title: Melanoma Cell Line WM8

city: Philadelphia

first: Katherine

last: Nathanson

address: 421 Curie Blvd

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: Hybridization was performed following Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol

scan_protocol: Hybridized arrays were scanned using Agilent’s High-Resolution C Scanner

data_processing: Data was extracted using Agilent Feature Extraction software

source_name: Melanoma Cell Line WM8

label_protocol: Samples were labeled using Invitrogen's BioPrime Total for Agilent aCGH

extract_protocol: Genomic DNA was extracted using Promega Wizard Genomic DNA Purification Kit following manufacturer's instructions.

value: BRAF/NRAS WT

source_name: Promega Human Female

value: Female Control DNA from Promega


title: genomic DNA from fresh cord blood sample 1 (BeadChip)

status: Public on Aug 27 2012

type: genomic

city: Cambridge

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: normal cord blood spot sample

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

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

data_processing: GenomeStudio softwarre

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from dried blood spot samples using the GenSolve kit as per manufacturers instructures.  DNA was extracted from other samples using the Qiagen DNeasy kit.

tag: sample id

tag: sample type

value: cord blood

tag: tissue

value: blood


title: genomic DNA from sperm (sample 4) (BeadChip)

description: normal sperm

value: sperm

tag: cell type


title: Melanoma Cell Line WM3438

state: PA

country: USA

source_name: Melanoma Cell Line WM3438

tag: genotype

tag: cell line


title: genomic DNA from sperm (sample 2) (BeadChip)

description: normal sperm


title: iPSIMR90Col1

city: Bad Nauheim

first: Jason

last: Lai

state: Hessen

address: Ludwigstrasse 43

department: Developmental Genetics

country: Germany

institute: Max Planck Institute For Heart and Lung Research

description: biological replicate 2

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Separate colors are background-subtracted followed by quantile normalization.

label: Cy3 and Cy5

source_name: Induced Pluripotent Stem Cell

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: Induced Pluripotent stem cell

tag: gender

value: female

tag: molecule type

value: Bisulfite converted DNA


title: Melanoma Cell Line WM3918 passage 65

source_name: Melanoma Cell Line WM3918 passage 65


title: Melanoma Cell Line WM3928F

source_name: Melanoma Cell Line WM3928F


title: IMR90P5

description: biological replicate 2

source_name: Human Fetal Lung Fibroblast

value: fetal lung fibroblast

value: IMR90 P6


title: Melanoma Cell Line WM3311

source_name: Melanoma Cell Line WM3311


title: genomic DNA from sample F2 dried blood spot (BeadChip)

description: normal dried blood spot sample

value: dried blood spot


title: Melanoma Cell Line WM3246

source_name: Melanoma Cell Line WM3246


title: iPCH460Col12

description: biological replicate 1

source_name: Induced Pluripotent Cancer Cell

value: induced pluripotent cancer cell

value: iPCH460 Col12

value: male


title: genomic DNA from sample F1 dried blood spot (BeadChip)

description: normal dried blood spot sample


title: H460P15

description: biological replicate 2

source_name: Lung Large Cell Carcinoma

value: lung large cell carcinoma


title: genomic DNA from sample M dried blood spot (BeadChip)

description: normal dried blood spot sample

source_name: M

value: M


title: Melanoma Cell Line WM209

source_name: Melanoma Cell Line WM209


title: Melanoma Cell Line WM1963

source_name: Melanoma Cell Line WM1963


title: Melanoma Cell Line C8161

source_name: Melanoma Cell Line C8161


title: Melanoma Cell Line WM852

source_name: Melanoma Cell Line WM852

value: NRAS p.Q61R


title: adult AML [UPN94]

city: Ulm

first: Frank

middle: G.

last: Ruecker

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University of Ulm

description: Hybridized to 250K_Nsp

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 AffymetrixGeneChip Scanner 3000 7G.

data_processing:
GenomeWideSNP_6
affymetrix-algorithm-name = birdseed-v2
affymetrix-algorithm-version = 2.4
program-name = Genotyping Console
Mapping250K_Sty and Mapping250K_Nsp
Results type: Genotyping
Algorithm: DynamicModel 3.0

label: biotin

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from CK-AML using DNAzol or Qiagen AllPrep DNA/RNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: DNA extracted from tumor cells obtained at diagnosis

tag: analyzed material

value: BM

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):RD

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):NA

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: H358P12

description: biological replicate 1

source_name: Lung Adenocarcinoma Cell Line

tag: cell type

value: lung adenocarcinoma

tag: cell line

tag: gender

tag: molecule type


title: iPCH460Col5

description: biological replicate 2

value: iPCH460 Col5


title: adult AML [UPN96]

description: Hybridized to 250K_Nsp

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):NA

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):NA


title: Melanoma Cell Line WM3702

source_name: Melanoma Cell Line WM3702

tag: genotype

value: NRAS p.Q61L

source_name: Promega Human Female

tag: sample type

value: Female Control DNA from Promega


title: Melanoma Cell Line WM3623

source_name: Melanoma Cell Line WM3623

value: NRAS p.Q61K


title: adult AML [UPN78]

description: Hybridized to 250K_Nsp

value: complete remission; RD:refractory disease; ED:early death):ED

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN86]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):CR

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):MUD

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)


title: adult AML [UPN77]

description: Hybridized to 250K_Nsp

value: PB

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)


title: adult AML [UPN8]

description: Hybridized to 250K_Nsp

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN85]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)


title: adult AML [UPN68]

description: Hybridized to 250K_Nsp

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)


title: Melanoma Cell Line WM3066

source_name: Melanoma Cell Line WM3066

tag: genotype

tag: cell line

tag: sample type


title: adult AML [UPN57]

description: Hybridized to 250K_Nsp

tag: cell type

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN98]

description: Hybridized to GenomeWideSNP_6

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)


title: Melanoma Cell Line WM2032

source_name: Melanoma Cell Line WM2032

tag: genotype

value: NRAS p.Q61R

tag: cell line

tag: sample type


title: adult AML [UPN83]

description: Hybridized to 250K_Nsp

tag: cell type

value: DNA extracted from tumor cells obtained at diagnosis

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):tAML


title: adult AML [UPN88]

description: Hybridized to GenomeWideSNP_6

tag: analyzed material

value: BM

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN6]

description: Hybridized to 250K_Nsp

tag: cell type

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)


title: Melanoma Cell Line WM1366

source_name: Melanoma Cell Line WM1366

tag: genotype

tag: cell line

tag: sample type


title: Melanoma Cell Line WM3451

source_name: Melanoma Cell Line WM3451


title: adult AML [UPN87]

description: Hybridized to GenomeWideSNP_6

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):NA

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml


title: adult AML [UPN55]

description: Hybridized to 250K_Nsp

tag: cell type

value: match urelated donor; MRD:match related donor):MRD

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: Melanoma Cell Line WM1361A

source_name: Melanoma Cell Line WM1361A

tag: genotype

tag: cell line

tag: sample type


title: Melanoma Cell Line WM2013

source_name: Melanoma Cell Line WM2013


title: adult AML [UPN56]

description: Hybridized to 250K_Nsp

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)


title: Melanoma Cell Line WM983B

source_name: Melanoma Cell Line WM983B

value: BRAF p.V600E


title: adult AML [UPN65]

description: Hybridized to 250K_Nsp

tag: cell type

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml


title: adult AML [UPN41]

description: Hybridized to 250K_Nsp

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):oAML

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN84]

description: Hybridized to GenomeWideSNP_6

tag: cell type

value: complete remission; RD:refractory disease; ED:early death):RD

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)


title: adult AML [UPN75]

description: Hybridized to GenomeWideSNP_6

value: complete remission; RD:refractory disease; ED:early death):NA

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: bm blasts (%)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):NA


title: adult AML [UPN49]

description: Hybridized to GenomeWideSNP_6

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation


title: Mo17_tass

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: This Sample represents 3 replicates.

hyb_protocol: 15ug of labeled DNAs (input DNA, IP DNA) were hybridized to a single subarray of the 3x1.4M arrays according to the array manufacturer protocol (42°C, 20hrs). Arrays were then washed according to the array manufacturer's protocol.

scan_protocol: Arrays were scanned according to the NimbleScan DNA methylation User Guide (v7.2) protocol, which specifies parameters for the MS200 Microarray Scanner (Roche Nimblegen) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software v2.6 (Roche NimbleGen) which produced .pair reports of raw data.
.pair files exported from NimbleScan were imported into 'Ringo' within the Bioconductor statistical environment (http://bioconductor.org/). Sample-dependent MeDIP enrichments were estimated for each probe by fitting a fixed linear model accounting for array, dye, and sample effects to the data using the limma package (Smyth, 2004). Contrasts between IP and input for each genotype and tissue contrast were developed (see manuscript). Moderated t-statistics and the log-odds score for differential MeDIP enrichment was computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05. Results were loaded into relational databases and a Generic Genome Browser for downstream analyses.

organism: Zea mays

source_name: Mo17, tassel, input

label_protocol: Amplified input DNA and immunoprecipitated methylated DNA (IP) were labeled (3 x 1ug per reaction) using Cy3 and Cy5, respectively.

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation. 15-30ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps). Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101), which contains the anti-5-methylcytosine monoclonal antibody. 50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

tag: inbred line

tag: tissue

value: tassel (immature 3-4cM)

tag: medip antibody

source_name: Mo17, tassel, IP

value: anti-5-methylcytosine monoclonal

tag: antibody vendor

value: Zymo Research

tag: antibody catalog #

tag: antibody lot#


title: adult AML [UPN51]

description: Hybridized to 250K_Nsp

tag: cell type

value: complete remission; RD:refractory disease; ED:early death):CR

value: match urelated donor; MRD:match related donor):MUD

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: Melanoma Cell Line WM9

source_name: Melanoma Cell Line WM9

tag: genotype

tag: cell line

tag: sample type

value: Female Control DNA from Promega


title: Melanoma Cell Line WM902B

source_name: Melanoma Cell Line WM902B


title: adult AML [UPN45]

description: Hybridized to 250K_Nsp

value: DNA extracted from tumor cells obtained at diagnosis

tag: analyzed material

value: PB

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation


title: adult AML [UPN95]

description: Hybridized to GenomeWideSNP_6

source_name: Leukemic cells obtained from bone marrow or blood at remission

tag: cell type

value: DNA extracted from germline cells

value: BM

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)


title: B73_tass

description: This Sample represents 3 replicates.

source_name: B73, tassel, input

tag: inbred line

tag: tissue

tag: medip antibody

source_name: B73, tassel, IP

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot#


title: Mo17_leaf

description: This Sample represents 3 replicates.

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the 2.1M arrays according to the array manufacturer protocol (42°C, 16-20hrs). Arrays were then washed according to the array manufacturer's protocol.

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the GenePix 4000B Scanner (Axon/Molecular Devices) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files exported from NimbleScan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Sample-dependent MeDIP enrichments were estimated for each probe by fitting a fixed linear model accounting for array, dye, and sample effects to the data using the limma package (Smyth, 2004). The following statistical contrasts were then fit: B73 seedling immunoprecipitation sample (IP) vs. B73 seedling genomic DNA control (input); B73 embryo IP vs. input; B73 endosperm IP vs. input; B73 tassel IP vs. input; Mo17 seedling IP vs. input; Mo17 embryo IP input; Mo17 endosperm IP vs. input; Mo17 tassel IP vs. input. Four between-genotype statistical contrasts were also fit: Mo17 seedling vs. B73 seedling; Mo17 embryo vs. B73 embryo; Mo17 endosperm vs. B73 endosperm; Mo17 tassel vs. B73 tassel. Finally, between-tissue statistical contrasts were developed for each genotype individually: Embryo vs. leaf; Embryo vs. Tassel; Endosperm vs. embryo; Endosperm vs. leaf; Endosperm vs. tassel; Leaf vs. tassel. Moderated t-statistics and the log-odds score for differential MeDIP enrichment was computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05. Results were formatted for the Integrative Genomics Viewer (IGV, Robinson et al., 2011) for downstream analysis.

source_name: Mo17, leaf, input

value: leaf (L3)

source_name: Mo17, leaf, IP


title: Melanoma Cell Line WM88

source_name: Melanoma Cell Line WM88

tag: genotype

tag: cell line

source_name: Promega Human Female

tag: sample type


title: adult AML [UPN38]

description: Hybridized to 250K_Nsp

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):NA

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):tAML

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN4]

description: Hybridized to 250K_Nsp

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):sAML


title: adult AML [UPN31]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML


title: B73_leaf

description: This Sample represents 3 replicates.

source_name: B73, leaf, input

tag: inbred line

tag: tissue

tag: medip antibody

source_name: B73, leaf, IP

tag: antibody vendor

tag: antibody catalog #


title: adult AML [UPN71]

description: Hybridized to GenomeWideSNP_6

value: complete remission; RD:refractory disease; ED:early death):NA

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: Mo17_endo

description: This Sample represents 3 replicates.

source_name: Mo17, endosperm, input

growth_protocol: Samples were harvested from pooled 14 DAP ears.

tag: inbred line

value: endosperm (14 DAP)

source_name: Mo17, endosperm, IP

tag: antibody lot#


title: adult AML [UPN37]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):NA


title: adult AML [UPN28]

description: Hybridized to 250K_Nsp

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml


title: adult AML [UPN25]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN39]

description: Hybridized to GenomeWideSNP_6

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)


title: Melanoma Cell Line WM793

source_name: Melanoma Cell Line WM793

tag: genotype

value: BRAF p.V600E

tag: cell line

tag: sample type


title: adult AML [UPN24]

description: Hybridized to 250K_Nsp

tag: cell type

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml


title: Melanoma Cell Line WM858

source_name: Melanoma Cell Line WM858


title: Melanoma Cell Line WM35 passage 44

source_name: Melanoma Cell Line WM35 passage 44


title: adult AML [UPN27]

description: Hybridized to 250K_Nsp

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):MRD

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: Melanoma Cell Line WM1617

source_name: Melanoma Cell Line WM1617

tag: genotype

tag: cell line

tag: sample type


title: Melanoma Cell Line WM1791C

source_name: Melanoma Cell Line WM1791C


title: Melanoma Cell Line WM164

source_name: Melanoma Cell Line WM164


title: B73_endo

description: This Sample represents 3 replicates.

source_name: B73, endosperm, input

extract_protocol: Genomic DNAs were extracted using the Qiagen DNeasy Plant Mini Kit. 10ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps). Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody. 50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

tag: inbred line

tag: tissue

value: endosperm

tag: medip antibody

source_name: B73, endosperm, IP

value: anti-5-methylcytosine monoclonal

tag: antibody vendor

value: Zymo Research

tag: antibody catalog #


title: B73_emb

description: This Sample represents 3 replicates.

source_name: B73, embryo, input

value: embryo (14 DAP)

source_name: B73, embryo, IP

tag: antibody lot#


title: Mo17_emb

description: This Sample represents 3 replicates.

source_name: Mo17, embryo, input

source_name: Mo17, embryo, IP


title: adult AML [UPN36]

description: Hybridized to GenomeWideSNP_6

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

tag: cell type

value: DNA extracted from tumor cells obtained at diagnosis

tag: analyzed material

value: PB

tag: age (years)

tag: remission status past double induction (cr

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml


title: adult AML [UPN231]

description: Hybridized to GenomeWideSNP_6

value: BM

value: complete remission; RD:refractory disease; ED:early death):RD

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):MUD

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: homozygous mutation

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN230]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):CR

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)


title: adult AML [UPN23]

description: Hybridized to 250K_Nsp

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)


title: adult AML [UPN229]

description: Hybridized to 250K_Nsp

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):NA

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):tAML

tag: homozygous mutation


title: adult AML [UPN232]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: os (days)

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN220]

description: Hybridized to GenomeWideSNP_6

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):sAML


title: CONTROL_sample_7

type: RNA

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: female, 54  years

data_processing: Data was processed using the softwares SDS 2.3 and RQ manager 1.2 from Applied Biosystems. Ct raw data were normalized against the median Ct values (deltaCt).

label: FAM

molecule: total RNA

source_name: biceps brachii, CONTROL

label_protocol: standard Taqman assay

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

tag: disease state

value: control

tag: age

value: 54 years

tag: gender

value: female

tag: tissue

value: biceps brachii biopsy


title: CONTROL_sample_8

description: female, 52  years

value: 52 years


title: CONTROL_sample_9

description: male, 62  years

value: 62 years

value: male


title: adult AML [UPN26]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML

tag: homozygous mutation


title: CONTROL_sample_6

description: male, 74  years

value: 74 years


title: Melanoma Cell Line WM1552C

source_name: Melanoma Cell Line WM1552C

tag: genotype

value: BRAF p.V600E

tag: cell line

source_name: Promega Human Female

tag: sample type

value: Female Control DNA from Promega


title: CONTROL_sample_5

description: male, 44  years

tag: disease state

tag: age

value: 44 years


title: adult AML [UPN227]

description: Hybridized to 250K_Nsp

value: DNA extracted from tumor cells obtained at diagnosis

value: PB

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):NA

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):NA

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN222]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

value: BM

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):NA

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):tAML

tag: homozygous mutation


title: CONTROL_sample_4

description: male, 37  years

tag: disease state

value: control

tag: age

value: 37 years

tag: gender

tag: tissue


title: Melanoma Cell Line 451Lu

source_name: Melanoma Cell Line 451Lu

tag: genotype

tag: cell line

tag: sample type


title: Melanoma Cell Line SKMel28

source_name: Melanoma Cell Line SKMel28


title: CONTROL_sample_3

description: male, 47  years

value: 47 years

value: biceps brachii biopsy


title: Melanoma Cell Line A375

source_name: Melanoma Cell Line A375


title: adult AML [UPN186]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: age (years)

tag: remission status past double induction (cr

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: Melanoma Cell Line 1205Lu

source_name: Melanoma Cell Line 1205Lu

tag: genotype


title: CONTROL_sample_2

description: male, 47 years

tag: disease state

tag: age

tag: gender

value: male

tag: tissue


title: adult AML [UPN212]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: age (years)

value: complete remission; RD:refractory disease; ED:early death):CR

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML

tag: homozygous mutation


title: adult AML [UPN219]

description: Hybridized to GenomeWideSNP_6

source_name: Leukemic cells obtained from bone marrow or blood at remission

value: DNA extracted from germline cells

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):RD

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: CONTROL_sample_1

description: male, 35 years

tag: disease state

tag: age

value: 35 years

tag: gender

tag: tissue


title: adult AML [UPN197]

description: Hybridized to GenomeWideSNP_6

tag: cell type

value: DNA extracted from tumor cells obtained at diagnosis

tag: analyzed material

tag: age (years)

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml


title: adult AML [UPN216]

description: Hybridized to 250K_Nsp

tag: remission status past double induction (cr

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):sAML

tag: homozygous mutation

tag: compound heterozygous mutations


title: adult AML [UPN218]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: age (years)

value: complete remission; RD:refractory disease; ED:early death):NA

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: biallelic aberration/function deletion


title: adult AML [UPN214]

description: Hybridized to 250K_Nsp

tag: remission status past double induction (cr

tag: os (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml


title: DM2_sample_9

description: male,47 years

source_name: biceps brachii,DM2

tag: disease state

value: Myotoni Dystrophy type 2

tag: age

tag: gender

tag: tissue


title: adult AML [UPN202]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

value: BM

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):NA

tag: homozygous mutation

tag: compound heterozygous mutations


title: adult AML [UPN205]

description: Hybridized to 250K_Nsp

value: PB

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):NA

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: biallelic aberration/function deletion


title: adult AML [UPN207]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: type aml (aml


title: adult AML [UPN18]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: homozygous mutation

tag: compound heterozygous mutations


title: DM2_sample_10

description: male,61 years

tag: disease state

tag: age

value: 61 years

tag: gender

tag: tissue


title: adult AML [UPN196]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: biallelic aberration/function deletion


title: adult AML [UPN191]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: type aml (aml

tag: homozygous mutation


title: adult AML [UPN199]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: compound heterozygous mutations


title: DM2_sample_8

description: male,70 years

tag: disease state

tag: age

value: 70 years

tag: gender

tag: tissue


title: adult AML [UPN192]

description: Hybridized to 250K_Nsp

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):ED

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: biallelic aberration/function deletion


title: adult AML [UPN17]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: type aml (aml

tag: homozygous mutation


title: adult AML [UPN185]

description: Hybridized to 250K_Nsp

tag: age (years)

tag: remission status past double induction (cr

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: rfs (days)

tag: compound heterozygous mutations


title: adult AML [UPN5]

description: Hybridized to 250K_Sty

tag: cell type

tag: analyzed material

value: match urelated donor; MRD:match related donor):MUD

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: biallelic aberration/function deletion


title: adult AML [UPN162]

description: Hybridized to GenomeWideSNP_6

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)


title: adult AML [UPN161]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):CR

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: type aml (aml

tag: homozygous mutation


title: DM2_sample_7

description: female,59 years

tag: disease state

tag: age

value: 59 years

tag: gender

value: female

tag: tissue

value: biceps brachii biopsy


title: adult AML [UPN174]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: compound heterozygous mutations

tag: biallelic aberration/function deletion


title: adult AML [UPN47]

description: Hybridized to 250K_Sty

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):RD

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: type aml (aml


title: DM2_sample_6

description: female, 59 years

tag: disease state

tag: age

tag: gender

tag: tissue


title: adult AML [UPN48]

description: Hybridized to 250K_Sty

tag: cell type

value: DNA extracted from tumor cells obtained at diagnosis

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML

tag: homozygous mutation

tag: compound heterozygous mutations


title: adult AML [UPN159]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: biallelic aberration/function deletion


title: adult AML [UPN137]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

value: complete remission; RD:refractory disease; ED:early death):NA

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: type aml (aml


title: adult AML [UPN145]

description: Hybridized to GenomeWideSNP_6

value: DNA extracted from germline cells

tag: age (years)

tag: remission status past double induction (cr

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: homozygous mutation

tag: compound heterozygous mutations


title: DM2_sample_5

description: male,62 years

tag: disease state

value: Myotoni Dystrophy type 2

tag: age

value: 62 years

tag: gender

value: male

tag: tissue


title: DM2_sample_4

description: male,64 years

value: 64 years


title: adult AML [UPN40]

description: Hybridized to 250K_Sty

tag: cell type

tag: analyzed material

value: PB

value: match urelated donor; MRD:match related donor):NA

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):sAML

tag: biallelic aberration/function deletion


title: adult AML [UPN171]

description: Hybridized to GenomeWideSNP_6

value: BM

tag: age (years)

tag: remission status past double induction (cr

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):NA

tag: homozygous mutation


title: adult AML [UPN134]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

value: match urelated donor; MRD:match related donor):MRD

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):tAML

tag: compound heterozygous mutations


title: adult AML [UPN173]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: biallelic aberration/function deletion


title: adult AML [UPN149]

description: Hybridized to GenomeWideSNP_6

source_name: Leukemic cells obtained from bone marrow or blood at relapse

value: DNA extracted from tumor cells obtained at relapse

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)


title: adult AML [UPN166]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: type aml (aml

tag: homozygous mutation


title: adult AML [UPN15]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):CR

value: match urelated donor; MRD:match related donor):MUD

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: compound heterozygous mutations


title: DM2_sample_1

description: male, 56 years

tag: disease state

tag: age

value: 56 years

tag: gender

tag: tissue

value: biceps brachii biopsy


title: adult AML [UPN115]

description: Hybridized to 250K_Nsp

tag: cell type

value: DNA extracted from tumor cells obtained at diagnosis

tag: analyzed material

value: complete remission; RD:refractory disease; ED:early death):ED

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: pb blasts (%)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML

tag: biallelic aberration/function deletion


title: DM2_sample_2

description: male,60 years

value: Myotoni Dystrophy type 2

value: 60 years

value: male


title: Borderline mucinous ovarian tumour_11552G

status: Public on Aug 26 2012

city: Melbourne

first: Sally

last: Hunter

state: VIC

address: 7 St Andrew's Pl

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
MOT_11552G
hybridized to SNP6

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

data_processing:
CHP files were generated using the Affymetrix Genotyping Console algorithm Birdseed v2. Total and allele-specific copy number analysis was performed using Partek Genomics Suite 6.5, using both paired copy number generation.
CEL and CHP files are provided for each sample in the study. Processed/normalized data for the germline DNA samples not provided because they themselves are normalised to a diploid copy number, making all the probe values 2, which is not informative.

source_name: Borderline mucinous ovarian tumour

extract_protocol: Genomic DNA was extracted from tissues (epithelium and stroma) microdissected mucinous ovarian tumours stained with haematoxylin and eosin, and from lymphcoytes obtained from peripheral blood (for matched normal DNA)  using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Qubit.

value: blood lymphocytes

tag: tumor histology

value: mucinous

tag: tumor diagnosis

value: borderline


title: adult AML [UPN32]

description: Hybridized to 250K_Sty

value: BM

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):NA

value: match urelated donor; MRD:match related donor):NA

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):sAML

tag: homozygous mutation

tag: compound heterozygous mutations


title: adult AML [UPN126]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

value: complete remission; RD:refractory disease; ED:early death):RD

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):tAML


title: DM2_sample_3

description: male,61 years

tag: disease state

tag: age

value: 61 years

tag: gender

tag: tissue


title: Borderline mucinous ovarian tumour_8566G

description:
MOT_8566G
hybridized to SNP6

tag: tumor histology

tag: tumor diagnosis


title: adult AML [UPN136]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation

tag: biallelic aberration/function deletion


title: adult AML [UPN114]

description: Hybridized to 250K_Nsp

tag: cell type

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: compound heterozygous mutations


title: adult AML [UPN3]

description: Hybridized to 250K_Sty

tag: age (years)

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)


title: Borderline mucinous ovarian tumour_6181G

description:
MOT_6181G
hybridized to SNP6

tag: tissue

tag: tumor histology

tag: tumor diagnosis


title: adult AML [UPN130]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: analyzed material

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: platelets (g/l)

tag: wbc (g/l)

tag: pb blasts (%)

tag: type aml (aml

tag: homozygous mutation

tag: biallelic aberration/function deletion


title: Borderline mucinous ovarian tumour_4884G

description:
MOT_4884G
hybridized to SNP6


title: adult AML [UPN13]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):CR

value: match urelated donor; MRD:match related donor):MRD

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: compound heterozygous mutations


title: adult AML [UPN127]

description: Hybridized to GenomeWideSNP_6

tag: cell type

value: DNA extracted from tumor cells obtained at diagnosis

tag: analyzed material

value: PB

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)


title: adult AML [UPN113]

description: Hybridized to 250K_Nsp

tag: age (years)

tag: platelets (g/l)

tag: wbc (g/l)

tag: pb blasts (%)

tag: type aml (aml

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):AML

tag: homozygous mutation

tag: biallelic aberration/function deletion


title: Borderline mucinous ovarian tumour_4779G

description:
MOT_4779G
hybridized to SNP6

tag: tissue

tag: tumor histology

tag: tumor diagnosis


title: Borderline mucinous ovarian tumour_5401G

description:
MOT_5401G
hybridized to SNP6


title: adult AML [UPN20]

description: Hybridized to 250K_Sty

tag: cell type

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: compound heterozygous mutations


title: adult AML [UPN11]

description: Hybridized to 250K_Nsp

tag: analyzed material

tag: age (years)

tag: allogeneic stem cell transplantation (mud

value: match urelated donor; MRD:match related donor):MUD

tag: response at date of transplantation

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: pb blasts (%)


title: adult AML [UPN194]

description: Hybridized to 250K_Sty

tag: cell type

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: type aml (aml

tag: homozygous mutation

tag: biallelic aberration/function deletion


title: adult AML [UPN176]

description: Hybridized to 250K_Sty

tag: analyzed material

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: compound heterozygous mutations


title: Borderline mucinous ovarian tumour_4691G

description:
MOT_4691G
hybridized to SNP6

tag: tissue

tag: tumor histology

tag: tumor diagnosis


title: Borderline mucinous ovarian tumour_4584G

description:
MOT_4584G
hybridized to SNP6


title: adult AML [UPN103]

description: Hybridized to 250K_Nsp

tag: cell type

tag: age (years)

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: pb blasts (%)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):oAML


title: adult AML [UPN107]

description: Hybridized to 250K_Nsp

tag: analyzed material

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: type aml (aml

tag: homozygous mutation

tag: biallelic aberration/function deletion


title: adult AML [UPN128]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: age (years)

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: compound heterozygous mutations


title: Borderline mucinous ovarian tumour_4515G

description:
MOT_4515G
hybridized to SNP6

tag: tissue

value: blood lymphocytes

tag: tumor histology

tag: tumor diagnosis


title: adult AML [UPN158]

description: Hybridized to 250K_Sty

tag: analyzed material

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: platelets (g/l)

tag: wbc (g/l)

tag: pb blasts (%)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):NA


title: adult AML [UPN125]

description: Hybridized to GenomeWideSNP_6

tag: cell type

value: DNA extracted from germline cells

tag: age (years)

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: ldh (u/l)

tag: type aml (aml

tag: homozygous mutation

tag: biallelic aberration/function deletion


title: Borderline mucinous ovarian tumour_4551G

description:
MOT_4551G
hybridized to SNP6

tag: tissue

tag: tumor histology

value: mucinous

tag: tumor diagnosis

value: borderline


title: adult AML [UPN109]

description: Hybridized to 250K_Nsp

tag: analyzed material

value: BM

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):ED

value: match urelated donor; MRD:match related donor):NA

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: compound heterozygous mutations


title: Borderline mucinous ovarian tumour_2063G

description:
MOT_2063G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_2895G

description:
MOT_2895G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_528G

description:
MOT_528G
hybridized to SNP6


title: adult AML [UPN104]

description: Hybridized to 250K_Sty

tag: cell type

tag: age (years)

value: complete remission; RD:refractory disease; ED:early death):RD

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)

tag: ldh (u/l)

tag: pb blasts (%)

value: de novo AML; sAML:secondary AML; tAML:therapy related AML):sAML


title: adult AML [UPN100]

description: Hybridized to GenomeWideSNP_6

tag: analyzed material

tag: remission status past double induction (cr

value: complete remission; RD:refractory disease; ED:early death):NA

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: type aml (aml

tag: homozygous mutation

tag: biallelic aberration/function deletion


title: adult AML [UPN12]

description: Hybridized to GenomeWideSNP_6

tag: cell type

tag: status efs (0=no event, 1=event)

tag: efs (days)

tag: status rfs (0=no event, 1=event)

tag: gender (1=male, 2=female)

tag: bm blasts (%)

tag: compound heterozygous mutations


title: adult AML [UPN118]

description: Hybridized to GenomeWideSNP_6

tag: age (years)

tag: allogeneic stem cell transplantation (mud

tag: response at date of transplantation

tag: rfs (days)

tag: hb (g/dl)

tag: platelets (g/l)

tag: wbc (g/l)


title: adult AML [UPN106]

description: Hybridized to GenomeWideSNP_6

tag: analyzed material

tag: remission status past double induction (cr

tag: status os (0=alive, 1=dead)

tag: os (days)

tag: ldh (u/l)

tag: pb blasts (%)

tag: type aml (aml


title: Borderline mucinous ovarian tumour_531G

description:
MOT_531G
hybridized to SNP6

tag: tissue

tag: tumor histology

tag: tumor diagnosis


title: Borderline mucinous ovarian tumour_537G

description:
MOT_537G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_11552S

description:
MOT_11552S
hybridized to SNP6

value: ovarian tumor stroma


title: Borderline mucinous ovarian tumour_388S

description:
MOT_388S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_11552T

description:
MOT_11552T
hybridized to SNP6

value: ovarian tumor epithelium


title: Borderline mucinous ovarian tumour_8566T

description:
MOT_8566T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4884S

description:
MOT_4884S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_387S

description:
MOT_387S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_6181S

description:
MOT_6181S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_322G

description:
MOT_322G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4884T

description:
MOT_4884T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_263G

description:
MOT_263G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4691S

description:
MOT_4691S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_186G

description:
MOT_186G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4691T

description:
MOT_4691T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_6181T

description:
MOT_6181T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_8566S

description:
MOT_8566S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_5401S

description:
MOT_5401S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4779S

description:
MOT_4779S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_92G

description:
MOT_92G
hybridized to SNP6


title: Benign mucinous ovarian tumour_11142G

description:
MOT_11142G
hybridized to SNP6

source_name: Benign mucinous ovarian tumour

value: benign


title: Borderline mucinous ovarian tumour_4779T

description:
MOT_4779T
hybridized to SNP6


title: Benign mucinous ovarian tumour_8676G

description:
MOT_8676G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4551S

description:
MOT_4551S
hybridized to SNP6


title: Benign mucinous ovarian tumour_8055G

description:
MOT_8055G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4584T

description:
MOT_4584T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4584S

description:
MOT_4584S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_2895S

description:
MOT_2895S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4515T

description:
MOT_4515T
hybridized to SNP6


title: Benign mucinous ovarian tumour_3788G

description:
MOT_3788G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_2895T

description:
MOT_2895T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_5401T

description:
MOT_5401T
hybridized to SNP6


title: Benign mucinous ovarian tumour_3045G

description:
MOT_3045G
hybridized to SNP6


title: Benign mucinous ovarian tumour_2845G

description:
MOT_2845G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_4551T

description:
MOT_4551T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_2063T

description:
MOT_2063T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_537T

description:
MOT_537T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_2063S

description:
MOT_2063S
hybridized to SNP6


title: Benign mucinous ovarian tumour_2408G

description:
MOT_2408G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_528S

description:
MOT_528S
hybridized to SNP6


title: Benign mucinous ovarian tumour_1735G

description:
MOT_1735G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_531T

description:
MOT_531T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_388T

description:
MOT_388T
hybridized to SNP6


title: Benign mucinous ovarian tumour_2362G

description:
MOT_2362G
hybridized to SNP6


title: Benign mucinous ovarian tumour_1249G

description:
MOT_1249G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_537S

description:
MOT_537S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_387T

description:
MOT_387T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_528T

description:
MOT_528T
hybridized to SNP6


title: Benign mucinous ovarian tumour_907G

description:
MOT_907G
hybridized to SNP6


title: Benign mucinous ovarian tumour_11142S

description:
MOT_11142S
hybridized to SNP6


title: Benign mucinous ovarian tumour_512G

description:
MOT_512G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_322S

description:
MOT_322S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_263T

description:
MOT_263T
hybridized to SNP6


title: Benign mucinous ovarian tumour_372S

description:
MOT_372S
hybridized to SNP6


title: Benign mucinous ovarian tumour_335S

description:
MOT_335S
hybridized to SNP6


title: Borderline mucinous ovarian tumour_92S

description:
MOT_92S
hybridized to SNP6


title: Benign mucinous ovarian tumour_11142T

description:
MOT_11142T
hybridized to SNP6


title: Benign mucinous ovarian tumour_8676T

description:
MOT_8676T
hybridized to SNP6


title: Benign mucinous ovarian tumour_294G

description:
MOT_294G
hybridized to SNP6


title: Borderline mucinous ovarian tumour_322T

description:
MOT_322T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_92T

description:
MOT_92T
hybridized to SNP6


title: Benign mucinous ovarian tumour_8055S

description:
MOT_8055S
hybridized to SNP6


title: Benign mucinous ovarian tumour_8676S

description:
MOT_8676S
hybridized to SNP6


title: Benign mucinous ovarian tumour_2845S

description:
MOT_2845S
hybridized to SNP6


title: Benign mucinous ovarian tumour_3788S

description:
MOT_3788S
hybridized to SNP6


title: Benign mucinous ovarian tumour_446G_Sty

description:
MOT_446G
hybridized to STYI 250K


title: Borderline mucinous ovarian tumour_186T

description:
MOT_186T
hybridized to SNP6


title: Benign mucinous ovarian tumour_3788T

description:
MOT_3788T
hybridized to SNP6


title: Benign mucinous ovarian tumour_276G

description:
MOT_276G
hybridized to SNP6


title: Benign mucinous ovarian tumour_3045T

description:
MOT_3045T
hybridized to SNP6


title: Benign mucinous ovarian tumour_94G

description:
MOT_94G
hybridized to SNP6


title: Benign mucinous ovarian tumour_446G_Nsp

description:
MOT_446G
hybridized to NSPI 250K


title: Borderline mucinous ovarian tumour_289G_Sty

description:
MOT_289G
hybridized to STYI 250K


title: Benign mucinous ovarian tumour_2845T

description:
MOT_2845T
hybridized to SNP6


title: Benign mucinous ovarian tumour_2408T

description:
MOT_2408T
hybridized to SNP6


title: Benign mucinous ovarian tumour_2362T

description:
MOT_2362T
hybridized to SNP6


title: Benign mucinous ovarian tumour_3045S

description:
MOT_3045S
hybridized to SNP6


title: Benign mucinous ovarian tumour_214G_Sty

description:
MOT_214G
hybridized to STYI 250K


title: Benign mucinous ovarian tumour_1735S

description:
MOT_1735S
hybridized to SNP6


title: Benign mucinous ovarian tumour_1249S

description:
MOT_1249S
hybridized to SNP6


title: Benign mucinous ovarian tumour_214G_Nsp

description:
MOT_214G
hybridized to NSPI 250K


title: Benign mucinous ovarian tumour_156G

description:
MOT_156G
hybridized to SNP6


title: Benign mucinous ovarian tumour_446T_Sty

description:
MOT_446T
hybridized to STYI 250K


title: Benign mucinous ovarian tumour_512S

description:
MOT_512S
hybridized to SNP6


title: Benign mucinous ovarian tumour_2408S

description:
MOT_2408S
hybridized to SNP6


title: Benign mucinous ovarian tumour_446T_Nsp

description:
MOT_446T
hybridized to NSPI 250K


title: Borderline mucinous ovarian tumour_289T_Sty

description:
MOT_289T
hybridized to STYI 250K


title: Benign mucinous ovarian tumour_1249T

description:
MOT_1249T
hybridized to SNP6


title: Benign mucinous ovarian tumour_2362S

description:
MOT_2362S
hybridized to SNP6


title: NSCLC_11_20111129

status: Public on Aug 25 2012

city: Vienna

first: Stefan

last: Kastner

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim RCV

hyb_protocol: The microarrays were incubated with 200µL hybridization cocktails overnight (16 hrs) at 45°C in an Affymetrix Hybridisation oven 640.

scan_protocol: The microarrays were washed/stained in an Affymetrix FS450 fluidics station using the GeneChip® Hybridization Wash and Stain Kit (protocol FS450_0001) and subsequently scanned in an Affymetrix 7G scanner.

data_processing: Raw (CEL) files were Robust Multichip Average-normalized using the affy package in R/Bioconductor.

source_name: Carcinoma of lung, squamous cell

label_protocol: Samples were processed following the Affymetrix GeneChip® Whole Transcript Sense Target Labeling Assay manual. 300 ng of total RNA were applied for first cycle cDNA synthesis (first and second strand). After in vitro transcription, 10 µg of antisense copy RNA were subjected to second cycle cDNA synthesis followed by hydrolysis of copy RNA by RNase H. The sense strand cDNA (5.5 µg) was fragmented and biotin end-labeled.

extract_protocol: Human RNA samples used for this study had been purchased from OriGene Technologies

value: primary tumor

tag: histology

value: Carcinoma of lung, squamous cell (spindle cell)

tag: age [y]

tag: Sex

value: Male

tag: Stage

value: IIB

tag: tumor grade

value: AJCC G2:Moderately differentiated

tag: tnm


title: Benign mucinous ovarian tumour_335T

description:
MOT_335T
hybridized to SNP6


title: NSCLC_10_20111129

value: IB

value: Not Reported


title: Benign mucinous ovarian tumour_214T_Sty

description:
MOT_214T
hybridized to STYI 250K

value: mucinous


title: NSCLC_8_20111129

value: Female


title: SCLC_4_20111129

source_name: Carcinoma of lung, small cell

value: Adenocarcinoma

value: IIIA


title: Benign mucinous ovarian tumour_1735T

description:
MOT_1735T
hybridized to SNP6


title: Borderline mucinous ovarian tumour_289T_Nsp

description:
MOT_289T
hybridized to NSPI 250K

value: borderline


title: NSCLC_18_20111129

source_name: Carcinoma of lung, large cell

value: Carcinoma of lung, large cell (giant, clear)


title: NSCLC_9_20111129


title: SCLC_7_20111129

source_name: Carcinoma of lung, small cell, lymph node metastatic

value: metastasis (LN)

value: Carcinoma

value: IIA

value: AJCC G3:Poorly differentiated


title: normal_13_20111129

source_name: normal lung

value: normal lung

value: normal

value: Not applicable


title: Benign mucinous ovarian tumour_214T_Nsp

description:
MOT_214T
hybridized to NSPI 250K

value: ovarian tumor epithelium

value: benign


title: NSCLC_17_20111129

source_name: Adenocarcinoma of lung

value: primary tumor

value: Adenocarcinoma of lung (acin,pap,bronchalv,solid w/mucus)

value: IB


title: Benign mucinous ovarian tumour_8055T

description:
MOT_8055T
hybridized to SNP6

value: mucinous


title: Benign mucinous ovarian tumour_907T

description:
MOT_907T
hybridized to SNP6


title: NSCLC_14_20111129

value: Female

value: IA

value: AJCC G2:Moderately differentiated


title: Benign mucinous ovarian tumour_512T

description:
MOT_512T
hybridized to SNP6


title: NSCLC_7_20111129

source_name: Carcinoma of lung, non-small cell

value: Carcinoma of lung, squamous cell (spindle cell)

value: Male

value: IIB


title: NSCLC_13_20111129


title: NSCLC_6_20111129

source_name: Carcinoma of lung, neuroendocrine

value: Carcinoma of lung, large cell, neuroendocrine

value: Not Reported


title: NSCLC_15_20111129

value: AJCC G3:Poorly differentiated


title: Borderline mucinous ovarian tumour_289G_Nsp

description:
MOT_289G
hybridized to NSPI 250K

value: blood lymphocytes

value: borderline


title: Benign mucinous ovarian tumour_294S

description:
MOT_294S
hybridized to SNP6

value: ovarian tumor stroma


title: Benign mucinous ovarian tumour_372T

description:
MOT_372T
hybridized to SNP6

value: ovarian tumor epithelium

value: benign


title: NSCLC_1_20111129

value: primary tumor

value: Adenocarcinoma of lung (acin,pap,bronchalv,solid w/mucus)


title: NSCLC_4_20111129

value: IIIA


title: V4097

value: Small cell (oat, intermediate cell, combined oat)

value: Female

value: IB


title: V4098


title: NSCLC_5_20111129

value: Carcinoma of lung, large cell (giant, clear)


title: V4099


title: V4095

value: normal lung

value: normal

value: Not applicable


title: V4092

value: metastasis (LN)

value: Carcinoma

value: Male

value: IIA


title: V4096


title: V4094


title: V4093

value: AJCC G3:Poorly differentiated


title: NSCLC_2_20111129


title: NSCLC_3_20111129


title: Benign mucinous ovarian tumour_294T

description:
MOT_294T
hybridized to SNP6

value: ovarian tumor epithelium

value: mucinous


title: V4087

value: primary tumor

value: IA

value: Not Reported


title: V4089

value: Small cell (oat, intermediate cell, combined oat)


title: V4090


title: V4084

value: Adenocarcinoma

value: IIIA


title: V4088

value: IB


title: V4091


title: V4081

value: Adeno and small cell carcinoma

value: IIIB


title: V4086


title: V4080


title: Benign mucinous ovarian tumour_156S

description:
MOT_156S
hybridized to SNP6

value: ovarian tumor stroma

value: benign


title: V4074

value: normal lung

value: normal

value: Not applicable


title: V4079

value: Male

value: AJCC G3:Poorly differentiated


title: V4077


title: iSox2-DAOY_+Dox_rep1

city: Omaha

first: Angie

last: Rizzinio

state: NE

address: 986805 Nebraska Medical Center

department: Eppley Institute for Research in Cancer and Allied Diseases

institute: University of Nebraska Medical Center

description: 4F +Dox

hyb_protocol: Hybridization for 16 hours at 45C using the GeneChip® WT Terminal Labeling and Hybridization on Affymetrix GeneChip Human Gene 1.0 ST. Washing and staining were performed with the Affymetrix Fluidics Station 450.

scan_protocol: The gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G by the University of Nebraska Medical Center DNA Microarray Core Facility.

data_processing: Data was analyzed with Affymetrix Expression Console software (version 1.1.2 (64-Bit), Affymetrix, Santa Clara, CA) using Robust Multichip Analysis (RMA) for normalization.

source_name: iSox2-DAOY_doxycycline (0.5 µg/mL)_24 hours

label_protocol: Sense-strand cDNA was generated from 300ng total RNA using the Ambion WT Expression kit for Affymetrix Whole Transcript Expression Arrays. This cDNA was fragmented and labeled using the GeneChip® WT Terminal Labeling and Hybridization.

growth_protocol: Stock cultures of iSox2-DAOY (engineered from DAOY, obtained from ATCC, HTB-186, Manassas, VA) were cultured as described previously (Kingsley-Kallesen,M., 2001, PMID: 11776974).

extract_protocol: RNA isolation has been described previously (Kopp,J.L., 2008, PMID: 18238855).

treatment_protocol: FACS sorted CD133 low iSox2-DAOY cells were subculture onto tissue culture plastic at a density of 7.3x10^3 cells per cm^2. Twenty-four hours after subculture, doxycycline was added to the culture medium (0.5 µg/mL) of the +Dox sample. The -Dox sample was refed fresh medium without doxycycline. Twenty-four hours after the addition of doxycycline, RNA was isolated from iSox2-DAOY cells.

tag: cell line background

value: DAOY (ATCC, HTB-186)

tag: genotype/variation

value: expressing epitope-tagged Sox2 under the control of a doxycycline inducible promoter (iSox2-DAOY)

tag: cell type

value: medulloblastoma cells

tag: cell sub-popuation

value: FACS sorted CD133 low iSox2-DAOY cells

tag: treated with

value: doxycycline (0.5 µg/mL) for 24 hours


title: V4076

value: primary tumor

value: Small cell (oat, intermediate cell, combined oat)

value: Not Reported


title: V4078


title: Benign mucinous ovarian tumour_907S

description:
MOT_907S
hybridized to SNP6

value: mucinous


title: ESC scr shRNA

description: Gene expression data from D3 undifferentiated ES cells

hyb_protocol: Hybridization for 16 hours at 45C using the GeneChip® WT Terminal Labeling and Hybridization on Affymetrix GeneChip Mouse Gene 1.0 ST. Washing and staining were performed with the Affymetrix Fluidics Station 450.

data_processing: Data was analyzed with Affymetrix Expression Console software (Affymetrix, Santa Clara, CA) using Robust Multichip Analysis (RMA) for normalization.

organism: Mus musculus

source_name: D3 ESC treated with lentivirus expressing scr shRNA

growth_protocol: Stock cultures of D3 mouse ESC (ATCC number CRL-1934, obtained from T. Doetschman) were cultured as described previously (Kopp,J.L., 2008, PMID: 18238855). Culture medium was supplemented with 5 ng/ml leukemia inhibitory factor. Production of lentiviruses in 293T cells, including the lentivirus that expresses the scrambled shRNA sequence used in this study, has been described previously (Cox,J.L., 2011, PMID: 21750191). Lentiviral vectors for expression of shRNA sequences that target mouse Msi2 were obtained from Open Biosystems (RMM4534-NM_054043, Huntsville, AL). Msi2 shRNA lentiviral construct #1 used in this study corresponds to TRCN0000071973 with the mature sense sequence: CCCAGCTTAATATCTAGTTAA (Open Biosystems).

treatment_protocol: For treatment with the Msi2 shRNA #1 or scr shRNA, D3 ESC were seeded at a density of 100,000 cells per well in a 6-well plate. One day later, cells were infected with lentiviruses that express either the scrambled shRNA or shRNA #1 targeting Msi2. The protocol for infection of D3 ESC with lentiviruses has been described previously (Cox,J.L., 2011, PMID: 21750191). D3 ESC were infected with lentiviruses for 24 hours followed by selection with puromycin for 24 hours. Cells were subcultured 48 hours after puromycin selection at a low density (4,500 cells per cm2). Cells were maintained for 4 days in normal ES cell media followed by RNA isolation.

tag: knockdown

value: scramble

tag: cell line

value: D3 undifferentiated ES cells


title: V4075


title: ESC Msi2 shRNA

description: Gene expression data from D3 differentiated cells due to the knockdown of Msi2

source_name: D3 ESC treated with lentivirus expressing Msi2 shRNA

value: Msi2 shRNA

value: D3 differentiated cells


title: V4085

value: IA


title: V4073

value: normal lung

value: normal

value: Not applicable


title: Benign mucinous ovarian tumour_94S

description:
MOT_94S
hybridized to SNP6

value: ovarian tumor stroma

value: benign


title: V4071

value: Male

value: IIIA


title: V4070


title: WT STR PDE10i 13

city: Groton

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

description: Snap-frozen microdissected mouse brain region

hyb_protocol: Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 Gene Chips for 18 hours, then washed/stained according to manufacturer's recommendations using the Affymetrix 450 fluidics station.

scan_protocol: Gene chips were scanned using an Affymetrix 3000 array scanner.

data_processing: R/Bioconductor was used to apply the Robust Multi-Array Average (RMA) methodology to generate expression values for the combined samples.

source_name: WT striatum PDE10i

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed.

tag: strain

tag: genotype

value: WT

value: striatum

tag: treatment


title: Benign mucinous ovarian tumour_156T

description:
MOT_156T
hybridized to SNP6

tag: tissue

value: ovarian tumor epithelium

tag: tumor histology

tag: tumor diagnosis


title: Knockout 3

city: Montréal

first: greg

last: VOISIN

state: QC

address: 3840 Saint-Urbain

department: Département de Médecine, Centre de Recherche

country: Canada

institute: Centre Hospitalier de l'Université de Montréal Hôtel Dieu

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was preprocessed by the Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized.

source_name: breast tumor, Cyp27b1 knockout

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

growth_protocol: In vivo

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

value: Cyp27b1 flox/flox;Cre+

value: breast tumor

tag: genetic background

value: FVB


title: V5380

description: CI0000007037 - CR560698 - RN00001061

tag: histology

tag: age [y]

tag: Sex

value: Female

tag: Stage


title: iSox2-DAOY_-Dox_rep1

description: 4F -Dox

tag: cell line background

value: DAOY (ATCC, HTB-186)

tag: genotype/variation

value: expressing epitope-tagged Sox2 under the control of a doxycycline inducible promoter (iSox2-DAOY)

value: medulloblastoma cells

value: FACS sorted CD133 low iSox2-DAOY cells

value: none (control)


title: Knockout 2


title: Benign mucinous ovarian tumour_94T

description:
MOT_94T
hybridized to SNP6

value: mucinous


title: WT STR PDE10i 14


title: WT STR PDE10i 15


title: WT STR PDE10i 12


title: WT STR PDE10i 11


title: V5378

description: CI0000007037 - CR560698 - RN00001061

value: normal lung

value: normal

value: Not applicable

tag: tumor grade

tag: tnm


title: WT STR Veh 5

source_name: WT striatum Veh

value: vehicle control


title: Control 1

source_name: breast tumor, control

value: Cyp27b1 flox/flox;Cre-


title: WT STR Veh 4

value: WT

value: striatum


title: Benign mucinous ovarian tumour_276T

description:
MOT_276T
hybridized to SNP6

value: ovarian tumor epithelium

value: benign


title: WT STR Veh 3


title: WT STR PDE10i 10


title: V4082

value: primary tumor

value: Adenocarcinoma

value: Male

value: IIIA

value: Not Reported


title: Knockout 1

value: Cyp27b1 flox/flox;Cre+

value: breast tumor

value: FVB


title: Control 3


title: WT STR Veh 2


title: V5379

description: CI0000007037 - CR560698 - RN00001061

value: normal lung

value: Female


title: V5375

description: CI0000013164 - CR560573 - RN00001A55

value: normal

value: Not applicable


title: WT STR Veh 1

value: vehicle control


title: Control 2

value: Cyp27b1 flox/flox;Cre-


title: V5376

description: CI0000013164 - CR560573 - RN00001A55


title: KO STR PDE10i 39

source_name: KO striatum PDE10i

value: PDE10A KO

value: striatum


title: V4072

value: Small cell (oat, intermediate cell, combined oat)


title: WT HPC PDE10i 11

source_name: WT hippocampus PDE10i

value: WT

value: hippocampus


title: KO STR PDE10i 34


title: WT HPC PDE10i 14


title: V5371

description: CI0000013181 - CR560571 - RN00001A56

value: Male


title: WT HPC PDE10i 10


title: KO STR Veh 30

source_name: KO striatum Veh


title: V5369

description: CI0000013181 - CR560571 - RN00001A56


title: V5374

description: CI0000000104 - CR560046 - RN00000FC6


title: KO STR PDE10i 37


title: KO STR PDE10i 35


title: V5373

description: CI0000000104 - CR560046 - RN00000FC6


title: V5372

description: CI0000000104 - CR560046 - RN00000FC6


title: WT HPC PDE10i 15


title: KO STR Veh 28


title: V5367

description: CI0000018461 - CR562424 - RN000023E4


title: gills_pool3_Alberoni

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

institute: University of Padova

description: Pool consisting of 5 gills

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing:
Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software
Normalized intensities (null corresponds to missing spot; empty corresponds to control spot not included in the normalization)

organism: Ruditapes philippinarum

source_name: Pool of Ruditapes philippinarum gills sampled in Alberoni

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

value: gills

tag: sampling site

value: Alberoni


title: V5368

description: CI0000018461 - CR562424 - RN000023E4


title: KO STR Veh 26


title: WT HPC Veh 6

source_name: WT hippocampus Veh


title: A329P

city: Leicester

first: James

middle: Howard

last: Pringle

state: Leicestershire

address: Robert Kilpatrick Clinical Sciences Building Leicester Royal Infirmary

department: Department of Cancer Studies and Molecular Medicine

institute: University of Leicester

hyb_protocol: standard illumina hybridisation protocol

scan_protocol: standard illumina scanning protocol

data_processing: the data was normalised using quantile normalisation with the lumi package available in R

source_name: adenomatous polyp

label_protocol: Biotinylated cDNA was made using the Whole-Genome DASL Assay Profiling Reagent Kit

extract_protocol: RNA was extracted using TriReagent, followed by clean-up with QIAGEN RNeasy mini kit in accodance with the protocol described within the kit. QC was undertaken using qRT-PCR with RPL13a primers in accordance with Illumina's suggested QC protocol

treatment_protocol: Samples were microdissected and pre-treated with PK to allow overnight digestion prior to RNA extraction

tag: sample type

value: adenomatous polyp

tag: gender

value: female

tag: age


title: WT HPC PDE10i 12

tag: strain

tag: genotype

tag: treatment


title: A190P


title: KO STR Veh 25

tag: tissue


title: V5370

description: CI0000013181 - CR560571 - RN00001A56

source_name: normal lung


title: V5366

description: CI0000018461 - CR562424 - RN000023E4


title: A257P

value: male


title: WT HPC Veh 5


title: WT HPC PDE10i 13


title: KO STR Veh 29


title: gills_pool1_Alberoni

description: Pool consisting of 5 gills


title: A151P


title: A161P


title: V5365

description: CU0000005278 - CR561576 - RN00000A9A

value: normal lung


title: gills_pool3_Marghera

description: Pool consisting of 5 gills

source_name: Pool of Ruditapes philippinarum gills sampled in Marghera

value: Marghera


title: A53P


title: WT HPC Veh 4


title: V5364

description: CU0000005278 - CR561576 - RN00000A9A

value: normal

value: Female


title: gills_pool2_Marghera

description: Pool consisting of 5 gills


title: WT HPC Veh 2

value: vehicle control


title: V5363

description: CU0000005278 - CR561576 - RN00000A9A

value: Not applicable


title: KO HPC PDE10i 39

source_name: KO hippocampus PDE10i

value: PDE10A KO


title: V5362

description: CI0000008641 - CR561107 - RN00001208


title: Digestive gland_pool4_Alberoni

description: Pool consisting of 5 digestive glands

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Alberoni

value: digestive gland


title: HP161

source_name: hyperplastic polyp

value: hyperplastic polyp


title: Digestive gland_pool3_Alberoni

description: Pool consisting of 5 digestive glands


title: WT HPC Veh 3

value: WT


title: WT HPC Veh 1

value: hippocampus


title: A4P


title: V5361

description: CI0000008641 - CR561107 - RN00001208


title: gills_pool1_Marghera

description: Pool consisting of 5 gills


title: A10P


title: gills_pool2_Alberoni

description: Pool consisting of 5 gills


title: HP75


title: Digestive gland_pool1_Alberoni

description: Pool consisting of 5 digestive glands


title: KO HPC PDE10i 36


title: KO HPC PDE10i 35


title: V5322

description: CI0000008641 - CR561107 - RN00001208


title: V5321

description: CU0000005332 - CR561589 - RN0000095F

value: Male


title: Digestive gland_pool2_Marghera

description: Pool consisting of 5 digestive glands

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Marghera


title: KO HPC PDE10i 37


title: HP39


title: Digestive gland_pool3_Marghera

description: Pool consisting of 5 digestive glands


title: HP27


title: V5320

description: CU0000005332 - CR561589 - RN0000095F


title: HP25


title: KO HPC PDE10i 34


title: V5318

description: CU0000005967 - CR561388 - RN000017B3


title: V5319

description: CU0000005332 - CR561589 - RN0000095F


title: HP3


title: HP10


title: KO HPC Veh 30

source_name: KO hippocampus Veh


title: V5317

description: CU0000005967 - CR561388 - RN000017B3


title: KO HPC Veh 26


title: KO HPC Veh 28


title: V5316

description: CU0000005967 - CR561388 - RN000017B3


title: Digestive gland_pool1_Marghera

description: Pool consisting of 5 digestive glands


title: KO HPC Veh 25


title: S/shRB-E2F7 IMR90, biological rep2

city: New York

first: Ozlem

last: Aksoy

state: NY

address: 415 East 68th Street

department: Watson School of Biological Sciences

institute: CSHL

description: Gene expression data from Ras expressing IMR90 cells with RB and E2F7 hairpin

hyb_protocol: Hybridization was as described in Expression Analysis Technical Manual Affymetrix P/N 702232 Rev 2, (16 hours, 45 degress at 60 rpm), the Wash and Stain Protocol was as described in FS450_0004 using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Scanning was performed using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with the gc-RMA (Robust Multi-Array Averaging with GC content correction) method of BioConductor R package to subtract background normalize intensities and summarize gene expression level.

source_name: Ras expressing  IMR90 with both RB and E2F7 hairpin_B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human IMR90 cells with different conditions were grown at 37C at 5%CO2. Total RNA was extracted seven (7) days after the end of puromycin selection.

extract_protocol: Total RNA was extracted with the Rneasy Mini Kit (QUIAGEN), utilized for cRNA expression with Message AmpII (Ambion) and hybridized to U133 Plus 2.0 microarray (Affymetrix) according to the manufacturer's instructions.

treatment_protocol: Cells were infected with retroviruses expressing shRNA and ras.

tag: cell line

tag: cell state

value: senescent

value: infected with Ras and RB and E2F7 hairpins


title: S/shE2F7 IMR90, biological rep2

description: Gene expression data from Ras expressing IMR90 cells with E2F7 hairpin

source_name: Ras expressing  IMR90 with E2F7 hairpin_B

value: infected with Ras and E2F7 hairpin


title: KO HPC Veh 29


title: V5314

description: CU0000005265 - CR561643 - RN00000964

tag: histology

tag: age [y]


title: S/shRB-E2F7 IMR90, biological rep1

source_name: Ras expressing  IMR90 with both RB and E2F7 hairpin_A


title: NC68

source_name: normal colonic mucosa

value: normal colonic mucosa

value: female


title: NC292


title: NC54


title: V5315

description: CU0000005265 - CR561643 - RN00000964

value: normal lung

tag: Sex

tag: Stage


title: NC49

value: male


title: V5312

description: CI0000000029 - CR560259 - RN00000E25

value: normal


title: HP13


title: NC37


title: S/shRB IMR90, biological rep2

description: Gene expression data from Ras expressing IMR90 cells with RB hairpin

source_name: Ras expressing  IMR90 with RB hairpin_B

value: infected with Ras and RB hairpin


title: V5313

description: CU0000005265 - CR561643 - RN00000964


title: V5310

description: CI0000000029 - CR560259 - RN00000E25

value: Female


title: S/shE2F7 IMR90, biological rep1

source_name: Ras expressing  IMR90 with E2F7 hairpin_A


title: NC3


title: S/shRB IMR90, biological rep1

source_name: Ras expressing  IMR90 with RB hairpin_A


title: S/shLuc IMR90, biological rep2

description: Gene expression data from Ras expressing IMR90 cells with control hairpin (shLuciferase)

source_name: Ras expressing IMR90 with control hairpin shLuciferase_B

value: infected with Ras and control hairpin (shLuciferase)


title: V5311

description: CI0000000029 - CR560259 - RN00000E25

value: Not applicable


title: S/shLuc IMR90, biological rep1

source_name: Ras expressing IMR90 with control hairpin shLuciferase_A


title: V5308

description: CI0000006947 - CR559282 - RN00001060


title: NC5


title: Growing IMR90, biological rep2

description: Gene expression data from growing IMR90 cells

source_name: Growing IMR90_B

value: growing


title: Growing IMR90, biological rep1

source_name: Growing IMR90_A


title: V5309

description: CI0000006947 - CR559282 - RN00001060

source_name: normal lung


title: NC2


title: V5307

description: CI0000006947 - CR559282 - RN00001060


title: V5377

description: CI0000013164 - CR560573 - RN00001A55


title: 9688 micro PSY 3

status: Public on Aug 24 2012

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum strain 9688 grown microaerobically

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com).

organism: Bradyrhizobium japonicum

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase which corresponded to an OD600 of 0.4 to 0.5 in microoxic cultures (PSY-arabinose medium)

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

treatment_protocol: Where indicated cultures were treated with 2 mM H2O2 for 10 min immediately prior to cell harvest

tag: growth condition

value: microaerobiosis

tag: medium

value: PSY


title: 9688 micro 2mM H2O2 10min PSY 3

description: B. japonicum strain 9688 grown microaerobically treated with 2 mM H2O2 for 10 min

source_name: B. japonicum strain 9688 grown microaerobically stressed with 2 mM H2O2 for 10 min

value: 2 mM H2O2, 10 min


title: 9688 micro PSY 2

source_name: B. japonicum strain 9688 grown microaerobically


title: 9688 micro 2mM H2O2 10min PSY 2


title: 0202 micro 2mM H2O2 10min PSY 2

description: B. japonicum strain 0202 grown microaerobically treated with 2 mM H2O2 for 10 min

source_name: B. japonicum strain 0202 grown microaerobically stressed with 2 mM H2O2 for 10 min


title: 9692 micro PSY 2

description: B. japonicum strain 9692 grown microaerobically


title: 9692 micro PSY 1

source_name: B. japonicum strain 9692 grown microaerobically


title: 9688 micro 2mM H2O2 10min PSY 1


title: 9688 micro PSY 1


title: 0202 micro PSY 2

description: B. japonicum strain 0202 grown microaerobically


title: 0202 micro PSY 1

source_name: B. japonicum strain 0202 grown microaerobically


title: 110spc4 micro 2mM H2O2 10min PSY 3

description: B. japonicum strain 110spc4 grown microaerobically treated with 2 mM H2O2 for 10 min

source_name: B. japonicum strain 110spc4 grown microaerobically stressed with 2 mM H2O2 for 10 min

value: 110spc4 (wild type)


title: 110spc4 micro 2mM H2O2 10min PSY 1


title: 0202 micro 2mM H2O2 10min PSY 1


title: 9692 micro PSY 3


title: LIVER EXP2 Liver13 GluMspI

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

institute: University of Toronto

description: Post mortem liver samples from databanks: Curline & Cambridge Biosci.

hyb_protocol: Approximately 9 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. All array sets were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000 7G

data_processing:
We distinguished between three types of probes on the tiling microarray: “target probes”, which contain the restriction site CCGG, “flanking probes”, which do not contain the recognition sequence but could lie up to 200 bp upstream or downstream of a target probe (sheared DNA fragments were of average 200 bp), and “non-target probes” that neither contain a target sequence nor are within 200 bp (on either side) of the target sequence. After comparing different array preprocessing algorithms, we chose to use a sequence-based algorithm after Potter et al (Supplementary Note). The model (Supplementary Note, equation 1) was applied to non-target probes matched proportionally to target probes by GC content.  Normalized intensities were obtained by subtracting the fitted value from raw probe intensities, resulting in a normal distribution of probe-level intensities.  Each chip was independently normalized.  All downstream analyses were carried out at the single-probe level (i.e. without windowing or peak-calling) and solely on target probes. Probes overlapping repeats were excluded. Probes were required to have a ‘CCGG’ in both the Affymetrix probe sequence and the chromosomal sequence downloaded from UCSC; probes that did not meet this criterion were excluded.
EXP2_Human_BrainLiver_sample_metadata.xls, HumanBrain_sample_metadata.xls
BED files of normalized intensities for target probes. Unless otherwise specified, probes overlapping repeats are excluded. Unless otherwise specified, target probes that did not contain a CCGG in the UCSC genome sequence were also excluded.

source_name: Liver

label_protocol: 9 ug of PCR amplified DNA products were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: Human and mouse untreated tissues were analyzed in this study

extract_protocol: Genomic DNA was extracted applying standard phenol chloroform and isopropanol precipitation method. Genomic DNA was then sheared to 200bp fragment length on Covaris S2 sonifier (Covaris, USA); blunt ended and ligated to adaptors before subjecting for glucosylation and restriction enzyme digestion. Glucosylation reaction was performed in presence of 200 µM uridine-5’-diphospho-α -D-glucose (UDP-Glc, Sigma) and 80ng BGT (Lariviere, Kurzeck et al. 2002) in 100mM Tris-HCl (pH 8.0) and 25mM MgCl2 for 3 h at 37ºC.

treatment_protocol: No treatment for human and mouse tissues. Only one human cell line underwent SAHA treatment protocol; stated in the sample description.

tag: age (y)

value: F

tag: post-mortem interval

value: Liver

tag: enzymatic digestion

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: LIVER EXP2 Liver8 GluMspI

value: M


title: LIVER EXP2 Liver4 GluMspI


title: LIVER EXP2 Liver2 GluMspI