title: VIN.2824-1

source_name: VIN.2824-1, Vastus intermedius

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of all RNA extractions


title: SME.2824-1

status: Public on Oct 30 2012

type: RNA

city: Aarhus

first: Henrik

last: Hornshøj

address: Brendstrupgårdsvej 100

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: Statistical analysis was carried out in the R computing environment version 2.6 using the package Linear Models for Microarray Analysis (Limma, version 2.9.17) which is part of the Bioconductor project. The log2-transformed ratios of Alexa-647 to Alexa-555 were normalized within-slide using the global-loess method with default parameters as implemented in Limma.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press ""button"" on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press ""button"" and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox)

scan_protocol: Scanner: GenePix Autoloader 4200AL, 5 µm resolution, 90 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.22, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = MorphologicalClosingFollowedByOpening

data_processing: Muscle tissue samples from heart (HEA), Vastus intermedius (VIN), Infraspinatus (ISP), Supraspinatus (SSP), Biceps femoris (BFE), Longissimus dorsi (LDO), Semimembranosus (SME), Semitendinosus (STE) and Triceps brachii (TBR). A reference sample was constructed by combining all samples. The exact same tissue samples were used for expression profiling with cDNA microarrays and 70-mer long oligonucleotide microarrays.

molecule: total RNA

organism: Sus scrofa

source_name: SME.2824-1, Semimembranosus

label_protocol: 20 µg total RNA was labelled with Alexa-647 using the Superscript Plus Direct cDNA Labeling System (Invitrogen) following the enclosed protocol. Spike-in RNA (red) from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen)

tag: Breed

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semimembranosus

source_name: reference: pool of all extractions

label_protocol: 20 µg total RNA was labelled with Alexa-555 using the Superscript Plus Direct cDNA Labeling System (Invitrogen) following the enclosed protocol. Spike-in RNA (green) from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions.


title: MFP tumor from Control cells 2

status: Public on Oct 29 2012

city: Clayton

first: Konstantin

last: Knoblich

state: VIC

address: 15 Innovation Walk

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.

scan_protocol: The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Data are processed using GenePattern. The ExpressionFileCreator module is used to normalize (RMA normalization algorithm) and create processed file (gct)

label: biotin

organism: Homo sapiens

source_name: tumor

label_protocol: RNA is converted to cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements.The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Tumors were grown in mammary fat pads of Nu/Nu nude mice for 34 days

extract_protocol: Tumors were extracted with a scalpel and frozen. Piece of the the tumor was used to extract and purify total RNA using Rneasy kit (Qiagen)

tag: genotype/variation

value: Control


title: NH17 WT LPS

city: Linköping

first: Namik

last: Hamzic

address: Linköpings Universitet

department: Institution for clinical and experimental medicin

country: Sweden

institute: University of Health

description: Gene expression data from mouse hypothalamus

hyb_protocol: Following fragmentation, 2 µg of cRNA were hybridized for 16-18hr at 45 °C on GeneChip Mouse 1.0 ST Array. GeneChips were washed and stained in the Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring software using RMA as normalization method.

label: Biotin

organism: Mus musculus

source_name: Mouse hypothalamus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 200 ng total RNA.

growth_protocol: 9-12 weeks old C57bl6 male mice deficient in interleukin-6 and their corresponding wild-type littermates originating from the same parental animals were used. All animals were housed one per cage in a pathogen-free facility at ambient temperature of 20-21 °C with food and water available ad libitum, and on a 12-h light, 12-h dark cycle.

extract_protocol: The mice were perfused with 0.9% saline solution transcardially before samples of hypothalamus were collected. Total RNA from the hypothalamus was extracted using RNeasy Lipid Tissue Kit (Qiagen) according to the manufacturer’s instructions, including deoxyribonuclease treatment with ribonuclease-free deoxyribonuclease set (Qiagen).

treatment_protocol:
LPS
Mice were stimulated with a single intraperitoneal injection of lipopolysaccharide from Escherichia coli in a dose of 120 µg/kg body weight. Control animals were given vehicle (saline) only. The mice were sacrificied three hours after the injection of LPS or saline using coldioxide.

tag: strain

tag: treatment

tag: tissue

value: Hypothalamus

value: WT


title: NH13 IL-6 KO SALINE

treatment_protocol:
SALINE
Mice were stimulated with a single intraperitoneal injection of lipopolysaccharide from Escherichia coli in a dose of 120 µg/kg body weight. Control animals were given vehicle (saline) only. The mice were sacrificied three hours after the injection of LPS or saline using coldioxide.

value: saline

value: IL-6 KO


title: NH12 WT LPS

value: lipopolysaccharide from Escherichia coli in a dose of 120 µg/kg body weight


title: NH10 WT LPS


title: NH7 IL-6 KO SALINE


title: NH14 IL-6 KO LPS


title: MFP tumor from Control cells 1


title: NH9 WT LPS


title: NH8 WT SALINE


title: NH3 WT LPS


title: NH21 IL-6 KO SALINE


title: NH4 IL-6 KO LPS


title: NH11 WT SALINE


title: NH15 IL-6 KO LPS


title: NH5 WT LPS


title: NH16 IL-6 KO LPS


title: NH1 IL-6 KO LPS


title: NH6 WT SALINE


title: NH2 WT LPS


title: PI02

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: gene expression from biopsies

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using RMA

source_name: gingival tissue, Parodontitis patient

extract_protocol: RNA extracted using RNeasy (Qiagen) according to the manufacturers guidelines

tag: cell type

value: primary tissue, biopsy


title: PI49

description: gene expression from biopsies

source_name: gingival tissue, periimplantitis patient

label_protocol: according to the manufacturers guidelines (Affymetrix)


title: PI05

description: gene expression from biopsies


title: PI12

description: gene expression from biopsies


title: PI10

description: gene expression from biopsies


title: PI09

description: gene expression from biopsies


title: PI44

description: gene expression from biopsies


title: PI01

description: gene expression from biopsies


title: PI13

description: gene expression from biopsies


title: PI50

description: gene expression from biopsies


title: PI70

description: gene expression from biopsies

source_name: gingival tissue, healthy individual


title: PI11

description: gene expression from biopsies


title: PI75

description: gene expression from biopsies


title: PI43

description: gene expression from biopsies


title: PI78

description: gene expression from biopsies


title: PI45

description: gene expression from biopsies


title: PI29

description: gene expression from biopsies


title: PI41

description: gene expression from biopsies


title: PI06

description: gene expression from biopsies


title: PI48

description: gene expression from biopsies


title: PI46

description: gene expression from biopsies


title: DNA from NT22

type: genomic

city: Esplugues de Llobregat

first: Cinzia

last: Lavarino

state: Barcelona

address: Santa Rosa 39-57

department: Oncology

country: Spain

institute: Hospital Sant Joan de Déu

description: Sample name: HSJD-C9

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 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
Matrix signal intensities value definition: Unmethylated and methylated signal intensities.  The Matrix of signal intensities is  linked as a supplementary file on the Series record.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated from snap-frozen samples using Cell Lysis Solution from Promega and proteinase K from Sigma following manufacturers’ protocols

tag: gender

value: male

value: tumoral tissue

tag: tumor stage (inss classification)

value: stage 4

tag: mycn status

value: non amplified

tag: age at diagnosis (months)


title: DNA from NT23

description: Sample name: HSJD-C10

value: female

value: ganglioneuroblastoma


title: DNA from fetal brain

description: Sample name: HSJD-D8

source_name: Fetal brain

value: normal brain tissue


title: DNA from NT24

description: Sample name: HSJD-C12

value: stage 3

value: amplified


title: DNA from NT21

description: Sample name: HSJD-C8

value: ganglioneuroma


title: PI47

description: gene expression from biopsies


title: DNA from NT25

description: Sample name: HSJD-D4

value: stage 4s


title: DNA from adrenal gland

description: Sample name: HSJD-D9

source_name: Adrenal gland

value: normal adrenal gland tissue


title: P4 - 2MED

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

country: USA

institute: Mount SinaiSchool of Medicine

description: whole skin tisue

hyb_protocol: RNA was hybridized to HG U133A 2.0 chips to measure relative gene expression according to manufacturer's protocol

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: whole skin tisue

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen Valencia, CA) according to manufacturer’s protocol with on-column Dnase digestion

tag: patient

tag: group


title: DNA from NT15

description: Sample name: HSJD-B12

value: stage 1


title: DNA from NT16

description: Sample name: HSJD-C2


title: DNA from NT18

description: Sample name: HSJD-C4


title: DNA from NT20

description: Sample name: HSJD-C6


title: DNA from NT17

description: Sample name: HSJD-C3


title: DNA from NT19

description: Sample name: HSJD-C5


title: DNA from NT11

description: Sample name: HSJD-B4


title: DNA from NT13

description: Sample name: HSJD-B6


title: DNA from NT8

description: Sample name: HSJD-A12


title: DNA from NT10

description: Sample name: HSJD-B2


title: DNA from NT12

description: Sample name: HSJD-B5


title: USC-HN1-GFP-G2 A

city: Los Angeles

first: Masood

last: Rizwan

department: Otolaryngology-Head and Neck Surgery

institute: University of Southern California

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw signal intensities were imported and analyzed using GenomeStudio® data analysis software. Data was background subtracted, and the quantile normalized signal intensities were exported to the Partek® genomics expression analysis suite using “Partek’s Report Plug-in” option in the GenomeStudio® software. Differentially expressed genes were identified using the “gene expression” workflow in the Partek® software.

label_protocol: Gene expression profiling was performed using the BeadChip HumanHT-12 v4 Expression kit from Illumina®, which contains 47,231 gene probes (Illumina® Inc., San Diego, California).

extract_protocol: Total RNA from these cell lines were isolated using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, California following the manufacturer’s recommendations.

value: Alveolar Ridge Squamous Cell Carcinoma metastatic to mouse lymph node from generation 1


title: USC-HN1-GFP-G2 C


title: DNA from NT6

description: Sample name: HSJD-A6


title: USC-HN1-GFP-G2 D


title: DNA from NT9

description: Sample name: HSJD-B1


title: USC-HN1-GFP-G1 B

value: Alveolar Ridge Squamous Cell Carcinoma metastatic to mouse lymph node from parental generation


title: USC-HN1-GFP-G1 A


title: DNA from NT3

description: Sample name: HSJD-A3


title: USC-HN1-GFP D

value: Alveolar Ridge Squamous Cell Carcinoma


title: DNA from NT14

description: Sample name: HSJD-B7


title: USC-HN1-GFP-G2 B


title: USC-HN1-GFP-G1 D


title: DNA from NT7

description: Sample name: HSJD-A11


title: USC-HN1-GFP-G1 C


title: DNA from NT5

description: Sample name: HSJD-A5


title: DNA from NT4

description: Sample name: HSJD-A4


title: Pim-1-/- aortic endothelial cells replicate 3

city: Zürich

first: Thomas

last: Walpen

address: Gloriastrasse 30 H09

department: Research Unit Division Internal Medicine

country: Switzerland

institute: University Hospital Zürich

description: Biological replicate 3 of 3. Pim1 knockout vs. wildtype mouse aortic endothelail cells

hyb_protocol: Agilent Gene Expression kit for oligo microarrays (Agilent, order number 5188-5242, protocol G4140-90050).

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Agilent Feature Extraction software 9.5.3.1.

source_name: Aortic endothelial cells

label_protocol: 1.6 - 4 μg of total RNA were reverse transcribed to cDNA, and amplified and labeled to cRNA with the Agilent Low RNA Input Linear Amplification Kit PLUS (order number 5184-3525, Agilent).

growth_protocol: MAECs were isolated from aortae of FVB/N wildtype and Pim1-/- mouse strains as described previously [Humar et al., 2002]. For all experiments cell culture dishes were precoated with 0.1% gelatine gold (Carl Roth GmbH, Karlsruhe, Germany) for 20 minutes at 37°C. Cells were maintained in DMEM (Biochrom, Berlin, Germany) complemented with 10% FBS, 1% sodium pyruvate, 1% non-essential amino acids and 1% penicillin-streptomycin (Invitrogen, LuBioScience GmbH, Luzern, Switzerland). 8×104 cells/cm2 were seeded, washed with phosphate-buffered saline (Invitrogen) after 24 hours and trypsinized (TripLE express, Invitrogen) to isolate total RNA

extract_protocol: Total RNA was isolated using a RNAeasy Mini kit (Qiagen) and the RNAse free DNAse set (Qiagen) following manufacturer's instructions.

value: FVB/N Pim1 knockout

tag: primary cells

value: mouse aortic endothelial cells (MAEC)

tag: age

value: 12 weeks

source_name: Aortic endothelial cells wildtype

value: FVB/N wildtype


title: DNA from NT2

description: Sample name: HSJD-A2

value: male

value: tumoral tissue

value: non amplified


title: USC-HN1-GFP C


title: USC-HN1-GFP B


title: USC-HN1-GFP A


title: Pim-1-/- aortic endothelial cells replicate 2

description: Biological replicate 2 of 3. Pim1 knockout vs. wildtype mouse aortic endothelail cells

value: female


title: PBMC P3  IL1 -2h 6334175029_C

status: Public on Oct 28 2012

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

scan_protocol: Standard Illumina scanning protocol and scanned with Illumina iScan

data_processing: The data were background subtracted and average normalized using Illumina Genome Studio

source_name: PBMC

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the Illumina TotalPrep RNA Amplification Kit from Ambion

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

tag: disease state

value: HOIL deficiency

tag: subject

value: HOIL deficiency 3

tag: stimulation

tag: time

value: 2 hours

value: PBMC


title: DNA from NT1

description: Sample name: HSJD-A1

value: ganglioneuroma


title: PBMC P3  TNF -6h 6334175045_C

value: TNF-a

value: 6 hours


title: PBMC P1 TNF -6h 6334175036_C

value: HOIL deficiency 1


title: PBMC P2  TNF -2h 6334175046_I

value: HOIL deficiency 2


title: PBMC P3  TNF -2h 6334175036_J


title: PBMC P3  IL1 -6h 6334175026_J


title: PBMC P3  Non stimulate -2h 6334175031_E

value: Medium


title: PBMC P2  Non stimulate -2h 6334175031_G


title: PBMC P3  Non stimulate -6h 6334175045_E


title: PBMC P2  IL1 -2h 6334175045_L


title: Pim-1-/- aortic endothelial cells replicate 1

description: Biological replicate 1 of 3. Pim1 knockout vs. wildtype mouse aortic endothelail cells

value: FVB/N Pim1 knockout

value: mouse aortic endothelial cells (MAEC)


title: PBMC P2  Non stimulate -6h 6334175044_F


title: PBMC P1 Non stimulate -6h 6334175026_H


title: PBMC P2  TNF -6h 6334175036_G


title: PBMC P2  IL1 -6h 6334175027_E


title: PBMC P1 IL1 -6h 6334175029_E


title: PBMC MYD88-(2)  Non stimulate -6h 6334175036_H

value: Myd88 deficiency

value: Myd88 deficiency 2


title: MWS57

scan_protocol: Illumina BeadArray Reader

data_processing: The data were analysed using BeadStudio version using the average chip normalization method.

source_name: Whole blood

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the Illumina TotalPrep RNA Amplification Kit from Ambion.

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems) according to the manufacturer's instructions

value: whole blood

value: MWS


title: MWS81


title: MVK272

value: MVK


title: MWS56


title: MVK271


title: MWS11


title: PBMC MYD88-(2)  TNF -6h 6334175036_A


title: PBMC MYD88-(2)  Non stimulate -2h 6334175040_L


title: MWS12


title: CINCA06

value: CINCA


title: PBMC MYD88-(2)  TNF -2h 6334175030_H


title: CINCA05


title: PBMC MYD88-(1)  TNF -2h 6334175036_B

value: Myd88 deficiency 1


title: PBMC MYD88-(2)  IL1 -2h 6334175029_D

value: 2 hours


title: PBMC MYD88-(1)  TNF -6h 6334175048_C

value: PBMC


title: PBMC MYD88-(1)  Non stimulate -2h 6334175031_I


title: PBMC MYD88-(1)  IL1 -6h 6334175029_B


title: PBMC C3  Non stimulate -2h 6334175027_L

value: Healthy

value: Healthy 3


title: PBMC MYD88-(1)  IL1 -2h 6334175030_K


title: PBMC MYD88-(2)  IL1 -6h 6334175036_K

value: 6 hours


title: PBMC C3  Non stimulate -6h 6334175040_J


title: PBMC MYD88-(1)  Non stimulate -6h 6334175040_D


title: PBMC C3  TNF -2h 6334175026_C

value: TNF-a


title: H192


title: H1246


title: P1

value: HOIL dificiency


title: H996


title: H1181


title: H1242


title: PBMC C3  TNF -6h 6334175045_J


title: H1239


title: H332


title: H289


title: PBMC C3  IL1 -6h 6334175030_L


title: H1183


title: H646


title: H1245


title: PBMC C2  TNF -6h 6334175030_D


title: H287


title: H257


title: PBMC C2  Non stimulate -2h 6334175044_H

value: Healthy 2

value: Medium


title: PBMC C2  Non stimulate -6h 6334175044_A


title: PBMC C2  IL1 -2h 6334175027_A


title: PBMC C2  TNF -2h 6334175045_H


title: PBMC C2  IL1 -6h 6334175048_A


title: H288


title: H256


title: PBMC C1  TNF -2h 6334175027_I

value: Healthy 1


title: H229


title: H241


title: H240


title: H231


title: PBMC C1  Non stimulate -6h 6334175046_L


title: PBMC C1  IL1 -6h 6334175036_L


title: PBMC C1  TNF -6h 6334175045_B


title: P3 TNF - 2h (6334175026_I)

description: P3 TNF - 2h

scan_protocol: We used Illumina iScan.

source_name: fibroblast

value: HOIL deficiency

value: HOIL deficiency 3


title: H228

value: whole blood


title: H220


title: H225


title: PBMC C1  IL1 -2h 6334175045_G


title: H226


title: H219


title: P3 TNF - 6h (6334175046_A)

description: P3 TNF - 6h


title: H213


title: PBMC C1  Non stimulate -2h 6334175027_F


title: H244


title: H275


title: P3 Non stimulate (6334175030_G)

description: P3 Non stimulate


title: P3 IL1 - 6h (6334175040_H)

description: P3 IL1 - 6h


title: P2 TNF - 2h (6334175030_E)

description: P2 TNF - 2h

value: HOIL deficiency 2


title: H205


title: P3 IL1 - 2h (6334175027_G)

description: P3 IL1 - 2h


title: P2 Non stimulate (6334175026_L)

description: P2 Non stimulate


title: P3 Non stimulate (6334175029_G)

description: P3 Non stimulate


title: P2 Non stimulate (6334175031_K)

description: P2 Non stimulate


title: Top2b-/- Cardiomyocytes 72hr after PBS rep4

city: Houston

first: Sui

last: Zhang

state: TX

address: 1400 Pressler St.

department: Cardiology

institute: U.T. M.D. Anderson Cancer Center

description:
Gene expression 72 hr after PBS injection (i.p.)
72 hr Top2b Del Ctr4

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (FES, Version 10.7.3.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Version 7.2)

source_name: Top2b-/- Cardiomyocytes 72hr after PBS

label_protocol: One hundred nanograms of each total RNA sample were used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from the isolated cardiomyocytes with TRIZOL reagent (Invitrogen), RNA was then purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Mice were first injected with doxorubicin (25mg/kg, i.p.) or PBS (i.p.). Hearts were removed 16hr or 72 hr after injection. Live cardiomyocytes were isolated from the heart immediately by using a Langendorff aparatus.

tag: strain background

value: male

value: 6 weeks

tag: genotype/variation

value: Top2b-/- (cardiac specific deletion of Top2b)

tag: injected with

value: PBS (i.p.)

value: heart

value: primary cardiomyocytes


title: H164

tag: tissue

value: Healthy


title: Top2b-/- Cardiomyocytes 72hr after doxorubicin rep4

description:
Gene expression 72 hr after Doxorubicin injection (i.p.)
72 hr Top2b Del Dox4

value: doxorubicin (25mg/kg, i.p.) or PBS (i.p.)

tag: cell type


title: P2 TNF - 6h (6334175030_J)

description: P2 TNF - 6h

value: TNF-a

value: 6 hours


title: H199


title: H198


title: P2 IL1 - 2h (6334175036_F)

description: P2 IL1 - 2h

value: 2 hours


title: Top2b-/- Cardiomyocytes 72hr after doxorubicin rep3

description:
Gene expression 72 hr after Doxorubicin injection (i.p.)
72 hr Top2b Del Dox3

tag: gender


title: H201


title: WT Cardiomyocytes 72hr after doxorubicin rep4

description:
Gene expression 72 hr after Doxorubicin injection (i.p.)
72 hr WT Dox4

value: wild type


title: P1 TNF - 6h (6334175044_C)

description: P1 TNF - 6h


title: H202


title: P1 TNF - 2h (6334175040_B)

description: P1 TNF - 2h

value: HOIL deficiency 1


title: P2 IL1 - 6h (6334175031_D)

description: P2 IL1 - 6h

value: HOIL deficiency


title: P1 IL1 - 2h (6334175036_E)

description: P1 IL1 - 2h


title: H184


title: P1 IL1 - 6h (6334175046_B)

description: P1 IL1 - 6h


title: H204


title: P1 Non stimulate (6334175045_A)

description: P1 Non stimulate

value: Medium


title: WT Cardiomyocytes 72hr after PBS rep4

description:
Gene expression 72 hr after PBS injection (i.p.)
72 hr WT Ctr4

source_name: WT Cardiomyocytes 72hr after PBS


title: H200

value: whole blood


title: PBMC C3  IL1 -2h 6334175048_B

value: Healthy 3

value: PBMC


title: H155


title: WT Cardiomyocytes 72hr after doxorubicin rep3

description:
Gene expression 72 hr after Doxorubicin injection (i.p.)
72 hr WT Dox3

value: male

value: 6 weeks


title: NEMO IL1 - 6 hour (6334175046_E)

description: NEMO IL1 - 6 hour

value: NEMO deficeincy


title: NEMO TNF - 6 hour (6334175044_J)

description: NEMO TNF - 6 hour


title: Myd88 TNF - 6 hour (6334175046_K)

description: Myd88 TNF - 6 hour

value: Myd88 deficiency


title: P1 Non stimulate (6334175029_F)

description: P1 Non stimulate


title: C4 TNF - 6h (6334175046_F)

description: C4 TNF - 6h

value: Healthy 4


title: Top2b-/- Cardiomyocytes 72hr after PBS rep3

description:
Gene expression 72 hr after PBS injection (i.p.)
72 hr Top2b Del Ctr3

value: Top2b-/- (cardiac specific deletion of Top2b)

value: PBS (i.p.)

value: heart

value: primary cardiomyocytes


title: Myd88 IL1 - 6 hour (6334175031_H)

description: Myd88 IL1 - 6 hour

value: 6 hours


title: WT Cardiomyocytes 72hr after doxorubicin rep2

description:
Gene expression 72 hr after Doxorubicin injection (i.p.)
72 hr WT Dox2

value: wild type

value: doxorubicin (25mg/kg, i.p.) or PBS (i.p.)


title: WT Cardiomyocytes 72hr after PBS rep3

description:
Gene expression 72 hr after PBS injection (i.p.)
72 hr WT Ctr3


title: Top2b-/- Cardiomyocytes 72hr after PBS rep2

description:
Gene expression 72 hr after PBS injection (i.p.)
72 hr Top2b Del Ctr2


title: NEMO Non stimula (6334175040_I)

description: NEMO Non stimula

value: 2 hours


title: NEMO TNF - 2h (6334175029_J)

description: NEMO TNF - 2h

value: TNF-a


title: Top2b-/- Cardiomyocytes 72hr after doxorubicin rep2

description:
Gene expression 72 hr after Doxorubicin injection (i.p.)
72 hr Top2b Del Dox2


title: Myd88 Non stimul (6334175036_I)

description: Myd88 Non stimul

value: Medium


title: Myd88 IL1 - 2h (6334175031_B)

description: Myd88 IL1 - 2h


title: NEMO IL1 - 2 hour (6334175044_L)

description: NEMO IL1 - 2 hour


title: B.oleracea_drought_rep1

city: Poznan

first: Agnieszka

middle: Wioletta

last: Ludwików

address: Umultowska 89

department: Biotechnology

country: Poland

institute: Adam Mickiewicz University

description: A total 522 features were spotted

hyb_protocol: Purified radiolabelled cDNA was used for hybridization with custom nylon membrane arrays. To minimize nonspecific binding, labeled DNA in 4xSSC, 0.1% SDS was mixed with 0.1 mg/ml poly(dA) DNA, denatured at 95ºC for 5 min and hybridized at 65ºC for 1 h. Prehybridization step was carried out at 65ºC for 3 h in 15 ml of Church buffer (250 mM Na2HPO4 pH 7.2, 1 mM EDTA, 7% SDS and 1% BSA) with 10 mg/ml Salmon sperm DNA. Hybridization using denatured labeled cDNA was performed at 65ºC up to 18 h. After washing: once in 2 x SSC, 0.1% SDS, twice in 0.5 SSC, 0.1% SDS and once at 0.1 x SSC, 0.1% SDS each at 65ºC.

scan_protocol: The membranes were exposed to a storage screens for 48 h and then scanned at 200 micron resolution (PhosphorImager Fuji) into the supplied Multi Gauge V2.2 Software.

data_processing: Raw data were normalized to the mean hybridization signal for ACT2. The average expression values for each condition were calculated from three independent biological replicates. Normalization software: ImageQuantTL.

organism: Brassica oleracea

source_name: B.oleracea,drought-treated 5 days

label_protocol: 10 µg of total RNA was used for 33P-CTP labeling with LabelStar Array Kits (Qiagen) according to the instruction

growth_protocol: Seeds were sterilized with bleach, chilled for 4 days than transferred to the growth chamber with 16 h photoperiod (~300 µmol –2 s-1 photon density, 75% relative humidity) and grown 3-5 plants per pot. Plants were watered daily; once a week plants were irrigated with mineral nutrient solution.

extract_protocol: Total RNA was isolated from leaves of 5 plants in triplicate using Qiagen RNA isolation kit. The corresponding total RNA samples were pooled and usued for labelling

treatment_protocol: For drought stress treatment, plants were not watered for 5-days until relative water content (RWC) of the leaves reached an average 45%±15. Control plants were watered regularly.

tag: subspecies

value: alboglabra line A12DH

value: 4 week old

tag: stress

value: drought

value: leaf


title: Myd88 TNF - 2 hour (6334175044_E)

description: Myd88 TNF - 2 hour


title: B.oleracea_drought_rep2

description: A total 522 features were spotted


title: B.oleracea_drought_rep3

description: A total 522 features were spotted


title: NEMO Non stimula (6334175044_B)

description: NEMO Non stimula

value: NEMO deficeincy


title: WT Cardiomyocytes 72hr after PBS rep2

description:
Gene expression 72 hr after PBS injection (i.p.)
72 hr WT Ctr2

value: male

value: 6 weeks


title: H037

value: whole blood

value: Healthy


title: H127


title: Myd88 Non stimul (6334175030_C)

description: Myd88 Non stimul

value: Myd88 deficiency


title: H159


title: H153


title: C4 TNF - 2h (6334175044_D)

description: C4 TNF - 2h

value: Healthy 4


title: B.oleracea_control_rep4

description: A total 522 features were spotted

value: control


title: B.oleracea_control_rep1

description: A total 522 features were spotted


title: B.oleracea_control_rep2

description: A total 522 features were spotted


title: A.thaliana_drought_rep2

description: A total 522 features were spotted

organism: Arabidopsis thaliana

source_name: A.thaliana,drought-treated 5 days

tag: ecotype

value: Columbi (Col-0 obtained from ABRC)


title: A.thaliana_drought_rep3

description: A total 522 features were spotted


title: A.thaliana_drought_rep1

description: A total 522 features were spotted


title: B.oleracea_control_rep3

description: A total 522 features were spotted


title: C3 TNF - 2h (6334175030_F)

description: C3 TNF - 2h

value: Healthy 3


title: C3 IL1 - 2h (6334175029_A)

description: C3 IL1 - 2h

value: 2 hours


title: Top2b-/- Cardiomyocytes 16hr after PBS rep3

description:
Gene expression 16 hr after PBS injection (i.p.)
16 hr Top2b Del Ctr3

source_name: Top2b-/- Cardiomyocytes 16hr after PBS

value: wild type

value: PBS (i.p.)

value: heart

value: primary cardiomyocytes


title: Top2b-/- Cardiomyocytes 16hr after doxorubicin rep1

description:
Gene expression 16 hr after Doxorubicin injection (i.p.)
16 hr Top2b Del Dox1

value: doxorubicin (25mg/kg, i.p.) or PBS (i.p.)


title: Top2b-/- Cardiomyocytes 16hr after doxorubicin rep2

description:
Gene expression 16 hr after Doxorubicin injection (i.p.)
16 hr Top2b Del Dox2

value: Top2b-/- (cardiac specific deletion of Top2b)


title: C3 Non stimulate (6334175040_K)

description: C3 Non stimulate

value: Medium

value: 6 hours


title: C3 IL1 - 6h (6334175026_E)

description: C3 IL1 - 6h


title: C4 IL1 - 2h (6334175030_B)

description: C4 IL1 - 2h


title: C4 Non stimulate (6334175030_I)

description: C4 Non stimulate


title: Top2b-/- Cardiomyocytes 16hr after PBS rep2

description:
Gene expression 16 hr after PBS injection (i.p.)
16 hr Top2b Del Ctr2

value: male

value: 6 weeks


title: C2 TNF - 6h (6334175040_G)

description: C2 TNF - 6h

value: Healthy

value: TNF-a


title: C3 TNF - 6h (6334175031_L)

description: C3 TNF - 6h


title: A.thaliana_control_rep4

description: A total 522 features were spotted

source_name: A.thaliana, non treated

value: 4 week old

value: leaf


title: Top2b-/- Cardiomyocytes 16hr after doxorubicin rep3

description:
Gene expression 16 hr after Doxorubicin injection (i.p.)
16 hr Top2b Del Dox3


title: Top2b-/- Cardiomyocytes 16hr after PBS rep1

description:
Gene expression 16 hr after PBS injection (i.p.)
16 hr Top2b Del Ctr1


title: C3 Non stimulate (6334175031_A)

description: C3 Non stimulate


title: C4 IL1 - 6h (6334175046_H)

description: C4 IL1 - 6h

value: Healthy 4


title: C4 Non stimulate (6334175026_D)

description: C4 Non stimulate


title: C2 IL1 - 6h (6334175030_A)

description: C2 IL1 - 6h

value: Healthy 2


title: WT Cardiomyocytes 16hr after doxorubicin rep3

description:
Gene expression 16 hr after Doxorubicin injection (i.p.)
16 hr WT Dox3


title: WT Cardiomyocytes 16hr after doxorubicin rep1

description:
Gene expression 16 hr after Doxorubicin injection (i.p.)
16 hr WT Dox1


title: C2 IL1 - 2h (6334175046_J)

description: C2 IL1 - 2h

value: 2 hours


title: C2 Non stimulate (6334175031_C)

description: C2 Non stimulate


title: WT Cardiomyocytes 16hr after doxorubicin rep2

description:
Gene expression 16 hr after Doxorubicin injection (i.p.)
16 hr WT Dox2

value: wild type


title: C2 Non stimulate (6334175026_B)

description: C2 Non stimulate


title: C2 TNF - 2h (6334175027_K)

description: C2 TNF - 2h


title: A.thaliana_control_rep3

description: A total 522 features were spotted

value: Columbi (Col-0 obtained from ABRC)

value: control


title: A.thaliana_control_rep2

description: A total 522 features were spotted


title: A.thaliana_control_rep1

description: A total 522 features were spotted


title: C1 TNF - 6h (6334175036_D)

description: C1 TNF - 6h

value: Healthy 1


title: WT Cardiomyocytes 16hr after PBS rep3

description:
Gene expression 16 hr after PBS injection (i.p.)
16 hr WT Ctr3

source_name: WT Cardiomyocytes 16hr after PBS

value: PBS (i.p.)

value: heart

value: primary cardiomyocytes


title: WT Cardiomyocytes 16hr after PBS rep1

description:
Gene expression 16 hr after PBS injection (i.p.)
16 hr WT Ctr1


title: C1 Non stimulate (6334175031_J)

description: C1 Non stimulate

value: Medium

value: 6 hours


title: C1 IL1 - 6h (6334175046_G)

description: C1 IL1 - 6h


title: C1 Non stimulate (6334175026_A)

description: C1 Non stimulate


title: Pin1 RNAi

status: Public on Oct 27 2012

city: Buffalo

first: ROOPA

last: THAPAR

address: 700 Ellicott Street

department: Structural Biology

institute: Hauptman Woodward Medical Research Institute

description:
Sample2
Average of three replicates.

hyb_protocol: 750ng of the labeled probes was then mixed with hybridization reagents and hybridized overnight at 58°C to the HumanRef-8 v3 BeadChips.

scan_protocol: Following washing and staining with a Cy3-streptavidin conjugate, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: The intensity of the signal corresponded to the quantity of the respective mRNA in the original sample. BeadChip data files were analyzed with Illumina's GenomeStudio (v2010.1) gene expression module (v1.6.0) to report both un-normalized and quantile-normalized, background-corrected gene expression signal levels. The experimental data set provided represents three biological replicates from a single data set that showed the best knockdown for the Pin1 siRNA-treated RNA. Three experimental datasets were collected in all with varying degrees of knockdown. Good quality of microarray data was obtained in all cases.

source_name: HeLa cell line, Pin siRNA

label_protocol: Initially, 500 ng total RNA was converted to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per the manufacturer's instructions.

growth_protocol: HeLa cells were cultured in DMEM with 10% Fetal Bovine Serum.

extract_protocol: Total RNA from frozen cell pellets was prepared using the RNeasy midi kits (Qiagen, Inc.) following the manufacturer's instructions. After elution, RNA samples were concentrated by ethanol precipitation and resuspended in nuclease-free water. Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 50 nM control or Pin1 siRNA was used and cells were harvested 72 hrs after the second hit.

tag: cell line

value: HeLa

value: immortal cervical cancer cell line

tag: sirna


title: C1 IL1 - 2h (6334175040_A)

description: C1 IL1 - 2h

value: Healthy


title: Motor neurons-wt-rep3

first: Polyxeni

last: Philippidou

address: 550 1st ave

institute: NYU Medical Center

description: FACS sorted cells

data_processing: quantile normalized using BSGX Version 1.0.6

source_name: cervical motor neurons, wt

label_protocol: Illumina TotalPrep RNA Amplification kit

extract_protocol: Papain/Dnase dissociation

treatment_protocol: FACS sorting from HB9::GFP embryos

value: cervical motor neurons

tag: developmental stage

tag: strain

value: mix of c57/bl6, balbc, fvb


title: Pin1 control

description:
Sample1
Average of three replicates.

source_name: HeLa cell line, control siRNA


title: Motor neurons-mut-rep2

description: FACS sorted cells

source_name: cervical motor neurons, Hox5 mut

value: Hox5 mut


title: Motor neurons-mut-rep1

description: FACS sorted cells


title: Motor neurons-mut-rep3

description: FACS sorted cells


title: MALC, quiescent, sample 1

city: TOULOUSE

first: Pauline

last: GRAVELLE

address: CHU Purpan, Pavillon Lefebvre

country: France

institute: INSERM UMR1037

hyb_protocol: Labaled complementary RNA (cRNA)  from these samples was then fragmented and hybridized to Affymetrix GeneChip arrays HG-U133 plus 2,0

scan_protocol: the chips were then washed, scanned on the Affymetrix Fluidics Station 400 and analyzed with Genechip Operating Software

data_processing: The data were analyzed with Microarray Suite version 5,0 (MAS 5,0) using Affymetrix default analysis settings and global scaling as normalization method

source_name: Human B lymphoid RL cell line (ATCC: CRL-2261), MALC, 14 days, quiescent cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30 ng total RNA , amplified and labeled following the one-cycle target labelling protocol (Affymetrix, Santa Clara, CA, USA).

growth_protocol: MALC were cultured for 14 days, stained for pyronin Y and then quiescent and cycling cells of these MALC were sorted on a BD LSRII cytometer

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

treatment_protocol: Pyronin Y staining for sorting

tag: genotype

tag: phenotype

value: Pyronin Y dull


title: MALC, cycling, sample 3

source_name: Human B lymphoid RL cell line (ATCC: CRL-2261), MALC, 14 days, cycling cells

value: Pyronin Y bright


title: Suspension cells, sample 2

source_name: Human B lymphoid RL cell line (ATCC: CRL-2261), exponential

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA , amplified and labeled following the one-cycle target labelling protocol (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Suspension cells were collected in exponential growth phase ; MALC were collected after 10 days culture,

treatment_protocol: No treatment


title: MALC, cycling, sample 1


title: Motor neurons-wt-rep1

description: FACS sorted cells

value: wild type


title: MALC, quiescent, sample 3


title: MALC, quiescent, sample 2


title: MALC, cycling, sample 2


title: WT Cardiomyocytes 16hr after PBS rep2

description:
Gene expression 16 hr after PBS injection (i.p.)
16 hr WT Ctr2

value: male

tag: age

value: 6 weeks


title: MALC, cycling, sample 4


title: MALC, quiescent, sample 4


title: Suspension cells, sample 3


title: C1 TNF - 2h (6334175044_I)

description: C1 TNF - 2h

tag: disease state

tag: subject

value: Healthy 1

tag: stimulation

value: TNF-a

tag: time

value: 2 hours


title: 2A3-3-asTF, replicate3

city: Leiden

first: Henri

middle: H

last: Versteeg

address: Albinusdreef 2

department: Einthoven Lab for Experimental Vascular Medicine

country: Netherlands

institute: Leiden University Medical Center

description: replicate 3

data_processing: The data were normalised by using loess normalisation via a Lumi library

label_protocol: RNA was amplified and labeled using Illumina TotalprepTM -96 RNA Amplification Kit (Ambion, #4393543)

growth_protocol: Cells were seeded in 6-wells plates and grown for three days

extract_protocol: RNA was extracted using Nucleospin II (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol.

value: MCF-7-based 2A3-3

value: breast cancer

tag: genotype/variation

value: alternatvively spliced tissue factor (asTF)


title: 2A3-3-asTF, replicate2

description: replicate 2

tag: cell type


title: Suspension cells, sample 1


title: MALC, sample 3

source_name: Human B lymphoid RL cell line (ATCC: CRL-2261), MALC, 10 days


title: Motor neurons-wt-rep2

description: FACS sorted cells

tag: tissue


title: 2A3-3-asTF, replicate1

description: replicate 1


title: Liver_Control

city: Nanchang

first: xl

last: tang

address: Xuefu road

country: China

institute: Nanchang university

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

organism: Rattus norvegicus

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

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

treatment_protocol: The type 2 diabetic model group  was injected intraperitoneally with a low dose of STZ (30 mg/kg).

value: Sprague–Dawley

value: 8 weeks

value: Liver


title: Liver_Diabetes


title: 2A3-3-flTF, replicate2

description: replicate 2

value: full length tissue factor (flTF)


title: 2A3-3-flTF, replicate3

description: replicate 3


title: 2A3-3-flTF, replicate1

description: replicate 1


title: MALC, sample 2


title: Skeletal Muscle_Diabetes

source_name: Skeletal Muscle_Diabetes

value: Skeletal Muscle


title: 2A3-3-pcDNA, replicate4

description: replicate 4

value: empty vector


title: 2A3-3-pcDNA, replicate2

description: replicate 2


title: 2A3-3-pcDNA, replicate3

description: replicate 3


title: Skeletal Muscle_Control

source_name: Skeletal Muscle_Control


title: Pre-treatment breast cancer cells sample 21

status: Public on Oct 26 2012

city: Vienna

first: Florian

middle: Leopold

last: Klinglmueller

address: Spitalgasse 23

department: Medizinische Statistik und Informatik

country: Austria

institute: Medizinische Universitaet Wien

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: We used R Bioconductor (2.3) to do the processing of the arrays. Normalization (etc) has been done using the function rma() with default options from package affy (1.20.2).

source_name: Pre-treatment breast cancer cells

label_protocol: standard affymetrix protocol

extract_protocol: Trizol extraction, followed by purification with RNeasy mini kit (Qiagen).

value: breast cancer cells

tag: treatment response in vivo

tag: treatment response in vitro

tag: ki67 reduction


title: Pre-treatment breast cancer cells sample 18


title: Pre-treatment breast cancer cells sample 17


title: Pre-treatment breast cancer cells sample 20


title: Pre-treatment breast cancer cells sample 16


title: Pre-treatment breast cancer cells sample 10


title: 2A3-3-pcDNA, replicate1

description: replicate 1

tag: cell line


title: Pre-treatment breast cancer cells sample 11


title: Pre-treatment breast cancer cells sample 9


title: Pre-treatment breast cancer cells sample 15


title: Pre-treatment breast cancer cells sample 14


title: Pre-treatment breast cancer cells sample 19


title: Pre-treatment breast cancer cells sample 12


title: Pre-treatment breast cancer cells sample 13


title: MALC, sample 1


title: Pre-treatment breast cancer cells sample 7


title: Pre-treatment breast cancer cells sample 8


title: Pre-treatment breast cancer cells sample 1


title: Pre-treatment breast cancer cells sample 3


title: Pre-treatment breast cancer cells sample 4


title: OxPAPC BXH20/KccJ-21

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format.  All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene. To avoid detecting variation signal intensity as an artifact of SNP variation in transcripts, prior to RMA normalization we excluded individual probes in probe-sets that aligned to sequences with SNPs, and excluded entire probe-sets where at least 8 of the probes in the set aligned to a sequence with SNPs.

source_name: macrophage

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

growth_protocol: 16 week male mice maintained on 12 hr light dark cycle fed a chow diet

extract_protocol: Total RNA was extracted from macrophage samples using RNeasy columns (Qiagen, Valencia, CA), using on-column DNase digestion (Qiagen) and according to manufacturer’s instructions.

treatment_protocol: Cells were washed once with PBS the day after plating and incubated for 4 hours with 1%FBS DMEM media in control-treated cells, with control media plus 2ng/mL LPS (List Biological Inc., Campbell, CA, 201), or with control media plus 50μg/mL OxPAPC. OxPAPC was prepared from PAPC (Avanti Polar Lipids, Alabaster, AL) as previously described (Watson et al., 1997). After treatment, media was removed and cells were washed once with PBS.

tag: gender

value: 16 weeks

tag: treatment condition

value: OxPAPC

value: macrophage


title: OxPAPC C57L/J-7

value: male

tag: strain


title: OxPAPC BXD39/TyJ-7


title: Pre-treatment breast cancer cells sample 2


title: OxPAPC SM/J-32

value: SM/J


title: Pre-treatment breast cancer cells sample 6


title: Pre-treatment breast cancer cells sample 5


title: OxPAPC NON/ShiLtJ-9

value: NON/ShiLtJ


title: OxPAPC C57L/J-8


title: OxPAPC C57BL/6J-39


title: OxPAPC C57BL/6J-37


title: OxPAPC BXD39/TyJ-8


title: OxPAPC BXH9/TyJ-16


title: OxPAPC BXH20/KccJ-41


title: OxPAPC SM/J-34


title: OxPAPC NON/ShiLtJ-10


title: OxPAPC BXA24/PgnJ-14


title: OxPAPC BXA24/PgnJ-15


title: OxPAPC BXH9/TyJ-15


title: OxPAPC BXD8/TyJ-7


title: OxPAPC BXH20/KccJ-40


title: OxPAPC BXA14/PgnJ-8


title: OxPAPC BXH7/TyJ-36


title: OxPAPC BXD15/TyJ-10


title: OxPAPC BXD8/TyJ-8


title: OxPAPC BXD11/TyJ-10


title: OxPAPC BXH20/KccJ-20


title: OxPAPC BXA14/PgnJ-9


title: OxPAPC BXH20/KccJ-42


title: OxPAPC BXD36/TyJ-9


title: OxPAPC BXD38/TyJ-7


title: OxPAPC NOD/ShiLtJ-21

value: NOD/ShiLtJ


title: OxPAPC PL/J-9

value: PL/J


title: OxPAPC BXD36/TyJ-12


title: OxPAPC KK/HlJ-16

value: KK/HlJ


title: OxPAPC BXD36/TyJ-8


title: OxPAPC BXD33/TyJ-16


title: OxPAPC PL/J-8


title: OxPAPC BXH7/TyJ-34


title: OxPAPC BALB/cJ-35

value: BALB/cJ


title: OxPAPC BALB/cJ-34


title: OxPAPC NOD/ShiLtJ-19


title: OxPAPC BXD33/TyJ-5


title: OxPAPC BXD19/TyJ-6


title: OxPAPC BXD19/TyJ-5


title: OxPAPC KK/HlJ-15


title: OxPAPC BXD33/TyJ-18


title: OxPAPC BXD2/TyJ-7


title: OxPAPC BXD2/TyJ-8


title: OxPAPC BXH14/TyJ-28


title: OxPAPC BXH14/TyJ-29


title: OxPAPC BXA8/PgnJ-13


title: OxPAPC AXB12/PgnJ-8


title: OxPAPC AXB12/PgnJ-9


title: OxPAPC BXA8/PgnJ-14


title: OxPAPC BXD33/TyJ-4


title: OxPAPC BXD42/TyJ-8


title: OxPAPC BXD24/TyJ-7


title: Pre-treatment breast cancer cells sample 22


title: OxPAPC BXD5/TyJ-5


title: OxPAPC BXD28/TyJ-6


title: OxPAPC BXD5/TyJ-6


title: OxPAPC BXD24/TyJ-6


title: OxPAPC BXD32/TyJ-5


title: OxPAPC BXD28/TyJ-4


title: OxPAPC BXD31/TyJ-6


title: OxPAPC BXD21/TyJ-5


title: OxPAPC BXA7/PgnJ-8


title: OxPAPC RIIIS/J-7

value: RIIIS/J


title: OxPAPC BXD29-Tlr4<lps-2J>/J-7


title: OxPAPC BXD31/TyJ-5


title: OxPAPC BXH8/TyJ-16


title: OxPAPC BXD29-Tlr4<lps-2J>/J-9


title: OxPAPC BXA2/PgnJ-7


title: OxPAPC BXH8/TyJ-17


title: OxPAPC BXA1/PgnJ-5


title: OxPAPC RIIIS/J-8


title: OxPAPC BXD20/TyJ-8


title: OxPAPC BXA2/PgnJ-8


title: OxPAPC BXD20/TyJ-9


title: OxPAPC BXA7/PgnJ-9


title: OxPAPC BXA26/PgnJ-6


title: OxPAPC AXB1/PgnJ-9


title: OxPAPC BXA26/PgnJ-5


title: OxPAPC BXA1/PgnJ-7


title: OxPAPC A/J-5

value: A/J


title: OxPAPC BXD9/TyJ-7


title: OxPAPC BXD22/TyJ-5


title: OxPAPC AXB1/PgnJ-8


title: OxPAPC AKR/J-14

value: AKR/J


title: OxPAPC BXH10/TyJ-25


title: OxPAPC BXH10/TyJ-24


title: OxPAPC MA/MyJ-9

value: MA/MyJ


title: OxPAPC BTBR T<+> tf/J-9

value: BTBR T<+> tf/J


title: OxPAPC SEA/GnJ-8

value: SEA/GnJ


title: OxPAPC MA/MyJ-8


title: OxPAPC AXB4/PgnJ-7


title: OxPAPC AXB15/PgnJ-4


title: OxPAPC NZW/LacJ-13

value: NZW/LacJ


title: OxPAPC AXB15/PgnJ-3

value: 16 weeks


title: OxPAPC SEA/GnJ-9

value: OxPAPC


title: OxPAPC BXD18/TyJ-11

value: macrophage


title: OxPAPC AXB5/PgnJ-9

value: male


title: OxPAPC BXH6/TyJ-16


title: OxPAPC AXB4/PgnJ-9


title: OxPAPC BXD24/TyJ-Cep290<rd16>/J-9


title: OxPAPC CBA/J-4

value: CBA/J


title: OxPAPC BXD22/TyJ-6


title: OxPAPC BTBR T<+> tf/J-8


title: OxPAPC C58/J-15


title: OxPAPC C3H/HeJ-31


title: OxPAPC SWR/J-18

value: SWR/J


title: OxPAPC BXD18/TyJ-9


title: OxPAPC BXD24/TyJ-Cep290<rd16>/J-7


title: OxPAPC C58/J-14


title: OxPAPC BXA12/PgnJ-8


title: OxPAPC C3H/HeJ-32


title: OxPAPC BXA12/PgnJ-18


title: OxPAPC AXB5/PgnJ-7


title: OxPAPC CBA/J-5


title: OxPAPC BXH6/TyJ-15


title: OxPAPC BXH22/KccJ-11


title: OxPAPC SWR/J-17


title: OxPAPC AXB13/PgnJ-7


title: OxPAPC BXH19/TyJ-26


title: OxPAPC BXD40/TyJ-18


title: OxPAPC BXD40/TyJ-16


title: OxPAPC BXD12/TyJ-8


title: OxPAPC B6cC3-1/KccJ-40


title: OxPAPC BXD27/TyJ-9


title: OxPAPC BXH19/TyJ-27


title: OxPAPC BXH2/TyJ-27


title: OxPAPC BXA12/PgnJ-9


title: OxPAPC BUB/BnJ-7

value: BUB/BnJ


title: OxPAPC BXD12/TyJ-7


title: OxPAPC B6cC3-1/KccJ-41


title: OxPAPC BXA12/PgnJ-17


title: OxPAPC BXH22/KccJ-10


title: OxPAPC BXH2/TyJ-28


title: OxPAPC BXD38/TyJ-8


title: OxPAPC AXB13/PgnJ-9


title: OxPAPC LG/J-10

value: LG/J


title: OxPAPC BXD6/TyJ-7


title: OxPAPC BXD27/TyJ-8


title: OxPAPC BXD1/TyJ-6


title: OxPAPC BXD6/TyJ-8


title: OxPAPC LG/J-12


title: OxPAPC BUB/BnJ-8


title: OxPAPC AXB8/PgnJ-3


title: OxPAPC AXB24/PgnJ-5


title: OxPAPC AXB19/PgnJ-8


title: OxPAPC AXB2/PgnJ-5


title: OxPAPC AXB19/PgnJ-9


title: LPS NON/ShiLtJ-5

value: NON/ShiLtJ

value: LPS


title: OxPAPC AXB19a/PgnJ-7


title: OxPAPC BXD1/TyJ-5


title: OxPAPC AXB19a/PgnJ-8


title: LPS BXH20/KccJ-39


title: OxPAPC AXB2/PgnJ-4


title: OxPAPC AXB23/PgnJ-6


title: LPS C57BL/6J-36


title: LPS C57BL/6J-35


title: LPS BXH9/TyJ-13


title: OxPAPC AXB10/PgnJ-9


title: LPS BXH20/KccJ-36


title: OxPAPC AXB10/PgnJ-12


title: LPS SM/J-29

value: SM/J


title: LPS SM/J-28


title: OxPAPC AXB24/PgnJ-6


title: LPS BXH7/TyJ-31


title: LPS BXD39/TyJ-6


title: LPS BXH20/KccJ-18


title: LPS C57L/J-6


title: LPS BXH20/KccJ-17


title: LPS BXH9/TyJ-14


title: LPS C57L/J-4


title: LPS BXD39/TyJ-5


title: LPS BXH20/KccJ-38


title: LPS BXH7/TyJ-32


title: LPS BXH20/KccJ-37


title: LPS BXD8/TyJ-6


title: LPS BXA24/PgnJ-12


title: LPS NON/ShiLtJ-6


title: LPS BXD33/TyJ-7


title: LPS BXD27/TyJ-4


title: LPS BXA7/PgnJ-6


title: LPS BXA14/PgnJ-5


title: LPS BXD8/TyJ-5


title: LPS BXA14/PgnJ-4


title: LPS BXD22/TyJ-4


title: LPS BALB/cJ-26

value: BALB/cJ


title: LPS BXD11/TyJ-8


title: LPS BXD33/TyJ-13


title: LPS BALB/cJ-29


title: LPS BXD11/TyJ-4


title: LPS BXD11/TyJ-7


title: LPS BXA24/PgnJ-13


title: LPS BXD36/TyJ-4


title: LPS BXH20/KccJ-16


title: LPS KK/HlJ-14

value: KK/HlJ


title: LPS PL/J-4

value: PL/J


title: LPS NOD/ShiLtJ-18

value: NOD/ShiLtJ


title: LPS BXD36/TyJ-6


title: LPS PL/J-6


title: LPS NOD/ShiLtJ-17


title: LPS KK/HlJ-13


title: LPS BXH14/TyJ-24


title: LPS BXD19/TyJ-4


title: LPS BXD11/TyJ-3


title: LPS BXA8/PgnJ-9


title: LPS BXA8/PgnJ-4


title: LPS AXB12/PgnJ-5


title: LPS BXA8/PgnJ-10


title: LPS BXD36/TyJ-11


title: LPS BXD33/TyJ-8


title: LPS BXD33/TyJ-14


title: LPS BXD2/TyJ-5


title: LPS AXB12/PgnJ-6


title: LPS BXD2/TyJ-6


title: LPS I/LnJ-4

value: I/LnJ


title: LPS BXA8/PgnJ-5


title: LPS BXD28/TyJ-8


title: LPS BXH14/TyJ-21


title: LPS BXD31/TyJ-3


title: LPS BXD5/TyJ-3


title: LPS BXD28/TyJ-7


title: LPS RIIIS/J-4

value: RIIIS/J


title: LPS BXD31/TyJ-4

value: 16 weeks


title: LPS BXD32/TyJ-4


title: LPS BXD5/TyJ-4


title: LPS BXH8/TyJ-15


title: LPS BXD24/TyJ-5


title: LPS BXD21/TyJ-4


title: LPS BXD24/TyJ-4


title: LPS BXD20/TyJ-5


title: LPS BXH8/TyJ-13


title: LPS BXD29-Tlr4<lps-2J>/J-3


title: LPS BXA26/PgnJ-9


title: LPS BXD29-Tlr4<lps-2J>/J-4


title: LPS BXD42/TyJ-4


title: LPS BXA1/PgnJ-10


title: LPS BXD20/TyJ-6


title: LPS BXD21/TyJ-3


title: LPS CE/J-5

value: CE/J


title: LPS AXB1/PgnJ-5

value: macrophage


title: LPS BXA1/PgnJ-9

value: male


title: LPS BXA26/PgnJ-8


title: LPS BXD22/TyJ-3


title: LPS BXA2/PgnJ-6


title: LPS BXD9/TyJ-4


title: LPS DBA/2J-28


title: LPS A/J-3

value: A/J


title: LPS AXB1/PgnJ-6


title: LPS RIIIS/J-6


title: LPS 129X1/SvJ-14


title: LPS BXH10/TyJ-29


title: LPS DBA/2J-29


title: LPS MA/MyJ-4

value: MA/MyJ


title: LPS NZW/LacJ-9

value: NZW/LacJ


title: LPS BXA7/PgnJ-4


title: LPS AKR/J-15

value: AKR/J


title: LPS NZW/LacJ-10


title: LPS AXB6/PgnJ-3


title: LPS BXA2/PgnJ-4


title: LPS MA/MyJ-5


title: LPS CE/J-6


title: LPS BXD9/TyJ-5


title: LPS BXD24/TyJ-Cep290<rd16>/J-6


title: LPS 129X1/SvJ-13


title: LPS SJL/J-2

value: SJL/J


title: LPS BXH10/TyJ-27

value: LPS


title: LPS SEA/GnJ-5

value: SEA/GnJ


title: LPS SEA/GnJ-6


title: LPS AXB15/PgnJ-6


title: LPS BXD18/TyJ-5


title: LPS AXB4/PgnJ-4


title: LPS BTBR T<+> tf/J-5

value: BTBR T<+> tf/J


title: LPS BTBR T<+> tf/J-6


title: LPS AXB15/PgnJ-5


title: LPS AXB5/PgnJ-5


title: LPS BXD34/TyJ-3


title: LPS CBA/J-8

value: CBA/J


title: LPS BXH6/TyJ-12


title: LPS AXB4/PgnJ-5


title: LPS AXB5/PgnJ-4


title: LPS BXA4/PgnJ-6


title: LPS C3H/HeJ-28


title: LPS BXA16/PgnJ-1


title: LPS CBA/J-7


title: LPS BXD18/TyJ-7


title: LPS C3H/HeJ-27


title: LPS C58/J-7


title: LPS C58/J-8


title: LPS BXH19/TyJ-23


title: LPS SWR/J-21

value: SWR/J


title: LPS BXA16/PgnJ-2


title: LPS BXD34/TyJ-4


title: LPS BXA12/PgnJ-6


title: LPS AXB13/PgnJ-5


title: LPS BXH2/TyJ-25


title: LPS BXH6/TyJ-14


title: LPS BXD24/TyJ-Cep290<rd16>/J-5


title: LPS BXA12/PgnJ-13


title: LPS BXH2/TyJ-26


title: LPS BXA4/PgnJ-5


title: LPS BXA12/PgnJ-4


title: LPS BXH19/TyJ-20


title: LPS AXB13/PgnJ-4


title: LPS SWR/J-20


title: LPS BXA12/PgnJ-14


title: LPS BXD40/TyJ-13


title: LPS BXD6/TyJ-4


title: LPS BXH22/KccJ-9


title: LPS BXD38/TyJ-5


title: LPS LG/J-7

value: LG/J


title: LPS LG/J-3


title: LPS LG/J-2


title: LPS B6cC3-1/KccJ-33


title: LPS B6cC3-1/KccJ-35


title: LPS BXD6/TyJ-6


title: LPS BXD40/TyJ-15


title: LPS BXD27/TyJ-6


title: LPS AXB8/PgnJ-2


title: LPS BXD38/TyJ-6


title: LPS LG/J-9


title: LPS AXB24/PgnJ-3


title: LPS FVB/NJ-18

value: FVB/NJ


title: LPS AXB2/PgnJ-8


title: LPS BUB/BnJ-9

value: BUB/BnJ


title: LPS AXB19/PgnJ-4

value: 16 weeks


title: LPS BXD12/TyJ-4


title: LPS BXD12/TyJ-5


title: LPS AXB23/PgnJ-9


title: LPS AXB19/PgnJ-5


title: LPS AXB10/PgnJ-5


title: LPS AXB19a/PgnJ-4


title: LPS AXB24/PgnJ-4


title: Control C57L/J-2

value: Control


title: Control BXH20/KccJ-33

value: macrophage


title: Control NON/ShiLtJ-2

value: male

value: NON/ShiLtJ


title: Control BXH9/TyJ-9


title: LPS AXB10/PgnJ-11


title: Control SM/J-27

value: SM/J


title: LPS AXB2/PgnJ-7


title: LPS AXB23/PgnJ-8


title: Control C57BL/6J-33


title: Control SM/J-25


title: LPS BUB/BnJ-10


title: Control BXH9/TyJ-11


title: LPS AXB19a/PgnJ-6


title: Control C57BL/6J-31


title: LPS BXD1/TyJ-9


title: Control NON/ShiLtJ-1


title: Control BXH20/KccJ-13


title: Control BXA14/PgnJ-3


title: Control BXA24/PgnJ-9


title: Control BXD8/TyJ-3


title: Control C57L/J-1


title: Control BXA24/PgnJ-2


title: Control BXH7/TyJ-30


title: Control BXH20/KccJ-31


title: Control BXA24/PgnJ-10


title: Control BXH7/TyJ-29


title: Control BXA14/PgnJ-2


title: Control NON/ShiLtJ-4


title: Control BALB/cJ-20

value: BALB/cJ


title: Control BXD15/TyJ-9


title: Control BXD31/TyJ-1


title: Control BXD20/TyJ-3


title: Control BXA14/PgnJ-1


title: Control BXD12/TyJ-2


title: Control NOD/ShiLtJ-13

value: NOD/ShiLtJ


title: Control BXD24/TyJ-Cep290<rd16>/J-1


title: Control BXD20/TyJ-2


title: Control BXA24/PgnJ-1


title: Control BALB/cJ-22


title: Control BXD19/TyJ-2


title: Control BXD33/TyJ-11


title: Control BXD36/TyJ-10


title: Control PL/J-3

value: PL/J


title: Control BXD33/TyJ-2


title: Control BXD39/TyJ-3


title: Control BXD11/TyJ-1


title: Control BXD36/TyJ-1


title: Control BXH14/TyJ-18


title: Control BXD19/TyJ-1


title: Control BXD33/TyJ-1


title: Control NOD/ShiLtJ-15


title: EBV-LCL 0 Gy 4 hr RS44LCL_0G_4H (3May07)

city: East Melbourne

first: Jason

last: Li

address: St Andrews Pl

institute: Peter MacCallum Cancer Centre

hyb_protocol: Followed the exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix).

scan_protocol: Chips were scanned with a Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using aroma.affymetrix (R package). RMA background correction were applied to probe intensities, gene level expression were quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Blood sample

growth_protocol: EBV-transformed lymphoblast cell lines were grown in RPMI medium and fibroblasts in DMEM medium, both supplemented with 10% FBS and gentamicin and incubated in a 5% CO2 humidified incubator at 37oC.

extract_protocol: Cells were grown to a density of 1 x 107, pelleted, resuspended in 3 ml PBS and an equal volume of Trizol (Invitrogen, Carlsbad, CA, USA) was added, mixed and the aqueous layer was mixed with and equal volume of 70 percent ethanol and added onto a RNeasy column (Qiagen, Venlo, The Netherlands). The RNA extraction was continued by using the RNeasy method as per manufactures recommendation except starting with the addition of the sample of Buffer RW1. RNA concentration and integrity was determined by analysing on a bioanalyzer (Agilent, Santa Clara, CA, USA). RNA was determined to be high enough quality if a minimum RIN of 8.5 was obtained.

treatment_protocol: Approximately 1x 108  lymphoblast cells or 1x107 primary fibroblasts were irradiated with 0 Gy, 2 Gy or 10 Gy IR at RT using a Cs137 source with a dose rate of 1.7min/Gy

value: primary lymphoblast cell line

tag: individual

value: radiosensitive

tag: treatment

value: 0 Gy

tag: time (h)


title: Control PL/J-2

tag: age


title: EBV-LCL 10 Gy 4 hr RS7LCL_10G_4H (3May07)

label_protocol: Followed the exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix).

tag: phenotype

value: 10 Gy


title: Control BXD2/TyJ-2


title: Control BXA8/PgnJ-6


title: EBV-LCL 0 Gy 4 hr RS7LCL_0G_4H (3May07)


title: EBV-LCL 10 Gy 4 hr RS44LCL_10G_4H (3May07)


title: Control BXD33/TyJ-12


title: Control BXD2/TyJ-1


title: EBV-LCL 5 Gy 4 hr RS32LCL_5G_4H (2-3-7)

value: 5 Gy


title: Control BXD36/TyJ-3


title: Control BXH14/TyJ-19


title: Control BXA8/PgnJ-7


title: EBV-LCL 2 Gy 4 hr RS32LCL_2G_4H (2-3-6)

value: 2 Gy


title: EBV-LCL 20 Gy 4 hr RS32LCL_20G_4H (2-3-12)

value: 20 Gy


title: Control I/LnJ-1

value: I/LnJ


title: EBV-LCL 10 Gy 48 hr RS32LCL_10G_48H (2-3-11)


title: Control AXB12/PgnJ-1

value: 16 weeks


title: Control BXA8/PgnJ-1

value: Control


title: EBV-LCL 10 Gy 4 hr RS32LCL_10G_4H (3May07)


title: EBV-LCL 10 Gy 8 hr RS32LCL_10G_8H (2-3-9)


title: EBV-LCL 10 Gy 2 hr RS32LCL_10G_2H (2-3-8)


title: EBV-LCL 10 Gy 24 hr RS32LCL_10G_24H (2-3-10)


title: Control AXB12/PgnJ-3

value: macrophage


title: Control BXD32/TyJ-2

value: male


title: EBV-LCL 5 Gy 4 hr RS21LCL_5G_4H (2-2-2)


title: EBV-LCL 1 Gy 4 hr RS32LCL_1G_4H (2-3-5)

value: 1 Gy


title: Control BXD32/TyJ-1


title: EBV-LCL 10 Gy 4 hr RS22LCL_10G_4H (3May07)


title: EBV-LCL 2 Gy 4 hr RS21LCL_2G_4H (2-2-1)


title: EBV-LCL 1 Gy 4 hr RS21LCL_1G_4H (2-1-12)


title: EBV-LCL 0 Gy 4 hr RS22LCL_0G_4H (3May07)


title: Control RIIIS/J-1

value: RIIIS/J


title: EBV-LCL 20 Gy 4 hr RS21LCL_20G_4H (2-2-8)


title: EBV-LCL 0 Gy 4 hr RS32LCL_0G_4H (3May07)


title: Control BXD28/TyJ-2


title: Control I/LnJ-2


title: EBV-LCL 10 Gy 48 hr RS21LCL_10G_48H (2-2-7)


title: Control BXD42/TyJ-1


title: EBV-LCL 10 Gy 8 hr RS21LCL_10G_8H (2-2-5)


title: Control BXD31/TyJ-2


title: Control BXD8/TyJ-2


title: Control RIIIS/J-2


title: EBV-LCL 10 Gy 4 hr RS21LCL_10G_4H (2-2-4)


title: Control BXH8/TyJ-12


title: EBV-LCL 10 Gy 2 hr RS21LCL_10G_2H (2-2-3)


title: Control BXH8/TyJ-10


title: EBV-LCL 10 Gy 24 hr RS21LCL_10G_24H (2-2-6)


title: Control BXD29-Tlr4<lps-2J>/J-1


title: Control BXD21/TyJ-2


title: EBV-LCL 0 Gy 4 hr RS20LCL_0G_4H (3May07)


title: Control BXA26/PgnJ-2


title: Control BXD21/TyJ-1


title: EBV-LCL 0 Gy 4 hr RS21LCL_0G_0H (2-1-11)


title: Control AXB1/PgnJ-3


title: Control BXD5/TyJ-1


title: EBV-LCL 10 Gy 4 hr RS20LCL_10G_4H (3May07)


title: EBV-LCL 0 Gy 4 hr RS103LCL_0G_4H (3May07)


title: Control BXA2/PgnJ-3


title: EBV-LCL 0 Gy 4 hr CL44LCL_0G_4H (3May07)

value: control


title: EBV-LCL 10 Gy 4 hr CL7LCL_10G_4H (3May07)


title: Control NOD/ShiLtJ-14

value: NOD/ShiLtJ


title: EBV-LCL 5 Gy 4 hr CL32LCL_5G_4H (2-2-11)


title: EBV-LCL 10 Gy 4 hr CL44LCL_10G_4H (3May07)


title: Control AXB1/PgnJ-2


title: Control BXA7/PgnJ-1


title: Control BXA2/PgnJ-1


title: Control BXA1/PgnJ-2


title: EBV-LCL 10 Gy 4 hr RS103LCL_10G_4H (3May07)


title: EBV-LCL 2 Gy 4 hr CL32LCL_2G_4H (2-2-10)


title: Control BXA7/PgnJ-2


title: EBV-LCL 20 Gy 4 hr CL32LCL_20G_4H (2-3-4)


title: EBV-LCL 0 Gy 4 hr CL7LCL_0G_4H (3May07)


title: Control SJL/J-1

value: SJL/J


title: Control BXA1/PgnJ-1


title: EBV-LCL 1 Gy 4 hr CL32LCL_1G_4H (2-2-9)

value: primary lymphoblast cell line


title: Control LP/J-18

value: LP/J


title: Control BXA26/PgnJ-1


title: Control KK/HlJ-10

value: KK/HlJ


title: Control AXB6/PgnJ-1


title: EBV-LCL 10 Gy 4 hr CL32LCL_10G_4H (3May07)

value: 10 Gy


title: Control BXD22/TyJ-1


title: EBV-LCL 10 Gy 8 hr CL32LCL_10G_8H (2-3-1)


title: EBV-LCL 10 Gy 2 hr CL32LCL_10G_2H (2-2-12)


title: Control DBA/2J-25


title: EBV-LCL 0 Gy 4 hr CL32LCL_0G_4H (3May07)

value: 0 Gy


title: EBV-LCL 10 Gy 4 hr CL25LCL_10G_4H (3May07)


title: Control CE/J-2

value: CE/J


title: Control LP/J-17


title: Control BXD5/TyJ-2


title: EBV-LCL 0 Gy 4 hr CL22LCL_0G_4H (3May07)


title: EBV-LCL 2 Gy 4 hr CL21LCL_2G_4H (2-1-3)

value: 2 Gy


title: EBV-LCL 10 Gy 48 hr CL32LCL_10G_48H (2-3-3)


title: Control AXB6/PgnJ-2


title: Control DBA/2J-26


title: EBV-LCL 10 Gy 4 hr CL22LCL_10G_4H (3May07)


title: Control AKR/J-13

value: AKR/J


title: EBV-LCL 20 Gy 4 hr CL21LCL_20G_4H (2-1-10)

value: 20 Gy


title: Control CE/J-3

value: 16 weeks

value: Control


title: Control BXA13/PgnJ-5

value: male

value: macrophage


title: EBV-LCL 0 Gy 4 hr CL25LCL_0G_4H (3May07)


title: Control 129X1/SvJ-11


title: Control BXD22/TyJ-2


title: Control MA/MyJ-1

value: MA/MyJ


title: EBV-LCL 5 Gy 4 hr CL21LCL_5G_4H (2-1-4)

value: control

value: 5 Gy


title: EBV-LCL 10 Gy 8 hr CL21LCL_10G_8H (2-1-7)


title: EBV-LCL 10 Gy 4 hr CL21LCL_10G_4H (2-1-6)


title: EBV-LCL 1 Gy 4 hr CL21LCL_1G_4H (2-1-2)

value: 1 Gy


title: Control NZW/LacJ-6

value: NZW/LacJ


title: Control BXD28/TyJ-1


title: EBV-LCL 10 Gy 24 hr CL21LCL_10G_24H (2-1-8)

value: primary lymphoblast cell line


title: EBV-LCL 0 Gy 4 hr CL21LCL_0G_OH (2-1-1)


title: Control SEA/GnJ-1

value: SEA/GnJ


title: Control BXH10/TyJ-21


title: EBV-LCL 10 Gy 2 hr CL21LCL_10G_2H (2-1-5)

value: 10 Gy


title: EBV-LCL 0 Gy 4 hr CL20LCL_0G_4H (3May07)

value: 0 Gy


title: Control BXD9/TyJ-2


title: Control MA/MyJ-2


title: EBV-LCL 10 Gy 4 hr CL20LCL_10G_4H (3May07)


title: Control NZW/LacJ-5


title: Primary fibroblast 2 Gy 4 hr RS7FB_2G_4H (1-2-8)

source_name: Skin punch biopsy

value: Fibroblast

value: radiosensitive


title: Control BTBR T<+> tf/J-3

value: BTBR T<+> tf/J


title: Control AXB4/PgnJ-3


title: Control BXH10/TyJ-17


title: Primary fibroblast 0 Gy 4 hr RS7FB_0G_4H (1-2-7)


title: Primary fibroblast 2 Gy 4 hr RS42FB_2G_4H (1-3-8)

value: 2 Gy


title: Primary fibroblast 10 Gy 4 hr RS42FB_10G_4H (1-3-9)


title: Control SEA/GnJ-2

value: 16 weeks


title: Control AXB4/PgnJ-2

value: Control


title: Control 129X1/SvJ-12

value: male


title: Primary fibroblast 10 Gy 4 hr RS7FB_10G_4H (1-2-9)


title: Control BTBR T<+> tf/J-2

value: macrophage


title: Control BXD24/TyJ-Cep290<rd16>/J-2


title: Primary fibroblast 5 Gy 4 hr RS32FB_5G_4H (3-3-7)


title: Control AXB15/PgnJ-1


title: Primary fibroblast 0 Gy 4 hr RS42FB_0G_4H (1-3-7)


title: Control AXB15/PgnJ-2


title: Primary fibroblast 2 Gy 4 hr RS32FB_2G_4H (3-3-6)


title: Primary fibroblast 2 Gy 4 hr RS32FB_2G_4H (1-3-5)


title: Control BXD34/TyJ-1


title: Control C3H/HeJ-24


title: Control CBA/J-2

value: CBA/J


title: Primary fibroblast 10 Gy 4 hr RS32FB_10G_4H (1-3-6)


title: Primary fibroblast 1 Gy 4 hr RS32FB_1G_4H (3-3-5)


title: Primary fibroblast 0 Gy 4 hr RS32FB_0G_4H (1-3-4)


title: Primary fibroblast 10 Gy 24 hr RS32FB_10G_24H (3-3-10)


title: EBV-LCL 10 Gy 48 hr CL21LCL_10G_48H (2-1-9)

value: control


title: Primary fibroblast 20 Gy 4 hr RS32FB_20G_4H (3-3-12)

value: 20 Gy


title: Control BXA12/PgnJ-1


title: Control SWR/J-15

value: SWR/J


title: Control CBA/J-3


title: Primary fibroblast 10 Gy 2 hr RS32FB_10G_2H (3-3-8)


title: Control BXH6/TyJ-10


title: Primary fibroblast 5 Gy 4 hr RS21FB_5G_4H (3-2-2)

value: 5 Gy


title: Primary fibroblast 10 Gy 8 hr RS32FB_10G_8H (3-3-9)


title: Control BXA12/PgnJ-11


title: Control C3H/HeJ-22


title: Control BXH22/KccJ-5


title: Control BXH6/TyJ-9


title: Control C58/J-1


title: Primary fibroblast 10 Gy 48 hr RS32FB_10G_48H (3-3-11)


title: Primary fibroblast 2 Gy 5 hr RS21FB_2G_4H (3-2-1)


title: Primary fibroblast 20 Gy 4 hr RS21FB_20G_4H (3-2-8)


title: Primary fibroblast 10 Gy 8 hr RS21FB_10G_8H (3-2-5)


title: Control AXB13/PgnJ-1


title: Control B6cC3-1/KccJ-27


title: Control BXA12/PgnJ-3


title: Primary fibroblast 1 Gy 4 hr RS21FB_1G_4H (3-1-12)

value: 1 Gy


title: Primary fibroblast 10 Gy 4 hr RS21FB_10G_4H (1-3-3)


title: Control BXA12/PgnJ-10


title: Primary fibroblast 10 Gy 48 hr RS21FB_10G_48H (3-2-7)


title: Control B6cC3-1/KccJ-28


title: Primary fibroblast 2 Gy 4 hr RS21FB_2G_4H (1-3-2)


title: Control AXB13/PgnJ-2


title: Primary fibroblast 10 Gy 2 hr RS21FB_10G_2H (3-2-3)


title: Primary fibroblast 0 Gy 0 hr RS21FB_0G_0H (3-1-11)


title: Primary fibroblast 2 Gy 4 hr RS20FB_2G_4H (1-2-11)


title: Control BXH22/KccJ-6


title: Primary fibroblast 2 Gy 4 hr RS121FB_2G_4H (1-3-11)


title: EBV-LCL 10 Gy 24 hr CL32LCL_10G_24H (2-3-2)

value: primary lymphoblast cell line


title: Primary fibroblast 10 Gy 24 hr RS21FB_10G_24H (3-2-6)

value: 10 Gy


title: Control BXH19/TyJ-18


title: Control BXH19/TyJ-14


title: Primary fibroblast 10 Gy 4 hr RS21FB_10G_4H (3-2-4)


title: Control BXH2/TyJ-21


title: Primary fibroblast 10 Gy 4 hr RS121FB_10G_4H (1-3-12)


title: Primary fibroblast 10 Gy 4 hr RS20FB_10G_4H (1-2-12)


title: Control SWR/J-13


title: Control BXH2/TyJ-22


title: Primary fibroblast 0 Gy 4 hr RS20FB_0G_4H (1-2-10)

value: 0 Gy


title: Control BXD38/TyJ-3


title: Primary fibroblast 0 Gy 4 hr RS121FB_0G_4H (1-3-10)

value: Fibroblast


title: Primary fibroblast 10 Gy 4 hr CL35FB_10G_4H (1-2-6)


title: Control LG/J-1

value: LG/J


title: Primary fibroblast 0 Gy 4 hr CL35FB_0G_4H (1-2-4)


title: Control LG/J-6


title: Primary fibroblast 0 Gy 4 hr RS21FB_0G_4H (1-3-1)

value: radiosensitive


title: Primary fibroblast 5 Gy 4 hr CL32FB_5G_4H (3-2-11)


title: Primary fibroblast 2 Gy 4 hr CL32FB_2G_4H (1-2-2)

value: 2 Gy


title: Primary fibroblast 2 Gy 5 hr CL32FB_2G_4H (3-2-10)


title: Primary fibroblast 2 Gy 4 hr CL35FB_2G_4H (1-2-5)


title: Primary fibroblast 1 Gy 4 hr CL32FB_1G_4H (3-2-9)


title: Control BXD6/TyJ-1

value: 16 weeks


title: Primary fibroblast 10 Gy 2 hr CL32FB_10G_2H (3-2-12)


title: Primary fibroblast 10 Gy 8 hr CL32FB_10G_8H (3-3-1)


title: Primary fibroblast 2 Gy 4 hr CL29FB_2G_4H (1-1-11)


title: Primary fibroblast 20 Gy 4 hr CL32FB_20G_4H (3-3-4)


title: Control BXD40/TyJ-10

value: Control


title: Primary fibroblast 10 Gy 48 hr CL32FB_10G_48H (3-3-3)


title: Primary fibroblast 0 Gy 4 hr CL32FB_0G_4H (1-2-1)


title: Primary fibroblast 10 Gy 24 hr CL32FB_10G_24H (3-3-2)


title: Primary fibroblast 10 Gy 4 hr CL32FB_10G_4H (1-2-3)


title: Control BXD40/TyJ-12

value: male


title: Control LG/J-5

value: macrophage


title: Control BXD38/TyJ-2


title: Primary fibroblast 0 Gy 4 hr CL29FB_0G_4H (1-1-10)


title: Primary fibroblast 2 Gy 4 hr CL22FB_2G_4H (1-1-8)


title: Primary fibroblast 10 Gy 4 hr CL22FB_10G_4H (1-1-9)


title: Primary fibroblast 10 Gy 4 hr CL29FB_10G_4H (1-1-12)


title: Control BXD6/TyJ-2


title: Control BUB/BnJ-4

value: BUB/BnJ


title: Primary fibroblast 2 Gy 4 hr CL21FB_2G_4H (1-1-5)

value: control


title: Control BXD27/TyJ-3


title: Primary fibroblast 2 Gy 5 hr CL21FB_2G_4H (3-1-3)


title: Control BXD1/TyJ-3


title: Control BUB/BnJ-1


title: Primary fibroblast 20 Gy 4 hr CL21FB_20G_4H (3-1-10)

value: 20 Gy


title: Primary fibroblast 0 Gy 4 hr CL22FB_0G_4H (1-1-7)


title: Primary fibroblast 5 Gy 4 hr CL21FB_5G_5H (3-1-4)


title: Primary fibroblast 10 Gy 8 hr CL21FB_10G_8H (3-1-7)


title: Primary fibroblast 1 Gy 4 hr CL21FB_1G_4H (3-1-2)


title: Primary fibroblast 10 Gy 4 hr CL21FB_10G_4H (3-1-6)


title: Control BXD1/TyJ-1


title: Control AXB8/PgnJ-1


title: Primary fibroblast 10 Gy 4 hr CL21FB_10G_4H (1-1-6)


title: Primary fibroblast 10 Gy 2 hr CL21FB_10G_2H (3-1-5)


title: Control BXD27/TyJ-2


title: Primary fibroblast 10 Gy 24 hr CL21FB_10G_24H (3-1-8)


title: Primary fibroblast 0 Gy 4 hr CL21FB_0G_4H (1-1-4)


title: Primary fibroblast 0 Gy 4 hr CL20FB_0G_4H (1-1-1)


title: Primary fibroblast 2 Gy 4 hr CL20FB_2G_4H (1-1-2)


title: Primary fibroblast 10 Gy 4 hr CL20FB_10G_4H (1-1-3)


title: Control BXD12/TyJ-1


title: Control AXB23/PgnJ-3


title: Control AXB24/PgnJ-1


title: Primary fibroblast 0 Gy 0 hr CL21FB_0G_0H (3-1-1)


title: Control FVB/NJ-17

value: FVB/NJ


title: Control AXB23/PgnJ-2


title: Control-rep3

city: Tucson

first: Megha

last: Padi

state: AZ

address: 1071 East Lowell St.

department: Molecular and Cellular Biology

institute: University of Arizona

hyb_protocol: Samples were hybridized to Human Gene U133 Plus 2.0 arrays according to the manufacturer's instructions.

scan_protocol: Scanning of microarrays was performed by following Affymetrix protocols at the Dana-Farber Cancer Institute microarray core facility.

data_processing: Data were normalized by RMA using R/Bioconductor package affy.

source_name: U-2 OS cells expressing empty vector

label_protocol: RNA was converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA, according to the standard Affymetrix protocol.

growth_protocol: U-2 OS cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Cellgro) supplemented with 10% Fetal Clone-I serum (HyClone), penicillin and streptomycin.

extract_protocol: Total RNA from LT-expressing U-2 OS cell lines was extracted using TRIzol (Invitrogen) and purified in RNeasy columns (Qiagen). RNA integrity was determined using a Bioanalyzer (Agilent).

value: U-2 OS

value: expressing empty vector


title: T1-rep3

source_name: U-2 OS cells expressing full-length SV40 LT

value: expressing full-length SV40 LT


title: T6-rep3

source_name: U-2 OS cells expressing SV40 LT fragment T6

value: expressing SV40 LT fragment T6


title: Control AXB2/PgnJ-2


title: T16-rep2

source_name: U-2 OS cells expressing SV40 LT fragment T16

value: expressing SV40 LT fragment T16


title: Control AXB2/PgnJ-3


title: T16-rep3


title: T8-rep2

source_name: U-2 OS cells expressing SV40 LT fragment T8

value: expressing SV40 LT fragment T8


title: Primary fibroblast 10 Gy 48 hr CL21FB_10G_48H (3-1-9)

value: Fibroblast

value: 10 Gy


title: CTGF overexpressed

city: Taipei

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University

description:
microRNA expression profile of CTGF-expressed cell
SAS-CTGF

hyb_protocol: Standard Illumina microRNA protocol for beadchip

data_processing: The data were normalised using quantile normalization with Illumina GenomeStudio

source_name: Head and neck cell line

label_protocol: Standard Illumina microRNA protocol: Cy3-labled PCR product

growth_protocol: Cells were cultivated in DMEM+ 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

treatment_protocol: Establish stable transfectants of pcDNA3-CTGF in SAS cells

value: oral cancer cell line SAS

value: CTGF overexpressed


title: HCC tissue54025

city: Shanghai

first: jie

last: hu

address: 180 Fenglin Road

institute: Zhongshan hospital, Fudan University

description: Hybridized to SNP 6.0

hyb_protocol: Formalin-fixed paraffin-embedded  tumor DNA was hybridized on Affymetrix GeneChip Human Mapping SNP6.0 using the Human mapping SNP6.0 assay kit (Affymetrix Inc., Santa Clara, USA) and following the manufacturer’s protocol. The only modification to the manufacturer’s protocol occurred after digestion and adaptor ligation, when the DNA was split into nine plates instead of three. Independent PCR reactions were set up using TITANIUM Taq DNA polymerase (Clontech Laboratories, Inc. Mountain View, USA), for the recommended 35 cycles. The nine PCR products were then pooled.

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

data_processing: CEL files (generated by Affymetrix GTYPE using the DM algorithm) were processed by Genotyping Console 3.0.1. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758.

source_name: HCC patients

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: HCC Tumor cells were manually microdissected from three consecutive 10-μm sections for each sample under a dissecting microscope to obtain high-purity (>80%) tumor DNA. Fixative removal was performed twice in xylene and absolute ethanol washes. The pellets were digested with proteinase K and then processed according to the QIAamp DNA FFPE Tissue protocol (Qiagen Inc. GmbH, Germany). The concentration was determined by Nanodrop (Thermo Scientific Inc., Wilmington, DE, USA)

value: Hepatocellular carcinoma


title: control

description:
microRNA expression profile of control cells
SAS-NEO


title: HCC tissue62130

description: Hybridized to SNP 6.0


title: T6-rep2


title: HCC tissue62132

description: Hybridized to SNP 6.0


title: Control AXB19a/PgnJ-3

value: male

value: 16 weeks

value: Control


title: T8-rep3


title: Control AXB19/PgnJ-3

value: macrophage


title: T1-rep2


title: HCC tissue38717

description: Hybridized to SNP 6.0


title: HCC tissue39327

description: Hybridized to SNP 6.0


title: Control-rep2


title: HCC tissue24169

description: Hybridized to SNP 6.0


title: Control AXB23/PgnJ-1


title: HCC tissue33372

description: Hybridized to SNP 6.0


title: Control AXB24/PgnJ-2


title: HCC tissue24029

description: Hybridized to SNP 6.0


title: LT-HSC Zbtb7a F/F Mx1-Cre+ #3

city: Boston

first: Takahiro

last: Maeda

state: MA

address: One Blackfan Circle

institute: Brigham and Women's Hospital

description:
B658_MG430 2-(6_2851+2821FF)
Gene expression data from FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-).

hyb_protocol: Affymetrix GeneChip Mouse Genome 430 v2.0 arrays (Affymetrix, Santa Clara, CA) were hybridized with fragmented cRNA targets (20 μg) and washed and stained with streptavidin-PE.

scan_protocol: Affymetrix GeneChip images were scanned using a high-resolution GeneChip Scanner 3000 (Hewlett-Packard).

data_processing: The raw data is normalized by Robust Multi-array Average (RMA) using Affymetrix Expression Console.

source_name: LT-HSCs of LRF knockout mouse

label_protocol: Biotinylated cRNA was generated using two rounds of in vitro transcription by T7 RNA polymerase.

extract_protocol: RNA samples were prepared using the Absolutely RNA Microprep Kit (Stratagene).

treatment_protocol: LT-HSCs were FACS-sorted from three Lrf knockout (Zbtb7a Flox/Flox Mx1-Cre+) and two control (Zbtb7a Flox/+ Mx1-Cre+) mice, nine days after the first pIpC injection. pIpC (250μg) was injected twice to induce Cre recombinase.

tag: strain/background

value: Zbtb7a Flox/Flox Mx1-Cre+ (LRF homozygous knockout)

value: 4 weeks

tag: time point

value: 9 days after 1st pIpC injection


title: HCC tissue27643

description: Hybridized to SNP 6.0


title: T8-rep1

value: U-2 OS

tag: genotype/variation


title: HCC tissue34868

description: Hybridized to SNP 6.0


title: LT-HSC Zbtb7a F/F Mx1-Cre+ #2

description:
B657_MG430 2-(5_2950FF)
Gene expression data from FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-).

tag: cell type


title: HCC tissue29417

description: Hybridized to SNP 6.0

tag: tissue


title: HCC tissue29350

description: Hybridized to SNP 6.0


title: Control AXB19a/PgnJ-1


title: LT-HSC Zbtb7a F/F Mx1-Cre+ #1

description:
B656_MG430 2-(4_2846FF)
Gene expression data from FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-).


title: T6-rep1


title: LT-HSC Zbtb7a F/+ Mx1-Cre+ #2

description:
B655_MG430 2-(2_2849F+)
Gene expression data from FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-).

source_name: LT-HSCs of control mouse

value: Zbtb7a Flox/+ Mx1-Cre+ (LRF heterozygous)


title: T16-rep1


title: Control AXB19/PgnJ-2


title: HCC tissue23937

description: Hybridized to SNP 6.0


title: T1-rep1

value: expressing full-length SV40 LT


title: Control AXB10/PgnJ-3


title: Control-rep1

value: expressing empty vector


title: HCC tissue19093

description: Hybridized to SNP 6.0


title: A3-1 mRNA microarray - siGFP rep1

status: Public on Oct 25 2012

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: A3-1 treated with control siRNA

hyb_protocol: Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human gene 1.0 ST arrays for 17 hr at 45˚C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: All gene array data was analyzed using tools in Expression Console software (Affymetrix). The Robust Multi-array Analysis (RMA) (Irizarry, Hobbs, Collin, Beazer-Barclay, Antonellis, Scherf, and Speed 2003) algorithm was used for probeset (gene-level) intensity analysis.

source_name: cultured mouse embryonic stem cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Wt sensetarget label manual, 2007, Affymetrix).

growth_protocol: Mouse embryonic stem cell were incubated in DMEM media containing 20% FBS, non-essentail amino acid and LIF at 37˚C.

extract_protocol: Total RNA was purified with Trizol reagent (Invitrogen) according to manufacturer's protocol

treatment_protocol: Mouse embryonic stem cell were treated with siRNA for GFP or for Lin28a and incubated for 48 hours.

tag: sirna sequence


title: A3-1 mRNA microarray - untreated rep2

description: A3-1 untreated


title: A3-1 mRNA microarray - untreated rep1

description: A3-1 untreated


title: A3-1 mRNA microarray - siLin28a rep2

description: A3-1 treated with siLin28a


title: Control AXB10/PgnJ-10


title: HCC tissue13295

description: Hybridized to SNP 6.0


title: A3-1 mRNA microarray - siGFP rep2

description: A3-1 treated with control siRNA


title: HCC tissue39488

description: Hybridized to SNP 6.0


title: HCC tissue17495

description: Hybridized to SNP 6.0


title: T cell lymphomas in TCF-1 KO mice, biological rep 3

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

description: Gene expression data from T cell lymphoma cells in TCF-1 KO mice

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

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

data_processing:
The data were analyzed with Partek GS v 6.4 using default RMA as normalization method.
probe group file: MoGene-1_0-v1.r4.pgf
meta-probeset file: MoGene-1_0-v1.r4.mps

source_name: Mouse T cell lymphoma in TCF-1 KO mice

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

growth_protocol: DN3 thymocytes were isolated by cell sorting from WT or TCF-1-deficient mice. T cell lymphomas were sorted from the thymuses of TCF-1 KO mice that have developed the diseases.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by further purification on RNeasy columns.

treatment_protocol: DN3 thymocytes or T cell lymphoma cells were sorted directly into Trizol LS reagent.

value: thymus

value: T cell lymphoma

tag: genotype

value: TCF-1 KO


title: T cell lymphomas in TCF-1 KO mice, biological rep 1


title: T cell lymphomas in TCF-1 KO mice, biological rep 5


title: T cell lymphomas in TCF-1 KO mice, biological rep 2


title: HCC tissue65403

description: Hybridized to SNP 6.0


title: A3-1 mRNA microarray - siLin28a rep1

description: A3-1 treated with siLin28a


title: HCC tissue11023

description: Hybridized to SNP 6.0


title: HCC tissue11703

description: Hybridized to SNP 6.0


title: WT DN3 thymocytes, biological rep 1

description: Gene expression data from WT DN3 thymocytes

source_name: Mouse WT DN3 thymocytes

value: thymocytes

value: wild-type


title: TCF-1 KO DN3 thymocytes, biological rep 2

description: Gene expression data from TCF-1-deficient DN3 thymocytes

source_name: Mouse TCF-1 KO DN3 thymocytes


title: WT DN3 thymocytes, biological rep 2


title: WT DN3 thymocytes, biological rep 3


title: TCF-1 KO DN3 thymocytes, biological rep 3


title: HCC tissue12839

description: Hybridized to SNP 6.0

value: Hepatocellular carcinoma


title: T cell lymphomas in TCF-1 KO mice, biological rep 6


title: LM464

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

institute: The University of Texas M.D. Anderson Cancer Center

description:
LM001_525_AGE_1_LM464_03_30_10
Inclusion number in the clinical trial : 299

hyb_protocol: Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol.

scan_protocol: Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

data_processing: Raw data of microarrays were processed using quantile normalization and RMA algorithm (RMAExpress); expression values were log2 transformed

source_name: BATTLE_trial_core biopsy_chemorefractory non-small cell lung cancer

label_protocol: WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols.

growth_protocol: Core biopsies from patients included in the Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE)

extract_protocol: RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.

treatment_protocol: Samples were OCT-embedded and frozen before RNA extraction

tag: egfr mutation

tag: kras mutation

tag: 8_week_disease control_1yes_0no

tag: progression-free survival status

tag: progression-free survival time (months)


title: LT-HSC Zbtb7a F/+ Mx1-Cre+ #1

description:
B654_MG430 2-(1_2823F+)
Gene expression data from FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-).


title: LM476

description:
LM001_525_AGE_1_LM476_03_31_10
Inclusion number in the clinical trial : 324

value: sorafenib


title: TCF-1 KO DN3 thymocytes, biological rep 1

tag: strain


title: LM423

description:
LM001_525_AGE_1_LM423_07_30_09
Inclusion number in the clinical trial : 237

tag: treatment


title: HCC tissue11648

description: Hybridized to SNP 6.0


title: LM226

description:
LM001_525_AGE_1_LM226_10_08_08
Inclusion number in the clinical trial : 174


title: LM462

description:
LM001_525_AGE_1_LM462_03_30_10
Inclusion number in the clinical trial : 157

value: erlotinib+bexarotene


title: LM438

description:
LM001_525_AGE_1_LM438_07_31_09
Inclusion number in the clinical trial : 265


title: LM481

description:
LM001_525_AGE_1_LM481_03_31_10
Inclusion number in the clinical trial : 332

label_protocol: RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit. For all experiments, the manufacturers' protocols were strictly followed. WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively.

value: WT

tag: egfr index

value: erlotinib

tag: randomization date

tag: date of progression


title: HCC tissue8100

description: Hybridized to SNP 6.0


title: LM478

description:
LM001_525_AGE_1_LM478_03_31_10
Inclusion number in the clinical trial : 326


title: T cell lymphomas in TCF-1 KO mice, biological rep 4

tag: age


title: LM477

description:
LM001_525_AGE_1_LM477_03_31_10
Inclusion number in the clinical trial : 325

value: Mutant

tag: egfr activating mutation

value: Yes

tag: concomitant t790m

tag: egfr mutation exon

value: Exon 21/Exon 20

tag: egfr mutation pattern


title: LM485

description:
LM001_525_AGE_1_LM485_04_01_10
Inclusion number in the clinical trial : 338


title: LM470

description:
LM001_525_AGE_1_LM470_03_30_10
Inclusion number in the clinical trial : 313


title: LM474

description:
LM001_525_AGE_1_LM474_03_31_10
Inclusion number in the clinical trial : 320


title: LM467

description:
LM001_525_AGE_1_LM467_03_30_10
Inclusion number in the clinical trial : 308


title: LM479

description:
LM001_525_AGE_1_LM479_03_31_10
Inclusion number in the clinical trial : 329


title: LM469

description:
LM001_525_AGE_1_LM469_03_30_10
Inclusion number in the clinical trial : 311


title: LM468

description:
LM001_525_AGE_1_LM468_03_30_10
Inclusion number in the clinical trial : 310

value: Unknown

value: Exon 20


title: LM472

description:
LM001_525_AGE_1_LM472_03_31_10
Inclusion number in the clinical trial : 316


title: LM465

description:
LM001_525_AGE_1_LM465_03_30_10
Inclusion number in the clinical trial : 303

value: Exon 19


title: HCC tissue8099

description: Hybridized to SNP 6.0

data_processing:
CEL files (generated by Affymetrix GTYPE using the DM algorithm) were processed by Genotyping Console 3.0.1. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758.
primary data description: CEL files were generated by Affymetrix GTYPE using the DM algorithm

tag: tissue


title: HCC tissue6454

description: Hybridized to SNP 6.0


title: LM463

description:
LM001_525_AGE_1_LM463_03_30_10
Inclusion number in the clinical trial : 269


title: LM460

description:
LM001_525_AGE_1_LM460_03_30_10
Inclusion number in the clinical trial : 137


title: LM459

description:
LM001_525_AGE_1_LM459_03_30_10
Inclusion number in the clinical trial : 137


title: LM442

description:
LM001_525_AGE_1_LM442_08_19_09
Inclusion number in the clinical trial : 275


title: LM448

description:
LM001_525_AGE_1_LM448_08_19_09
Inclusion number in the clinical trial : 285


title: LM447

description:
LM001_525_AGE_1_LM447_08_19_09
Inclusion number in the clinical trial : 283


title: HCC tissue2358

description: Hybridized to SNP 6.0


title: HCC tissue5219

description: Hybridized to SNP 6.0


title: LM458

description:
LM001_525_AGE_1_LM458_08_05_09
Inclusion number in the clinical trial : 255


title: LM445

description:
LM001_525_AGE_1_LM445_08_19_09
Inclusion number in the clinical trial : 280


title: LM440

description:
LM001_525_AGE_1_LM440_07_31_09
Inclusion number in the clinical trial : 267


title: HCC tissue1326

description: Hybridized to SNP 6.0


title: HCC tissue5400

description: Hybridized to SNP 6.0


title: LM452

description:
LM001_525_AGE_1_LM452_08_19_09
Inclusion number in the clinical trial : 289


title: LM439

description:
LM001_525_AGE_1_LM439_07_31_09
Inclusion number in the clinical trial : 266

value: Exon 19/Exon 20


title: LM437

description:
LM001_525_AGE_1_LM437_07_31_09
Inclusion number in the clinical trial : 263


title: LM436

description:
LM001_525_AGE_1_LM436_07_31_09
Inclusion number in the clinical trial : 261


title: LM435

description:
LM001_525_AGE_1_LM435_07_31_09
Inclusion number in the clinical trial : 259


title: LM425

description:
LM001_525_AGE_1_LM425_07_30_09
Inclusion number in the clinical trial : 242


title: LM430

description:
LM001_525_AGE_1_LM430_07_31_09
Inclusion number in the clinical trial : 249


title: LM428

description:
LM001_525_AGE_1_LM428_07_30_09
Inclusion number in the clinical trial : 245


title: LM434

description:
LM001_525_AGE_1_LM434_07_31_09
Inclusion number in the clinical trial : 258


title: LM426

description:
LM001_525_AGE_1_LM426_07_30_09
Inclusion number in the clinical trial : 243


title: HCC tissue987

description: Hybridized to SNP 6.0


title: LM427

description:
LM001_525_AGE_1_LM427_07_30_09
Inclusion number in the clinical trial : 244


title: LM418

description:
LM001_525_AGE_1_LM418_07_30_09
Inclusion number in the clinical trial : 231


title: LM324

description:
LM001_525_AGE_1_LM324_01_23_09
Inclusion number in the clinical trial : 228


title: LM321

description:
LM001_525_AGE_1_LM321_01_23_09
Inclusion number in the clinical trial : 224

value: Exon 18


title: LM320

description:
LM001_525_AGE_1_LM320_01_23_09
Inclusion number in the clinical trial : 223


title: LM323

description:
LM001_525_AGE_1_LM323_01_23_09
Inclusion number in the clinical trial : 227


title: LM318

description:
LM001_525_AGE_1_LM318_01_22_09
Inclusion number in the clinical trial : 219


title: LM312

description:
LM001_525_AGE_1_LM312_01_22_09
Inclusion number in the clinical trial : 207


title: Ovarian cancer tissue from Taiwan LD148

city: Singapore

first: Liang

last: Goh

address: College Road

country: Singapore

institute: Duke-NUS graduate medical school

description:
Epithelial ovarian cancers
primary_data_description:  Log relative ratio calclulated by Affymetric Genotyping Console

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

scan_protocol: Affymetrix standard procedure

data_processing: CEL files and CHP files are processed and normalized with Hapmap CHB using the Affymetric Genotyping Console.

source_name: Ovarian Cancer tissue

extract_protocol: Tumor genomic DNAs were extracted by using phenol-chloroform extraction method. Tumor RNAs were extracted by using Qiazol followed by column clean-up using miRNeasy kit (Qiagen).

tag: histotype

value: Clear Cell


title: LM310

description:
LM001_525_AGE_1_LM310_01_22_09
Inclusion number in the clinical trial : 204

tag: egfr mutation


title: Ovarian cancer tissue from Taiwan LB957


title: Ovarian cancer tissue from Taiwan LD157


title: Ovarian cancer tissue from Taiwan LB771


title: LM308

description:
LM001_525_AGE_1_LM308_01_22_09
Inclusion number in the clinical trial : 199

tag: kras mutation


title: Ovarian cancer tissue from Taiwan LB542

value: Serous


title: Ovarian cancer tissue from Taiwan LA347

value: Mucinous


title: Ovarian cancer tissue from Taiwan LA810


title: LM238

description:
LM001_525_AGE_1_LM238_10_20_08
Inclusion number in the clinical trial : 196


title: Ovarian cancer tissue from Taiwan LD108


title: Ovarian cancer tissue from Taiwan LD029


title: Ovarian cancer tissue from Taiwan LA243


title: LM236

description:
LM001_525_AGE_1_LM236_10_20_08
Inclusion number in the clinical trial : 192


title: Ovarian cancer tissue from Taiwan L991


title: Ovarian cancer tissue from Taiwan LD085


title: Ovarian cancer tissue from Taiwan LD050


title: Ovarian cancer tissue from Taiwan LD037


title: Ovarian cancer tissue from Taiwan LB625


title: Ovarian cancer tissue from Taiwan LB699


title: Ovarian cancer tissue from Taiwan LA097


title: Ovarian cancer tissue from Taiwan LB630


title: LM228

description:
LM001_525_AGE_1_LM228_10_20_08
Inclusion number in the clinical trial : 176


title: LM230

description:
LM001_525_AGE_1_LM230_10_20_08
Inclusion number in the clinical trial : 181


title: Ovarian cancer tissue from Taiwan LD041


title: Ovarian cancer tissue from Taiwan LA436


title: LM232

description:
LM001_525_AGE_1_LM232_10_20_08
Inclusion number in the clinical trial : 184


title: LM234

description:
LM001_525_AGE_1_LM234_10_20_08
Inclusion number in the clinical trial : 187


title: Ovarian cancer tissue from Taiwan LB392