title: JCW25 Vs JCW26 0min (replicate 2)

description: JCW25 Vs JCW26 0min (P2)

source_name: Saccharomyces cerevisiae JCW25 strain, 0min

value: Grown to log phase at 26C

source_name: Saccharomyces cerevisiae JCW26 strain, 0min


title: 7214T_r3 (Affymetrix A354-09)

status: Public on Dec 03 2009

type: genomic

city: Cambridge

first: Christina

last: Curtis

address: Robinson Way

department: Computational Biology/Oncology

country: United Kingdom

institute: University of Cambridge

description:
Genomic DNA extracted breast tumours was profiled for copy number alterations using the Affymetrix SNP5.0 platform
Data were corrected for allelic-crosstalk and fragment length. Probe-level data were summarized such that probe signals for SNP probes were averaged across replicates and summarized between alleles, while non-polymorphic probes were reported as is.

hyb_protocol: Samples were hybridized according to the manurfacturer's protocol

scan_protocol: Samples were scanned according to the manurfacturer's protocol

data_processing: Data were processed using SNP-RMA implemented in the aroma.affymetrix package

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast carcinoma

label_protocol: Samples were labeled according to the manurfacturer's protocol

extract_protocol: Genomic DNA from breast tumors and matched normals was extracted with Qiagen's Dneasy kit. The extractions were not done manually but using Qiagen's Quiacube. Input = 20x10um sections per sample.

tag: sample


title: CHOP0054

type: RNA

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

country: USA

institute: Childrens Hospital of Philadelphia

hyb_protocol: Illumina Human 6 expression Bead chip standard protocol

molecule: total RNA

source_name: tumor RNA

extract_protocol: Trizol RNA extraction reagent protocol

tag: tissue type

value: neuroblastoma

value: primary tumor

tag: mycn status

tag: gender

tag: inss

tag: risk

tag: ploidy

tag: age

tag: shimada


title: 7207T_r2 (Affymetrix A354-05)


title: 7206T_r3 (Affymetrix A354-03)


title: 7214T_r1 (Affymetrix A354-07)


title: 7195T_r1 (Affymetrix A354-10)


title: CHOP0166

scan_protocol: Illumina Human 6 expression Bead chip standard protocol


title: CHOP0249

data_processing: Illumina Human 6 expression Bead chip standard protocol


title: CHOP0237

label_protocol: Illumina Human 6 expression Bead chip standard protocol


title: CHOP0060

growth_protocol: Illumina Human 6 expression Bead chip standard protocol


title: CHOP0038

treatment_protocol: Illumina Human 6 expression Bead chip standard protocol


title: CHOP0047


title: 7207T_r3 (Affymetrix A354-06)


title: JCW25 Vs JCW26 120min (replicate 1)

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

country: Spain

institute: IDAEA-CSIC

description: JCW25 Vs JCW26 120min (P1)

hyb_protocol: Microarray prehybridization was performed in 5x SSC (SSC: 150 mM NaCl, 15mM Na-citrate, pH 7.0), 0.1% SDS, 1%BSA at 42ºC for 45 min. (Fluka, Sigma-Aldrich, Buchs SG, Switzerland). Labeled cDNA was dried in a vacuum trap and used as probe after resuspension in 110 μl of hybridization solution (50% Formamide, 5xSSC, 0.1% SDS, 100 μg/ml salmon sperm from Invitrogen, Carlsbad, CA, USA). Hybridization and washing were performed in a Lucidea Slide Pro System (GE Healthcare, Uppsala, Sweden).

scan_protocol: GenePix 4000B fluorescence scanner and analyzed by Genepix® Pro 6.0 software (Axon Instruments, MDS Analytical Technologies, Toronto, Canada).

data_processing: Data was filtered according to spot quality. Only those spots with intensities at least twice the background signal and with at least 75% of pixels with intensities above background plus two standard deviations were selected for further calculations. Following these  criteria, over 70% of spots in each array were usually found suitable for further analysis. Ratio of medians was used to calculate the VALUEs.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae JCW25 strain, 120min

label_protocol: 20 µg of total RNA were used for cDNA synthesis and labeling with Cy3-dUTP and Cy5-dUTP fluorescent nucleotides, following indirect labeling protocol (CyScribe postlabeling kit, GE-Healthcare). Labeling efficiency was evaluated by measuring Cy3 or Cy5 absorbance in Nanodrop Spectrophotometer.

growth_protocol: Yeast cells were grown in minimal media until logarithmic phase.

extract_protocol: Total RNA extracted by RiboPure RNA extraction kit (Ambion) following manufacturer's instructions.

treatment_protocol: Upon reaching logarithmic phase, cells were passed to 35C to inactivate top2. Samples were taken at 0 and 120 min top2 inactivation (35C).

tag: strain

tag: treatment

value: After growth to log phase, 120min at 35C

source_name: Saccharomyces cerevisiae JCW26 strain, 120min

tag: genotype

value: FY251 carrying allele top2-4


title: JCW25 Vs JCW26 0min (replicate 3)

description: JCW25 Vs JCW26 0min (P3)


title: 7207T_r1 (Affymetrix A354-04)


title: 7206T_r2 (Affymetrix A354-02)


title: 7214T_r2 (Affymetrix A354-08)


title: JCW25 Vs JCW26 0min (replicate 1)

description: JCW25 Vs JCW26 0min (P1)


title: Streptococcus suis 40C vs 37C

status: Public on Dec 02 2009

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

country: China

institute: Institute of Microbiology and Epidemiology

description: Streptococcus suis serotype 2 (SS2) is able to cause human infections ranging from superficial wounded skin infections to severe invasive infections such as meningitis and streptococcal toxic shock-like syndrome (STSLS). During its infection cycle, SS2 must acclimatize itself to temperature shift. Herein, a whole-genome DNA microarray was used to investigate the global transcriptional regulation of an invasive SS2 strain grown to late-exponential phase at 40 relative to 37°C. The detecting differentially regulated genes included those encoding virulence factors, antigenic proteins, ABC transporters and unknown functions. Our data provided a global profile of gene transcription induced by temperature alteration and shed light on some unforeseen lines for further pathogenesis investigation.

hyb_protocol: For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Accordingly, for each time point, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5X SSC, 0.1% SDS and 0.1% BSA) at 42°C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then blown to dry with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt’s solution, and 0.5 µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98°C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42°C for 18 to 20 hr in a hybridization incubator (Robbins Scintific). After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 1 min. The slides were blown dry for scanning.

scan_protocol: The hybridized slides were scanned at a resolution of 10 µm by using a GenePix Personal 4100A Microarray Scanner (Axon Instruments). The scanning images were processed and the data were further analyzed by using GenePix Pro 5.0 software (Axon Instruments) combined with Microsoft Excel software.

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 5.0 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two folds of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods. The normalized log2 ratio of reference/test signal for each spot was recorded. Genes with less than four data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the four replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software using one class mode. After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.

label: Cy3 or Cy5

organism: Streptococcus suis 05ZYH33

source_name: Streptococcus suis, reference 37°C

label_protocol: A cDNA microarray imprinted with 2194 genes representing about 97% of Streptococcus.suis genome was used for transcriptome analysis. For two-sample (reference versus test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Accordingly, for each time point, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. 20 µg of total RNA was mixed with 3µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript Ⅲ reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 50°C for 1 hr, after which an additional 200 U of Superscript Ⅲ reverse transcriptase was added. The mixture was then incubated at 50°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 15 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then was labeled by the addition of 1/10 of one reaction vial of Cy3 or Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark.

extract_protocol: Before bacterial harvest, double-volume of RNAprotect Bacteria Reagent (Qiagen) was added immediately to each cell culture. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter) as mentioned in our previous report . RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

tag: growth

value: late exponential growth phase

source_name: Streptococcus.suis, test 40°C


title: Ketogenic diet replicate 2

city: Gangneung

first: Dojun

last: Yoon

state: Gangwon

address: 522 Naegokdong

department: Biochemistry, Medical College

country: South Korea

institute: Kwandong University

description: Duplicated in one chip

hyb_protocol: 20ml hybridization buffer were applied and samples were incubated at 58 oC for 16 h

scan_protocol: Scanned on ScanArray Lite (Packard BioScience) and quantified using GenePix Pro software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Rattus norvegicus

source_name: Ketogenic diet-fed rat brain

label_protocol: Indirect labeling of 40 mg total RNA

growth_protocol: Rats were fed diet for 4 weeks.

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

treatment_protocol: Kainic acid (8mg/kg) were administered i.p.

value: Sprague-Dawley

value: male

source_name: Normal diet-fed rat brain


title: Ketogenic diet replicate 1

description: Duplicated in one chip


title: Streptococcus suis 29C vs 37C

description: Streptococcus suis serotype 2 (SS2) is able to cause human infections ranging from superficial wounded skin infections to severe invasive infections such as meningitis and streptococcal toxic shock-like syndrome (STSLS). During its infection cycle, SS2 must acclimatize itself to temperature shift. Herein, a whole-genome DNA microarray was used to investigate the global transcriptional regulation of an invasive SS2 strain grown to late-exponential phase at 29 relative to 37°C. The detecting differentially regulated genes included those encoding virulence factors, antigenic proteins, ABC transporters and unknown functions. Our data provided a global profile of gene transcription induced by temperature alteration and shed light on some unforeseen lines for further pathogenesis investigation.

source_name: Streptococcus.suis, test 29°C


title: MEFs mTR WT 1

status: Public on Dec 01 2009

city: Baltimore

first: Carol

last: Greider

state: MD

address: 725 N Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis and processing used GCOS 1.4 with the Expression Console PLIER algorithm and the manufacturer’s specifications.

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter random primers for cDNA synthesis, and Invitrogen SuperScript II reverse transcriptase (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol:
DMEM + 10% FBS + 1X PSG + 1X Normocin
37C, 5% CO2
passage number: 5

extract_protocol:
extraction with Trizol reagent
clean-up with RNeasy kit (QIAGEN)

value: mTR WT

tag: cell type

value: embryonic fibroblasts

tag: developmental stage

tag: passage number


title: MEFs mTR KO G1 1

growth_protocol:
DMEM + 10% FBS + 1X PSG + 1X Normocin
37C, 5% CO2
passaged every 3 days

extract_protocol:
extraction using Trizol reagent
clean-up using RNeasy kit (QIAGEN)

value: mTR KO

tag: generation


title: OM-OECs vs. OB-OECs, 1

city: Rouen

first: nicolas

last: guerout

state: Normandy

address: 22 Bd Gambetta

country: France

institute: Faculty of medecine of Rouen

description: Biological replicate 1 of 4.

hyb_protocol: The corresponding Cy3- and Cy5-labeled cDNAs were combined and hybridized overnight (17 hours, 65°C) to Agilent Whole Rat Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Agilent's DNA microarray scanner (Agilent Technologies).

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.1). Agilent Feature Extraction Software was used for background subtraction and Linear LOWESS normalization.

molecule: polyA RNA

source_name: Olfactory mucosa OECs

label_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure. The amplification is based on a global PCR protocol using mRNA-derived cDNA. 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec's undisclosed protocol. OM-OECs are labeled with Cy5 and OB-OECs are labeled with Cy3.

growth_protocol: OM-OECs and OB-OECs were cultivated with the same protocol (A. Ramon-Cueto and M. Nieto-Sampedro, 1992).

extract_protocol: Cell samples were lysed using SuperAmp Lysis Buffer and stored appropriately according to the instructions of the SuperAmp Preparation Kit (Miltenyi Biotec). mRNA was isolated via magnetic bead technology.

value: Fischer

tag: tissue

value: olfactory mucosa

value: olfactory ensheathing cells

source_name: Olfactory bulb OECs

value: olfactory bulb


title: OM-OECs vs. OB-OECs, 3

description: Biological replicate 3 of 4.


title: MEFs mTR KO G1 3


title: 7206T_r1 (Affymetrix A354-01)

tag: sample


title: CHOP0008

tag: tissue type

tag: mycn status


title: MEFs mTR KO G1 2

tag: gender


title: OM-OECs vs. OB-OECs, 4

description: Biological replicate 4 of 4.


title: MEFs mTR WT 3


title: MEFs mTR WT 2


title: Liver mTR WT 2

source_name: liver, homogenized in Trizol

value: liver


title: MEFs mTERT KO G1 3

value: mTERT KO


title: Liver mTR WT 3


title: OM-OECs vs. OB-OECs, 2

description: Biological replicate 2 of 4.


title: Liver mTR KO G1 3


title: MEFs mTERT WT 1

value: mTERT WT


title: Liver mTR KO G1 2


title: MEFs mTERT WT 3


title: MEFs mTERT KO G1 2


title: MEFs mTERT KO G1 1


title: MEFs mTERT WT 2


title: Liver mTERT WT 3


title: Liver mTERT KO G1 2


title: Liver mTERT WT 2


title: Liver mTR WT 1


title: Liver mTERT WT 1


title: Liver mTERT KO G1 3


title: Liver mTERT KO G1 1


title: Liver mTR KO G1 1


title: T790M 2

city: Nashville

first: William

last: Pao

state: TN

address: 2220 Pierce Avenue, 777 Prestion Research Building

institute: Vanderbilt University

description: T790M tumor

hyb_protocol: Hybridization was performed as per standard protocols from the MSKCC Genomics Core Laboratory.

scan_protocol: GCOS image processing

data_processing: The data were normalized using the robust multichip average (RMA) method using the R/Bioconductor package rma.

source_name: lung

label_protocol: Biotin-labeling was performed as per standard protocols  from the MSKCC Genomics Core Laboratory.

growth_protocol: Harvested tissue was flash frozen immediately in liquid nitrogen.

extract_protocol: Total mRNA was extracted using Trizol (Invitrogen) as per manufacturer's instructions.

treatment_protocol: The following samples were analyzed: macro-dissected visible tumor nodules from bitransgenic animals (C/L858R (n=4), C/L+T (n=5) and C/T790M (n=5)) fed a dox-containing diet for 3 to 6 months, and normal lung tissue (n=10) derived from transgene-negative or mono-transgenic littermates on dox.

value: FVB

tag: type

value: bitransgenic T790M


title: T790M 3

description: T790M tumor


title: Normal 3

description: normal lung

value: FVB mixed

value: normal


title: T790M 1

description: T790M tumor


title: Grape berry pool

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: Scanning was performed on a GenePix 4000B scanner. Laser was set at 33% power and PMT at 650.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software.

organism: Vitis vinifera

source_name: Berry pool

label_protocol: Five µg of the same pool of total RNA used for 454 sequencing were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

growth_protocol: Vitis vinifera cv Corvina (clone 48) plants were grown in an experimental vineyard in the Verona Province (San Floriano, Verona, Italy).

extract_protocol: Total RNA was extracted according to Rezaian (doi:10.1016/S0166-0934(00)00211-1) from samples at each time point and equal quantities of total RNA were pooled together for a total of 300 ug of total RNA.

treatment_protocol:
30 clusters were collected for each sampling time-point, and 12 berries were sampled from each cluster to form a pool for each time-point.
Collection date Sample Name
03/08/05 Véraison
22/08/05 Ripening I
15/09/05 Ripening II
18/10/05 Withering I
17/11/05 Withering II
14/12/05 Withering III

tag: Cultivar

value: Corvina


title: Normal 5

description: normal lung


title: T790M 4

description: T790M tumor


title: L858R+T790M 4

description: L858R+T790M tumor

value: bitransgenic L858R+T790M


title: L858R+T790M 5

description: L858R+T790M tumor


title: Normal 1

description: normal lung


title: Normal 2

description: normal lung


title: L858R+T790M 3

description: L858R+T790M tumor


title: L858R+T790M 1

description: L858R+T790M tumor


title: L858R+T790M 2

description: L858R+T790M tumor


title: L858R 4

description: L858R tumor

value: bitransgenic L858R


title: L858R 3

description: L858R tumor


title: T790M 5

description: T790M tumor


title: L858R 2

description: L858R tumor


title: Normal 4

description: normal lung


title: control 5

description: normal lung


title: NP14_aGS

city: Lübeck

first: Jens

middle: K

last: Habermann

address: Ratzeburger Allee 160

department: Department of Surgery

country: Germany

institute: University Clinic Schleswig-Holstein (UKSH), Campus Lübeck

description: for clinical data please see table 1 in habermann jk et al. the gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome. int j cancer 2009; 124: 1552-1564

hyb_protocol: Sample RNA and universal human reference RNA (Stratagene, La Jolla, CA) were then amplified for one round using RiboAmp RNA Amplification Kit (Arcturus, Mountain View, CA).  All amplified RNA samples were hybridized against amplified reference RNA using a slightly modified protocol from Hedge and colleagues (Hegde P et al. A concise guide to cDNA microarray analysis. BioTechniques 2000;29(3):548-50, 52-4, 56 passim.). Each sample was hybridized against the reference RNA in a humid chamber (ArrayltTM Hybridization Cassette, TeleChem Intl., Sunnyvale, CA) for 16 hours at 42ºC and washed.  In order to account for potential amplification bias, total RNA was hybridized following the same protocol for 11 samples (20 ug each).  We used customized arrays obtained from the National Cancer Institute’s microarray core facility.  Arrays were used from one print batch and composed of 9,128 cDNAs denatured and immobilized on a poly-L-lysine-coated glass surface.  The gene annotation file (GAL file) used (Hs-UniGEM2-v2px-32Bx18Cx18R.gal) can be found at the facilities website http://nciarray.nci.nih.gov.

scan_protocol: Each sample was scanned by the Axon GenePix 4000B Scanner (Axon Instruments, Union City, CA). GenePix software version 4.0.1.17 was used to apply the GAL file through an interactive gridding process (Korn EL et al. An objective method of comparing DNA microarray image analysis systems. BioTechniques 2004;36(6):960-7.)

data_processing: All values that did not meet the quality control criteria were treated as missing values (Supplementary Materials, Habermann JK et al. The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome. Int J Cancer 2009; 124:1552-1564) Intensity ratios were calculated using the background corrected median intensities that were normalized with the locally weighted scatter plot smoother (LOWESS) algorithm for each print-tip group.  The fraction of data points used in the local regression (f) was 0.1 and other parameters were adjusted as suggested by Cleveland (Cleveland WS. Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc 1979;74(368):829-36)  The value of f was determined using two self versus self experiments.  All within-slide normalized ratios were log-transformed (natural base).

source_name: Breast cancer

label_protocol: In brief, 3 ug of amplified RNA was reverse transcribed using random primers and converted into cDNA using reverse transcriptase.  After incorporation of aminoallyl-conjugated nucleotides, the RNA was indirectly labelled with Cy3 (tumor RNA) and Cy5 (reference RNA, Amersham, Piscataway, NJ).

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) followed by Qiagen RNeasy column purification (Qiagen, Valencia, CA).

treatment_protocol: Tumor tissue was removed surgically, and later snap frozen.

tag: ploidy

value: aGS

source_name: cancer cell lines

extract_protocol: Total RNA was supplied by Stratagene, La Jolla, CA

value: Universal human reference RNA


title: A06_aGU

value: aGU


title: D15_dGS

value: dGS


title: NP12_aGS

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) followed by RNeasy column purification (Qiagen).


title: D14_dGS


title: control 4

description: normal lung


title: A05_aGU


title: NP17_aGS


title: L858R 1

description: L858R tumor


title: A15_aGU


title: A17_aGU


title: A18_aGU


title: D12_dGS


title: A10_aGU


title: NP11_aGS


title: D08_dGS


title: control 2

description: normal lung


title: control 1

description: normal lung


title: NP16_aGS


title: A19_aGU


title: NP10_aGS


title: A12_aGU


title: A04_aGU


title: control 3

description: normal lung


title: D21_dGS


title: D23_dGS


title: D09_dGS


title: NP20_aGS


title: D19_dGS


title: NP08_aGS

source_name: Breast tumor


title: NP13_aGS


title: A16_aGU


title: D16_dGS


title: NP06_aGS


title: D03_dGS


title: A03_aGU


title: NP01_aGS


title: A02_aGU


title: A14_aGU


title: A07_aGU


title: D25_dGS


title: NP02_aGS


title: NP18_aGS


title: NP22_aGS


title: A20_aGU


title: A01_aGU


title: D05_dGS


title: Berry_pool_2

source_name: Berry pool from 6 time points from veraison to whitering

growth_protocol: Vitis vinifera cv Corvina (clone 48) were grown in an experimental vineyard in the Verona Province (San Floriano, Verona, Italy).


title: D07_dGS


title: NF1-unaffected #21

status: Public on Nov 30 2009

city: Bethesda

first: Alexander

last: Pemov

address: 49 Convent Drive

institute: National Institutes of Health

hyb_protocol: Amplified biotinylated cRNA (1.5 ug) were hybridized to HumanWG-6_v2 Sentrix BeadChips. In all steps, care was exercised to avoid batch effects. Samples were hybridized to the microarrays at 55ºC for 16-17 hours. Microarrays were washed to remove non-specifically bound cRNA, stained with 1 mg/mL Streptavidin-Cy3 (GE Healthcare, Piscataway, NJ, USA) and dried.

scan_protocol: Microarrays were scanned in BeadStation 500 scanner. Image acquisition and initial image analysis were done with Illumina BeadScan and BeadStudio applications.

data_processing:
Raw data from the Illumina BeadChips was corrected for background and quantile normalized using BeadExplorer (version 1.5.0), a Bioconductor module developed for quality control, normalization, annotation and exploration of Illumina BeadChip data. Average detection value was calculated for each transcript, and the transcripts with average detection values below 0.99 were excluded from further analysis.

Non-normalized data is available in the 'GSE18444_non-normalized_data.txt' file, which is linked to the Series GSE18444 record as a supplementary file.

source_name: Coriell Cell Repository, LCL GM09688

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit (Ambion Inc., Austin, TX) per the manufacturer's instuctions.

growth_protocol: All NF1-affected and -unaffected banked lymphoblastoid cell lines (LCLs; Epstein-Barr virus (EBV)-transformed peripheral blood B-cell lymphocytes) from human kindred with neurofibromatosis type 1 were obtained from the Coriell Institute (pedigree 2176; Camden, NJ, USA). Cultures were maintained in an incubator at 37oC with 5% CO2 in T25 flasks in medium with RPMI 1640 supplemented with 2 mM L-glutamine, 100 Units/mL penicillin, 100 mg/mL streptomycin and 15% heat inactivated fetal bovine serum (all tissue culture reagents were from Gibco/Invitogen, Carlsbad, CA, USA).  Cultures were grown to a density from 0.9 x 106 to 1.3 x 106 cells/mL and harvested in Trizol reagent (Invitrogen, Carlsbad, CA, USA).

extract_protocol: Trizol cell lysates were mixed with chloroform (1/5 of lysate volume), vortexed for one minute and centrifuged in a table-top centrifuge at 13,000 rpm for 15 min at 4ºC. The aqueous phase was used for RNA isolation. The aqueous phase was mixed with equal volume of 70% ethanol and immediately loaded onto RNeasy mini columns (Qiagen, Valencia, CA, USA), with subsequent steps performed as per the manufacturer’s protocol. The RNA quality was estimated on a 2100 Bioanalyzer, RNA 6000 Nano Chips (Agilent, Santa Clara, CA, USA). Samples with RNA integrity number (RIN) of 8.0 and above were used for further analysis.

treatment_protocol: None.

value: lymphoblastoid cells

tag: nf1-affectation status

value: Unaffected

tag: age (years)

value: Not available

value: Male


title: NF1-unaffected #16

source_name: Coriell Cell Repository, LCL GM09638

value: Female


title: NF1-unaffected #20

source_name: Coriell Cell Repository, LCL GM09652


title: NF1-unaffected #15

source_name: Coriell Cell Repository, LCL GM09635


title: D13_dGS


title: Berry_pool_1

label_protocol: ive µg of the same pool of total RNA used for 454 sequencing were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

extract_protocol: Total RNA was extracted according to Rezaian (doi:10.1016/S0166-0934(00)00211-1) from samples at each time point and equal quantities of total RNA were pooled together for  a total of 300 ug of total RNA.

treatment_protocol:
30 clusters were collected for each sampling time-point, and 12 berries were sampled from each cluster to form a pool for each time-point.
Collection date	Sample Name
03/08/05	Véraison
22/08/05	Ripening I
15/09/05	Ripening II
18/10/05	Withering I
17/11/05	Withering II
14/12/05	Withering III


title: NF1-unaffected #19

source_name: Coriell Cell Repository, LCL GM09651


title: NF1-unaffected #4

source_name: Coriell Cell Repository, LCL GM09617


title: NF1-unaffected #6

source_name: Coriell Cell Repository, LCL GM09625


title: NF1-affected #24

source_name: Coriell Cell Repository, LCL GM09693

value: Affected


title: NF1-affected #8

source_name: Coriell Cell Repository, LCL GM09627


title: NF1-affected #1

source_name: Coriell Cell Repository, LCL GM09534


title: TEL-AML1-SNP-#38-remission-50kxba

status: Public on Sep 02 2009

city: Memphis

first: Charles

middle: G

last: Mullighan

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Leukemia remission samples that correspond to those leukemia blast samples that have specific genetic lesions.

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

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

data_processing: CEL files were generated using GeneChip Operating Software v 3.0 and SNP calls generated using GeneChip DNA Analysis Software (GDAS) v 3.0 or Affymetrix GeneChip Genotyping Analysis Software (GTYPE) v 4.0.  The summary files (containing both expression values and SNP calls) were generated by dChipSNP, and a modified array normalization algorithm that accounts for gross cytogenetic abnormalities in the blast samples (described in the paper).

label: Biotin

source_name: Remission samples.

extract_protocol: Genomic DNA from remission samples was extracted by the Qiagen method or phenol/Chloroform. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: Remission samples that correspond to those tumor samples that have copy number abnormalities in specific genes.


title: NF1-unaffected #10

source_name: Coriell Cell Repository, LCL GM09630


title: Microvinification UCD522/P29, 1

status: Public on Nov 13 2009

description: High-sulfide (UCD522) vs low-sulfide (P29) yeast strains.

hyb_protocol: Microarray prehybridization was performed in 5x SSC (SCC, 150 mM NaCl, 15 mM Na-citrate, pH 7.0), 0.1% SDS, 1%BSA at 42ºC for 45 min. Labeled cDNA was dried in a vacuum trap and used as probe after resuspension in 110 µl of hybridization solution (50% formamide, 5xSSC, 0.1% SDS, 100 µg/ml salmon sperm DNA). Hybridization and washing were performed in a Lucidea Slide Pro System (GE Healthcare, Uppsala, Sweden).

scan_protocol: Arrays were scanned with a GenePix 4000B fluorescence scanner and analyzed by Genepix 5.0 Pro software (Axon Instruments, MDS Analytical Technologies, Toronto, Canada).

data_processing: Genepix 5.0 Pro software. Data was filtered according to spot quality. Only those spots whose intensity was twice background signal and, at least 75% of pixels had intensities above background plus two standard deviations, were selected for further calculations. Gene definition and characterization, as well as their classification by gene ontology (GO) in biological process category, were performed at the Saccharomyce Genome Database (SGD) page. Microarray datasets were analyzed using the TIGR MeV program.

label_protocol: Fifteen µg of total RNA were used for cDNA synthesis and labeling with Cy3-dUTP and Cy5-dUTP fluorescent nucleotides, following an indirect labeling protocol (CyScribe post labeling kit, GE-Healthcare, New York, NY, USA). Labeling efficiency was evaluated by spectrophotometric measurement of Cy3 or Cy5 absorbance.

growth_protocol: Yeast strains used in this study were Saccharomyces cerevisiae UCD522 and P29. Fermentation media was pasteurized grape juice in 1 L glass bottle. Fermentation temperature was controlled by a HotCold Incubator (Selecta, Barcelona, Spain), set at 18ºC, and continuous rotation was provided by a Rotabit from Selecta. Wine analysis was done by official or equivalent methods. Fermentation was monitored by weight loss in a 2000g scale (Precisa, Madrid, Spain).

extract_protocol: Yeast cells (approximately 2 X 10e8 cells) were harvested by centrifugation, washed with distilled water, treated with RNA Later (Sigma-Aldrich, St. Louis, MO), and kept in the freezer until extracted by the hot acidic phenol method.

tag: strain

tag: sulfide production

value: low

value: high


title: NF1-affected #23

source_name: Coriell Cell Repository, LCL GM09692

tag: cell type


title: NF1-affected #13

source_name: Coriell Cell Repository, LCL GM09633


title: NF1-affected #14

source_name: Coriell Cell Repository, LCL GM09634


title: Hyperdip50-SNP-#28-remission-50kxba


title: NF1-affected #3

source_name: Coriell Cell Repository, LCL GM09616


title: NF1-unaffected #12

source_name: Coriell Cell Repository, LCL GM09632


title: NF1-affected #5

source_name: Coriell Cell Repository, LCL GM09619


title: HUES6 ES_2

status: Public on Oct 20 2009

city: La Jolla

first: Alysson

middle: R

last: Muotri

state: CA

address: 9500 Gilman Drive

department: Pediatrics/CMM

institute: University of California San Diego

description: Gene expression data

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: Human Gene U133_2 arrays were analyzed by using affymetrix power tools (apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Pl  us_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM08111  02B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110  RA.CEL CM081110RB.CEL CM081110RC.CEL )

source_name: HUES6 ES

label_protocol: according to Affymetrix protocol

growth_protocol: Human fetal NSCs (ReNCell VM, Chemicon) were cultured on laminin-coated dishes in ReNcell maintenance medium (Chemicon) in the presence of basic fibroblast growth factor 2 (bFGF2), following the manufacturer’s instructions. Human ESC and iPSC were grwon in feeder-free conditions, on matrigel-coated dishes (BD) using mTeSRTM1 .

extract_protocol: Total cellular RNA was extracted from ~5x106 cells using the RNeasy Protect Mini kit (Qiagen, Valencia, CA), according to the manufacturer's instructions, and reverse transcribed using the SuperScript III First-Strand Synthesis System RT-PCR from Invitrogen. The cDNA was amplified by PCR using Accuprime Taq DNA polymerase system (Invitrogene).

treatment_protocol: Cells were collected at 50% confluency. For hESC and hiPSC, we first removed any differentiated cell on the plate by manual microdissociation based on morphology.

value: Human Embryonic Stem Cells


title: HUES6 ES_3

description: Gene expression data


title: iPS Clone 2_3

description: Gene expression data

source_name: hiPSC footprint-free clone 2

value: Human induced pluripotent stem cells


title: TEL-AML1-SNP-#33-remission-50kxba


title: HUES6 ES_1

description: Gene expression data


title: iPS Clone 2_2

description: Gene expression data


title: TEL-AML1-SNP-#32-remission-50kxba


title: T-ALL-SNP-#49-remission-50kxba


title: NF1-affected #9

source_name: Coriell Cell Repository, LCL GM09628


title: TEL-AML1-SNP-#42-remission-50kxba


title: TEL-AML1-SNP-#46-remission-50kxba


title: NPC 3

description: Gene expression data

source_name: ReNCell

value: neural progenitor cells


title: NPC 2

description: Gene expression data


title: NPC 1

description: Gene expression data


title: iPS Clone 1_3

description: Gene expression data

source_name: hiPSC footprint-free clone 1


title: T-ALL-SNP-#3-remission-50kxba


title: iPS Clone 2_1

description: Gene expression data


title: Hypodip-SNP-#1-remission-50kxba


title: Pseudodip-SNP-#2-remission-50kxba


title: Hypodip-SNP-#8-remission-50kxba


title: Hypodip-SNP-#7-remission-50kxba


title: E2A-PBX1-SNP-#11-remission-50kxba


title: E2A-PBX1-SNP-#16-remission-50kxba


title: E2A-PBX1-SNP-#10-remission-50kxba


title: E2A-PBX1-SNP-#13-remission-50kxba


title: BCR-ABL-SNP-#9-remission-50kxba


title: iPS Clone 1_2

description: Gene expression data


title: Hypodip-SNP-#9-remission-50kxba


title: Hyperdip50-SNP-#24-remission-50kxba


title: Pseudodip-SNP-#13-remission-50kxba


title: Hyperdip47-50-SNP-#19-remission-50kxba


title: Other-SNP-#14-remission-50kxba


title: Hypodip-SNP-#2-remission-50kxba


title: BCR-ABL-SNP-#1-remission-50kxba


title: Hypodip-SNP-#10-remission-50kxba


title: TEL-AML1-SNP-#5-remission-50kxba


title: Pseudodip-SNP-#1-remission-50kxba


title: Hyperdip50-SNP-#17-remission-50kxba


title: Hyperdip47-50-SNP-#6-remission-50kxba


title: Hyperdip47-50-SNP-#20-remission-50kxba


title: iPS Clone 1_1

description: Gene expression data


title: TEL-AML1-SNP-#26-remission-50kxba


title: T-ALL-SNP-#19-remission-50kxba


title: T-ALL-SNP-#20-remission-50kxba


title: TEL-AML1-SNP-#27-remission-50kxba


title: TEL-AML1-SNP-#28-remission-50kxba


title: TEL-AML1-SNP-#19-remission-50kxba


title: Other-SNP-#5-remission-50kxba


title: Other-SNP-#7-remission-50kxba


title: Hyperdip47-50-SNP-#8-remission-50kxba


title: Hyperdip47-50-SNP-#5-remission-50kxba


title: Pseudodip-SNP-#11-remission-50kxba


title: Pseudodip-SNP-#9-remission-50kxba


title: Pseudodip-SNP-#6-remission-50kxba


title: Hyperdip47-50-SNP-#9-remission-50kxba


title: Other-SNP-#4-remission-50kxba


title: Hypodip-SNP-#6-remission-50kxba


title: Hypodip-SNP-#4-remission-50kxba


title: Other-SNP-#3-remission-50kxba


title: Hypodip-SNP-#5-remission-50kxba


title: MLL-SNP-#2-remission-50kxba


title: E2A-PBX1-SNP-#8-remission-50kxba


title: Hypodip-SNP-#3-remission-50kxba


title: BCR-ABL-SNP-#4-remission-50kxba


title: TEL-AML1-SNP-#18-remission-50kxba


title: TEL-AML1-SNP-#23-remission-50kxba


title: T-ALL-SNP-#6-remission-50kxba


title: E2A-PBX1-SNP-#6-remission-50kxba


title: Reference_56-50kxba

description: 242 pediatric acute lymphoblastic leukemia blast samples were analyzed.

source_name: Pediatric acute lymphoblastic leukemia (ALL) blast samples or reference leukemic blast samples.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: Leukemic blasts from 242 pediatric acute lymphoblastic leukemia (ALL) patients, or reference leukemic blast samples used for DNA copy number analysis.


title: TEL-AML1-SNP-#15-remission-50kxba


title: Reference_64-50kxba


title: Reference_51-50kxba


title: Reference_50-50kxba


title: Reference_63-50kxba


title: TEL-AML1-SNP-#9-remission-50kxba


title: Reference_62-50kxba


title: Reference_57-50kxba


title: TEL-AML1-SNP-#11-remission-50kxba


title: Reference_60-50kxba


title: Reference_58-50kxba


title: Reference_59-50kxba


title: Reference_47-50kxba


title: Reference_46-50kxba


title: Reference_61-50kxba


title: Reference_66-50kxba


title: Reference_43-50kxba


title: Pseudodip-SNP-#4-remission-50kxba


title: Reference_42-50kxba


title: Reference_44-50kxba


title: Reference_10-50kxba


title: Reference_22-50kxba


title: Reference_65-50kxba


title: Reference_40-50kxba


title: Reference_06-50kxba


title: Reference_01-50kxba


title: Reference_48-50kxba


title: Reference_08-50kxba


title: Reference_03-50kxba


title: Reference_39-50kxba


title: Reference_49-50kxba


title: Reference_38-50kxba


title: Reference_36-50kxba


title: Reference_33-50kxba


title: Reference_35-50kxba


title: Reference_34-50kxba


title: Reference_41-50kxba


title: Reference_29-50kxba


title: Reference_31-50kxba


title: Reference_30-50kxba


title: Reference_28-50kxba


title: Reference_25-50kxba


title: Reference_26-50kxba


title: Reference_23-50kxba


title: Reference_27-50kxba


title: Reference_20-50kxba


title: Reference_19-50kxba


title: Reference_18-50kxba


title: Reference_24-50kxba


title: Reference_45-50kxba


title: Reference_32-50kxba


title: Reference_21-50kxba


title: Reference_15-50kxba


title: Reference_17-50kxba


title: Reference_05-50kxba


title: Reference_16-50kxba


title: Reference_13-50kxba


title: Reference_12-50kxba


title: Reference_14-50kxba


title: Reference_02-50kxba


title: Reference_04-50kxba


title: Reference_11-50kxba


title: Reference_07-50kxba


title: BCR-ABL-SNP-#8-50kxba


title: BCR-ABL-SNP-#1-50kxba


title: Reference_09-50kxba


title: BCR-ABL-SNP-#9-50kxba


title: BCR-ABL-SNP-#2-50kxba


title: BCR-ABL-SNP-#6-50kxba


title: BCR-ABL-SNP-#3-50kxba


title: Reference_37-50kxba


title: BCR-ABL-SNP-#7-50kxba


title: BCR-ABL-SNP-#5-50kxba


title: TEL-AML1-SNP-#46-50kxba


title: TEL-AML1-SNP-#47-50kxba


title: TEL-AML1-SNP-#45-50kxba


title: TEL-AML1-SNP-#42-50kxba


title: TEL-AML1-SNP-#41-50kxba


title: TEL-AML1-SNP-#37-50kxba


title: TEL-AML1-SNP-#39-50kxba


title: TEL-AML1-SNP-#40-50kxba


title: TEL-AML1-SNP-#38-50kxba


title: TEL-AML1-SNP-#43-50kxba


title: TEL-AML1-SNP-#36-50kxba


title: BCR-ABL-SNP-#4-50kxba


title: TEL-AML1-SNP-#34-50kxba


title: TEL-AML1-SNP-#33-50kxba


title: TEL-AML1-SNP-#31-50kxba


title: TEL-AML1-SNP-#2-50kxba


title: TEL-AML1-SNP-#7-50kxba


title: TEL-AML1-SNP-#5-50kxba


title: TEL-AML1-SNP-#6-50kxba


title: TEL-AML1-SNP-#3-50kxba


title: TEL-AML1-SNP-#4-50kxba


title: TEL-AML1-SNP-#8-50kxba


title: TEL-AML1-SNP-#44-50kxba


title: TEL-AML1-SNP-#35-50kxba


title: TEL-AML1-SNP-#28-50kxba


title: TEL-AML1-SNP-#25-50kxba


title: TEL-AML1-SNP-#1-50kxba


title: TEL-AML1-SNP-#27-50kxba


title: TEL-AML1-SNP-#26-50kxba


title: TEL-AML1-SNP-#32-50kxba


title: TEL-AML1-SNP-#24-50kxba


title: TEL-AML1-SNP-#22-50kxba


title: TEL-AML1-SNP-#21-50kxba


title: TEL-AML1-SNP-#29-50kxba


title: TEL-AML1-SNP-#23-50kxba


title: TEL-AML1-SNP-#17-50kxba


title: TEL-AML1-SNP-#9-50kxba


title: TEL-AML1-SNP-#14-50kxba


title: E2A-PBX1-SNP-#15-50kxba


title: TEL-AML1-SNP-#12-50kxba


title: TEL-AML1-SNP-#16-50kxba


title: TEL-AML1-SNP-#15-50kxba


title: TEL-AML1-SNP-#20-50kxba


title: E2A-PBX1-SNP-#16-50kxba


title: E2A-PBX1-SNP-#13-50kxba


title: TEL-AML1-SNP-#13-50kxba


title: TEL-AML1-SNP-#10-50kxba


title: TEL-AML1-SNP-#19-50kxba


title: E2A-PBX1-SNP-#3-50kxba


title: TEL-AML1-SNP-#11-50kxba


title: E2A-PBX1-SNP-#1-50kxba


title: E2A-PBX1-SNP-#9-50kxba


title: TEL-AML1-SNP-#18-50kxba


title: E2A-PBX1-SNP-#10-50kxba


title: E2A-PBX1-SNP-#12-50kxba


title: E2A-PBX1-SNP-#11-50kxba


title: E2A-PBX1-SNP-#14-50kxba


title: E2A-PBX1-SNP-#17-50kxba


title: E2A-PBX1-SNP-#6-50kxba


title: E2A-PBX1-SNP-#4-50kxba


title: E2A-PBX1-SNP-#5-50kxba


title: T-ALL-SNP-#50-50kxba


title: E2A-PBX1-SNP-#2-50kxba


title: T-ALL-SNP-#49-50kxba


title: T-ALL-SNP-#46-50kxba


title: T-ALL-SNP-#41-50kxba


title: T-ALL-SNP-#48-50kxba


title: T-ALL-SNP-#47-50kxba


title: T-ALL-SNP-#45-50kxba


title: T-ALL-SNP-#39-50kxba


title: T-ALL-SNP-#42-50kxba


title: T-ALL-SNP-#37-50kxba


title: T-ALL-SNP-#35-50kxba


title: T-ALL-SNP-#31-50kxba


title: T-ALL-SNP-#40-50kxba


title: T-ALL-SNP-#38-50kxba


title: E2A-PBX1-SNP-#7-50kxba


title: T-ALL-SNP-#36-50kxba


title: T-ALL-SNP-#32-50kxba


title: T-ALL-SNP-#33-50kxba


title: T-ALL-SNP-#30-50kxba


title: E2A-PBX1-SNP-#8-50kxba


title: T-ALL-SNP-#34-50kxba


title: T-ALL-SNP-#29-50kxba


title: T-ALL-SNP-#3-50kxba


title: T-ALL-SNP-#1-50kxba


title: T-ALL-SNP-#2-50kxba


title: T-ALL-SNP-#28-50kxba


title: T-ALL-SNP-#5-50kxba


title: T-ALL-SNP-#43-50kxba


title: T-ALL-SNP-#24-50kxba


title: T-ALL-SNP-#27-50kxba


title: T-ALL-SNP-#21-50kxba


title: T-ALL-SNP-#25-50kxba


title: T-ALL-SNP-#23-50kxba


title: T-ALL-SNP-#22-50kxba


title: T-ALL-SNP-#20-50kxba


title: T-ALL-SNP-#19-50kxba


title: T-ALL-SNP-#18-50kxba


title: T-ALL-SNP-#14-50kxba


title: T-ALL-SNP-#15-50kxba


title: T-ALL-SNP-#17-50kxba


title: T-ALL-SNP-#4-50kxba


title: T-ALL-SNP-#13-50kxba


title: T-ALL-SNP-#9-50kxba


title: T-ALL-SNP-#12-50kxba


title: T-ALL-SNP-#7-50kxba


title: T-ALL-SNP-#10-50kxba


title: Pseudodip-SNP-#16-50kxba


title: T-ALL-SNP-#11-50kxba


title: Pseudodip-SNP-#15-50kxba


title: T-ALL-SNP-#44-50kxba


title: Pseudodip-SNP-#19-50kxba


title: T-ALL-SNP-#16-50kxba


title: T-ALL-SNP-#6-50kxba


title: T-ALL-SNP-#8-50kxba


title: Pseudodip-SNP-#20-50kxba


title: Pseudodip-SNP-#14-50kxba


title: Pseudodip-SNP-#2-50kxba


title: Pseudodip-SNP-#18-50kxba


title: Pseudodip-SNP-#17-50kxba


title: T-ALL-SNP-#26-50kxba


title: Pseudodip-SNP-#1-50kxba


title: Pseudodip-SNP-#11-50kxba


title: Pseudodip-SNP-#10-50kxba


title: Pseudodip-SNP-#9-50kxba


title: Pseudodip-SNP-#8-50kxba


title: Pseudodip-SNP-#4-50kxba


title: Pseudodip-SNP-#7-50kxba


title: Pseudodip-SNP-#6-50kxba


title: Pseudodip-SNP-#12-50kxba


title: Other-SNP-#1-50kxba


title: Other-SNP-#12-50kxba


title: Other-SNP-#16-50kxba


title: Other-SNP-#15-50kxba


title: Other-SNP-#8-50kxba


title: Other-SNP-#14-50kxba


title: Other-SNP-#9-50kxba


title: Other-SNP-#10-50kxba


title: Other-SNP-#6-50kxba


title: Pseudodip-SNP-#13-50kxba


title: Other-SNP-#3-50kxba


title: Other-SNP-#13-50kxba


title: Other-SNP-#4-50kxba


title: Other-SNP-#2-50kxba


title: Other-SNP-#5-50kxba


title: MLL-SNP-#11-50kxba


title: Pseudodip-SNP-#3-50kxba


title: MLL-SNP-#8-50kxba


title: Other-SNP-#7-50kxba


title: Pseudodip-SNP-#5-50kxba


title: MLL-SNP-#10-50kxba


title: Other-SNP-#11-50kxba


title: MLL-SNP-#7-50kxba


title: MLL-SNP-#9-50kxba


title: MLL-SNP-#3-50kxba


title: MLL-SNP-#5-50kxba


title: MLL-SNP-#2-50kxba


title: Hypodip-SNP-#1-50kxba


title: MLL-SNP-#4-50kxba


title: MLL-SNP-#1-50kxba


title: Hypodip-SNP-#8-50kxba


title: Hypodip-SNP-#7-50kxba


title: Hypodip-SNP-#9-50kxba


title: Hypodip-SNP-#2-50kxba


title: Hypodip-SNP-#5-50kxba


title: Hypodip-SNP-#6-50kxba


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title: T-ALL-SNP-#30-50khind


title: Hyperdip47-50-SNP-#16-250ksty


title: Hypodip-SNP-#6-250ksty


title: T-ALL-SNP-#29-50khind


title: T-ALL-SNP-#1-50khind


title: T-ALL-SNP-#4-50khind


title: T-ALL-SNP-#2-50khind


title: T-ALL-SNP-#3-50khind


title: Hyperdip47-50-SNP-#1-250ksty


title: Hyperdip47-50-SNP-#23-250ksty


title: Hypodip-SNP-#3-250ksty


title: T-ALL-SNP-#44-50khind


title: T-ALL-SNP-#28-50khind


title: Hyperdip47-50-SNP-#22-250ksty


title: T-ALL-SNP-#5-50khind


title: T-ALL-SNP-#27-50khind


title: T-ALL-SNP-#26-50khind


title: Hyperdip47-50-SNP-#20-250ksty


title: T-ALL-SNP-#25-50khind


title: Hyperdip47-50-SNP-#19-250ksty


title: T-ALL-SNP-#23-50khind


title: Hyperdip47-50-SNP-#18-250ksty


title: Hyperdip47-50-SNP-#3-250ksty


title: T-ALL-SNP-#24-50khind


title: Hyperdip47-50-SNP-#17-250ksty


title: T-ALL-SNP-#22-50khind


title: T-ALL-SNP-#19-50khind


title: T-ALL-SNP-#21-50khind


title: Hyperdip47-50-SNP-#12-250ksty


title: T-ALL-SNP-#20-50khind


title: T-ALL-SNP-#18-50khind


title: Hyperdip47-50-SNP-#13-250ksty


title: Hyperdip47-50-SNP-#2-250ksty


title: Hyperdip47-50-SNP-#9-250ksty


title: Hyperdip47-50-SNP-#11-250ksty


title: Hyperdip47-50-SNP-#14-250ksty


title: Hyperdip47-50-SNP-#15-250ksty


title: Hyperdip47-50-SNP-#8-250ksty


title: T-ALL-SNP-#17-50khind


title: T-ALL-SNP-#9-50khind


title: T-ALL-SNP-#16-50khind


title: T-ALL-SNP-#14-50khind


title: Hyperdip47-50-SNP-#21-250ksty


title: Hyperdip47-50-SNP-#6-250ksty


title: Hyperdip47-50-SNP-#5-250ksty


title: Hyperdip47-50-SNP-#4-250ksty


title: T-ALL-SNP-#10-50khind


title: T-ALL-SNP-#11-50khind


title: T-ALL-SNP-#8-50khind


title: T-ALL-SNP-#12-50khind


title: BCR-ABL-SNP-#8-250ksty


title: BCR-ABL-SNP-#1-250ksty


title: T-ALL-SNP-#7-50khind


title: Hyperdip47-50-SNP-#10-250ksty


title: BCR-ABL-SNP-#7-250ksty


title: BCR-ABL-SNP-#3-250ksty


title: T-ALL-SNP-#6-50khind


title: BCR-ABL-SNP-#6-250ksty


title: Pseudodip-SNP-#16-50khind


title: BCR-ABL-SNP-#5-250ksty


title: Pseudodip-SNP-#2-50khind


title: BCR-ABL-SNP-#9-250ksty


title: T-ALL-SNP-#13-50khind


title: BCR-ABL-SNP-#4-250ksty


title: Pseudodip-SNP-#20-50khind


title: Pseudodip-SNP-#18-50khind


title: MLL-SNP-#10-250ksty


title: MLL-SNP-#11-250ksty


title: Pseudodip-SNP-#14-50khind


title: Pseudodip-SNP-#17-50khind


title: T-ALL-SNP-#15-50khind


title: MLL-SNP-#9-250ksty


title: Pseudodip-SNP-#19-50khind


title: Pseudodip-SNP-#15-50khind


title: MLL-SNP-#8-250ksty


title: MLL-SNP-#7-250ksty


title: Hyperdip47-50-SNP-#7-250ksty


title: Pseudodip-SNP-#1-50khind


title: Pseudodip-SNP-#11-50khind


title: MLL-SNP-#6-250ksty


title: Pseudodip-SNP-#10-50khind


title: MLL-SNP-#3-250ksty


title: MLL-SNP-#4-250ksty


title: Pseudodip-SNP-#9-50khind


title: MLL-SNP-#2-250ksty


title: Pseudodip-SNP-#8-50khind


title: Pseudodip-SNP-#7-50khind


title: Pseudodip-SNP-#5-50khind


title: TEL-AML1-SNP-#47-250ksty


title: BCR-ABL-SNP-#2-250ksty


title: TEL-AML1-SNP-#45-250ksty


title: Pseudodip-SNP-#4-50khind


title: Pseudodip-SNP-#12-50khind


title: TEL-AML1-SNP-#43-250ksty


title: TEL-AML1-SNP-#41-250ksty


title: TEL-AML1-SNP-#40-250ksty


title: TEL-AML1-SNP-#42-250ksty


title: Pseudodip-SNP-#3-50khind


title: Other-SNP-#1-50khind


title: MLL-SNP-#1-250ksty


title: Other-SNP-#9-50khind


title: TEL-AML1-SNP-#38-250ksty


title: Other-SNP-#8-50khind


title: Other-SNP-#15-50khind


title: TEL-AML1-SNP-#39-250ksty


title: Pseudodip-SNP-#13-50khind


title: TEL-AML1-SNP-#37-250ksty


title: Other-SNP-#16-50khind


title: Pseudodip-SNP-#6-50khind


title: TEL-AML1-SNP-#46-250ksty


title: Other-SNP-#14-50khind


title: TEL-AML1-SNP-#36-250ksty


title: TEL-AML1-SNP-#33-250ksty


title: TEL-AML1-SNP-#34-250ksty


title: Other-SNP-#13-50khind


title: TEL-AML1-SNP-#35-250ksty


title: Other-SNP-#12-50khind


title: Other-SNP-#11-50khind


title: TEL-AML1-SNP-#31-250ksty


title: Other-SNP-#6-50khind


title: Other-SNP-#3-50khind


title: Other-SNP-#4-50khind


title: Other-SNP-#2-50khind


title: TEL-AML1-SNP-#7-250ksty


title: TEL-AML1-SNP-#30-250ksty


title: Other-SNP-#7-50khind


title: Other-SNP-#5-50khind


title: TEL-AML1-SNP-#5-250ksty


title: TEL-AML1-SNP-#3-250ksty


title: TEL-AML1-SNP-#44-250ksty


title: TEL-AML1-SNP-#2-250ksty


title: MLL-SNP-#11-50khind


title: Other-SNP-#10-50khind


title: MLL-SNP-#9-50khind


title: MLL-SNP-#8-50khind


title: TEL-AML1-SNP-#8-250ksty


title: MLL-SNP-#7-50khind


title: TEL-AML1-SNP-#4-250ksty


title: MLL-SNP-#6-50khind


title: TEL-AML1-SNP-#1-250ksty


title: MLL-SNP-#5-250ksty


title: MLL-SNP-#5-50khind


title: MLL-SNP-#3-50khind


title: TEL-AML1-SNP-#29-250ksty


title: MLL-SNP-#10-50khind


title: MLL-SNP-#4-50khind


title: TEL-AML1-SNP-#28-250ksty


title: TEL-AML1-SNP-#27-250ksty


title: TEL-AML1-SNP-#25-250ksty


title: MLL-SNP-#2-50khind


title: TEL-AML1-SNP-#26-250ksty


title: TEL-AML1-SNP-#24-250ksty


title: MLL-SNP-#1-50khind


title: Hypodip-SNP-#1-50khind


title: TEL-AML1-SNP-#23-250ksty


title: Hypodip-SNP-#10-50khind


title: Hypodip-SNP-#8-50khind


title: Hypodip-SNP-#9-50khind


title: TEL-AML1-SNP-#20-250ksty


title: TEL-AML1-SNP-#18-250ksty


title: Hypodip-SNP-#7-50khind


title: TEL-AML1-SNP-#19-250ksty


title: TEL-AML1-SNP-#21-250ksty


title: Hypodip-SNP-#2-50khind


title: Hypodip-SNP-#6-50khind


title: Hypodip-SNP-#5-50khind


title: TEL-AML1-SNP-#17-250ksty


title: TEL-AML1-SNP-#16-250ksty


title: Hypodip-SNP-#4-50khind


title: TEL-AML1-SNP-#15-250ksty


title: TEL-AML1-SNP-#13-250ksty


title: Hypodip-SNP-#3-50khind


title: Hyperdip47-50-SNP-#17-50khind


title: TEL-AML1-SNP-#14-250ksty


title: Hyperdip47-50-SNP-#16-50khind


title: Hyperdip47-50-SNP-#1-50khind


title: TEL-AML1-SNP-#11-250ksty


title: TEL-AML1-SNP-#12-250ksty


title: Hyperdip47-50-SNP-#23-50khind


title: TEL-AML1-SNP-#6-250ksty


title: TEL-AML1-SNP-#9-250ksty


title: Hyperdip47-50-SNP-#22-50khind


title: TEL-AML1-SNP-#10-250ksty


title: Hyperdip47-50-SNP-#19-50khind


title: E2A-PBX1-SNP-#15-250ksty


title: E2A-PBX1-SNP-#17-250ksty


title: Hyperdip47-50-SNP-#21-50khind


title: E2A-PBX1-SNP-#14-250ksty


title: Hyperdip47-50-SNP-#18-50khind


title: Hyperdip47-50-SNP-#20-50khind


title: E2A-PBX1-SNP-#16-250ksty


title: Hyperdip47-50-SNP-#3-50khind


title: Hyperdip47-50-SNP-#2-50khind


title: TEL-AML1-SNP-#22-250ksty


title: E2A-PBX1-SNP-#13-250ksty


title: TEL-AML1-SNP-#32-250ksty


title: Hyperdip47-50-SNP-#15-50khind


title: Hyperdip47-50-SNP-#14-50khind


title: E2A-PBX1-SNP-#10-250ksty


title: E2A-PBX1-SNP-#12-250ksty


title: Hyperdip47-50-SNP-#13-50khind


title: E2A-PBX1-SNP-#1-250ksty


title: E2A-PBX1-SNP-#11-250ksty


title: Hyperdip47-50-SNP-#11-50khind


title: E2A-PBX1-SNP-#3-250ksty


title: Hyperdip47-50-SNP-#10-50khind


title: E2A-PBX1-SNP-#9-250ksty


title: Hyperdip47-50-SNP-#12-50khind


title: Hyperdip47-50-SNP-#8-50khind


title: E2A-PBX1-SNP-#6-250ksty


title: Hyperdip47-50-SNP-#6-50khind


title: E2A-PBX1-SNP-#8-250ksty


title: Hyperdip47-50-SNP-#9-50khind


title: E2A-PBX1-SNP-#2-250ksty


title: E2A-PBX1-SNP-#4-250ksty


title: Hyperdip47-50-SNP-#4-50khind


title: Hyperdip47-50-SNP-#7-50khind


title: E2A-PBX1-SNP-#7-250ksty


title: Hyperdip50-SNP-#38-50khind


title: Hyperdip50-SNP-#37-250ksty


title: Hyperdip50-SNP-#37-50khind


title: Hyperdip50-SNP-#38-250ksty


title: Hyperdip50-SNP-#35-250ksty


title: Hyperdip50-SNP-#35-50khind


title: Hyperdip50-SNP-#36-50khind


title: Hyperdip50-SNP-#34-250ksty


title: E2A-PBX1-SNP-#5-250ksty


title: Hyperdip50-SNP-#34-50khind


title: Hyperdip50-SNP-#36-250ksty


title: Hyperdip50-SNP-#33-250ksty


title: Hyperdip47-50-SNP-#5-50khind


title: Hyperdip50-SNP-#32-250ksty


title: Hyperdip50-SNP-#32-50khind


title: Hyperdip50-SNP-#30-50khind


title: Hyperdip50-SNP-#31-50khind


title: Hyperdip50-SNP-#29-50khind


title: Hyperdip50-SNP-#30-250ksty


title: Hyperdip50-SNP-#27-250ksty


title: Hyperdip50-SNP-#28-50khind


title: Hyperdip50-SNP-#31-250ksty


title: Hyperdip50-SNP-#29-250ksty


title: Hyperdip50-SNP-#33-50khind


title: Hyperdip50-SNP-#27-50khind


title: Hyperdip50-SNP-#26-250ksty


title: Hyperdip50-SNP-#26-50khind


title: Hyperdip50-SNP-#25-50khind


title: Hyperdip50-SNP-#25-250ksty


title: Hyperdip50-SNP-#24-50khind


title: Hyperdip50-SNP-#39-250ksty


title: Hyperdip50-SNP-#39-50khind


title: Hyperdip50-SNP-#28-250ksty


title: Hyperdip50-SNP-#2-50khind


title: Hyperdip50-SNP-#1-250ksty


title: Hyperdip50-SNP-#3-50khind


title: Hyperdip50-SNP-#2-250ksty


title: Hyperdip50-SNP-#22-250ksty


title: Hyperdip50-SNP-#1-50khind


title: Hyperdip50-SNP-#20-250ksty


title: Hyperdip50-SNP-#21-250ksty


title: Hyperdip50-SNP-#21-50khind


title: Hyperdip50-SNP-#19-250ksty


title: Hyperdip50-SNP-#3-250ksty


title: Hyperdip50-SNP-#20-50khind


title: Hyperdip50-SNP-#22-50khind


title: Hyperdip50-SNP-#19-50khind


title: Hyperdip50-SNP-#18-50khind


title: Hyperdip50-SNP-#17-250ksty


title: Hyperdip50-SNP-#24-250ksty


title: Hyperdip50-SNP-#18-250ksty


title: Hyperdip50-SNP-#16-250ksty


title: Hyperdip50-SNP-#17-50khind


title: Hyperdip50-SNP-#16-50khind


title: Hyperdip50-SNP-#13-250ksty


title: Hyperdip50-SNP-#9-50khind


title: Hyperdip50-SNP-#13-50khind


title: Hyperdip50-SNP-#10-250ksty


title: Hyperdip50-SNP-#14-250ksty


title: Hyperdip50-SNP-#15-250ksty


title: Hyperdip50-SNP-#9-250ksty


title: Hyperdip50-SNP-#11-50khind


title: Hyperdip50-SNP-#10-50khind


title: Hyperdip50-SNP-#12-250ksty


title: Hyperdip50-SNP-#12-50khind


title: Hyperdip50-SNP-#14-50khind


title: Hyperdip50-SNP-#8-50khind


title: Hyperdip50-SNP-#11-250ksty


title: Hyperdip50-SNP-#23-250ksty


title: Hyperdip50-SNP-#23-50khind


title: Hyperdip50-SNP-#8-250ksty


title: Hyperdip50-SNP-#7-250ksty


title: Hyperdip50-SNP-#15-50khind


title: Hyperdip50-SNP-#6-250ksty


title: Hyperdip50-SNP-#7-50khind


title: Hyperdip50-SNP-#6-50khind


title: Hyperdip50-SNP-#5-50khind


title: Hyperdip50-SNP-#4-50khind


title: Hyperdip50-SNP-#5-250ksty


title: Hyperdip50-SNP-#4-250ksty


title: retinoblastoma URb HPV neg_Folio 50

status: Public on May 21 2008

city: Mexico City

first: Martha

middle: Veronica

last: Ponce-Castañeda

address: Av. Cuauhtemoc 330

department: Hospital de Pediatría, CMN SXXI

country: Mexico

institute: Instituto Mexicano del Seguro Social IMSS

description: Total RNA from each primary retinoblastoma culture was extracted using TRIzol reagent. Total RNA from exponentially growing Saccharomyces cerevisiae was extracted using an organic extraction protocol. 10 g of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 for yeast and dUTP-Cy5 for retinoblastoma.  RNA was reverse-transcribed into cDNA with  CyScribe First strand cDNA labeling kit (Amersham) following manufacturer’s instructions. After cleanup, fluorophore incorporation was analyzed  by spectrophotometric absorbance at 555nm for Cy3 and 655nm for Cy5. The 10K human oligos microarray was hybridized with equal amounts of labeled cDNA from yeast and retinoblastoma using  hybridization solution UniHyb (TeleChem International Inc. Sunnyvale,CA)  for 14 hr at 42°C. After hybridization acquisition and quantification of microarrays images  was performed using ScanArray 4000 scanner and its accompanying software from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10 m resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and corresponding background mean value were calculated with ArrayPro Analyzer from Media Cibernetics

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the ten thousand human oligos arrays for 14 h at 42°C

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: Raw data was normalized by Local Lowess with MIDAS V2.19 (The Institute for Genomics Reseach, Wei Linag and John Quackenbush, 2004). We used block mode and a smoothing parameter of 0.33.  Replicates on the same array were averaged and the log2 ratio was calculated of Sc5/Sc3. For expressions of zero the log ratio is null.

source_name: Saccharomyces cerevisiae

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm

growth_protocol: YPD medium

extract_protocol: Total RNA was extracted with a Phenol/Chloroform/Isoamyl-alcohol protocol

tag: reference

source_name: Rb tumor, Hpv -, Unilateral

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Cy5 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 655 nm for Cy5

growth_protocol: Immediately after surgery, tumor cells were isolated using a ficoll gradient, and maintained in RPMI medium 15% FBS for a week without antibiotics

extract_protocol: Tumors cells were harvested by centrifugation, drained and total RNA was extracted using TRIzol reagent according to manufacturer’s instructions. (Invitrogen, Carlsbad, CA)

value: Retinoblastoma tumor. Status:Hpv negative, unilateral.  Folio 50


title: retinoblastoma URb HPV pos_Folio 86_Array 236

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics

value: RNA from exponentially growing Saccharomyces cerevisiae

source_name: Rb tumor, Hpv +, Unilateral

value: Retinoblastoma tumor. Status:Hpv positive, unilateral.  Folio 86


title: retinoblastoma URb HPV pos_Folio 72

value: Retinoblastoma tumor. Status:Hpv positive, unilateral.  Folio 72


title: retinoblastoma BRb HPV pos_Folio 73_Array 238

source_name: Rb tumor, Hpv +, Bilateral

value: Retinoblastoma tumor. Status:Hpv positive, bilateral.  Folio 73


title: retinoblastoma URb HPV pos_Folio 78

value: Retinoblastoma tumor. Status:Hpv positive, unilateral.  Folio 78


title: retinoblastoma URb HPV pos_Folio 85_Array 237

value: Retinoblastoma tumor. Status:Hpv positive, unilateral.  Folio 85


title: retinoblastoma BRb HPV neg_Folio 1

source_name: Rb tumor, Hpv -, Bilateral

value: Retinoblastoma tumor. Status:Hpv negative, bilateral.  Folio 1


title: retinoblastoma BRb HPV pos_Folio 73_Array 234

value: Retinoblastoma tumor. Status:Hpv positive, Bilateral.  Folio 73


title: retinoblastoma BRb HPV pos_Folio 37_Array 235

value: Retinoblastoma tumor. Status:Hpv positive, Bilateral.  Folio 37


title: retinoblastoma BRb HPV pos_Folio 37_Array239

value: Retinoblastoma tumor. Status:Hpv positive, bilateral.  Folio 37


title: retinoblastoma BRb HPV pos_Folio 74

value: Retinoblastoma tumor. Status:Hpv positive, Bilateral.  Folio 74


title: retinoblastoma BRb HPV neg_Folio 54

value: Retinoblastoma tumor. Status:Hpv negative, Bilateral.  Folio 54


title: retinoblastoma BRb HPV pos_Folio 32

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the ten thousand human oligos arrays for 14 h at 42°C.

value: Retinoblastoma tumor. Status:Hpv positive, bilateral.  Folio 32


title: retinoblastoma URb HPV neg_Folio 87

value: Retinoblastoma tumor. Status:Hpv negative, unilateral.  Folio 87


title: retinoblastoma URb HPV pos_Folio 85_Array 229


title: retinoblastoma URb HPV pos_Folio 86_ Array 228


title: retinoblastoma URb HPV pos_Folio 33

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm.

extract_protocol: Total RNA was extracted with a Phenol/Chloroform/Isoamyl-alcohol protocol.

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Cy5 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 655 nm for Cy5.

growth_protocol: Immediately after surgery, tumor cells were isolated using a ficoll gradient, and maintained in RPMI medium 15% FBS for a week without antibiotics.

value: Retinoblastoma tumor. Status:Hpv positive, unilateral.  Folio 33.


title: Nuclear scaffold attachment of Aortic Adventitial Fibroblast (AoAF) chromatin Replicate 2

status: Public on Mar 11 2009

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 East Hancock Avenue

institute: Wayne State University

description: The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications.  Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively.  We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in AoAF cells.

hyb_protocol: Hybridized at NimbleGen facilities as per NimbleGen protocol

scan_protocol: Scanned at NimbleGen facilities as per NimbleGen protocol

data_processing: Dual channel array data was q spline normalized using the NimbleGen data analysis suite.  Normalized signal ratios were analyzed for enrichment in either the loop or matrix fraction.

source_name: Scaffold attachment profile of AoAF DNA: LIS Loop Replicate 2

label_protocol: Labeled at NimbleGen facilities

extract_protocol: Nuclear halos were prepared in solution from isolated AoAF nuclei with dounce homogenization in the presence of 25 mM LIS (lithium 3,5-diiodosalicylate) using approximately 1 x 107 cells.  After extraction, the halos were pelleted at 1000 x g for 5 minutes at 4°C then washed gently in REact® 3 restriction buffer (Invitrogen, Carlsbad, CA) on a rocker platform for 20 minutes at room temperature then centrifuged at 1000 x g for 5 minutes at 4°C then the supernatant discarded.  This washing procedure was repeated an additional two times.  After the third wash, the halos were resuspended in restriction buffer and the loops separated from the nuclear scaffold associated DNA by digestion with 400 U of EcoRI (Invitrogen, Carlsbad, CA) at 37°C for 3 hours.  Subsequent to restriction digestion, the scaffold fraction was pelleted by centrifugation at 16,000 x g for 5 minutes at 4°C and the loop containing supernatant was removed and placed in a separate tube.  The scaffold fraction was resuspended, and then washed in restriction buffer, immediately pelleted at 16,000 x g for 5 minutes at 4°C and supernatant discarded.  The nuclear scaffold containing pellet fraction was washed an additional two times.  Both loop and scaffold restriction fragments were then freed from any nuclear proteins by overnight digestion at 55°C with 50 µg/mL of proteinase K buffered with 50 mM Tris-HCl buffer, pH 8.0, containing 50 mM NaCl, 25 mM EDTA and 0.5% SDS.  DNA was recovered and purified using a Quantum-prep matrix (BioRad, Hercules, CA) then resuspended in deionized water.

value: Aortic adventitial fibroblast cell line

source_name: Scaffold attachment profile of AoAF DNA: LIS Scaffold Replicate 2


title: Nuclear scaffold and matrix attachment of HeLa chromatin (LIS_1)

status: Public on Feb 27 2009

address: 275 East Hancock, CS Mott Center

description: The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in HeLa cells.

hyb_protocol: Hybridized at NimbleGen facilities in accordance with NimbleGen protocol

scan_protocol: Scanned at NimbleGen facilities in accordance with NimbleGen protocol

data_processing: Dual channel array data was q spline normalized using the NimbleGen data analysis suite. Normalized signal ratios were analyzed for enrichment in either the loop or matrix fraction.

source_name: Scaffold attachment profile of HeLa DNA: LIS Loop Replicate 1

label_protocol: Labeled at NimbleGen facilities in accordance with manufacturer's protocol

extract_protocol: Nuclear halos were prepared in solution from isolated HeLa nuclei with dounce homogenization in the presence of 25 mM LIS using approximately 1 x 107 cells.  After extraction, the halos were pelleted at 1000 x g for 5 minutes at 4°C then washed gently in REact® 3 restriction buffer (Invitrogen, Carlsbad, CA) on a rocker platform for 20 minutes at room temperature then centrifuged at 1000 x g for 5 minutes at 4°C then the supernatant discarded.  This washing procedure was repeated an additional two times.  After the third wash, the halos were resuspended in restriction buffer and the loops separated from the nuclear scaffold associated DNA by digestion with 400 U of EcoRI (Invitrogen, Carlsbad, CA) at 37°C for 3 hours.  Subsequent to restriction digestion, the scaffold fraction was pelleted by centrifugation at 16,000 x g for 5 minutes at 4°C and the loop containing supernatant was removed and placed in a separate tube.  The scaffold fraction was resuspended, and then washed in restriction buffer, immediately pelleted at 16,000 x g for 5 minutes at 4°C and supernatant discarded.  The nuclear scaffold containing pellet fraction was washed an additional two times.  Both loop and scaffold restriction fragments were then freed from any nuclear proteins by overnight digestion at 55°C with 50 µg/mL of proteinase K buffered with 50 mM Tris-HCl buffer, pH 8.0, containing 50 mM NaCl, 25 mM EDTA and 0.5% SDS.  DNA was recovered and purified using a Quantum-prep matrix (BioRad, Hercules, CA) then resuspended in deionized water.

value: female

value: cultured HeLa S3 cells

source_name: Scaffold attachment profile of HeLa DNA: LIS Matrix Replicate 1