title: T113_Tissue

description: SNP and copy number calls.

source_name: Metastatic tumor tissue

value: metastatic melanoma

value: III

value: paired

value: tissue (amplified)

value: cell line isolated via passage


title: T-ALL tumor 38 (non-aneuploid)

status: Public on Jul 01 2014

type: genomic

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description:
38Th
non-aneuploid; genotype in Sup data 1 accompanying paper

hyb_protocol: Labeled DNA was hybridyzed to Agilent 244K oligo arrays (mm9 build, design 014695) using manufacturer's standard protocols

scan_protocol: Arrays were scanned on an Agilent 2565BA scanner

data_processing: Data was imported into Agilent Genomc Workbench, quantile normalized and log 2 Cy5/Cy3 ratios were exported to Excel.

molecule: genomic DNA

organism: Mus musculus

source_name: control p53 null T-ALL sample

label_protocol: Tumor DNA and reference DNA were labeled with Cy3 and Cy5 dNTP respectively using Exo Klenow fragment and Agilent random primers using Agilent standard protocols

growth_protocol: Mice were sacrificed when gravely ill (in vast majority of cases because of T-ALL) See for details Supplementary info S1 accompanying paper

extract_protocol: Tissue was homogenized using bead-homogenization in Qiagen DNA-easy buffer 1. DNA was then purified using DNA-easy columns using Qiagen protocols

treatment_protocol: Thymus was dissected and stored at -80 in pieces for subsequent analysis

tag: strain

tag: chromosome instability

value: non-CIN

tag: gender

value: male

tag: disease state

value: T-ALL

tag: tissue

value: p53 f/f control tumor

source_name: sex-matched control liver

value: sex-matched liver (mix several litter mates)


title: T-ALL tumor 37 (non-aneuploid)

description:
37Th
non-aneuploid; genotype in Sup data 1 accompanying paper

value: female


title: genomic DNA from normal colon biopsies 351A

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k Beadchip using standard Illumina protocol.

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

data_processing: Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. Beta values were calculated after performing smoothQuantileNrmalization for color balance adjustment followed by background level corection and quantile based probe level normalization. We masked data point as “NA” for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.01 were also replaced as NA. Furthermore, probes containing at least one “NA” across the normal sample set were masked as “NA”. Beta value was calculated as M/(M+U).

label: Cy5 and Cy3

organism: Homo sapiens

source_name: normal colon

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from normal colon biopsies using Qiagen DNeasy Kit according to standard instructions.

tag: colonic location

value: proximal

value: normal

tag: age

tag: aspirin

value: nonuser

tag: hrt

tag: bmi

value: high

tag: smoking


title: ccRCC tumor 2.29

city: Umeå

first: Linda

last: Köhn

address: Building 6M

department: Medical Biosciences/pathology

country: Sweden

institute: Umeå University

description: Genomic DNA extracted from clear cell renal cell carcinoma tumors was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from clear cell renal cell carcinoma was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

label: A-DNP, C-Bio

source_name: clear cell renal cell carcinoma

label_protocol: 200 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA was done using a BioRobot M48 Workstation with MagAttract technology (Qiagen)

tag: tumor stage

value: metastasized tumor

value: Male

value: Kidney

value: carcinoma


title: ccRCC tumor 2.42

value: un-metastasized tumor

value: Female


title: genomic DNA from normal colon biopsies 168C

value: distal


title: ccRCC tumor 2.04


title: ccRCC tumor 2.08


title: genomic DNA from normal colon biopsies 245A


title: Day 5 EB_GemOE_control_rep1

type: RNA

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

country: USA

institute: Washington University School of Medicine

description: Day 5 EB, rep 1, control

hyb_protocol: RNA was hybridized to Affymetrix Mouse Gene 1.0 ST microarrays and washed and stained with the GeneChip Fluidics Station 450 (Affymetrix) according to standard protocols.

scan_protocol: Array image acquisition was done with GeneChip Scanner 3000 7G (Affymetrix) and image processing with Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/) after normalization to exclude probe sets that did not meet the following preliminary cutoff values: 1) expression, represented by model-based expression indices (MBEI), was changed more than 1.2-fold in treated versus untreated samples (E/B >1.2) groups; 2) MBEI differences were larger than 30 (E-B > 30); and 3) expression was claimed as present (P) in at least one sample in each experiment. For each sample type, the entire experiment was repeated three times. Probe sets were considered putatively Geminin-regulated if they met microarray cutoff values in at least 2 of the 3 experiments.

label: biotin

molecule: total RNA

source_name: day 5 embryoid bodies, GemOE, no dox control

label_protocol: 1 microgram of RNA was prepared by the Whole Transcript Sense Target Labeling (Affymetrix) standard protocol to add biotin label.

growth_protocol: ES cells were differentiated into embryoid bodies for 4 or 5 days. ES cells were maintained on irradiated MEFs in DMEM plus 15% fetal bovine serum (HyClone), 1mM sodium pyruvate, 0.1mM non-essential amino acids (Gibco), 2mM Glutamine, 1000U/mL LIF (Chemicon) and 100μM 2-mercaptoethanol (Sigma). For EB formation, ES cells were feeder subtracted and plated at 6,000/ml on 10 cm petri dishes treated with 5% polyheme to prevent cell adhesion and were differentiated in IMDM with 15% FCS, 1% L-glutamine, 50µg/ml ascorbic acid and 4.5X10-4 M MTG. Dox is added at 0.5 µg/ml to induce overexpression of Gem or miRNAs targeting endogenous Gem transcripts.

extract_protocol: RNA was prepped with the Qiagen RNeasy kit.

treatment_protocol: Embryoid bodies from the Gem knockdown line were collected on day 4. Embryoid bodies from the Gem overexpression line were collected on days 4 or 5.

tag: background/strain

tag: es cell line

tag: es cell line type

value: Geminin overexpression

tag: cell type

value: embryoid bodies

tag: differentiation day

tag: dox addition

value: no Dox


title: T-ALL tumor 50 (aneuploid)

description:
50Th
aneuploid; genotype in Sup data 1 accompanying paper

source_name: aneuploid T-ALL sample

tag: strain

tag: chromosome instability

value: CIN

value: male

value: T-ALL

value: Mps1DK p53f/f of Mps1DK p53f/+ tumor

value: non-CIN


title: Staphylococcus aureus  planktonic cells_control 60min_replicate2

city: Changchun

first: lu

last: yu

state: Jilin

address: Xi’an Road 5333#

department: Institute of Zoonosis

country: China

institute: Jilin University

description: Gene expression data from Staphylococcus aureus  planktonic cells  at 60min

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.0

organism: Staphylococcus aureus

label_protocol: Conversion to cDNA and labeling was performed as described in Hutter et al., Antimicrobial agents and chemotherapy, 2004, 48(8):2838-284

growth_protocol: S. aureus strain ATCC29213 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of TSB, after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of TSB in 250-ml Erlenmeyer flasks, the planktonic cells were grown at 37°C at 200 rpm to an OD600 of 0.3. Within biofilm, the overnight culture were inoculated to an initial OD600 and diluted in TSBg to obtain the final concentration of 1× 105cfu/ml, 30 ml bacterial suspension diluted in 2% glucose-supplemented TSB containing 1 × 105 cfu/ml into the culture dish, then incubated in air for 48 h at 37°C

extract_protocol: Total bacterial RNA was isolated as described by Hutter et al., 2004, 48(8):2838-2844

treatment_protocol: Licochalcone A stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 1/2× MIC (2 μg/ml), and the final concentration of DMSO was 0.1% (vol/vol) as control group. Biofilms washed once with PBS to remove any unbound bacteria, Licochalcone A stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 4× MIBC (64 μg/ml), and the final concentration of DMSO was 0.1% (vol/vol) as control group. Then, the bacterial planktonic and biofilm cells were further incubated for 60 min at 37°C

value: Standard strain ATCC29213

value: planktonic cells


title: Staphylococcus aureus  planktonic cells_control 60min_replicate1


title: Staphylococcus aureus  planktonic cells_Licochalcone A 60 min_replicate1

description: Gene expression data from Staphylococcus aureus  planktonic cells with Licochalcone A treatment at 60min


title: T-ALL tumor 52 (aneuploid)

description:
52Th
aneuploid; genotype in Sup data 1 accompanying paper

tag: gender

tag: disease state

value: sex-matched liver (mix several litter mates)


title: ccRCC tumor 6.41

value: metastasized tumor

value: Male

tag: tissue


title: genomic DNA from normal colon biopsies 155C

value: female

tag: colonic location

value: normal

tag: age

value: nonuser


title: genomic DNA from normal colon biopsies 183A

value: proximal

tag: aspirin

tag: hrt

value: user


title: cell line L-428, knock-down of DUSP5

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: Gene expression data from established Hodgkin's lymphoma cell line after knock-down of DUSP5

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on HG_U133A Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed using the MAS5.0 algorithm and Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Hodgkin’s lymphoma cell line L-428, transfected with vector pcDNA6.2-GW/EmGFP-miR-DUSP5

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Established Hodgkin's lymphoma cells were grown under standard conditions.

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

treatment_protocol: Cells were transfected with empty control vector pcDNA6.2-GW/EmGFP-miR-neg or with vector pcDNA6.2-GW/EmGFP-miR-DUSP5

value: Hodgkin’s lymphoma cell line

tag: cell line

tag: transfection

value: vector pcDNA6.2-GW/EmGFP-miR-DUSP5


title: kidney cortex 6.41

description: Genomic DNA extracted from normal kidney cortex was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

source_name: kidney cortex

tag: tumor stage

value: not applicable

value: Kidney

value: carcinoma


title: T117_CTC

city: Santa Monica

first: Neal

middle: Percy

last: Kawas

state: CA

address: 2200 Santa Monica Blvd

department: Molecular Oncology

institute: John Wayne Cancer Institute

description: SNP and copy number calls.

hyb_protocol: Following fragmentation, 3ug of gDNA was annealed for 16 hours at a temperature of 50C to Affymetrix Genomewide SNP Array 6.0 at a pH of 6.6.

scan_protocol: Scanned on 7G 3000 manufactured by Affymetrix.

data_processing: SNPs were called using the Birdseed v2 algorithm (.CHP files), and copy number variations were called using the CN5 algorithm (.CNCHP files) using Affymetrix Genotyping Console 4.0 under good laboratory practice (GLP) conditions. Sample table and .CNCHP data are based on genome build NCBI36 (hg18).

label: Biotin

source_name: Blood

label_protocol: Biotinylated gDNA was prepared according to the standard Affymetrix protocol from3 ug of gDNA.

growth_protocol: Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol: DNA extraction from frozen tumor tissues, and cell lines was carried out with the QIAamp DNA mini kit (QIAGEN, Valencia, CA). DNA extraction from CTCs was carried out using DNAzol (Molecular Research Center, Cincinnati, OH) according to the manufacturer's instructions.

treatment_protocol: No treatment.

value: metastatic melanoma

tag: cancer stage

value: III

tag: patient group

value: paired

tag: pair number

value: CTC (amplified)

tag: isolation method

value: GM3, GM2, GD4


title: T114_Tissue

description: SNP and copy number calls.

tag: cell type

value: tissue (amplified)

value: cell line isolated via passage


title: genomic DNA from normal colon biopsies 580C

value: female

value: distal

tag: bmi

value: high

tag: smoking


title: S662_CTC

description: SNP and copy number calls.

value: GM3, GM2, GD2


title: T116_CTC

description: SNP and copy number calls.

value: GM3, GM2, GD3


title: T-ALL tumor 49 (aneuploid)

description:
49Th
aneuploid; genotype in Sup data 1 accompanying paper

tag: strain

tag: chromosome instability

value: CIN

tag: gender

value: male

value: T-ALL

value: Mps1DK p53f/f of Mps1DK p53f/+ tumor

value: non-CIN

value: sex-matched liver (mix several litter mates)


title: T-ALL tumor 25 (aneuploid)

description:
25Th
aneuploid; genotype in Sup data 1 accompanying paper

tag: disease state

tag: tissue


title: genomic DNA from normal colon biopsies 392A

tag: colonic location

value: proximal

value: normal

tag: age

tag: aspirin

value: nonuser

value: user


title: kidney cortex 6.21

value: not applicable

value: Male

value: Kidney

value: carcinoma


title: T-ALL tumor 24 (aneuploid)

description:
24Th
aneuploid; genotype in Sup data 1 accompanying paper


title: T112_Tissue

description: SNP and copy number calls.

value: metastatic melanoma

value: III

value: paired

value: tissue (amplified)

value: cell line isolated via passage


title: kidney cortex 6.07


title: genomic DNA from normal colon biopsies 193C

value: female

value: distal

tag: hrt

value: high


title: genomic DNA from normal colon biopsies M025C


title: genomic DNA from normal colon biopsies M033A


title: Sxi (+)

city: Madison

first: Christina

last: Hull

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry, Medical Microbiology and Immunology

institute: University of Wisconsin- Madison

hyb_protocol: Slides were incubated in pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) for 1 hour at 42ºC. cDNAs were then applied to slides in 1X formamide buffer (25% formamide, 5X SSC, 0.1% SDS) containing 10 µg each sheared salmon sperm DNA (Eppendorf, Westbury, NY) and yeast tRNA (Sigma-Aldrich, St. Louis MO). Hybridizations were incubated at 42ºC for 12 hours. Slides were washed (1x SSC, .05XSSC) and dried before scanning.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Molecular Devices, Sunnyvale CA) at the University of Wisconsin-Madison Gene Expression Center.

data_processing: The resulting spot intensities were extracted using GenePix Pro 4.0. Data were analyzed using Limma (Bioconductor) [Smyth, 2004]. Analysis included a background correction, normalization within the arrays, fitting of a linear model (lmFit), and a moderated T-Test using the Empirical Bayes package.

label: Cy3, Cy5

organism: Cryptococcus deneoformans

source_name: SXI-Inducible cells 6 hrs after Induction [experimental]

label_protocol: cDNA was synthesized using the SuperScript III Direct Labeling Kit (Invitrogen, Carlsbad CA). The cDNA was purified over a QiaQuick MinElute PCR Purification Kit (Qiagen, Valencia CA), both according to manufacturer’s instructions.

extract_protocol: RNA was extracted using the Hot-Acid Phenol Method for yeast found in Current Protocols

tag: genotype

value: MATα ade2 ura5 sxi1α::NATR pGPD:SXI1α-TAP URA5 pGAL7:SXI2a-ADE2

source_name: Sxi-Deletion Haploid 6 hrs after induction [control]

value: MATa sxi1α::URA5


title: Sxi (-)

source_name: Δsxi1α x Δsxi2a cross 16 hrs after plating [experimental]

value: MATa sxi1a::URA5 x MATa sxi2a::URA5

source_name: JEC20 x JEC21 cross 16 hrs after plating [control]

value: MATα x MATa


title: peripheral blood 6.21

description: Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

source_name: peripheral blood

tag: tumor stage

value: Blood


title: Staphylococcus aureus  planktonic cells_Licochalcone A 60 min_replicate2

value: Standard strain ATCC29213

value: planktonic cells


title: T-ALL tumor 48 (aneuploid)

description:
48Th
aneuploid; genotype in Sup data 1 accompanying paper

value: CIN

value: male

value: T-ALL

value: Mps1DK p53f/f of Mps1DK p53f/+ tumor

value: non-CIN

value: sex-matched liver (mix several litter mates)


title: T115_Tissue

description: SNP and copy number calls.

value: metastatic melanoma

tag: cancer stage

value: III

tag: patient group

value: paired

value: tissue (amplified)

value: cell line isolated via passage


title: T-ALL tumor 21 (aneuploid)

description:
21Th
aneuploid; genotype in Sup data 1 accompanying paper


title: T111_Tissue

description: SNP and copy number calls.

tag: pair number

tag: isolation method


title: T-ALL tumor 20 (aneuploid)

description:
20Th
aneuploid; genotype in Sup data 1 accompanying paper


title: cell line L-428, vector control

description: Gene expression data from established Hodgkin's lymphoma cell line

source_name: Hodgkin’s lymphoma cell line L-428, transfected with control vector pcDNA6.2-GW/EmGFP-miR-neg

tag: cell type

value: Hodgkin’s lymphoma cell line

tag: cell line

tag: transfection


title: T-ALL tumor 23 (aneuploid)

description:
23Th
aneuploid; genotype in Sup data 1 accompanying paper

tag: strain

tag: chromosome instability


title: genomic DNA from normal colon biopsies M022C

tag: gender

value: female

value: distal

tag: disease state

value: normal

value: nonuser

tag: bmi

value: high

tag: smoking


title: kidney cortex 5.11

value: not applicable

value: Male

tag: tissue

value: Kidney

value: carcinoma


title: T-ALL tumor 36 (non-aneuploid)

description:
36Th
non-aneuploid; genotype in Sup data 1 accompanying paper

value: non-CIN

value: male

value: T-ALL

value: p53 f/f control tumor


title: peripheral blood 6.07

value: Blood


title: ccRCC tumor 6.07

description: Genomic DNA extracted from clear cell renal cell carcinoma tumors was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

value: un-metastasized tumor


title: genomic DNA from normal colon biopsies 60C

tag: colonic location

tag: age

tag: aspirin

tag: hrt


title: peripheral blood 5.11

tag: tumor stage


title: T-ALL tumor 46 (aneuploid)

description:
46Th
aneuploid; genotype in Sup data 1 accompanying paper

value: CIN

value: Mps1DK p53f/f of Mps1DK p53f/+ tumor

value: sex-matched liver (mix several litter mates)


title: T-ALL tumor 19 (aneuploid)

description:
19Th
aneuploid; genotype in Sup data 1 accompanying paper

value: female


title: ccRCC tumor 2.07

value: metastasized tumor


title: genomic DNA from normal colon biopsies 137C

value: distal

value: normal

value: nonuser


title: T-ALL tumor 47 (aneuploid)

description:
47Th
aneuploid; genotype in Sup data 1 accompanying paper


title: genomic DNA from normal colon biopsies M026A

value: proximal

value: high


title: genomic DNA from normal colon biopsies 580A

value: user


title: T-ALL tumor 22 (aneuploid)

description:
22Th
aneuploid; genotype in Sup data 1 accompanying paper

value: non-CIN


title: T-ALL tumor 45 (aneuploid)

description:
45Th
aneuploid; genotype in Sup data 1 accompanying paper


title: T-ALL tumor 44 (aneuploid)

description:
44Th
aneuploid; genotype in Sup data 1 accompanying paper

value: male


title: peripheral blood 6.41

value: not applicable

value: Male

value: carcinoma


title: genomic DNA from normal colon biopsies 168A


title: T-ALL tumor 39 (aneuploid)

description:
39Th
aneuploid; genotype in Sup data 1 accompanying paper

value: T-ALL


title: ccRCC tumor 5.09

value: un-metastasized tumor

value: Female

value: Kidney


title: kidney cortex 5.09

description: Genomic DNA extracted from normal kidney cortex was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).


title: genomic DNA from normal colon biopsies 193A

value: female


title: genomic DNA from normal colon biopsies 155A


title: kidney cortex 5.07


title: genomic DNA from normal colon biopsies M025A


title: T-ALL tumor 16 (aneuploid)

description:
16Th
aneuploid; genotype in Sup data 1 accompanying paper

value: CIN

value: Mps1DK p53f/f of Mps1DK p53f/+ tumor

value: sex-matched liver (mix several litter mates)


title: T-ALL tumor 18 (aneuploid)

description:
18Th
aneuploid; genotype in Sup data 1 accompanying paper


title: genomic DNA from normal colon biopsies 40C

value: distal

value: normal

value: nonuser


title: T-ALL tumor 15 (aneuploid)

description:
15Th
aneuploid; genotype in Sup data 1 accompanying paper


title: T-ALL tumor 43 (aneuploid)

description:
43Th
aneuploid; genotype in Sup data 1 accompanying paper


title: genomic DNA from normal colon biopsies M020C

value: high


title: peripheral blood 5.09

description: Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

value: Blood


title: peripheral blood 4.20


title: peripheral blood 5.07


title: T-ALL tumor 14 (aneuploid)

description:
14Th
aneuploid; genotype in Sup data 1 accompanying paper

value: non-CIN


title: T-ALL tumor 17 (aneuploid)

description:
17Th
aneuploid; genotype in Sup data 1 accompanying paper

value: male


title: genomic DNA from normal colon biopsies K724C


title: genomic DNA from normal colon biopsies M022A

value: proximal


title: genomic DNA from normal colon biopsies 95C

value: user


title: T-ALL tumor 12 (aneuploid)

description:
12Th
aneuploid; genotype in Sup data 1 accompanying paper

value: T-ALL


title: genomic DNA from normal colon biopsies 60A


title: genomic DNA from normal colon biopsies 373C


title: T-ALL tumor 11 (aneuploid)

description:
11Th
aneuploid; genotype in Sup data 1 accompanying paper


title: genomic DNA from normal colon biopsies 137A


title: T-ALL tumor 13 (aneuploid)

description:
13Th
aneuploid; genotype in Sup data 1 accompanying paper


title: gul2-1 bri1-5 mutant, biological rep2

city: Seoul

first: Sunghwa

last: Choe

address: Gwanak-Gu Shillim-Dong

department: Biological sciences

country: South Korea

institute: Seoul National University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis (ATH1) GenChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: All raw data from each array were processed by background correction and quantile normalization using CodeLink from the R package (Gautier et al., 2004). In addition, all array data were processed to calculate the robust multi-array average (RMA) (Irizarry et al., 2003) using AFFY (Gautier et al., 2004). Expression values were computed by applying the RMA model of probespecific correction to perfect-match probes. These corrected probe values were then subjected to quantile normalization (Bolstad et al., 2003). The resulting RMA expression values were log2  ransformed.

organism: Arabidopsis thaliana

source_name: 7d-old gul2-1bri1-5 double mutant seedling grown under red light

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

growth_protocol: Arabidopsis seedlings of each genotype were grown in controlled environment of growth chamber. Seedlings were grown for 7 days under continuous red light.

extract_protocol: Total RNAs were prepared using Quiagen Rneasy kit

tag: genotype/variation

value: gul2-1 bri1-5 mutant

value: 7 day-old whole seedlings


title: genomic DNA from normal colon biopsies 56C


title: peripheral blood 4.13

value: not applicable

value: Male

value: carcinoma


title: T-ALL tumor 10 (aneuploid)

description:
10Th
aneuploid; genotype in Sup data 1 accompanying paper

value: CIN

value: Mps1DK p53f/f of Mps1DK p53f/+ tumor


title: T-ALL tumor 7 (aneuploid)

description:
7Th
aneuploid; genotype in Sup data 1 accompanying paper

value: female

value: sex-matched liver (mix several litter mates)


title: genomic DNA from liver (fetal) control

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: control

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

source_name: liver (fetal) control

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extraction was performed using standard methods

tag: disease status

value: control


title: kidney cortex 4.13

value: Kidney


title: genomic DNA from lung (fetal) control

description: control

source_name: lung (fetal) control


title: genomic DNA from liver, child_3

source_name: liver, child_3

value: patient


title: gul2-1 bri1-5 mutant, biological rep1


title: gul2-1 mutant, biological rep3

source_name: 7d-old gul2-1 mutant seedling grown under red light

value: gul2-1 mutant


title: gul2-1 mutant, biological rep2


title: kidney cortex 4.10


title: ccRCC tumor 4.10

description: Genomic DNA extracted from clear cell renal cell carcinoma tumors was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).

source_name: clear cell renal cell carcinoma

value: metastasized tumor


title: peripheral blood 4.10

value: Blood


title: kidney cortex 4.05

value: Female


title: kidney cortex 4.20


title: genomic DNA from lung, child_3

description: control

source_name: lung, child_3


title: gul2-1 mutant, biological rep1


title: genomic DNA from muscle, child_3

source_name: muscle, child_3


title: genomic DNA from muscle (fetal) control

description: control

source_name: muscle (fetal) control


title: Wild type, biological rep3

source_name: 7d-old wild type seedling grown under red light

value: Wild type


title: bri1-5 mutant, biological rep3

source_name: 7d-old bri1-5 mutant seedling grown under red light

value: bri1-5 mutant


title: bri1-5 mutant, biological rep2

value: 7 day-old whole seedlings


title: genomic DNA from muscle (fetal) control, sample b

description: control

source_name: muscle (fetal) control, sample a


title: bri1-5 mutant, biological rep1


title: peripheral blood 4.05

value: not applicable


title: genomic DNA from muscle (fetal) control, sample a

description: control


title: ccRCC tumor 4.13

value: Male


title: kidney cortex 4.08

source_name: kidney cortex

value: carcinoma


title: gul2-1 bri1-5 mutant, biological rep3

value: gul2-1 bri1-5 mutant


title: kidney cortex 3.19


title: ccRCC tumor 4.08

value: un-metastasized tumor


title: genomic DNA from muscle, child_1, sample b

source_name: muscle, child_1, sample b


title: Wild type, biological rep1


title: genomic DNA from muscle, child_1, sample a

source_name: muscle, child_1, sample a


title: genomic DNA from fibroblasts (scrotal), control sample 15b

description: control


title: peripheral blood 3.12

source_name: peripheral blood


title: Wild type, biological rep2


title: peripheral blood 3.19


title: genomic DNA from fibroblasts (scrotal), control sample 13b

description: control


title: kidney cortex 3.14


title: genomic DNA from fibroblasts (scrotal), control sample 15a

description: control


title: peripheral blood 3.14


title: peripheral blood 3.06


title: genomic DNA from fibroblasts (scrotal), control sample 12b

description: control


title: kidney cortex 3.01


title: peripheral blood 3.01


title: genomic DNA from fibroblasts (scrotal), control sample 13a

description: control


title: genomic DNA from fibroblasts (scrotal), control sample 12a

description: control


title: genomic DNA from fibroblasts (scrotal), control sample 11b

description: control


title: genomic DNA from fibroblasts (scrotal), control sample 11a

description: control


title: male CLC -197,C159-261

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

hyb_protocol: according to Agilent instructions

scan_protocol: slides were scanned at a resolution of 3 μm with a G2505C DNA Microarray Scanner (Agilent Technologies)

data_processing: raw data filtered for wabg (wabg=1 for at least 4 samples), vsn normalisation with vsn2 method of R-package vsn

source_name: liver

label_protocol: Cy3-labeled cRNA was produced with the Quick Amp Labeling Kit, One-Color (Agilent Technologies)

growth_protocol: Mice were kept under SPF conditions, and were fed stadardized rodent chow (V1536, Ssniff, Soest, DE).

extract_protocol: trizol

treatment_protocol: Mice of all groups scheduled for RNA analysis were put on a grid at 9 o’clock a.m. with no access to chow, where they could not reach other organic material (bedding, feces). Water was given ad libitum. Sections started exactly 6 hours later and performed as fast as possible. Preparation of liver for RNA analysis was done by extracting a central piece of the left liver lobe, ca. 4x4x8mm. This work was done on an ice-cooled glass plate (ca. 4°C). The piece was stored in RNAlater® (Ambion [part of Invitrogen], Darmstadt, DE) at 4°C overnight and was transferred to a -20 or -80°C freezer on the next day.

value: liver

tag: genotype

value: fl/fl | +/wt

value: 6 week

tag: date of birth

tag: Sex

value: male

tag: transgene


title: kidney cortex 2.44

value: Kidney


title: male CLC -105,200/201-246

value: fl/fl | wt/wt


title: male CLC -197,C159-260


title: genomic DNA from fibroblasts (scrotal), control sample 9b

description: control

value: control


title: male CLC -105,200/201-245


title: genomic DNA from fibroblasts (scrotal), control sample 9a

description: control


title: peripheral blood 2.44

value: Blood


title: male CLC -105,200/201-244


title: genomic DNA from fibroblasts (scrotal), control sample 5b

description: control


title: kidney cortex 2.42

value: Female


title: peripheral blood 2.42


title: kidney cortex 2.08


title: male CLC -105,200/201-243


title: genomic DNA from fibroblasts (scrotal), control sample 5a

description: control


title: male CLC -220/219,C156-294

value: 3 week


title: peripheral blood 2.29


title: peripheral blood 2.07


title: kidney cortex 2.29


title: peripheral blood 2.08


title: male CLC -220/219,C156-293


title: kidney cortex 2.07


title: genomic DNA from fibroblasts (scrotal), control sample 4a

description: control


title: male CLC -220/219,C156-292


title: genomic DNA from fibroblasts (scrotal), control sample 3b

description: control


title: male CLC -190,195-275


title: genomic DNA from fibroblasts (scrotal), control sample 4b

description: control


title: genomic DNA from fibroblasts (scrotal), control sample 3a

description: control


title: male CLC -190,195-274


title: kidney cortex 2.04


title: genomic DNA from fibroblasts, child_2, sample b

source_name: fibroblasts, child_2, sample b

value: patient


title: peripheral blood 2.04


title: genomic DNA from lymphoblastoid cell line, control d

description: control

source_name: lymphoblastoid cell line, control d


title: male CLC -190,195-273


title: male CLC -220/219-C156-291

value: 1 week


title: genomic DNA from fibroblasts, child_2, sample a

source_name: fibroblasts, child_2, sample a


title: male CLC -217,189-285


title: genomic DNA from lymphoblastoid cell line, control b

description: control

source_name: lymphoblastoid cell line, control b


title: male CLC -220/219-C156-289


title: male CLC -217,189-284


title: genomic DNA from lymphoblastoid cell line, control c

description: control

source_name: lymphoblastoid cell line, control c


title: genomic DNA from lymphoblastoid cell line, control a

description: control

source_name: lymphoblastoid cell line, control a


title: genomic DNA from lymphoblastoid cell line, child_2, sample b


title: genomic DNA from lymphoblastoid cell line, child_2, sample a


title: genomic DNA from peripheral blood, healthy control t

description: control

source_name: peripheral blood, healthy control t


title: Blood B2126b

city: Aarhus N

first: Philippe

last: Lamy

address: Brendstrupgårdsvej 100

department: Department of molecular medecine

country: Denmark

institute: MOMA

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

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

data_processing:
Call and signal intensities were done using the birdseedv2 algorithm. For copy number, CEL files were analysed using the arome.affymetrix R package. All probes from each allele were combined in one value per probeset (SNP or CN). Segmentation was done using the Rseg R package.
The log2 ratio was calculated as the log2 ratio between the theta estimates from the tumor sample and the theta estimates from the blood sample from the same patient for chromosomes 1 to 22 and chromosome X.

source_name: Blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA from the paired-WGS set was extracted from frozen tumor tissue and blood using the Puregene DNA purification kit (Gentra Systems, Minneapolis, MN, USA). Amplification Kit, GE Healthcare)

tag: cell type

value: Blood cells


title: genomic DNA from peripheral blood, healthy control r

description: control

source_name: peripheral blood, healthy control r


title: Urothelial bladder tumor B1992s1

source_name: Bladder Carcinoma

value: Bladder Carcinoma

value: Carcinoma cells

tag: gender


title: Blood B1992b


title: Urothelial bladder tumor B1992s3


title: Urothelial bladder tumor B1829s3

value: Male


title: Blood B1829b


title: genomic DNA from peripheral blood, healthy control o

description: control

source_name: peripheral blood, healthy control o


title: genomic DNA from peripheral blood, healthy control s

description: control

source_name: peripheral blood, healthy control s


title: genomic DNA from peripheral blood, healthy control q

description: control

source_name: peripheral blood, healthy control q


title: X462_Brain Melanoma Metastasis

description: Copy number calls only.

data_processing: Copy number variations were called using the CN5 algorithm (.CNCHP files) using Affymetrix Genotyping Console 4.0 under good laboratory practice (GLP) conditions. Sample table and .CNCHP data are based on genome build NCBI36 (hg18).

source_name: Metastatic tumor tissue

tag: disease state

value: metastatic melanoma

tag: cancer stage

value: IV

tag: patient group

value: brain melanoma metastasis

tag: pair number

value: unpaired

value: tissue

tag: isolation method

value: cell line isolated via passage


title: genomic DNA from peripheral blood, healthy control n

description: control

source_name: peripheral blood, healthy control n


title: genomic DNA from peripheral blood, healthy control p

description: control

source_name: peripheral blood, healthy control p


title: Urothelial bladder tumor B1829s1

tag: tissue


title: Urothelial bladder tumor B2126s1


title: X463_Brain Melanoma Metastasis

description: Copy number calls only.


title: Urothelial bladder tumor B2126s4


title: genomic DNA from peripheral blood, healthy control m

description: control

source_name: peripheral blood, healthy control m


title: X465_Brain Melanoma Metastasis

description: Copy number calls only.


title: genomic DNA from peripheral blood, healthy control k

description: control

source_name: peripheral blood, healthy control k


title: genomic DNA from peripheral blood, healthy control j

description: control

source_name: peripheral blood, healthy control j


title: X461_Brain Melanoma Metastasis

description: Copy number calls only.


title: genomic DNA from peripheral blood, healthy control h

description: control

source_name: peripheral blood, healthy control h


title: X460_Brain Melanoma Metastasis

description: Copy number calls only.


title: X464_Brain Melanoma Metastasis

description: Copy number calls only.


title: X457_Brain Melanoma Metastasis

description: Copy number calls only.


title: X458_Brain Melanoma Metastasis

description: Copy number calls only.


title: X455_Brain Melanoma Metastasis

description: Copy number calls only.


title: X456_Brain Melanoma Metastasis

description: Copy number calls only.


title: genomic DNA from peripheral blood, healthy control l

description: control

source_name: peripheral blood, healthy control l


title: genomic DNA from peripheral blood, healthy control g

description: control

source_name: peripheral blood, healthy control g


title: genomic DNA from peripheral blood, healthy control e

description: control

source_name: peripheral blood, healthy control e


title: genomic DNA from peripheral blood, healthy control d

description: control

source_name: peripheral blood, healthy control d


title: genomic DNA from peripheral blood, healthy control c

description: control

source_name: peripheral blood, healthy control c


title: genomic DNA from peripheral blood, healthy control f

description: control

source_name: peripheral blood, healthy control f


title: X454_Brain Melanoma Metastasis

description: Copy number calls only.


title: X830_Liver Melanoma Metastasis

description: Copy number calls only.

value: liver melanoma metastasis


title: genomic DNA from peripheral blood, healthy control b

description: control

source_name: peripheral blood, healthy control b

value: control


title: genomic DNA from peripheral blood, healthy control i

description: control

source_name: peripheral blood, healthy control i


title: X453_Brain Melanoma Metastasis

description: Copy number calls only.


title: X831_Liver Melanoma Metastasis

description: Copy number calls only.


title: genomic DNA from peripheral blood, healthy control a

description: control

source_name: peripheral blood, healthy control a


title: genomic DNA from peripheral blood, father, sample a

description: control

source_name: peripheral blood, father, sample b


title: X452_Brain Melanoma Metastasis

description: Copy number calls only.

source_name: Metastatic tumor tissue


title: X459_Brain Melanoma Metastasis

description: Copy number calls only.


title: genomic DNA from peripheral blood, mother, sample b

description: control

source_name: peripheral blood, mother, sample b


title: genomic DNA from peripheral blood, child_2, sample b

source_name: peripheral blood, child_2, sample b


title: genomic DNA from peripheral blood, mother, sample a

description: control


title: X826_Lung Melanoma Metastasis

description: Copy number calls only.

value: lung melanoma metastasis


title: genomic DNA from peripheral blood, father, sample b

description: control


title: genomic DNA from peripheral blood, child_2, sample a

source_name: peripheral blood, child_2, sample a


title: BRCA2 knockout technical replicate 3

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

country: Canada

institute: British Columbia Cancer Agency

description: HCT116 BRCA2 knockout cells

hyb_protocol: Labelled RNA was probed on Human Exon Array 1.0 ST chips (Affymetrix, Santa Clara, California) for gene expression analysis and scanned at the CTAG Facility of the British Columbia Cancer Agency, Vancouver, BC, Canada.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix)

data_processing:
The microarray data were analyzed using the oneChannelGUI package of the R statistical programming language (R version 2.11.1, R Development Core Team, 2010).  Raw intensity calls were normalized using quantile normalization (Bolstad et al 2003) and probeset summarization (core plus extended) undertaken with RMA (Irizarry et al 2003)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HCT116 BRCA2 knockout cells

label_protocol: Samples with a resulting total RNA of 1 µg or greater and with a RNA integrity number (RIN) of 7.0 or greater were used and the whole transcript sense target labeling procedure followed the Affymetrix protocol, including the RiboMinus™ rRNA removal step. Three technical replicates were compared for each of the genotypes (HCT116 homozygous BRCA2-/- and isogenic wild type) for a total of six experiments.

growth_protocol: Cells were incubated in 6mm plates.  HCT116 human colon carcinoma cells were maintained in McCoy’s 5A media (Gibco, Invitrogen) supplemented with 10 % fetal bovine serum (Sigma-Aldrich, St. Louis, MO) and 20 mM L-glutamine, at 37 C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated from frozen HCT116 samples (three wild type and three BRCA2-/-) using QIAzol™ lysis reagent (Qiagen, Maryland, USA). The tissues were homogenized in 800 µL QIAzol and transferred to Phase Lock Gel tubes (2 mL, heavy) (Eppendorf AG, Hamburg, Germany) to which 200 µL chloroform was added. Samples were centrifuged and the aqueous phase was removed and transferred to a new tube with an equal volume of isopropanol. After centrifugation, the supernatant was removed from the precipitated RNA pellets, and the pellets were washed with 70% ethanol. The air-dried RNA was dissolved in RNase/DNase free water and stored frozen at -80 °C. Total RNA samples were analyzed on a NanoDrop (Thermo Fisher Scientific, Waltham, MA) spectrophotometer to determine RNA quality and concentration. One µL of the RNA (was adjusted within a range of 25-500 ng/µL) was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) using the RNA 6000 Nano kit.

treatment_protocol: The wild-type HCT116 line was obtained from ATCC (ATCC number CCL-247). Isogenic BRCA2-deficient lines were generated by sequentially targeting both alleles of the BRCA2 gene by homologous recombination (J. Xian and C. Caldas).

tag: cell line

value: BRCA2 knockout


title: X451_Brain Melanoma Metastasis

description: Copy number calls only.


title: X827_Lung Melanoma Metastasis

description: Copy number calls only.


title: X829_Liver Melanoma Metastasis

description: Copy number calls only.


title: BRCA2 knockout technical replicate 2

description: HCT116 BRCA2 knockout cells


title: BRCA2 knockout technical replicate 1

description: HCT116 BRCA2 knockout cells


title: X824_Lung Melanoma Metastasis

description: Copy number calls only.


title: X828_Liver Melanoma Metastasis

description: Copy number calls only.


title: Wild type technical replicate 1

description: HCT116 wild type cells

source_name: HCT116 wild type cells

value: Wild type


title: X822_Bowel Melanoma Metastasis

description: Copy number calls only.

value: bowel melanoma metastasis


title: Wild type technical replicate 3

description: HCT116 wild type cells


title: X825_Lung Melanoma Metastasis

description: Copy number calls only.


title: Wild type technical replicate 2

description: HCT116 wild type cells


title: O874_Poor LN

description:
Lymph node melanoma metastasis, poor': patient had metastatic melanoma to a lymph node, and had disease-free survival <2 years.
Copy number calls only.

value: III

value: lymph node melanoma metastasis, poor

value: cell line


title: O876_Good LN

description:
Lymph node melanoma metastasis, good': patient had metastatic melanoma to a lymph node, and had disease-free survival >5 years.
Copy number calls only.

value: lymph node melanoma metastasis, good


title: O875_Good LN


title: Breast Carcinoma 133.placebo

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

hyb_protocol: affymetrix

scan_protocol: affymetrix

data_processing: RMA

source_name: Breast Carcinoma

label_protocol: biotin label

value: N

tag: plasma genistein (ng/ml)

tag: menopausal status

value: post

tag: treatment

value: placebo

tag: predicted molecular subtype

value: LumB


title: O878_Poor LN

value: metastatic melanoma

value: unpaired


title: O877_Poor LN

value: cell line isolated via passage


title: X821_Bowel Melanoma Metastasis

description: Copy number calls only.

value: IV

value: tissue


title: Breast Carcinoma 131.soy

value: P

value: pre

value: soy


title: Breast Carcinoma 136.placebo

value: LumA


title: Breast Carcinoma 129.soy


title: Breast Carcinoma 124.soy


title: Breast Carcinoma 122.soy

value: Basal


title: Breast Carcinoma 121.soy


title: X823_Bowel Melanoma Metastasis

description: Copy number calls only.

value: bowel melanoma metastasis


title: X820_Bowel Melanoma Metastasis

description: Copy number calls only.


title: Breast Carcinoma 103.placebo


title: O872_Poor LN

value: III

value: lymph node melanoma metastasis, poor

value: cell line


title: Breast Carcinoma 105.soy


title: O873_Poor LN


title: O866_Good LN

value: lymph node melanoma metastasis, good


title: O868_Poor LN


title: O870_Poor LN


title: O865_Poor LN


title: O869_Poor LN


title: Breast Carcinoma 101.placebo

value: placebo


title: Breast Carcinoma 95.soy

value: post


title: Breast Carcinoma 94.soy


title: O861_Poor LN

value: metastatic melanoma


title: O871_Good LN

value: unpaired


title: O867_Good LN

value: cell line isolated via passage


title: Breast Carcinoma 91.placebo


title: Breast Carcinoma 88.placebo

value: LumB


title: Breast Carcinoma 87.soy


title: Breast Carcinoma 80.placebo


title: Breast Carcinoma 81.placebo

value: N


title: O864_Good LN


title: Breast Carcinoma 77.soy

value: P


title: Breast Carcinoma 78.soy

value: pre


title: Breast Carcinoma 75.placebo


title: Breast Carcinoma 73.soy

value: soy


title: O858_Good LN


title: Breast Carcinoma 76.placebo

value: LumA


title: O857_Good LN


title: O860_Good LN


title: O863_Good LN


title: O853_Good LN


title: Breast Carcinoma 72.soy


title: Breast Carcinoma 69.soy


title: O856_Good LN


title: O854_Good LN


title: Breast Carcinoma 68.soy

value: Basal


title: O851_Poor LN


title: Breast Carcinoma 66.placebo


title: Breast Carcinoma 61.soy


title: Breast Carcinoma 65.soy


title: O850_Poor LN


title: O844_Good LN


title: O855_Poor LN


title: O862_Poor LN


title: Breast Carcinoma 56.soy


title: O848_Good LN


title: O843_Poor LN


title: Breast Carcinoma 49.placebo


title: Breast Carcinoma 50.placebo


title: HL-1_PCI_6h_rep.3

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

hyb_protocol: Hybridization was in agreement with the Whole-Genome Gene Expression Assay protocol from Illumina.

scan_protocol: Arrays were read with the detection system iScan from Illumina.

data_processing: Raw data were pre-processed using GenomeStudio (v 1.9.0). Robust spline normalization (rsn) and detection filtering were performed by the lumi package within R statistics software and Bioconductor for HL-1 and NNC samples separately. One outlier LPS 12h (rep.4) was detected and removed.

source_name: HL-1 cardiomyocytes, stimulated with murine PCI serum, 6h

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).

growth_protocol: All cells were grown in an incubator at 37°C, in an atmosphere of 5 % CO2 and 95 % air at a relative humidity of approximately 95 %.

extract_protocol: RNA was isolated from cardiomyocytes (HL-1 cells, murine neonatal cardiomyocytes) using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.

treatment_protocol: HL-1 cells and murine neonatal cardiomyocytes (NNC) were cultivated in 12- and 6-well plates, respectively, until required confluence was reached. For stimulation experiments the appropriate culture medium was prepared serum-free and supplemented with the following additives immediately before stimulation: a) 5 % murine control serum, b) 5 % murine PCI serum, c) 5 % murine control serum + 200 ng/ml LPS (from Escherichia coli 0111:B4; Sigma-Aldrich), d) 5 % murine control serum + cytokine mix. The mix consisted of (final concentrations): 50 ng/ml TNF-α, 10 ng/ml IL-1β, 50 ng/ml IL-6, 10 ng/ml IFN-γ (all cytokines purchased from Hiss/Novitec) and 100 ng/ml LPS. Stimulation was performed for 6 or 12 h at 37°C

value: immortalized murine cardiomyocytes


title: O842_Poor LN

value: III


title: O859_Good LN


title: Breast Carcinoma 48.placebo


title: Breast Carcinoma 47.soy


title: X840_CTC

description: SNP and copy number calls.

source_name: Blood

value: paired

value: CTC (amplified)

value: GM3, GM2, GD11


title: Breast Carcinoma 54.soy


title: O840_Poor LN

value: lymph node melanoma metastasis, poor

value: cell line


title: HL-1_PCI_6h_rep.2


title: HL-1_PCI_6h_rep.1


title: Breast Carcinoma 53.soy


title: Breast Carcinoma 44.placebo

value: post

value: placebo


title: U015_Tissue

description: SNP and copy number calls.

value: metastatic melanoma

value: tissue (amplified)

value: cell line isolated via passage


title: HL-1_CON_6h_rep.3

source_name: HL-1 cardiomyocytes, stimulated with murine control serum, 6h


title: T464_Tissue

description: SNP and copy number calls.


title: HL-1_CON_6h_rep.4


title: Breast Carcinoma 43.soy

value: N


title: HL-1_CON_6h_rep.2


title: Breast Carcinoma 27.soy

value: P

value: LumB


title: O839_Poor LN

value: unpaired


title: Breast Carcinoma 33.placebo

value: pre

value: LumA


title: HL-1_CON_6h_rep.1

value: immortalized murine cardiomyocytes


title: T462_Tissue

description: SNP and copy number calls.

value: III

value: paired


title: HL-1_PCI_6h_rep.4


title: Breast Carcinoma 23.placebo


title: Breast Carcinoma 24.soy

value: soy


title: NNC_PCI_12h_rep.4

description: NNC

source_name: isolated neonatal cardiomyocytes, 12h after stimulation with PCI serum

value: isolated neonatal cardiomyocytes, murine


title: Breast Carcinoma 20.placebo


title: Breast Carcinoma 25.soy


title: NNC_LPS_6h_rep.4

description: NNC

source_name: isolated neonatal cardiomyocytes, 6h after stimulation with LPS


title: NNC_CM_6h_rep.4

description: NNC

source_name: isolated neonatal cardiomyocytes, 6h after stimulation with cytokine mix


title: NNC_CM_12h_rep.4

description: NNC

source_name: isolated neonatal cardiomyocytes, 12h after stimulation with cytokine mix


title: Breast Carcinoma 15.soy

value: Basal


title: U014_CTC

description: SNP and copy number calls.

value: CTC (amplified)

value: GM3, GM2, GD13


title: NNC_CON_12h_rep.4

description: NNC

source_name: isolated neonatal cardiomyocytes


title: X841_Tissue

description: SNP and copy number calls.

value: metastatic melanoma


title: T455_CTC

description: SNP and copy number calls.

value: GM3, GM2, GD11


title: Breast Carcinoma 13.placebo

value: post

value: placebo


title: G319 rep 2

city: Boston

first: Svitlana

last: Tyekucheva

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: See manufacturer's website: www.nanostring.com

data_processing: background subtracted counts were multiplied by scaling factors proportional to the sum of counts for spiked-in positive control probes to account for individual assay efficiency variation, and to the geometric average of the housekeeping gene probes (CLTC, GAPDH, GUSB, HPRT1, PGK1 and TUBB) to account for variability in the mRNA content. Background signal was calculated as a median value of the negative hybridization control probes. Normalized counts were log-transformed.

source_name: ovarian cancer

extract_protocol: RNA was extracted from paraffin scrolls using the RNeasy FFPE kit (Qiagen) with modification.  In brief, 1 ml of xylene was first added to a 25 μm paraffin scroll, vortexed vigorously for 10 sec and centrifuged at full speed for 2 min.  Supernatant was then removed and 1 ml of ethanol (100%) was added to the pellet, mixed by vortexing and centrifuged at full speed for 2 min.  Supernatant was removed and the tube was incubated at room temperature from 10 min with lid opened.  Subsequently, RNA was extracted using reagents provided in the RNeasy FFPE extraction kit according to the manufacturer’s instruction.  Finally, purified RNA was eluted from the RNeasy MinElute spin column using 30 μl RNase-free water.

tag: block age

tag: diagnosis

value: serous carcinoma

tag: percent tumor

tag: percent necrosis

tag: amount

tag: tissue type

value: ovarian cancer tumor


title: NNC_CON_6h_rep.4

description: NNC

tag: cell type


title: G319 rep

scan_protocol: See manufacturer's website: www.nanostring.com


title: NNC_PCI_6h_rep.4

description: NNC

source_name: isolated neonatal cardiomyocytes, 6h after stimulation with PCI serum


title: Breast Carcinoma 8.placebo

value: P

value: LumB


title: NNC_CM_6h_rep.3

description: NNC


title: NNC_CM_12h_rep.3

description: NNC


title: Breast Carcinoma 6.placebo


title: Breast Carcinoma 2.soy

value: pre


title: NNC_LPS_12h_rep.3

description: NNC

source_name: isolated neonatal cardiomyocytes, 12h after stimulation with LPS


title: NNC_LPS_6h_rep.3

description: NNC


title: NNC_PCI_12h_rep.3

description: NNC


title: G800 rep

label_protocol: See manufacturer's website: www.nanostring.com

value: clear cell carcinoma


title: NNC_CON_12h_rep.3

description: NNC


title: T454_CTC

description: SNP and copy number calls.

tag: disease state

tag: cancer stage

value: III

value: GM3, GM2, GD10


title: G901 rep


title: Breast Carcinoma 5.soy

value: N

value: soy


title: Breast Carcinoma 3.soy


title: T460_Tissue

description: SNP and copy number calls.

source_name: Metastatic tumor tissue

tag: patient group

value: paired

tag: pair number

value: tissue (amplified)

value: cell line isolated via passage


title: G765 rep


title: Follicular Lymphoma_68

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description: Gene expression data from  pretreated FL biopsy

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Affymetrix Scanning Protocol

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. The trimmed mean target intensity of each array was arbitrarily set to 100. Further supervised analysis (e.g., mutant vs WT) was carried using BRB-ArrayTools version (3.7.0).

source_name: Pre-treated fresh frozen FL biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All  tissue biopsies were fresh frozen and stored below -70 degree C prior to total RNA isolation.

extract_protocol: Total RNA was extracted with AllPrep DNA/RNA Mini Kit  (Qiagen, Valencia, CA) and quality was estimated with Bioanalyzer( Agilent Technologies Genomics)  prior to gene expression profiling.

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction

tag: tissue

value: Follicular Lymphoma

tag: ezh2 mutation

value: WT

tag: age

tag: fl grade


title: NNC_CON_6h_rep.3

description: NNC

value: isolated neonatal cardiomyocytes, murine


title: G403 rep


title: Follicular Lymphoma_67


title: Follicular Lymphoma_66


title: T461_Tissue

description: SNP and copy number calls.

value: metastatic melanoma

tag: isolation method


title: G969 rep

value: serous carcinoma


title: T457_CTC

description: SNP and copy number calls.

value: CTC (amplified)

value: GM3, GM2, GD12


title: T452_CTC

description: SNP and copy number calls.

value: GM3, GM2, GD8


title: NNC_LPS_12h_rep.2

description: NNC


title: T453_CTC

description: SNP and copy number calls.

value: GM3, GM2, GD9


title: NNC_PCI_6h_rep.3

description: NNC


title: G653 rep

value: ovarian cancer tumor


title: NNC_CM_12h_rep.2

description: NNC


title: Follicular Lymphoma_64


title: Follicular Lymphoma_63


title: Breast Carcinoma 4.placebo

value: P

tag: plasma genistein (ng/ml)

tag: menopausal status

value: pre

tag: treatment

value: placebo

tag: predicted molecular subtype

value: LumA


title: NNC_PCI_12h_rep.2

description: NNC


title: Follicular Lymphoma_65


title: T458_Tissue

description: SNP and copy number calls.

value: III

value: paired


title: G678 rep

tag: block age

tag: diagnosis

tag: percent tumor

tag: percent necrosis


title: G366 rep

value: clear cell carcinoma

tag: amount

tag: tissue type


title: G794 rep


title: G776 rep


title: T459_Tissue

description: SNP and copy number calls.

tag: disease state

tag: cancer stage

tag: patient group

tag: cell type

value: tissue (amplified)

value: cell line isolated via passage


title: Follicular Lymphoma_61

tag: tissue

value: Follicular Lymphoma

tag: ezh2 mutation

value: WT

tag: age


title: G319

value: serous carcinoma


title: O846_Poor LN

value: metastatic melanoma

value: lymph node melanoma metastasis, poor

tag: pair number

value: unpaired

value: cell line

tag: isolation method


title: NNC_LPS_6h_rep.2

description: NNC

value: isolated neonatal cardiomyocytes, murine


title: NNC_CM_6h_rep.2

description: NNC


title: G901

value: ovarian cancer tumor


title: Follicular Lymphoma_62

tag: fl grade


title: Follicular Lymphoma_60


title: NNC_CON_12h_rep.2

description: NNC


title: NNC_PCI_6h_rep.2

description: NNC


title: G800


title: Follicular Lymphoma_57


title: T451_CTC

description: SNP and copy number calls.

value: CTC (amplified)

value: GM3, GM2, GD7


title: Follicular Lymphoma_56


title: Follicular Lymphoma_59


title: NNC_PCI_12h_rep.1

description: NNC


title: NNC_CM_12h_rep.1

description: NNC


title: Follicular Lymphoma_58


title: NNC_CON_6h_rep.2

description: NNC


title: NNC_CON_12h_rep.1

description: NNC


title: NNC_LPS_12h_rep.1

description: NNC


title: Follicular Lymphoma_55


title: G800 rep 2


title: G403


title: G969


title: Follicular Lymphoma_54


title: G653


title: G765


title: G678


title: Follicular Lymphoma_69


title: G776


title: G366


title: G794


title: p31 Normal rep2 X3725137N_100.1

source_name: prostate

extract_protocol: Areas of high-density tumor were identified, and 0.6 mm punches were taken from both tumor and adjacent non-tumor prostatic tissue for RNA extraction. The cores were deparaffinized using 800 μL Citrisolv (Fisher Scientific, Pittsburgh, PA) at 60°C for 20 minutes followed by 1.2 mL Citrisolv:absolute alcohol (2:1) at room temperature for 10 minutes. Cores were subsequently washed with absolute alcohol, dried at 55°C, and incubated overnight at 45°C in 300 μL lysis buffer (10 mM NaCl, 500 mM Tris [pH 7.6], 20 mM EDTA, 1% sodium dodecyl sulfate) containing 1 mg/mL proteinase K (Ambion, Austin, TX).  RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion). Post tissue digestion, following the manufacturer’s protocol, samples were incubated in 10x DNase (Ambion) and column purified to elute RNA.

value: Normal prostate

tag: gleason score


title: p8 Tumor rep2 X1675210T_100.2

tag: block age

value: Prostate tumor


title: NNC_CM_6h_rep.1

description: NNC


title: Follicular Lymphoma_49


title: Follicular Lymphoma_48


title: p8 Normal X1675210N_100


title: p8 Tumor rep X1675210T_100.1


title: NNC_CON_6h_rep.1

description: NNC


title: NNC_LPS_6h_rep.1

description: NNC


title: Follicular Lymphoma_53


title: p8 Normal X1675210N_200


title: p31 Tumor rep2 X3725137T_100.1


title: p19 Normal X3739759N_150


title: Follicular Lymphoma_51


title: Follicular Lymphoma_47


title: Follicular Lymphoma_52


title: NNC_PCI_6h_rep.1

description: NNC


title: p31 Tumor rep X3725137T_200


title: Follicular Lymphoma_50


title: Follicular Lymphoma_45


title: p16 Normal rep X1535389N_100


title: p14 Tumor rep2 X2927390T_100


title: Follicular Lymphoma_46


title: Follicular Lymphoma_44


title: Follicular Lymphoma_43


title: Follicular Lymphoma_40


title: Follicular Lymphoma_41


title: Follicular Lymphoma_42


title: Follicular Lymphoma_38


title: p14 Normal X2927390N_100


title: p19 Tumor rep2 X3739759T_200.1


title: Follicular Lymphoma_39


title: Naïve_B cell_ replicate2

description: Gene expression data from normal Naïve B cells

source_name: Purified from normal reactive tonsil

value: Naïve_B cell


title: Naïve_B cell_ replicate1


title: p31 Normal rep X3725137N_200.2


title: p19 Normal X3739759N_100


title: p14 Normal X2927390N_200


title: p19 Tumor rep X3739759T_200


title: p14 Tumor rep X2927390T_200.1


title: p16 Tumor X1535389T_200


title: p31 Normal X3725137N_100


title: Centroblast_replicate2

description: Gene expression data from normal centroblasts

value: Centroblast


title: Centrocyte_replicate2

description: Gene expression data from normal centrocyte

value: Centrocyte


title: Centroblast_replicate1


title: p14 Tumor X2927390T_200


title: Follicular Lymphoma_30


title: Follicular Lymphoma_29


title: p31 Tumor X3725137T_100


title: Follicular Lymphoma_27


title: Follicular Lymphoma_28


title: Sporozoite

city: Seattle

first: Robert

middle: D

last: Morrison

state: WA

address: 307 Westlake Ave N

institute: Center for Infectious Disease Research

description: SPZ

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

organism: Plasmodium falciparum

source_name: cultured NF54 sporozoites

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Blood stage Plasmodium falciparum (Strain NF54) were cultured in vitro in erythrocyte isolated from whole blood (Trager and Jensen, Science, 1976,;193(4254):673-5); Sporozoites were isolated from dissected salivary gland from infected mosquitoes (Ozaki, Gwadz et al. J Parasitol. 1984, 70(5):831; Guebre-Xabier, Schwenk et al. Eur J Immunology, 1999; 29(12):3978); HC-04 cells were infected with Plasmodium falciparum sporozoites [growth medium DMEM/F12 supplemented with 10% FBS, Penicillin (100 U.ml) and Streptomycine (100 ug.ml)] and infected cells were isolated at 24 and 48h time post infection for RNA Isolation (Sinns P et al., Methods Mol Biol, 2013, 923; 385))

extract_protocol: Total RNA was isolated from mixed blood stage, sporozoites and at two different time points of Liver stage using Qiagen Rneasy mini kit (Qiagen, USA). RNA was colum purified and DNA were removed by oncolum DNAse-I digestion (Qiagen, USA). RNA quality was verified by  Bio-analyzer (Agilent, USA). RNA samples were sent to Roche-Nimblegen for hybridizztion (Roche Nimblegen, Inc, USA).

treatment_protocol: Mixed blood stage, SPZ and isolated liver stage were washed separately with RNAse free PBS.

tag: strain

tag: developmental stage

value: sporozoite stage


title: Centrocyte_replicate1


title: LiverStage_24hour

source_name: NF54 sporozoites axenically cultured for 24 hours

value: early liver stage


title: p16 Normal X1535389N_200


title: p19 Tumor X3739759T_100


title: LiverStage_48hour

source_name: NF54 sporozoites axenically cultured for 48 hours


title: BloodStage_NonAnemic_4

source_name: peripheral blood field isolate

value: mixed blood stage


title: BloodStage_NonAnemic_5


title: Follicular Lymphoma_26

value: Follicular Lymphoma

value: WT


title: Follicular Lymphoma_31


title: p8 Tumor X1675210T_150


title: BloodStage_NonAnemic_3


title: Follicular Lymphoma_25


title: Follicular Lymphoma_23


title: Follicular Lymphoma_24


title: Mutant_liquid_medium_rep3

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

description:
Aspergillus nidulans
gcn li3

hyb_protocol: Hybridizations were done automatically for 16h at 45 ºC using the GeniomRT® Analyzer. The biochip underwent a stringent wash. Following the labeling procedure, a microfluidic-based primer extension assay was performed. This assay utilizes the bound mRNAs as a primer for an enzymatic elongation with labeled nucleotides. The elongation was done with Klenow Fragment and biotinylated nucleotides at 37 ºC for 15 minutes. Finally, the Biochip was washed automatically.

scan_protocol: Detection was achieved with streptavidin-phycoerythrin using Cy3 filter set in a GeniomRT® Analyzer.

data_processing: Raw intensity values were background subtracted, i.e., for each array the global background was computed and subtracted from the measured intensity. Data were normalized by VSN (variance stabilizing normalization, LIMMA package).

organism: Aspergillus nidulans

source_name: ∆gcnE mutant strain liquid medium

label_protocol: For each array, 1 µg of total RNA was labelled with MessageAmpTMII-Biotin Enhanced RNA Kit (Ambion) according to the manufacturer's instructions.

extract_protocol: Samples were frozen in liquid nitrogen upon harvesting and stored at -80ºC until processing. RNA was isolated from strains grown in liquid or solid media. RNA samples were quality controlled with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit.

tag: strain/background

tag: genotype/variation

value: ∆gcnE mutant

tag: growth medium

value: liquid


title: Follicular Lymphoma_22


title: Mutant_liquid_medium_rep2

description:
Aspergillus nidulans
gcn li2


title: Follicular Lymphoma_21


title: Wild_type_liquid_medium_rep2

description:
Aspergillus nidulans
wt li 2

source_name: wild type strain in liquid medium

value: wild type


title: Mutant_liquid_medium_rep1

description:
Aspergillus nidulans
gcn li1


title: Mutant_conidation_rep3

description:
Aspergillus nidulans
gcn co3

source_name: ∆gcnE mutant strain conidation

value: solid


title: Follicular Lymphoma_20


title: WP3Δhns-20C rep6

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description:
raw data file: 8210 WP3cy5-hnscy3.LSR
WP3Δhns cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing: S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model. Normalized log2 ratio (Cy5/Cy3) representing test/reference. In all of the experiments, WP3hns is the test sample and WP3 wild-type is the reference sample. Microarray spots with P values <0.001 in the F-test and log2 ratio were regarded as differentially expressed genes. In addition, all of the DEGs were confirmed with Significance Analysis of Microarrays (SAM) software.

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) shaking at  220 rpm at 20°C

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

tag: growth protocol

value: cultured at 20C in 2216E medium

value: WP3 wild-type


title: Wild_type_liquid_medium_rep1

description:
Aspergillus nidulans
wt li 1


title: Follicular Lymphoma_18


title: Follicular Lymphoma_17


title: WP3Δhns-20C rep4


title: WP3Δhns-20C rep5


title: ce_SRFcko_E9.0_rep2

city: Berlin

first: Phillip

last: Grote

address: Ihnestr. 73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio software

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

growth_protocol: homozygous and heterozygous embryos were obtained by crossing SRF(flex1/+); T:cre/T:cre females to SRF(flex1/+); T:cre/T:cre males

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: embryose were dissected in PBS on ice and staged accordingly before tissue preparation.

tag: genotype

tag: Stage

value: embryo

value: unsegmented caudal end


title: ce_SRFcko_E9.0_rep4

description: replicate 4


title: ce_wt_E9.0_rep4

description: replicate 4


title: Follicular Lymphoma_19


title: Mutant_conidation_rep2

description:
Aspergillus nidulans
gcn co2


title: Wild_type_liquid_medium_rep3

description:
Aspergillus nidulans
wt li 3


title: Follicular Lymphoma_14


title: ce_SRFcko_E9.0_rep1

description: replicate 1


title: WP3Δhns-20C rep3

description:
raw data file: 8209 WP3cy3-hnscy5.LSR
WP3Δhns cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3

tag: cell type


title: Follicular Lymphoma_16

tag: tissue


title: KO with DAC

city: Hannover

first: Michael

last: Heuser

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: Agilent Feature Extraction Software (v 10.5) was used for background subtraction and LOWESS normalization.

growth_protocol: Leukemic cells were kept in the Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (Stemcell Technologies, Vancouver, Canada ), 10 ng/mL of human interleukin-6 (hIL-6), 6 ng/mL of murine interleukin-3 (mIL-3), and 20 ng/mL of murine stem cell factor (mSCF; all from Peprotech, Hamburg, Germany).

extract_protocol: Genomic DNA from 10x106 cells treated or untreated cells were extracted and enriched for methylated DNA using the MagMeDIP kit (Diagenode, Belgium), following the manufacturer’s instructions. A fraction of the initial DNA was kept as reference input DNA. Both the MeDIP DNA and input DNA were amplified with the GenomePlex Complete Whole Genome Amplification (WGA) Kit (Sigma-Aldrich, Germany) for subsequent labeling with fluorescent dyes for microarray hybridization.

treatment_protocol: Cells were treated with or without decitabine (20nM) every 24 hours for 3 consecutive days and were harvested at 72 hours.

value: HOXA9 KO

tag: treatment

value: Decitabine

tag: cell line


title: WT with DAC


title: Mutant_conidation_rep1

description:
Aspergillus nidulans
gcn co1


title: ce_SRFcko_E9.0_rep3

description: replicate 3


title: KO no DAC


title: WP3Δhns-20C rep2


title: Follicular Lymphoma_15

tag: ezh2 mutation

tag: age


title: Wild_type_conidation_rep3

description:
Aspergillus nidulans
wt co3

source_name: wild type strain conidation


title: ce_wt_E9.0_rep3

description: replicate 3


title: Wild_type_conidation_rep1

description:
Aspergillus nidulans
wt co1


title: WP3Δhns-20C rep1


title: Wild_type_conidation_rep2

description:
Aspergillus nidulans
wt co2


title: ce_wt_E9.0_rep2

description: replicate 2


title: ce_wt_E9.0_rep1

description: replicate 1


title: WP3Δhns-4C-rep6

description:
raw data file: 8191 WP3cy5+hnscy3.LSR
WP3Δhns cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) shaking at  220 rpm at 4°C

value: cultured at 4C in 2216E medium

tag: genotype/variaton


title: WP3Δhns-4C-rep5


title: WT no DAC


title: ce_SRFcko_E8.75_rep4

description: replicate 4


title: WP3Δhns-4C-rep4


title: Follicular Lymphoma_11

tag: fl grade


title: ce_SRFcko_E8.75_rep2

description: replicate 2


title: WP3Δhns-4C-rep3

description:
raw data file: 8192 WP3cy3+hnscy5.LSR
WP3Δhns cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3


title: WP3Δhns-4C-rep1


title: WP3Δhns-4C-rep2


title: Follicular Lymphoma_10


title: Follicular Lymphoma_12


title: Follicular Lymphoma_09


title: ce_SRFcko_E8.75_rep1

description: replicate 1


title: ce_SRFcko_E8.75_rep3

description: replicate 3


title: Follicular Lymphoma_07


title: 142ab-/- WKMs, biological rep 2

first: Hongbo

last: Fan

address: 320 Yueyang Road, Shanghai, China

department: Institute of Health Sciences

institute: Chinese Academy of Sciences

description: Gene expression data from WKMs(without erythrocytes) in zebrafish kidney

hyb_protocol: 10μg fragmented, labeled cRNA were hybridized for 16 hours at 45℃ on Affymetrix Zebrafish 1.0 ST array.

scan_protocol: GeneChips were scanned with GeneChip® Scanner 3000.

data_processing: The data were analyzed according to the GeneChip® Expression Analysis Manual (Affymetrix).

organism: Danio rerio

source_name: zebrafish kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneAtlas® WT Expression User Manual, 2012, Affymetrix).

growth_protocol: Zebrafish embryos were raised up in standard conditions (as described in The Zebrafish Book).

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

treatment_protocol: The kidney was dissected from 60 dpf zebrafish on ice, rinsed with 0.9 x PBS and 10% FBS, and then passed through the 40 μm filter. Myelomonocytes or WKMs (without erythrocytes) were sorted from the single cell suspension.

value: kidney

value: WKMs(without erythrocytes) sorted from kidney

value: miR-142-3p double knockout

value: 60 dpf


title: Follicular Lymphoma_13

value: Follicular Lymphoma


title: Follicular Lymphoma_08


title: Follicular Lymphoma_06


title: ce_wt_E8.75_rep3

description: replicate 3


title: wild-type WKMs, biological rep 2


title: ce_wt_E8.75_rep4

description: replicate 4


title: Follicular Lymphoma_05


title: wild-type WKMs, biological rep 1


title: 142ab-/- myelomonocytes, biological rep 1

description: Gene expression data from myelomonocytes in zebrafish kidney

value: myelomonocytes sorted from kidney


title: Follicular Lymphoma_03


title: 142ab-/- myelomonocytes, biological rep 2


title: Follicular Lymphoma_02


title: ce_wt_E8.75_rep2

description: replicate 2


title: 142ab-/- WKMs, biological rep 1


title: ce_SRFcko_E8.5_rep4

description: replicate 4


title: Follicular Lymphoma_04


title: 1833-Treatment-2

city: Chicago

first: Miao

last: Sun

institute: University of Chicago

description: Biological replicate 2 of S153E-RKIP expression

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to miRCURYTM LNA Array Version 11.0 - annotated to miRBase 13.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat.

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: Background correction was conducted to remove non-biological contributions.  The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: MDA-MB-231 1833 cells expressing S153E-RKIP

label_protocol: The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 500 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Cells were cultured in a complete medium consisting of DMEM supplemented with 10% FBS, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was isolated from cells using miRNeasy Mini Kit following the manufacturer’s instructions.

treatment_protocol: RKIP expressing cells were generated by transducing the cells with S153E-RKIP expression vector in a lentiviral vector, and were selected and maintained in 0.5 μg/ml puromycin.

value: breast cancer cells

tag: transduction

source_name: Common reference for ms1-ms6

value: breast cancer cells expressing control or S153E-RKIP


title: Follicular Lymphoma_01


title: wild-type myelomonocytes, biological rep 2

value: wild type


title: ce_wt_E8.75_rep1

description: replicate 1

tag: strain


title: 1833-Treatment-3

description: Biological replicate 3 of S153E-RKIP expression


title: ce_SRFcko_E8.5_rep3

description: replicate 3

tag: developmental stage


title: 1833 S153E-RKIP, biological replicate 2

description: gene expression data from S153E-RKIP expressing cells

hyb_protocol: Following fragmentation, 5.5 ug cRNA were hybridized on GeneChip Human Genome U133plus2.0 Array using GeneChip Hybridization, Wash and Stain Kit according to manufacturer's protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Using fluidics protocol FS450_0007, and scan with Fluidics Station 450.

data_processing: Hybridization and background correction according to the standard protocols, the quantified signals were normalized using Robust Multi-array Average (RMA).

source_name: MDA-MB-231 1833 cells expressing HMGA2 shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA Using GeneChip WT terminal Labeling Kit.

growth_protocol: Cells were cultured in complete medium consisting of DMEM supplemented with 10% FBS, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit following the manufacturer’s instructions.

value: breast cancer cell line


title: wild-type myelomonocytes, biological rep 1


title: 1833-Treatment-1

description: Biological replicate 1 of S153E-RKIP expression


title: 1833 S153E-RKIP, biological replicate 1


title: ce_wt_E8.5_rep4

description: replicate 4


title: 1833-Control-2

description: Biological replicate 2 of control

source_name: MDA-MB-231 1833 cells expressing control vector


title: ce_SRFcko_E8.5_rep2

description: replicate 2


title: 1833-Control-1

description: Biological replicate 1 of control


title: ce_SRFcko_E8.5_rep1

description: replicate 1


title: ce_wt_E8.5_rep3

description: replicate 3


title: ce_wt_E8.5_rep1

description: replicate 1


title: 1833 S153E-RKIP, biological replicate 3


title: S2-cells_DENRdsRNA-translated_1

status: Public on Jun 30 2014

city: Heidelberg

first: Aurelio

middle: A

last: Teleman

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center (DKFZ)

description: RNA from 80S and polysome peaks of a polysome profile performed on S2 cells treated with DENR dsRNA

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

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

data_processing: The data were analyzed with Expression Profiler from the EBI using RMA normalization.

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

label_protocol: Biotinylated cRNA were prepared according to Affymetrix protocol

treatment_protocol: S2 cells treated with dsRNA

value: wildtype

value: DENR dsRNA

tag: sample type


title: ce_wt_E8.5_rep2

description: replicate 2

value: embryo


title: Patient75_arthritic cartilage

city: Vienna

first: Manuela

last: Hofner

address: Muthgasse 11/2

department: Molecular Diagnostics

country: Austria

institute: Austrian Institute of Technology - AIT

description: DNA-Methylation pattern analysis of non-arthritic knee cartilage, patient 75

hyb_protocol: Array hybridization was performed according to manufacturer`s instructions. For each array 5 µg of Cy3-labeled DNA were mixed with 50 µg of Human Cot-1 DNA in 1x Agilent Blocking Agent and 1x Agilent Hybridization Buffer in a total volume of 520 µl. Hybridization mixture was heated at 95°C for 3 minutes and incubated afterwards at 37°C for 30 minutes, then mixture was hybridized onto Agilent`s Human Promoter ChIP-on-chip microarrays (G4489A) for 40 hours at 65°C in a rotating Agilent hybridization oven (20 RPM). Agilent`s Human Promoter Microarray Set consists of 2 244k arrays (1 array per slide), therefore each patient sample was prepared in duplicate and hybridized onto one of the 2 different arrays. After hybridization microarrays were washed  5 minutes  at room temperature in Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 5 minutes with 31°C prewarmed Oligo aCGH/ChIP-on-chip Wash Buffer 2 (Agilent). Then they were dried immediately by centrifugation (1000xg).

scan_protocol: Slides were scanned immediately after washing  on the Agilent Microarray scanner (G2505C) using one colour settings for 1x244k array slides (Scan area 61x21.6 mm; Scan resolution 5 µm; Dye channel set to Green and Green PMT set to 100%).

data_processing: Raw data analysis of scanned images was performed using the Feature Extraction Software 10.5.1 (Agilent) using protocol GE1_105_Dec08 and grid 014706_D_F_20080627 to receive background subtracted and spatially detrended signal intensities. Statistical analysis and data normalization was performed using the BRB-ArrayTools software 3.7.1, using the option of this program to combine both array data sets per sample (array A and array B) to one normalized data file. Values of Human Promoter ChIP-on-chip arrays were log2 transformed and a global normalization was used to median center the log intensity values within one experiment (Data provided in Matrix1_Norm. Data). For subsequent analysis only normalized data of a selection of 57138  target probes were included corresponding to generated DNA fragments (during methylation-specific enrichment procedure) providing no cut site for methylation-unspecific restriction enzymes  and at least one cut-site for one methylation-specific enzyme (Data provided in Matrix2_Selected Norm. Data).

source_name: knee cartilage, arthritic area

label_protocol: 4 µg of each DNA amplicon was labeled with Cyanine-3 (Cy3) in two separate reactions (2 µg/reaction) using the Agilent Genomic DNA Labeling Kit PLUS according to the manufacturer`s instructions. DNA yield and dye incorporation were determined using a NanoDrop ND-1000 Spectrophotometer (DNA yield > 5 µg per reaction, Specific activity > 3 pmol/µg).

extract_protocol: Cartilage samples were collected from patients undergoing total knee Arthroplasty due to severe osteoarthritis. Samples were harvested from macroscopic arthritic and non-arthritic areas of the medial or lateral femoral condyle with the use of an eight millimetres gouge in each patient`s knee. Cartilage samples (approximately 2 mg weight) were ground in liquid nitrogen and genomic DNA was isolated using the QIAamp DNA Micro Kit (QIAgen) according to the manufacturer`s instructions and quantified using  a Nanodrop ND-1000 Spectrophotometer. To mainly enrich methylated DNA a specific amplification protocol was performed based on combinations of different methylation-sensitive and -insensitive restriction digestion steps and a rolling circle amplification (RCA).

value: cartilage derived from medial/lateral femoral condyle

tag: disease

value: arthritic cartilage area

tag: gender

value: female


title: S2-cells_GFPdsRNA-total_2

description: total RNA extracted from S2 cells treated with control (GFP) dsRNA

tag: genotype/variation

value: (GFP) dsRNA

value: total RNA


title: S2-cells_GFPdsRNA-translated_1

description: RNA from 80S and polysome peaks of a polysome profile performed on S2 cells treated with control (GFP) dsRNA


title: S2-cells_DENRdsRNA-total_2

description: total RNA extracted from S2 cells treated with DENR dsRNA


title: 1833 control, biological replicate 3

description: gene expression data from control cells

source_name: MDA-MB-231 1833 cells

value: control


title: S2-cells_DENRdsRNA-translated_2


title: Patient75_non-arthritic cartilage

description: DNA-Methylation pattern analysis of arthritic knee cartilage, patient 75

source_name: knee cartilage, non-arthritic area

value: non-arthritic cartilage area


title: S2-cells_GFPdsRNA-translated_2


title: 1833 control, biological replicate 1

description: gene expression data from control cells


title: 1833 control, biological replicate 2

description: gene expression data from control cells


title: Patient72_non-arthritic cartilage

description: DNA-Methylation pattern analysis of arthritic knee cartilage, patient 72


title: 1833-Control-3

description: Biological replicate 3 of control


title: Patient69_non-arthritic cartilage

description: DNA-Methylation pattern analysis of arthritic knee cartilage, patient 69


title: S2-cells_GFPdsRNA-total_1


title: Patient72_arthritic cartilage

description: DNA-Methylation pattern analysis of non-arthritic knee cartilage, patient 72


title: S2-cells_DENRdsRNA-total_1


title: Patient69_arthritic cartilage

description: DNA-Methylation pattern analysis of non-arthritic knee cartilage, patient 69


title: DK-final

status: Public on May 15 2014

city: Chapel Hill

first: Silva

last: Markovic-Plese

state: NC

address: 105 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

hyb_protocol: 15 ug of cRNA was used for gene array hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip® Hybridization Oven 640.The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip® Fluidics Station 400.

scan_protocol: The arrays were scanned with the Hewlett Packard GeneArray Scanner.

data_processing: Affymetrix GeneChip® Microarray Suite 5.0 software

source_name: PBMCs from CIS patient after IFNb-1a in-vivo treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA.

extract_protocol: Total RNA was extracted using a Rneasy kit according to the manufacturer's instructions.

treatment_protocol: 6x107 PBMCs were separated from 6 CIS patients at baseline and after 12 months of IFNb-1a (44 ug s.q. tiw) treatment.

value: PBMCs

value: after IFNb-1a in-vivo treatment


title: DK-first

source_name: PBMCs from CIS patient before IFNb-1a in-vivo treatment

value: before IFNb-1a in-vivo treatment


title: AEP-final


title: RS-first


title: PS-final


title: WSD-final


title: RS-final


title: PS-first


title: WSD-first


title: Aortic valve leaflet juvenile WT 2

status: Public on Apr 15 2014

city: Madison

first: Ana

middle: Maria

last: Porras

address: 1550 Engineering Drive #2153

department: Biomedical Engineering

institute: UW-madison

description: Wild Type 2

hyb_protocol: After fragmentation, 10ug of aRNA were applied to each Affymetrix Porcine array. Samples were hybridized at 45C for 16 hours. Postprocessing of the GeneChips on the Affymetrix Fluidics 450 Station following the protocols and procedures outline for the Affymetrix Porcine array.

scan_protocol: GeneChips were scanned on a GC3000 G7 scanner. Data were extracted and processed using the Affymetrix Command Console v3.1.1.1229.

data_processing: Microarray data were analyzed using the open source statistical language R v2.15.2 and the libraries in the Bioconductor Project32. The raw expression values from the *.CEL files were background-corrected and normalized using the Robust Multi-array Analysis method.

organism: Sus scrofa

source_name: Aortic valve leaflet, WT, juvenile

label_protocol: 400 ng of total RNA were labeled with the Ambion MessageAmp Premier IVT kit according to manufacturer's instructions.

growth_protocol: Swine were maintained on a standard chow diet.

extract_protocol: Leaflets were mechanically homogenized with a BulletBlend tube agitator according to manufacturer's instructions. Total RNA was isolated using the Qiagen RNeasy fibrous tissue spin-column kit following manufacturer's instructions.

treatment_protocol: Swine were stunned and euthanized by exsanguination. Within one hour of death, aortic valve leaflets were isolated and stored in RNAlater.

tag: breed

value: Rapacz Wisconsin Miniature Swine

value: wild type (RFH -/-)

value: 3 months

tag: Sex

value: aortic valve leaflet


title: KM-final


title: KM-first


title: Aortic valve leaflet juvenile WT 1

description: Wild Type 1


title: islets of non-pregnant female mouse, biological rep 4

status: Public on Feb 14 2014

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

country: Belgium

institute: KULeuven

description: Gene expression data from islets of non-pregnant female mice

hyb_protocol: Labeled DNA was hybridized to the array during 16h at 45°C

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

data_processing: All image files were generated using the Affymetrix GeneChip command console (AGCC). The raw data were analyzed with RMA sketch using the standard settings for Gene 1.0 ST arrays of Expression Console in the AGCC software (affymetrix).

source_name: mouse islets, C57bl6/J, NP

label_protocol: according to manufacturer’s manual 701880Rev4 (Affymetrix, Santa Clara, CA). Briefly, in the first cycle, double stranded cDNA was prepared with random hexamers tagged with a T7 promoter sequence followed by the generation of cRNA using the GeneChip WT Synthesis and Amplification kit (Affymetrix). cRNA concentration after cleanup was measured with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW). In the second cycle, sense oriented single-stranded DNA containing dUTP is generated and the concentration is, after cleanup, measured using the nanodrop. The cRNA is hydrolysed and the single stranded DNA is fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) (GeneChip WT terminal Labeling kit, Affymetrix). The quality of fragmentation (fragments should be between 40 and 70 nucleotides) is checked on the bioanalyzer (Agilent, Waldbronn, Germany). The fragmented DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix).

extract_protocol: The absolute RNA microprep kit of Strategene was used to extract total RNA according to the manufacturer's instructions. The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

tag: genotype

value: wild type

tag: pregnancy day

value: NP

value: pancreatic islets


title: islets of non-pregnant female mouse, biological rep 3

tag: tissue


title: Patient67_arthritic cartilage

description: DNA-Methylation pattern analysis of non-arthritic knee cartilage, patient 67

value: cartilage derived from medial/lateral femoral condyle


title: 6801-1023165-#63-GFP+-CD19+splen

status: Public on Jun 27 2014

first: Karen

middle: Dyer

last: Montgomery

address: 504 S Rosa Rd, Ste 101

department: Cytogenetics

institute: WiCell

hyb_protocol: NimbleGen Arrays User's Guide: CGH Analysis - Hybridization and Washing

scan_protocol: NimbleGen Arrays User's Guide: CGH Analysis - Two-Color Array Scanning utilizing the Axon 4000B GenePix Dual Laser Scanner

data_processing:
NimbleGen Arrays User's Guide: CGH Analysis - NimbleScan Data Analysis
infoQuant - cghFusion data analysis is based on the examination of unaveraged and/or 10X averaged data tracks. Settings for data analysis in infoQuant include an average log-ratio threshold of 0.2, a minimum aberration length of 5 probes, p-value of 0.001.  Additional analysis of this data may be performed using different ratio settings and different window averaging to enhance resolution.

source_name: #63_GFP+_CD19+ splen

label_protocol: Add 1500ng genomic DNA to 80uL water for sonication. Sonicate samples to between 500bp-2000bp. Follow NimbleGen Arrays User's Guide: CGH Analysis - Sample Labeling

extract_protocol: Cells arrived pelleted and frozen in 1.5mL microcentrifuge tubes, which were stored at -80C until extraction. Incubate samples in 37C waterbath for ~5 min. until completely thawed. Follow Qiagen DNeasy Blood and Tissue Kit with RNase A digestion.

tag: cell line

value: #63_GFP+_CD19+ splen

value: Female

value: B cell cancer

tag: ctr#

tag: dna#

source_name: healthy, wild type control

value: reference


title: AEP-first

tag: treatment


title: Patient68_non-arthritic cartilage

description: DNA-Methylation pattern analysis of arthritic knee cartilage, patient 68

value: female


title: islets of pregnancy day 12.5, biological rep 4

description: Gene expression data from islets of mice that were 12.5 day pregnant

source_name: mouse islets, C57bl6/J, P12.5


title: islets of non-pregnant female mouse, biological rep 2


title: Patient68_arthritic cartilage

description: DNA-Methylation pattern analysis of non-arthritic knee cartilage, patient 68

value: arthritic cartilage area


title: islets of non-pregnant female mouse, biological rep 1


title: Aortic valve leaflet juvenile WT 3

description: Wild Type 3

tag: age