title: 548530_A02_532

source_name: Minipig  6_M_210758

tag: tissue

value: male

value: 1 year old minipig

value: circa 20 kg

value: Ellegaard, Denmark


title: 548530_A03_532

status: Public on Dec 16 2015

type: RNA

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: total RNA recovered from fresh frozen tissue from untreated minipigs

hyb_protocol: Hybridization was performed following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

scan_protocol: Scanning was performed on a NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to background correction, quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.). In addition this RMA normalized data was GRSN normalized according to the method of Pelz et al. (Pelz C et al. BMC Bioinformatics 2008, 9:520).

molecule: total RNA

organism: Sus scrofa

source_name: Minipig  5_M_210690

label_protocol: Labeling was performed using 10 ng of total RNA as input following the standard operating protocol on a Biomek FXp workstation (Beckman Coulter Inc., Brea, CA, USA) with the NuGen Ovation Pico WTA System V2 (NuGEN Technologies, Inc., SanCarlos, CA, USA; see http://www.nugeninc.com). Cy3 labeling of cDNA was performed with  the Roche NimbleGen One Color DNA Labeling Kit according to manufacturer's instructions (NimbleGen Systems Inc., Madison, WI USA. (See www.nimblegen.com).

growth_protocol: the tissue samples were collected from drug-naive, untreated animals of GLP drug safety studies carried out in accordance with current animal protection standards. Tissues were stored at -80°C until RNA extraction.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) . DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

value: liver

tag: gender

tag: age

tag: weigth

tag: facility


title: whole blood, PBS treated, Animal 71Y

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Sheep Genome microarrays 8x15K Design ID 019921 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Ovis aries

source_name: Whole Blood_PBS treated

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using Arcturus RiboAmp HS reagents (Molecular Devices, Sunnyvale, CA).  Alternatively, MessageAMP II (Applied Biosystems, Foster City, CA) was used.  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Sheep whole blood was incubated with 1microg LPS or  10 microg MPLA for 90 minutes

value: Whole Blood


title: Roscovitine rep2

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description:
4482545065_D
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw probe expression values were log2 transformed and normalized with quantiles normalization functions as implemented in the GeneSpring GX12 package.

label: biotin

organism: Homo sapiens

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 and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue source

value: prostate

tag: cell line

value: LNCaP

tag: cell type

value: prostate adenocarcinoma cells

tag: treated with

value: 20uM Roscovitine (positive control)


title: 11578 Primary

city: saint louis

first: chidananda

last: Mudalagiriyappa

state: Missouri

address: 4940 Parkview Pl.

department: Surgery

institute: washington university in saint louis

description: Gene expression data from primary tumor Breast cancer patients

hyb_protocol: Hybridization was done following NuGEN’s recommendations using Affymetrix fluidic stations and Affymetrix hybridization, wash and stain kit.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Affymetrix CEL files were imported into Partek Genomics Suite v6.5 and processed using the RMA algorithm without probe filtering.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Primary Tumor

label_protocol: lablelling was done using NuGEN Encore Biotin module.

extract_protocol: Total RNA was isolated from Breast tumor samples using Trizol reagent (Invitrogen) according to manufacturer’s protocol.  The extracted RNA was quantified and qualitatively assessed using an Agilent Bioanalyzer and RNA NanoChip assay. cDNA synthesis and amplification was performed using the Ovation Pico SL kit from NuGEN.

tag: phenotype

value: Primary Tumor

value: Breast Tissue

tag: reference id

tag: pre/post therapy

value: Pre

tag: date of randomisation (month/date/year)

tag: allocated treatment

value: zometa

tag: menopausal   status

tag: er

value: pos

tag: pr

value: neg

tag: dtc positive(ihc)

value: Yes

tag: date of   recurrence

tag: date of death or date patient last known to be alive (month/date/year)


title: CPT rep1

description:
4482545065_E
replicate 1

value: 500nM Campthotecin (positive control)


title: 11577 Primary

tag: tissue

value: No


title: 548530_A08_532

source_name: Minipig  M_208393

tag: gender

value: male

tag: age

value: 1 year old minipig

tag: weigth

value: circa 20 kg

tag: facility


title: Bortezomib rep1

description:
4482545065_G
replicate 1

tag: tissue source

tag: cell line

tag: cell type

tag: treated with

value: 50 nM Bortezomib (positive control)


title: SMIP004 rep2_1

description:
4482545037_G
replicate 1

value: prostate

value: 40 uM SMIP004 for 24 h


title: 11575 Primary

tag: phenotype

tag: reference id

tag: pre/post therapy

tag: date of randomisation (month/date/year)


title: 11574 Primary

tag: allocated treatment

tag: menopausal   status

tag: er

tag: pr


title: SMIP004 rep2_2

description:
4482545037_H
replicate 2

value: LNCaP

value: prostate adenocarcinoma cells


title: Roscovitine rep1

description:
4482545065_C
replicate 1

value: 20uM Roscovitine (positive control)


title: 548530_A09_532

source_name: Minipig  M_208431

tag: tissue

value: liver

value: Ellegaard, Denmark


title: 548530_A01_532

source_name: Minipig  4_F_306227

tag: gender

value: female


title: 11576 Primary

value: Primary Tumor

value: Breast Tissue

value: Pre

value: zometa

value: Post

value: pos

tag: dtc positive(ihc)

tag: date of   recurrence

tag: date of death or date patient last known to be alive (month/date/year)


title: 548530_A07_532

source_name: Minipig  2_F_306273

tag: age

value: 1 year old minipig

tag: weigth

tag: facility


title: DMSO rep2

description:
4482545037_B
replicate 2

tag: tissue source

tag: cell line

tag: cell type

tag: treated with

value: DMSO (vehicle)


title: SMIP004 rep1_2

description:
4482545037_F
replicate 2


title: DMSO rep1

description:
4482545037_A
replicate 1


title: 11573 Primary

tag: phenotype

tag: reference id

tag: pre/post therapy

tag: date of randomisation (month/date/year)

value: neg

value: No


title: 548530_A04_532

source_name: Minipig  3_F_306298

value: circa 20 kg


title: whole blood, PBS treated, Volunteer 6

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays 8x60K v2 Design ID 039494 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

treatment_protocol: Human whole blood was incubated with 1microg LPS or  10 microg MPLA for 90 minutes

value: Whole Blood


title: whole blood, PBS treated, Volunteer 5


title: whole blood, LPS treated, Volunteer 6

source_name: Whole Blood_LPS treated


title: 548530_A11_532

source_name: Minipig  1_F_306285


title: whole blood, MPLA treated, Volunteer 6

source_name: Whole Blood_MPLA treated


title: 11572 Primary

tag: allocated treatment

tag: menopausal   status

tag: er

tag: pr


title: 11570 Primary

tag: tissue

tag: dtc positive(ihc)

tag: date of   recurrence


title: SMIP004 rep1_1

description:
4482545037_E
replicate 1

value: prostate

value: LNCaP

value: prostate adenocarcinoma cells

value: 40 uM SMIP004 for 24 h


title: 548530_A06_532

source_name: Minipig  F_304342

value: liver

tag: gender

value: female

tag: age

tag: weigth

value: Ellegaard, Denmark


title: whole blood, PBS treated, Volunteer 4


title: whole blood, MPLA treated, Volunteer 5


title: 11571 Primary

value: Primary Tumor

value: Breast Tissue

tag: date of death or date patient last known to be alive (month/date/year)


title: 11537 Primary


title: whole blood, LPS treated, Volunteer 4


title: whole blood, LPS treated, Volunteer 3


title: whole blood, MPLA treated, Volunteer 4


title: whole blood, PBS treated, Volunteer 3


title: whole blood, MPLA treated, Volunteer 3


title: 544062_A09_532

source_name: Minipig  8_M_210733

value: kidney (medulla & cortex)

value: male

tag: facility


title: 11535 Primary

value: Pre

value: no

value: Yes


title: 544062_A01_532

source_name: Minipig  7_M_210995

value: 1 year old minipig


title: 548530_A10_532

source_name: Minipig  F_304362

value: circa 20 kg


title: 544062_A10_532


title: whole blood, PBS treated, Volunteer 2

value: Whole Blood


title: whole blood, MPLA treated, Volunteer 2


title: 11534 Primary


title: whole blood, LPS treated, Volunteer 2


title: whole blood, MPLA treated, Volunteer 1


title: 11533 Primary

value: Post

value: pos

value: neg


title: whole blood, PBS treated, Volunteer 1


title: whole blood, LPS treated, Volunteer 5


title: 11532 Primary

value: zometa


title: whole blood, LPS treated, Volunteer 1


title: 544062_A08_532


title: 11536 Primary

value: No


title: 11531 Primary


title: 544062_A05_532

value: kidney


title: 544062_A04_532

value: Ellegaard, Denmark


title: 544062_A02_532

value: female


title: 11530 Primary

value: Primary Tumor

value: Breast Tissue


title: 544062_A06_532

value: kidney (medulla & cortex)


title: 544062_A11_532


title: 11527 Primary


title: 11528 Primary


title: 11529 Primary

value: Pre


title: 544062_A03_532


title: 544062_A07_532


title: 11526 Primary

value: no


title: 11525 Primary


title: HK-6943 whole blood NSD1 variant genomic DNA

type: genomic

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Using an Illumina HiScan

data_processing: Using an Illumina HiScan

label: Cy5 and Cy3

molecule: genomic DNA

source_name: whole blood genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: All genomic DNA were extracted from either whole blood or fibroblast using standard procedures. 1 microgram of genomic DNA was sodium bisulfite modified using the Qiagen EZ DNA Methylation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Modified genomic DNA was then processed and analyzed on the Infinium HumanMethylation450 BeadChip from Illumina (Illumina 450K) according to the manufacturer’s protocol.

value: male

tag: disease state

value: NSD1 variant

value: whole blood


title: 544062_A12_532

value: 1 year old minipig

value: circa 20 kg


title: 11524 Primary

tag: phenotype

value: Post


title: HK-14867 whole blood NSD1 variant genomic DNA


title: HK-11767 whole blood NSD1 variant genomic DNA


title: 545234_A01_532

value: heart


title: HK-435 whole blood NSD1 variant genomic DNA


title: 545234_A06_532


title: HK-3326 whole blood NSD1 variant genomic DNA


title: DL159025 whole blood NSD1 variant genomic DNA


title: 11522 Primary

tag: reference id


title: HK-12366 whole blood NSD1 variant genomic DNA


title: 11523 Primary

tag: pre/post therapy


title: 11521 Primary

tag: date of randomisation (month/date/year)

value: zometa

value: neg


title: HK-5474 whole blood NSD1 variant genomic DNA


title: 545234_A11_532


title: HK-5581 whole blood NSD1 variant genomic DNA


title: HK-9776 whole blood NSD1 variant genomic DNA


title: HK-11693 whole blood NSD1 variant genomic DNA


title: 545234_A04_532


title: DL208122 whole blood NSD1 variant genomic DNA


title: DL136303 whole blood NSD1 variant genomic DNA


title: A117 whole blood Weaver genomic DNA

value: Weaver


title: DL73286 whole blood NSD1 variant genomic DNA


title: 11519 Primary

tag: allocated treatment

value: Yes


title: DL129940 whole blood Weaver genomic DNA


title: 548581_A10_532

value: female

value: Ellegaard, Denmark


title: 545234_A10_532


title: 11518 Primary

value: Primary Tumor

value: Breast Tissue

tag: menopausal   status


title: F0123 whole blood Weaver genomic DNA


title: 11517 Primary

tag: er


title: DL199861 whole blood NSD1 variant genomic DNA


title: 11520 Primary

value: Pre

value: pos

tag: pr

value: No


title: A212 whole blood Weaver genomic DNA

tag: tissue


title: DL181344 whole blood NSD1 variant genomic DNA

value: male

value: NSD1 variant


title: A1359 whole blood Weaver genomic DNA

value: whole blood


title: 548581_A12_532

value: 1 year old minipig

value: circa 20 kg


title: A120W whole blood Weaver genomic DNA


title: HK-5977 whole blood Sotos genomic DNA

value: Sotos


title: 11516 Primary

tag: dtc positive(ihc)


title: A134W whole blood Weaver genomic DNA


title: A123W whole blood Weaver genomic DNA


title: 548581_A11_532

value: heart


title: 545234_A12_532


title: HK-10067 whole blood Sotos genomic DNA


title: HK11807 whole blood Sotos genomic DNA


title: 11513 Primary

tag: date of   recurrence


title: 545234_A03_532

tag: gender


title: HK-6779 whole blood Sotos genomic DNA


title: 11515 Primary


title: 545234_A08_532

tag: age


title: 11514 Primary


title: 11512 Primary


title: HK-4470 whole blood Sotos genomic DNA


title: HK-5589 whole blood Sotos genomic DNA


title: HK-2129 whole blood Sotos genomic DNA


title: HK-6966 whole blood Sotos genomic DNA


title: 545234_A07_532

source_name: Minipig  6_M_210758

tag: weigth


title: Kidney_2_years_male_repetition_8

description: Gene expression values of a 2 year old male minipig kidney

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and 40ul hybridized to Agilent SurePrint G3 Custom GE Array 8x60K (Design-ID 050244) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on a Roche/Nimblegen MS200 Scanner using one color scan setting (Laser 532nm against Cy3, Laser power 50%, Scan resolution 2um, Gain 15%)

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12) to obtain background subtracted and spatially detrended Processed Signal intensities. gProcessedSignal values were quantile normalized and log2 transformed.

source_name: Total RNA from Kidney tissue, 2 years, male

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Agilent Low Input Quick Amp Labeling kit (One-Color) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer. Specific activity of Cy3 was above 6 as intended in manufacturer's instructions.

growth_protocol: Minipig Tissue samples were obtained from Ellegaard Goettingen Minipigs A/S, Dalmose, Denmark; SMP (E) Food by Special Diets Services, Essex; water ad libitum; 12h day/night rythm; euthanasia was performed 3-4h after start of the day phase by pentobarbital (Euthasol 40% by Virbac S.A., Carros) with a dose of 0,3 ml/kg. Exceptions were made for the 2 year old male minipig which was raised 74 days after birth at F. Hoffmann-LaRoche AG with food from Provimi Kliba AG, Kaiseraugst (#3000); Euthanasia in this pig was performed with pentobarbital (Esconarkon by Streuli Pharma AG, Uznach) 150mg/kg.

extract_protocol: Total RNA was isolated from 40-50mg tissue. 1,2ml QIAzol was added and shaken in a Lysing Matrix D (MP Biomedicals) by a Savant FastPrep FP120 for 20 seconds (setting 6.0). Supernatant was transferred to a new tube after centrifugation (17.000g, 3min) and incubated at room temperature for 5 min. 200ul chloroform was added, the tube vortexed and incubated at room temperature for 2 min. After a centrifugation (4°C, 12.000g, 15min) the aqueous phase was transferred to a new tube and mixed with the same volume of 70% EtOH. An RNeasy Mini kit by Qiagen was used afterwards to clean up the RNA solution. For that the mixture was centrifugated in a column (30s, 8.000g) and washed with 700ul buffer RW1 and two times with 500ul buffer RPE. After dry centrifugating an eluation was performed with 50ul water. All samples had a 260/280nm value of over 2,0, a 260/230nm value of over 1,85 and a RIN value of over 7 (4 exceptions with 6,2; 6,7; 6,8 and 6,9)

treatment_protocol: Tissues were immediately fresh frozen on dry ice and crushed right before RNA extraction. For that a tissueTUBE TT1 and a cryoPrep Impactor by Covaris were used

value: Kidney

value: 2 years


title: HK-4913 whole blood Sotos genomic DNA


title: 11511 Primary

tag: date of death or date patient last known to be alive (month/date/year)


title: Bone_Marrow_2_years_male

description: Gene expression values of a 2 year old male minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 2 years, male

value: Bone Marrow


title: Liver_2_years_male

description: Gene expression values of a 2 year old male minipig liver

source_name: Total RNA from Liver tissue, 2 years, male

value: Liver


title: HK-13565 whole blood Sotos genomic DNA

value: female


title: HK-7783 whole blood Sotos genomic DNA


title: Testis_2_years_male

description: Gene expression values of a 2 year old male minipig testis

source_name: Total RNA from Testis tissue, 2 years, male

value: Testis


title: 11509 Primary

source_name: Primary Tumor

value: Primary Tumor

value: Breast Tissue


title: HK-5530 whole blood Sotos genomic DNA


title: 11507 Primary


title: HK-11302 whole blood Sotos genomic DNA


title: HK-5439 whole blood Sotos genomic DNA


title: 11510 Primary


title: HK-5533 whole blood Sotos genomic DNA


title: HK-15438 whole blood Sotos genomic DNA


title: Kidney_renal_pelvis_2_years_male

description: Gene expression values of a 2 year old male minipig renal pelvis

source_name: Total RNA from Kidney renal pelvis tissue, 2 years, male

value: Kidney renal pelvis


title: HK-1540 whole blood Sotos genomic DNA


title: Kidney_2_years_male_repetition_6


title: 11508 Primary


title: SF155 fibroblast Sotos genomic DNA

source_name: fibroblast genomic DNA

tag: cell type

value: fibroblast


title: 11506 Primary


title: Kidney_2_years_male_repetition_5

value: male


title: 8413 Primary

value: Pre

value: no

value: neg

value: Yes


title: HK-5107 whole blood Sotos genomic DNA

tag: disease state

value: Sotos

value: whole blood


title: MutuI.2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
control
SAMPLE 5

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis, resulting in the reduced data set of 21,731 ID_REFs

source_name: MutuI cell line

label_protocol: Standard Illumina labeling protocol

growth_protocol: EBV positive B-cell (Mutu I, LCL) were grown in RPMI with 10% FBS and Glutamax

extract_protocol: Total RNA was isolated with High Pure RNA Paraffin Kit (Roche Applied Science, Branford, CT).

treatment_protocol: no treatment

tag: cell line

value: MutuI

value: EBV positive B lymphocyte line


title: Cortex_2_years_male

description: Gene expression values of a 2 year old male minipig cortex

source_name: Total RNA from Cortex tissue, 2 years, male

value: Cortex

value: 2 years


title: 8415 Primary

tag: phenotype

tag: reference id


title: DL89813 whole blood Sotos genomic DNA


title: HK-15164 whole blood Sotos genomic DNA

value: female


title: Spleen_2_years_male

description: Gene expression values of a 2 year old male minipig spleen

source_name: Total RNA from Spleen tissue, 2 years, male

value: Spleen


title: 8414 Primary

value: Primary Tumor

tag: pre/post therapy

tag: date of randomisation (month/date/year)

value: pos

value: No


title: MutuI.1

description:
control
SAMPLE 4


title: 51537F fibroblast Sotos genomic DNA

value: fibroblast


title: 8410 Primary

value: Breast Tissue

tag: allocated treatment

value: zometa

tag: menopausal   status

value: Post


title: DL141677 fibroblast Sotos genomic DNA

value: male


title: 8412 Primary

value: Pre

value: no

tag: er

tag: pr

value: Yes


title: 8409 Primary

tag: tissue

tag: dtc positive(ihc)


title: 8411 Primary

value: neg


title: Kidney_2_years_male_repetition_3

value: Kidney

tag: gender


title: LCL.2

description:
control
SAMPLE 2

source_name: LCL cell line

value: LCL

value: EBV positive B lymphocyte line


title: LCL.3

description:
control
SAMPLE 3


title: Kidney_2_years_male_repetition_7

tag: age

value: 2 years


title: DL94609 whole blood Sotos genomic DNA

value: Sotos

value: whole blood


title: 8408 Primary

value: Primary Tumor

value: pos

tag: date of   recurrence


title: DL87406 whole blood Sotos genomic DNA


title: Kidney_2_years_male_repetition_1


title: DL76010 whole blood Sotos genomic DNA

value: female


title: DL50452 whole blood Sotos genomic DNA


title: DL50448 whole blood Sotos genomic DNA


title: 3DAY

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

description: Mitochondria signature for HCC

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12  Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

source_name: SNU354 cells was transfected by NUPR1 siRNA

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser.

value: hepatoma cell


title: Hypothalamus_2_years_male

description: Gene expression values of a 2 year old male minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 2 years, male

value: Hypothalamus


title: DL50450 whole blood Sotos genomic DNA


title: 8407 Primary

value: Breast Tissue

tag: date of death or date patient last known to be alive (month/date/year)


title: LCL.1

description:
control
SAMPLE 1

tag: cell type


title: Kidney_2_years_male_repetition_4

value: male


title: Cerebellum_2_years_male

description: Gene expression values of a 2 year old male minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 2 years, male

value: Cerebellum


title: 8406 Primary

value: Pre

value: no

value: Post


title: Kidney_2_years_male_repetition_2

value: Kidney


title: Liver_4_months_male

description: Gene expression values of a 4 month old male minipig liver

source_name: Total RNA from Liver tissue, 4 months, male

value: Liver

value: 4 months


title: Hypothalamus_4_weeks_female

description: Gene expression values of a 4 week old female minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 4 weeks, female

value: 4 weeks


title: Bone_Marrow_2_months_female

description: Gene expression values of a 2 month old female minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 2 months, female

value: Bone Marrow

value: 2 months


title: 8403 Primary

value: Primary Tumor

value: neg

value: No


title: 8210 Primary

value: zometa

value: pos

value: Yes


title: negative control

description: Mitochondria signature for HCC

source_name: negative control

value: hepatoma cell


title: 2DAY

description: Mitochondria signature for HCC


title: MDA-MB-435_rho 0

description: Mitochondria signature for HCC

source_name: breast cancer cell without mitochondrial DNA

value: breast cancer cell


title: 8404 Primary

value: Breast Tissue

value: Pre


title: MutuI.3

description:
control
SAMPLE 6

value: MutuI

value: EBV positive B lymphocyte line


title: DL179067 whole blood Sotos genomic DNA

source_name: whole blood genomic DNA

value: male

tag: disease state

value: Sotos

value: whole blood


title: DL168744 whole blood Sotos genomic DNA


title: DL159249 whole blood Sotos genomic DNA

value: female


title: MDA-MB-435_WT

description: Mitochondria signature for HCC

source_name: breast cancer cell


title: DL38402 whole blood Sotos genomic DNA


title: Cerebellum_1_week_female

description: Gene expression values of a 1 week old female minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 1 week, female

value: Cerebellum

value: 1 week


title: DL151889 whole blood Sotos genomic DNA


title: Ovary_1_week_female

description: Gene expression values of a 1 week old female minipig ovary

source_name: Total RNA from Ovary tissue, 1 week, female

value: Ovary


title: 8206 Primary

source_name: Primary Tumor

value: Primary Tumor

value: no

value: Post

value: neg

value: No


title: 8209 Primary

value: pos


title: Testis_4_months_male

description: Gene expression values of a 4 month old male minipig testis

source_name: Total RNA from Testis tissue, 4 months, male

value: Testis

value: 4 months


title: 8207 Primary

value: Breast Tissue

value: Pre


title: H2O2_3day

description: Mitochondria signature for HCC

source_name: Ch-L clone was exposed to hydrogen peroxide

value: Ch-L clone


title: 8205 Primary

value: zometa


title: 8204 Primary


title: H2O2_6hr

description: Mitochondria signature for HCC


title: A1208 whole blood Sotos genomic DNA

value: Sotos

value: whole blood


title: TTFA

description: Mitochondria signature for HCC

source_name: Ch-L clone was exposed to mitochondrial inhibitor, TTFA


title: Antimycin A

description: Mitochondria signature for HCC

source_name: Ch-L clone was exposed to mitochondrial inhibitor, Antimycin A


title: Oligomycin

description: Mitochondria signature for HCC

source_name: Ch-L clone was exposed to mitochondrial inhibitor, Oligomycin


title: Cortex_4_weeks_female

description: Gene expression values of a 4 week old female minipig cortex

source_name: Total RNA from Cortex tissue, 4 weeks, female

value: Cortex

value: 4 weeks

value: female


title: Cortex_1_week_male

description: Gene expression values of a 1 week old male minipig cortex

source_name: Total RNA from Cortex tissue, 1 week, male

value: 1 week

value: male


title: Spleen_1_week_female

description: Gene expression values of a 1 week old female minipig spleen

source_name: Total RNA from Spleen tissue, 1 week, female

value: Spleen


title: 8203 Primary

description: Gene expression data from primary tumor Breast cancer patients

value: Primary Tumor

value: no

value: neg


title: DL122057 whole blood Sotos genomic DNA


title: Kidney_4_weeks_female

description: Gene expression values of a 4 week old female minipig kidney

source_name: Total RNA from Kidney tissue, 4 weeks, female

value: Kidney


title: DL117330 whole blood Sotos genomic DNA


title: 8200 Primary

value: Yes


title: Rotenone

description: Mitochondria signature for HCC

source_name: Ch-L clone was exposed to mitochondrial inhibitor, Rotenone


title: Bone_Marrow_4_months_male

description: Gene expression values of a 4 month old male minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 4 months, male

value: Bone Marrow

value: 4 months


title: Spleen_4_months_male

description: Gene expression values of a 4 month old male minipig spleen

source_name: Total RNA from Spleen tissue, 4 months, male


title: Liver_2_months_female

description: Gene expression values of a 2 month old female minipig liver

source_name: Total RNA from Liver tissue, 2 months, female

value: Liver

value: 2 months


title: 8197 Primary

value: Breast Tissue

value: Pre

value: pos


title: SNU387

description: Mitochondria signature for HCC

source_name: hepatoma cell

value: hepatoma cell


title: Ch-L

description: Mitochondria signature for HCC

source_name: Ch-L

value: Ch-L clone


title: 8194 Primary


title: SNU423

description: Mitochondria signature for HCC


title: 8195 Primary

value: zometa

value: No


title: 8199 Primary


title: Bone_Marrow_4_weeks_female

description: Gene expression values of a 4 week old female minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 4 weeks, female

value: 4 weeks

value: female


title: Hypothalamus_2_months_male

description: Gene expression values of a 2 month old male minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 2 months, male

value: Hypothalamus

value: male


title: Cerebellum_1_week_male

description: Gene expression values of a 1 week old male minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 1 week, male

value: Cerebellum

value: 1 week


title: 47407F06 fibroblast Control genomic DNA

source_name: fibroblast genomic DNA

value: Control

value: fibroblast


title: SNU354

description: Mitochondria signature for HCC


title: 8193 Primary

source_name: Primary Tumor

value: Primary Tumor


title: 11D/6637 whole blood Sotos genomic DNA

source_name: whole blood genomic DNA

value: Sotos

value: whole blood


title: SF156 fibroblast Control genomic DNA


title: 11D/0326 whole blood Sotos genomic DNA


title: 11D/0328 whole blood Sotos genomic DNA


title: 11D/6718 whole blood Sotos genomic DNA


title: HL-659 whole blood Control genomic DNA


title: HL-910 whole blood Control genomic DNA


title: Spleen_1_week_male

description: Gene expression values of a 1 week old male minipig spleen

source_name: Total RNA from Spleen tissue, 1 week, male

value: Spleen


title: 8192 Primary

value: Breast Tissue

value: Post

value: no

value: Pre

value: neg


title: HL-994 whole blood Control genomic DNA


title: Kidney_2_months_male

description: Gene expression values of a 2 month old male minipig kidney

source_name: Total RNA from Kidney tissue, 2 months, male

value: Kidney

value: 2 months


title: 46163F05 fibroblast Control genomic DNA

value: female


title: Testis_4_weeks_male

description: Gene expression values of a 4 week old male minipig testis

source_name: Total RNA from Testis tissue, 4 weeks, male

value: Testis

value: 4 weeks

value: male


title: 8191 Primary

value: No


title: HL-3274 whole blood Control genomic DNA

value: Control


title: Cortex_2_months_female

description: Gene expression values of a 2 month old female minipig cortex

source_name: Total RNA from Cortex tissue, 2 months, female

value: Cortex


title: 8188 Primary

value: Primary Tumor

value: zometa

value: pos

value: Yes


title: HL-2970 whole blood Control genomic DNA

value: whole blood


title: 13142F03 fibroblast Control genomic DNA

value: fibroblast


title: Liver_1_week_female

description: Gene expression values of a 1 week old female minipig liver

source_name: Total RNA from Liver tissue, 1 week, female

value: Liver

value: 1 week


title: 8189 Primary

value: Breast Tissue

value: Pre

value: neg


title: 8190 Primary

value: no


title: Hypothalamus_4_months_female

description: Gene expression values of a 4 month old female minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 4 months, female

value: Hypothalamus

value: 4 months

value: female


title: 8185 Primary

value: No


title: 8186 Primary

value: Post


title: 8187 Primary

value: Primary Tumor


title: Hypothalamus_4_months_male

description: Gene expression values of a 4 month old male minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 4 months, male

value: male


title: Cerebellum_4_weeks_female

description: Gene expression values of a 4 week old female minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 4 weeks, female

value: Cerebellum

value: 4 weeks


title: 8183 Primary

value: zometa

value: Yes


title: Spleen_4_weeks_male

description: Gene expression values of a 4 week old male minipig spleen

source_name: Total RNA from Spleen tissue, 4 weeks, male

value: Spleen


title: Ovary_2_months_female

description: Gene expression values of a 2 month old female minipig ovary

source_name: Total RNA from Ovary tissue, 2 months, female

value: Ovary

value: 2 months


title: Kidney_4_months_male

description: Gene expression values of a 4 month old male minipig kidney

source_name: Total RNA from Kidney tissue, 4 months, male

value: Kidney


title: HL-1917 whole blood Control genomic DNA

value: Control

value: whole blood


title: 8180 Primary

description: Gene expression data from primary tumor Breast cancer patients

value: Breast Tissue

value: Pre

value: pos

value: neg


title: HL-1685 whole blood Control genomic DNA

value: female


title: 8182 Primary

value: Primary Tumor

value: Post

value: No


title: 8181 Primary


title: EP61W whole blood Control genomic DNA


title: Ovary_4_weeks_female

description: Gene expression values of a 4 week old female minipig ovary

source_name: Total RNA from Ovary tissue, 4 weeks, female

value: 4 weeks


title: EP8W whole blood Control genomic DNA

value: male


title: HL-1845 whole blood Control genomic DNA


title: 8177 Primary

value: zometa


title: 8178 Primary


title: EP60W whole blood Control genomic DNA


title: Cortex_4_months_male

description: Gene expression values of a 4 month old male minipig cortex

source_name: Total RNA from Cortex tissue, 4 months, male

value: Cortex

value: 4 months


title: Gut Chip + VSL#3-2

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: Caco-2 cells cultured in the gut-on-a-chip with flow and cyclic peristalsis-like motions in the presence of VSL#3 probiotic bacteria Replicate 2

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix Human Gene 1.0 ST Array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA normalized using Expression Console

source_name: Human Caco-2BBE cell line

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: Human Caco-2BBE cells were grown in DMEM containing 10 % fetal bovine serum (FBS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM of L-glutamine andSodium pyruvate. Total RNA was collected for microarray

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

tag: cell line


title: Hypothalamus_4_weeks_male

description: Gene expression values of a 4 week old male minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 4 weeks, male

value: Hypothalamus


title: EP58W whole blood Control genomic DNA


title: EP55W whole blood Control genomic DNA


title: 8174 Primary

source_name: Primary Tumor

tag: phenotype


title: 8172 Primary

tag: reference id


title: Cerebellum_4_months_female

description: Gene expression values of a 4 month old female minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 4 months, female

value: Cerebellum


title: Gut Chip + VSL#3-1

description: Caco-2 cells cultured in the gut-on-a-chip with flow and cyclic peristalsis-like motions in the presence of VSL#3 probiotic bacteria Replicate 1


title: Gut Chip-2

description: Caco-2 cells cultured in the gut-on-a-chip with flow and cyclic peristalsis-like motions Replicate 2


title: Kidney_2_months_female

description: Gene expression values of a 2 month old female minipig kidney

source_name: Total RNA from Kidney tissue, 2 months, female

value: Kidney

value: 2 months


title: Bone_Marrow_2_months_male

description: Gene expression values of a 2 month old male minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 2 months, male

value: Bone Marrow


title: Gut Chip-1

description: Caco-2 cells cultured in the gut-on-a-chip with flow and cyclic peristalsis-like motions Replicate 1


title: 8176 Primary

value: Breast Tissue

tag: pre/post therapy

value: no

value: Pre

value: Yes


title: Liver_1_week_male

description: Gene expression values of a 1 week old male minipig liver

source_name: Total RNA from Liver tissue, 1 week, male

value: Liver

value: 1 week


title: EP56W whole blood Control genomic DNA

source_name: whole blood genomic DNA

value: female

value: Control

value: whole blood


title: EP59W whole blood Control genomic DNA

value: male


title: EP5W whole blood Control genomic DNA


title: Testis_2_months_male

description: Gene expression values of a 2 month old male minipig testis

source_name: Total RNA from Testis tissue, 2 months, male

value: Testis


title: Transwell-2

description: Caco-2 cells cultured in static Transwell Replicate 2


title: EP57W whole blood Control genomic DNA


title: 8171 Primary

value: Primary Tumor

tag: date of randomisation (month/date/year)

value: zometa

value: neg


title: Cortex_1_week_female

description: Gene expression values of a 1 week old female minipig cortex

source_name: Total RNA from Cortex tissue, 1 week, female

value: Cortex


title: 8170 Primary

tag: allocated treatment

value: No


title: Transwell-1

description: Caco-2 cells cultured in static Transwell Replicate 1


title: EP52W whole blood Control genomic DNA


title: 8169 Primary

tag: menopausal   status

value: pos


title: EP53W whole blood Control genomic DNA


title: EP54W whole blood Control genomic DNA


title: Cerebellum_4_months_male

description: Gene expression values of a 4 month old male minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 4 months, male

value: Cerebellum

value: 4 months


title: EP51W whole blood Control genomic DNA


title: EP4W whole blood Control genomic DNA


title: EP50W whole blood Control genomic DNA


title: Kidney_1_week_male

description: Gene expression values of a 1 week old male minipig kidney

source_name: Total RNA from Kidney tissue, 1 week, male

value: Kidney


title: 8168 Primary

description: Gene expression data from primary tumor Breast cancer patients

value: Breast Tissue

value: Pre

value: Post

tag: er


title: Hypothalamus_2_months_female

description: Gene expression values of a 2 month old female minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 2 months, female

value: Hypothalamus

value: 2 months

value: female


title: Control:  Anti_SLBP+peptide2

city: Hanover

last: Whitfield

state: NH

address: Geisel School of Medicine; HB 7400

institute: Geisel School of Medicine at Dartmouth

description: RIP-ChIP negative control

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Axon scanner

data_processing: Images were quantified using GenePixPro; Probes were considered present when the mean intensity/median background >= 1.5.   Genes were included in the analysis only when 80% of the data points associated with that gene were present (i.e. if missing data on > 20% of the samples analyzed, the probe is then discarded).  Data points were excluded if they were manually flagged as aberrant or did not have a mean intensity/median background >= 1.5.

source_name: RNA isolated from pellet after IP from HeLa Polyribosomes (Control; Anti-SLBP pre-incubated with antigenic peptide)

label_protocol: Purified RNAbound to SLBP, or isolated in control experiments, was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3.  Total polyribosomal RNA not bound to SLBP, or isolated in the control samples, was prepared from each supernatant and reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy5.

growth_protocol: HeLa S3 cells were grown to log phase in spinner flask and polyribosomes isolated

extract_protocol: Polyribosomes were isolated form HeLa cells.  Immunoprecipitations were performed essentially as previously described (Whitfield et al. 2004 Nuc Acids Res). The SLBP antibody and affinity purified antibody have been previously described in detail (Wang et al. 1996 Genes Dev; Whitfield et al. 2000 Mol Cell Biol). Polyribosomes (30–40 mg of polyribosomal RNA) were diluted into 100 mL of NP-40 lysis buffer (0.1% Tergitol type NP-40, 50 mM Tris-HCl at pH 7.5, 150 mM NaCl, 50 mM NaF, 1 mM DTT, 10 mM EDTA, 40 U RNasin [Promega]). Nonspecific interactions between the poly- ribosomes and protein-A agarose beads were precleared by the addition of 20 mL of the 1:1 protein A bead:NP40LB slurry and incubation at 4°C for 30 min with rotation. Protein A beads were removed by centrifugation at 1500g, and the precleared superna- tant incubated for 1 h at 4°C with either 1.5 mg affinity-purified anti-SLBP, anti-SLBP preincubated with the 13 AA C-terminal peptide, or without any antibody. Antibody–protein complexes were isolated by incubation for 1 h at 4°C with a 20-mL Protein A agarose bead slurry. Beads were recovered by centrifugation at 400g and washed three times with NP-40 lysis buffer. RNA was prepared from both beads and supernatant as previously described (Whitfield et al. 2004 Nuc. Acids Res). Urea lysis buffer (7 M urea, 2% SDS, 0.35 M NaCl, 10 mM EDTA, 10 mM Tris-HCl at pH 7.5) was added to an equal volume of the supernatant (100 mL), and 200 mL added to the pellet. RNA from both was extracted in phenol:[chloroform:isoamyl alcohol (24:1)] and precipitated with ethanol.  RNA isolated from the supernatant and the precipitate of each IP reaction was labeled for microarray analysis.  The Agilent Direct Labeling Kit was used to label RNA for hybridization to the Agilent oligonucleotide microarrays.  Hybridization and washing procedures were consistent with the manufacturer’s protocol. Agilent data were centered on their mean values in both the gene and array dimensions.

value: HeLa S3

tag: protocol

value: RIP-Chip

tag: rna source

value: RNA isolated from pellet after immunopreciptation

source_name: RNA isolated from supernatent after IP (control; ant-SLBP pre-incubated with antigenic peptide)

value: supernatent

value: RIP-ChIP


title: Bone_Marrow_4_months_female

description: Gene expression values of a 4 month old female minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 4 months, female

tag: tissue

value: Bone Marrow


title: EP49W whole blood Control genomic DNA

tag: gender

value: male

value: Control

value: whole blood


title: wild-type

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

hyb_protocol: Following fragmentation, 1.9 μg of cDNAs were hybridized for 16 hours at 45oC, 60 rpm on GeneChip® Mouse Gene 1.0 ST arrays . The chips were then washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0

data_processing: CEL files were processed to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms

organism: Mus musculus

source_name: control

label_protocol: Biotinylated cDNA targets were prepared from 150 ng of total RNA using  Ambion WT Expression Kit (Cat # 4411974) and  Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: strain

tag: genotype/variation

value: wild-type

value: gastrocnemius


title: PGC-1β(i)skm-/-

source_name: PGC-1β(i)skm-/- mutant


title: Liver_4_weeks_male

description: Gene expression values of a 4 week old male minipig liver

source_name: Total RNA from Liver tissue, 4 weeks, male

value: Liver

tag: age

value: 4 weeks


title: 8165 Primary

source_name: Primary Tumor

value: Primary Tumor

value: Breast Tissue

value: Pre

value: zometa

value: pos

tag: pr

value: neg

tag: dtc positive(ihc)

value: No

tag: date of death or date patient last known to be alive (month/date/year)


title: Control:  Anti_SLBP+peptide4

description: RIP-ChIP negative control

tag: cell line

value: HeLa S3

value: RIP-Chip

value: RNA isolated from pellet after immunopreciptation

value: supernatent


title: 8166 Primary

tag: phenotype

tag: reference id

value: no

value: Post


title: Spleen_2_months_female

description: Gene expression values of a 2 month old female minipig spleen

source_name: Total RNA from Spleen tissue, 2 months, female

value: Spleen

value: 2 months

value: female


title: Control:  Anti_SLBP+peptide3

description: RIP-ChIP negative control

value: RIP-ChIP


title: 8163 Primary

value: Primary Tumor

tag: pre/post therapy

tag: date of randomisation (month/date/year)

value: Yes


title: Bone_Marrow_1_week_female

description: Gene expression values of a 1 week old female minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 1 week, female

value: Bone Marrow

value: 1 week


title: 8164 Primary

value: Breast Tissue

value: Pre

tag: allocated treatment

tag: menopausal   status

value: pos


title: 8162 Primary

value: zometa

tag: er

value: neg

tag: date of   recurrence


title: Control:  Anti_SLBP+peptide6

description: RIP-ChIP negative control

value: HeLa S3

tag: protocol

value: RIP-Chip

tag: rna source

value: RNA isolated from pellet after immunopreciptation


title: Control:  Anti_SLBP+peptide1

description: RIP-ChIP negative control

value: supernatent


title: EP48W whole blood Control genomic DNA

tag: gender

tag: disease state

value: Control

tag: tissue

value: whole blood


title: EP47W whole blood Control genomic DNA

value: female


title: Liver_2_months_male

description: Gene expression values of a 2 month old male minipig liver

source_name: Total RNA from Liver tissue, 2 months, male

value: Liver

tag: age

value: 2 months

value: male


title: Cerebellum_4_weeks_male

description: Gene expression values of a 4 week old male minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 4 weeks, male

value: Cerebellum

value: 4 weeks


title: EP45W whole blood Control genomic DNA

source_name: whole blood genomic DNA


title: Anti_SLBP_RIP_ChIP_IP7

description: RIP-ChIP antiSLBP IP

source_name: RNA isolated from pellet after IP from HeLa Polyribosomes (anti-SLBP)

source_name: RNA isolated from supernatent after IP (anti-SLBP)

value: RIP-ChIP


title: 8161 Primary

value: Primary Tumor

value: Breast Tissue

value: Pre

tag: pr

tag: dtc positive(ihc)

value: No


title: 8167 Primary

value: Post

value: zometa

value: pos

value: neg

tag: date of death or date patient last known to be alive (month/date/year)


title: 8179 Primary

tag: phenotype

value: no


title: Anti_SLBP_RIP_ChIP_IP4

description: RIP-ChIP antiSLBP IP

tag: cell line

value: HeLa S3

value: RIP-Chip

value: RNA isolated from pellet after immunopreciptation

value: supernatent


title: Testis_1_week_male

description: Gene expression values of a 1 week old male minipig testis

source_name: Total RNA from Testis tissue, 1 week, male

value: Testis

value: 1 week

value: male


title: 8160 Primary

tag: reference id

tag: pre/post therapy


title: Anti_SLBP_RIP_ChIP_IP5

description: RIP-ChIP antiSLBP IP

value: RIP-ChIP


title: Anti_SLBP_RIP_ChIP_IP6

description: RIP-ChIP antiSLBP IP


title: Spleen_4_months_female

description: Gene expression values of a 4 month old female minipig spleen

source_name: Total RNA from Spleen tissue, 4 months, female

value: Spleen

value: 4 months

value: female


title: Cortex_4_months_female

description: Gene expression values of a 4 month old female minipig cortex

source_name: Total RNA from Cortex tissue, 4 months, female

value: Cortex


title: 8158 Primary

value: Primary Tumor

value: Breast Tissue

value: Pre

tag: date of randomisation (month/date/year)

tag: allocated treatment

value: Post

value: No


title: Control:  Anti_SLBP+peptide5

description: RIP-ChIP negative control

source_name: RNA isolated from pellet after IP from HeLa Polyribosomes (Control; Anti-SLBP pre-incubated with antigenic peptide)

value: HeLa S3


title: EP41W whole blood Control genomic DNA

value: Control

value: whole blood


title: 8159 Primary

value: no

tag: menopausal   status

tag: er

value: neg

value: Yes


title: EP42W whole blood Control genomic DNA


title: EP39W whole blood Control genomic DNA


title: Anti_SLBP_RIP_ChIP_IP3

description: RIP-ChIP antiSLBP IP

tag: protocol

value: RIP-Chip

value: RNA isolated from pellet after immunopreciptation

value: supernatent


title: EP46W whole blood Control genomic DNA

value: male


title: 8156 Primary

value: zometa

value: pos

tag: date of   recurrence


title: Kidney_4_weeks_male

description: Gene expression values of a 4 week old male minipig kidney

source_name: Total RNA from Kidney tissue, 4 weeks, male

value: Kidney

value: 4 weeks

tag: gender


title: 8157 Primary

value: Primary Tumor

value: Breast Tissue

value: Pre


title: Cerebellum_2_months_male

description: Gene expression values of a 2 month old male minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 2 months, male

value: Cerebellum

value: 2 months


title: Ovary_4_months_female

description: Gene expression values of a 4 month old female minipig ovary

source_name: Total RNA from Ovary tissue, 4 months, female

value: Ovary

value: 4 months

value: female


title: Anti_SLBP_RIP_ChIP_IP1

description: RIP-ChIP antiSLBP IP

value: HeLa S3

tag: rna source

value: RIP-ChIP


title: EP38W whole blood Control genomic DNA

tag: disease state

value: Control

tag: tissue

value: whole blood


title: 7425 Primary

value: Post

tag: pr

value: No


title: Anti_SLBP_RIP_ChIP_IP2

description: RIP-ChIP antiSLBP IP

value: RIP-Chip

value: RNA isolated from pellet after immunopreciptation

value: supernatent


title: No Antibody Control 1 for Anti-SLBP

description: RIP-ChIP negative control

source_name: RNA isolated from pellet after IP from HeLa Polyribosomes (Control; No antibody)

source_name: RNA isolated from supernatent after IP (no antibody control)


title: 7424 Primary

source_name: Primary Tumor

value: Primary Tumor

value: no

value: neg

tag: dtc positive(ihc)


title: EP43W whole blood Control genomic DNA


title: Hypothalamus_1_week_male

description: Gene expression values of a 1 week old male minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 1 week, male

value: Hypothalamus

tag: age

value: 1 week

value: male


title: Cortex_2_months_male

description: Gene expression values of a 2 month old male minipig cortex

source_name: Total RNA from Cortex tissue, 2 months, male

value: Cortex

value: 2 months


title: EP34W whole blood Control genomic DNA

value: female


title: EP37W whole blood Control genomic DNA


title: No Antibody Control 2 for Anti-SLBP

description: RIP-ChIP negative control

value: HeLa S3

value: RIP-ChIP


title: 7423 Primary

tag: phenotype

value: Breast Tissue

value: Pre

value: zometa

value: pos

value: Yes

tag: date of death or date patient last known to be alive (month/date/year)


title: EP35w whole blood Control genomic DNA

value: Control

value: whole blood


title: Liver_4_weeks_female

description: Gene expression values of a 4 week old female minipig liver

source_name: Total RNA from Liver tissue, 4 weeks, female

value: Liver

value: 4 weeks


title: 7422 Primary

description: Gene expression data from primary tumor Breast cancer patients

value: Primary Tumor

tag: reference id

value: Post

value: neg


title: 7420 Primary

tag: pre/post therapy


title: Kidney_4_months_female

description: Gene expression values of a 4 month old female minipig kidney

source_name: Total RNA from Kidney tissue, 4 months, female

value: Kidney

value: 4 months


title: EP33W whole blood Control genomic DNA

source_name: whole blood genomic DNA

value: male


title: Spleen_4_weeks_female

description: Gene expression values of a 4 week old female minipig spleen

source_name: Total RNA from Spleen tissue, 4 weeks, female

value: Spleen

value: female


title: EP32W whole blood Control genomic DNA


title: EP31W whole blood Control genomic DNA


title: Kidney_1_week_female

description: Gene expression values of a 1 week old female minipig kidney

source_name: Total RNA from Kidney tissue, 1 week, female

value: 1 week


title: EP30W whole blood Control genomic DNA


title: 7417 Primary

value: Breast Tissue

value: Pre

tag: date of randomisation (month/date/year)

value: no


title: Bone_Marrow_1_week_male

description: Gene expression values of a 1 week old male minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 1 week, male

value: Bone Marrow


title: 7421 Primary

tag: allocated treatment

value: zometa

value: No


title: Cerebellum_2_months_female

description: Gene expression values of a 2 month old female minipig cerebellum

source_name: Total RNA from Cerebellum tissue, 2 months, female

value: Cerebellum

value: 2 months


title: 7418 Primary

value: Primary Tumor

tag: menopausal   status

value: pos

value: Yes


title: 7413 Primary

value: Post

tag: er

value: neg


title: Cortex_4_weeks_male

description: Gene expression values of a 4 week old male minipig cortex

source_name: Total RNA from Cortex tissue, 4 weeks, male

value: Cortex

value: 4 weeks

value: male


title: Liver_4_months_female

description: Gene expression values of a 4 month old female minipig liver

source_name: Total RNA from Liver tissue, 4 months, female

value: Liver

value: 4 months

value: female


title: 7415 Primary

value: Breast Tissue

value: Pre

value: no


title: EP29W whole blood Control genomic DNA

value: Control

value: whole blood


title: Spleen_2_months_male

description: Gene expression values of a 2 month old male minipig spleen

source_name: Total RNA from Spleen tissue, 2 months, male

value: Spleen

value: 2 months


title: Bone_Marrow_4_weeks_male

description: Gene expression values of a 4 week old male minipig bone marrow

source_name: Total RNA from Bone Marrow tissue, 4 weeks, male

value: Bone Marrow


title: 7416 Primary

value: Primary Tumor

value: pos

value: Yes


title: 7419 Primary

value: zometa

value: Post

value: neg


title: 7414 Primary


title: EP28w whole blood Control genomic DNA


title: EP2W whole blood Control genomic DNA


title: T4-5

status: Public on Dec 15 2015

city: shanghai

first: xin

last: ge

address: xietu road

country: China

institute: xybiotech

hyb_protocol: we use the Oligo GEArray® HybPlate Express Protocol(Option 3) to simplify and accelerate the hybridization(as short as 3 hours) and washing process.

scan_protocol: The chemiluminescent array image were captured by a high quality, cooled CCD camera.

data_processing: Using the RVM model, we would find the different genes included genes from Microarray data (more details in data_processing_details.pdf).

source_name: second time palliative resection

label_protocol: Conversion of experimental RNA to labeled cRNA target by using the TrueLabeling-AMP™ 2.0 Kit (GA-030)

extract_protocol: HCC tissue from nude mice bearing HCC xenografts were prepared for eatraction of toal RNA without the contamination of proteins or salts.

tag: tissue source

value: nude mice bearing HCC xenografts

value: hepatocellular carcinoma (HCC)

tag: sample group

value: palliative resection group

tag: tissue group

value: T4; 2nd time surgically removed from palliative resection


title: T4-4


title: T4-3


title: T3-1

source_name: first time blank control

value: blank control (without further surgical intervention)

value: T3; 1st time surgically removed from blank control group


title: T3-4


title: EP27W whole blood Control genomic DNA

tag: gender

value: male

value: Control


title: T2-3

source_name: first time sham operation

value: sham operation group

value: T2; 2nd time surgically removed HCC tissues from sham operation group


title: T2-4


title: T3-2


title: T4-1


title: T2-5


title: T2-2


title: T4-2


title: T3-3


title: T2-1


title: T3-5


title: EP22W whole blood Control genomic DNA

tag: disease state

value: whole blood


title: 7412 Primary

source_name: Primary Tumor

value: Primary Tumor

tag: tissue

value: Breast Tissue

value: Pre

tag: date of   recurrence


title: T1-5

source_name: first time palliative resection

value: T1; 1st time surgically removed from palliative resection


title: Hypothalamus_1_week_female

description: Gene expression values of a 1 week old female minipig hypothalamus

source_name: Total RNA from Hypothalamus tissue, 1 week, female

value: Hypothalamus

value: 1 week

value: female


title: EP16W whole blood Control genomic DNA


title: EP15W whole blood Control genomic DNA


title: EP17W whole blood Control genomic DNA


title: EP13W whole blood Control genomic DNA


title: T1-4

value: nude mice bearing HCC xenografts

value: hepatocellular carcinoma (HCC)


title: T1-1

value: palliative resection group


title: 41373W whole blood Control genomic DNA


title: T1-2


title: T1-3


title: EP14W whole blood Control genomic DNA


title: EP12w whole blood Control genomic DNA


title: Diabetic 5

city: Camperdown, Sydney

first: Rima

last: Chaudhuri

state: NSW

address: D17 Johns Hopkins Drive

department: Charles Perkins Center

country: Australia

institute: University of Sydney

description: Diabetic

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.

source_name: 27633_Diabetic_skeletal muscle

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).

extract_protocol: Total RNA was prepared using Qiagen protocol.

treatment_protocol: Muscle tissue is collected under postprandial condition.

value: skeletal muscle

tag: metabolic class

value: Diabetic

source_name: Universal human reference

tag: reference rna source

value: RNA from 10 human cell lines


title: Obese Insulin sensitive 4

description: Obese Insulin sensitive

source_name: 27634_Obese Insulin sensitive_skeletal muscle

value: Obese Insulin sensitive


title: Diabetic 2

description: Diabetic


title: Obese Insulin sensitive 2

description: Obese Insulin sensitive


title: Obese Insulin sensitive 6

description: Obese Insulin sensitive


title: Obese Insulin sensitive 1

description: Obese Insulin sensitive


title: Diabetic 7

description: Diabetic


title: Obese Insulin sensitive 7

description: Obese Insulin sensitive


title: Obese Insulin sensitive 5

description: Obese Insulin sensitive


title: Diabetic 3

description: Diabetic


title: Diabetic 4

description: Diabetic


title: Diabetic 1

description: Diabetic


title: Diabetic 6

description: Diabetic


title: Obese Insulin Resistant 3

description: Obese Insulin Resistant

source_name: 27632_Obese Insulin Resistant_skeletal muscle

value: Obese Insulin Resistant


title: Obese Insulin Resistant 5

description: Obese Insulin Resistant


title: Obese Insulin sensitive 3

description: Obese Insulin sensitive


title: Obese Insulin Resistant 6

description: Obese Insulin Resistant


title: Obese Insulin Resistant 2

description: Obese Insulin Resistant


title: Lean Control 7

description: Lean Control

source_name: 27631_Lean Control_skeletal muscle

value: Lean Control


title: Lean Control 2

description: Lean Control


title: Obese Insulin Resistant 7

description: Obese Insulin Resistant


title: Lean Control 5

description: Lean Control


title: Obese Insulin Resistant 4

description: Obese Insulin Resistant


title: Lean Control 4

description: Lean Control


title: Lean Control 1

description: Lean Control


title: Lean Control 3

description: Lean Control


title: Obese Insulin Resistant 1

description: Obese Insulin Resistant


title: Lean Control 6

description: Lean Control


title: EP24W whole blood Control genomic DNA

source_name: whole blood genomic DNA

value: Control

value: whole blood


title: Cftr-Wildtype Mouse Small Intestine rep3

city: Minneapolis

first: Ying

last: Zhang

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

scan_protocol: Standard Illumina scan protocol

data_processing: The BeadArray data was processed via R/Bioconductor and packages lumi and limma.

label: Biotin

source_name: Mouse small intestinal epithelium

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

growth_protocol: Apc+/+ Cftr+/+ and Apc+/+ Cftrfl/fl-Villin-Cre mice were maintained in colonies at the University of Minnesota-Medical School Duluth until the age of 12 weeks.

extract_protocol: For the small intestine, villi were removed from the distal quarter of the proximal quarter, tissue was then flash frozen in liquid nitrogen. For the colon, whole tissue was removed and flash frozen in liquid nitrogen. Small intestinal and colonic tissues were extracted using QIAGEN RNeasy Mini Kit with an additional DNAse Digestion step. Quality control was performed using Agilent Bioanalyzer.

treatment_protocol: Mouse small intestine and colon tissues were removed, opened longitudinally, and rinsed in PBS.

value: small intestine

tag: cell type

value: epithelium

tag: strain

tag: genotype

value: Apc+/+ Cftr+/+-Villin-Cre

tag: age

value: 3 months


title: Cftr-Wildtype Mouse Small Intestine rep1


title: Cftr-Mutant Mouse Small Intestine rep2

value: Apc+/+ Cftrfl/fl-Villin-Cre


title: Cftr-Mutant Mouse Colon rep3

source_name: Mouse colonic epithelium

value: colon


title: Cftr-Mutant Mouse Small Intestine rep3


title: Cftr-Mutant Mouse Colon rep1


title: Cftr-Mutant Mouse Colon rep2


title: Cftr-Wildtype Mouse Colon rep2


title: Cftr-Wildtype Mouse Small Intestine rep2


title: 7411 Primary

tag: phenotype

value: Primary Tumor

value: Breast Tissue

tag: reference id

tag: pre/post therapy

value: Pre

tag: date of randomisation (month/date/year)

value: no

value: neg

tag: pr

value: pos

tag: dtc positive(ihc)

value: Yes

tag: date of death or date patient last known to be alive (month/date/year)


title: Cftr-Mutant Mouse Small Intestine rep1


title: Cftr-Wildtype Mouse Colon rep1


title: WAP-Cre:PTENp53 Tumor TW53-88

first: Jeff

last: Liu

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

description: Gene expression data from primary WAP-Cre:PTENp53 tumor

hyb_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek software and absolute expression values were obtained. Batch-correction was performed by Partek

source_name: Mouse Mammary Tumor

growth_protocol: Samples from independent primary mammary tumors from MMTV-Neu,WAP-Cre:PTEN:p53-R270H, WAP-Cre:PTEN:p53 models and wild-type mammary glands were frozen and kept in -80 degree.

extract_protocol: Total RNA was extracted with Trizol reagent twice. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Total RNA obtained from primary tumors were used for microarray analysis to determine differentially regulated genes among different mouse models.  Cluster analysis and pathway analysis based on gene expression were then performed to determine significant genes/pathways

tag: sample

value: Mammary Tumor less than 1.0 cm diameter

tag: histology

value: Spindle


title: WAP-Cre:PTENp53 Tumor TW53-63

scan_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

tag: tissue


title: WAP-Cre:PTENp53 Tumor TW53-227

label_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

value: Mixed Spindle and Epithelial


title: WAP-Cre:PTENp53 Tumor TW53-70


title: Cftr-Wildtype Mouse Colon rep3


title: WAP-Cre:PTENp53 Tumor TW53-51


title: WAP-Cre:PTENp53 Tumor TW53-104b


title: CIP4G_00180

city: Shenzhen

first: zhong

last: chen

address: No 89, Taoyuan Road, Nanshan district, Shenzhen 518052, China.

institute: the Affiliated Shenzhen Nanshan Hospital, Guangdong Medical College

hyb_protocol: 1.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing Agilent fragmentation buffer and Agilent blocking agent according to the manufacturer protocol. After fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 custom 8×60K Microarrays (G4102A) for 17 hours at 65°C in a rotating hybridization oven (Agilent).  Then the Microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Microarrays were scanned after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed using the Feature Extraction Software (Agilent) with default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Escherichia coli

source_name: cDNA of EPEC strain

label_protocol: The fluorescent dye of Cyanine-3 (Cy3) was used for cRNA label. The amount of 0.5 ug RNA was used for cRNA label by the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). The cRNA yield were assayed by the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Trizol Reagent and a RiboPure kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol. RNA integrity was assessed using an Agilent 2100 bioanalyser (Agilent, Palo Alto, CA, USA).

value: EPEC

tag: time point

value: 180 min

tag: treatment

value: 4ug/ml of ciprofloxacin


title: WAP-Cre:PTENp53 Tumor TW53-105


title: CIP2G_00180

value: 2ug/ml of ciprofloxacin


title: WAP-Cre:PTENp53 Tumor TW53-80


title: CIPSG_00180

value: saline


title: CIPSG_00135

value: 135 min


title: WAP-Cre:PTENp53 Tumor TW53-102

description: Gene expression data from primary MMTV-Neu tumor


title: WAP-Cre:PTENp53 Tumor TW53-104


title: CIP2G_00135


title: CIP2G_00090

value: 90 min


title: WAP-Cre:PTEN:p53-R270H Tumor LSL334-3R

value: Primary Tumor


title: WAP-Cre:PTEN:p53-R270H Tumor LSL88

value: Poorly Differentiated


title: MMTV-Neu Tumor N362

value: MMTV-Neu

value: Epithelial


title: WAP-Cre:PTENp53 Tumor TW53-102b


title: WAP-Cre:PTEN:p53-R270H Tumor LSL372-3L


title: WAP-Cre:PTEN:p53-R270H Tumor LSL211-L5


title: WAP-Cre:PTEN:p53-R270H Tumor LSL165


title: MMTV-Neu Tumor N334


title: WAP-Cre:PTEN:p53-R270H Tumor LSL228-2R


title: CIPSG_00045

value: 45 min


title: CIP4G_00090


title: WAP-Cre:PTEN:p53-R270H Tumor LSL245 R3


title: WAP-Cre:PTEN:p53-R270H Tumor LSL285-2-2L


title: MMTV-Neu Tumor N348


title: WAP-Cre:PTEN:p53-R270H Tumor J287-R


title: CIP4G_00135


title: CIPSG_00000


title: CIP2G_00000


title: WAP-Cre:PTEN:p53-R270H Tumor LSL276-3R


title: Wild Type Mammary Gland FvB6L

source_name: Mouse Mammary Gland

value: Mammary Epithelial

value: Wild Type

value: Purified Mammary Epithelial lin- cells


title: CIP2G_00045


title: WAP-Cre:PTEN:p53-R270H Tumor LSL374-2R

value: Mammary Tumor less than 1.0 cm diameter


title: WAP-Cre:PTEN:p53-R270H Tumor LSL314

value: Spindle


title: WAP-Cre:PTEN:p53-R270H Tumor LSL243 R2


title: WAP-Cre:PTEN:p53-R270H Tumor J356 R


title: Wild Type Mammary Gland FvB5L


title: CIPSG_00090

value: EPEC


title: CIP4G_00045


title: CIP4G_00000


title: Wild Type Mammary Gland FvB4L


title: ISL1_D14_1

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
Growth factor receptors expressed on differentiated cardiac cell types_replicate 1
Gene expression data from fetal heart cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HumanHT-12 v4 Beadchip Array.

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

data_processing: The data were normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 20.

source_name: ISL1+ differentiated cardiac cell

growth_protocol: The ISL1+ progenitor cell was cultured in basal medium (CGM) comprising of 35% complete IMDM/65% DMEM–Ham F-12 mix, containing 2% B27, 2% BSA Fraction V, 0.1 mmol/L 2-mercaptoethanol, 4 ng/ml epidermal growth factor (EGF), 10 ng/ml basic fibroblast growth factor (bFGF), 40 nmol/L cardiotrophin-1, 40 nmol/L thrombin, 1% Pen/Strep and 1% L-Glutamine. Endothelin-1 and WNT3A were supplemented fresh into the medium.

treatment_protocol: Differentiation of ISL1+ progenitor cells towards endothelial cells was achieved by culturing the cells in low serum (5%) containing basal medium (DMEM-Ham F-12). The medium was supplemented with VEGF (50ng/ml), Pen/strep (1%) and L-glutamine (1%).

tag: tissue type

value: fetal heart


title: OFT_11_R1

description:
Human Fetal Heart Week 11_Outflow Tract_replicate 1
Gene expression data from fetal heart cells

source_name: Fetal Heart


title: OFT_11_R3

description:
Human Fetal Heart Week 11_Outflow Tract_replicate 3
Gene expression data from fetal heart cells


title: RV_11_R3

description:
Human Fetal Heart Week 11_Right Ventricle_replicate 3
Gene expression data from fetal heart cells


title: ISL1_D7_2

description:
Growth factor receptors expressed on ISL1+ progenitor cell_replicate 2
Gene expression data from fetal heart cells

source_name: ISL1+ progenitor


title: RA_11_R2

description:
Human Fetal Heart Week 11_Right Atrium_replicate 2
Gene expression data from fetal heart cells


title: LV_11_R2

description:
Human Fetal Heart Week 11_Left Ventricle_replicate 2
Gene expression data from fetal heart cells


title: RV_11_R1

description:
Human Fetal Heart Week 11_Right Ventricle_replicate 1
Gene expression data from fetal heart cells


title: ISL1_D7_1

description:
Growth factor receptors expressed on ISL1+ progenitor cell_replicate 1
Gene expression data from fetal heart cells


title: RA_11_R3

description:
Human Fetal Heart Week 11_Right Atrium_replicate 3
Gene expression data from fetal heart cells


title: RV_11_R2

description:
Human Fetal Heart Week 11_Right Ventricle_replicate 2
Gene expression data from fetal heart cells


title: LV_11_R3

description:
Human Fetal Heart Week 11_Left Ventricle_replicate 3
Gene expression data from fetal heart cells


title: LV_11_R1

description:
Human Fetal Heart Week 11_Left Ventricle_replicate 1
Gene expression data from fetal heart cells


title: LA_11_R2

description:
Human Fetal Heart Week 11_Left Atrium, replicate 2
Gene expression data from fetal heart cells


title: LA_11_R1

description:
Human Fetal Heart Week 11_Left Atrium, replicate 1
Gene expression data from fetal heart cells


title: 608_2

city: Yongin

first: Young-Chul

last: Choi

state: Gyeonggi-do

address: 1 Seocheon-dong Giheung-gu

institute: Kyung Hee University

description: test 2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human HT-12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using LPE test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: A549 cells transfected with miR-608 mimic

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: A549 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturer's protocol.

treatment_protocol: A549 cells were transfected with miR-552-3p, miR-608 and negative control mimics using Lipofectamine RNAiMAX and total RNA was prepared 24 hour post-transfection.

tag: cell line

tag: cell type

value: lung cancer


title: LA_11_R3

description:
Human Fetal Heart Week 11_Left Atrium, replicate 3
Gene expression data from fetal heart cells


title: OFT_11_R2

description:
Human Fetal Heart Week 11_Outflow Tract_replicate 2
Gene expression data from fetal heart cells


title: RA_11_R1

description:
Human Fetal Heart Week 11_Right Atrium_replicate 1
Gene expression data from fetal heart cells


title: NC_2

description: control 2

source_name: A549 cells transfected with negative control mimic


title: RCSC clone 1

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

data_processing: The data were normalised using quantile normalisation with Genespring 11.0

source_name: human kidney_RCSCs

extract_protocol: Total RNA was extracted from a minimum of 10^6 cells/line cultured in under EGM-MV medium (Lonza, Valais, Switzerland) supplemented with 20% FBS (Sigma-Aldrich) using the miRNeasy Mini Kit (Qiagen Group) The RNA concentrationwas determined with NanoDrop Spectrophotometer (Nanodrop Technologies). The RNA quality was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies), and only samples with RNA integrity number >8.5 were used.

tag: tissue origin

value: kidney

value: Renal Cancer Stem Cells (RCSCs)


title: RCSC clone 3


title: RCSC clone 6


title: NC_1

description: control 1


title: 552_2

description: test 4

source_name: A549 cells transfected with miR-552-3p mimic


title: RCSC clone 4


title: RCSC clone 5


title: 552_1

description: test 3


title: RCSC clone 2


title: 608_1

description: test 1


title: tARPC clone 6

source_name: human kidney_tARPCs

value: tubular Adult Renal Progenitor Cells (tARPCs)


title: tARPC clone 5


title: MSC clone 3

source_name: human bone marrow_MSCs

value: Bone marrow

value: Mesenchymal Stem Cells (MSC).


title: tARPC clone 3


title: MSC clone 1


title: tARPC clone 2


title: tARPC clone 1


title: RPTEC clone 2

source_name: human kidney_RPTECs

value: Renal Proximal Tubular Cells (RPTEC)


title: RPTEC clone 1


title: MSC clone 2


title: RPTEC clone 3


title: HepG2_0.5_%_DMSO_3_72h_rep3

city: Maastricht

first: Jian

last: Jiang

address: Maastricht University

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files v14.1 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the Arrayanalysis.org web service. This resulted in 18,988 probe sets.

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) (Sigma-Aldrich, Zwijndrecht, The Netherlands) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Total RNA was isolated after 24 hours of incubation with compound or solvent control in HepG2 total RNA was isolated from cells using miRNeasy mini Kit (Qiagen Westburg bv, Leusden, the Netherlands) according to the manufacturer’s instructions and followed by a DNAse I (Qiagen Inc.) treatment. RNA quantity was measured on a spectrophotometer and quality was determined on a BioAnalyzer (Agilent Technologies, Breda, the Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with a RIN level higher than 8 were used.

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% v/v DMSO or 0.5/10mM acetaminophen)

tag: compound, dose

tag: time

value: hepatocellular carcinoma cell line


title: HepG2_500_µM_Acetominophen_72h_rep1

value: APAP, 500 µM


title: HepG2_0.5_%_DMSO_3_72h_rep1


title: HepG2_0.5_%_DMSO_3_72h_rep2


title: HepG2_500_µM_Acetominophen_72h_rep2


title: HepG2_10000_µM_Acetominophen_72h_rep3

value: APAP, 10000 µM


title: HepG2_500_µM_Acetominophen_72h_rep3


title: HepG2_10000_µM_Acetominophen_72h_rep2


title: HepG2_10000_µM_Acetominophen_48h_rep3


title: HepG2_0.5_%_DMSO_3_48h_rep2


title: HepG2_500_µM_Acetominophen_48h_rep3


title: HepG2_0.5_%_DMSO_3_48h_rep3


title: HepG2_10000_µM_Acetominophen_72h_rep1


title: HepG2_500_µM_Acetominophen_48h_rep1


title: HepG2_10000_µM_Acetominophen_48h_rep1


title: HepG2_10000_µM_Acetominophen_48h_rep2


title: HepG2_0.5_%_DMSO_3_48h_rep1


title: HepG2_500_µM_Acetominophen_48h_rep2


title: HepG2_0.5_%_DMSO_3_24h_rep3


title: HepG2_0.5_%_DMSO_3_24h_rep2


title: BL2 Cont rep1

city: New Haven

first: Yasuhiro

last: Nakayama

state: CT

address: 1 Gilbert St

department: Genetics

institute: Yale University

description: SAMPLE 2

hyb_protocol: Standard Illumina hybridizatiion protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized and analyzed in R

label_protocol: RNA was labelled according to the manufacturer's protocol

growth_protocol: The cell line was grown in RPMI1640 medium (Gibco/BRL, Gaithersburg, MD) supplemented with10% FCS and was maintained in a 5% CO2 incubator at 37C.

extract_protocol: Total RNA was extracted according to the manufacturer's protocol

treatment_protocol: shRNA experiments were performed using Mission lentiviral transduction particles (Sigma-aldrich). These had four different target sequences (TRCN14764-14767) aimed against the same RNA. Among them TRCN0000014674 showed significant suppression and was thus used for the present study. Results were further independently confirmed by other siRNAs targeting to different regions of the mRNA. pLKO1.puro(Open Biosystems) was used for silencing short RNA hairpin constructs containing IRF4 target sequences.  Lentivirus Packaging was performed in HEK293T cells with VSV-G and target hairpin RNA. Puromycin kill curves in BL2 cells showed a 100% cell death at 1 ug/mL, which was subsequently used for all of our studies. The lentiviral tranducing particles had TU8x10^6/ml. 0.43x10^6/50ul multiplicity of infection (MOI)1. Just before infection we added 8ug/ml of hexadimethrine bromide for transducing viral particles. We infected BL2 cells at 3 different concentrations; Moi.1, 2, and 5. Viral particle-containing media were replaced with fresh cell culture medium the following day. Half of the media were replaced with fresh media containing puromycin at 1ug/ml subsequently. We replaced puromycine containing medium every 3 days. After significant IRF4 reduction was confirmed by q-PCR, IRF4 KO sample swere processed for Illumina Beads Expression Arrays (SABiosciences A Qiagen), and their expression value differences with respect to controls were recorded.

value: Burkitt's lymphoma-derived B cell line

tag: infected with

value: lentivirus expressing shRNA for IRF5


title: HepG2_500_µM_Acetominophen_24h_rep1


title: HepG2_0.5_%_DMSO_3_24h_rep1


title: HepG2_10000_µM_Acetominophen_24h_rep3


title: embryo at E11.5, Wild-type, whole-body

city: Bunkyo-ku

first: Noriko

last: Funato

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression data from E11. 5 Wild-type embryos

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner3000 (Affymetrix 00-0074).

data_processing: The data were analyzed with GeneChip Operating Software ver1.4 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to  500.

source_name: mouse wild-type embryos at E11.5

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT Express Kit User Manual, P/N 702646 Rev.1 Affymetrix).

growth_protocol: Wild-type and Hand2 mutant (Hand2 CAT/+; Wnt1-Cre) embryos were collected at E11.5 or E12.5.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) and Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS and placed on ice in the Trizol solution (GibcoBRL).

tag: genotype

value: wildtype

value: whole-body

tag: developmental stage

tag: background strain

value: mixed C57BL/6J x ICR


title: BL2 shIRF4 rep1

description: SAMPLE 1

value: lentivirus expressing shRNA for control


title: HepG2_10000_µM_Acetominophen_24h_rep2


title: HepG2_500_µM_Acetominophen_24h_rep3


title: Cells treated with 1D11 TGFB1 inhibitor replicate 1

city: Mountain View

first: Afshin

last: Beheshti

address: Moffett Blvd

institute: NASA Ames Research Center

description: Gene expression data from LLC Cells with 1D11 treatment

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

scan_protocol: GeneChips were scanned using the Affymetrix 3000 laser scanner.

data_processing: The data were analyzed with RMAExpress which performs background adjustments and quantile normalization

source_name: LLC tumor treated with 1D11

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

extract_protocol: RNA was isolated using RNeasy Minikit (Qiagen)

treatment_protocol: LLC cells (1X 105) were subcutaneously injected into the right flank of 6 to 8 week-old C57BL/6 female mice. When tumors were 60-80 mm3, Mice were randomized to achieve comparable mean tumor size for each treatment group. Tumors were collected for gene expression profiling study at day19 post-injection.

value: LLC


title: embryo at E12.5, Wild-type, head

description: Gene expression data from E12. 5 Wild-type embryos

source_name: mouse wild-type embryos at E12.5

value: head


title: HepG2_500_µM_Acetominophen_24h_rep2


title: Cells treated with 1D11 TGFB1 inhibitor and radiation replicate 2

description: Gene expression data from LLC Cells with 1D11 and 2Gy of radiatioin

source_name: LLC tumor treated with 1D11 + Radiation

value: 1D11 + 5 X 6Gy Radiation


title: embryo at E12.5, Hand2 mutant, head

description: Gene expression data from E12. 5 Hand2 mutant embryos

source_name: mouse Hand2 mutant embryos at E12.5

value: Hand2 mutant (Hand2 CAT/+; Wnt1-Cre)


title: HepG2_10000_µM_Acetominophen_24h_rep1


title: Cells treated with 1D11 TGFB1 inhibitor and radiation replicate 1


title: Cells treated with radiation replicate 1

description: Gene expression data from LLC Cells with 2Gy of radiatioin

source_name: LLC tumor treated with Radiation

value: 13C4 + 5 X 6Gy Radiation


title: embryo at E11.5, Hand2 mutant, whole-body

description: Gene expression data from E11. 5 Hand2 mutant embryos

source_name: mouse Hand2 mutant embryos at E11.5


title: Cells treated with radiation replicate 2


title: HepG2_0.5_%_DMSO_3_12h_rep3


title: Cells treated with 1D11 TGFB1 inhibitor replicate 2


title: Cells treated with 1D11 TGFB1 inhibitor and radiation replicate 3


title: Cells treated with radiation replicate 3


title: HepG2_0.5_%_DMSO_3_12h_rep2


title: Control Replicate 3

description: Gene expression data from LLC Cells as Controls

source_name: LLC tumor Control


title: Control Replicate 2


title: Cells treated with 1D11 TGFB1 inhibitor replicate 3


title: HepG2_500_µM_Acetominophen_12h_rep3


title: HepG2_500_µM_Acetominophen_12h_rep2


title: HepG2_500_µM_Acetominophen_12h_rep1


title: Control Replicate 1


title: HepG2_0.5_%_DMSO_3_12h_rep1


title: HepG2_10000_µM_Acetominophen_12h_rep2


title: HepG2_10000_µM_Acetominophen_12h_rep1


title: HepG2_10000_µM_Acetominophen_12h_rep3


title: TRAMPxPWK F2 prostate tumor P503

city: Bethesda

first: Nigel

last: Crawford

state: MD

address: 50 South Drive, Room 5154

institute: Human Genome Research Institute

description: gene expression data from Tg+ F2 male prostate tumor

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to The Affymetrix mouse GeneChip® 2.0 ST chips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described. by Affymetrix.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Data was processed using Partek.

source_name: TRAMPxPWK tumor

label_protocol: Labeling performed using GeneChip® Terminal Labeling kit according to manufacturer's protocol.

growth_protocol: Transgene-positive F2 male tumor growth and metastases were quantified either at 30 weeks or when humane experimental endpoints were reached.

extract_protocol: Total RNA was isolated from tumor samples using QIAGEN RNeasy mini kit.

treatment_protocol: Prostate tumor sample were collected and snap frozen in liquid nitrogen, then stored at -80 degrees until ready for RNA extraction.

tag: cross

value: TRAMPxPWK/PhJ F2

value: mouse prostate tumor

tag: genetic background

value: F2 mice from a mixed (C57BL/6-Tg(TRAMP)8247Ng/J x PWK/PhJ) background


title: TRAMPxPWK F2 prostate tumor P1394


title: TRAMPxPWK F2 prostate tumor P217


title: TRAMPxPWK F2 prostate tumor P268


title: TRAMPxPWK F2 prostate tumor P502


title: TRAMPxPWK F2 prostate tumor P474


title: TRAMPxPWK F2 prostate tumor P569


title: tARPC clone 4

hyb_protocol: Standard Illumina hybridization protocol

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

value: kidney

value: tubular Adult Renal Progenitor Cells (tARPCs)


title: TRAMPxPWK F2 prostate tumor P757


title: TRAMPxPWK F2 prostate tumor P509


title: TRAMPxPWK F2 prostate tumor P1218


title: TRAMPxPWK F2 prostate tumor P500


title: TRAMPxPWK F2 prostate tumor P237


title: TRAMPxPWK F2 prostate tumor P609


title: TRAMPxPWK F2 prostate tumor P912


title: B3-Hr76-3

city: Chicago

first: Wei

address: 680 N. Lake Shore Drive, Suite 1400

institute: Northwestern University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio
Unmethylated and methylated signal intensities

source_name: iCell Neurons 3

label_protocol: Standard Illumina Protocol

extract_protocol: At each timepoint, DNA was extracted by adding 50 ul per well of tissue digestion buffer (100 mM NaCl, 50 mM Tris 8.0, 100 mM EDTA, 1% SDS) along with 2 mg/ml Proteinase K (Denville Scientific; South Plainfield, NJ). The plate was sealed with parafilm and agitated overnight at 55°C using 200 RPM in an Innova orbital shaker (Eppendorf; Enfield, CT). The digested cells from each well was combined and DNA extracted with equal volume of phenol:chloroform (Invitrogen), vortexing for 10 minutes (Lab Vortex-setting of 4) and the samples were centrifuged for 5 minutes at 14000 g.   The aqueous phase was collected, extracted with equal volume of chloroform and repeated two times. The DNA was precipitated with equal volume 100% ethanol and centrifuged for 10 minutes as 14000 g. Two washes with 70% ethanol produced a pellet that was air dried for 10 minutes at room temperature and finally dissolved in 50 µl of 10 mM Tris (8.0) for 3 days at 4°C then stored at -70°C.

value: 76 hrs

value: iCell Neurons

tag: disease state

value: normal


title: Ar-N2-CAP-2

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description:
U937 cells were treated with Ar-N2-CAP for 2 min followed by culturing  at 37°C for 3 h (2)
Ar-N2-CAP-2

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
GeneChip Analysis Suite

source_name: Human myelomonocytic lymphoma cell line U937

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: The human myelomonocytic lymphoma U937 cells were obtained from the Human Science Research Resources Bank of the Japan Health Sciences Foundation (Tokyo, Japan). The cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, and maintained at 37°C in humidified air with 5% CO2 and 95% air.

extract_protocol: Total RNA was extracted from cells using a NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: The cells in a well of 24-well-plate were exposed to Ar-CAP or Ar containing 2.5 % of N2 (Ar-N2-CAP) generated by using a 20 kHz low frequency at 18 kV at a flow rate of 2 L/min for 2 min at room temperature. After CAP-treatment, the cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C for 3 h.

tag: gender

value: male

tag: age

value: 37 years

value: lymphoma, diffuse histiocytic, monocyte-like characteristics

tag: life span

value: infinite

tag: morphology

value: diffuse histiocytic lymphoma

value: myelomonocytic lymphoma cell line U937


title: Ar-N2-CAP-1

description:
U937 cells were treated with Ar-N2-CAP for 2 min followed by culturing  at 37°C for 3 h (1)
Ar-N2-CAP-1

tag: tissue

tag: treatment


title: TRAMPxPWK F2 prostate tumor P1225


title: B3-Hr4-2

tag: time point

value: 4 hrs

tag: cell type


title: Ar-CAP-1

description:
U937 cells were treated with Ar-CAP for 2 min followed by culturing  at 37°C for 3 h (1)
Ar-CAP-1

tag: cell line

value: Ar-CAP


title: TRAMPxPWK F2 prostate tumor P902


title: B1-Hr28-3

source_name: iCell Neurons 1

value: 28 hrs


title: TRAMPxPWK F2 prostate tumor P311

value: TRAMPxPWK/PhJ F2


title: B3-Hr28-3


title: B3-Hr4-3


title: Ar-CAP-2

description:
U937 cells were treated with Ar-CAP for 2 min followed by culturing  at 37°C for 3 h (2)
Ar-CAP-2


title: B2-Hr28-2

source_name: iCell Neurons 2


title: B3-Hr0-3

value: 0 hr


title: B3-Hr4-4


title: B2-Hr28-3


title: B1-Hr76-3


title: Control (nontreatment)-2

description:
U937 cells were cultured at  37°C for 3 h (2)
Ctr-2

value: Control


title: B4-Hr0-2

source_name: iCell Neurons 4


title: B2-Hr4-3


title: B4-Hr0-3


title: B3-Hr76-4

label: Cy5 and Cy5


title: B1-Hr28-2


title: TRAMPxPWK F2 prostate tumor P1469

value: mouse prostate tumor

value: F2 mice from a mixed (C57BL/6-Tg(TRAMP)8247Ng/J x PWK/PhJ) background


title: B4-Hr0-1


title: B3-Hr28-4

label: Cy5 and Cy4


title: RPTEC clone 3 +INF-alpha

data_processing:
The data were normalised using Shift to 75 percentile with Genespring 11.0 (baseline transformation: median of all samples)
Please note that the data in the sample data table just normalized values without additional processing/normalization. However, additional processing/normalization procedure were performed to filter statistical significant probes.

source_name: RPTECs_INF-alpha stimulated

extract_protocol: Total RNA was isolated with RNA easy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions and quantified by NanoDrop ND-1000 Spectrophotometer  (NanoDrop Technologies, Inc.) and its quality was assessed by  Agilent 2100 Bioanalyzer (Agilent Technologies), and only samples with RNA integrity number >8.5 were used.

value: kidney

value: human renal proximal tubular epithelial cells (RPTECs)

tag: stimulated with

value: 100U/ml INF-alpha  for 48 hrs


title: Control (nontreatment)-1

description:
U937 cells were cultured at  37°C for 3 h (1)
Ctr-1

value: male


title: RPTEC clone 1 +INF-alpha


title: TRAMPxPWK F2 prostate tumor P219


title: RPTEC clone 2 +INF-alpha


title: TRAMPxPWK F2 prostate tumor P1276


title: TRAMPxPWK F2 prostate tumor P235


title: B2-Hr28-1

value: iCell Neurons

value: normal


title: TRAMPxPWK F2 prostate tumor P803


title: TRAMPxPWK F2 prostate tumor P233


title: RPTEC clone 2

value: none (unstimulated control)


title: B2-Hr76-3

value: 76 hrs


title: RPTEC clone 1


title: B3-Hr28-2


title: B1-Hr4-2


title: TRAMPxPWK F2 prostate tumor P425


title: B1-Hr76-2


title: TRAMPxPWK F2 prostate tumor P966


title: B3-Hr76-2


title: TRAMPxPWK F2 prostate tumor P471


title: TRAMPxPWK F2 prostate tumor P619


title: B3-Hr0-2