title: evolved polyploid cell 6, replicate 4

description:
Sample name: evo6-rep4
Derived from anc6.
Technical replicate 4 of 4. Polyploid/haploid cells.


title: evolved polyploid cell 6, replicate 3

status: Public on Oct 11 2016

type: genomic

city: Taipei

first: Jun-Yi

last: Leu

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

country: Taiwan

institute: Institute of Molecular Biology

description:
Sample name: evo6-rep3
Derived from anc6.
Technical replicate 3 of 4. Polyploid/haploid cells.

hyb_protocol: The hybridization protocol was adapted from Microarray Core Facility, Institute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html).

scan_protocol: Arrays were scanned for F635 (Cy5) and F532 (Cy3) fluorescence intensities using AXON 4000B (Molecular Device, Sunnyvale, CA).

data_processing: LOWESS normalized, background subtracted data obtained from signals. Agilent GeneSpring GX 7.3 was used.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae polyploid cells at 1000 generations

label_protocol: The labeling protocol was adapted from Microarray Core Facility, Institute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html).

growth_protocol: Yeast cells were grown in YPD medium at 23 degrees Celsius.

extract_protocol: Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit.

tag: strain/background

tag: ploidy

value: polyploid

tag: sample type

value: evolved

source_name: S. cerevisiae haploid cells

value: haploid


title: Bp072_UC NR W4/6_IFX_43

type: RNA

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Colonic mucosal biopsy from UC non-responder (NR) 43 week (W) 4-6 after infliximab (IFX) therapy

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

tag: study individual number

tag: week (w)

tag: induction therapy_maintenance therapy

value: IFX

tag: mayo endoscopic subscore

tag: tissue

value: colonic mucosal biopsy


title: mammary carcinoma induced by postpubertal irradiation, replicate3

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: M1148 Mt.4

hyb_protocol: Labeled DNAs (3.5 µg) were combined and mixed with rat Cot-1 DNA (10 mM final concentration; Applied Genetics Laboratories, Melbourne, FL, USA), the Agilent Blocking Agent, de-ionized formamide, and the Agilent Hybridization Buffer at 67°C for 40 hours.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)  and analyzed with Agilent Genomic Workbench standard Edition 6.5 software for methylation analysis.

organism: Rattus norvegicus

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent Genomic DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Rats were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (CE-2; Clea Japan, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was isolated by proteinase K digestion, followed by phenol/chloroform extraction.

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (2 Gy, 0.6 Gy/min) at 3 or 7 weeks of age. Rats were fed AIN-76A diet containing 23.5% corn oil (Clea Japan) after 9 weeks of age.

tag: disease status

value: carcinoma

tag: gender

value: female

tag: strain

value: Sprague-Dawley

tag: age at irradiation

value: 7 weeks

tag: isolation of methylated dna

value: methyl-CpG binding domain-based protein

value: mammary carcinoma


title: mammary carcinoma induced by postpubertal irradiation, replicate4

description: M1182 Mt.1


title: mammary carcinoma induced by postpubertal irradiation, replicate5

description: M1192 Mt.1


title: Bp069_Active UC W0_IFX_43

description: Colonic mucosal biopsy from active UC patient 43 before infliximab (IFX) therapy


title: mammary carcinoma induced by postpubertal irradiation, replicate1

description: M1113 Mt.2


title: mammary carcinoma induced by postpubertal irradiation, replicate2

description: M1113 Mt.3


title: evolved polyploid cell 6, replicate 2

description:
Sample name: evo6-rep2
Derived from anc6.
Technical replicate 2 of 4. Polyploid/haploid cells.


title: evolved polyploid cell 6, replicate 1

description:
Sample name: evo6-rep1
Derived from anc6.
Technical replicate 1 of 4. Polyploid/haploid cells.


title: evolved polyploid cell 5, replicate 2

description:
Sample name: evo5-rep2
Derived from anc5.
Technical replicate 2 of 4. Polyploid/haploid cells.


title: evolved polyploid cell 5, replicate 4

description:
Sample name: evo5-rep4
Derived from anc5.
Technical replicate 4 of 4. Polyploid/haploid cells.


title: MMTV_PyMT_375_Macro

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: Breast cancer GEM, Tumor 375

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 48C on Human Gene 2.1 ST array. GeneChips were washed and stained in the Affymetrix GeneTitan.

scan_protocol: GeneChips were scanned in the Affymetrix GeneTitan.

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

organism: Mus musculus

source_name: tumor

label_protocol: RNA was amplified by WT expression kit (Ambion) and Biotinylated by WT terminal labeling kit (Affymetrix)

growth_protocol: Tumor and tumor-associated stromal cells were obtained after tissue dissociation of 1500mm3 tumors

extract_protocol: Total RNA was isolated from the sorted fractions using the RNAeasy Plus Micro kit (Qiagen, Inc.)

treatment_protocol: Dissociation of tumors was performed using an procedure optimized for our tumors described in Petit et al. [ Petit V, Massonnet G, Maciorowski Z, Touhami J, Thuleau A, Nemati F, et al. Optimization of tumor xenograft dissociation for the profiling of cell surface markers and nutrient transporters. Lab Invest. 2013].

tag: tumor type

value: Breast cancer

tag: model type

value: Genetically Engineered Model

tag: cell type

value: Mouse macrophages (M1+M2)

tag: mouse type

value: FVB

tag: patient id


title: mammary carcinoma induced by prepubertal irradiation, replicate7

description: M1501 Mt.4

value: 3 weeks


title: evolved polyploid cell 5, replicate 1

description:
Sample name: evo5-rep1
Derived from anc5.
Technical replicate 1 of 4. Polyploid/haploid cells.

tag: strain/background

tag: ploidy


title: MMTV_PyMT_375_Cell_Tum

description: Breast cancer GEM, Tumor 375

value: Mouse tumor cells


title: mammary carcinoma induced by prepubertal irradiation, replicate5

description: M1499 Mt.2


title: evolved polyploid cell 4, replicate 4

description:
Sample name: evo4-rep4
Derived from anc4.
Technical replicate 4 of 4. Polyploid/haploid cells.

value: polyploid

tag: sample type


title: evolved polyploid cell 5, replicate 3

description:
Sample name: evo5-rep3
Derived from anc5.
Technical replicate 3 of 4. Polyploid/haploid cells.

value: evolved


title: MMTV_PyMT_360_Cell_Tum

description: Breast cancer GEM, Tumor 360


title: MMTV_PyMT_360_Macro

description: Breast cancer GEM, Tumor 360


title: mammary carcinoma induced by prepubertal irradiation, replicate6

description: M1501 Mt.2


title: mammary carcinoma induced by prepubertal irradiation, replicate4

description: M1496 Mt.4


title: MMTV_PyMT_369_Macro

description: Breast cancer GEM, Tumor 369


title: BC256_LEV_37_Macro

description: Breast cancer PDX n° 256, Tumor 37

value: Patient-Derived xenograft (PDX)

value: Nude

value: LEV


title: mammary carcinoma induced by prepubertal irradiation, replicate3

description: M1495 Mt.1

value: carcinoma


title: normal mammary gland, replicate3

source_name: normal mammary gland

value: normal

value: female

value: non-irradiated

value: mammary gland


title: MMTV_PyMT_369_Cell_Tum

description: Breast cancer GEM, Tumor 369


title: BC256_LEV_26_Macro

description: Breast cancer PDX n° 256, Tumor 26


title: BC111_VINC_2_Macro

description: Breast cancer PDX n° 111, Tumor 2

value: VINC


title: evolved polyploid cell 4, replicate 3

description:
Sample name: evo4-rep3
Derived from anc4.
Technical replicate 3 of 4. Polyploid/haploid cells.

value: haploid


title: mammary carcinoma induced by prepubertal irradiation, replicate1

description: M1180 Mt.1

value: Sprague-Dawley

value: methyl-CpG binding domain-based protein

value: mammary carcinoma


title: normal mammary gland, replicate2


title: mammary carcinoma induced by prepubertal irradiation, replicate2

description: M1493 Mt.1

value: 3 weeks


title: normal mammary gland, replicate1


title: evolved 2/ ancestral 2 cells, replicate 2

description:
Sample name: evo2-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.

scan_protocol: Arrays were scanned for F635 (Alexa Fluor 647) and F532 (Alexa Fluor 555) fluorescence intensities using AXON 4000B (Molecular Device, Sunnyvale, CA).

label: Alexa Fluor 647

growth_protocol: Cells were grown to log phase in YPD medium at 36 degrees Celsius.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Midi Kit (Qiagen, Valencia, CA).

label: Alexa Fluor 555

source_name: S. cerevisiae polyploid cells, ancestral

value: ancestral


title: evolved polyploid cell 3, replicate 1

description:
Sample name: evo3-rep1
Derived from anc3.
Technical replicate 1 of 2. Polyploid/haploid cells.

value: polyploid


title: evolved polyploid cell 3, replicate 2

description:
Sample name: evo3-rep2
Derived from anc3.
Technical replicate 2 of 2. Polyploid/haploid cells.

value: evolved


title: evolved polyploid cell 4, replicate 2

description:
Sample name: evo4-rep2
Derived from anc4.
Technical replicate 2 of 4. Polyploid/haploid cells.


title: evolved polyploid cell 4, replicate 1

description:
Sample name: evo4-rep1
Derived from anc4.
Technical replicate 1 of 4. Polyploid/haploid cells.


title: evolved polyploid cell 2, replicate 1

description:
Sample name: evo2-rep1
Derived from anc2.
Technical replicate 1 of 2. Polyploid/haploid cells.


title: evolved polyploid cell 1, replicate 1

description:
Sample name: evo1-rep1
Derived from anc1.
Technical replicate 1 of 2. Polyploid/haploid cells.


title: ancestral polyploid cell 5

description:
Sample name: anc5
Polyploid/haploid cells.


title: ancestral polyploid cell 6

description:
Sample name: anc6
Polyploid/haploid cells.


title: evolved polyploid cell 1, replicate 2

description:
Sample name: evo1-rep2
Derived from anc1.
Technical replicate 2 of 2. Polyploid/haploid cells.


title: BC_PyMT_18_Macro

description: Breast cancer GEM, Tumor 18

value: Breast cancer

value: Genetically Engineered Model

value: Mouse macrophages (M1+M2)


title: BC_PyMT_18_Cell_Tum

description: Breast cancer GEM, Tumor 18

value: Mouse tumor cells

value: Nude


title: BC_PyMT_14_Macro

description: Breast cancer GEM, Tumor 14


title: ancestral polyploid cell 7

description:
Sample name: anc7
Polyploid/haploid cells.


title: BC_PyMT_24_Cell_Tum

description: Breast cancer GEM, Tumor 24


title: ancestral polyploid cell 8

description:
Sample name: anc8
Polyploid/haploid cells.


title: evolved polyploid cell 2, replicate 2

description:
Sample name: evo2-rep2
Derived from anc2.
Technical replicate 2 of 2. Polyploid/haploid cells.


title: B334_RO_2_Macro

description: Breast cancer PDX n° 334, Tumor 2

value: Patient-Derived xenograft (PDX)

value: RO


title: BC_PyMT_14_Cell_Tum

description: Breast cancer GEM, Tumor 14


title: B256_LEV_40_Macro

description: Breast cancer PDX n° 256, Tumor 40

value: LEV


title: BC111_VINC_1_Macro

description: Breast cancer PDX n° 111, Tumor 1

value: VINC


title: B334_RO_4_Macro

description: Breast cancer PDX n° 334, Tumor 4


title: BC_PyMT_24_Macro

description: Breast cancer GEM, Tumor 24


title: ancestral polyploid cell 4

description:
Sample name: anc4
Polyploid/haploid cells.

value: haploid


title: ancestral polyploid cell 1

description:
Sample name: anc1
Polyploid/haploid cells.


title: B111_VINC_3_Macro

description: Breast cancer PDX n° 111, Tumor 3


title: ancestral polyploid cell 2

description:
Sample name: anc2
Polyploid/haploid cells.


title: B334_RO_1_Macro

description: Breast cancer PDX n° 334, Tumor 1


title: ancestral polyploid cell 3

description:
Sample name: anc3
Polyploid/haploid cells.


title: Experiment3 Isoproterenol Rep2

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

country: USA

institute: UCLA

description: Illumina MouseRef-8 v2.0 expression beadchip

hyb_protocol: Standard Illumina hybridization protocol (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

source_name: BMDM

label_protocol: Biotinylated cRNA were prepared with Ambion TotalPrep for Illumina arrays (carried out by UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from BMDM samples lysed in RLT buffer following the protocol from a QIAGEN RNeasy mini kit on a QIACube instrument and included DNase I treatment.

tag: experiment #

tag: activator

value: Isoproterenol

tag: replicate #


title: Experiment3 IL4 Rep2


title: Experiment3 IFNg Rep1

value: IFNg


title: Experiment3 Control Rep1

value: media only


title: Experiment3 Control Rep2


title: Experiment3 Isoproterenol Rep1


title: Experiment2 IL4 Rep1


title: Experiment3 IL4 Rep1


title: Experiment2 Isoproterenol Rep2


title: Experiment3 IFNg Rep2


title: Experiment2 IL4 Rep2


title: Experiment2 IFNg Rep1


title: Experiment2 IFNg Rep2


title: Experiment1 Isoproterenol Rep1


title: Experiment2 Isoproterenol Rep1


title: BC334_RO_4_Cell_Tum

description: Breast cancer PDX n° 334, Tumor 4

value: Human tumor cells


title: Experiment1 IFNg Rep1


title: BC334_RO_2_Cell_Tum

description: Breast cancer PDX n° 334, Tumor 2


title: Experiment1 IL4 Rep2


title: Experiment2 Control Rep1


title: BC241_MINC_p6_Frag

description: Breast cancer PDX n° 241, in vivo passage 6

value: All human tumor

value: MINC


title: BC256_LEV_37_Cell_Tum

description: Breast cancer PDX n° 256, Tumor 37


title: BC256_LEV_26_Cell_Tum

description: Breast cancer PDX n° 256, Tumor 26


title: BC111_VINC_2_Cell_Tum

description: Breast cancer PDX n° 111, Tumor 2


title: BC111_VINC_3_Cell_Tum

description: Breast cancer PDX n° 111, Tumor 3


title: Experiment1 Isoproterenol Rep2


title: Experiment1 IFNg Rep2


title: BC256_LEV_40_Cell_Tum

description: Breast cancer PDX n° 256, Tumor 40


title: BC334_RO_1_Cell_Tum

description: Breast cancer PDX n° 334, Tumor 1


title: Experiment2 Control Rep2


title: Experiment1 Control Rep2


title: Experiment1 IL4 Rep1


title: BC73_BON_p17_Frag

description: Breast cancer PDX n° 73, in vivo passage 17

value: BON


title: BC52_EDW_p15_Frag

description: Breast cancer PDX n° 52, in vivo passage 15

value: Breast cancer

value: EDW


title: Experiment1 Control Rep1


title: BC111_VINC_1_Cell_Tum

description: Breast cancer PDX n° 111, Tumor 1


title: PDX.36.DAC.2

status: Public on Oct 10 2016

city: Groningen

first: G. Bea

middle: A.

last: Wisman

state: Groningen

address: Hanzeplein 1

department: Department of Gynecologic Oncology

country: Netherlands

institute: University of Groningen, University Medical Centre Groningen

description: PDX tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2 and R packages (Minfi, CHAMP)
Beta-mixture quantile (BMIQ) normalized Average Beta values and filtered probes (388,696 only) after removal of failed probes on detection p value, X-Y chromosomes based probed and probes cross-hybrid with mouse DNA

label: Cy5 and Cy3

source_name: HGSOC PDX tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: PDXs and cell lines were treated with demethylating agent decitabine and cisplatin

tag: pdx model

tag: tumor

value: HGSOC PDX tumor

tag: tumor generation

value: Third (F3)

tag: treatment

value: Decitabine

value: Female

value: High grade serous ovarian


title: SKOV3 DAC

description: Cancer cell line

source_name: Cancer cell line

tag: cell line

value: Ovarian cancer cell line SKOV3

tag: gender


title: PDX.36.CisPt.2

description: PDX tumor

value: Cisplatin

tag: tumor type


title: PDX.36.CisPt.1

description: PDX tumor


title: PDX.36.DAC.3

description: PDX tumor


title: PDX.36.CisPt.3

description: PDX tumor


title: PDX.37.F3

description: PDX tumor


title: PDX.36.Control.2

description: PDX tumor

value: Control


title: PDX.37.F1

description: PDX tumor

value: First (F1)


title: T.2543

city: PITTSBURGH

first: SAMEER

last: AGNIHOTRI

state: Pennsylvania

address: Rangos Research Center, 7th Floor, ROOM 7126, 530, 45th Street

department: MacFeeters-Hamilton Brain Tumour Centre

institute: University of Pittsburgh

description: DNA from a Schwannoma patient

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing: Raw IDAT files were imported into Genome Studio and average methylation ( average beta values) were exported as a tab delimited file [ratio of methylated to (methylated + unmethylated probes].

source_name: genomic DNA from Schwannoma patient

extract_protocol: genomic DNA was extracted and purified from schwannoma patient samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: Schwannoma


title: PDX.56.F2

description: PDX tumor

value: Second (F2)


title: PDX.36.F2

description: PDX tumor


title: PDX.56.F1

description: PDX tumor


title: PDX.36.DAC.1

description: PDX tumor


title: PDX.36.F0

description: Patient tumor

source_name: HGSOC patient tumor

value: HGSOC patient tumor

value: Primary patient (F0)


title: PDX.37.F2

description: PDX tumor


title: PDX.36.F1

description: PDX tumor


title: PDX.36.F3

description: PDX tumor


title: T.3045

description: DNA from a Schwannoma patient


title: T.2106

description: DNA from a Schwannoma patient


title: PDX.56.F3

description: PDX tumor


title: PDX.56.F0

description: Patient tumor


title: T.1822

description: DNA from a Schwannoma patient


title: PDX.37.F0

description: Patient tumor


title: PDX.36.Control.3

description: PDX tumor


title: T.3067

description: DNA from a Schwannoma patient


title: T.3022

description: DNA from a Schwannoma patient


title: T.3090

description: DNA from a Schwannoma patient


title: T.3179

description: DNA from a Schwannoma patient


title: SKOV3 Control

description: Cancer cell line

value: DMSO


title: T.2762

description: DNA from a Schwannoma patient


title: T.2741

description: DNA from a Schwannoma patient


title: T.2610

description: DNA from a Schwannoma patient


title: T.2736

description: DNA from a Schwannoma patient


title: T.1793

description: DNA from a Schwannoma patient


title: T.2201

description: DNA from a Schwannoma patient


title: T.2505

description: DNA from a Schwannoma patient


title: T.1780

description: DNA from a Schwannoma patient


title: T.2488

description: DNA from a Schwannoma patient


title: T.2553

description: DNA from a Schwannoma patient


title: MD79

description: DNA from a Schwannoma patient


title: T.1679

description: DNA from a Schwannoma patient


title: MD9

description: DNA from a Schwannoma patient


title: T.2551

description: DNA from a Schwannoma patient


title: MD76

description: DNA from a Schwannoma patient


title: T.2160

description: DNA from a Schwannoma patient


title: T.3086

description: DNA from a Schwannoma patient


title: T.2067

description: DNA from a Schwannoma patient


title: T.2921

description: DNA from a Schwannoma patient


title: T.2494

description: DNA from a Schwannoma patient


title: MD78

description: DNA from a Schwannoma patient


title: T.2051

description: DNA from a Schwannoma patient


title: T.2538

description: DNA from a Schwannoma patient


title: T.2523

description: DNA from a Schwannoma patient


title: T.2336

description: DNA from a Schwannoma patient


title: MD75

description: DNA from a Schwannoma patient


title: T.1971

description: DNA from a Schwannoma patient


title: MD7

description: DNA from a Schwannoma patient


title: MD69

description: DNA from a Schwannoma patient


title: T.2212

description: DNA from a Schwannoma patient


title: MD72

description: DNA from a Schwannoma patient


title: MD67

description: DNA from a Schwannoma patient


title: MD63

description: DNA from a Schwannoma patient


title: MD68

description: DNA from a Schwannoma patient


title: MD74

description: DNA from a Schwannoma patient


title: MD64

description: DNA from a Schwannoma patient


title: MD59

description: DNA from a Schwannoma patient


title: MD66

description: DNA from a Schwannoma patient


title: MD52

description: DNA from a Schwannoma patient


title: MD62

description: DNA from a Schwannoma patient


title: MD41

description: DNA from a Schwannoma patient


title: MD57

description: DNA from a Schwannoma patient


title: MD56

description: DNA from a Schwannoma patient


title: MD58

description: DNA from a Schwannoma patient


title: MD50

description: DNA from a Schwannoma patient


title: MD4

description: DNA from a Schwannoma patient


title: MD51

description: DNA from a Schwannoma patient


title: MD37

description: DNA from a Schwannoma patient


title: MD53

description: DNA from a Schwannoma patient


title: MD5

description: DNA from a Schwannoma patient


title: MD55

description: DNA from a Schwannoma patient


title: MD39

description: DNA from a Schwannoma patient


title: MD38

description: DNA from a Schwannoma patient


title: MD45

description: DNA from a Schwannoma patient


title: MD73

description: DNA from a Schwannoma patient


title: MD6

description: DNA from a Schwannoma patient


title: MD36

description: DNA from a Schwannoma patient


title: MD40

description: DNA from a Schwannoma patient


title: MD32

description: DNA from a Schwannoma patient


title: MD21

description: DNA from a Schwannoma patient


title: MD33

description: DNA from a Schwannoma patient


title: MD23

description: DNA from a Schwannoma patient


title: MD31

description: DNA from a Schwannoma patient


title: MD22

description: DNA from a Schwannoma patient


title: MD26

description: DNA from a Schwannoma patient


title: MD15

description: DNA from a Schwannoma patient


title: MD13

description: DNA from a Schwannoma patient


title: T.932

description: DNA from a Schwannoma patient


title: MD11

description: DNA from a Schwannoma patient


title: MD2

description: DNA from a Schwannoma patient


title: MD20

description: DNA from a Schwannoma patient


title: T.1918

description: DNA from a Schwannoma patient


title: T.2267

description: DNA from a Schwannoma patient


title: T.1945

description: DNA from a Schwannoma patient


title: T.1800

description: DNA from a Schwannoma patient


title: MD48

description: DNA from a Schwannoma patient


title: T.1248

description: DNA from a Schwannoma patient


title: T.2246

description: DNA from a Schwannoma patient


title: MD12

description: DNA from a Schwannoma patient


title: T.1535

description: DNA from a Schwannoma patient


title: MD19

description: DNA from a Schwannoma patient


title: T.1640

description: DNA from a Schwannoma patient


title: T.2422

description: DNA from a Schwannoma patient


title: MD17

description: DNA from a Schwannoma patient


title: T.3777

description: DNA from a Schwannoma patient


title: T.1011

description: DNA from a Schwannoma patient


title: MD10

description: DNA from a Schwannoma patient


title: T.1927

description: DNA from a Schwannoma patient


title: T.2432

description: DNA from a Schwannoma patient


title: T.2034

description: DNA from a Schwannoma patient


title: T.3789

description: DNA from a Schwannoma patient


title: T.2310

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT059

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
JWT059
Dgcr8 wild type, four months.
Biological replicate 5 of 7.

hyb_protocol: Microarray hybridization was performed at 55°C for 20 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer's recommended protocols.

scan_protocol: Microarray was scanned in an Agilent scanner at 5μm resolution, and the array data was extracted with Agilent Feature Extraction software using the miRNA_105_Jan09 protocol.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for extracting the signal intensity, followed by a log2 transformation and quantile normalization between arrays among the entire dataset.

source_name: Thalamus, Dgcr8 wild type, 4 months

label_protocol: 100ng of total RNA were labeled with Cy3 according to Agilent's labeling protocol.

extract_protocol: Total RNA was extracted with mirVana isolation kit (Ambion). RNA quality was confirmed by analysis on the Agilent 2100 Bioanalyzer.

tag: genotype/variation

value: wild type

tag: age

value: four months

tag: tissue

value: medial geniculate nucleus of the thalamus


title: Medial geniculate nucleus of the thalamus, JWT063

description:
JWT063
Dgcr8 wild type, four months.
Biological replicate 7 of 7.

tag: strain/background


title: Medial geniculate nucleus of the thalamus, JWT062

description:
JWT062
Dgcr8 wild type, four months.
Biological replicate 6 of 7.


title: T.3412

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT055

description:
JWT055
Dgcr8 wild type, four months.
Biological replicate 4 of 7.


title: T.3437

description: DNA from a Schwannoma patient


title: T.3130

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT050

description:
JWT050
Dgcr8 wild type, four months.
Biological replicate 1 of 7.


title: T.2408

description: DNA from a Schwannoma patient


title: T.3535

description: DNA from a Schwannoma patient


title: T.3006

description: DNA from a Schwannoma patient


title: T.3141

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT061

description:
JWT061
Dgcr8+/- mutant, four months.
Biological replicate 7 of 7.

source_name: Thalamus, Dgcr8+/- mutant, 4 months

value: Dgcr8+/- mutant


title: Medial geniculate nucleus of the thalamus, JWT060

description:
JWT060
Dgcr8+/- mutant, four months.
Biological replicate 6 of 7.


title: Medial geniculate nucleus of the thalamus, JWT058

description:
JWT058
Dgcr8+/- mutant, four months.
Biological replicate 5 of 7.


title: T.3098

description: DNA from a Schwannoma patient


title: T.3569

description: DNA from a Schwannoma patient


title: iNPC-derived human oligodendrocyte line 17, sporadic ALS

city: Sheffield

first: Laura

last: Ferraiuolo

address: 385a Glossop Road

country: United Kingdom

institute: University of Sheffield

description:
iOlig_17
cells derived from genetic reprogramming

hyb_protocol: Samples were fragmented for 15min, 1 ug of cDNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 GeneChips, according to Affymetrix protocols. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned in the GeneChip 3000 Scanner

data_processing: CHP files were imported in Affymetrix Expression Console and data normalized using the RMA algorithm

source_name: iNPC-derived human oligodendrocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: RNA was isolated using Trizol

tag: disease

value: sporadic ALS

tag: cell type

value: iNPC-derived oligodendrocytes

tag: line


title: Medial geniculate nucleus of the thalamus, JWT057

description:
JWT057
Dgcr8+/- mutant, four months.
Biological replicate 4 of 7.


title: T.1316

description: DNA from a Schwannoma patient


title: T.3570

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT051

description:
JWT051
Dgcr8+/- mutant, four months.
Biological replicate 1 of 7.


title: T.1831

description: DNA from a Schwannoma patient


title: T.2338

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT045

description:
JWT045
Dgcr8 wild type, two months.
Biological replicate 7 of 7.

source_name: Thalamus, Dgcr8 wild type, 2 months

value: two months


title: T.1650

description: DNA from a Schwannoma patient


title: T.2837

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT041

description:
JWT041
Dgcr8 wild type, two months.
Biological replicate 5 of 7.


title: T.1763

description: DNA from a Schwannoma patient


title: T.1365

description: DNA from a Schwannoma patient


title: iNPC-derived human oligodendrocyte line 155 unaffected

description:
iOlig_155
cells derived from genetic reprogramming

value: unaffected


title: T.3457

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT039

description:
JWT039
Dgcr8 wild type, two months.
Biological replicate 4 of 7.


title: T.3205

description: DNA from a Schwannoma patient


title: T.1317

description: DNA from a Schwannoma patient


title: T.2493

description: DNA from a Schwannoma patient


title: iNPC-derived human oligodendrocyte line 170 unaffected

description:
iOlig_170
cells derived from genetic reprogramming


title: T.3419

description: DNA from a Schwannoma patient


title: T.2669

description: DNA from a Schwannoma patient


title: iNPC-derived human oligodendrocyte line 12, sporadic ALS

description:
iOlig_12
cells derived from genetic reprogramming


title: Medial geniculate nucleus of the thalamus, JWT053

description:
JWT053
Dgcr8+/- mutant, four months.
Biological replicate 2 of 7.


title: Medial geniculate nucleus of the thalamus, JWT054

description:
JWT054
Dgcr8 wild type, four months.
Biological replicate 3 of 7.


title: Medial geniculate nucleus of the thalamus, JWT038

description:
JWT038
Dgcr8 wild type, two months.
Biological replicate 3 of 7.


title: Medial geniculate nucleus of the thalamus, JWT036

description:
JWT036
Dgcr8 wild type, two months.
Biological replicate 2 of 7.


title: T.3549

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT042

description:
JWT042
Dgcr8+/- mutant, two months.
Biological replicate 8 of 9.

source_name: Thalamus, Dgcr8+/- mutant, 2 months


title: T.2621

description: DNA from a Schwannoma patient


title: Medial geniculate nucleus of the thalamus, JWT044

description:
JWT044
Dgcr8+/- mutant, two months.
Biological replicate 9 of 9.


title: Medial geniculate nucleus of the thalamus, JWT034

description:
JWT034
Dgcr8 wild type, two months.
Biological replicate 1 of 7.


title: Medial geniculate nucleus of the thalamus, JWT040

description:
JWT040
Dgcr8+/- mutant, two months.
Biological replicate 7 of 9.


title: Medial geniculate nucleus of the thalamus, JWT037

description:
JWT037
Dgcr8+/- mutant, two months.
Biological replicate 6 of 9.


title: iNPC-derived human astrocyte line 17, sporadic ALS

description:
iA_17
cells derived from genetic reprogramming

source_name: iNPC-derived human astrocytes

value: iNPC-derived astrocytes


title: iNPC-derived human astrocyte line 170 unaffected

description:
iA_170
cells derived from genetic reprogramming


title: iNPC-derived human astrocyte line 155 unaffected

description:
iA_155
cells derived from genetic reprogramming


title: Medial geniculate nucleus of the thalamus, JWT035

description:
JWT035
Dgcr8+/- mutant, two months.
Biological replicate 5 of 9.


title: Medial geniculate nucleus of the thalamus, JWT052

description:
JWT052
Dgcr8 wild type, four months.
Biological replicate 2 of 7.


title: Medial geniculate nucleus of the thalamus, JWT033

description:
JWT033
Dgcr8+/- mutant, two months.
Biological replicate 4 of 9.


title: Medial geniculate nucleus of the thalamus, JWT032

description:
JWT032
Dgcr8+/- mutant, two months.
Biological replicate 3 of 9.


title: Medial geniculate nucleus of the thalamus, JJW025_2

description:
JJW025_2
Df(16)1/+ wild type, four months.
Biological replicate 4 of 4, technical replicate 2 of 2.

source_name: Thalamus, Df(16)1/+ wild type, 4 months


title: Medial geniculate nucleus of the thalamus, JWT030

description:
JWT030
Dgcr8+/- mutant, two months.
Biological replicate 1 of 9.


title: Medial geniculate nucleus of the thalamus, JWT031

description:
JWT031
Dgcr8+/- mutant, two months.
Biological replicate 2 of 9.


title: Medial geniculate nucleus of the thalamus, JJW025_1

description:
JJW025_1
Df(16)1/+ wild type, four months.
Biological replicate 4 of 4, technical replicate 1 of 2.


title: Medial geniculate nucleus of the thalamus, JJw022_1

description:
JJw022_1
Df(16)1/+ wild type, four months.
Biological replicate 3 of 4, technical replicate 1 of 2.


title: Medial geniculate nucleus of the thalamus, JJW022_2

description:
JJW022_2
Df(16)1/+ wild type, four months.
Biological replicate 3 of 4, technical replicate 2 of 2.


title: iNPC-derived human astrocyte line 12, sporadic ALS

description:
iA_12
cells derived from genetic reprogramming


title: Human primary fibroblast #11 unaffected

description:
FB_11
primary cells expanded in vitro

source_name: Human primary fibroblast

value: primary fibroblast


title: Human primary fibroblast #13 unaffected

description:
FB_13
primary cells expanded in vitro


title: Medial geniculate nucleus of the thalamus, JJW021_1

description:
JJW021_1
Df(16)1/+ wild type, four months.
Biological replicate 2 of 4, technical replicate 1 of 2.


title: Human primary fibroblast #2 unaffected

description:
FB_2
primary cells expanded in vitro


title: Medial geniculate nucleus of the thalamus, JJW020_1

description:
JJW020_1
Df(16)1/+ wild type, four months.
Biological replicate 1 of 4, technical replicate 1 of 2.


title: Medial geniculate nucleus of the thalamus, JJW020_2

description:
JJW020_2
Df(16)1/+ wild type, four months.
Biological replicate 1 of 4, technical replicate 2 of 2.


title: Medial geniculate nucleus of the thalamus, JJW027_2

description:
JJW027_2
Df(16)1/+ mutant, four months.
Biological replicate 4 of 4, technical replicate 2 of 2.

source_name: Thalamus, Df(16)1/+ mutant, 4 months

value: Df(16)1/+ mutant


title: Medial geniculate nucleus of the thalamus, JJW026_2

description:
JJW026_2
Df(16)1/+ mutant, four months.
Biological replicate 3 of 4, technical replicate 2 of 2.


title: Medial geniculate nucleus of the thalamus, JJW026_1

description:
JJW026_1
Df(16)1/+ mutant, four months.
Biological replicate 3 of 4, technical replicate 1 of 2.


title: Medial geniculate nucleus of the thalamus, JJW024_2

description:
JJW024_2
Df(16)1/+ mutant, four months.
Biological replicate 2 of 4, technical replicate 2 of 2.


title: Medial geniculate nucleus of the thalamus, JWT043

description:
JWT043
Dgcr8 wild type, two months.
Biological replicate 6 of 7.


title: Medial geniculate nucleus of the thalamus, JJW021_2

description:
JJW021_2
Df(16)1/+ wild type, four months.
Biological replicate 2 of 4, technical replicate 2 of 2.


title: Medial geniculate nucleus of the thalamus, JWT020

description:
JWT020
Df(16)1/+ wild type, two months.
Biological replicate 6 of 6.

source_name: Thalamus, Df(16)1/+ wild type, 2 months


title: Medial geniculate nucleus of the thalamus, JJW023_2

description:
JJW023_2
Df(16)1/+ mutant, four months.
Biological replicate 1 of 4, technical replicate 2 of 2.


title: Medial geniculate nucleus of the thalamus, JJW023_1

description:
JJW023_1
Df(16)1/+ mutant, four months.
Biological replicate 1 of 4, technical replicate 1 of 2.


title: Medial geniculate nucleus of the thalamus, JWT016

description:
JWT016
Df(16)1/+ wild type, two months.
Biological replicate 4 of 6.


title: Medial geniculate nucleus of the thalamus, JWT019

description:
JWT019
Df(16)1/+ wild type, two months.
Biological replicate 5 of 6.


title: Medial geniculate nucleus of the thalamus, JJW027_1

description:
JJW027_1
Df(16)1/+ mutant, four months.
Biological replicate 4 of 4, technical replicate 1 of 2.


title: Medial geniculate nucleus of the thalamus, JWT018

description:
JWT018
Df(16)1/+ mutant, two months.
Biological replicate 4 of 4.

source_name: Thalamus, Df(16)1/+ mutant, 2 months


title: Medial geniculate nucleus of the thalamus, JWT011

description:
JWT011
Df(16)1/+ wild type, two months.
Biological replicate 1 of 6.


title: Medial geniculate nucleus of the thalamus, JWT012

description:
JWT012
Df(16)1/+ wild type, two months.
Biological replicate 2 of 6.


title: Medial geniculate nucleus of the thalamus, JWT017

description:
JWT017
Df(16)1/+ mutant, two months.
Biological replicate 3 of 4.


title: Medial geniculate nucleus of the thalamus, JJW024_1

description:
JJW024_1
Df(16)1/+ mutant, four months.
Biological replicate 2 of 4, technical replicate 1 of 2.


title: Sh251664

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

description: Patient received neoadjuvant treatment(paclitaxel followed by carboplatin)

hyb_protocol: The labeled cDNA was hybridized onto a HG U133 Plus 2.0 Array (Affymetrix) in a hybridization oven (Hybridization Oven 640, Agilent Technologies) with 60 rotations per min at 50 C for 18 h. The HG U133 Plus 2.0 Array contained 54,675 probe sets representing approximately 39,000 of the best-characterized human genes.

scan_protocol: After hybridization, the arrays were washed and stained according to the Affymetrix protocol (EukGE-WS2v4) using a GeneChip Fluidics Station 450 (Affymetrix). The arrays were scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Quality control analyses were performed according to the suggestions of standard Affymetrix parameters. Based on the evaluation criteria, all of our experiments fulfilled the minimal quality requirements. The Affymetrix expression arrays were preprocessed by Robust Multi-chip Average (RMA) with background correction, quantile normalization and median polish summarization. Probe sets with extreme signal intensity (lower than 50 or higher than 2E14) were filtered out. Then, annotation based filtering was performed according to the Entrez Gene database. Probe sets without Entrez Gene ID annotation were removed. To reduce the likelihood of batch effects, a normalization algorithm (http://statistics.byu.edu/johnson/ComBat/) was applied to the filtered expression data. The ComBat method applied either a parametric or nonparametric empirical Bayes framework for adjusting batch effects in a given data set.

label: Biotin

source_name: Breast tumor biopsied tissue

label_protocol: Fifty nanograms of total RNA was then reverse transcribed and linearly amplified to single strand cDNA using the Ribo-SPIA™ kit with the WT-Ovation™ RNA Amplification System (NuGEN Technologies Inc., San Carlos, CA, USA) according to the manufacturer’s standard protocol. Products were purified with a QIAquick PCR purification kit (QIAGEN GmbH, Hilden, Germany). A total of 2 lg of amplified and purified cDNA were subsequently fragmented with RQ1 RNase-Free DNase (Promega Corp., Fitchburg, WI, USA) and labeled with biotinylated deoxynucleoside triphosphates by terminal transferase (Roche Diagnostics Corp., Indianapolis, IN, USA) and GeneChip DNA Labeling Reagent (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: Before RNA extraction, a 5-lm section of biopsied tissue was hematoxylin and eosin (H&E) stained to confirm that the tissue contained at least 50% tumor cells. Total RNA was extracted with Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. The quantity of total RNA was measured by a spectrophotometer at an optical density of 260 nm, and the quality was assessed using the RNA 6000 Nano LabChip Kit on a BioAnalyzer Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA). Only samples with an RNA integrity number between 7 and 10 were analyzed.

value: Breast tumor

value: F


title: Sh249317


title: Sh252144


title: Sh249360


title: Medial geniculate nucleus of the thalamus, JWT014

description:
JWT014
Df(16)1/+ mutant, two months.
Biological replicate 2 of 4.


title: Medial geniculate nucleus of the thalamus, JWT013

description:
JWT013
Df(16)1/+ mutant, two months.
Biological replicate 1 of 4.


title: Sh246173


title: Sh246490


title: Sh246744


title: Sh245596_1


title: Medial geniculate nucleus of the thalamus, JWT015

description:
JWT015
Df(16)1/+ wild type, two months.
Biological replicate 3 of 6.


title: Human primary fibroblast #1 unaffected

description:
FB_1
primary cells expanded in vitro


title: Sh248050


title: Sh252197


title: Sh246064_1


title: Sh245968_1


title: Sh245981_1


title: Sh250720


title: Medial geniculate nucleus of the thalamus, JWT056

description:
JWT056
Dgcr8+/- mutant, four months.
Biological replicate 3 of 7.


title: Sh252648


title: Sh252540


title: Sh245205_1


title: Colon cancer tissue samples (FFPE) 113

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description: Normal colon mucosa from the same patient as the tumor was used as reference in the oaCGH experiments

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: The profiles were dewaved (van de wiel et al, Bioinformatics. 2009, median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al, Bioinformatics. 2007)

source_name: colon cancer

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al, J Pathol. 2010

value: colon cancer (FFPE)

tag: Stage

tag: disease free survival (months)

tag: disease recurrence

value: yes

tag: follow-up (months)

tag: death by crc

source_name: normal colon mucosa

value: normal colon mucosa obtained from the same patient as ch1


title: Sh245155_1


title: Colon cancer tissue samples (FFPE) 114

value: no


title: Colon cancer tissue samples (FFPE) 111


title: Colon cancer tissue samples (FFPE) 112


title: Shnodata2


title: Sh251154


title: Sh249025


title: Sh247361


title: Colon cancer tissue samples (FFPE) 107


title: Colon cancer tissue samples (FFPE) 102


title: Sh241222


title: Colon cancer tissue samples (FFPE) 101


title: Colon cancer tissue samples (FFPE) 110


title: Colon cancer tissue samples (FFPE) 109


title: Colon cancer tissue samples (FFPE) 108


title: Sh244815_1


title: Colon cancer tissue samples (FFPE) 105


title: Colon cancer tissue samples (FFPE) 103


title: Colon cancer tissue samples (FFPE) 106


title: Colon cancer tissue samples (FFPE) 104


title: Sh247942


title: Colon cancer tissue samples (FFPE) 100


title: Sh244244_1


title: Sh238919_2


title: Colon cancer tissue samples (FFPE) 99


title: Sh249528


title: Sh242229_1


title: Sh241327_1


title: Sh253021


title: Sh239723_1


title: Colon cancer tissue samples (FFPE) 98


title: Colon cancer tissue samples (FFPE) 97


title: Sh248560


title: Colon cancer tissue samples (FFPE) 96


title: Colon cancer tissue samples (FFPE) 95


title: cotton adaptation3

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

institute: University of Ghent

description: replication 3 of cotton adaptation

hyb_protocol: Labeled cRNA were pooled and hybridized on a custom-made Agilent 8x60k array using the Gene Expression Hybridization Kit (Agilent Technologies). Prior to washing (Gene Expression Wash Buffer Kit (Agilent Technologies)), slides were kept in a rotating hybridization oven for 17 hrs.

scan_protocol: All arrays were scanned using an Agilent Microarray High Resolution Scanner (default settings for two-color GE micro-arrays).

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.5 (GE2_107_Sep09 protocol). Data was transferred to limma (Smyth, 2004) for final statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was assessed.

organism: Tetranychus urticae

source_name: London-COTTON

label_protocol: Cy5- and Cy3-labeled cRNA was synthesized from RNA following the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: All mites and host plants were reared and maintained in climatically controlled rooms at 26 °C, 60% RH and 16h:8h light:dark photoperiod

extract_protocol: Spider mite RNA was isolated using the RNeasy minikit (Qiagen) using 100-150 pooled mites and was subsequently treated with DNase (Turbo DNA-free kit, Ambion).

tag: strain

value: London

tag: life stage

value: adult

value: female

tag: host plant

value: COTTON

value: whole spider mite

source_name: London (bean reared)

tag: host

value: bean


title: Sh248548

tag: gender


title: Shnodata3


title: Colon cancer tissue samples (FFPE) 94


title: Colon cancer tissue samples (FFPE) 92


title: maize adaptation3

description: replication 3 of maize adaptation

source_name: London-MAIZE

value: MAIZE


title: cotton adaptation2

description: replication 2 of cotton adaptation


title: cotton adaptation1

description: replication 1 of cotton adaptation


title: maize adaptation4

description: replication 4 of maize adaptation


title: Colon cancer tissue samples (FFPE) 90


title: Colon cancer tissue samples (FFPE) 91


title: Sh248103


title: Sh248231


title: Sh252521


title: Sh248230


title: Colon cancer tissue samples (FFPE) 88


title: Colon cancer tissue samples (FFPE) 89


title: Colon cancer tissue samples (FFPE) 93


title: maize adaptation1

description: replication 1 of maize adaptation


title: Sh248052


title: soy adaptation4

description: replication 4 of soy adaptation

source_name: London-SOY

value: SOY


title: Sh248243


title: Sh248164


title: Colon cancer tissue samples (FFPE) 87


title: Colon cancer tissue samples (FFPE) 85


title: Colon cancer tissue samples (FFPE) 84


title: Sh247462


title: Sh247690


title: soy adaptation1

description: replication 1 of soy adaptation


title: Sh246630


title: soy adaptation2

description: replication 2 of soy adaptation


title: Sh242445


title: Sh246780


title: maize adaptation2

description: replication 2 of maize adaptation


title: Sh246031


title: Sh245968_2


title: Colon cancer tissue samples (FFPE) 83


title: soy adaptation3

description: replication 3 of soy adaptation


title: Sh246309


title: Colon cancer tissue samples (FFPE) 80


title: Colon cancer tissue samples (FFPE) 81


title: Colon cancer tissue samples (FFPE) 82


title: Colon cancer tissue samples (FFPE) 86


title: Shnodata1


title: Colon cancer tissue samples (FFPE) 77


title: Colon cancer tissue samples (FFPE) 76


title: Sh244289


title: Colon cancer tissue samples (FFPE) 79


title: Colon cancer tissue samples (FFPE) 78


title: Colon cancer tissue samples (FFPE) 71


title: Sh245981_2


title: Sh238019_1


title: Colon cancer tissue samples (FFPE) 73


title: Colon cancer tissue samples (FFPE) 72


title: Colon cancer tissue samples (FFPE) 70


title: Colon cancer tissue samples (FFPE) 75


title: Sh244815_2


title: Sh245596_2


title: Colon cancer tissue samples (FFPE) 69


title: Sh245563


title: Sh246561


title: Colon cancer tissue samples (FFPE) 67


title: Sh246064_2


title: Fusion positive cells 3, biological rep3

description: Immortalized Schwann Cells expressing the fusion gene

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. CHECK WITH FACILITY

scan_protocol: GeneChips were scanned at The Centre for Applied Genomics (TCAG), SickKids Hospital Toronto, Canada

data_processing: The data were normalized with Affymetrix Expression Console Software using RMA analysis.

source_name: Immortalized Schwann Cells

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

growth_protocol: Cells were grown in DMEM media supplemented with 10% fetal bovine serum ((Sigma F6886) and  2uM Forskolin

extract_protocol: RNA was extracted with the RNeasy Mini Kit (Qiagen, Cat#74104 ) using the manufacturer's protocol.

treatment_protocol: Cells were transfected with empty vector or fusion positve cDNA and stable cells were generated using puromycin selection

value: Human Peripheral Nerve


title: Colon cancer tissue samples (FFPE) 74


title: Sh242229_2


title: Colon cancer tissue samples (FFPE) 66


title: Fusion positive cells 2, biological rep2


title: Sh244630


title: Sh245155_2


title: Fusion positive cells 1, biological rep1


title: Colon cancer tissue samples (FFPE) 64


title: Sh244857


title: Colon cancer tissue samples (FFPE) 65


title: Sh244244_2


title: Colon cancer tissue samples (FFPE) 68


title: Colon cancer tissue samples (FFPE) 62


title: Colon cancer tissue samples (FFPE) 63


title: Colon cancer tissue samples (FFPE) 61


title: Sh245205_2


title: Sh242535


title: Colon cancer tissue samples (FFPE) 60


title: Colon cancer tissue samples (FFPE) 59


title: Empty Vector Control cells 2, biological rep 2

description: Immortalized Schwann Cells expressing empty vector control


title: Empty Vector Control cells 3, biological rep 3


title: Sh241696


title: Sh239723_2


title: Sh241327_2


title: mRNA_TLT-C-093-TT

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

institute: Baylor College of Medicine

description:
HB
Affymetrix GeneChip 3’ IVT Express Kit

hyb_protocol: Human Genome U133 Plus 2.0 arrays, Affymetrix GeneChip 3’ IVT Express Kit

scan_protocol: scan protocol - Affymetrix GeneChip Scanner 3000

data_processing: Data analysis focused on probe sets with maximum signal log ratio (normalized relative expression) above 6, and standard deviation > 0.4 across tumors and normal samples. Consequently, 7,896 probe sets, associate with 5,823 unique genes, were selected. Hierarchical clustering based on these probe sets, of our tumors and tumors profiled by Cairo et al. (Cairo et al., 2008) was performed using hcluster in R with Pearson Correlation and average linkage. The resulting hierarchy pointed to 3 distinct molecular clusters.

molecule: polyA RNA

source_name: Tumor

label_protocol: not provided

extract_protocol: RNA from frozen hepatic tumor specimens and matched normal liver tissue specimens was isolated using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Dnase 1

value: Tumor

tag: age (yrs)

tag: Sex

tag: race

value: Caucasian

tag: histology

value: Epithelial, embryonal and  small cell (minor)


title: Empty Vector Control cells 1, biological rep 1

tag: tissue


title: Sh251107

value: Breast tumor

tag: age

value: F


title: CEF_TAM67_NY72-4_37˚C_rep1

city: Hamilton

first: Bart

middle: Michal

last: Maslikowski

state: Ontario

address: 1280 Main St. West

department: Biology

country: Canada

institute: McMaster University

description:
Gene expression data from CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 37˚C
CEF_NY72-4_TAM67_37C_1

hyb_protocol: cRNA was fragmented and hybridized onto Affymetrix Chicken GeneChip arrays for 16 hours at 45˚C. Washing, staining and scanning was done in accordance with the Affymetrix EukGE-WS2v4 protocol.

scan_protocol: Scanning was done using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were analysed using Affymetrix Expression Console software v1.1. Array data were normalized and probe intensities were estimated using the Affymetrix probe logarithmic intensity error (PLIER) algorithm.

organism: Gallus gallus

source_name: CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 37˚C, biological replicate 1

label_protocol: 15 µg of total RNA was used to prepare biotin labeled complimentary RNA (cRNA). cDNA was generated by one-cycle target labeling protocol using SuperScript II (Invitrogen). Biotinylated cRNA was generated from purified cDNA using the Enzo IVT kit.

growth_protocol: CEFs were cultured at 41.5˚C in Dulbecco-modified Eagle medium (DMEM) with 5% heat-inactivated calf serum, 5% tryptose phosphate broth, L-glutamine, and penicillin/streptomycin.

extract_protocol: Total cell RNA was isolated using Trizol reagent (Invitrogen) according to manufacturer's instructions. RNA quality was assessed by gel electrophoresis and examined by Bioanalyzer (Agilent). RNA samples with a RNA Integrity Index of less than 9.7 were discarded.

treatment_protocol: Early passages (n<10) of CEFs were cultured at 41.5˚C and transfected with B-type RSV viral vectors expressing JunD shRNA, GFP control, or the c-Jun TAM67 dominant negative mutant using the calcium phosphate method. CEFs were superinfected with the temperature sensitive A-type NY72-4 RSV one passage following transfection and cultured for three passages or until the apoptosis phenotype was observed in response to AP-1 inhibition and transformation. Infected CEFs were cultured at the non-permissive temperature of 41.5˚C until such time when temperature shift was performed. Temperature shift was performed for six to eight hours at 37.5˚C.

value: white leghorn

tag: cell type

value: chicken embryonic fibroblast cells derived from day 10 embryos

tag: transfection

tag: infection

value: temperature sensitive A-type NY72-4 RSV

tag: temperature


title: Sh240387


title: CEF_TAM67_NY72-4_41.5˚C_rep3

description:
Gene expression data from CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_TAM67_42C_3

source_name: CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 41.5˚C, biological replicate 3


title: Colon cancer tissue samples (FFPE) 55

value: colon cancer (FFPE)

tag: Stage

tag: disease free survival (months)

tag: disease recurrence

value: no

tag: follow-up (months)

value: normal colon mucosa obtained from the same patient as ch1


title: mRNA_TLT-C-091-TT

value: Epithelial, embryonal, nesting pattern (small cell)


title: Colon cancer tissue samples (FFPE) 58

value: yes

tag: death by crc


title: CEF_TAM67_NY72-4_41.5˚C_rep2

description:
Gene expression data from CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_TAM67_42C_2

source_name: CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 41.5˚C, biological replicate 2

tag: strain


title: CEF_GFP-shRNA_NY72-4_37˚C_rep3

description:
Gene expression data from CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_RCASB_37C_3

source_name: CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 37˚C, biological replicate 3

value: RCAS(B)-GFP shRNA


title: Colon cancer tissue samples (FFPE) 52


title: Colon cancer tissue samples (FFPE) 51


title: Colon cancer tissue samples (FFPE) 53


title: CEF_TAM67_NY72-4_37˚C_rep2

description:
Gene expression data from CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 37˚C
CEF_NY72-4_TAM67_37C_2

source_name: CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 37˚C, biological replicate 2


title: mRNA_TLT-C-089-TT

value: Hispanic

value: Epithelial hepatoblastoma


title: CEF_GFP-shRNA_NY72-4_37˚C_rep2

description:
Gene expression data from CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_RCASB_37C_2

source_name: CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 37˚C, biological replicate 2


title: Colon cancer tissue samples (FFPE) 54


title: Colon cancer tissue samples (FFPE) 57


title: mRNA_TLT-C-087-TT

value: M


title: mRNA_TLT-C-086-TT

value: Tumor

value: African American

value: Epithelial hepatoblastoma, fetal


title: Colon cancer tissue samples (FFPE) 49


title: CEF_GFP-shRNA_NY72-4_41.5˚C_rep3

description:
Gene expression data from CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_RCASB_42C_3

source_name: CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 41.5˚C, biological replicate 3


title: CEF_TAM67_NY72-4_41.5˚C_rep1

description:
Gene expression data from CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_TAM67_42C_1

source_name: CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 41.5˚C, biological replicate 1


title: CEF_GFP-shRNA_NY72-4_37˚C_rep1

description:
Gene expression data from CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_RCASB_37C_1

source_name: CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 37˚C, biological replicate 1


title: mRNA_TLT-C-088-TT

value: Caucasian

value: Epithelial, embryonal, fetal, minor small cell


title: CEF_GFP-shRNA_NY72-4_41.5˚C_rep2

description:
Gene expression data from CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_RCASB_42C_2

source_name: CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 41.5˚C, biological replicate 2

value: white leghorn


title: mRNA_TLT-C-085-TT


title: CEF_JunD-shRNA_NY72-4_37˚C_rep6

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_JunD_KD_37C_6

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C, biological replicate 6

value: chicken embryonic fibroblast cells derived from day 10 embryos

value: RCAS(B)-JunD shRNA


title: Colon cancer tissue samples (FFPE) 48

source_name: colon cancer

value: colon cancer (FFPE)

source_name: normal colon mucosa


title: mRNA_TLT-C-083-TT

value: Normal liver


title: Colon cancer tissue samples (FFPE) 46

value: no

value: normal colon mucosa obtained from the same patient as ch1


title: Colon cancer tissue samples (FFPE) 50


title: mRNA_TLT-C-084-TT

value: Epithelial hepatoblastoma, embryonal


title: Colon cancer tissue samples (FFPE) 45


title: mRNA_TLT-C-082-TT

value: Epithelial hepatoblastoma, mitotically active fetal


title: CEF_JunD-shRNA_NY72-4_37˚C_rep4

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_JunD_KD_37C_4

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C, biological replicate 4

value: temperature sensitive A-type NY72-4 RSV


title: mRNA_TLT-C-080-TT

value: F

value: Epithelial hepatoblastoma, crowded fetal


title: mRNA_TLT-C-081-TT

value: Tumor

value: M

value: Epithelial hepatoblastoma


title: mRNA_TLT-C-079-TT

value: Caucasian

value: Epithelial hepatoblastoma, embryonal and fetal


title: CEF_JunD-shRNA_NY72-4_37˚C_rep5

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_JunD_KD_37C_5

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C, biological replicate 5

value: white leghorn


title: Colon cancer tissue samples (FFPE) 43

description: Normal colon mucosa from the same patient as the tumor was used as reference in the oaCGH experiments

value: yes


title: CEF_TAM67_NY72-4_37˚C_rep3

description:
Gene expression data from CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 37˚C
CEF_NY72-4_TAM67_37C_3

source_name: CEF transfected with RCAS(B)-TAM67, infected with NY72-4, grown at 37˚C, biological replicate 3

value: chicken embryonic fibroblast cells derived from day 10 embryos


title: mRNA_TLT-C-074-TT

source_name: Tumor

value: Epithelial hepatoblastoma, fetal


title: CEF_JunD-shRNA_NY72-4_37˚C_rep3

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_JunD_KD_37C_3

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C, biological replicate 3

value: RCAS(B)-JunD shRNA


title: CEF_JunD-shRNA_NY72-4_37˚C_rep2

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_JunD_KD_37C_2

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C, biological replicate 2


title: mRNA_TLT-C-078-TT

description:
HB
Affymetrix GeneChip 3’ IVT Express Kit

value: Epithelial hepatoblastoma, embryonal  and fetal


title: CEF_JunD-shRNA_NY72-4_37˚C_rep1

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C
CEF_NY72-4_JunD_KD_37C_1

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 37˚C, biological replicate 1


title: CEF_JunD-shRNA_NY72-4_41.5˚C_rep3

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_JunD_KD_42C_3

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 41.5˚C, biological replicate 3


title: mRNA_TLT-C-075-TT

value: Asian

value: Epithelial hepatoblastoma, embryonal and fetal


title: Colon cancer tissue samples (FFPE) 44

value: colon cancer (FFPE)

value: no

value: normal colon mucosa obtained from the same patient as ch1


title: Colon cancer tissue samples (FFPE) 56


title: mRNA_TLT-C-070-TT

value: Hispanic

value: Epithelial hepatoblastoma, embryonal


title: CEF_JunD-shRNA_NY72-4_41.5˚C_rep2

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_JunD_KD_42C_2

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 41.5˚C, biological replicate 2

value: temperature sensitive A-type NY72-4 RSV


title: Colon cancer tissue samples (FFPE) 41


title: Colon cancer tissue samples (FFPE) 42


title: CEF_JunD-shRNA_NY72-4_41.5˚C_rep1

description:
Gene expression data from CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_JunD_KD_42C_1

source_name: CEF transfected with RCAS(B)-JunD shRNA, infected with NY72-4, grown at 41.5˚C, biological replicate 1


title: Colon cancer tissue samples (FFPE) 39


title: Colon cancer tissue samples (FFPE) 40


title: mRNA_TLT-C-066-TT

value: Tumor

value: M

value: Epitthelial hepatoblastoma, embryonal and blastemal


title: mRNA_TLT-C-068-TT

value: Unknown


title: Colon cancer tissue samples (FFPE) 37


title: mRNA_TLT-C-064-TT

value: F

value: Caucasian


title: mRNA_TLT-C-062-TT


title: Colon cancer tissue samples (FFPE) 35


title: mRNA_TLT-C-052-TT

value: Epithelial hepatoblastoma, fetal (70%), embryonal (10%), small cell (20%)


title: mRNA_TLT-C-053-TT

value: Mixed epithelial and mesenchymal, fetal (60%), embryonal (20%), stromal (10%), blastema (5%) and small cell (2%)


title: Colon cancer tissue samples (FFPE) 38


title: mRNA_TLT-C-050-TT

value: Epithelial hepatoblastoma, fetal, embryonal with rare small cell


title: mRNA_TLT-C-052-LV

description:
NL
Affymetrix GeneChip 3’ IVT Express Kit

source_name: Normal Liver

value: Normal Liver


title: mRNA_TLT-C-058-TT

value: Epithelial, hepatoblastoma embryonal, fetal, some anaplastia, telangiectatic


title: Colon cancer tissue samples (FFPE) 33

value: colon cancer (FFPE)

value: yes


title: Colon cancer tissue samples (FFPE) 29

value: normal colon mucosa obtained from the same patient as ch1


title: mRNA_TLT-C-048-LV

value: Other


title: mRNA_TLT-C-065-TT

value: Epithelial hepatoblastoma, fetal and embryonal


title: mRNA_TLT-C-060-TT

value: Epithelial hepatoblastoma, embryonal


title: mRNA_TLT-C-049-TT

value: Tumor

value: African American

value: Epithelial hepatoblastoma, embryonal, fetal and 15-20% small cell


title: Colon cancer tissue samples (FFPE) 32


title: Colon cancer tissue samples (FFPE) 31


title: Colon cancer tissue samples (FFPE) 24

value: no


title: Colon cancer tissue samples (FFPE) 27


title: mRNA_TLT-C-047-LV

value: M


title: Colon cancer tissue samples (FFPE) 26


title: mRNA_TLT-C-048-TT

value: Epithelial hepatoblastoma , embryonal


title: Colon cancer tissue samples (FFPE) 25


title: mRNA_TLT-C-043-TT

value: F

value: Caucasian

value: Epithelial hepatoblastoma, pure fetal


title: CEF_GFP-shRNA_NY72-4_41.5˚C_rep1

description:
Gene expression data from CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 41.5˚C
CEF_NY72-4_RCASB_42C_1

source_name: CEF transfected with RCAS(B)-GFP shRNA, infected with NY72-4, grown at 41.5˚C, biological replicate 1

value: white leghorn

value: chicken embryonic fibroblast cells derived from day 10 embryos

value: RCAS(B)-GFP shRNA

value: temperature sensitive A-type NY72-4 RSV


title: Colon cancer tissue samples (FFPE) 23

value: colon cancer (FFPE)

value: yes

value: normal colon mucosa obtained from the same patient as ch1


title: Colon cancer tissue samples (FFPE) 30


title: Colon cancer tissue samples (FFPE) 28


title: Colon cancer tissue samples (FFPE) 34


title: mRNA_TLT-C-042-TT

value: Asian

value: Epithelial hepatoblastoma, embryonal (65%) and fetal (15%)


title: mRNA_TLT-C-040-TT

value: Tumor

value: Epithelial hepatoblastoma, fetal (20%), embryonal (70%) and small cell (10%)


title: mRNA_TLT-C-041-LV

value: Normal Liver


title: mRNA_TLT-P-039-TT

value: M

value: Epithelial hepatoblastoma, embryonal and fetal


title: Colon cancer tissue samples (FFPE) 22


title: Colon cancer tissue samples (FFPE) 47

value: no


title: Colon cancer tissue samples (FFPE) 20


title: mRNA_TLT-P-036-TT

value: F

value: Caucasian

value: Epithelial hepatoblastoma


title: mRNA_TLT-P-023-TT


title: mRNA_TLT-P-038-TT

value: Hispanic


title: mRNA_TLT-P-028-TT

value: Epithelial hepatoblastoma, predominately embryonal


title: mRNA_TLT-P-033-TT

value: Mixed hepatoblastoma, predominately meshenchymal, 14% fetal  and 1% embryonal


title: Colon cancer tissue samples (FFPE) 13

value: colon cancer (FFPE)


title: Colon cancer tissue samples (FFPE) 21


title: mRNA_TLT-P-027-TT

value: Epithelial hepatoblastoma, mixed fetal and small cell


title: Colon cancer tissue samples (FFPE) 14

value: yes

value: normal colon mucosa obtained from the same patient as ch1


title: Colon cancer tissue samples (FFPE) 19


title: mRNA_TLT-P-016-TT

value: Epithelial hepatoblastoma, embryonal, fetal and minor small cell


title: Colon cancer tissue samples (FFPE) 17


title: mRNA_TLT-P-024-TT

value: Tumor

value: Mixed epithelial and mesenchymal hepatoblastoma


title: Colon cancer tissue samples (FFPE) 11


title: Colon cancer tissue samples (FFPE) 15


title: Colon cancer tissue samples (FFPE) 18


title: Colon cancer tissue samples (FFPE) 12


title: Colon cancer tissue samples (FFPE) 9


title: Colon cancer tissue samples (FFPE) 10


title: Patient27_GT30_mRNA_PMBL_NFKBIE_wildtype

status: Public on Oct 09 2016

city: Berlin

first: Daniel

last: Noerenberg

address: Augustenburger Platz 1

department: Hematooncology

country: Germany

institute: Charité University Medicine

description: NFKBIE wildtype sample

hyb_protocol: Hybridization was performed according to the manufacturer's protocol (NanoString.com) with 5µl of adjusted RNA overnight for a minimum of 18h at 65°C.

scan_protocol: Purification and binding of the hybridized probes to the cartridge was performed on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer's instruction. For each assay, a high-density scan with 600 FOV (fields of view) was performed.

data_processing: RCC files from the NanoString Digital Analyzer were imported into nSolver3.0 software and checked for data quality using default QC settings. In total, 29 of 26 samples passed prior RNA integrity and/or quality control. Tthe data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls.

label: NanoString PanCancer Pathway and Custom probes

source_name: Primary mediastinal B-cell lymphoma (PMBL)

label_protocol: 150ng of the adjusted RNA was used in 5µl with specific mRNA tag probes using the NanoString GX PanCancer Pathway Panel including 606 pathway genes, 124 cancer driver genes and 40 reference genes and a custom CodeSet including additional 30 genes of interest.

extract_protocol: RNA isolation of paraffin-embedded tumor tissue was performed in 36 human PMBL samples using AllPrep DNA/RNA Kit (Quiagen) or Maxwell RSC RNA FFPE Kit (Promega) accoring to the manufacturer's protocol. RNA was quantified via QubitTM 3.0 Fluorometer. For quality assessment, all samples were run on an Fragment Analyzer. The degree of RNA integrity was assessed using the smear analysis function in the PROSize software. The desired target input of 150 ng FFPE-extracted RNA was corrected for suboptimal RNA integrity, based on the percentage of degraded RNA between 30-300 nt.

value: PMBL tumor tissue

tag: biopsy location

tag: estimated tumor content


title: mRNA_TLT-P-021-TT

tag: age (yrs)

tag: Sex

value: Other

value: Mixed hepatoblastoma, predominately epithelial (fetal and embryonal), small area of osteoid


title: Patient25_ESP15_mRNA_PMBL_NFKBIE_mutated_VAF_14

description: NFKBIE variant allele frequency 14%

value: cervical lymphnode


title: Patient28_CH115_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample

value: mediastinum


title: Patient29_CH116_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient26_GT26_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient23_GT14_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Colon cancer tissue samples (FFPE) 36

value: no


title: Colon cancer tissue samples (FFPE) 16


title: mRNA_TLT-D-001-TT

value: M

tag: race

value: Caucasian

tag: histology

value: Epithelial hepatoblastoma, fetal, embryonal and minor small cell


title: Patient24_GT15_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample

tag: tissue


title: mRNA_TLT-P-003-TT

value: F

value: Epithelial hepatoblastoma mitotically active fetal and embryonal


title: Colon cancer tissue samples (FFPE) 7

value: colon cancer (FFPE)


title: mRNA_TLT-P-011-TT

value: Epithelial hepatoblastoma predominantly fetal and embryonal


title: Patient22_GT11_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient21_CH8_mRNA_PMBL_NFKBIE_mutated_VAF_21

description: NFKBIE variant allele frequency 21%


title: mRNA_TLT-S-010-TT

value: Epithelial hepatoblastoma, fetal and embryonal


title: mRNA_TLT-S-008-TT

value: Epithelial hepatoblastoma, embryonal and small cell


title: Colon cancer tissue samples (FFPE) 6

value: normal colon mucosa obtained from the same patient as ch1


title: Colon cancer tissue samples (FFPE) 5


title: mRNA_TLT-P-004-TT

value: Tumor


title: mRNA_TLT-D-009-TT

value: Hepatocellular neoplasm, NOS


title: Colon cancer tissue samples (FFPE) 2

value: yes


title: mRNA_TLT-D-001-LV

value: Normal Liver


title: Colon cancer tissue samples (FFPE) 1


title: Colon cancer tissue samples (FFPE) 4


title: Patient20_WU103_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample

value: PMBL tumor tissue


title: Colon cancer tissue samples (FFPE) 3


title: Patient18_ESP4_mRNA_PMBL_NFKBIE_mutated_VAF_41

description: NFKBIE variant allele frequency 41%

value: mediastinum


title: Patient17_ESP2_mRNA_PMBL_NFKBIE_mutated_VAF_25

description: NFKBIE variant allele frequency 25%

value: supraclavicular lymphnode


title: Patient15_GN2_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Colon cancer tissue samples (FFPE) 8

value: no


title: Patient14_RH104_mRNA_PMBL_NFKBIE_mutated_VAF_62

description: NFKBIE variant allele frequency 62%


title: Patient13_CH6_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient16_CH121_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient11_CH2_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient19_CH120_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient12_CH5_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient10_GT35_mRNA_PMBL_NFKBIE_mutated_VAF_45

description: NFKBIE variant allele frequency 45%


title: Patient9_GT36_mRNA_PMBL_NFKBIE_mutated_VAF_47

description: NFKBIE variant allele frequency 47%


title: Patient8_GT33_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient7_GT29_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: Patient6_GN1_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: HeyA8_mono_complete medium 24h_replicate2

first: Prahlad

middle: T.

last: Ram

address: 7435 Fannin St.

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and variance-stabilizing transformation using the beadarray and lumi packages in R

source_name: ovarian cancer cell

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit

growth_protocol: Day 0: HeyA8 cells are seeded in 6 well plates under RPMI 1640, Day1: 3 wells of HeyA8 cells are cocultured with CAFs, which are seeded on 6 well inserts, Day4: fresh medium(medium with or without glutamine) were replaced and cells were collected after 24 hours

extract_protocol: RNA was extracted with the mirVana miRNA Isolation kit in accordance with the prescribed protocol provided with the kit for total RNA extraction.

tag: cell line

tag: cell type

value: ovarian cancer cell

tag: media

value: complete

tag: culture

value: mono


title: Patient5_UU9_mRNA_PMBL_NFKBIE_mutated_VAF_17

description: NFKBIE variant allele frequency 17%


title: Patient3_ST108_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: HeyA8_mono_complete medium 24h_replicate3


title: HeyA8_coculturing with cancer associated fibroblasts_glutamine deprivation 24h_replicate3

value: glutamine deprivation

value: coculture


title: Patient2_WU107_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: HeyA8_mono_glutamine deprivation 24h_replicate2


title: Patient1_WU102_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample


title: HeyA8_coculturing with cancer associated fibroblasts_glutamine deprivation 24h_replicate1


title: HeyA8_coculturing with cancer associated fibroblasts_glutamine deprivation 24h_replicate2


title: HeyA8_mono_glutamine deprivation 24h_replicate1


title: U266_WT

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

label_protocol: 200 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: All myeloma cell lines were cultured in RPMI 1640 medium containing 2 mM L-glutamine and 10% fetal bovine serum (FBS). In addition, ANBL-6 and KAS-6/1 cells (both wild type and carfilzomib resistant) were cultured with added IL-6 (1 ng/ml).

extract_protocol: Total RNA was isolated by using TRIzol reagent (life Technologies), then further purified using the RNeasy plus Mini kit (Qiagen).

treatment_protocol: Drug-naive ANBL-6, KAS-6/1, U266, and OPM-2 myeloma cells were initially exposed to carfilzomib with  concentrations that were 10% of the maximal inhibitory concentration (IC10). Over several months, drug concentrations were serially increased following the verification of proliferative ability. After carfilzomib resistant (CR) cell lines ANBL-6/CR, KAS-6/1/CR, U266/CR, and OPM-2/CR were established, all experiments were done after removal of carfilzomib for at least 10 days.

value: human myeloma cell line

tag: phenotype

value: drug-naïve


title: U266_CR

source_name: U266_carfilzomib resistant

value: carfilzomib-resistant (CR)


title: HeyA8_mono_complete medium 24h_replicate1


title: mRNA_TLT-P-031-TT

value: M

value: Caucasian

value: Epithelial hepatoblastoma, mitotically active fetal

tag: Stage


title: ANBL6_WT


title: OPM2_CR

source_name: OPM2_carfilzomib resistant

value: carfilzomib resistant (CR)


title: KAS6/1_WT

value: drug-naive


title: KAS6/1_CR

source_name: KAS6/1_carfilzomib resistant


title: Patient4_ST111_mRNA_PMBL_NFKBIE_wildtype

description: NFKBIE wildtype sample

value: PMBL tumor tissue


title: KO2-Inf-3

status: Public on Oct 08 2016

city: Tokyo

first: Yayoi

last: Fukuoka

address: Hachioji Takakuracho

institute: Agilent

hyb_protocol: Each 600 ng of labeled cRNA was hybridized to SurePrint G3 Human Gene Expression microarray 8x60K v3 at 65°C for 17 hours.

scan_protocol: Washed slides were scanned by Agilent's SureScan microarray scanner.

data_processing: The scanned images were anlyzed with Feature Extraction and text files were imported to GeneSpring GX to analyze differentially expressed transcripts.

source_name: enSLiT07573 Knockout HeLa cells

label_protocol: Total RNA(100 ng) was reverse transcribed and labeled by Low Input Quick Amp WT Labeling kit (Agilent technologies) according to the manufacturer's instructions.

growth_protocol: HeLa TO cells were grown in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% foetal bovine serum (FBS) and antibiotics at 37°C in a humidified incubator with 5% CO2.

extract_protocol: To obtain RNA,  RNAiso plus was added and followed by RNA isolation in accordance with the manufacturer’sinstructions, using chloroform and 2-propanol.

treatment_protocol: The S. enterica serovar Typhimurium virulent strain used in this study was χ3306. A total of 1 × 105 HeLa cells in each well of a 12-well plate were challenged with Salmonella at a multiplicity of infection (m.o.i.) of 75, unless otherwise stated. The plate was centrifuged for 5 min at 500 ×g to enhance and synchronise infection. The cells were incubated for 1 h at 37°C to permit phagocytosis, and the free bacteria were removed by three washes with prewarmed phosphate-buffered saline (PBS). DMEM containing 10% heat-inactivated FBS and 100 μg/ml gentamicin was added and the cells were incubated for an additional 2 h at 37°C in a humidified incubator with 5% CO2. The cells were subsequently incubated with DMEM containing 10% heat-inactivated FBS and 10 μg/ml gentamicin at 37°C in a humidified incubator with 5% CO2 for the indicated period.

tag: infection

value: Salmonella


title: ANBL6_CR

source_name: ANBL6_carfilzomib resistant


title: OPM2_WT


title: KO2-NI-1

value: non-infected


title: KO2-Inf-2


title: KO2-Inf-1


title: KO2-NI-2


title: KO1-NI-2


title: KO1-Inf-3


title: KO1-Inf-1


title: HeLa-Inf-3

source_name: HeLa cells


title: KO1-NI-3


title: KO1-Inf-2


title: HeLa-NI-3


title: KO2-NI-3


title: Msn2A6_0min R2

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

hyb_protocol: The labelled Samples were hybridized to the Microarray slides, according to the standard protocol of the manufacturer.

scan_protocol: The slides were scanned with an Agilent Technologies Scanner G2505C, according to the standard protocol (GE1_107_Sep09) using grid 016322_D_F_20120509 as supplied by the manufacturer. Information from probe features was extracted from microarray scan images using the Agilent Feature Extraction software v10.7.3.

data_processing: The raw intensities were imported into Bioconductor and processed with the limma package.  Manufacturer control features were removed for further analysis.

source_name: S.c. strain BY4741

label_protocol: RNA quality was checked on RNA 6000 Nano chips using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Agilent's Low Input Quick Amp Labeling Kit, one-color (Kat. No.: 5190-2305) was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using Promega's SV Total RNA Isolation System. and hybridized to Agilent Yeast (V2) Gene Expression Microarrays 8x15K. Microarray slides were washed and scanned with an Agilent Scanner, according to the standard protocol of the manufacturer.

growth_protocol: Yeast cells were pre-grown in liquid YPD medium over night. After dilution to OD 0.1 in fresh YPD grown to OD 0.5 were 17ß-Estradiol  was added to final concentration of  and were harvested after 90 minutes.

extract_protocol: Cells were harvested by centrifugation washed and frozen. Extracts were made with bead beating with the phenol chloroform method. RNA was precipitated with ethanol, and dissolved in RNAse free water.

treatment_protocol: 50ml cultures in YPD at 30°C to OD600nm of about 1 before 17-ß-Estradiol was added to a final concentration of 6nM. After 90 minutes cells were harvested and immediately frozen

tag: estradiol treatment

value: no


title: HeLa-NI-2


title: LinSLiT08211KO2-WT-3

source_name: LinSLiT08211 Kockout HeLa cells


title: Msn2A6_0min R1


title: Msn2A6_90min R1

value: yes


title: HeLa-NI-1


title: LinSLiT08211KO2-NoInfection-3


title: Msn2A6_90min R2


title: LinSLiT08211KO2-WT-1


title: LinSLiT08211KO2-NoInfection-2


title: KO1-NI-1


title: LinSLiT08211KO2-NoInfection-1


title: LinSLiT08211KO2-WT-2


title: LinSLiT08211KO1-WT-3


title: LinSLiT08211KO1-WT-1


title: HeLa-Inf-2


title: LinSLiT08211KO1-WT-2


title: LinSLiT08211KO1-NoInfection-3


title: LinSLiT08211KO1-NoInfection-1


title: LinSLiT08211KO1-NoInfection-2


title: HeLa-WT-1


title: HeLa-WT-3


title: HeLa-WT-2


title: HeLa-NoInfection-2


title: HeLa-NoInfection-3


title: HeyA8_mono_glutamine deprivation 24h_replicate3

value: ovarian cancer cell


title: HeLa-NoInfection-1


title: challenge, 70 days [CH-70-51]

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Each hybridization mixture was made up from 1.1 µg Test (Cy3) and 1.1 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of the appropriate sample tracking control (STC, Roche Nimblegen) was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 95°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto a 12x135k Mus musculus microarray (Catalog no. 05543797001, Design 090901 MM9 EXP HX12) containing 44,170 genes with 3 probes per target gene. Microarrays were hybridized for 20 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen). Afterwards, the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0

scan_protocol: Slides were scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

data_processing: Raw microarray signal data were normalised in R (www.r-project.org), using a four step approach: (1) natural log-transformation, (2) quantile normalisation of all scans, (3) correcting the sample spot signal for the corresponding reference spot signal and (4) averaging data from replicate oligo spots. Normalised data for the resulting 44170 oligonucleotides were further analysed in R and Microsoft Excel. Further calculations were based on logratios compared to uninfected animals.

source_name: lung

label_protocol: Per sample, 500 ng total RNA was amplified according to the Agilent QuickAmp kit manual (Agilent technologies).  Amino-allyl modified nucleotides were incorporated during the aRNA synthesis (2.5 mM rGAU (GE Healthcare), 0.75 mM  rCTP (GE Healthcare), 0.75 mM AA-rCTP (TriLink Biotechnologies).  Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek). Test samples were labeled with Cy3 and a Reference sample (made by pooling equimolar amounts of RNA from Test samples) was labeled with Cy5.  5 µg of aRNA was dried down and dissolved in 50 mM carbonate buffer pH 8.5. Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). The labeled aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit. The yields of aRNA and CyDye incorporation were measured on the NanoDrop ND-1000.

growth_protocol: Female BALB/c mice (Harlan, The Netherlands), 8-week-old, were divided in groups of three animals and housed in cages (macrolon III including filter top).

extract_protocol: RNA isolation was performed using a miRNeasy Mini Kit with DNAse treatment (Qiagen). RNA concentrations were determined using UV spectroscopy (Tech3 module, Synergy Mx, BioTek). RNA quality was determined using electrophoresis (RNA nano 6000 kit, 2100 Bioanalyzer, Agilent).

treatment_protocol: Three healthy mice were euthanized at day 0 and considered as naïve group. Mice assigned to the challenge groups were  were intranasally infected under anesthesia (isoflurane/oxygen), with 2x10^5 cfu Bordetella pertussis B1917 in 40 µl Verweij medium at day 0. For both primary and secondary infections, mice were  were intranasally infected under anesthesia (isoflurane/oxygen), with 2x10^5 cfu Bordetella pertussis B1917 in 40 µl Verweij medium at day 56.

tag: treatment

value: challenge (secondary infection)

tag: time

value: 70 days

tag: sample type

value: common reference


title: NCI-H460

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: NCI60 panel

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: Lung

label_protocol: Standard Illumina labelling protocol

extract_protocol: unknown

value: Lung

value: Cancer cell line


title: HeLa-Inf-1


title: MDA-MB-468

description: NCI60 panel

source_name: Breast

value: Breast


title: RXF393

description: NCI60 panel

source_name: Kidney

value: Kidney


title: SF-539

description: NCI60 panel

source_name: Central Nervous System

value: Central Nervous System


title: HOP-92

description: NCI60 panel


title: SNB-75

description: NCI60 panel


title: challenge, 70 days [CH-70-50]


title: LOX_IMVI

description: NCI60 panel

source_name: Skin

value: Skin


title: BT-549

description: NCI60 panel


title: HOP-62

description: NCI60 panel


title: SF-268

description: NCI60 panel


title: OVCAR-8

description: NCI60 panel

source_name: Ovary

value: Ovary


title: KM12

description: NCI60 panel

source_name: Large Intestine

value: Large Intestine


title: challenge, 66 days [CH-66-43]

value: 66 days


title: DU-145

description: NCI60 panel

source_name: Prostate

value: Prostate


title: ACHN

description: NCI60 panel

value: ACHN


title: A549_ATCC

description: NCI60 panel


title: challenge, 66 days [CH-66-45]


title: U031

description: NCI60 panel


title: challenge, 70 days [CH-70-49]


title: SK-MEL-5

description: NCI60 panel


title: SN12C

description: NCI60 panel


title: SF-295

description: NCI60 panel


title: challenge, 63 days [CH-63-42]

value: 63 days


title: challenge, 63 days [CH-63-40]


title: MCF7

description: NCI60 panel


title: challenge, 66 days [CH-66-44]


title: NCI-H522

description: NCI60 panel


title: challenge, 58 days [CH-58-39]

value: 58 days


title: challenge, 58 days [CH-58-38]


title: NCI-H226

description: NCI60 panel


title: challenge, 63 days [CH-63-41]


title: RPMI-8226

description: NCI60 panel

source_name: Haematopoietic and Lymphoid Tissue

value: Haematopoietic and Lymphoid Tissue


title: challenge, 56.4 days [CH-56.4-35]

value: challenge (secondary infection)

value: 56 days + 4h


title: challenge, 58 days [CH-58-37]

value: common reference


title: T47D

description: NCI60 panel


title: SNB-19

description: NCI60 panel


title: 786-O

description: NCI60 panel


title: SK-MEL-2

description: NCI60 panel


title: challenge, 56.4 days [CH-56.4-34]


title: IGR-OV1

description: NCI60 panel


title: challenge, 56 days [CH-56-32]

value: 56 days


title: challenge, 56 days [CH-56-31]


title: challenge, 56 days [CH-56-33]


title: primary infection, 70 days [PI-70-62]

value: primary infection

value: 70 days


title: TK10

description: NCI60 panel

value: Kidney

value: Cancer cell line


title: primary infection, 70 days [PI-70-61]


title: primary infection, 70 days [PI-70-63]


title: challenge, 56.4 days [CH-56.4-36]


title: MDA-MB-435

description: NCI60 panel

value: Skin


title: COLO-205

description: NCI60 panel


title: primary infection, 63 days [PI-63-60]


title: primary infection, 63 days [PI-63-58]


title: primary infection, 63 days [PI-63-59]


title: primary infection, 58 days [PI-58-57]


title: NCI-H322M

description: NCI60 panel

value: Lung


title: HCT-15

description: NCI60 panel

value: Large Intestine


title: primary infection, 58 days [PI-58-55]


title: primary infection, 58 days [PI-58-56]


title: MDA-MB-231

description: NCI60 panel

value: Breast


title: CAKI-1

description: NCI60 panel


title: SK-MEL-28

description: NCI60 panel


title: primary infection, 56.4 days [PI-56.4-54]


title: naive, 0 days [PI-0-3]

value: naive

value: 0 days


title: primary infection, 56.4 days [PI-56.4-52]


title: MOLT-4

description: NCI60 panel


title: naive, 0 days [PI-0-1]


title: OVCAR-4

description: NCI60 panel

value: Ovary


title: U251

description: NCI60 panel

value: Central Nervous System


title: primary infection, 56.4 days [PI-56.4-53]


title: H96118699A pancreatic ductal adenocarcinoma

status: Public on Oct 07 2016

city: ChongQing

first: ShiXiang

last: Guo

state: ChongQing

address: GaoTanYan street No.29，ShaPingBa district

department: Southwest hospital，Third Military Medical University

country: China

institute: institute of Hepatopancreatobiliary Surgery

description: The pancreatic ductal adenocarcinoma sample was collected from the Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University, and stored in liquid nitrogen.

hyb_protocol: The labeled cRNAs were hybridized onto an Arraystar Human circRNA Array (8×15K, Arraystar)and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After the slides were washed, the arrays were scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Statistical differences in circRNA expression between the two groups were determined with Volcano Plot filtering. Differentially expressed circRNAs between the two sample sets were identified through Fold Change filtering. Hierarchical Clustering was performed to show distinguishable circRNAs expression patterns among samples.

source_name: pancreatic ductal adenocarcinoma

label_protocol: total RNA was digested with RNase R (Epicentre, Inc.) to remove linear RNAs and to enrich for circRNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA from pancreatic ductal adenocarcinoma samples and paracancerous tissues was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The RNA extractions were stored at 80°C. Total RNA from each sample was quantified using a NanoDrop ND-1000. Sample preparation and microarray hybridization were performed based on Arraystar’s standard protocols.

treatment_protocol: Twenty fresh-frozen PDAC samples and twenty paracancerous tissues were collected from the Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University. The paracancerous samples were obtained from the same patient. All tissue samples were stored in liquid nitrogen, and pathologists from the Department of Pathology in the Southwest Hospital performed pathologic diagnosis.

value: pancreatic ductal adenocarcinoma sample

tag: age

tag: gender

value: male


title: H69276948P paracancerous tissue

description: The paracancerous tissue was obtained from the same patient, and stored in liquid nitrogen.

source_name: paracancerous tissue

value: paracancerous tissue

value: female


title: H69276948A pancreatic ductal adenocarcinoma


title: H96118699P paracancerous tissue


title: naive, 0 days [PI-0-2]

value: common reference


title: H55478397P paracancerous tissue


title: Human liver biopsy (11_GW)

city: Cambridge

first: Naomi

last: Habib

state: MA

address: 75 Ames st

department: Zhang

institute: Broad Institute

hyb_protocol: RNA was hybridized to an Affymetrix GeneChip. Samples were hybridized using Affymetrix hybridization kit (following manufacturer's protocol)

scan_protocol: Affymetrix GeneChip scanner

data_processing: Following robust multi-array average (RMA) procedure and quantile normalization, the probes were filtered using BioDiscovery’s Nexus Expression software (El Segundo, CA). Probes with a variance less than 0.2 and intensity less than 4.0 were removed.

source_name: Human liver biopsy

label_protocol: Affymetrix labeling protocol

growth_protocol: Primary human hepatocytes were mixed with lung endothelial cells and seeded in a humidified incubator conditioned by a gas mixture of 95% oxygen and 5% CO2. Following overnight seeding under 95% oxygen the cultures were returned to atmospheric levels of oxygen and 5% CO2.

extract_protocol: Liver biopsy samples were flash frozen, then RNA was extracted for array analysis. RNA from primary samples was collected at day 11 post infection.

treatment_protocol: HCV infection of primaty hepatocytes (JFH-1 virus) was carried 1 day post seeding. Liver biopsy samples were collected from 5 patients, at early stages of HCV infection (genotypes 2B, 1A, 2A, 3A), following an overnight fast.

value: 25 to 39 years

value: liver

value: HCV-infected


title: K-562

description: NCI60 panel

value: Haematopoietic and Lymphoid Tissue

value: Cancer cell line


title: Human liver biopsy (13_KS)


title: HCC-2998

description: NCI60 panel


title: Human liver biopsy (09-JA)


title: SR

description: NCI60 panel

value: SR


title: UACC-62

description: NCI60 panel

value: Skin


title: H46809281P paracancerous tissue


title: H46809281A pancreatic ductal adenocarcinoma


title: Human liver biopsy (03_ScS)


title: Human liver biopsy (01_SS)


title: SK-OV-3

description: NCI60 panel


title: H23616671A pancreatic ductal adenocarcinoma


title: H23616671P paracancerous tissue


title: H12560130P paracancerous tissue


title: H12560130A pancreatic ductal adenocarcinoma


title: H9383468P paracancerous tissue


title: OVCAR-3

description: NCI60 panel


title: HS_578T

description: NCI60 panel

value: Breast


title: A498

description: NCI60 panel

value: Kidney


title: H9383468A pancreatic ductal adenocarcinoma


title: H8795243A pancreatic ductal adenocarcinoma


title: H8795243P paracancerous tissue


title: NCI-ADR-RES

description: NCI60 panel

value: NCI-ADR-RES


title: HL-60_TB

description: NCI60 panel


title: H8741820P paracancerous tissue


title: MALME-3M

description: NCI60 panel