiagen RNeasy Mini Kit.

tag: strain background

tag: medium

value: Minimal galactose-based medium

tag: growth condition

value: controlled fermenter kept at pH 5.0

tag: sampling time

value: mid exponential phase


title: HeJ, 48 hr Ozone, biological rep 1

description: 3SRK 13-11


title: 5DU1

description:
Sample 1
rep1

source_name: reconstructed mutant_5DU_ galactose medium


title: EBP1

description:
Sample 13
rep1


title: RBP1

description:
Sample 11
rep1


title: OuJ, 48 hr Ozone, biological rep 2

description: 3SRK 10-111

value: C3H/ HeOuJ


title: RAU2

description:
Sample 4
rep2

source_name: reconstructed mutant_RAU_ galactose medium


title: HeJ, 6 hr Ozone, biological rep 2

description: 3SRK 3-33b


title: RAU1

description:
Sample 3
rep1


title: EBP2

description:
Sample 14
rep2


title: RBU2

description:
Sample 6
rep2

source_name: reconstructed mutant_RBU_ galactose medium


title: 5DU2

description:
Sample 2
rep2


title: HeJ, air, biological rep 1

description: 3SRK 3-21


title: RAP2

description:
Sample 10
rep2


title: RAP1

description:
Sample 9
rep1


title: OuJ, 48 hr Ozone, biological rep 3

description: 3SRK 10-112


title: OuJ, 48 hr Ozone, biological rep 1

description: 3SRK 10-110


title: EBU2

description:
Sample 8
rep2

source_name: reconstructed mutant_EBU_ galactose medium


title: RBU1

description:
Sample 5
rep1


title: EBU1

description:
Sample 7
rep1


title: OuJ, air, biological rep 2

description: 3SRK 3-2


title: OuJ, 24 hr Ozone, biological rep 1

description: 3SRK 10-100


title: OuJ, air, biological rep 1

description: 3SRK 3-1


title: OuJ, 6 hr Ozone, biological rep 3

description: 3SRK 3-13


title: OuJ, 24 hr Ozone, biological rep 2

description: 3SRK 10-101


title: OuJ, 6 hr Ozone, biological rep 1

description: 3SRK 3-11


title: OuJ, 6 hr Ozone, biological rep 2

description: 3SRK 3-12


title: OuJ, air, biological rep 3

description: 3SRK 3-3


title: OuJ, 24 hr Ozone, biological rep 3

description: 3SRK 10-102


title: Wild-type_stimulated_sample 3

city: DUNDEE

first: Maria

middle: N

last: Navarro

address: Dow Street

department: Cell Signallig and Immunology

country: United Kingdom

institute: University of Dundee

description: 6  Wt802 peptide treated

hyb_protocol: Performed by Turku Centre for Biotechnology

data_processing: CHP files were generated using Expression Console V1.1

source_name: Wild-type_stimulated with antigenic peptide (gp33-41)

growth_protocol: Lymph nodes were harvested, disaggregated and cell suspensions were cultured for 4 hours

extract_protocol: Qiagen Rneasy minikit according to manufacturer's instructions.

treatment_protocol: Cells were stimulated with antigenic peptide gp33-41 (62.5 ng/ml) for 4 hours or left unstimulated

tag: genotype/variation

value: wild type

value: lymph nodes


title: PKD2-null_stimulated_sample 1

description: 8  KO219 peptide treated

scan_protocol: Performed by Turku Centre for Biotechnology

source_name: PKD2-null_stimulated with antigenic peptide (gp33-41)

value: PKD2 null


title: Wild-type_unstimulated_sample 3

description: 5  Wt802 untreated

label_protocol: Performed by Turku Centre for Biotechnology


title: PKD2-null_unstimulated_sample 3

description: 11  KO216 untreated


title: PKD2-null_stimulated_sample 3

description: 12  KO216 peptide treated


title: PKD2-null_stimulated_sample 2

description: 10  KO215 peptide treated


title: Wild-type_unstimulated_sample 2

description: 3  Wt274 untreated


title: Wild-type_stimulated_sample 1

description: 2  Wt273 peptide treated


title: Wild-type_stimulated_sample 2

description: 4  Wt274 peptide treated


title: PKD2-null_unstimulated_sample 2

description: 9  KO215 untreated


title: dka070

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

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

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.5  using the RMA method batch correction for amplficiation assay followed using the three repeated samples assayed by both methods in STATA/SE 11.  Data provided in the spreadsheet is the corrected data.

label: Biotin (Affyexpress)

source_name: Myc tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol).  Some samples were amplified and labelled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction.

growth_protocol: For Shh-type medulloblastoma [dka001-005, 009, 033 and 034] and [dka050-057], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] and [Cdkn2c-/-; Ptch1+/-] (Uziel et al.,2005 Genes Dev) were used, respectively.  For Myc [dka010-022, 037, 046, 049 and 058-71] and Mycn [dka023-032, 036 and 047] were generated by orthotopic injection of either Myc or Mycn overexpression in Cdkn2c-/-, Trp53-/- cerebellar cells into immunocompromised nude mice.  For Wnt-type medulloblastomas [pgr003, 016 and 066], spontaneously developed tumors from CTNNB1+/lox (ex3); BLBP-Cre; Trp53Fl/Fl (Gibson et al., Nature, 2010) were removed for RNA extraction.

extract_protocol: Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.

treatment_protocol: Tumor cells were dissociated and purified by percoll-gradient before RNA extraction.

value: cmyc MB - GFP positive


title: dka068

value: cmyc MB - GFP negative


title: pgr066

label: Biotin (One cycle kit)

source_name: Wnt-type medulloblastoma


title: pgr003


title: Wild-type_unstimulated_sample 1

description: 1  Wt273 untreated


title: PKD2-null_unstimulated_sample 1

description: 7  KO219 untreated


title: pgr016


title: dka069


title: dka071


title: dka067

description: dka067 is repeated measure of dka049

value: cmyc MB


title: dka066

description: dka066 is repeated measure of dka016


title: dka064


title: dka063


title: Seeds (15-20-25 DAP) of W134 line rep.1 [GPL13298]

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

country: Italy

institute: University of Verona

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 °C.  Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as the following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST wash solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software, and a quantile normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the SAM analysis (T-MEV 4.3)

organism: Petunia x hybrida

source_name: Seeds

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions

growth_protocol: Petunia axillaris plants were grown in soil under normal greenhouse conditions.

extract_protocol: Total RNA was isolated using Trizol reagent (Life Technologies, Cleveland, OH) according to the manufacturer instructions.

tag: line

value: Seeds


title: dka065

description: dka065 is repeated measure of dka012


title: Seeds (15-20-25 DAP) of W134 line rep.2 [GPL13298]


title: dka062


title: Seeds (15-20-25 DAP) of W134 line rep.3 [GPL13298]


title: dka061


title: Fertilized ovary (17 DAP)rep.3 [GPL13298]

organism: Petunia axillaris

source_name: Fertilized ovary

value: Fertilized ovary


title: dka056

source_name: Shh-type medulloblastoma

value: Ptc+/-, Cdkn2c-/-


title: Fertilized ovary (17 DAP)rep.1 [GPL13298]


title: Seeds (15-20-25 DAP) of R27 line rep.1 [GPL13298]


title: dka055


title: Seeds (15-20-25 DAP) of R27 line rep.3 [GPL13298]


title: dka059


title: dka057


title: dka051


title: dka054


title: dka058

value: p53-/-, Cdkn2c-/-, Math1-GFP infected with mcMyc/mRFP


title: Seedling rep.3 [GPL13298]

source_name: Seedling

value: Seedling


title: Seeds (15-20-25 DAP) of R27 line rep.2 [GPL13298]


title: Fertilized ovary (17 DAP)rep.2 [GPL13298]


title: dka053


title: dka060


title: Seedling rep.1 [GPL13298]


title: Seedling rep.2 [GPL13298]


title: dka052


title: Inflorescence rep.3 [GPL13298]

source_name: inflorescence

value: inflorescence


title: dka047

source_name: Mycn tumor

value: p53-/-, Cdkn2c-/-, Math1-GFP  infected with mMycn/mRFP


title: Inflorescence rep.2 [GPL13298]


title: Callus rep.1 [GPL13298]

source_name: Callus

value: Callus


title: dka050


title: Inflorescence rep.1 [GPL13298]


title: dka046


title: Callus rep.2 [GPL13298]


title: Callus rep.3 [GPL13298]


title: dka049


title: dka044

source_name: control for the Myc infected mutants (prepared from FACS-sorted GFP+ cells from P6 Cdkn2c-/-, Trp53-/-, Atoh1-GFP cerebella)

value: p53-/-, Cdkn2c-/-, Math1-GFP FACS sort for GFP+


title: Floral bud rep.2 [GPL13298]

source_name: Floral bud

value: Floral bud


title: dka042


title: Floral bud rep.1 [GPL13298]


title: dka038


title: WT15_Favorable Histology Wilms Tumor

city: Chicago

first: Elizaebth

middle: J

last: Perlman

state: IL

address: 2373 North Lincoln Avenue

department: Pathology

institute: Northwestern University

hyb_protocol: The labeled, fragmented cRNA was hybridized to the Affymetrix HG - U133A oligonucleotide array for 16 hours at 45°C according to Affymetrix protocol. Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols.

scan_protocol: The arrays were scanned in an HP GeneArray Scanner.

data_processing: Positional-dependent-nearest-neighbor model (PDNN) software was used to translate the scanned images into expression analysis files and to normalize the data across all arrays (http://www.r-project.org/).  The normalized value of each probeset for each tumor is provided within Sample table.

organism: Homo sapiens

source_name: Favorable Histology Wilms Tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by Trizol (Invitrogen, Carlsbad, CA) extraction and treated with DNase I (Roche, Indianapolis, IN).

tag: tumor type

value: Wilms Tumor

value: Pretreatment tumor tissue


title: WT12_Favorable Histology Wilms Tumor


title: dka036


title: WT14_Favorable Histology Wilms Tumor


title: WT11_Favorable Histology Wilms Tumor


title: WT13_Favorable Histology Wilms Tumor


title: WT10_Favorable Histology Wilms Tumor


title: dka032

value: p53-/-, Cdkn2c-/- infected with mMycn/GFP


title: dka037


title: WT9_Favorable Histology Wilms Tumor


title: dka031


title: dka040


title: Floral bud rep.3 [GPL13298]


title: WT7_Favorable Histology Wilms Tumor


title: WT5_Favorable Histology Wilms Tumor


title: dka030


title: dka034

value: p53floxed, Nestin-Cre, Cdkn2c-/-


title: WT6_Favorable Histology Wilms Tumor


title: WT4_Favorable Histology Wilms Tumor


title: dka026


title: WT3_Favorable Histology Wilms Tumor


title: dka029


title: dka027


title: WT2_Favorable Histology Wilms Tumor


title: dka025


title: WT8_Favorable Histology Wilms Tumor


title: WT1_Favorable Histology Wilms Tumor


title: dka023


title: dka024


title: dka022


title: dka020


title: dka019

value: p53-/-, Cdkn2c-/- infected with hcMyc/GFP


title: RT5_Rhabdoid Tumor

source_name: Rhabdoid Tumor

value: Rhabdoid Tumor


title: dka017


title: RT3_Rhabdoid Tumor


title: RT9_Rhabdoid Tumor


title: RT15_Rhabdoid Tumor


title: dka021


title: dka018


title: RT10_Rhabdoid Tumor


title: dka014


title: dka016


title: RT12_Rhabdoid Tumor


title: dka015


title: RT7_Rhabdoid Tumor


title: RT8_Rhabdoid Tumor


title: dka013


title: RT14_Rhabdoid Tumor


title: CCSK18_Clear Cell Sarcoma of the Kidney

source_name: Clear Cell Sarcoma of the Kidney

value: Clear Cell Sarcoma of the Kidney


title: dka012


title: RT1_Rhabdoid Tumor


title: dka011


title: CCSK16_Clear Cell Sarcoma of the Kidney


title: dka010


title: CCSK17_Clear Cell Sarcoma of the Kidney


title: CCSK14_Clear Cell Sarcoma of the Kidney


title: dka005


title: dka009


title: CCSK12_Clear Cell Sarcoma of the Kidney


title: dka004


title: dka003


title: dka002


title: CCSK5_Clear Cell Sarcoma of the Kidney


title: CCSK7_Clear Cell Sarcoma of the Kidney


title: CCSK10_Clear Cell Sarcoma of the Kidney


title: CCSK6_Clear Cell Sarcoma of the Kidney


title: CCSK3_Clear Cell Sarcoma of the Kidney


title: CCSK9_Clear Cell Sarcoma of the Kidney


title: CCSK2_Clear Cell Sarcoma of the Kidney


title: CCSK4_Clear Cell Sarcoma of the Kidney


title: dka001


title: CCSK11_Clear Cell Sarcoma of the Kidney


title: CCSK8_Clear Cell Sarcoma of the Kidney


title: CCSK1_Clear Cell Sarcoma of the Kidney


title: Dedifferentiated RPE 1

city: Philadelphia

first: Jeffrey

last: Adijanto

state: PA

address: 1020 Locust Street

department: Anatomy, Pathology, and Cell Biology

institute: Thomas Jefferson University

description: Sample 5

hyb_protocol: Agilent's miRNA labeling reagent and hybridization kit were used according to protocol.

scan_protocol: Agilent Technologies Scanner G2505 C.

data_processing: Images were quantified and processed using Feature Extraction software version 10.5.1.1 (Agilent).  Sample values from the raw fluorescence data were normalized to the average fraction of miR-24 and miR-130a for each sample.  To determine fractions for each samples, the values of miR-24 and miR-130a for sample 1 were set to a value of one.  The data in the Sample data tables include positive and negative controls that were excluded from the data used in SAM analysis.

source_name: fetal human retinal pigment epithelium, dedifferentiated

label_protocol: 100 ng of total RNA from each sample was labeled and hybridized to an Agilent-019118 Human miRNA Microarray 2.0 G4470B.

growth_protocol: hfRPE cells grown on T25 flasks were trypsinized and seeded on transwell filters (12mm) for at least 3 weeks prior to RNA extraction.  These hfRPE cells differentiate into highly pigmented and hexagonally packed monolayers with high total tissue resistance (> 500 ohm.cm2).  Dedifferentiated RPE cells are cells that have migrated from the free-edge of an intact hfRPE monolayer and continued to proliferate.

extract_protocol: Trizol reagent was used to extract total RNA according to the manufacturer's protocol.

treatment_protocol: No treatment.

tag: cell type

value: fetal human retinal pigment epithelium cells

tag: morphology

value: fibroblastic


title: Dedifferentiated RPE 2

description: Sample 6


title: Dedifferentiated RPE 3 (tech. rep. of Dediff. RPE 1)

description: Sample 7


title: Sample22 RC

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

description: stored, frozen Bone Marrow cells

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GC3000 7G

data_processing: The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org]

source_name: MDS sample

label_protocol: Biotinylated cRNA were prepared according to the One Cycle Assay Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA purification using selective binding columns

treatment_protocol: Stored, frozen bone marrow or peripheral blood cells

value: Bone Marrow

tag: diagnosis

value: refractory cytopenia sample at diagnosis


title: Sample24 RC

description: stored, frozen Bone Marrow cells


title: Partially Differentiated RPE 1

description: Sample 4

source_name: fetal human retinal pigment epithelium, partially differentiated

value: epithelial/fibroblastic


title: Sample 20 RC

description: stored, frozen Bone Marrow cells


title: Sample23 RAEB-t

description: stored, frozen Bone Marrow cells

value: refractory anemia with excess of blast in transformation sample at diagnosis


title: Sample21 RC

description: stored, frozen Bone Marrow cells


title: CMN13_Cellular Mesoblastic Nephroma

source_name: Cellular Mesoblastic Nephroma

value: Cellular Mesoblastic Nephroma


title: CMN12_Cellular Mesoblastic Nephroma


title: dka033


title: CMN11_Cellular Mesoblastic Nephroma


title: Differentiated RPE 3

description: Sample 3

source_name: fetal human retinal pigment epithelium, differentiated

value: epithelial


title: Differentiated RPE 2

description: Sample 2


title: Differentiated RPE 1

description: Sample 1


title: CMN6_Cellular Mesoblastic Nephroma


title: CMN9_Cellular Mesoblastic Nephroma


title: Sample18 RC

description: stored, frozen Peripheral Blood cells

value: Peripheral Blood


title: Seeds (15-20-25 DAP) of W134 line rep.1 [GPL13299]

source_name: Seeds

value: Seeds


title: Sample16 RAEB-t

description: stored, frozen Peripheral Blood cells


title: Sample19 RAEB

description: stored, frozen Peripheral Blood cells

value: refractory anemia with excess of blast sample at diagnosis


title: Array 30_vivo_16-cell rep3

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description: Array 30

hyb_protocol: A total of 825 ng of each labeled sample were incubated in a solution containing 2X blocking agent and 1X fragmentation buffer in a volume of 55 μl at 65 °C for 15 min, and were then put on ice. Fifty-five microliters of 2X GEx Hybridization Buffer HI-RPM was added for a final volume of 110 μl. The hybridization mix was added onto the array and hybridization was performed at 65 °C for 17 hr using an Agilent Hybridization chamber in a rotating oven

scan_protocol: Slides were scanned using Agilent’s High-Resolution C Scanner (Agilent Technologies, CA, USA) and features were extracted with the Agilent's Feature Extraction software (Agilent Technologies, CA, USA).

data_processing: Data were submitted to a simple background correction, a Loess within array normalization and a Quantile between array normalization.

organism: Bos taurus

source_name: Blastocyst cultured in vivo until 16-cell stage

label_protocol:
Amplification of RNA has been done using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
Labelling aRNA was performed using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol: Total RNA extraction was performed using the PicoPure RNA Isolation Kit (ARCTURS, Munich, Germany) according to the manufacturer's instruction.

tag: sample type

tag: breed (cattle)

value: Simmental

tag: reproductive status (cattle)

value: Heifer

source_name: in vivo control blastocyst


title: CMN8_Cellular Mesoblastic Nephroma

value: Pretreatment tumor tissue


title: Seeds (15-20-25 DAP) of R27 line rep.3 [GPL13299]


title: Sample17 RC

description: stored, frozen Bone Marrow cells


title: CMN7_Cellular Mesoblastic Nephroma


title: Sample12 RAEB

description: stored, frozen Peripheral Blood cells


title: Sample15 RC

description: stored, frozen Bone Marrow cells


title: Seeds (15-20-25 DAP) of R27 line rep.2 [GPL13299]


title: Seeds (15-20-25 DAP) of W134 line rep.2 [GPL13299]


title: Sample14 RAEB

description: stored, frozen Bone Marrow cells


title: Seeds (15-20-25 DAP) of W134 line rep.3 [GPL13299]


title: CMN4_Cellular Mesoblastic Nephroma


title: Sample11 RAEB-t

description: stored, frozen Bone Marrow cells


title: Fertilized ovary (17 DAP)rep.3 [GPL13299]

organism: Petunia integrifolia subsp. inflata

source_name: Fertilized ovary

value: Fertilized ovary


title: CMN5_Cellular Mesoblastic Nephroma


title: Seeds (15-20-25 DAP) of R27 line rep.1 [GPL13299]


title: Sample13 RC

description: stored, frozen Bone Marrow cells


title: CMN3_Cellular Mesoblastic Nephroma


title: Fertilized ovary (17 DAP)rep.2 [GPL13299]


title: CMN2_Cellular Mesoblastic Nephroma


title: Array 26_vivo_16-cell rep1

description: Array 26


title: Array 29_vivo_16-cell rep3

description: Array 29


title: Array 28_vivo_16-cell rep2

description: Array 28


title: Sample9 RAEB-t

description: stored, frozen Bone Marrow cells


title: Fertilized ovary (17 DAP)rep.1 [GPL13299]


title: Seedling rep.3 [GPL13299]

source_name: Seedling

value: Seedling


title: Array 25_vivo_16-cell rep1

description: Array 25


title: Array 27_vivo_16-cell rep2

description: Array 27


title: IFS3_Infantile Fibrosarcoma

source_name: Infantile Fibrosarcoma

value: Infantile Fibrosarcoma


title: CMN1_Cellular Mesoblastic Nephroma


title: Array 24_vivo_4-cell rep3

description: Array 24

source_name: Blastocyst cultured in vivo until 4-cell stage


title: Sample10 RC

description: stored, frozen Bone Marrow cells


title: Inflorescence rep.2 [GPL13299]

source_name: inflorescence

value: inflorescence


title: Seedling rep.2 [GPL13299]


title: IFS2_Infantile Fibrosarcoma


title: Array 21_vivo_4-cell rep2

description: Array 21


title: Sample7 RAEB

description: stored, frozen Bone Marrow cells


title: Sample6 RC

description: stored, frozen Bone Marrow cells


title: Sample4 RAEB

description: stored, frozen Bone Marrow cells


title: Array 23_vivo_4-cell rep3

description: Array 23


title: Array 22_vivo_4-cell rep2

description: Array 22


title: Seedling rep.1 [GPL13299]


title: Sample8 RC

description: stored, frozen Bone Marrow cells


title: Sample5 RC

description: stored, frozen Bone Marrow cells


title: Inflorescence rep.1 [GPL13299]


title: Inflorescence rep.3 [GPL13299]


title: Sample3 RAEB

description: stored, frozen Bone Marrow cells


title: Callus rep.1 [GPL13299]

source_name: Callus

value: Callus


title: rin mutant fruit, plant 1, biol rep1  (mutant3_RR)

city: Delhi

first: arun

middle: k.

last: sharma

state: Delhi

address: Benito-juarez road

department: Plant Molecular Biology

country: India

institute: Delhi university

description: Gene expression data of rin mutant fruit, plant 1, biological rep. 1

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using Avadis 4.2 prophetic software (Strandgenomics, Bangalore, India)

organism: Solanum lycopersicum

source_name: 45th DAP red-ripe fruit of rin mutant fruit

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

growth_protocol: Seedlings were raised on MS medium without antibiotic selection for 15 days.

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

treatment_protocol: Untreated seedlings were used for shoot tissue

tag: variety

value: Pusa Ruby

value: rin mutant

tag: age

value: 45 days after planting (DAP)

tag: developmental stage

value: red-ripe fruit

value: pericarp


title: Array 17_IVP rep3

description: Array 17

source_name: in vitro produced blastocyst


title: Floral bud rep.3 [GPL13299]

source_name: Floral bud

tag: tissue

value: Floral bud


title: rin mutant fruit, plant 2, biol rep2 (mutant8_RR)

description: Gene expression data of rin mutant fruit, plant 2, biological rep. 2


title: rin mutant fruit, plant 3, biol rep3 (mutant9_RR)

description: Gene expression data of rin mutant fruit, plant 3, biological rep. 3


title: Array 20_vivo_4-cell rep1

description: Array 20


title: Sample2 RAEB

description: stored, frozen Bone Marrow cells

value: Bone Marrow


title: Array 14_IVP rep1

description: Array 14


title: Array 19_vivo_4-cell rep1

description: Array 19


title: Array 15_IVP rep2

description: Array 15


title: rin mutant fruit, plant3, biol rep3 (mutant9_B)

source_name: 40st DAP breaker fruit of rin mutant fruit

value: 40 days after planting (DAP)

value: breaker fruit


title: Array 18_IVP rep3

description: Array 18

value: Simmental


title: Floral bud rep.1 [GPL13299]


title: rin mutant fruit, plant 2, biol rep2 (mutant8_B)


title: dka225

data_processing: The data were analyzed with Partek Genomics Suite version 6.5  using the RMA method.

source_name: Myc-type secondary tumor

label_protocol: Biotinylated cRNA were prepared and labeled according to the standard Affymetrix one-Cycle protocol).

growth_protocol: Myc-type tumors [dka201-203] were generated by orthotopic injection of Myc-infected cerebellar cells from Cdkn2c-/-, Trp53-/-, Atoh1-GFP mice into the cerebral cortex of immunocompromised nude mice. For Shh-type medulloblastomas [dka204-206], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] (Uziel et al.,2005 Genes Dev) were used.  FACS-sorted GFP-positive [dka220-222] and GFP-negative [dka211, 212 and 219] populations were obtained from postnatal day 6 Cdkn2c-/-, Trp53-/-, Atoh1-GFP cerebella.  Myc-type secondary tumors [dka223-225] were generated by orthotopic transplantation of cultured sphere cells from Myc-type primary tumors.

tag: tissue type

value: Myc-type secondary tumor


title: Array 16_IVP rep2

description: Array 16

value: Heifer


title: Sample1 RAEB-t

description: stored, frozen Bone Marrow cells

source_name: MDS sample

value: refractory anemia with excess of blast in transformation sample at diagnosis


title: Callus rep.2 [GPL13299]


title: Array 12_vitro_16-cell rep3

description: Array 12

source_name: Blastocyst cultured in vitro until 16-cell stage


title: rin mutant fruit, plant 1, biol rep1  (mutant6_B)


title: Floral bud rep.2 [GPL13299]


title: Array 13_IVP rep1

description: Array 13


title: dka224


title: dka223


title: Array 10_vitro_16-cell rep2

description: Array 10


title: SBS treatment_jejunum_4

city: Haifa

first: Igor

last: Sukhotnik

address: 47 Golomb St., P.O.B. 4940

department: Dept of Pediatric Surgery and Pathology,  Bnai Zion Medical Center, Haifa

country: Israel

institute: The Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology

hyb_protocol: Biotinylated cRNAs was purified, fragmented, and subsequently hybridized to an Illumina RatRef-12 Expression BeadChip V1 for genome-wide expression analysis containing 21,910 probes selected primarily from the NCBI RefSeq database (Release 16) according to the Direct Hybridization assay (Illumina Inc.). The hybridized chip capable of querying 12 samples in parallel was stained with streptavidin-Cy3 (AmershamTM) and scanned with an Illumina BeadArray 500GX Reader. The scanned images were imported into GenomeStudio (Illumina Inc.) for extraction and quality control, generating an output file for statistical analysis.

scan_protocol: The hybridized chip capable of querying 12 samples (control ileum-3, treatment ileum-4, control jejunum-1, treatment jejunum -4)   in parallel was stained with streptavidin-Cy3 (AmershamTM) and scanned with an Illumina BeadArray 500GX Reader. The scanned images were imported into GenomeStudio (Illumina Inc.) for extraction and quality control, generating an output file for statistical analysis.

data_processing: Differentially expressed transcripts in the SBS group (P<.05) were imported into Ingenuity Pathways Analysis (IPA, v7.5; Ingenuity Systems, Redwood City, CA(www.ingenuity.com). Transcripts’ gene identifiers were mapped to their corresponding gene object in the Ingenuity Pathways Knowledge Base

organism: Rattus norvegicus

source_name: 75% bowel resection (Short Bowel Syndrome)

label_protocol: The RNA was amplified into cRNA and biotinylated by in vitro transcription using the TargetAmp Nano-g Biotin-aRNA labeling kit for the Illumina system (picentre Biotechnologies) according to the manufacturer's protocol, with 200 ng of total RNA as input material. Biotinylated cRNAs was purified, fragmented, and subsequently hybridized to an Illumina RatRef-12 Expression BeadChip V1 for genome-wide expression analysis containing 21,910 probes selected primarily from the NCBI RefSeq database (Release 16) according to the Direct Hybridization assay (Illumina Inc.).

extract_protocol: Total RNA was isolated using a TRIzol (Invitrogen, Carlsbad, CA) extraction protocol with chloroform interphase separation, isopropanol precipitation, and ethanol wash steps. Precipitated total RNA was resuspended in RNAse-free water.

treatment_protocol: Animals were divided randomly into two experimental groups of 6 rats each. Group A rats underwent bowel transection and re-anastomosis (Sham), Group B animals underwent 75% bowel resection (SBS). Illumina's Digital Gene Expression (DGE) analysis using Illumina Rat Quad BeadChips was used to determine PDGF-related gene expression profiling.

tag: strain

value: Spraque Dawley

tag: gender

value: male

tag: tissue source

value: jejunum

value: intestinal mucosa


title: dka219

source_name: GFP negative spontaneous tumor

value: GFP negative spontaneous tumor


title: Array 9_vitro_16-cell rep2

description: Array 9


title: wild type fruit, plant 1, biol rep1  (control7_RR)

description: Gene expression data of wild type fruit, plant 1, biological rep. 1

source_name: 45th DAP red-ripe fruit of wild type fruit

value: Pusa Ruby

tag: genotype/variation

value: wild type


title: dka211


title: dka212


title: Array 11_vitro_16-cell rep3

description: Array 11

source_name: in vivo control blastocyst


title: dka221

source_name: GFP positive spontaneous tumor

value: GFP positive spontaneous tumor


title: SBS treatment_jejunum_2


title: dka222


title: wild type fruit, plant 2, biol rep2 (control8_RR)

description: Gene expression data of wild type fruit, plant 2, biological rep. 2

value: 45 days after planting (DAP)

value: red-ripe fruit

value: pericarp


title: dka220


title: SBS treatment_jejunum_1


title: dka206

source_name: Shh tumors

value: Shh tumor


title: rin mutant fruit, plant 3, biol rep3 (mutant9_IMG)

source_name: 35th DAP immature green fruit of rin mutant plant

value: rin mutant

value: 35 days after planting (DAP)

value: immature green fruit


title: wild type fruit, plant 3, biol rep3 (control10_RR)

description: Gene expression data of wild type fruit, plant 3, biological rep. 3


title: rin mutant fruit, plant 2, biol rep2 (mutant8_IMG)


title: rin mutant fruit, plant 1, biol rep1  (mutant6_IMG)


title: wild type fruit, plant 3, biol rep3 (control10_B)

source_name: 40st DAP breaker fruit of wild type fruit

value: 40 days after planting (DAP)

value: breaker fruit


title: SBS treatment_jejunum_3

value: Spraque Dawley


title: Array 8_vitro_16-cell rep1

description: Array 8

value: Simmental

value: Heifer


title: Callus rep.3 [GPL13299]

value: Callus


title: Array 7_vitro_16-cell rep1

description: Array 7


title: Array 6_vitro_4-cell rep3

description: Array 6

source_name: Blastocyst cultured in vitro until 4-cell stage


title: SBS treatment_ileum_3

value: male

value: ileum

value: intestinal mucosa


title: SBS treatment_ileum_4


title: SBS treatment_ileum_2


title: Array 5_vitro_4-cell rep3

description: Array 5


title: Array 4_vitro_4-cell rep2

description: Array 4


title: Array 3_vitro_4-cell rep2

description: Array 3


title: dka204


title: dka205


title: Array 2_vitro_4-cell rep1

description: Array 2


title: wild type fruit, plant 3, biol rep3 (control7_IMG)

source_name: 35th DAP immature green fruit of wild type plant

value: Pusa Ruby

value: wild type


title: PC8_normal_paraffinsection_rep1

status: Public on Feb 28 2012

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

description: miRNA expression profile of prostate cancer

hyb_protocol: Following the Agilent product’s processing protocol.

data_processing: Raw data are imported into software of the GeneSpring GX 11, and then normalized under the setting of percentile shift normalization algorithm.  The data was further analyzed with the selected subset samples (C2,C3,C4,C5_cancer_frozen and N2,N3,N4, N5_normal_frozen) because clustering result of the paraffin section data and C1, N1 sample data is obviously in the different tree [Matrix-ExcludeC1N1andParaffin.txt available as a Series Supplementary file].

source_name: prostate cancer paraffin section tissue

extract_protocol: Total RNA was prepared using the mirVana RNA Isolation Kit (Applied Biosystem) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fresh tissue are fast protected by Liquid nitrogen and then kept in -80℃. Frozen tissues are confirmed by HE staining before choosing. Paraffin section are pick up from hospital phsilogical department and confirmed by HE staining before choosing.

value: prostate

tag: t- psa

tag: f- psa

tag: gleason

tag: patient no

tag: source type

value: Paraffin section


title: PB1_normal_paraffinsection_rep1

scan_protocol: Following the Agilent product’s processing protocol.

source_name: benign prostatic hyperplasia paraffin section tissue, pool

value: BPH Pool


title: PC2_cancer_paraffinsection_rep1

label_protocol: Following the Agilent product’s processing protocol.


title: PC3_cancer_paraffinsection_rep2


title: N6_normal_frozen_rep6

source_name: benign prostatic hyperplasia frozen tissue

value: no data

value: Frozen section


title: PC4_cancer_paraffinsection_rep3


title: sham_ileun_1

source_name: bowel transection and re-anastomosis (Sham)


title: Array 1_vitro_4-cell rep1

description: Array 1

tag: sample type


title: wild type fruit, plant 2, biol rep2 (control7_B)

value: pericarp


title: dka202

source_name: Myc tumors

value: Myc tumor


title: wild type fruit, plant 2, biol rep2 (control5_IMG)

value: 35 days after planting (DAP)

value: immature green fruit


title: wild type fruit, plant 1, biol rep1  (control6_B)

value: 40 days after planting (DAP)

value: breaker fruit


title: sham_ileun_3

value: Spraque Dawley


title: N5_normal_frozen_rep5

value: male


title: SBS treatment_ileum_1

value: ileum


title: wild type fruit, plant 1, biol rep1  (control1_IMG)


title: dka201


title: N2_normal_frozen_rep2

source_name: benign prostate tissue of prostate cancer


title: dka203


title: sham_jejunum_1

value: jejunum

value: intestinal mucosa


title: sham_ileun_2


title: N4_normal_frozen_rep4


title: N1_normal_frozen_rep1


title: C5_cancer_frozen_rep5

source_name: prostate cancer frozen tissue


title: C4_cancer_frozen_rep4


title: C3_cancer_frozen_rep3


title: C2_cancer_frozen_rep2


title: C1_cancer_frozen_rep1


title: ear_seismic_rep1

city: St. John's

first: Catherine

middle: Dawn

last: Andrews

state: NL

address: 80 East White Hills Road

department: Science Branch

country: Canada

institute: Fisheries and Oceans Canada

hyb_protocol: Stock solutions of 10% SDS and 20X SSC (Ambion Inc., Austin, TX) used in microarray slide preparation and post-hybridization washes were diluted to working concentrations using UltraPure DNase/RNase-free distilled water (Invitrogen, Burlington, ON). Microarrays were prepared for hybridization by washing at room temperature 2 X 5 min in 0.1% SDS, 2 X 5 min in UltraPure DNase/RNase-free distilled water (Invitrogen) and 1 X 3 min in UltraPure DNase/RNase-free distilled water (Invitrogen), with gentle agitation in 50 ml sterile conical tubes, followed by a 3 min dip in 95°C UltraPure DNase/RNase-free distilled water (Invitrogen) and dried by centrifugation (2000 rpm, 5 min, in loosely-capped 50 ml sterile conical tubes) at room temperature. Arrays were placed in a slide box and left in a hybridization oven at 48°C until ready for use. Microarray targets were prepared using the 3DNA Array 900 Detection Kit and instructions (Genisphere, Hatfield, PA) and Superscript II (Invitrogen). Microarray hybridizations were performed using the 3DNA Array 900 Detection Kit and instructions (Genisphere). The salmon ear cDNAs contained an anchor for one of the Cy dye labeled Capture Reagents e.g. Cy3-labeled seismic exposed ear cDNA with Cy5-labeled control ear cDNA (technical replicates) and Cy5-labeled seismic exposed ear cDNA with Cy3-labeled control ear cDNA (dye-swaps). To each cDNA hybridization mix, 3 μl of Cy5-labeled GFP spike, 2 µl of LNA dT blocker (Genisphere) and 35 μl of 2X formamide-based hybridization buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt’s solution) (Genisphere) were added and the reaction mixtures were incubated at 80°C for 10 minutes in a Tetrad thermal cycler (BioRad) with a heated lid. The cDNA hybridization mixtures were placed in a 48°C hybridization oven until applied to the arrays. Microarray hybridizations were performed under low light due to the light sensitivity of the fluorescent Cy3 and Cy5 fluors. The cDNA targets (60 µl) were hybridized to the pre-warmed arrays by application of 22x60mm HybriSlip coverslips (Grace Biolabs, Bend, OR, USA), in Corning microarray hybridization chambers (Corning, NY, USA) in a 50°C water bath for 16 hours in the dark. Coverslips were floated off the arrays in 49°C, 2X SSC, 0.2% SDS. Arrays were then washed once in 49°C, 2X  SSC, 0.2% SDS for 15 minutes, then at room temperature 2X SSC for 15 min and finally 0.2X SSC for 15 minutes then dried by centrifugation (2000 rpm for 5 min) at room temperature. Arrays were incubated at 48°C until application of 3DNA capture reagent. The 3DNA capture hybridization mixture was prepared by addition of 25 µl UltraPure DNase/RNase-free distilled water (Invitrogen) and 2.5 µl of each of the Cy3 and Cy5 capture reagents (Genisphere), to 30 µl of 2X formamide-based buffer (Genisphere). The mixtures were kept in a 48°C hybridization oven until use. 3DNA capture hybridization mixture (57 μl) was added to each array and left to hybridize at 50°C for 4 hours in the dark. Coverslips were floated off the arrays and arrays were washed and dried as previously described.

scan_protocol: Fluorescent images of hybridized arrays were acquired immediately using a ScanArray GX Plus Microarray Scanner (Perkin Elmer, Wellesley, MA, USA) at 10 µm resolution using ScanArray Express software (Perkin Elmer). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively, using 90% laser power and photomultiplier tube (PMT) settings set at PMT 75 for Cy5 and PMT 78 for Cy3.

data_processing:
Fluorescent intensity data were extracted from TIFF image data using ImaGene 5.5 software (BioDiscovery, El Segundo, CA, USA). Briefly, microarray elements were manually gridded, spot sizes adjusted automatically, and spatial effects were manually flagged. Fluorescent intensity measurements were made and and ImaGene files were imported into GeneSpring GX version 7.3.1 (Silicon Genetics, Agilent Technologies, Palo Alto, CA, USA) for data transformation (background correction, and setting background values <0.01 to 0.01) and normalization (Lowess) to generate Background Corrected Lowess Normalized (BCLN) data. Fluorescent threshold levels for determining of genes were present were set for each slide by calculating the mean of the median local background values plus three standard deviations for all spots in the dominant channel using raw data generated from ImaGene. In the “up-regulated in seismic compared to control” gene list, seismic is the “dominant channel” (i.e. the channel with the higher transcript expression); in the “down-regulated in seismic compared to control” gene list, control is the “dominant channel”. Genes differentially regulated greater than 1.75-fold in at least three slides of the study (including at least one dye-swap) with BCLN signal above threshold on all 4 slides were selected as high trust data.
Log2 Average Background Corrected Lowess Normalized (BCLN) data representing seismic/control (Cy3/Cy5 for GG003011 and GG003012; Cy5/Cy3 for GG003013 and GG003014)

organism: Salmo salar

label_protocol: Fifty ng mRNA from right inner ear of seismic exposed and control fish (n=12 individuals per pool) were reverse transcribed (4 reactions for each treatment) for 2.5 h at 42 °C using 100 Units of Superscript II and the manufacturer’s 5X Superscript II buffer (Invitrogen) and oligo d(T) primers with unique 5-prime sequence overhangs for the Cy3 or Cy5 Capture Reagents (Genisphere). To two of the seismic exposed ear mRNA pools and two of the control ear mRNA pools, reverse transcription (RT) primer with 3DNA capture sequence specific for Cy3 Capture Reagent was added. To the remaining two mRNA samples from seismic exposed and control ear, RT primer with 3DNA capture sequence specific for Cy5 Capture Reagent was added.

extract_protocol: Total RNA was extacted from flash frozen individual salmon ears using TRIzol Reagent (Invitrogen) following manufacturer’s instructions with modifications. Samples were disrupted using disposable RNase-free pellet pestles in 1.5 ml microtubes followed by homogenization using QIAshredders (QIAGEN, Mississauga, ON) following manufacturer’s instructions. Individual total RNA samples were treated with 6.8 Kunitz units DNaseI (RNase-free DNase set, QIAGEN) at room temperature for 10 min to remove any residual genomic DNA then column purified using RNeasy MinElute Cleanup Kit (QIAGEN) following manufacturer’s instructions, and eluted with 12 μl nuclease-free water (Invitrogen, Burlington, ON). Column purified total RNA pools were prepared from the right ears of 12 seismic exposed and 12 control individuals, each contributing 4.0 µg total RNA. Poly(A)+ RNA (mRNA) was isolated from 48.0 µg total RNA pools using MicroPoly (A) Purist Small Scale mRNA Purification Kit (Ambion Inc., Austin TX) following manufacturer’s instructions.

treatment_protocol: Fish were held in two 1m3 cages, one each for control (non-exposed) and exposed groups, in a 15,000L aquarium at ambient seawater temperature (0.2°C) and acclimated for two weeks. Each cage was placed the same distance from the water intake, and airstones were placed next to each cage. Fish were fasted for two days prior to exposure. Whole inner ears from 16 control, non-exposed, fish from one cage were sampled prior to seismic activity. Immediately following sampling of control fish, 17 fish in the remaining cage were placed 2m from a 10in3 Texas Instruments airgun. Seismic airgun exposures were conducted by Fugro-Jacques Ltd, St. John’s, NL and sound metrics were recorded by Oceans Ltd, St. John’s, NL. Fish were subjected to 50 exposures, 1 exposure every 10 seconds, at an average SPL of ~204 dB peak-to-peak re 1µPa. Received levels were measured with a Reson Model TC 4014 hydrophone and particle velocity was calculated using the pressure gradient between two hydrophones. Whole inner ears from 17 seismic exposed fish were sampled 16 h following exposure.

value: juvenile

value: smolt

tag: organ

value: whole ear

tag: treatment


title: ear_seismic_rep4


title: ear_seismic_rep2


title: ear_seismic_rep3


title: Pten null, biological rep1

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: Gene expression data from murine prostate tumor

hyb_protocol: As recommended by manufacturer

scan_protocol: GeneChip Scanner 3000 7G was used for scanning.  Affymetrix GeneChip Command Console software (AGCC 3.2) was used for image processing

data_processing: Data was normalized by RMA (R/Bioconductor).

source_name: murine Pten null prostate

label_protocol: As recommended by manufacturer

extract_protocol: total RNA was extracted using the miRNeasy Mini Kit (Qiagen) per manufacturer's instruction

value: prostate tumor

tag: genotype

value: Pten null

value: older than 20 weeks


title: Pten null, biological rep2

tag: age


title: ctrl_2hr_2_1

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: ctrl set

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9).

data_processing: Agilent Feature Extraction Software (v 9) was used for background subtraction and LOWESS normalization. In house scripts were then used for downstream processing of the data. Upon fitting exponentia decay rates to each time-point series, a t-test based score was calculated for each transcript. This score ranging from -1 (significant reduction in decay rate in HNRPA2B1 knock-down samples) to 1 (significant increase), is calculated based on equation s*(1-p) where p is the t-test p-value between decay rates in the HNRPA2B1-KD samples and control samples and s is the sign of the difference between the average values (+1 if HNRPA2B1-KD values are greater than controls and -1 otherwise). Data provided in GSE35756_HNRNPA2B1_differential_decay_rate_processed.txt.

label_protocol: Agilent Gene Expression Hybridization Kit was used to gybridize labeled samples.

growth_protocol: MDA-MB-231 cells at 80% confluency were transfected with siRNA (Dharmacon) and control oligo (Invitrogen) using Lipofectamin 2000 reagent (Invitrogen) according to manufacturer’s recommendations. Experiments were performed in duplicates for each set.

extract_protocol: 200ng of total RNA were labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions

treatment_protocol: Forty-eight hours post-transfection, cells were exposed to 5ug/mL alpha-amanitine (Sigma) and total RNA was extracted using Norgen Biotek Total RNA Purification Kit at 0, 1, 2 and 4hr timepoints.

tag: transfection

value: control

tag: protocol

value: growth in the presence of alpha-amanitine

tag: time point

value: 2 hr


title: ctrl_4hr_1_1

description: ctrl set

value: 4 hr


title: ctrl_2hr_2_2

description: ctrl set


title: ctrl_2hr_1_1

description: ctrl set


title: ctrl_2hr_1_2

description: ctrl set


title: Pb-Cre+;PtenL/W;K-rasG12D/W, biological rep1

tag: tissue


title: N3_normal_frozen_rep3

tag: gender

value: prostate

value: Frozen section


title: ctrl_1hr_2_2

description: ctrl set

value: 1 hr


title: HNRPA2B1_KD_1

description: set 1 of 3.

hyb_protocol: Agilent Gene Expression Hybridization Kit was used to gybridize labeled samples.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9).

data_processing: Agilent Feature Extraction Software (v 9) was used for background subtraction and LOWESS normalization. In house scripts were then used for downstream processing of the data. GSE35757_HNRNPA2B1_KD_processed.txt: Average LOWESS-normalized log10 ratio (siRNA/BLOCK-it control)

label_protocol: 200ng of total RNA were labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions

extract_protocol: Forty-eight hours post-transfection, total RNA was extracted using Norgen Biotek Total RNA Purification Kit.

value: siRNA transfection (set 1)

value: BLOCK-it control transfection


title: ctrl_4hr_1_2

description: ctrl set


title: Pten null, biological rep3


title: Pb-Cre+;PtenL/W;K-rasG12D/W, biological rep3


title: ctrl_4hr_2_1

description: ctrl set


title: HNRPA2B1_KD_2

description: set 2 of 3.

value: siRNA transfection (set 2)


title: ctrl_0hr_2_2

description: ctrl set

value: 0 hr


title: ctrl_0hr_2_1

description: ctrl set


title: HNRPA2B1_KD_3

description: set 3 of 3.

value: siRNA transfection (set 3)


title: ctrl_1hr_1_2

description: ctrl set


title: ctrl_4hr_2_2

description: ctrl set


title: ctrl_1hr_2_1

description: ctrl set


title: ctrl_1hr_1_1

description: ctrl set


title: S. epidermidis3

city: Houston

first: Mohan

last: Pammi Venkatesh

state: TX

address: One Baylor Plaza

department: Pediatrics

institute: Baylor College of Medicine

description: Custom 40K Staphylococcus epidermidis RP62A MYcroarrays and each slide has one array composed of 40,960 spots

hyb_protocol: CUST-40K-Staphylococcus_epidermidis_RP62A. Custom 40K Staphylococcus epidermidis RP62A MYcroarrays were manufactured. Each MYcroarray slide has one array composed of 40,960 spots, of which 33,715  spots contain 45mer  probes for S. epi genes, 525 features are “empty” (i.e., they contain no probe), 608 features contain MYcroarray in-house QC probes and 112 features contain positive control probes for assessing hybridization and washing stringency. There are 5 identical replicates of each S. epi probe such that a total of 6,743 S. epi genes are surveyed by each array. In addition, there are 6000 probes for randomly selected Candida genes.     Single color Hybridizations. cRNA derived from all samples was coupled to Alexa Fluor 555. Eight micrograms of each target was hybridized separately to one array.  Since the customer sent 3 biological replicates of two sample types (pure culture and cultured with Candida) each of the 6 targets was hybridized separately to one array. Hybridization was performed for >18hrs at 45oC in a proprietary hybridization buffer.  Wash and Scan Arrays. The array sandwich was opened submerged in 6X SSPE at 22oC and stored briefly (<2min) in fresh 6X SSPE until all arrays were ready to wash. The arrays were washed twice in 1X SSPE at 22oC for 3 minutes per wash while the wash solution was gently circulated over the arrays. The arrays were washed in 1X SSPE at 45C for 5 min. Finally, the arrays were allowed to cool to 22oC for 3 minutes in 1X SSPE then exposed to 0.25X SSPE for 30sec and spun dry in a microarray centrifuge. The arrays were scanned in an Axon 4000B Scanner (Molecular Devices) set at 5m per pixel resolution. The PMT setting was adjusted to appreciate the maximum dynamic range of signal. This was accomplished by increasing the PMT until a few features showed at least some saturation.

scan_protocol: Scanned images were quantified using GenePix Pro Software (version 6.1.0.4). For signal extraction, circular feature indicators (35um diameter) were centered over each spot. Median feature pixel intensity was extracted.   Saturated Spots or Spots Manually Flagged “Bad”. Some spots had some saturation due to adjusting the PMT until the full dynamic range was appreciated. Nonetheless, the PMT for this study was 375 (adjustable PMT range is 85 - 850) suggesting very robust signal while background values were no higher than 0.14% of the full dynamic range. This study, therefore, had excellent signal to background noise. Table 1 lists the frequency and percent of spots with at least 10% saturation (>=SAT10). There were so few spots with saturation that spots with saturation were permitted to be analyzed.  All spots were reviewed manually and some spots were flagged “bad” (a value of -100 in the “flags” field in the raw data [.gpr] files) due to issues such as dust, bubbles or proximity to gaskets. Table 1 reports the distribution of good (not flagged bad) spots in all probe sets (PS, each has 5 technical probe replicates; n = 6743/array). The data show that a trimmed mean (intra-array normalized signal value) was calculated for 99.77% of the probe sets (n = 26,972) in the study. A mean was used to calculate the signal value for the remaining few probes sets (n=60) because they had only 2 or 3 good probe replicates.

data_processing:
Due to the manufacturing process, the area immediately surrounding a spot should not be used to estimate background levels. We know that when probes do not bind target, the residual signal is very different compared with the surrounding area. A global background correction algorithm within each array is used instead of a local background correction factor. Empty” spots  was not used as a measure of background because they lack probe sequences and behave differently (to nonspecific hybridization) compared to spots containing probes.  Consequently, the background value was determined by the 5th percentile darkest feature from the distribution of median signal intensities for all Staphylococcus epidermidis RP62A spots for each array. To use local background values would over-estimate the contribution of background signal in the extracted signal intensity of each probe.     Normalization. To adjust for differences in dye incorporation, a scale factor was created to equalize signal across all arrays. Only probes that met the following criteria were used to calculate the scale factor: only S. epi spots were used; spots must have less than 10% saturated pixels; spots could not be flagged “bad”; median signal had to be more than 4 fold background; and all arrays had to have each spot qualify as a normalization spot. There were 15,554 qualifying spots. The average signal for these qualifying probes, called normalization features (NF), was calculated for each array.            Present Call. An estimation of whether or not a transcript was detected by a probe was calculated. The estimation is a “present” call. The present call is based on the trimmed mean signal for each gene relative to the global background level on each array. For each gene (probe), if the trimmed mean signal was greater than 3 times the background signal (see “Background Correction” above), then the transcript was considered “present”.  Analysis Strategy. Samples S1 and SC1 were sent separately from samples S2, S3, SC2 and SC3. Samples S1 and SC1 replaced the original samples that had failed QC. The fresh S1 and SC1 samples passed QC and were included in the study. Unfortunately, the “on-array” behavior of SC1 suggested that it was substantially different from the other samples. Table 2 lists several on-array characteristics for each sample. While S1 had a bit higher background and about 10% less genes considered to be “present”, this sample was omitted given that its matched pair SC1 had significant issues (very low signal resulting in a huge scale factor and consequently very few genes considered present); this despite the fact that both S1 and SC1 samples had very good QC parameters for dye incorporation and mean fragment size. So both SC1 and S1 were omitted from the following analysis.
Signal intensity values were extracted from scanned images using GenePix® Pro 6 software (Molecular Devices). Briefly, a 30-micron circular feature indicator was centered on each spot and median feature pixel intensity was extracted. Saturated signals were replaced by lower PMT scan values. The raw gpr files were loaded in Genespring GX 11.5, the data log2 transformed; background corrected, and normalized using the Quantile algorithm. Hierarchical clustering map was generating using Euclidean algorithm with the average linkage rule. Differential gene expression between the two samples groups (S. epidermidis and mixed-species biofilms) was evaluated by unsupervised unpaired t-test on the log2 transformed mean data. A fold-change ratio (mixed-species biofilms vs. S. epidermidis biofilms) was calculated with a fold change cutoff of 1.5 and p-value of 0.05. Probe set lists were trimmed to represent S. epidermidis and analyzed using unpaired t-test and Benjamini-Hochber multiple-testing correction to generate targeted lists of differential expression. Microarray expression patterns were validated using real-time PCR using three up regulated and two down-regulated genes. The comparison is Mixed-species biofilms vs. S. epidermidis biofilms. However, there are only two biologic replicates per condition [S2 and S3; SC2 and SC3]. It is likely that type II errors are prevalent.     3. A fold change ratio (SC/S) of 2 (or less than 0.5).     Under these filtering conditions, there were 416 interesting genes (there are some genes that are surveyed by more than one probe set). You have file that is called HotGeneList.xlsx. This is an Excel 2007 file. This Excel file is active. You can enter your own filtering criteria. You can enter a p value threshold in the yellow box (cell T9) and or a ratio threshold in the light orange box (cell U9). Then use the filter in cell W10 (Potentially a Hot Gene = 1) to retrieve only genes with a value of “1” in that field, which means the genes meet the filtering criteria.  If you change the filter in either U9 or T9, you must select “all” genes in cell W10 first before re-filtering on “1” in cell W10.   At a p value of 0.05 (and without a ratio filter), we expect by chance alone that 337 genes (out of 6743) will be significantly different (comparing the two groups). Yet we see many more significant genes (n=1059) than can be expected by chance alone a p<0.05. I conclude that there is some real difference between S and SC samples.

label: Alexa Fluor 555

organism: Staphylococcus epidermidis

source_name: S.epidernmidis biofilm3

label_protocol: Alexa Fluor 555 (Invitrogen A32756) was coupled to cRNA following the manufacturer’s instructions. Unincorporated dye was removed using RNeasy Mini Columns (Qiagen 74104). The Qiagen’s quick clean-up protocol was followed. cRNA Fragmentation. cRNA coupled to fluorescent dye was fragmented using proprietary technology. The expected mean fragment length is 100 -125 nucleotides. Fragmented cRNA is considered sufficiently fragmented for use on MYcroarrays if the mean fragment length less than 200 nucleotides.

growth_protocol: Single species biofilms of S. epidermidis (strain 1457) and C. albicans (strain 32354) and mixed-species biofilms were formed on 6-well tissue culture plates. Five ml of organism suspensions (O.D. 0.3, S. epidermidis 107 CFU/ml or C. albicans 105 CFU/ml)  or 2.5 ml each for mixed-species biofilms for 24 hr.

extract_protocol: RNA was harvested from single species and mixed-species biofilms using RNeasy Mini kit (Qiagen), a Fast-RNA Pro-BLUE kit (MP Biomedicals) according to manufacturer’s instructions (47, 49).  Microbial cells were lysed in a high-speed homogenizer (FastPrep24 instrument), and the isolated RNA was treated with RNAse-free DNAse-I. An aliquot of RNA was centrifuged and the pellet was washed with 80% ethanol. Following centrifugation, the supernatant was carefully aspirated, the residual ethanol was removed by brief drying (37oC) and the pellet was suspended in RNase free water. Total RNA was quantified with the use of a NanoDrop-1000 spectrophotometer. In addition, the integrity of the total RNA was analyzed (Agilent 2100 Bioanalyzer). Enrichment of mRNA. Ten micrograms of total RNA was converted to enriched mRNA using Applied Biosystem’s (Ambion) MicrobExpressTm Kit (AM1905). The manufacturer’s protocol was followed. Enriched mRNA was analyzed by the Agilent 2100 Bioanalyzer. The expected yield of enriched mRNA from ten micrograms of total RNA is typically 1.0 - 2.5μg.     Production of cRNA. Enriched mRNA (200ng) was converted to cRNA using Applied Biosystem’s (Ambion) MessageAmp™ II-Bacteria RNA Amplification Kit (AM1790). Amino-allyl-UTP was incorporated into the cRNA during the IVT reaction. The manufacturer’s protocol was followed. The expected yield from 200ng is about 100μg.

tag: population

value: Single species biofilm


title: Mixed-species2

organism:
Staphylococcus epidermidis
Candida albicans

source_name: Mixed-species biofilm2

value: Mixed-species biofilm


title: NM4_normal mucosa

city: Zurich

first: Giancarlo

last: Marra

address: Winterthurerstrasse 190

department: Molecular Cancer Research

country: Switzerland

institute: University of Zurich

description: surgical biopsy

hyb_protocol: 45C for 16 hours in a Affymetrix hybridization station.  Then, washings were performed in the Affymetrix Fluidics Station 450 (protocol FS450_0001 and reagents from Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Cell intensities (.CEL files) were captured by the Affymetrix GeneChip Operating Software (GCOS) and Affymetrix Expression Console Software was used to perform quality assessment.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: normal mucosa

label_protocol: biotin (Whole Transcript Sense Target Labeling kit of Affymetrix).

extract_protocol: Qiagen RNeasy.

value: colorectum

tag: colon segment

value: cecum


title: HNRPA2B1_KD_4hr_2_2

description: siRNA set

value: siRNA-mediated HNRPA2B1 knock-down


title: S. epidermidis2

source_name: S.epidernmidis biofilm2


title: Mixed-species3

source_name: Mixed-species biofilm3


title: P6_polypoid

description: endoscopic biopsy

source_name: polypoid

value: ascending


title: NM6_normal mucosa

description: endoscopic biopsy


title: ctrl_0hr_1_2

description: ctrl set

value: control

value: growth in the presence of alpha-amanitine


title: NP5_nonpolypoid

description: endoscopic biopsy

source_name: nonpolypoid


title: HNRPA2B1_KD_4hr_1_1

description: siRNA set

value: 4 hr


title: NM5_normal muocsa

description: endoscopic biopsy

source_name: normal muocsa


title: HNRPA2B1_KD_4hr_2_1

description: siRNA set


title: Ecad_Mut_1

city: Milwaukee

first: Michele

middle: A

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

hyb_protocol: Affymetrix Whole Transcript Sense Protocol

data_processing: dChip 2010

source_name: E18.5 E-cadherin cKO

label_protocol: Affymetrix Whole Transcript Sense Labeling

growth_protocol: Embryonic small intestine was harvested at E18.5.

extract_protocol: Qiagen Rneasy Mini

treatment_protocol: Small intestinal tissue was harvested, washed in PBS, and stored in RNALater until RNA preparation.

value: small intestine

tag: genotype/variation

value: E-cadherin cKO


title: CRC3_colorectal cancer

description: surgical biopsy

source_name: colorectal cancer


title: Ipsi_spinal_cord_SC

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

description: pool of 6 animals; 5125380031_F

hyb_protocol: The obtained labeled copy RNA samples (1,500 ng) were hybridized 18 h at 58°C to a MouseRef-8 v2.0 Expression BeadChip (Illumina) according to the manufacturer's instructions. BeadChips were then washed and developed using fluorolink streptavidin-Cy3 (GE Healthcare).

scan_protocol: BeadChips were scanned using an Illumina BeadArray Reader.

data_processing: The raw data were processed using Feature Extraction software version 10.5. The initial analysis and normalization to the median were performed using GeneSpring GX software (Agilent). Differentially expressed mRNAs with signal intensities higher than two-fold over the background standard deviation were filtered by t-test with p<0.05. Only the statistically significant data (p<0.05) were used to calculate gene expression ratios in the samples.

source_name: spinal cord day 5 post-injury

label_protocol: Samples of total RNA (500 ng) were labeled using an Illumina RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was extracted from nerves and DRG using TRIzol reagent and purified using the RNeasy columns (Qiagen). The RNA purity was estimated by measuring the OD260/280 and the 260/230 ratios. The integrity of the RNA samples was validated using an Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: Adult female C57Bl6 mice were used. Nerve crush was performed to study the mechanisms of nerve repair. Nerve transection was performed to differentiate the distal (degenerating) and proximal (regenerating) events of nerve injury. Animals were anesthetized with 4% isofluorane (Aearrane; Baxter, IL) in 55% Oxygen and the sciatic nerves were exposed unilaterally at the mid-thigh level. Nerves were transected using surgical scissors or crushed using fine, smooth-surface forceps twice for 5 sec each in rats or once for 3 sec in mice. Sham-operated control includes the sciatic nerve exposure without otherwise any manipulation. Animals were sacrificed by an i.p. injection of rodent anesthesia cocktail containing Nembutal (50 mg/ml, Ovation Pharmaceuticals, IL) and Diazepam (5 mg/ml, Hospira inc., Lake Forest, IL) in 0.9% saline (Steris Labs, Phoenix, AZ), followed by lethal i.p. injection of Beuthanasia (100-150 mg/ml, Schering-Plough Animal Health, Canada). The sciatic nerve and lumbar (L) 4 and 5 dorsal root ganglia (DRG) ipsilateral and contralateral to injury were isolated for analyses. Animals were handled in accordance with the NIH Guide for the Care and Use of Laboratory Animals and the protocols approved by the VA San Diego Institutional Animal Care and Use Committee.

tag: strain

value: spinal cord


title: ctrl_0hr_1_1

description: ctrl set


title: Pb-Cre+;PtenL/W;K-rasG12D/W, biological rep2

value: prostate tumor

value: older than 20 weeks


title: CRC4_colorectal cancer

description: surgical biopsy


title: Ecad_Mut_3

scan_protocol: Affymetrix Whole Transcript Sense Protocol


title: Ecad_Mut_2


title: HNRPA2B1_KD_4hr_1_2

description: siRNA set


title: HNRPA2B1_KD_2hr_2_1

description: siRNA set

value: 2 hr


title: D1_Injured_nerve_LND1

description: pool of 6 animals; 5125380031_B

source_name: Left nerve day 1 post-injury

value: sciatic nerve


title: Normal_DRG_RL4-5

description: pool of 6 animals; 5125380031_D

source_name: Normal dorsal root ganglia (DRG)

value: dorsal root ganglia


title: Ipsi_DRG_LL4-5

description: pool of 6 animals; 5125380031_E

source_name: DRG day 5 post-injury


title: NM3_normal mucosa

description: surgical biopsy


title: HNRPA2B1_KD_2hr_2_2

description: siRNA set


title: D5_Injured_nerve_LND1

description: pool of 6 animals; 5125380031_C

source_name: Left nerve day 5 post-injury


title: 8_152: Telomerase immortalised human keratinocytes (N/TERT) transduced with EGFP

type: genomic

city: London

first: Emilios

last: Gemenetzidis

address: 4 Newark Street

institute: Queen Mary University of London

description: Hybridized to 10K SNP

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

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

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from human keratinocytes using the Nucleon Genomic DNA Extraction Kit BACC3( (Amersham) according to manufacturer's instructions

tag: cell type

value: Human Epidermal Keratinocytes


title: 7_152: Telomerase immortalised human keratinocytes (N/TERT)

description: Hybridized to 10K SNP


title: NM2_normal mucosa

description: surgical biopsy


title: HNRPA2B1_KD_1hr_2_2

description: siRNA set

value: 1 hr


title: NM1_normal mucosa

description: surgical biopsy

value: colorectum


title: Normal_nerve_RN

description: pool of 6 animals; 5125380031_A

source_name: Normal right nerve control


title: 9_152: Telomerase immortalised human keratinocytes (N/TERT) transduced with EGFP-GLI2DeltaN

description: Hybridized to 10K SNP


title: 1_136: Normal human epidermal keratinocytes

description: Hybridized to 10K SNP

source_name: Primary human cells (reference)


title: 1_132: Normal human epidermal keratinocytes

description: Hybridized to 10K SNP


title: CRC2_colorectal cancer

description: surgical biopsy


title: HNRPA2B1_KD_0hr_2_2

description: siRNA set

value: 0 hr


title: Ecad_Con_2

source_name: E18.5 control

value: wildtype


title: 5_39dox+

city: Turku

first: Nelly

last: Rahkonen

address: Tykistökatu 6 A

country: Finland

institute: Turku Centr for Biotechnology

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was analyzed with R language and environment for statistical computing (version 2.10.1) using the Bioconductor module (version 2.5), quantile normalization method from limma package was used. Limma package computed normalized signal intensities.

source_name: NT2D1 cell line, total RNA

label_protocol: Ambion's Illumina RNA TotalPrep Amplification kit (cat no AMIL1791)

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen). To eliminate genomic DNA DNase I (Qiagen) digestion in column was included. RNA/cRNA concentrations where checked with Nanodrop ND-1000 and RNA/cRNA quality was controlled by BioRad’s Experion electrophoresis station

value: embryonal carcinoma cell line

tag: cell line

value: stably expressing TetR3 and L1TD1shRNA

tag: dox treatment

value: dox+

value: Day 6


title: CRC1_colorectal cancer

description: surgical biopsy

value: cecum


title: HNRPA2B1_KD_2hr_1_2

description: siRNA set

value: siRNA-mediated HNRPA2B1 knock-down

value: growth in the presence of alpha-amanitine


title: 5_40dox+

description: replicate 6


title: HNRPA2B1_KD_1hr_2_1

description: siRNA set


title: HNRPA2B1_KD_1hr_1_2

description: siRNA set


title: HNRPA2B1_KD_0hr_1_1

description: siRNA set


title: Ecad_Con_1

value: small intestine


title: HNRPA2B1_KD_2hr_1_1

description: siRNA set


title: Rat lung suzu-00002

city: Sapporo

first: Satoru

last: Tsunemine

country: Japan

institute: Contract Research Laboratory, GeneticLab Co., Ltd.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA

source_name: Yusuke Suzuki

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Extraction of total RNA was performed according to RNeasy Mini Kit（QIAGEN）.

value: lung

tag: experimenter

value: Yusuke Suzuki


title: 5_28dox-

description: replicate 5

value: dox-


title: HNRPA2B1_KD_1hr_1_1

description: siRNA set


title: rat_high-dosed_animal 8

city: Wuhan

first: Xiu-Ju

last: ZHAO

state: Hubei

address: No.68 South Xuefu Road, Changqing Garden

department: School of Biology and Pharmaceutical Engineering

institute: Wuhan Polytechnic University

description:
Rat_H8
Gene expression data from liver, high-dosed

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: high-dosed mequindox

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

value: liver

value: Wistar

value: week 10


title: 5_23dox-

description: replicate 4


title: 5_34dox+

description: replicate 4


title: 1_15dox+

description: replicate 3


title: HNRPA2B1_KD_0hr_2_1

description: siRNA set


title: 1_12dox+

description: replicate 2


title: 1_6dox-

description: replicate 3


title: HNRPA2B1_KD_0hr_1_2

description: siRNA set


title: rat_high-dosed_animal 6

description:
Rat_H6
Gene expression data from liver, high-dosed

value: week 9


title: 1_3dox-

description: replicate 2


title: HNRPA2B1_RIP_chip_1

description: rep 1

hyb_protocol: Agilent Gene Expression Hybridization Kit was used to hybridize labeled samples.

data_processing: Agilent Feature Extraction Software (v 9) was used for background subtraction and LOWESS normalization. In house scripts were then used for downstream processing of the data. GSE35753_HNRPA2B1_RIP_chip_processed.txt: Average LOWESS-normalized log10 ratio (RIP/input)

label_protocol: co-IP and input samples were differentially labeled using Low Input Quick Amp Labeling Kits per manufacturer's instructions.

growth_protocol: MDA-MB-231 cells at 50% confluency were transfected with tagged HNRPA2B1 (Origene) using Lipofectamin LTX reagent (Invitrogen) according to manufacturer’s recommendations.

extract_protocol: Seventy-two hours post-transfection, cells were UV-crosslinked and lysed. Samples were taken prior and after immunoprecipitation.

tag: fraction

value: co-IP sample

tag: antibody

tag: antibody vendor

value: Origene

value: input sample


title: 1_10dox+

description: replicate 1

value: embryonal carcinoma cell line

value: stably expressing TetR3 and L1TD1shRNA


title: decoy_vs_scrambled_2_1

description: Biological replicate 3 of 4.

data_processing: Agilent Feature Extraction Software (v 9) was used for background subtraction and LOWESS normalization. In house scripts were then used for downstream processing of the data. GSE35749_decoy_vs_scrambled_processed.txt: Average LOWESS-normalized log10 ratio (decoy/scrambled)

growth_protocol:
Two decoy/scrambled sets were then chemically synthesized (IDT). An upstream T7 promoter was used to transcribe the constructs in vitro using Megascript T7 kit (Ambion). In order to reduce cytotoxicity, RNA molecules were capped and poly-A tailed using Cap Analog (Ambion) and poly-A polymerase (NEB).
MDA-MB-231 cells at 80% confluency were transfected with the resulting RNA oligos using Lipofectamin 2000 reagent (Invitrogen) according to manufacturer’s recommendations. Experiments were performed in duplicates for each set.

value: Set2 decoy transfection

value: Set2 scrambled transfection


title: decoy_vs_scrambled_1_2

description: Biological replicate 2 of 4.

value: Set1 decoy transfection

value: Set1 scrambled transfection


title: decoy_vs_scrambled_2_2

description: Biological replicate 4 of 4.


title: rat_high-dosed_animal 4

description:
Rat_H4
Gene expression data from liver, high-dosed

tag: genotype

tag: age


title: HNRPA2B1_RIP_chip_2

description: rep 2


title: rat_high-dosed_animal 5

description:
Rat_H5
Gene expression data from liver, high-dosed


title: rat_high-dosed_animal 3

description:
Rat_H3
Gene expression data from liver, high-dosed


title: rat_high-dosed_animal 10

description:
Rat_H10
Gene expression data from liver, high-dosed


title: rat_high-dosed_animal 2

description:
Rat_H2
Gene expression data from liver, high-dosed


title: A1-2_ETOH#2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
0.1% ethanol treatment 8h
251485051236_1_4

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: 48 hours in DMEM supplemented with 5% charcoal dextran treated FBS

extract_protocol: Trizol Plus with on column DNase digestion per manufactures protocol

treatment_protocol: 100 nM dexamethasone or 0.1% ethanol vehicle for 8 hours.

value: A1-2 breast cancer cells

tag: agent

value: ethanol


title: rat_control_animal 9

description:
Rat_B9
Gene expression data from liver, control

source_name: control


title: Rat lung matsu-00001

source_name: So Matsuzawa

value: lung

value: So Matsuzawa


title: decoy_vs_scrambled_1_1

description: Biological replicate 1 of 4.

tag: transfection


title: A1-2_ETOH#3

description:
0.1% ethanol treatment 8h
251485051282_1_1


title: rat_high-dosed_animal 11

description:
Rat_H11
Gene expression data from liver, high-dosed

tag: tissue

value: liver


title: A1-2_ETOH#1

description:
0.1% ethanol treatment 8h
251485051281_1_3


title: A1-2_DEX#2

description:
100 nm Dexamethasone treatment 8h
251485051282_1_3

value: dexamethasone


title: Mice_mammary_Ecoli_Rep2.2

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242

scan_protocol: Microarry slides were scanned using Agilent Microarray Scanner at 3micron resolution

data_processing: Microarray data was normalized and analysed using GeneSpring Gx v 11.5 software

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis)

extract_protocol: Qiagen’s RNeasy minikit Cat#74104

value: Swiss albino

value: mammary gland


title: rat_control_animal 2

description:
Rat_B2
Gene expression data from liver, control

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

value: Wistar

value: week 9


title: A1-2_DEX#1

description:
100 nm Dexamethasone treatment 8h
251485051236_1_2


title: Mice_mammary_Ecoli_Rep2.1


title: Mice_mammary_PBS_Rep1.1


title: 1_1dox-

description: replicate 1

value: dox-

tag: time point

value: Day 6


title: Brain Tumor 1 cell rep2

status: Public on Feb 27 2012

city: San Diego

first: Craig

last: April

address: 9885 Towne Centre Drive

institute: Illumina, Inc.

description: replicate 2

data_processing: Raw data was analyzed using GenomeStudio v2.0

source_name: Brain Tumor 1 cell

label_protocol: Standard Illumina labelling protocol

extract_protocol: HeLa.S-Fucci RNA was extracted using TRIzol

tag: group

value: low input

tag: sample type

value: Brain Tumor 1 cell

value: Brain tumor cell


title: Tumorspheres rep1

description: replicate 1

source_name: Tumorspheres

value: Tumorspheres

value: Tumorsphere cells


title: Adherent Cells

description: replicate 1

source_name: Adherent Cells

value: Adherent Cells

value: Adherent cells


title: HeLa.S-Fucci 5 cells rep2

description: replicate 2

source_name: HeLa.S-Fucci 5 cells

value: HeLa.S-Fucci 5 cells


title: HeLa.S-Fucci 1 ng rep2

description: replicate 2

source_name: HeLa.S-Fucci 1 ng

value: high input

value: HeLa.S-Fucci 1 ng


title: Brain Tumor 1 cell rep1

description: replicate 1


title: rat_control_animal 1

description:
Rat_B1
Gene expression data from liver, control

value: liver


title: A1-2_DEX#3

description:
100 nm Dexamethasone treatment 8h
251485051281_1_4

value: A1-2 breast cancer cells

value: dexamethasone


title: HeLa.S-Fucci 1 ng rep3

description: replicate 3


title: Tumorspheres rep2

description: replicate 2


title: HeLa.S-Fucci 5 cells rep3

description: replicate 3


title: Brain Tumor 1 cell rep3

description: replicate 3


title: Ecad_Con_3

value: small intestine

tag: genotype/variation

value: wildtype


title: HeLa.S-Fucci 1 ng rep1

description: replicate 1


title: HeLa.S-Fucci 5 cells rep1

description: replicate 1


title: 50pg FirstChoice Human Brain Reference RNA rep3

description: replicate 3


title: HeLa.S-Fucci 1 cell rep3

description: replicate 3

source_name: HeLa.S-Fucci 1 cell

value: HeLa.S-Fucci 1 cell


title: 10pg FirstChoice Human Brain Reference RNA rep1

description: replicate 1


title: 10pg Universal Human Reference RNA rep2

description: replicate 2

source_name: 10pg Universal Human Reference RNA

value: 10pg Universal Human Reference RNA


title: 50pg Universal Human Reference RNA rep3

description: replicate 3

source_name: 50pg Universal Human Reference RNA

value: low input

value: 50pg Universal Human Reference RNA


title: 1ng Universal Human Reference RNA rep2

description: replicate 2

source_name: 1ng Universal Human Reference RNA

value: 1ng Universal Human Reference RNA


title: 10pg FirstChoice Human Brain Reference RNA rep3

description: replicate 3


title: HeLa.S-Fucci 1 cell rep2

description: replicate 2


title: 10pg Universal Human Reference RNA rep1

description: replicate 1


title: 1ng FirstChoice Human Brain Reference RNA rep3

description: replicate 3


title: 10pg FirstChoice Human Brain Reference RNA rep2

description: replicate 2


title: 1ng Universal Human Reference RNA rep3

description: replicate 3


title: HeLa.S-Fucci 1 cell rep1

description: replicate 1


title: 1ng FirstChoice Human Brain Reference RNA rep2

description: replicate 2


title: 1ng FirstChoice Human Brain Reference RNA rep1

description: replicate 1


title: 50pg Universal Human Reference RNA rep2

description: replicate 2


title: 50pg FirstChoice Human Brain Reference RNA rep1

description: replicate 1


title: Mice_mammary_PBS_Rep1.2

tag: strain

value: Swiss albino

value: mammary gland


title: 50pg FirstChoice Human Brain Reference RNA rep2

description: replicate 2


title: 50pg Universal Human Reference RNA rep1

description: replicate 1


title: 10pg Universal Human Reference RNA rep3

description: replicate 3


title: 1ng Universal Human Reference RNA rep1

description: replicate 1


title: CHC1201N

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: Paired normal sample for tumor CHC1201T

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from 3 mm3 frozen samples from tumor and nontumoral liver tissue using high salt precipitation (as described in PMID: 3344216).

tag: sample

value: Paired normal


title: CHC1192N

description: Paired normal sample for tumor CHC1192T


title: CHC1199N

description: Paired normal sample for tumor CHC1199T


title: CHC1199T

description: Hepatocellular carcinoma

value: Hepatocellular carcinoma

tag: hbv infection

value: no

tag: hcv infection

tag: alcool intake

tag: age (year)

tag: gender (m=male; f=female)

value: M

tag: tumor diameter (mm)


title: CHC1201T

description: Hepatocellular carcinoma

value: yes


title: CHC1065N

description: Paired normal sample for tumor CHC1065T


title: CHC1065T

description: Hepatocellular carcinoma


title: CHC1069T

description: Hepatocellular carcinoma


title: CHC1162N

description: Paired normal sample for tumor CHC1162T


title: CHC1146N

description: Paired normal sample for tumor CHC1146T


title: CHC1062T

description: Hepatocellular carcinoma


title: CHC1055N

description: Paired normal sample for tumor CHC1055T


title: CHC1192T

description: Hepatocellular carcinoma


title: CHC1154N

description: Paired normal sample for tumor CHC1154T


title: CHC1154T

description: Hepatocellular carcinoma


title: CHC1060N

description: Paired normal sample for tumor CHC1060T


title: CHC1069N

description: Paired normal sample for tumor CHC1069T


title: CHC1061N

description: Paired normal sample for tumor CHC1061T


title: CHC1052N

description: Paired normal sample for tumor CHC1052T


title: CHC1062N

description: Paired normal sample for tumor CHC1062T


title: CHC1053N

description: Paired normal sample for tumor CHC1053T


title: CHC1190N

description: Paired normal sample for tumor CHC1190T


title: CHC1040N

description: Paired normal sample for tumor CHC1040T


title: CHC1041N

description: Paired normal sample for tumor CHC1041T


title: CHC1060T

description: Hepatocellular carcinoma


title: CHC1146T

description: Hepatocellular carcinoma


title: CHC1190T

description: Hepatocellular carcinoma

value: F


title: CHC1044N

description: Paired normal sample for tumor CHC1044T


title: CHC1061T

description: Hepatocellular carcinoma


title: Breast Cancer serum (PD vs. BC) sample 30

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

hyb_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters and a pixel size of 5um.

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum (PD vs. BC) (PD vs. AD) results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.

label: Alexa Fluor 647

molecule: other

label_protocol: standard Invitrogen protocol

extract_protocol: All serum (PD vs. BC) (PD vs. AD) samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

tag: gender

value: Female

tag: mini mental state exam (mmse) score

value: serum

tag: disease state

value: Breast Cancer


title: Breast Cancer serum (PD vs. BC) sample 29

tag: age


title: CHC1162T

description: Hepatocellular carcinoma

tag: tissue


title: Breast Cancer serum (PD vs. BC) sample 28


title: Breast Cancer serum (PD vs. BC) sample 26


title: Breast Cancer serum (PD vs. BC) sample 24


title: Breast Cancer serum (PD vs. BC) sample 25


title: Breast Cancer serum (PD vs. BC) sample 23


title: Breast Cancer serum (PD vs. BC) sample 22


title: Breast Cancer serum (PD vs. BC) sample 19


title: Breast Cancer serum (PD vs. BC) sample 20


title: CHC1053T

description: Hepatocellular carcinoma


title: Breast Cancer serum (PD vs. BC) sample 21


title: Breast Cancer serum (PD vs. BC) sample 18


title: Breast Cancer serum (PD vs. BC) sample 17


title: Breast Cancer serum (PD vs. BC) sample 16


title: Breast Cancer serum (PD vs. BC) sample 15


title: Breast Cancer serum (PD vs. BC) sample 12


title: Breast Cancer serum (PD vs. BC) sample 13


title: Breast Cancer serum (PD vs. BC) sample 11


title: Breast Cancer serum (PD vs. BC) sample 10


title: Breast Cancer serum (PD vs. BC) sample 27


title: CHC1044T

description: Hepatocellular carcinoma


title: 4860956003_I

city: New Haven

first: Frank

last: Waldron-Lynch

state: CT

address: 300 George Street

department: Human Translational Immunology

institute: Yale University Medical School

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse Spleen

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: For in vitro treatment cells where grown in AIM-V serum free medium (GIBCO)

extract_protocol: Human CD4 cells from spleen were purified by positive selection on magnetic-activated Dynabeads (Invitrogen)

treatment_protocol: In vivo humanized mice were treated with teplizumab and sacrificed after 18 hours. In vitro splenocytes where isolated from humanized and treated with either teplizumab or hIg and then havested after 18 hours

tag: cell type

value: human CD4 from NOD/SCID IL2gc-/- (NSG) reconstituted with human CD34+ at birth

tag: treatment

value: Teplizumab in vitro


title: CHC1052T

description: Hepatocellular carcinoma


title: Breast Cancer serum (PD vs. BC) sample 9

tag: sample type


title: 4860956003_J

value: hIg in vitro


title: CHC793N

description: Paired normal sample for tumor CHC793T


title: Breast Cancer serum (PD vs. BC) sample 14


title: Breast Cancer serum (PD vs. BC) sample 8


title: Breast Cancer serum (PD vs. BC) sample 6


title: 4860956003_H


title: 4860956003_G

value: Teplizumab in vivo


title: Breast Cancer serum (PD vs. BC) sample 5


title: CHC1035N

description: Paired normal sample for tumor CHC1035T


title: Breast Cancer serum (PD vs. BC) sample 4


title: CHC1041T

description: Hepatocellular carcinoma


title: 4860956003_F


title: 4860956003_C


title: CHC1055T

description: Hepatocellular carcinoma


title: CHC1040T

description: Hepatocellular carcinoma


title: CHC891N

description: Paired normal sample for tumor CHC891T


title: CHC909N

description: Paired normal sample for tumor CHC909T


title: CHC983T

description: Hepatocellular carcinoma


title: CHC319N

description: Paired normal sample for tumor CHC320T


title: CHC614N

description: Paired normal sample for tumor CHC614T


title: 4860956003_D


title: Breast Cancer serum (PD vs. BC) sample 2


title: Breast Cancer serum (PD vs. BC) sample 1


title: CHC909T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 28

value: Parkinson's Disease


title: Parkinson's Disease serum (PD vs. BC) sample 29

value: Male


title: 4860956003_B


title: Breast Cancer serum (PD vs. BC) sample 3


title: Parkinson's Disease serum (PD vs. BC) sample 26


title: 4860956003_K


title: Parkinson's Disease serum (PD vs. BC) sample 27


title: Parkinson's Disease serum (PD vs. BC) sample 25

value: UNK


title: 4860956003_A


title: CHC1035T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 24


title: CHC429T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 21


title: CHC983N

description: Paired normal sample for tumor CHC983T


title: 4860956003_E


title: Parkinson's Disease serum (PD vs. BC) sample 23


title: Parkinson's Disease serum (PD vs. BC) sample 22


title: CHC891T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 19


title: Parkinson's Disease serum (PD vs. BC) sample 17


title: Breast Cancer serum (PD vs. BC) sample 7


title: Parkinson's Disease serum (PD vs. BC) sample 20


title: CHC614T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 15


title: Parkinson's Disease serum (PD vs. BC) sample 14


title: Parkinson's Disease serum (PD vs. BC) sample 16


title: Parkinson's Disease serum (PD vs. BC) sample 12


title: Parkinson's Disease serum (PD vs. BC) sample 11


title: Parkinson's Disease serum (PD vs. BC) sample 10


title: Parkinson's Disease serum (PD vs. BC) sample 8


title: Parkinson's Disease serum (PD vs. BC) sample 13


title: Parkinson's Disease serum (PD vs. BC) sample 18


title: CHC918T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 7


title: CHC961T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 9


title: CHC882T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 6


title: CHC918N

description: Paired normal sample for tumor CHC918T


title: Parkinson's Disease serum (PD vs. BC) sample 5


title: CHC428N

description: Paired normal sample for tumor CHC429T


title: Parkinson's Disease serum (PD vs. BC) sample 4


title: CHC794T

description: Hepatocellular carcinoma


title: CHC798T

description: Hepatocellular carcinoma


title: Parkinson's Disease serum (PD vs. BC) sample 3


title: CHC725N

description: Paired normal sample for tumor CHC725T


title: Parkinson's Disease serum (PD vs. BC) sample 2


title: CHC320T

description: Hepatocellular carcinoma


title: CHC794N

description: Paired normal sample for tumor CHC794T


title: CHC465T

description: Hepatocellular carcinoma


title: CHC961N

description: Paired normal sample for tumor CHC961T


title: CHC715N

description: Paired normal sample for tumor CHC715T


title: Multiple sclerosis serum (PD vs. MS) sample 10

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum (PD vs. AD) results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.

extract_protocol: All serum (PD vs. AD) samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

value: Multiple sclerosis


title: CHC725T

description: Hepatocellular carcinoma


title: CHC469T

description: Hepatocellular carcinoma


title: CHC882N

description: Paired normal sample for tumor CHC882T

value: Paired normal


title: CHC793T

description: Hepatocellular carcinoma

value: Hepatocellular carcinoma


title: CHC609T

description: Hepatocellular carcinoma

value: no


title: CHC609N

description: Paired normal sample for tumor CHC609T


title: Multiple sclerosis serum (PD vs. MS) sample 8


title: Multiple sclerosis serum (PD vs. MS) sample 7


title: Multiple sclerosis serum (PD vs. MS) sample 6


title: CHC715T

description: Hepatocellular carcinoma

value: M


title: CHC445N

description: Paired normal sample for tumor CHC445T


title: Parkinson's Disease serum (PD vs. BC) sample 1


title: CHC464N

description: Paired normal sample for tumor CHC465T


title: Multiple sclerosis serum (PD vs. MS) sample 5


title: CHC798N

description: Paired normal sample for tumor CHC798T


title: Multiple sclerosis serum (PD vs. MS) sample 3


title: Multiple sclerosis serum (PD vs. MS) sample 2


title: Multiple sclerosis serum (PD vs. MS) sample 4


title: Multiple sclerosis serum (PD vs. MS) sample 1


title: Parkinson's Disease serum (PD vs. MS) sample 28


title: Parkinson's Disease serum (PD vs. MS) sample 29


title: Multiple sclerosis serum (PD vs. MS) sample 9


title: Parkinson's Disease serum (PD vs. MS) sample 27


title: CHC445T

description: Hepatocellular carcinoma

value: yes


title: Parkinson's Disease serum (PD vs. MS) sample 25


title: Parkinson's Disease serum (PD vs. MS) sample 26


title: Parkinson's Disease serum (PD vs. MS) sample 24