title: Day 15 EEM from Male CSF2 Replicate 1

description:
raw data file: 252829810234_area1_2013_05_24_results.txt
Within the raw files, channel 1= Cy3 and channel 2= Cy5

source_name: Male CSF2 1


title: Day 15 EEM from Male CSF2 Replicate 2

status: Public on Oct 01 2014

type: RNA

city: Gainesville

first: Kyle

last: Dobbs

state: Florida

address: 2250 SW Shealy Drive

department: Animal Sciences

country: USA

institute: University of Florida

description:
raw data file: 252829810234_area2_2013_05_24_results.txt
Within the raw files, channel 1= Cy3 and channel 2= Cy5

hyb_protocol: 825 ng of one Cy3 labeled aRNA sample and 825 ng of one Cy5 aRNA sample were combined and hybridized to one area of a 4x44,000 Agilent EmbryoGene microarray slide

scan_protocol: Slides were scanned using a Agilent High-resolution C Scanner (Agilent Technologies, CA, USA) while features were extracted using Agilent's feature extraction software (Agilent)

data_processing: Data were sent to BioDiscovery Inc. (Hawthorne, CA ,USA) which generated separate datasets for each color (Cy3 and Cy5).  Spots were aligned to the corresponding Genepix aray list follwoed by examination for spots on the array that were larger than the spot or contaiend a bliemish.  Raw data was log transformed,normalized by both Loess and quantile normalization by JMP Genomic (SAS, Cary, NC, USA).

molecule: total RNA

organism: Bos taurus

source_name: Male CSF2 2

label_protocol: aRNA was labeled using the Universal Linkage System (ULS) by Kreatech for gene expression analysis.  Microarray slides were made by Agilent and designed by EmbryoGene.  ULS directly labels the aRNA through a non-enzymatic protocol which labels through the formation of a coordinate bond on the N7 position of guanine.  The Cy3 and Cy5 are linked by a spacer to the ULS molecule.

growth_protocol: Fertilized embryos were grown in culture to Day 7 after fertilization and transferred into Holstein recipients.  At Day 15, they were flushed from the recipient using DPBS/PVP

extract_protocol: RNA was extracted according to manufacturer's instructions using the Qiagen Allprep DNA/RNA mini kit

treatment_protocol: 10 ng/ml of CSF2 or Control (DPBS/BSA)  from Day 5-7 post-insemination during in vitro culture of bovine embryos.

tag: tissue

value: Filamentous Day 15 extra-embryonic membrane

tag: gender

value: male


title: EGF 72 - C7

city: brussels

first: aline

last: hébrant

address: 808 route de Lennik

department: iribhm

country: Belgium

institute: ulb

description:
raw data file 1: EGF721-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF721-hy5N-hy3EGF.gpr

hyb_protocol: samples were hybridized using Corning Pronto! Microarray Hybridization Kit, and were dye swapped. So for each sample, we have two microarray slide (raw data file 1 and raw data file 2 as indicated as description field). The raw data file 1 is labelled as 'tumor-Hy5+normal tissue-Hy3' and the raw data file 2 is labelled as tumor-Hy3+normal tissue-Hy5 as dye-swap experiments.

scan_protocol: the slides were scanned using a GenePix 4000B scanner (Axon, Sunnyvale, CA)

data_processing:
Please note that sample data table contains data combined across arrays. All hybridizations were performed in duplicates with dye swap and each probes are present in duplicate on the same array. For each probes, a mean was performed on their four replicates. We have kept the data for the probe for which we have at least 2 values.
A Normex + offset background correction and LOESS normalization were carried out by using functions of the LIMMA 3.4.5 package for the R 2.8.1 language. Data points were removed when intensity values for both dyes were below 200% of the background and absent calls were removed before subsequent statistical analyses.

label: Hy5, Hy3

organism: Homo sapiens

source_name: Primary Culture

label_protocol: total RNA was labelled using the miRCURY LNA microRNA Power Labelling Kit (Hy3/Hy5) (Exiqon, Copenhagen, Denmark), according to the manufacturer’s protocol. Labeled RNA was purified on a miRNeasy column (Qiagen)

extract_protocol: total RNA was extracted using a TRIzol Reagent kit (Invitrogen) followed by purification on miRNeasy columns (Qiagen, Hilden, Germany

treatment_protocol: Cells cultures were stoped using Trizol. Tissues were immediately dissected, placed on ice, snap-frozen in liquid nitrogen, and stored at -80°C until processing

tag: tissue/cell type

value: EGF treated Primary Culture

label: Hy3. Hy5

source_name: Control Cells

value: Non treated primary culture


title: 3.SIRT1 young

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised using quantile normalisation in R

label: Biotin

organism: Mus musculus

source_name: SIRT1 young

label_protocol: Biotinylated cRNA were prepared with Illumina  kit for Illumina arrays

extract_protocol: RNA was extracted  with standard methods

treatment_protocol: Adult microglia were isolated from SIRT1F/F or LysM-Cre/SIRT1F/F mice as described with some modifications. Brains were placed in a culture dish with enzyme solution and the digested brains were triturated with a 20-ml pipette and passed through 70-μm filter. After centrifugation, cells were incubated with anti-myelin microbeads, centrifuged, resuspendend and washed. Myelin-negative fractions were collected and further processed by incubating with anti-CD11b microbeads at 4°C for 15 min. After washing, the resuspended myelin negative fraction was passed through an autoMACS Pro Separator, and then the CD11b-positive population was separated from CD11b-negative population. Cells were centrifuged, and the pellets were lysed with RNA lysis buffer (QIAGEN) for microarray or quantitative RT-PCR.

tag: age

value: young

tag: genotype

tag: cell type

value: microglia

tag: genetic background

value: BL6 and 129/Sv


title: 24 hour biofilm vs Mixed Reference 4

city: San Francisco

first: Emily

middle: Patricia

last: Fox

address: 600 16th Street, GH - N374

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: 252016610066-block 9

hyb_protocol: 0.4 mg Cy3-labelled cDNA and 0.4 mg Cy5-labelled cDNA were hybridized onto custom Agilent 8*15k microarrays (AMADID #020166)

scan_protocol: Scanned on a 4000B Axon Instrument Scanner

data_processing: Arrays were gridded with Gene Pix Pro software version 7, Lowess normalization was performed using a Goulphar script for R, Probes were collapsed to a median value using a custom java script

organism: Candida albicans

source_name: 24 hour Biofilm (experiment 4)

label_protocol: cDNA was synthesized from 8 mg total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instruction, and using a mixture of 0.5 mM 3:2 aminoally-dUTP (Ambion 8437):dNTPs. cDNA was dye coupled to either Cy3 or Cy5 (GE Healthcare PA23001 or PA25001)

growth_protocol: C. albicans was grown in biofilms or in planktonic cultures at 30 deg or 37 deg in Spider media

extract_protocol: Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)

tag: source strain background

tag: strain

source_name: Mixed reference pool#4: cDNA from 252016610066 - blocks 5 - 10


title: Day 15 EEM from Male Control Replicate 1

source_name: Male Control 1


title: EGF 72 - C5

description:
raw data file 1: EGF722-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF722-hy5N-hy3EGF.gpr


title: EGF 3 - C7

description:
raw data file 1: EGF32-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF32-hy5N-hy3EGF.gpr


title: 8 hour biofilm vs Mixed Reference 4

description: 252016610065-block 8

source_name: 8 hour Biofilm (experiment 4)


title: EGF 16 - C5

description:
raw data file 1: EGF161-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF161-hy5N-hy3EGF.gpr


title: EGF 48 - C4

description:
raw data file 1: EGF482-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF482-hy5N-hy3EGF.gpr


title: 24 hour biofilm vs Mixed Reference 2

description: 252016610044-block 6

source_name: 24 hour Biofilm (experiment 2)

source_name: Mixed reference pool#2: cDNA from 252016610044 - blocks 1 - 8


title: 2.SIRT1 young


title: OV04-27_Om_B01

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description:
A891-21
Hybridised to SNP 6.0 array.

hyb_protocol: Hybridisation was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

scan_protocol: Scanning was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

data_processing: Data was processed using PICNIC using the 'primary' option.

molecule: genomic DNA

source_name: Ovarian cancer patient OV04-27, sample Om_B01

label_protocol: Labelling was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

extract_protocol: Samples were placed immediately into RNAlater at the time of collection. DNA extraction was performed using the Qiagen DNeasy Blood and Tissue Kit according to the manufacturer's instructions.

tag: study id

tag: sample id

tag: disease

value: ovarian cancer

value: omentum

tag: timepoint

value: laparoscopic biopsy

tag: response to treatment

value: partial response

tag: progression-free survival (months)


title: liver_wt_rep1

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: replicate 1

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

label: biotin

source_name: liver

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

value: wild type

tag: allele

value: 21 weeks

tag: mouse id

tag: Sex

value: liver


title: ESG 1.5 - C7

description:
raw data file 1: EGF1.52-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF1.52-hy5N-hy3EGF.gpr

tag: tissue


title: 8 hour biofilm vs Mixed Reference 2

description: 252016610044-block 5

source_name: 8 hour Biofilm (experiment 2)


title: OV04-21_ROv_S2

description:
A891-19
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-21, sample ROv_S2

value: right ovary

value: interval debulking surgery

value: stable disease


title: EGF 48 - C5

description:
raw data file 1: EGF481-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF481-hy5N-hy3EGF.gpr

tag: tissue/cell type


title: liver_wt_rep4

description: replicate 4

tag: age


title: 24 hour biofilm vs Mixed Reference 3

description: 252016610057-block 4

source_name: 24 hour Biofilm (experiment 3)

source_name: Mixed reference pool#3: cDNA from 252016610057 - blocks 1 - 5


title: EGF 1.5 - C5

description:
raw data file 1: EGF1.51-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF1.51-hy5N-hy3EGF.gpr


title: OV04-20_Unk_B1

description:
A891-18
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-20, sample Unk_B1

value: unknown

value: biopsy


title: TSH 72 - C9

description:
raw data file 1: TSH722-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH722-hy5N-hy3TSH.gpr

value: TSH treated Primary Culture


title: Log phase 37 degrees vs Mixed Reference 4

description: 252016610065-block 6

source_name: Planktonic Log Phase 37 degrees (experiment 4)


title: Log phase 37 degrees vs Mixed Reference 3

description: 252016610057-block 1

source_name: Planktonic Log Phase 37 degrees (experiment 3)


title: 48 hour biofilm vs Mixed Reference 3

description: 252016610057-block 5

source_name: 48 hour Biofilm (experiment 3)


title: Adhered biofilm cells vs Mixed Reference 2

description: 252016610044-block 3

source_name: Adhered Biofilm (experiment 2)


title: Adhered biofilm cells vs Mixed Reference 4

description: 252016610065-block 7

source_name: Adhered Biofilm (experiment 4)


title: Unadhered biofilm cells vs Mixed Reference 2

description: 252016610044-block 4

source_name: Planktonic Unadhered 37 degrees (experiment 2)


title: OV04-20_Om_S1

description:
A891-14
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-20, sample Om_S1


title: EGF 3 - C5

description:
raw data file 1: EGF33-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF33-hy5N-hy3EGF.gpr

source_name: Primary Culture

value: EGF treated Primary Culture

source_name: Control Cells

value: Non treated primary culture


title: OV04-21_ROv_S1

description:
A891-13
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-21, sample ROv_S1


title: EGF 3 - C4

description:
raw data file 1: EGF31-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF31-hy5N-hy3EGF.gpr


title: TSH 72  - C1

description:
raw data file 1: TSH723-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH723-hy5N-hy3TSH.gpr


title: TSH 72 - C4

description:
raw data file 1: TSH721-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH721-hy5N-hy3TSH.gpr


title: OV04-30_Om_S2

description:
A891-12
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-30, sample Om_S2

value: primary surgery


title: 8 hour biofilm vs Mixed Reference 3

description: 252016610057-block 3

source_name: 8 hour Biofilm (experiment 3)


title: Log phase 30degrees vs Mixed Reference 2

description: 252016610044-block 2

source_name: Planktonic Log Phase 30 degrees  (experiment 2)

source_name: Mixed reference pool#2: cDNA from 252016610044 - blocks 1 - 8


title: TSH 48 - C9

description:
raw data file 1: TSH482-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH482-hy5N-hy3TSH.gpr


title: 48 hour biofilm vs Mixed Reference 1

description: 252016610046-block 8

source_name: 48 hour Biofilm  (experiment 1)

source_name: Mixed reference pool#1: cDNA from 252016610046 - blocks 1 - 8


title: Stationary planktonic vs Mixed Reference 2

description: 252016610044-block 1

source_name: Planktonic Stationary Phase 30 degrees (experiment 2)


title: EGF 24 - C4

description:
raw data file 1: EGF241-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF241-hy5N-hy3EGF.gpr


title: OV04-20_LOv_S1

description:
A891-11
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-20, sample LOv_S1

value: left ovary


title: liver_hom_rep4

description: replicate 4

source_name: liver

tag: genotype

value: heterozygous

value: male


title: 1.SIRT1 young

source_name: SIRT1 young

value: young

tag: cell type

value: microglia

value: BL6 and 129/Sv


title: liver_hom_rep3

description: replicate 3

value: 21 weeks


title: EGF 24 - C5

description:
raw data file 1: EGF242-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF242-hy5N-hy3EGF.gpr


title: OV04-30_Ov_S1

description:
A891-10
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-30, sample Ov_S1

value: ovarian cancer

value: left ovarian tubule


title: TSH 48 - C4

description:
raw data file 1: TSH481-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH481-hy5N-hy3TSH.gpr


title: liver_hom_rep2

description: replicate 2

value: liver


title: 48 hour biofilm vs Mixed Reference 2

description: 252016610044-block 8

source_name: 48 hour Biofilm (experiment 2)


title: Adhered biofilm cells vs Mixed Reference 3

description: 252016610057-block 2

source_name: Adhered Biofilm (experiment 3)

source_name: Mixed reference pool#3: cDNA from 252016610057 - blocks 1 - 5


title: EGF 16 - C7

description:
raw data file 1: EGF162-hy5EGF-hy3N.gpr
raw data file 2 (dye-swap): EGF162-hy5N-hy3EGF.gpr

source_name: Primary Culture


title: OV03-17_Ascites_R1

description:
A891-09
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Ascites_R1

value: ascites

value: relapse

value: partial response


title: TSH 3 - C9

description:
raw data file 1: TSH32-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH32-hy5N-hy3TSH.gpr

value: TSH treated Primary Culture

source_name: Control Cells


title: TSH 3 - C4

description:
raw data file 1: TSH31-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH31-hy5N-hy3TSH.gpr


title: OV04-30_Om_S1

description:
A891-08
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-30, sample Om_S1

value: omentum

value: stable disease


title: Unadhered biofilm cells vs Mixed Reference 1

description: 252016610046-block 4

source_name: Planktonic Unadhered 37 degrees  (experiment 1)


title: liver_hom_rep1

description: replicate 1


title: OV04-21_LOv_S1

description:
A891-07
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV04-21, sample LOv_S1

value: interval debulking surgery


title: TSH 3 - C1

description:
raw data file 1: TSH33-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH33-hy5N-hy3TSH.gpr

value: Non treated primary culture


title: PB CD34+ cells from Healthy Donor Buffy Coat 8 (miEP)

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: Buffy Coat Peripheral Blood CD34+ cells from healthy donor

hyb_protocol: Regarding GEP, fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4). As for miEP, tagged RNA was hybridized to the Affymetrix Genechip miRNA array 2.0 using manufacturer's recommendations (FlashTag™ Biotin HSR RNA Labeling Kit, P/N 703095 Rev. 1). The miRNA arrays were washed and stained by GeneChip Hybridization, Wash and Stain Kit (Affymetrix) with Fluidic Station 450 using fluidic script FS450_003.

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.  Affymetrix Genechip miRNA arrays 2.0 were scanned using the Affymetrix GCS3000 7G Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: CTR Peripheral Blood Buffy Coat CD34+ Cells

label_protocol: Gene expression profiling (GEP) and miRNA expression profiling (miEP) were performed on the same RNA preparation. As regards GEP, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.As for miEP, total RNA (100ng for samples) were labeled using the FlashTag® Biotin HSR kit (Affymetrix).

growth_protocol: CD34+ cells were purified from 30–50 ml of PB collected from PMF patients, from 150 ml of PB from G-CSF untreated healthy donors, or from 5 ml of BM aspirates, all obtained in preservative free heparin.  Mononuclear cells were separated over a Ficoll-Paque gradient (Lympholyte; Cederlane Labs) and processed through two sequential steps of immunomagnetic CD34  selection (Miltenyi Biotec, Bergisch Gladbach,Germany,http://www.miltenyibiotec.com). Purity of the isolated CD34+ cell population was evaluated by flow cytometry after labeling with PE-HPCA2 anti-CD34 monoclonal antibody (BD Biosciences) and was always > 95%.

extract_protocol: CD34+ cells were purified from Peripheral Blood of PMF patients and immediately  lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from CD34+ cells was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations for Purification of Total RNA, Including Small RNAs, from Animal Cells. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: supplier

value: Vannucchi

value: CTR

value: PB CTR

value: neg

value: PB


title: TSH 24 -C4

description:
raw data file 1: TSH242-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH242-hy5N-hy3TSH.gpr


title: OV03-20_Om_S05

description:
A718-28
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_S05


title: OV03-13_Om_S06

description:
A718-25
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-13, sample Om_S06


title: OV03-25_Diaph_B1

description:
A718-26
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-25, sample Diaph_B1

value: diaphragm

value: laparoscopic biopsy


title: PB CD34+ cells from Healthy Donor Buffy Coat 7 (miEP)


title: TSH 24 - C9

description:
raw data file 1: TSH241-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH241-hy5N-hy3TSH.gpr


title: Adhered biofilm cells vs Mixed Reference 1

description: 252016610046-block 3

source_name: Adhered Biofilm  (experiment 1)

tag: source strain background

source_name: Mixed reference pool#1: cDNA from 252016610046 - blocks 1 - 8


title: TSH 16 - C4

description:
raw data file 1: TSH161-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH161-hy5N-hy3TSH.gpr


title: PB CD34+ cells from Healthy Donor Buffy Coat 9 (miEP)


title: liver_wt_rep3

description: replicate 3

source_name: liver

tag: strain

value: wild type

value: 21 weeks

value: male


title: Log phase 30degrees vs Mixed Reference 1

description: 252016610046-block 2

source_name: Planktonic Log Phase 30 degrees  (experiment 1)


title: 24 hour biofilm vs Mixed Reference 1

description: 252016610046-block 6

source_name: 24 hour Biofilm (experiment 1)


title: TSH 16 - C9

description:
raw data file 1: TSH162-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH162-hy5N-hy3TSH.gpr


title: OV03-13_P_B2

description:
A718-23
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-13, sample P_B2

tag: study id

value: ovarian cancer

value: peritoneal


title: Stationary planktonic vs Mixed Reference 1

description: 252016610046-block 1

source_name: Planktonic Stationary Phase 30 degrees (experiment 1)


title: liver_wt_rep2

description: replicate 2

value: liver


title: OV03-25_Om_B1

description:
A718-21
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-25, sample Om_B1

tag: sample id

value: omentum

value: partial response


title: TSH 1.5 - C9

description:
raw data file 1: TSH1.52-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH1.52-hy5N-hy3TSH.gpr

source_name: Primary Culture

value: TSH treated Primary Culture


title: TSH 1.5 - C4

description:
raw data file 1: TSH1.51-hy5TSH-hy3N.gpr
raw data file 2 (dye-swap): TSH1.51-hy5N-hy3TSH.gpr

source_name: Control Cells

value: Non treated primary culture


title: PB CD34+ cells from Healthy Donor Buffy Coat 6 (miEP)

value: Vannucchi

tag: disease


title: PB CD34+ cells from Healthy Donor Buffy Coat 18 (miEP)

value: CTR


title: PB CD34+ cells from Healthy Donor Buffy Coat 17 (miEP)

value: PB CTR


title: PB CD34+ cells from Healthy Donor Buffy Coat 3 (miEP)

value: neg


title: PB CD34+ cells from Healthy Donor Buffy Coat 5 (miEP)

value: PB


title: OV03-04_VV_B2

description:
A718-18
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample VV_B2

value: vaginal vault

tag: timepoint

value: stable disease


title: PB CD34+ cells from Healthy Donor Buffy Coat 2 (miEP)


title: PB CD34+ cells from Healthy Donor Buffy Coat 4 (miEP)


title: 252800415349-5

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: pcDNA3.1 (P375)

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Background correction and quantile normalization, paired differential analysis.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Kit nucleospin RNA II (Macherey Nagel)

treatment_protocol: Lung fibroblasts derived from 4 different IPF patients (P313, P355, P375 and P426) were transiently transfected with pcfoxf1 or control pcDNA3.1-constructs. Total RNAs were extracted 24 h after transfection.

value: Lung fibroblasts

tag: amount in (µg)

value: Idiopathic Pulmonary Fibrosis

tag: rin number


title: 252800415349-2

description: pcFOXF1 (P313)

source_name: pcFOXF1 (P313)


title: 252800415349-1

description: pcDNA3.1 (P313)


title: OV03-20_Om_S04

description:
A718-17
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_S04

value: interval debulking surgery

tag: response to treatment

tag: progression-free survival (months)


title: PTC 54

description:
raw data file 1: PTC54-hy5PTC-hy3N.gpr
raw data file 2 (dye-swap): PTC54-hy5N-hy3PTC.gpr

source_name: Tumor

value: Papillary carcinoma

source_name: Normal Tissue

value: Normal Tissue


title: OV03-10_Om_B01

description:
A718-15
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_B01

value: ovarian cancer

value: ultrasound-guided biopsy


title: OV03-13_Om_S05

description:
A718-13
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-13, sample Om_S05

value: omentum

value: partial response


title: PTC 53

description:
raw data file 1: PTC53-PTChy5-Nhy3.gpr
raw data file 2 (dye-swap): PTC53-Nhy5-PTChy3.gpr


title: PB CD34+ cells from Healthy Donor Buffy Coat 16 (miEP)

source_name: CTR Peripheral Blood Buffy Coat CD34+ Cells


title: PTC 50

description:
raw data file 1: PTC50-hy5PTC-hy3N.gpr
raw data file 2 (dye-swap): PTC50-hy5N-hy3PTC.gpr


title: OV03-25_Pelvic_B1

description:
A718-11
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-25, sample Pelvic_B1

value: pelvic

value: laparoscopic biopsy


title: OV03-20_SBM_S5

description:
A718-10
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample SBM_S5

value: small bowel mesentry


title: OV03-04_Bl_B3

description:
A718-09
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Bl_B3

value: bladder


title: PTC 4

description:
raw data file 1: PTC4-hy5PTC-hy3N.gpr
raw data file 2 (dye-swap): PTC4-hy5N-hy3PTC.gpr


title: PB CD34+ cells from Healthy Donor Buffy Coat 15 (miEP)

value: Vannucchi

value: CTR

value: PB CTR

value: neg


title: PB CD34+ cells from Healthy Donor Buffy Coat 11 (miEP)

value: PB


title: PB CD34+ cells from Healthy Donor Buffy Coat 10 (miEP)


title: 252800415349-4

description: pcFOXF1 (P355)

source_name: pcFOXF1 (P355)

value: Lung fibroblasts

value: Idiopathic Pulmonary Fibrosis


title: PTC 3

description:
raw data file 1: PTC3-hy5PTC-hy3N.gpr
raw data file 2 (dye-swap): PTC3-hy5N-hy3PTC.gpr

value: Papillary carcinoma


title: PB CD34+ cells from Healthy Donor Buffy Coat 14 (miEP)


title: 252800415349-7

description: pcDNA3.1 (P426)


title: PTC 13

description:
raw data file 1: PTC13-hy5PTC-hy3N.gpr
raw data file 2 (dye-swap): PTC13-hy5N-hy3PTC.gpr

value: Normal Tissue


title: OV03-13_Om_S04

description:
A718-06
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-13, sample Om_S04

value: ovarian cancer

value: interval debulking surgery


title: 252800415349-3

description: pcDNA3.1 (P355)


title: OV03-02_Adnexa_B1

description:
A718-05
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-02, sample Adnexa_B1

value: left adnexa


title: 252800415349-8

description: pcFOXF1 (P426)

source_name: pcFOXF1 (P426)


title: PB CD34+ cells from PMF patient PV_47 (miEP)

description: Peripheral Blood CD34+ cells from PMF patient

source_name: PMF Peripheral Blood CD34+ Cells

value: Barosi

value: MPD

value: PMF


title: PB CD34+ cells from Healthy Donor Buffy Coat 1 (miEP)


title: PB CD34+ cells from PMF patient PV_46 (miEP)

value: pos


title: 252800415349-6

description: pcFOXF1 (P375)

source_name: pcFOXF1 (P375)


title: OV03-20_SBM_S4

description:
A718-03
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample SBM_S4

value: small bowel mesentry

value: stable disease


title: PB CD34+ cells from PMF patient PV_41 (miEP)


title: PTC 12

description:
raw data file 1: PTC12-hy5PTC-hy3N.gpr
raw data file 2 (dye-swap): PTC12-hy5N-hy3PTC.gpr


title: FTC 130

description:
raw data file 1: FTC130-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC130-hy5N-hy3FTC.gpr

value: Follicular carcinoma


title: PTC 5

description:
raw data file 1: PTC5-hy5PTC-hy3N.gpr
raw data file 2 (dye-swap): PTC5-hy5N-hy3PTC.gpr


title: OV03-08_Om_S20

description:
A636-23
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S20

value: omentum

value: partial response


title: FTC 125

description:
raw data file 1: FTC125-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC125-hy5N-hy3FTC.gpr


title: OV03-08_Om_S18

description:
A636-20
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S18


title: OV03-08_Om_S17

description:
A636-19
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S17


title: OV03-08_Ascites_R1

description:
A636-24
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Ascites_R1

value: ascites

value: relapse


title: OV03-08_Om_S16

description:
A636-18
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S16


title: FTC 114

description:
raw data file 1: FTC114-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC114-hy5N-hy3FTC.gpr

source_name: Tumor

source_name: Normal Tissue


title: ATC 15

description:
raw data file 1: ATC15-ATChy5-Nhy3.gpr
raw data file 2 (dye-swap): ATC15-Nhy5-ATChy3.gpr

value: Anaplastic carcinoma


title: OV03-08_Om_S15

description:
A636-17
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S15


title: ATC 24

description:
raw data file 1: ATC24-hy5ATC-hy3N.gpr
raw data file 2 (dye-swap): ATC24-HY5N-hy3ATC.gpr


title: OV03-08_Om_S14

description:
A636-16
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S14


title: FTC 122

description:
raw data file 1: FTC122-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC122-hy5N-hy3FTC.gpr


title: PB CD34+ cells from PMF patient BG_6 (miEP)

value: Rambaldi

value: neg

value: PB


title: PB CD34+ cells from PMF patient PV_40 (miEP)


title: PB CD34+ cells from PMF patient BG_7 (miEP)


title: OV03-08_Om_S19

description:
A636-21
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S19

value: ovarian cancer

value: interval debulking surgery


title: PB CD34+ cells from PMF patient PV_12 (miEP)

value: Barosi


title: OV03-08_Om_S13

description:
A636-15
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S13


title: FTC 117

description:
raw data file 1: FTC117-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC117-hy5N-hy3FTC.gpr

value: Normal Tissue


title: OV03-08_SBM_S2

description:
A636-22
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample SBM_S2


title: PB CD34+ cells from PMF patient PV_27 (miEP)

value: MPD

value: PMF


title: ATC 22

description:
raw data file 1: ATC22-ATChy5-Nhy3.gpr
raw data file 2 (dye-swap): ATC22-Nhy5-ATC-hy3.gpr


title: FTC 119

description:
raw data file 1: FTC119-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC19-hy5N-hy3FTC.gpr


title: ATC 23

description:
raw data file 1: ATC23-ATChy5-Nhy3.gpr
raw data file 2 (dye-swap): ATC23-Nhy5-ATChy3.gpr


title: FTC 116

description:
raw data file 1: FTC116-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC116-hy5N-hy3FTC.gpr


title: OV03-08_Om_S12

description:
A636-14
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S12


title: ATC 21

description:
raw data file 1: ATC21-ATChy5-Nhy3.gpr
raw data file 2 (dye-swap): ATC21-Nhy5-ATC-hy3.gpr


title: PB CD34+ cells from PMF patient BG_5 (miEP)

value: pos


title: PB CD34+ cells from PMF patient PV_22 (miEP)


title: OV03-08_Om_S11

description:
A636-13
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S11


title: OV03-08_RPG_S3

description:
A636-25
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample RPG_S3

value: right paracolic gutter


title: OV03-08_Om_S10

description:
A636-12
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S10


title: OV03-08_Om_S09

description:
A636-11
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S09


title: FTC 123

description:
raw data file 1: FTC123-hy5FTC-hy3N.gpr
raw data file 2 (dye-swap): FTC123-hy5N-hy3FTC.gpr

value: Follicular carcinoma


title: OV03-08_Om_S08

description:
A636-10
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S08

value: omentum


title: PB CD34+ cells from PMF patient 5835 (miEP)

source_name: PMF Peripheral Blood CD34+ Cells

value: Vannucchi


title: PB CD34+ cells from PMF patient 5848 (miEP)


title: OV03-08_Om_S07

description:
A636-09
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S07

value: partial response


title: ATC 17

description:
raw data file 1: ATC17-ATChy5-Nhy3.gpr
raw data file 2 (dye-swap): ATC17-Nhy5-ATChy3.gpr


title: ATC 16

description:
raw data file 1: ATC16-ATChy5-Nhy3.gpr
raw data file 2 (dye-swap): ATC16-Nhy5-ATChy3.gpr


title: OV03-08_Om_S06

description:
A636-08
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S06


title: ATC 14

description:
raw data file 1: ATC14-hy5ATC-hy3N.gpr
raw data file 2 (dye-swap): ATC14-hy5N-hy3ATC.gpr


title: ATC 12

description:
raw data file 1: ATC12-ATChy5-Nhy3.gpr
raw data file 2 (dye-swap): ATC12-Nhy5-ATChy3.gpr


title: ATC 11

description:
raw data file 1: ATC11-hy5ATC-hy3N.gpr
raw data file 2 (dye-swap): ATC11-hy5N-hy3ATC.gpr


title: PB CD34+ cells from PMF patient PV_13 (miEP)

description: Peripheral Blood CD34+ cells from PMF patient


title: PB CD34+ cells from PMF patient BG_2 (miEP)


title: PB CD34+ cells from PMF patient 5807 (miEP)


title: OV03-08_Om_S05

description:
A636-07
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S05


title: ATC 13

description:
raw data file 1: ATC13-hy5ATC-hy3N.gpr
raw data file 2 (dye-swap): ATC13-hy5N-hy3ATC.gpr

source_name: Tumor


title: PB CD34+ cells from PMF patient PV_29 (miEP)


title: HN 78

description:
raw data file 1: AA78-AAHy5-NTHy3.gpr
raw data file 2 (dye-swap): AA78-NTHy5-AAHy3.gpr

value: Autonomous adenoma

source_name: Normal Tissue


title: HN 75

description:
raw data file 1: AA75-AAHy5-NTHy3.gpr
raw data file 2 (dye-swap): AA75-NTHy5-AAHy3.gpr


title: 8 hour biofilm vs Mixed Reference 1

description: 252016610046-block 5

source_name: 8 hour Biofilm  (experiment 1)

source_name: Mixed reference pool#1: cDNA from 252016610046 - blocks 1 - 8


title: OV03-08_Om_B02

description:
A636-05
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_B02

value: biopsy


title: PB CD34+ cells from PMF patient 5775 (miEP)


title: HN 71

description:
raw data file 1: AA71-AAHy5-NTHy3.gpr
raw data file 2 (dye-swap): AA71-NTHy5-AAHy3.gpr


title: PB CD34+ cells from PMF patient 5793 (miEP)


title: PB CD34+ cells from PMF patient 5776 (miEP)


title: OV03-08_Ov_S1

description:
A636-04
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Ov_S1

value: right ovary


title: OV03-08_Om_S03

description:
A636-03
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S03


title: OV03-08_Om_S02

description:
A636-02
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S02


title: OV03-08_Om_B01

description:
A636-01
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_B01


title: OV03-21_Om_S09

description:
A594-120
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S09


title: OV03-17_Om_B1

description:
A594-119
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_B1

value: laparoscopic biopsy


title: HN 68

description:
raw data file 1: AA68-AAHy5-NTHy3.gpr
raw data file 2 (dye-swap): AA68-NTHy5-AAHy3.gpr


title: PB CD34+ cells from PMF patient 5786 (miEP)

value: PB


title: HN 67

description:
raw data file 1: AA67-AAHy5-NTHy3.gpr
raw data file 2 (dye-swap): AA67-NTHy5-AAHy3.gpr


title: PB CD34+ cells from PMF patient 5767 (miEP)


title: OV03-08_Om_S04

description:
A636-06
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S04

value: ovarian cancer


title: OV03-22_Om_B04

description:
A594-118
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-22, sample Om_B04


title: PB CD34+ cells from PMF patient 5782 (miEP)

source_name: PMF Peripheral Blood CD34+ Cells


title: HN 61

description:
raw data file 1: AA61-AAHy5-NTHy3.gpr
raw data file 2 (dye-swap): AA61-NTHy5-AAHy3.gpr


title: PB CD34+ cells from PMF patient 5760 (miEP)


title: PB CD34+ cells from PMF patient 5757 (miEP)


title: HN 70

description:
raw data file 1: AA70-AAHy5-NTHy3.gpr
raw data file 2 (dye-swap): AA70-NTHy5-AAHy3.gpr


title: OV03-21_P_B1

description:
A594-116
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample P_B1

value: peritoneal


title: PB CD34+ cells from PMF patient 5733 (miEP)


title: OV03-08_RPG_S2

description:
A594-117
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample RPG_S2

value: interval debulking surgery


title: PB CD34+ cells from PMF patient 5715 (miEP)

value: neg


title: PB CD34+ cells from PMF patient 5719 (miEP)

value: MPD


title: PB CD34+ cells from PMF patient 5578 (miEP)

value: PMF


title: PB CD34+ cells from PMF patient 5724 (miEP)

value: pos


title: K562-pcDNA-ETO2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: K562 cells were maintained with RPMI-1640 containing 10% fetal bovine serum and 1% penicillin-streptomycin

extract_protocol: Total RNA was extracted with Trizol according to manufacture's instructions

treatment_protocol: In K562 cells, 10ug of pcDNA or pcDNA-ETO2 was transfected with amaxa nucleofector, at 0h and 24h.

tag: cell line

tag: transfection

value: K562 cells transfected with pcDNA-ETO2

value: hematopoietic cells


title: OV03-10_Om_S07

description:
A594-114
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_S07

tag: tissue

value: omentum

value: stable disease


title: OV03-13_Om_S03

description:
A594-111
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-13, sample Om_S03

value: partial response


title: OV03-20_Om_B03

description:
A594-113
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_B03


title: OV03-22_Om_B03

description:
A594-108
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-22, sample Om_B03


title: OV03-20_Om_B02

description:
A594-109
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_B02


title: K562 ETO2 siRNA

source_name: ETO2 siRNA

treatment_protocol: In K562 cells, 240pmol of control or ETO2 siRNA was transfected with amaxa nucleofector, at 0h and 24h.

value: K562 cells transfected with ETO2 siRNA


title: PB CD34+ cells from PMF patient 5408 (miEP)

value: Vannucchi


title: PB CD34+ cells from PMF patient 5566 (miEP)


title: K562-pcDNA

source_name: pcDNA

value: K562 cells transfected with pcDNA control


title: OV03-20_P_S1

description:
A594-106
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample P_S1

value: parietal peritoneum


title: PB CD34+ cells from PMF patient 5396 (miEP)

value: PB


title: PB CD34+ cells from PMF patient 5196 (miEP)


title: PB CD34+ cells from PMF patient 5415 (miEP)


title: PB CD34+ cells from PMF patient 5035 (miEP)


title: PB CD34+ cells from PMF patient 5024 (miEP)


title: OV03-17_Ov_B1

description:
A594-104
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Ov_B1

value: ovarian cancer

value: surface of ovary

value: laparoscopic biopsy


title: Strain Y2209 (LEP) Replicate 1

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

department: Biology

institute: Dickinson College

description: Biological replicate 1 of 2.

hyb_protocol: Arrays were hybridized in a NimbleGen hybridization system 12 (BioMicro) following the standard NimbleGen

scan_protocol: Arrays were scanned using a GenePix 4000B scanning laser (Molecular Devices) following the standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al.  (2004) Genome Biol 5: R80).  The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of gDNA for each strain versus the genomic DNA control (Cy5/Cy3).  Gene-level copy number changes were summarized with the median value of each probe set contained completely within each predicted ORF.

organism: Saccharomyces cerevisiae

source_name: Strain Y2209 (LEP) gDNA from log-phase culture

label_protocol: Samples were labeled using amino-allyl dUTP (Ambion), Klenow exo-polymerase (New England Biolabs), and random hexamers, and coupled with cyanine dyes (Amersham).

growth_protocol: Each strain was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase.  Cells were collected by centrifugation at OD600 1.0 - 2.0.

extract_protocol: gDNA was obtained with phenol/chloroform extraction and isoamyl alcohol precipitation.

source_name: Strain DBY8268 gDNA from log-phase culture


title: PB CD34+ cells from PMF patient PV_21 (miEP)

value: Barosi


title: Strain Y2209 (LEP) Replicate 2

description: Biological replicate 2 of 2.


title: Strain Y389 (MUSH) Replicate 2

description: Biological replicate 2 of 2.

source_name: Strain Y389 (MUSH) gDNA from log-phase culture

value: Y389 (MUSH)


title: PB CD34+ cells from PMF patient 5017 (miEP)

value: MPD

value: PMF

value: neg


title: K562-control siRNA

source_name: control siRNA

value: K562 cells transfected with control siRNA

value: hematopoietic cells


title: OV03-21_Om_S08

description:
A594-103
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S08

value: omentum

value: interval debulking surgery


title: OV03-01_P_B09

description:
A594-102
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B09

value: peritoneal

value: partial response


title: OV03-10_Om_S06

description:
A594-101
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_S06

value: stable disease


title: OV03-01_P_B10

description:
A594-105
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B10


title: PB CD34+ cells from PMF patient 5008 (miEP)

source_name: PMF Peripheral Blood CD34+ Cells

value: Vannucchi

value: pos


title: breast carcinoma MDA-MB-231 cells were co-transfected with myocardin and ERα rep2

city: Wuhan

first: da

middle: lin

last: lu

address: Wuhan university of science and tecnology

country: China

institute: Wuhan university of science and technology

hyb_protocol: Following fragmentation, 1 ug RNA were hybridized for 16 hr at 48C on GeneChip  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

source_name: mammary gland

label_protocol: Biotinylated microRNA were prepared according to the standard Affymetrix protocol from 1000ng total RNA (Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kits).

growth_protocol: Breast carcinoma cells were grown in Dulbecco’s modified Eagle’s medium (GIBCO) supplemented with 10% fetal bovine serum at 37℃ in a 5% CO2 incubator.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions(QIAGEN miRNAeasy Mini Kit).

treatment_protocol: MDA-MB-231 breast carcinoma cells were separately transfected with myocardin, ERα，myocardin+ERα and pcDNA3.1

value: co-transfected with myocardin and ERα


title: Strain YB-210 (CRB) Replicate 2

description: Biological replicate 2 of 2.

source_name: Strain YB-210 (CRB) gDNA from log-phase culture


title: breast carcinoma MDA-MB-231 cells were co-transfected with myocardin and ERα rep1


title: Strain Y389 (MUSH) Replicate 1

description: Biological replicate 1 of 2.


title: Strain YB-210 (CRB) Replicate 1

description: Biological replicate 1 of 2.


title: breast carcinoma MDA-MB-231 cells were transfected with ERα rep2

value: transfected with ERα


title: OV03-17_Om_S8

description:
A594-096
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S8

value: ovarian cancer


title: OV03-21_Om_S06

description:
A594-097
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S06


title: OV03-21_Om_S07

description:
A594-099
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S07


title: PB CD34+ cells from PMF patient 4771 (miEP)

value: PB


title: PB CD34+ cells from PMF patient 4831 (miEP)


title: PB CD34+ cells from PMF patient 5005 (miEP)


title: breast carcinoma MDA-MB-231 cells were co-transfected with myocardin and ERα rep3


title: OV03-22_Pelvis_B1

description:
A594-092
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-22, sample Pelvis_B1

value: right pelvis

value: laparoscopic biopsy


title: OV03-20_Om_S03

description:
A594-088
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_S03


title: OV03-13_P_B1

description:
A594-091
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-13, sample P_B1


title: OV03-17_Om_S7

description:
A594-094
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S7


title: breast carcinoma MDA-MB-231 cells were transfected with myocardin rep 3

value: transfected with myocardin


title: OV03-17_Om_S6

description:
A594-090
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S6


title: OV03-17_Om_S5

description:
A594-086
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S5


title: breast carcinoma MDA-MB-231 cells were transfected with ERα rep3


title: OV03-01_P_B07

description:
A594-084
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B07


title: OV03-04_VV_B1

description:
A594-082
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample VV_B1

value: vaginal vault


title: OV03-01_P_B08

description:
A594-085
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B08


title: OV03-21_Om_S05

description:
A594-079
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S05


title: breast carcinoma MDA-MB-231 cells were transfected with ERα rep1


title: OV03-08_RPG_S1

description:
A594-080
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample RPG_S1

value: right paracolic gutter


title: OV03-22_Ov_B1

description:
A594-078
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-22, sample Ov_B1

value: left ovary


title: OV03-01_P_B06

description:
A594-077
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B06


title: breast carcinoma MDA-MB-231 cells were transfected with myocardin rep 2

source_name: mammary gland


title: breast carcinoma MDA-MB-231 cells were transfected with myocardin rep 1


title: breast carcinoma MDA-MB-231 cells were transfected with pcDNA3.1 as control rep 2

value: transfected with pcDNA3.1 as control


title: OV03-22_Om_B02

description:
A594-076
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-22, sample Om_B02

value: omentum


title: breast carcinoma MDA-MB-231 cells were transfected with pcDNA3.1 as control rep 1


title: breast carcinoma MDA-MB-231 cells were transfected with pcDNA3.1 as control rep 3


title: OV03-04_Bl_B1

description:
A594-073
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Bl_B1

value: bladder


title: OV03-10_Om_S04

description:
A594-072
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_S04

value: interval debulking surgery


title: OV03-10_Om_S05

description:
A594-074
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_S05

value: stable disease


title: OV03-20_Om_S02

description:
A594-071
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_S02


title: OV03-17_Om_S4

description:
A594-069
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S4

value: partial response


title: OV03-13_Om_S02

description:
A594-068
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-13, sample Om_S02

value: ovary


title: OV03-07_P_B01

description:
A594-063
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-07, sample P_B01

value: peritoneal


title: tCNT4h.0h [A25 2-4+8]

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Pool19+Pool20_US23502401_252800516534_S01_GE2_1100_Jul11_1_2.txt

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays, , according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

source_name: tangled carbon nanotubes 4h.0h

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Female C57BL/6 mice (7-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.

extract_protocol: RNA isolation from the lung samples was done with TRIsure and the quantity and purity was determined by NanoDrop spectrophotometer. Further quality check of the total RNA was performed with the Agilent BioAnalyzer, according to the manufacturer's recommendations.

treatment_protocol: Nanomaterials were aerosolized with a fluidized bed aerosol generator, Mice were placed inside the exposure chamber and moved back to animal room after 4 h exposure. The animals were sacrified immediately after exposure or after 24h.

value: lung

tag: mice

value: Female

tag: time point

value: 4 h exposure


title: UT [A25 1-7+8]

description: Pool15+Pool16_US23502401_252800516533_S01_GE2_1100_Jul11_2_4.txt

source_name: untreated

value: Untreated


title: OV03-10_Om_S03

description:
A594-066
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_S03

value: ovarian cancer


title: OV03-21_Om_S03

description:
A594-064
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S03


title: UT [A25 1-5]

description: Pool11+Pool12_US23502401_252800516533_S01_GE2_1100_Jul11_2_2.txt


title: tCNT4h.24h [A22 1-3+2]

source_name: tangled carbon nanotubes 4h.24h

value: 4 h exposure, sacrifice after 24 h


title: tCNT4h.24h [A221-5+6]

description: Pool9+Pool10_US23502401_252800516533_S01_GE2_1100_Jul11_2_1.txt


title: rCNT4h.24h [A23 1-1+9]

description: Pool23+Pool24_US23502401_252800516534_S01_GE2_1100_Jul11_1_4.txt

source_name: rigid rod-like carbon nanotubes 4h.24h


title: OV03-01_P_B05

description:
A594-062
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B05

value: laparoscopic biopsy


title: UT [A25 1-2+3]

description: Pool17+Pool18_US23502401_252800516534_S01_GE2_1100_Jul11_1_1.txt


title: rCNT 4h.0h [A23 5-7+3]

description: Pool21+Pool22_US23502401_252800516534_S01_GE2_1100_Jul11_1_3.txt

source_name: rigid rod-like carbon nanotubes  4h.0h


title: OV03-20_SBM_S3

description:
A594-067
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample SBM_S3

value: small bowel mesentry


title: rCNT4h.24h [A23 1-3+5]

description: Pool13+Pool14_US23502401_252800516533_S01_GE2_1100_Jul11_2_3.txt


title: tCNT4h.0h [A25 2-3+5]

description: Pool5+Pool6_US23502401_252800516533_S01_GE2_1100_Jul11_1_3.txt


title: rCNT4h.24h [A23 1-7+8]

description: Pool1+Pool2_US23502401_252800516533_S01_GE2_1100_Jul11_1_1.txt


title: tCNT4h.0h [A25 2-2+6]


title: UT [A25 1-4+6]


title: rCNT 4h.0h [A23 5-6+4]

description: Pool7+Pool8_US23502401_252800516533_S01_GE2_1100_Jul11_1_4.txt


title: rCNT4h.24h [A23 1-6+4]


title: rCNT 4h.0h [A23 5-8+9]


title: 557289A12 - oxi1_stress_BR2 vs oxi1_control_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Transcriptomic analysis on the effect of oxi1 mutation under high light stress?

hyb_protocol: oxi1_control_BR2 Cy5 / oxi1_stress_BR2 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media=Soil Temperature=24°C/18°C Light=16h light/8h night

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype/variation

value: mutant (oxi1)

tag: dev.stage (boyes et al. plant cell 2001)

treatment_protocol: Name:high light and low temperature - abiotic stress - light and temperature,light and temperature:time 25hour . 5 weeks old mutant (oxi1) and wild type (WT) plants were exposed to high light and low temperature (1300-1350 µmol photons m-2s-1, 7°C/14°C day/night and 380ppm CO2) for 25 hours. ~100 mg fresh weight leaves were harvested, and total RNA prepared from them.


title: 557289A11 - oxi1_control_BR2 vs oxi1_stress_BR2

hyb_protocol: oxi1_stress_BR2 Cy5 / oxi1_control_BR2 Cy3 : 30pmol.


title: OV03-22_Om_B01

description:
A594-060
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-22, sample Om_B01

value: omentum


title: rCNT 4h.0h [A23 5-5+2]

tag: strain


title: OV03-17_Om_S3

description:
A594-059
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S3

tag: study id


title: OV03-01_P_B04

description:
A594-058
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B04

tag: sample id


title: OV03-23_Om_B01

description:
A594-057
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-23, sample Om_B01

tag: disease

value: ultrasound-guided biopsy


title: 557289A10 - oxi1_stress_BR1 vs oxi1_control_BR1

hyb_protocol: oxi1_control_BR1 Cy5 / oxi1_stress_BR1 Cy3 : 30pmol.


title: tCNT4h.0h [A25 2-1+7]

description: Pool3+Pool4_US23502401_252800516533_S01_GE2_1100_Jul11_1_2.txt


title: OV03-01_P_B03

description:
A594-055
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B03

tag: timepoint


title: Notch_CFU_Gfi1KO-4

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

description: Gene expression after 1 week in 4-OHT containing methylcellulose

hyb_protocol: Samples were hybridized to the SurePrint G3 Mouse GE 8x60K Microarray (AMADID 028005).

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner.

data_processing: The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.10 (FE). This data is stored in the FE '.txt' files. Reading in the FE extraction files and extraction the median intensity values for each probe on the array. These intensities are not background corrected (this has been shown to only introduce noise), but are corrected for any scanner offset that was added to the original raw values. The dataset was filtered to remove positive control elements and any elements that have been flagged as outliers. Present (P), Marginal (M) or Absent (A) calls were made for each element on the array using in-house methodologies that take into account both the results of FE probe detection statistics and the intensities of the negative controls elements on the array. The median green (Cy3) intensities were normalized between the arrays using the Quantile Normalization package in 'R' (Bolstad et al., 2003).

source_name: Lin- BM

label_protocol: Sample labeling and hybridization was performed according to the manufacturer's protocols using the One-Color Microarray-Based Gene Expression Analysis Manual (Low Input Quick Amp Version).

growth_protocol: Cells were flushed from tibias, femurs and iliac crests using PBS with 2% FBS and 1mM EDTA, lineage depleted using magnetic beads and put into StemSpan serum free media with cytokine support.  Two days later, cells were transduced with MigR1-Notch1IC-GFP retroviral supernatants and FACS sorted 72 hours later.  GFP+ cells were placed in methylcellulose for 7 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the Qiagen RNeasy kit following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer Lab-On-A-ChIP Agilent 6000 Series II (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After 7 days, CFU were disrupted, counted and replated in 4-OHT (1uM) containing methylcellulose for an additional 7 days at 37 ºC in a humidified incubator with 5% CO2.

tag: notch1 status

tag: gfi1 ex4-5 status

value: KO


title: OV03-02_Pelvic_B1

description:
A594-049
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-02, sample Pelvic_B1

value: pelvic

tag: response to treatment


title: OV03-10_Om_S02

description:
A594-056
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_S02

value: interval debulking surgery

value: stable disease

tag: progression-free survival (months)


title: 557289A09 - oxi1_control_BR1 vs oxi1_stress_BR1

hyb_protocol: oxi1_stress_BR1 Cy5 / oxi1_control_BR1 Cy3 : 30pmol.


title: VE14089ΔluxS with DPD rep2

city: Oeiras

first: Neuza

last: Teixeira

address: Av. da República, Estação Agronómica Nacional

country: Portugal

institute: ITQB

description: VE14089ΔluxS with DPD

hyb_protocol: standard NimbleGen Protocol

scan_protocol: GeneChips were scanned at the University of Iowa DNA Core Facility.

data_processing: standard NimbleGen Protocol

organism: Enterococcus faecalis V583

source_name: VE14089ΔluxS with DPD

label_protocol: Biotinylated cRNA were prepared with the BioArray Terminal Labeling Kit (Enzo Life Sciences).

growth_protocol: E. faecalis strains were grown in BHI, at 37ºC, until 0.4 OD (600nm). At this point, purified GBAP was added to a final concentration of 10nM in the culture. For others samples we did the same protocol but without GBAP.

extract_protocol: RNA was stabilized with RNA protect (Qiagen) and RNA was isolated with RNeasy columns per the manufacturer's instructions (Qiagen). Samples were treated with RNase-free DNase I (Roche) to remove contaminating DNA

value: E. faecalis V583

tag: genotype

tag: treatment

value: DPD


title: OV03-08_SBM_S1

description:
A594-054
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample SBM_S1

tag: tissue

value: partial response


title: Notch_CFU_Gfi1WT-3

value: WT


title: OV03-20_RPG_S1

description:
A594-048
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample RPG_S1

value: right paracolic gutter


title: Notch_CFU_Gfi1WT-4


title: VE14089ΔluxS rep2


title: 557289A08 - oxi1_stress_BR2 vs WT_stress_BR2

hyb_protocol: WT_stress_BR2 Cy5 / oxi1_stress_BR2 Cy3 : 30pmol.

value: wildtype


title: VE14089ΔluxS with DPD rep1

description: VE14089ΔluxS with DPD


title: 557289A03 - WT_control_BR2 vs oxi1_control_BR2

hyb_protocol: oxi1_control_BR2 Cy5 / WT_control_BR2 Cy3 : 30pmol.


title: Notch_CFU_Gfi1KO-1


title: OV03-08_Om_S01

description:
A594-047
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-08, sample Om_S01

value: ovarian cancer


title: Notch_CFU_Gfi1KO-2


title: 557289A05 - WT_stress_BR1 vs oxi1_stress_BR1

hyb_protocol: oxi1_stress_BR1 Cy5 / WT_stress_BR1 Cy3 : 30pmol.


title: 557289A02 - oxi1_control_BR1 vs WT_control_BR1

hyb_protocol: WT_control_BR1 Cy5 / oxi1_control_BR1 Cy3 : 30pmol.


title: 557289A01 - WT_control_BR1 vs oxi1_control_BR1

hyb_protocol: oxi1_control_BR1 Cy5 / WT_control_BR1 Cy3 : 30pmol.


title: 557289A06 - oxi1_stress_BR1 vs WT_stress_BR1

hyb_protocol: WT_stress_BR1 Cy5 / oxi1_stress_BR1 Cy3 : 30pmol.


title: VE14089ΔluxS rep1


title: Notch_CFU_Gfi1WT-2


title: Notch_CFU_Gfi1KO-3


title: OV03-20_SBM_S2

description:
A594-046
Hybridised to SNP 6.0 array.

hyb_protocol: Hybridisation was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

source_name: Ovarian cancer patient OV03-20, sample SBM_S2


title: 557289A04 - oxi1_control_BR2 vs WT_control_BR2

hyb_protocol: WT_control_BR2 Cy5 / oxi1_control_BR2 Cy3 : 30pmol.


title: OV03-21_Om_S02

description:
A594-045
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S02


title: OV03-20_Om_S01

description:
A594-043
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_S01


title: Notch_CFU_Gfi1WT-1


title: VE14089 rep2


title: Patient replicate HV10

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV10
high grade serous ovarian cancer specimen from a high-volume ascites case

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (Genome Studio Version 2011.1)

data_processing: The data were normalised using quantile normalisation in Genespring (version 12.1) followed by median centered normalization

label_protocol: Biotinylated cDNA were prepared with the Illumina 96 RNA prep Kit (LifeTech)

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

tag: tumour stage

value: Stage III-IV

tag: ascites volume

value: >= 1000cc measured ascites volume

value: Snap-frozen tissue specimen containing > 70% tumour


title: OV03-20_SBM_S1

description:
A594-040
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample SBM_S1

value: small bowel mesentry


title: OV03-20_Om_B01

description:
A594-038
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-20, sample Om_B01

value: omentum

value: laparoscopic biopsy


title: Brd4 siRNA, biological rep3

city: Philadelphia

first: Jianxin

last: You

address: 3610 Hamilton Walk

department: Department of Microbiology

institute: University of Pennsylvania Perelman School of Medicine

description:
Gene expression data from Brd4 siRNA
Reagents, Vendors, CatalogNumbers:
Knockout DMEM/F12 medium, Life technologies, 12660-012
N-2 supplement, Life technologies, 17502-048
B27 Supplement Minus Vitamin A, Life technologies, 12587-010
Bovine Albumin Fraction V (7.5% solution), Life technologies, 15260-037
GlutaMAX , Life technologies, 35050-061
Ambion WT Expression Kit, Life technologies, 4411973
human BMP4 , R&D systems, 314-BP-010
ESGRO® Leukemia Inhibitory Factor (LIF), Millipore, ESG1107
EmbryoMax® 0.1% Gelatin Solution, Millipore, ES-006-B
1-thioglycerol , Sigma, M6145
PD173074, Sigma, P2499
Genechip WT Terminal Labeling Kit, Affymetrix, 900670

hyb_protocol: Following fragmentation and labeled, samples were hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix) in a GeneChip Hyb Oven 640 (Affymetrix) for 16 hours at 45C. Arrays were washed and stained using the GeneChip Hyb, Wash and Stain kit (Affymetrix) with a GeneChip Fluidics Station 450 (Affymetrix) according to standard protocol.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix), and image processing was performed using AGCC version 3.1.

data_processing: For data procession, We used the CEL files (after the chip is scanned)analyzed by Affymetrix Expression Console Software (new version) to create the Intensity QC and CHP File.RMA from Affymetrix package  was applied to the data for preprocessing and normalization. Limma was used for detection of differentially expressed genes. Benjamini & Hochberg correction was applied for the multiple comparisons.

source_name: Embryonic stem cells

label_protocol: Microarray target preparation from total RNA (250ng/each sample for input) was done using Ambion WT Expression Kit(Life Technologies) following standard Affymetrix protocol. Sense strand cDNA (5.5ug) was fragmented and labeled using Genechip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mouse TL1 ESCs were maintained feeder-free on gelatin-coated tissue culture dishes in Knockout DMEM/F12 medium (Life technologies) with 0.5% N-2 supplement (Life technologies), 1% B27 supplement Minus vitamin A (Life technologies), 0.05% BSA (Life technologies), 1% GlutaMAX (Life technologies), 10 ng/ml human BMP4 (R&D systems), 1000 U/ml LIF (Millipore), 1.5x10-4 M 1-thioglycerol (Sigma), 100 nM FGF receptor inhibitor PD173074 (Sigma).

extract_protocol: At 48 h post-transfection, total RNAs were isolated using the RNeasy minikit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: TL1 ESCs were transfected with control siRNA, or Brd4 siRNA. At 18h post-transfection, the medium was changed to ESC medium without FGF receptor inhibitor PD173074 (Sigma)

tag: cell type

value: ESC

value: Brd4 loss


title: Brd4 siRNA, biological rep2

tag: genotype/variation


title: VE14089 rep1


title: OV03-01_P_B02

description:
A594-037
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B02

value: peritoneal


title: Control siRNA, biological rep1

description:
Gene expression data from control siRNA
Reagents, Vendors, CatalogNumbers:
Knockout DMEM/F12 medium, Life technologies, 12660-012
N-2 supplement, Life technologies, 17502-048
B27 Supplement Minus Vitamin A, Life technologies, 12587-010
Bovine Albumin Fraction V (7.5% solution), Life technologies, 15260-037
GlutaMAX , Life technologies, 35050-061
Ambion WT Expression Kit, Life technologies, 4411973
human BMP4 , R&D systems, 314-BP-010
ESGRO® Leukemia Inhibitory Factor (LIF), Millipore, ESG1107
EmbryoMax® 0.1% Gelatin Solution, Millipore, ES-006-B
1-thioglycerol , Sigma, M6145
PD173074, Sigma, P2499
Genechip WT Terminal Labeling Kit, Affymetrix, 900670

value: control


title: Control siRNA, biological rep2


title: Control siRNA, biological rep3


title: Patient replicate HV9

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV9
high grade serous ovarian cancer specimen from a high-volume ascites case


title: Alkanethiol/lipid Au NP treated HDF cells sample 1

city: Urbana

first: Elissa

middle: M

last: Grzincic

state: Illinois

address: A510 Chemical and Life Sciences Laboratory, 601 S. Goodwin Ave.

department: Chemistry

institute: University of Illinois at Urbana-Champaign

description:
Gene expression data from human dermal fibroblasts exposed to alkanethiol/lipid-coated gold nanoparticles
raw data file: slide4_D.gpr

hyb_protocol: Samples were hybridized in an Agilent Hybridization Cassette according to standard protocols.

scan_protocol: Scanned on an Axon GenePix 4000B scanner; Images were quantified using Axon GenePix 6.1.

data_processing: Median foreground intensites (no background subtraction) were normalized in R (version 3.0.1) using the quantile method in limma (version 3.16.7) for a separate channel analysis . Spots with -100 flags were weighted zero before normalization.

source_name: HDF, ATL, sample 1

label_protocol: 0.2 microgram of total RNA was labeled using the Agilent two color QuickAmp labeling kit according to the manufacturers protocol. The optional spike-in controls were not used.

growth_protocol: Standard mammalian cell culture methods

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

treatment_protocol: Cells were plated to confluency and then exposed to media containing no nanoparticles (untreated), or 20 nm gold nanoparticles surface-coated with citrate (CIT), alkanethiol/lipid (ATL, where C18SH covers the nanoparticle surface and forms a bilayer with 1:1 (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine: 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine) lipid solution), poly(allylamine hydrochloride) (PAH), or poly(allylamine hydrochloride)/lipid (PAHL, where the particle is coated with PAH first, followed by the formation of a 1:1 lipid bilayer on top of the PAH). HDF cells were treated with media containing 0.1 nM nanoparticles for 24-48 hours, and PC3 cells were treated with media containing 1 nM nanoparticles for 24-48 hours.

value: human dermal fibroblasts

tag: cell line

value: HDF

value: 0.1 nM alkanethiol/lipid-coated 20 nm gold nanoparticles


title: Patient replicate LV9

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV9
high grade serous ovarian cancer specimen from a low-volume ascites case

value: <= 200cc measured ascites volume


title: Patient replicate HV8

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV8
high grade serous ovarian cancer specimen from a high-volume ascites case


title: OV03-22_Ov_S1

description:
A594-036
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-22, sample Ov_S1

value: left ovary

value: interval debulking surgery

value: partial response


title: Patient replicate LV8

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV8
high grade serous ovarian cancer specimen from a low-volume ascites case

value: Stage III-IV


title: Brd4 siRNA, biological rep1

tag: strain


title: Patient replicate LV7

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV7
high grade serous ovarian cancer specimen from a low-volume ascites case


title: Patient replicate HV7

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV7
high grade serous ovarian cancer specimen from a high-volume ascites case

value: >= 1000cc measured ascites volume


title: OV03-01_P_B01

description:
A594-035
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample P_B01

tag: study id

value: ovarian cancer


title: OV03-17_Om_S2

description:
A594-034
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S2

tag: sample id


title: Poly(allylamine hydrochloride)/lipid Au NP treated PC3 cells sample 2

description:
Gene expression data from human prostate carcinoma exposed to poly(allylamine hydrochloride)/lipid-coated gold nanoparticles
raw data file: slide4_D.gpr

source_name: PC3, PAHL, sample 2

value: human prostate carcinoma cells

value: 1 nM poly(allylamine hydrochloride)/lipid-coated 20 nm gold nanoparticles


title: SUM159-spino2d

city: Graz

last: Pichler

address: Auenbruggerplatz 15

department: Internal medicine, Division of Oncology

country: Austria

institute: Medical University of Graz

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing: Affymetrix Genexpression Console (2.3) using Affymetrix default analysis settings for generation of CEL-files.  Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization)

source_name: SUM159 with silenced spinophilin

label_protocol: NuGen Applause WT-Amp Plus ST System (M01199v2-1); Encore Biotin Module (M0111v5); Linear Amplification.

extract_protocol: We used the miRNeasy Mini Kit (Qiagen) to isolate total RNA.


title: Citrate Au NP treated PC3 cells sample 1 technical replicate

description:
Gene expression data from human prostate carcinoma cells exposed to citrate-capped gold nanoparticles (technical replicate)
raw data file: slide4_C.gpr

source_name: PC3, CIT, sample 1, techical replicate

value: 1 nM citrate-capped 20 nm gold nanoparticles


title: SUM159-spino2


title: OV03-17_Om_S1

description:
A594-032
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-17, sample Om_S1

tag: disease

value: omentum


title: Poly(allylamine hydrochloride) Au NP treated PC3 cells sample 3

description:
Gene expression data from human prostate carcinoma exposed to poly(allylamine hydrochloride)-wrapped gold nanoparticles
raw data file: slide4_C.gpr

source_name: PC3, PAH, sample 3

value: 1 nM poly(allylamine hydrochloride)-wrapped 20 nm gold nanoparticles


title: Patient replicate HV6

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV6
high grade serous ovarian cancer specimen from a high-volume ascites case

value: Snap-frozen tissue specimen containing > 70% tumour


title: OV03-10_Om_S01

description:
A594-031
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-10, sample Om_S01

tag: timepoint

value: stable disease


title: OV03-02_Adnexa_B2

description:
A594-030
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-02, sample Adnexa_B2

value: left adnexa

value: laparoscopic biopsy


title: Citrate Au NP treated HDF cells sample 3

description:
Gene expression data from human dermal fibroblasts exposed to citrate-capped gold nanoparticles
raw data file: slide4_B.gpr

source_name: HDF, CIT, sample 3

value: human dermal fibroblasts

value: HDF

value: 0.1 nM citrate-capped 20 nm gold nanoparticles


title: SUM159-ctrl2d

source_name: SUM159 Control


title: SUM159-spino1


title: Patient replicate LV6

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV6
high grade serous ovarian cancer specimen from a low-volume ascites case

value: <= 200cc measured ascites volume


title: Poly(allylamine hydrochloride)/lipid Au NP treated HDF cells sample 1

description:
Gene expression data from human dermal fibroblasts exposed to poly(allylamine hydrochloride)/lipid-coated gold nanoparticles
raw data file: slide4_A.gpr

source_name: HDF, PAHL, sample 1

value: 0.1 nM poly(allylamine hydrochloride)/lipid-coated 20 nm gold nanoparticles


title: OV03-21_Om_S01

description:
A594-029
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-21, sample Om_S01

value: interval debulking surgery

value: partial response


title: Patient replicate HV5

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV5
high grade serous ovarian cancer specimen from a high-volume ascites case

value: Stage III-IV

value: >= 1000cc measured ascites volume


title: MicroRNA expression profile of 24 days mouse testis

city: Trivandrum

first: Pradeep

middle: G

last: Kumar

state: Kerala

address: Thycaud, Poojappura

department: Molecular Reproduction

country: India

institute: Rajiv Gandhi Centre for Biotechnology

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. . The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: Raw data values were thresholded to 1.0 for all those less than 0.0 and normalized by 75 percentile shift method.

source_name: 24 days mouse testis

label_protocol: The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. One µg total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Male Swiss albino mice were obtained from an inbred line maintained in  animal house facility.

extract_protocol: Total RNA extraction was performed using Guanidine Thiocyanate (GTC) based QIAzol lysis reagent, miRNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: None. Animals were reared in normal temperature, 26 ±1˚C and humidity controlled environment under 14h light: 10h dark conditions.

value: Testis

value: Swiss albino

source_name: mouse testis (pool of 6 samples)

value: testis


title: MicroRNA expression profile of 24 days mouse testis_REP1


title: Untreated PC3 cells sample 3

description:
Gene expression data from human prostate carcinoma cells
raw data file: slide4_B.gpr

source_name: PC3, control, sample 3

value: human prostate carcinoma cells

value: untreated


title: OV03-04_Om_S15

description:
A594-026
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S15

value: ovarian cancer

value: omentum

value: stable disease


title: BoM2 vs MCF7

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

country: Spain

institute: IRB Barcelona

hyb_protocol: 31 µg Cy3- and 31 µg Cy5-labeled DNA of each sample  were hybridized on 100718_HG18_WG_CGH_v3.1_HX3 Nimblegen microarray for 16 hours of hybridization at 42ºC; hybridization and washing was performed according to NimbleGen Array User Guide for CGH and CNV Arrays (Roche NimbleGen, http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Roche-Nimblegen MS200 Scanner was used according to  NimbleGen Array User Guide for CGH and CNV Arrays  (Roche NimbleGen, http://www.nimblegen.com/products/lit/lit.html)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan software for CGH-DNACopy Analysis.

source_name: Human BoM2 cell genomic DNA

label_protocol: 500 ng genomic DNA was labeled with either Cy3  or Cy5  according to NimbleGen Array User Guide for CGH and CNV Arrays (Roche NimbleGen, http://www.nimblegen.com/products/lit/lit.html)

growth_protocol: MCF7 media (Control media): DMEM (Life Technologies), 1X Glutamax (Gibco 35050) and 10% FBS (Biological Industires) when passaging.  See  growth conditions in Tarragona et al., Journal of Biological Chemistry, 2012), for more details.

extract_protocol: High-molecular DNA was isolated from in vitro cultured MCF7 and BoM2 cells using GeneElute™ Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) following manufacture’s instructions. DNA quantity and quality was determined by NanoDrop ND-1000 UV-Vis Spectrophotometer and electrophoresis in 1% agarose gel.

treatment_protocol: Cells were grown for 2 days following the growth protocol outlined above and DNA extracted

value: bone metastatic derivative

source_name: Human MCF7 cell genomic DNA

value: none-bone metastatic derivative


title: SUM159-ctrl1


title: Poly(allylamine hydrochloride) Au NP treated HDF cells sample 3

description:
Gene expression data from human dermal fibroblasts exposed to poly(allylamine hydrochloride)-wrapped gold nanoparticles
raw data file: slide3_D.gpr

source_name: HDF, PAH, sample 3+D37

value: human dermal fibroblasts

value: HDF

value: 0.1 nM poly(allylamine hydrochloride)-wrapped 20 nm gold nanoparticles


title: Patient replicate LV5

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV5
high grade serous ovarian cancer specimen from a low-volume ascites case

value: <= 200cc measured ascites volume

value: Snap-frozen tissue specimen containing > 70% tumour


title: Patient replicate HV4

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV4
high grade serous ovarian cancer specimen from a high-volume ascites case

value: Stage III-IV


title: 557289A07 - WT_stress_BR2 vs oxi1_stress_BR2

description: Transcriptomic analysis on the effect of oxi1 mutation under high light stress?

hyb_protocol: oxi1_stress_BR2 Cy5 / WT_stress_BR2 Cy3 : 30pmol.

tag: ecotype

value: columbia

value: mutant (oxi1)

tag: dev.stage (boyes et al. plant cell 2001)

value: wildtype


title: Patient replicate LV4

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV4
high grade serous ovarian cancer specimen from a low-volume ascites case


title: MicroRNA expression profile of 16 days mouse testis_REP1

source_name: 16 days mouse testis

value: Testis

value: Swiss albino

value: testis


title: MicroRNA expression profile of 8 days mouse testis_REP1

source_name: 8 days mouse testis


title: OV03-04_Om_S13

city: Pieve Emanuele

last: Ng

institute: Humanitas University

description:
A594-023
Hybridised to SNP 6.0 array.

scan_protocol: Scanning was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

data_processing: Data was processed using PICNIC using the 'primary' option.

source_name: Ovarian cancer patient OV03-04, sample Om_S13

label_protocol: Labelling was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

value: ovarian cancer

value: interval debulking surgery

tag: response to treatment


title: Citrate Au NP treated PC3 cells sample 3

description:
Gene expression data from human prostate carcinoma cells exposed to citrate-capped gold nanoparticles
raw data file: slide3_C.gpr

source_name: PC3, CIT, sample 3

value: human prostate carcinoma cells

value: 1 nM citrate-capped 20 nm gold nanoparticles


title: Patient replicate LV3

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV3
high grade serous ovarian cancer specimen from a low-volume ascites case


title: Alkanethiol/lipid Au NP treated HDF cells sample 2

description:
Gene expression data from human dermal fibroblasts exposed to alkanethiol/lipid-coated gold nanoparticles
raw data file: slide3_D.gpr

source_name: HDF, ATL, sample 2

value: 0.1 nM alkanethiol/lipid-coated 20 nm gold nanoparticles


title: SUM159-ctrl2


title: MicroRNA expression profile of 8 days mouse testis


title: Patient replicate HV3

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV3
high grade serous ovarian cancer specimen from a high-volume ascites case

value: >= 1000cc measured ascites volume


title: MicroRNA expression profile of 16 days mouse testis


title: Alkanethiol/lipid Au NP treated PC3 cells sample 3

description:
Gene expression data from human prostate carcinoma cells exposed to alkanethiol/lipid-coated gold nanoparticles
raw data file: slide4_A.gpr

source_name: PC3, ATL, sample 3

value: 1 nM alkanethiol/lipid-coated 20 nm gold nanoparticles


title: OV03-04_Om_S14

description:
A594-025-ny
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S14

value: omentum

value: stable disease

tag: progression-free survival (months)


title: mice_resting BMM

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

description: BMM, on 5d of M-CSF cluture

hyb_protocol: Hybridization was done overnight on a μParaflo microﬂuidic chip using a microcirculation pump (Atactic Technologies)

scan_protocol: After hybridization, images were collected and quantiﬁed by LC Sciences.

data_processing: data processing was preformed by LC Sciences.

source_name: mice_resting BMM

label_protocol: The small RNAs (<200 nt) were 3’-extended with apolyadenylate tail using polyadenylate (poly A) polymerase and then ligated to an oligonucleotide tag for later staining.

growth_protocol: Briefly, bone marrow progenitors were cultured for 72 hours in DMEM supplemented with 10% FBS, 20 ng/mL murine M-CSF. Non-adherent cells were gently removed; the remaining adherent cells were cultured for an additional 3 days to get mouse BMM.

extract_protocol: total RNA samples were isolated from BMM using Trizol agent.

treatment_protocol: resting BMM were untreated. IFNgamma primed BMM were stimulted with murine  (100U/ml) IFNgamma for 4h.

tag: age

value: 4 weeks old

value: mouse bone marrow derived macrophages

tag: gender

value: female

tag: rna subset

value: The small RNAs (<200 nt)


title: OV03-04_Om_S11

first: Charlotte

address: Via Rita Montalcini 4

description:
A594-020
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S11

extract_protocol: Samples were placed immediately into RNAlater at the time of collection. DNA extraction was performed using the Qiagen DNeasy Blood and Tissue Kit according to the manufacturer's instructions.

tag: tissue


title: OV03-01_Om_S08

description:
A594-018
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample Om_S08

value: partial response


title: Untreated HDF cells sample 3

description:
Gene expression data from human dermal fibroblasts
raw data file: slide3_C.gpr

source_name: HDF, control, sample 3

value: human dermal fibroblasts

value: HDF

tag: treatment

value: untreated


title: OV03-04_Om_S09

description:
A594-017
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S09

value: ovarian cancer


title: OV03-04_Om_S08

description:
A594-016
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S08

value: interval debulking surgery


title: OV03-04_Om_S12

description:
A594-022
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S12


title: Patient replicate LV2

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV2
high grade serous ovarian cancer specimen from a low-volume ascites case

tag: tumour stage

value: Stage III-IV

tag: ascites volume

value: <= 200cc measured ascites volume

value: Snap-frozen tissue specimen containing > 70% tumour


title: OV03-01_Om_S07

description:
A594-015
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample Om_S07


title: Patient replicate HV2

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV2
high grade serous ovarian cancer specimen from a high-volume ascites case

value: >= 1000cc measured ascites volume


title: OV03-04_Om_S07

description:
A594-014
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S07


title: Poly(allylamine hydrochloride)/lipid Au NP treated HDF cells sample 2

description:
Gene expression data from human dermal fibroblasts exposed to poly(allylamine hydrochloride)/lipid-coated gold nanoparticles
raw data file: slide3_B.gpr

source_name: HDF, PAHL, sample 2

tag: cell type

tag: cell line

value: 0.1 nM poly(allylamine hydrochloride)/lipid-coated 20 nm gold nanoparticles


title: Untreated PC3 cells sample 2

description:
Gene expression data from human prostate carcinoma cells
raw data file: slide3_B.gpr

source_name: PC3, control, sample 2

value: human prostate carcinoma cells


title: OV03-04_Om_S06

description:
A594-013
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S06

tag: study id

value: omentum

value: stable disease


title: Control 3

first: jingyuan

last: fang

address: 145 Shandong Rd Middle

institute: Shanghai Institute of Digestive Disease

description: Gene expression after 24h for control treatment

hyb_protocol: The pre-hybridization of HOAV6 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on HOAV6 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: Control 3

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: Cells were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10% fetal bovine serum at 37 °C in an atmosphere of 5% CO2

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: The experiment groups were treated by drug.

value: gastric cancer cell

value: control


title: Poly(allylamine hydrochloride) Au NP treated HDF cells sample 1 technical replicate

description:
Gene expression data from human dermal fibroblasts exposed to poly(allylamine hydrochloride)-wrapped gold nanoparticles (technical replicate)
raw data file: slide3_A.gpr

source_name: HDF, PAH, sample 1, technical replicate

value: 0.1 nM poly(allylamine hydrochloride)-wrapped 20 nm gold nanoparticles


title: Patient replicate HV1

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with high-volume ascites. Patient replicate HV1
high grade serous ovarian cancer specimen from a high-volume ascites case


title: Control 2

source_name: Control 2


title: OV03-01_Om_S06

description:
A594-012
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample Om_S06

tag: sample id

value: partial response


title: OV03-04_Om_S05

description:
A594-011
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S05

tag: disease


title: Alkanethiol/lipid Au NP treated HDF cells sample 3

description:
Gene expression data from human dermal fibroblasts exposed to alkanethiol/lipid-coated gold nanoparticles
raw data file: slide2_D.gpr

source_name: HDF, ATL, sample 3

value: human dermal fibroblasts

value: 0.1 nM alkanethiol/lipid-coated 20 nm gold nanoparticles


title: Control 1

source_name: Control 1


title: Untreated HDF cells sample 2

description:
Gene expression data from human dermal fibroblasts
raw data file: slide2_B.gpr

source_name: HDF, control,sample 2

value: HDF

value: untreated


title: TMEFF2 adenovirus treatment 3

description: Gene expression after 24h for treatment

source_name: TMEFF2 adenovirus treatment 3

value: TMEFF2 adenovirus


title: TMEFF2 adenovirus treatment 1

description: Gene expression after 24h for treatment

source_name: TMEFF2 adenovirus treatment 1


title: OV03-04_Om_S04

description:
A594-008
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S04

value: ovarian cancer

tag: timepoint

value: interval debulking surgery


title: Alkanethiol/lipid Au NP treated PC3 cells sample 2

description:
Gene expression data from human prostate carcinoma cells exposed to alkanethiol/lipid-coated gold nanoparticles
raw data file: slide2_D.gpr

source_name: PC3, ATL, sample 2

value: 1 nM alkanethiol/lipid-coated 20 nm gold nanoparticles


title: OV03-04_Om_S03

description:
A594-007
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S03


title: Patient replicate LV1

description:
RNA obtained from a tumour resected from a high grade serous ovarian cancer patient presenting with low-volume ascites. Patient replicate LV1
high grade serous ovarian cancer specimen from a low-volume ascites case

value: Stage III-IV

value: <= 200cc measured ascites volume

value: Snap-frozen tissue specimen containing > 70% tumour


title: Poly(allylamine hydrochloride) Au NP treated PC3 cells sample 2

description:
Gene expression data from human prostate carcinoma exposed to poly(allylamine hydrochloride)-wrapped gold nanoparticles
raw data file: slide3_A.gpr

source_name: PC3, PAH, sample 2

value: human prostate carcinoma cells

value: 1 nM poly(allylamine hydrochloride)-wrapped 20 nm gold nanoparticles


title: TMEFF2 adenovirus treatment 2

description: Gene expression after 24h for treatment

source_name: TMEFF2 adenovirus treatment 2

value: gastric cancer cell