title: LS001-4

status: Public on Jan 31 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan) * Priming: 5xSSC, 0.1%SDS * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul * Hybridization: 45 min at 42C. * Wash 2x: milliQ * Wash: 5xSSC, 0.1%SDS * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul) * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC at 23C * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing:
genes, no bg corr, hybset spec. dye corr
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

organism: Canis lupus familiaris

label_protocol:
robot amplification and labeling v1.0:
All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).    mRNA amplification protocol description:  * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.  * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * plate is incubated @ 70C for 10 mins, cooled to 48C.  * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well.  * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.   * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.    Labeling protocol description:   * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).    All subsequent steps are performed by the robot script :  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

extract_protocol:
RNA isolation using Trizol v1.0 (tissue sections):
Trizol RNA isolation of tissue sections:    1. After sectioning, store sections in ice-cold RNAlater (~10 ml RNAlater per 20-mm section). Make sure that the sections do not thaw before they are in ice-cold RNAlater. 50 ml RNAlater.  2. Add X ml Trizol (10x volume of RNAlater) and mix by inverting the tube several times. 500 ml Trizol.  3. Incubate 5 min at room temperature.  4. Pre-incubate Proteinase K (10 mg/ml) at 37 C for at least 10 minutes.  5. Add 10 ml of the pre-heated Proteinase K solution to Trizol mixture. 10 ml Prot-K.  6. Incubate 30 min at 55 C.  7. Add X ml chloroform (20 ml per 100 ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 100 ml chloroform.  8. Centrifuge 20 min at 14000 rpm without brake at 4 C. After centrifugation, transfer the water-phase to a new 1.5 ml micro centrifuge tube (~300 ml).  9. Continue with RNeasy columns (Qiagen) for clean-up of RNA.  10. Adjust each sample to a volume of 300 ml with sterile MilliQ water. Add 160 ml buffer RLT to the samples, and mix (= lysis buffer).  11. Add 240 ml ethanol (100% stored at -20 C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipette and work as quickly as possible). Next lysate, and so on.  12. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flow-through and collection tube.  13. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 ml buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in step 5.  14. Pipette 500 ml buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.  15. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).  16. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipette 100 ml milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.  17. Pipette the eluate of step 7 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.

tag: tissue

value: nucleus palposus tissue

tag: tissue enriched for

tag: disease state

value: chondrodystrophic

value: mixed reference (consisting of a multitude of canine organs)


title: LS001-8

type: RNA

country: Netherlands

molecule: total RNA

value: non-chondrodystrophic


title: LS001-6


title: LS001-7


title: Glioma-EORTC26951 30 025.CEL

status: Public on Feb 01 2013

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

institute: Erasmus MC

description: Abbreviations: IGS: intrinsic glioma subtype; Trt: treatment; SS: survival in years; C: classical; P: proneural; M: mesenchymal; N:neural

hyb_protocol: Hybridization was performed according to the Affymetrix (Santa Clara, CA) Labelling Assay manual

scan_protocol: Genechip scanner 3000 7G

data_processing: RMA

label: biotin

organism: Homo sapiens

source_name: Glioma, clinical trial RT v RT+PCV

label_protocol: labelling was performed according to the Affymetrix (Santa Clara, CA) Labelling Assay manual

extract_protocol: Qiagen Rneasy

value: glioma

tag: sample

tag: igs

tag: tcga classification

value: P

tag: tissue type

value: FF

tag: cimp

value: CIMP+

tag: idhmut

value: mut

tag: 1p19q loh

value: LOH

tag: egfr

value: wt

tag: mgmt

value: meth

tag: trt

value: RT/PCV

tag: ss (y)

tag: event

value: deceased

tag: age

tag: Sex

value: M

tag: original diagnosis

value: AOD

tag: review diagnosis

tag: experiment

value: pt 2


title: LS001-9

tag: tissue

value: nucleus palposus tissue

tag: tissue enriched for

tag: disease state


title: DS2

type: genomic

city: Liverpool

first: Sarah

last: Lake

address: 6th Floor, Duncan Building, Daulby Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

description: Genome-wide Human SNP 6.0 array

hyb_protocol: Hybridised to Affymetrix SNP 6.0 arrays according to manufacturers protocol

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 7G Scanner with the GeneChip Command Console software.

data_processing:
SNP genotypes and confidence scores were generated by fitting two-dimensional Gaussian functions to the SNP data using a customised Expectation-Maximisation algorithm (Birdseed, Affymetrix). Subsequent data analysis was performed using the Partek Genomics Suite of software (Partek Inc, St Louis, USA). In the absence of DNA from matched normal tissues, the 794 sample HapMap baseline, available from Partek, was used. Copy number variation (CNV) and loss of heterozygosity (LOH) workflows were used to determine CNVs and LOH. Cross-platform normalisations were performed to adjust for local GC content and remove “GC-waves” (based on the regression model approach of Diskin et al.)[26] The binary logarithm was generated for all data and used in genomic segmentation (p=0.00001).
CHP files generated using Affymetrix Genotyping Console software. Copy number data generated in Partek Genomics Suite,  adjustment was made for local GC content and the log2 value of data generated prior to Genomic Segmentation P value 0.00001.

molecule: genomic DNA

source_name: Uveal melanoma, disomy chr 3, long-term survival

label_protocol: Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 Assay following the manufacturers protocol with the exception of doubling the number of PCR reactions to compensate for using FFPE material.

extract_protocol: Qiagen DNeasy blood and tissue kit following FFPE protocol. Final purification using GenElute (Sigma) following the manaufacturer's protocol.

value: Uveal melanoma

tag: genotype

value: disomy chr 3

tag: metastasis status

value: non-metastasising


title: LS001-24

value: non-chondrodystrophic

value: mixed reference (consisting of a multitude of canine organs)


title: LS001-5


title: LS001-3

value: chondrodystrophic


title: LS001-2


title: LS001-20


title: LS001-21


title: LS001-19


title: LS001-16


title: LS001-22


title: LS001-18


title: PBMC_CsA_anti-CD3/CD28_donor_4

city: Nutley

first: Kai

last: Lau

address: 340 Kingsland St

country: USA

institute: Hoffmann-La Roche

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure.  Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release.  As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis.  A total of 26,088 out of 54,675 probesets passed the QC and curation processes, corresponding to 13,464 unique genes.

label: Biotin

source_name: PBMC from donor 4 treatment: CsA_anti-CD3/CD28

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).

extract_protocol: Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

tag: donor

tag: cell type

value: PBMC

tag: treatment

tag: subject


title: LS001-15


title: LS001-23


title: LS001-17


title: PBMC_FK506_anti-CD3/CD28_donor_4

source_name: PBMC from donor 4 treatment: FK506_anti-CD3/CD28


title: PBMC_CsA_anti-CD3/CD28_donor_3

source_name: PBMC from donor 3 treatment: CsA_anti-CD3/CD28


title: PBMC_Untreated_donor_4

source_name: PBMC from donor 4 treatment: Untreated

value: Untreated


title: LS001-14


title: LS001-11


title: LS001-1


title: PBMC_anti-CD3/CD28_donor_4

source_name: PBMC from donor 4 treatment: anti-CD3/CD28


title: LS001-13


title: PBMC_FK506_anti-CD3/CD28_donor_2

source_name: PBMC from donor 2 treatment: FK506_anti-CD3/CD28


title: PBMC_Untreated_donor_3

source_name: PBMC from donor 3 treatment: Untreated


title: LS001-10


title: LS001-12


title: PBMC_CRACi_anti-CD3/CD28_donor_2

source_name: PBMC from donor 2 treatment: CRACi_anti-CD3/CD28


title: PBMC_anti-CD3/CD28_donor_2

source_name: PBMC from donor 2 treatment: anti-CD3/CD28


title: PBMC_anti-CD3/CD28_donor_3

source_name: PBMC from donor 3 treatment: anti-CD3/CD28


title: PBMC_CRACi_anti-CD3/CD28_donor_3

source_name: PBMC from donor 3 treatment: CRACi_anti-CD3/CD28


title: PBMC_FK506_anti-CD3/CD28_donor_1

source_name: PBMC from donor 1 treatment: FK506_anti-CD3/CD28


title: PBMC_CsA_anti-CD3/CD28_donor_1

source_name: PBMC from donor 1 treatment: CsA_anti-CD3/CD28


title: PBMC_FK506_anti-CD3/CD28_donor_3

source_name: PBMC from donor 3 treatment: FK506_anti-CD3/CD28


title: PBMC_anti-CD3/CD28_donor_1

source_name: PBMC from donor 1 treatment: anti-CD3/CD28


title: PBMC_CRACi_anti-CD3/CD28_donor_1

source_name: PBMC from donor 1 treatment: CRACi_anti-CD3/CD28


title: PBMC_Untreated_donor_1

source_name: PBMC from donor 1 treatment: Untreated


title: CD4 anti-CD3 B7-2 BTNL2_2

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

hyb_protocol: Procedure used standard Affymetrix protocol.

data_processing: Scans were imported into Rosetta Resolver and pre-processed using the 'Resolver APT RMA - Intensity Profile Builder (group dependent)' and the Affymetrix Rosetta - Intensity Experiment Builder (no normalization, no error-weighting)  pipelines

organism: Mus musculus

source_name: CD4-positive cells from spleen and lymph nodes from female C57BL/6 mice

label_protocol: Fifty nanograms of total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: Cultured cells were colelcted by centrifugation and RNA extracted using the Qiagen RNeasy kit

treatment_protocol: 12 well tissue culture plates were coated overnight in 1ml PBS containing 2ug/ml anti-CD3 (2C11), 3ug/ml rB7-2.Fc, and 11ug/ml rBTNL2.Fc or IgG1 control protein.  C57BL/6 splenocyte single cell suspensions were generated and RBC lysed.  Biotin anti-mouse CD25 (PC61.5) was added to cells, and CD25+ cells were positively selected away using Miltenyi anti-biotin beads and autoMACS pro separator.  CD25- cells were then mixed with Miltenyi anti-mouse CD4 beads, and CD4+CD25- cells were positively selected with autoMACS separator.  After washing coating proteins out of 12 well plates, 1 million purified CD4+CD25- mouse T cells were added to each well with 0.36ng/ml rhuTGF-beta and 10ng/ml rmIL-2.  Cultures were carried out for four days before harvesting cells and lysing for RNA purification.

tag: gender

value: female

tag: strain

value: anti-CD3 B7-2 BTNL2


title: CD4 anti-CD3 B7-2 BTNL2_1

scan_protocol: Procedure used standard Affymetrix protocol.


title: CD4 anti-CD3_1


title: CD4 anti-CD3 B7-2_2

value: anti-CD3 B7-2


title: wt_P10.5_rep4

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

hyb_protocol: 5.5 ug of fragmented and labelled cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Exon ST 1.0 arrays. GeneChips were washed and stained using the GenChip Hybridization, Wash and Stain Kit (Affymetrix) in the Affymetrix Fluidics Station 450.

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

data_processing: Expression scores from the Core-Meta Probeset (MoEx-1_0-st-v1.r2.dt1.mm9.core.mps) were obtained using Robust Multichip Average to do background correction, quantile normalization and Median Polish for summarization using Partek Genomic Suite (Partek). Normalized data was subjected to ANOVA for gene list generation.

source_name: wild type mouse retina at age postnatal day 10.5

label_protocol: Amplified cDNA were prepared using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) followed by the GeneChip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix) from 1 ug total RNA.

growth_protocol: Animals were grown to embryonic day 16.5, and postnatal days 0.5, 6.5, or 10.5 where eyes were enucleaded and retinas isolated.  4 retinas from two animals were combined per each sample.

extract_protocol: Total RNA was isolated from retinas using Rneasy Mini kit with the on-column DNaseI treatment protocol according to manufacture's instructions.

value: retina

value: postnatal day 10.5

tag: genotype/variation

value: wild type


title: wt_P10.5_rep2

tag: age


title: CD4 anti-CD3 B7-2_1


title: CD4 anti-CD3_2


title: wt_P10.5_rep3


title: mut_P6.5_rep1

source_name: Rx-Dnmt1-/- mouse retina at age postnatal day 6.5

value: postnatal day 6.5


title: mut_P10.5_rep4

source_name: Rx-Dnmt1-/- mouse retina at age postnatal day 10.5


title: wt_P6.5_rep4

source_name: wild type mouse retina at age postnatal day 6.5


title: mut_P10.5_rep3


title: wt_P6.5_rep1


title: mut_P10.5_rep2


title: mut_P6.5_rep3


title: mut_P6.5_rep2


title: mut_P6.5_rep4


title: wt_P6.5_rep3


title: wt_P10.5_rep1


title: mut_P10.5_rep1


title: wt_P6.5_rep2


title: mut_P0.5_rep1

source_name: Rx-Dnmt1-/- mouse retina at age postnatal day 0.5

value: postnatal day 0.5


title: mut_P0.5_rep2


title: mut_P0.5_rep4


title: wt_P0.5_rep3

source_name: wild type mouse retina at age postnatal day 0.5


title: wt_P0.5_rep4


title: wt_P0.5_rep1


title: wt_P0.5_rep2


title: mut_E16.5_rep4

source_name: Rx-Dnmt1-/- mouse retina at age embryonic day 16.5

value: embryonic day 16.5


title: mut_E16.5_rep2


title: mut_E16.5_rep3


title: mut_P0.5_rep3


title: wt_E16.5_rep2

source_name: wild type mouse retina at age embryonic day 16.5


title: wt_E16.5_rep1


title: mut_E16.5_rep1


title: wt_E16.5_rep4


title: wt_E16.5_rep3


title: Differentiated SH-5Y cells_Mock-(2)[mRNA]

status: Public on Jan 17 2013

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

state: PA

address: 3307 N. Broad Street

institute: Temple University

description:
Differentiated SH-5Y cells
Mock 2

hyb_protocol: Genechip hybridization control kit (Affymetrix #900454) was used as requested and described by Affymetrix.

scan_protocol: The scanner is the GeneAtlas scanner and the software control is GeneAtlas Instrument Control (GAIC) v. 1.0.6.

data_processing:
Two biological replicates were used and analysis was performed using Partek software and using RMA Statistical algorithm
GeneAtlas® array results were also correlated with the array design and annotation information using the NetAffxTM Analysis Center. Hierarchical cluster analysis and heat maps were generated using Spotfire DecisionSite 7.2.

source_name: 24 hour treated with untreated

label_protocol: Genechip WT terminal labeling kit (Affymetrix #901524) was used to label the DNA and Hybridize Affymetrix Human Gene 1.1 ST Array (#AF901626PR) using Accublock digital dry bath. Strips were washed and stained using kit (affymetrix #901667).   Housekeeping control genes and spike controls were routinely analyzed on the GeneAtlas® microarrays platform to confirm the successful labeling of target RNAs.

growth_protocol: Differentiated SH-SY5Y neuronal cell line  (5 x 105) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

extract_protocol: Total RNA using Sureprep true total RNA isolation kit from Fisher scientific (#BP2800-50). RNA yield was measured on eppendorf biophotometer plus and 100 ng of total RNA was used as suggested by Affymetrix – GeneAtlas WT Expression kit manual.  (Affymetrix, Santa Clara, CA), comprised of a total 33,297 probe sets.  Quality control measures were carried out to ensure that RNA isolated was not degraded or lost.

treatment_protocol: Cells were treated with Vpr (10 pg/ml) kindly received from Dr Eric Cohen (University of Montreal-Canada) for 24 hours.

tag: cell line

value: differentiated SH-SY5Y neuronal cell line

tag: agent

value: untreated


title: PBMC_CRACi_anti-CD3/CD28_donor_4

source_name: PBMC from donor 4 treatment: CRACi_anti-CD3/CD28


title: Differentiated SH-5Y cells treated with HIV-1 tat (2)[mRNA]

description:
Differentiated SH-5Y cells
HIV-1 tat (2)

source_name: 24 hour treated with HIV-1 Tat

treatment_protocol: Cells were treated with Tat (100 ng/ml) kindly received from NIH (AIDS reagnets Bank) for 24 hours.

value: HIV-1 Tat


title: Differentiated SH-5Y cells_Mock (2)[mRNA]

description:
Differentiated SH-5Y cells
Mock 2


title: Differentiated SH-5Y cells_Mock (1)[mRNA]

description:
Differentiated SH-5Y cells
Mock 1


title: Differentiated SH-5Y cells treated with HIV-1 Vpr (2)[mRNA]

description:
Differentiated SH-5Y cells
HIV-1 Vpr (2)

source_name: 24 hour treated with HIV-1 Vpr

value: HIV-1 Vpr


title: Mutant vs WT Cortical Progenitor Cells Replicate 2

city: Edinburgh

first: Ian

last: Simpson

address: 10 Crichton Street

department: Institute for Adaptive and Neural Computation

institute: University of Edinburgh

description: Biological replicate 2 of 3.  Pax6sey/sey vs. Pax6+/+ cortical progenitor cells from lateral cortex

hyb_protocol: Fluorescently labelled cRNA samples were hybridized to Agilent dual-dye whole mouse genome arrays (G4122A) in accordance with Agilent protocols.  750ng of cyanine 3- and 750ng of cyanine 5-labelled cRNA were hybridized at 60ºC for 17 hours in a rotating oven.

scan_protocol: After hybridization arrays were scanned in an Agilent scanner for Cy3 and Cy5 and images analysed using Agilent’s feature extraction software (version 7.1).

data_processing: Edwards' algorithm was used to remove background noise followed by Loess normalisation

source_name: Pax6sey/sey  cortical progenitor cells from lateral cortex

label_protocol: RNA was amplified and labelled with cyanine dyes.  The Agilent low RNA input linear amplification kit was used to amplify the RNA samples and to produce cRNA, labelled with either Cyanine 3 (Cy3) or Cyanine 5 (Cy5) fluorescent labels.  Briefly; a poly dT primer with a T7 polymerase promoter was annealed to the poly A+ RNA.  Reverse transcriptase was then added to the reaction and double stranded cDNA was synthesised.  Using T7 RNA polymerase, cRNA, incorporating either cyanine 3- or cyanine 5-labelled CTP, was synthesised from the cDNA.  Using this protocol approximately 1μg cRNA is produced from 50ng of starting material.

extract_protocol: RNA was extracted from FACS sorted cells using a Qiagen RNeasy kit.  Membranes were disrupted and the lysate homogenized on a QIAshredder spin column.  70% ethanol was added to facilitate binding of RNA to the silica-gel membrane of the RNeasy spin column.  Any traces of genomic DNA were removed by on-column DNase digestion.  Contaminants were removed by washing and then the RNA was eluted in RNase-free water.  RNA was stored at -80ºC.

treatment_protocol: Pax6+/+.DTy54+ and Pax6sey/sey.DTy54+  E12.5 embryos were dissected as follows: The brain was isolated by an incision between the eye and the base of the brain and the skin and membranes were removed.  The telencephalic lobes were dissected away from the rest of the brain by an incision on either side of the diencephalon and the two lobes were then separated.  A small incision was made, just dorsal to the PSPB, at the rostral end of each lobe and another at the caudal end.  These incisions allowed the lobes to be flattened, by folding back the dorsal telencephalon, so that the ventricular surface was uppermost.  In this orientation the stripe of intense GFP expression at the PSPB could be clearly seen.  The tissue could then be divided into three pieces with cuts being made on either side of the PSPB as labelled by GFP expression. The cells were then dissociated using the papain dissociation system (Worthington Biochem) and sorted by FACS using a DakoCytomation MoFlo MLS highh speed sorter.  Before experimental samples were sorted, dissociated telencephalic cells from a non-transgenic embryo were used to position the gate for collection so that no non-transgenic cells were within the gated region.  This very stringent cut-off eliminated both GFP-negative cells and cells with low levels of GFP when the experimental samples were sorted

value: Swiss Sey

tag: developmental stage

value: Lateral Cortex

tag: cells

value: high expression of GFP

tag: transgene

value: DTy54 Pax6 reporter


title: Mutant vs WT Cortical Progenitor Cells Replicate 1

description: Biological replicate 1 of 3.  Pax6sey/sey vs. Pax6+/+ cortical progenitor cells from lateral cortex

tag: tissue


title: Differentiated SH-5Y cells_Mock-(1)[mRNA]

description:
Differentiated SH-5Y cells
Mock 1


title: Differentiated SH-5Y cells treated with HIV-1 Vpr (1)[mRNA]

description:
Differentiated SH-5Y cells
HIV-1 Vpr


title: Differentiated SH-5Y cells treated with HIV-1 tat (1)[mRNA]

description:
Differentiated SH-5Y cells
HIV-1 tat


title: Mutant vs WT Cortical Progenitor Cells Replicate 3

description: Biological replicate 3 of 3.  Pax6sey/sey vs. Pax6+/+ cortical progenitor cells from lateral cortex


title: WT(2) v WT over-expressing Cj1103(2) array

status: Public on Dec 31 2012

city: Norwich

first: Bruce

middle: MacKenzie

last: Pearson

state: Norfolk

address: Colney Lane

department: Food Safety

institute: Institute of Food Research

hyb_protocol: Standard Agilent hybridization was carried out overnight at 62 °C. Both Hybridization and washing steps as per Manufacturer's instructions.

scan_protocol: Microarrays were scanned at 5µm resolution using an Axon 4000A scanner and images were acquired using GenePixPro 6.1 software (Axon).

data_processing: Data was block median normalized (using Excel Macro) prior to analysis.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Batch cultured control sample

label_protocol: Sample was labelled with Cy5-dUTP. RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences) and made to 12.4 µl total volume with water and supplemented on ice with 3 µl 10x RT buffer (Invitrogen), 0.6 µl 50x dNTPs mixture (25 mM each dCTP, dATP, dGTP and 10 mM dTTP), 3 µl 0.1 M DTT, 2 µl 1mM Cy5-dUTP (Perkin Elmer), and 200U Superscript II RNase H reverse transcriptase (Invitrogen). Incubation was at 37 °C overnight. Labelled cDNA was purified using a Qiaquick purification kit (Qiagen) and dried.

growth_protocol: Batch cultures of C. jejuni strains were grown in 50 ml volumes of Brucella broth in Tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5 % Oxygen, 10 % Carbon dioxide, 85 % Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 ºC.

extract_protocol: 50 ml samples mixed immediately on ice with 5 ml 95% ethanol and 5% phenol to stabilize the RNA. The cells were subsequently harvested by centrifugation. Total RNA was purified by using a Qiagen RNeasy Mini kit as recommended by the supplier.

value: WT

source_name: Batch cultured test sample

label_protocol: Sample was labelled with Cy3-dUTP. RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences) and made to 12.4 µl total volume with water and supplemented on ice with 3 µl 10x RT buffer (Invitrogen), 0.6 µl 50x dNTPs mixture (25 mM each dCTP, dATP, dGTP and 10 mM dTTP), 3 µl 0.1 M DTT, 2 µl 1mM Cy3-dUTP (Perkin Elmer), and 200U Superscript II RNase H reverse transcriptase (Invitrogen). Incubation was at 37 °C overnight. Labelled cDNA was purified using a Qiaquick purification kit (Qiagen) and dried.


title: WT(3) v Complemented Cj1103 knockout(3) array


title: WT(3) v WT over-expressing Cj1103(3) array


title: WT(1) v Complemented Cj1103 knockout(1) array


title: WT(2) v Complemented Cj1103 knockout(2) array


title: WT(1) v Cj1103 knockout(1) array


title: WT(1) v Cj0667 knockout(1) array

scan_protocol: Microarrays were scanned at 5um resolution using an Axon 4000A scanner and images were acquired using GenePixPro 6.1 software (Axon).


title: WT(2) v Cj1103 knockout(2) array


title: WT(3) v Cj1103 knockout(3) array


title: WT(1) v Cj0138 knockout(1) array


title: WT(1) v WT over-expressing Cj1103(1) array


title: WT(1) v Complemented Cj0138 knockout(1) array


title: WT(2) v WT(3) array


title: WT(1) v WT over-expressing Cj0138(1) array


title: WT(1) v WT over-expressing Cj0667(1) array


title: LTL313h_ICI_rep2

status: Public on Dec 27 2012

city: Vancouver

first: Hisae

last: Nakamura

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Agency

description: Gene expression of ICI-treated LTL313

hyb_protocol: 1.65μg of Cy3-cRNA is hybridized to the array at 65 degrees for 17 hours.

scan_protocol: After hybridization, the slides were washed twice in Agilent Wash Buffer and acetonitrile and scanned using an Agilent DNA Microarray Scanner (Agilent, Mississauga, ON).

data_processing: The data was processed using the Agilent Feature Extraction 10.5.1 and analyzed in Agilent GeneSpring 7.3.1 (Agilent, Mississauga, ON).

source_name: LTL313 prostate cancer xenograft, ICI-treated

label_protocol: Total RNA was converted into cDNA, which was used to generate cyanine-3-labeled cRNA by T7 RNA polymerase in the presence of Cy3.

growth_protocol: The establishment of two distinct human tumour lines,  LTL313, has been described previously (Andersen RJ,Mawji NR, et al. 2010, Watahiki A,Wang Y, et al. 2011, Hu P,Chu GC, et al. 2011).Briefly, they were derived from primary biopsy PCa specimen, which was grafted under the renal capsule of NOD-SCID male mice, where the tumour tissue receives sufficient amounts of oxygen and nutrients (Wang Y,Revelo MP, et al. 2005, Wang Y,Xue H, et al. 2005).

extract_protocol: Total RNA was extracted from snap-frozen LTL313h tumours that were untreated (control) or treated with either 10mg-genistein or ICI 182, 780 using the RNeasy mini kit following the manufacturer’s instructions (Qiagen, Toronto, ON). 1μg of total RNA per sample was submitted to the Vancouver Prostate Centre, Microarray Core Facility for gene expression microarray analysis.

value: LTL313 prostate cancer xenograft

tag: host

value: NOD-SCID male mice


title: LTL313h_genistein_rep3

description: Gene expression of genistein-treated LTL313

source_name: LTL313 prostate cancer xenograft, genistein-treated


title: LTL313h_control_rep1

description: Gene expression of non-treated LTL313

source_name: LTL313 prostate cancer xenograft, control (not-treated)


title: WT(2) v WT(1) array


title: LTL313h_genistein_rep2


title: LTL313h_genistein_rep1


title: LTL313h_ICI_rep3

description: Gene expression of ICI-treated LTL313


title: LTL313h_control_rep2

description: Gene expression of non-treated LTL313


title: LTL313h_control_rep3

description: Gene expression of non-treated LTL313


title: Differentiated SH-5Y cells treated with supernatant from HIV-infected U-937 (2) [mRNA]

status: Public on Dec 07 2012

description: Differentiated SH-5Y cells, HIV-JR-FL (2)

data_processing:
Quality control measures were carried out to ensure that RNA isolated was not degraded or lost. Housekeeping control genes and spike controls were routinely analyzed on the GeneAtlas® microarrays platform to confirm the successful labeling of target RNAs.
Two biological replicates were used and analysis was performed using Partek software and using RMA Statistical algorithm
GeneAtlas® array results were also correlated with the array design and annotation information using the NetAffxTM Analysis Center. Hierarchical cluster analysis and heat maps were generated using Spotfire DecisionSite 7.2.

source_name: 24 hour treated with supernatant isolated with HIV JR-FL

label_protocol: Genechip WT terminal labeling kit (Affymetrix #901524) was used to label the DNA and Hybridize Affymetrix Human Gene 1.1 ST Array (#AF901626PR) using Accublock digital dry bath. Strips were washed and stained using kit (affymetrix #901667).

extract_protocol: Total RNA using Sureprep true total RNA isolation kit from Fisher scientific (#BP2800-50). RNA yield was measured on eppendorf biophotometer plus and 100 ng of total RNA was used as suggested by Affymetrix – GeneAtlas WT Expression kit manual.  (Affymetrix, Santa Clara, CA), comprised of a total 33,297 probe sets.

treatment_protocol: Cells were treated for 24hrs with 0.1 pg/cell as calculated by p24 ELISA, of supernatant isolated from U-937-infected with HIV-1 JR-FL

value: neuronal cell line SH-SY5Y

value: supernatant from HIV-infected U-937


title: HIV-1 Tat (1)_HN [mRNA]

description: SAMPLE 1

hyb_protocol: Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.

data_processing:
RMA normalization using GeneSpring software.
Quality control measures were carried out to ensure that RNA isolated was not degraded or lost. Housekeeping control genes and spike controls were routinely analyzed on the GeneChip® microarrays to confirm the successful labeling of target RNAs. Preliminary data analysis was performed in conjunction with the Thomas Jefferson University Bioinformatics Program.
GeneChip® array results were also correlated with the array design and annotation information using the NetAffxTM Analysis Center. Hierarchical cluster analysis and heat maps were generated using Spotfire DecisionSite 7.2.

source_name: Primary human Neurons

growth_protocol: Primary human neurons (HN) (5 x 105) purchased from ScienCell Research Laboratories (Carlsbad, CA) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for Gene expression profiling that was performed using the Affymetrix GeneChip® [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]

treatment_protocol: Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) for 24 hours.

value: Tat


title: Differentiated SH-5Y cells treated with supernatant from HIV-infected U-937 (1) [mRNA]

description: Differentiated SH-5Y cells, HIV-JR-FL (1)


title: 6 month_starvation_culture_rep3

status: Public on Oct 25 2012

city: Heverle

first: Tekle Tafese

last: Fida

address: Kastelpark Arenberg 220

department: Earth and environmental Science

country: Belgium

institute: KU Leuven

description: gene expression in after 6 months of starvation

hyb_protocol: Sixty nanograms of labeled cDNA with an incorporation efficiency of cyanine-3-labeled dCTP between 4-5% were used for microarray analysis. The cDNA was hybridized with the array for 17 h at 65oC, washed, and scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

scan_protocol: The Agilent Feature Extraction software package (version 9.5.3; Agilent Technologies) was used to extract the hybridization signal intensities from the images scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

data_processing: Normalization of the signal intensities (Quantile normalization) and analysis of the data were done using the Genespring GX software package (version 11, Agilent technologies). To test for significantly differentially expressed genes, Welch’s t- test with unequal variances was first used to calculate p-values. The Benjamini and Hochberg procedure was then used to correct the p-vales for multiple hypothesis testing and convert the p-vales into false discovery rates (FDRs)

organism: Sphingomonas sp. LH128

source_name: 6 month_starvation_culture

label_protocol: The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript III reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 55oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer  The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript III reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 55oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer    The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript III reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 55oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer

growth_protocol: Cells were pregrown in phosphate buffered minimal medium containg 2 g per liter glucos

extract_protocol: RNA was immediately extracted from 1 ml of the cell suspensions from triplicate tubes of each condition using the RNeasy Protect Bacteria Mini Kit (Qiagen, Benelux, BV) according to the manufacturer’s instructions. RNA was further purified and precipitated by using sodium acetate and ethanol precipitation method.

treatment_protocol: Cells were pregrown to exponential phase (OD600 of 0.5) in triplicate of 50 ml MM containing 2 g l-1 glucose. Five ml of the cells each corresponding to about 1.4 x 109 CFU per ml, was centrifuged at 5000 x g for 10 min in a Becton Dickinson centrifuge (Benelux, NV), washed twice with 0.01M MgSO4 and finally resuspended in 5 ml of MgSO4 and  kept at 20°C for 6 months, during which CFU was determined at different time points. At the end of the experiment, the tubes were sacrificed for physiological analysis and RNA extraction. As a control, freshly prepared non-starved cells washed in 0.01M MgSO4 were similarly treated as the starved cells.

tag: growth condition

value: starved culture


title: HIV-1 Tat (2)_HN [mRNA]

description: SAMPLE 2

scan_protocol: Labeling, hybridization and detection of RNA were done at the Genomics Core Facility at Thomas Jefferson University and at HC-LITT according to recommendations by Affymetrix.


title: 6 month_starvation_culture_rep2


title: nonstarved_culture_rep3

description: gene expression in initial culture

value: nonstarved culture


title: nonstarved_culture_rep1

description: gene expression in initial culture


title: Differentiated SH-5Y cells (1) [mRNA]

description: Differentiated SH-5Y cells, Mock 1

source_name: 24 hour treated with U937 media

value: mock


title: MSC_ROPI4

status: Public on Aug 31 2012

city: Edmonton

first: Eliana

last: Lucchinetti

address: HMRC 408

institute: University of Alberta

hyb_protocol: Samples were hybridized using Affymetrix reagents according to the protocols established at the Functional Genomics Center Zurich (http://www.fgcz.uzh.ch). Washing using the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Microarray analysis was performed using customCDF from Brainarray (Brainarray Version 11.0.1, MoEx10stv1_Mm_ENSG). For more information, please see:  http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp . Background correction, normalization, and calculation of probe set summaries done with the Robust Multichip Average (RMA) method.

source_name: Mesenchymal stem cells

label_protocol: The cDNA was prepared from total RNA using the WT Ovation Pico System (NuGEN Technologies, Inc., San Carlos, CA).  The FL-Ovation cDNA Biotin Module V2 (NuGEN) was used to generate biotin-labeled single-stranded cDNA samples, which were subsequently fragmented randomly to 35 to 200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., Santa Clara, CA) and used to hybridize onto Affymetrix Exon 1.0 ST arrays (Affymetrix Inc.).

growth_protocol: Culture-expanded mesenchymal stem cells; passage 10; standard culture conditions

extract_protocol: Total RNA was isolated using the Qiagen RNeasy MiniKit (QIAGEN Inc., Toronto, ON)

treatment_protocol: Cells were treated for 24 hours with 100 mM ropivacaine (commonly used local anesthetic agent)

value: bone marrow

value: ropivacaine 100 uM

tag: sample collection time

value: 24 hrs


title: MSC_ROPI3


title: MSC_ROPI2


title: MSC_ROPI1


title: LTL313h_ICI_rep1

description: Gene expression of ICI-treated LTL313


title: MSC_control4

value: no treatment


title: swaPS2

status: Public on Jan 01 2013

city: New York

first: Daniel

last: Paull

address: 1995 Broadway

institute: The New York Stem Cell Foundation

description: Hybridized to SNP 6.0 Array

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: Arrays were  washed using Affymetrix 450 fluidics stations, and scanned using Affymetrix 7G Gene Chip Scanner 3000.

data_processing:
CNVs were detected using NEXUS 6.0 and the SNP-FASST2 Segmentation algorithm. High gains were set to the threshold of 0.7, gains at 0.1, losses at -0.15 and big losses at -1.1. A significance threshold of 5.0E-7 was used, with minimum number of 10 probes required per CNV call and a minimum size of 50Kbp (2 Copy losses/gains were analyzed to a minimum of 10Kbp). Following participation analysis to determine whether CNVs were novel or preexisting, each call was manually inspected for visual confirmation of the call.
The log2 intensity values generated following normalization in NEXUS against the Affymetrix/NEXUS Hapmap reference set (Generated from pooled hapmap samples: http://www.blog.biodiscovery.com/?p=392). Thus, sample data table contains log2 ratio of normalized intensity representing [test/HapMap reference set].
Complete processed data files containing the following columns are avaible as Sample supplementary file [*.data.txt];
ID_REF=Unique Identifier for the SNP or CNV probe set; Chromosome=Chromosome(1-22,X,Y); RANGE_START=The start base position for the 5'-most probe in the probe set; RANGE_STOP=The end base position of the 3'-most probe in the probe set; LogRatio = Log2 Ratio of Intensity.
Data file from Nexus 6.0 with analysis parameters and raw CNV calls including size and location for each cell line are also available as Sample supplementary file [*.Nexus_output.txt].

source_name: Swapped Pluripotent Stem Cell Line

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Cell lines grown under standard conditions.

extract_protocol: DNA extracted using High Pure PCR Template Preparation Kit as per manufacturer (Roche).

value: Swapped Pluripotent Stem (swaPS) Cell Line 2

value: Embryonic Stem Cell


title: MSC_control3


title: Tumor_MMTV_PyMT_167_HCI

status: Public on Aug 10 2012

city: Salt Lake City

first: Bryan

last: Welm

state: UT

address: 2000 Circle of Hope Drive

department: Oncological Science

institute: University of Utah, Huntsman Cancer Institute

hyb_protocol: Agilent One-color Gene Expression Hybridization and Wash Protocol

scan_protocol: Microarrays were scanned on an Agilent Technologies G2505C scanner at 5 micron resolution

data_processing:
Array images were processed in Agilent Feature Extraction software version 10.5.1.1, which produces spatially detrended intensity data
Array data was filtered to remove control features and any non-uniform features or population outlier features. Remaining features were averaged to yield a single value for each unique probe. Finally data were log2 transformed, quantile normalized, and adjusted for batch effects using ComBat.

source_name: Primary tumor MMTV-PyMT 167 generated from MMTV-PyMT transgenic mouse, adenosquamous histology

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

growth_protocol: Mammary epithelial cells were infected with specified lentivirus, then transplanted into cleared fat pads of recipient mice. Tumors were harvested at 2 cm and a portion was flash frozen.

extract_protocol: Qiagen Rneasy kit

treatment_protocol: No treatments

tag: tissue type

value: mouse mammary tumor

tag: lentivirus

tag: primary tumor

tag: histology

value: Adenocarcinoma

tag: number of insertion sites

tag: combat group


title: 6 month_starvation_culture_rep1


title: nonstarved_culture_rep2

description: gene expression in initial culture


title: Tumor_MMTV_PyMT_82_HCI

source_name: Primary tumor MMTV-PyMT 82 generated from MMTV-PyMT transgenic mouse, adenosquamous histology


title: Tumor_1656_HCI

source_name: Primary tumor 1656 generated from EF1α-PyMT9C lentivirus, adenosquamous histology

value: Adenosquamous

value: Unknown


title: MSC_control2

tag: strain


title: pES6

description: Hybridized to SNP 6.0 Array

source_name: Parthenognic Stem Cell Line

value: Parthenognic Stem (pES) Cell Line 6

tag: cell type


title: Tumor_1586_HCI

source_name: Primary tumor 1586 generated from EF1α-PyMT9C lentivirus, adenocarcinoma histology


title: Tumor_1614_ HCI

source_name: Primary tumor 1614 generated from EF1α-PyMT9C lentivirus, adenocarcinoma histology


title: pES4

description: Hybridized to SNP 6.0 Array

tag: cell line

value: Parthenognic Stem (pES) Cell Line 4


title: Differentiated SH-5Y cells (2) [mRNA]

description: Differentiated SH-5Y cells, Mock 2

value: neuronal cell line SH-SY5Y

tag: treatment


title: Tumor_1649_HCI

source_name: Primary tumor 1649 generated from EF1α-PyMT9C lentivirus, tubular  histology

value: Tubular


title: Tumor_1003_HCI

source_name: Secondary tumor 1003 regenerated from primary tumor 253 tissue, Muc-PyMT10C lentivirus, lipid rich histology

value: Lipid Rich

value: 4- same sites as tumor 253


title: swaPS4

description: Hybridized to SNP 6.0 Array

value: Swapped Pluripotent Stem (swaPS) Cell Line 4


title: Embryonic_HCI

source_name: Embryonic tissue sample

value: embryonic tissue


title: Tumor_1002_HCI

source_name: Secondary tumor 1002 regenerated from primary tumor 253 tissue, Muc-PyMT10C lentivirus, lipid rich histology


title: MSC_control1

value: bone marrow

tag: agent


title: Tumor_256_HCI

source_name: Primary tumor 256 generated from Muc-PyMT10C lentivirus, papillary histology

value: Papillary


title: Tumor_258_HCI

source_name: Primary tumor 258 generated from Muc-PyMT10C lentivirus, lipid rich histology


title: Tumor_253_HCI

source_name: Primary tumor 253 generated from Muc-PyMT10C lentivirus, lipid rich histology


title: pES3

description: Hybridized to SNP 6.0 Array

value: Parthenognic Stem (pES) Cell Line 3


title: swaPS3

description: Hybridized to SNP 6.0 Array

value: Swapped Pluripotent Stem (swaPS) Cell Line 3


title: Tumor_1004_HCI

source_name: Secondary tumor 1004 regenerated from primary tumor 253 tissue, Muc-PyMT10C lentivirus, lipid rich histology


title: Tumor_1001_HCI

source_name: Secondary tumor 1001 regenerated from primary tumor 253 tissue, Muc-PyMT10C lentivirus, lipid rich histology


title: 1058

description: Hybridized to SNP 6.0 Array

source_name: Somatic Cell

value: 1058 Somatic Cell

value: Somatic Cell


title: Tumor_252_HCI

source_name: Primary tumor 252 generated from Muc-PyMT10C lentivirus, papillary histology

value: mouse mammary tumor


title: pES7

description: Hybridized to SNP 6.0 Array

value: Parthenognic Stem (pES) Cell Line 7

value: Embryonic Stem Cell


title: pES1

description: Hybridized to SNP 6.0 Array

value: Parthenognic Stem (pES) Cell Line 1


title: Tumor_1058_HCI

source_name: Secondary tumor 1058 regenerated from primary tumor 27 tissue, EF1α-PyMT10C lentivirus, spindloid histology

value: Spindloid

value: Unknown


title: swaPS1

description: Hybridized to SNP 6.0 Array

source_name: Swapped Pluripotent Stem Cell Line

value: Swapped Pluripotent Stem (swaPS) Cell Line 1


title: Tumor_248_HCI

source_name: Primary tumor 248 generated from Muc-PyMT10C lentivirus, tubular histology

value: Tubular


title: Tumor_1055_HCI

source_name: Secondary tumor 1055 regenerated from primary tumor 25 tissue, EF1α-PyMT10C lentivirus, adenocarcinoma histology

value: Adenocarcinoma

value: 1- same site as tumor 25


title: Tumor_1041_HCI

source_name: Secondary tumor 1041 regenerated from primary tumor 24 tissue, EF1α-PyMT10C lentivirus, adenocarcinoma histology


title: 1110

description: Hybridized to SNP 6.0 Array

value: 1110 Somatic Cell


title: Tumor_1031_HCI

source_name: Secondary tumor 1031 regenerated from primary tumor 16 tissue, EF1α-PyMT10C lentivirus, adenocarcinoma histology


title: Tumor_449_HCI

source_name: Secondary tumor 449 regenerated from primary tumor 43 tissue, EF1α-PyMT10C lentivirus, adenocarcinoma histology


title: Tumor_38_HCI

source_name: Primary tumor 38 generated from EF1α-PyMT10C lentivirus, adenosquamous histology

value: Adenosquamous


title: Tumor_37_HCI

source_name: Primary tumor 37 generated from EF1α-PyMT10C lentivirus, adenosquamous histology


title: Tumor_39_HCI

source_name: Primary tumor 39 generated from EF1α-PyMT10C lentivirus, adenocarcinoma histology


title: Tumor_25_HCI

source_name: Primary tumor 25 generated from EF1α-PyMT10C lentivirus, adenoarcinoma histology


title: Tumor_24_HCI

source_name: Primary tumor 24 generated from EF1α-PyMT10C lentivirus, adenocarcinoma histology


title: Tumor_17_HCI

source_name: Primary tumor 17 generated from EF1α-PyMT10C lentivirus, adenocarcinoma histology


title: Tumor_63_HCI

source_name: Primary tumor 63 generated from EF1α-PyMT10C lentivirus, tubular histology


title: Tumor_10_HCI

source_name: Primary tumor 10 generated from EF1α-PyMT10C lentivirus, adenosquamous histology


title: Tumor_21_HCI

source_name: Primary tumor 21 generated from EF1α-PyMT10C lentivirus, adenosquamous histology


title: Tumor_23_HCI

source_name: Primary tumor 23 generated from EF1α-PyMT10C lentivirus, tubular histology


title: 1105

description: Hybridized to SNP 6.0 Array

source_name: Somatic Cell

value: 1105 Somatic Cell


title: 1034

description: Hybridized to SNP 6.0 Array

data_processing:
CNVs were detected using NEXUS 6.0 and the SNP-FASST2 Segmentation algorithm. High gains were set to the threshold of 0.7, gains at 0.1, losses at -0.15 and big losses at -1.1. A significance threshold of 5.0E-7 was used, with minimum number of 10 probes required per CNV call and a minimum size of 50Kbp (2 Copy losses/gains were analyzed to a minimum of 10Kbp). Following participation analysis to determine whether CNVs were novel or preexisting, each call was manually inspected for visual confirmation of the call.
The log2 intensity values generated following normalization in NEXUS against the Affymetrix/NEXUS Hapmap reference set (Generated from pooled hapmap samples: http://www.blog.biodiscovery.com/?p=392). Thus, sample data table contains log2 ratio of normalized intensity representing [test/HapMap reference set].
Complete processed data files containing the following columns are avaible as Sample supplementary file [*.data.txt];
ID_REF=Unique Identifier for the SNP or CNV probe set; Chromosome=Chromosome(1-22,X,Y); RANGE_START=The start base position for the 5'-most probe in the probe set; RANGE_STOP=The end base position of the 3'-most probe in the probe set; LogRatio = Log2 ratio of normalized intensity representing test/Hapmap .
Data file from Nexus 6.0 with analysis parameters and raw CNV calls including size and location for each cell line are also available as Sample supplementary file [*.Nexus_output.txt].

value: 1034 Somatic Cell


title: DGM-00708_lg

status: Public on Jun 20 2012

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: large airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: smoker


title: DGM-00752_lg


title: DGM-00612_lg


title: DGM-00663_lg


title: Tumor_249_HCI

source_name: Primary tumor 249 generated from Muc-PyMT10C lentivirus, adenosquamous histology


title: DGM-00537_lg


title: DGM-00613_lg


title: DGM-00599_lg


title: DGM-00626_lg


title: DGM-00641_lg


title: DGM-00761_lg


title: DGM-00764_lg


title: DGM-00732_lg


title: DGM-00583_lg


title: DGM-00567_lg


title: DGM-00332_lg


title: DGM-00447_lg


title: DGM-00321_lg


title: DGM-00413_lg


title: DGM-00552_lg


title: DGM-00469_lg


title: DGM-00451_lg


title: DGM-00446_lg


title: DGM-00464_lg


title: DGM-00515_lg


title: DGM-00300_lg


title: 1111

description: Hybridized to SNP 6.0 Array

value: 1111 Somatic Cell


title: DGM-00127_lg


title: DGM-00205_lg


title: 1126

description: Hybridized to SNP 6.0 Array

value: 1126 Somatic Cell

value: Somatic Cell


title: DGM-00751_lg

value: nonsmoker


title: DGM-00661_lg


title: DGM-00685_lg


title: DGM-00465_lg


title: DGM-00268_lg


title: DGM-00778_lg


title: DGM-00551_lg


title: DGM-00529_lg


title: DGM-00278_lg


title: DGM-00757_lg


title: DGM-00342_lg


title: DGM-00013_lg


title: Tumor_96_HCI

source_name: Secondary tumor 96 regenerated from primary tumor 17 tissue, EF1α-PyMT10C lentivirus, adenocarcinoma histology

value: mouse mammary tumor

value: 1- same site as tumor 17


title: DGM-00019_lg


title: DGM-00568_lg


title: DGM-00530_lg


title: DGM-00249_lg


title: DGM-00314_lg


title: Tumor_48_HCI

source_name: Primary tumor 48 generated from EF1α-PyMT10C lentivirus, adenocarcinoma histology


title: DGM-00696_lg


title: DGM-00273_lg


title: DGM-00192_lg


title: DGM-00073_lg


title: DGM-00041_lg


title: DGM-00044_lg


title: DGM-00052_lg


title: Cafeteria diet 2

status: Public on Mar 30 2012

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description: Gene expression data from the mesenteric adipose tissue surrounding the pancreas (pMES) in cafeteria diet fed Wistar rats for 30 days

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor on R language.

organism: Rattus norvegicus

source_name: cafeteria diet (obese group)

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

growth_protocol: Adult male Wistar rats (Charles River Laboratories, Wilmington, MA), 7 wk old (weighing 225–250 g), were caged individually in a 12-h light, 12-h dark cycle in a temperature- and humidity-controlled environment.

extract_protocol: Total RNA was extracted using the RNeasy minikit (QIAGEN, Hilden, Germany).

treatment_protocol: Animals were divided into two dietary sets for 30 days. One group was fed with standard chow diet (supplying 8% of calories as fat; type AO4 from Panlab, Barcelona, Spain). The second group was fed with a cafeteria diet (66% of calories as fat), as previously described (Endocrinology 146:4362–4369, 2005).

value: Wistar

tag: diet

value: Cafeteria diet


title: Cafeteria diet 1

tag: tissue

value: mesenteric adipose tissue surrounding the pancreas (pMES)


title: Standard diet 1

description: Gene expression data from the mesenteric adipose tissue surrounding the pancreas (pMES) in standard diet fed Wistar rats for 30 days

source_name: standard chow (lean group)

value: Standard diet


title: Standard diet 2


title: Standard diet 3


title: MPI-652_tissue

status: Public on Jun 24 2011

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)

source_name: tumor

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

tag: gender

value: male

tag: age

value: GCB

value: intermediate

value: Test

value: FISH data not available

value: FALSE


title: MPI-641_tissue

value: female

value: non-mBL


title: MPI-826_tissue


title: MPI-537_tissue


title: MPI-560_tissue

value: unclassified


title: MPI-768_tissue


title: MPI-714_tissue


title: MPI-555_tissue


title: MPI-414_tissue


title: MPI-423_tissue

value: Train

value: negative


title: MPI-304_tissue

value: ABC


title: MPI-389_tissue


title: MPI-334_tissue


title: MPI-320_tissue


title: MPI-356_tissue


title: MPI-291_tissue


title: MPI-302_tissue


title: MPI-331_tissue


title: Pt23_good_recovery

status: Public on Dec 03 2009

city: La Jolla

first: Christopher

last: Woelk

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California San Diego

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, and washing and scanning were performed according to the Illumina BeadStation 500x manual. Essentially the amplified, biotin-labeled human cRNA samples were resuspended in a solution of Hyb E1 buffer (Illumina) and 25% (v/v) formamide at a final concentration of 25 ng/µL. 1.5 µg of each cRNA were hybridized.

scan_protocol: The arrays were scanned on the Illumina BeadArray Reader.

data_processing: The data were log2 transformed, normalised using robust spline normalisation with Bioconductor package lumi in R and adjusted for batch effect using ComBat (http://statistics.byu.edu/johnson/ComBat/Usage.html).

source_name: PBMC

label_protocol: Biotinylated cRNA was prepared using the Illumina RNA Amplification Kit, Catalog #1L1791 (Ambion, Inc., Austin, TX) according to the manufacturer's directions starting with ~250 ng total RNA. mRNA was converted to cDNA, followed by an amplification/labeling step mediated by T7 DNA polymerase. The cDNA and cRNA filter cartridges (Ambion) were used according to the manufacturer's instructions for RT and IVT cleanup, respectively.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer.

value: PBMC

tag: sex

value: Male

value: 54 years

tag: race

value: White

tag: subsequent drug regimen

value: PI

tag: cell count (baseline cd4+ t cell count, cells/ul)

tag: final cell count (final week 48 cd4+ t cell count, cells/ul)

tag: change in cell count (change in cd4+ t cell count, cells/ml)

tag: batch


title: Pt18_poor_recovery

value: 24 years

value: American Indian


title: Pt22_good_recovery

value: 37 years

value: Asian


title: Pt19_good_recovery

value: 39 years


title: Pt20_poor_recovery

value: 34 years

value: African American


title: Pt17_good_recovery

value: 33 years


title: Pt15_poor_recovery

value: 58 years


title: Pt14_poor_recovery

value: 50 years


title: mESCs 72 hours after differentiation start

status: Public on Apr 11 2012

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

hyb_protocol: Affymetrix GeneChip Mouse Exon 1.0 ST microarrays were hybridized with 4.7 µg of labelled DNA

scan_protocol: Washes, staining and scan of microarrays were conducted using an Affymetrix GCS3000 platform

data_processing:
Microarrays were normalized using RMA (Robust Multi-array Analysis) as available in the bioconductor affy package (http://www.bioconductor.org), and annotated using the xmapcore database for Ensembl mouse version 62 (http://annmap.picr.man.ac.uk/download/). For each gene the expression is calculated by averaging over probesets that detect the maximum number of transcripts per gene
probe group file: MoEx-1_0-st-v1.r2.pgf

label_protocol: Affymetrix mouse Exon 1.0 ST arrays were hybridised according to Affymetrix's recommendations using the Ambion WT protocol (Life technologies) and Affymetrix labelling and hybridization kits. 100ng of total RNA (RIN=10) were processed and amplified in parallel with an external Universal Mouse Reference RNA (Agielent, #740100) to control robustness of the data. The mean yield of labelled DNA was   7.2 µg (min: 6.4µg; max: 7.7µg).

growth_protocol: Pgk12.1 ES cells were adapted, during passages 21-26, to 2i culture conditions, consisting of N2B27 medium (50% DMEM/F12 (Invitrogen), 50% Neurobasal medium (Invitrogen), NDiff supplement (Millipore), B27 supplement (Invitrogen), 2mM Glutamine, 100 µM β-Mercaptoethanol), supplemented with 3 µM Gsk3 inhibitor CT-99021, 1 µM Mek1 inhibitor PD-0325901 and 100U/ml LIF (Millipore).

extract_protocol: 200 µl of Chloroform was added and after 15 min centrifugation (12000xg, 4°C) the aqueous phase was mixed with 700 µl 70% ethanol and applied to a Silica column (Qiagen RNAeasy Mini kit). RNA was then purified according to the instruction of the manufacturer, including on-column DNAse digestion.

treatment_protocol: For EpiSC differentiation9 8*10^5 cells per well were seeded in a Fibronectin coated (10 µg/ml, Millipore) 6-well plate in differentiation medium (N2B27 medium, 20ng/ml Activin A, 12 ng/ml Fgf-basic, R&D), subsequently the medium was changed daily. At 6, 12, 18, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 66, 72 and 84 hours of differentiation, cells were lysed by direct addition of 1 ml Trizol to the wells

tag: hours


title: Pt13_poor_recovery

tag: cell type

value: 29 years


title: Pt21_good_recovery

value: 40 years


title: Pt12_good_recovery

value: PBMC

value: 19 years

value: NNRTI


title: Pt9_good_recovery

value: Male

value: 28 years

value: White


title: Pt11_poor_recovery


title: mESCs 84 hours after differentiation start

tag: cell line


title: mESCs 6 hours after differentiation start


title: mESCs 60 hours after differentiation start


title: mESCs 32 hours after differentiation start


title: Pt8_good_recovery

value: 38 years


title: Pt3_good_recovery

value: American Indian


title: Pt6_poor_recovery

value: 42 years


title: Pt4_good_recovery


title: Pt10_poor_recovery

value: Asian


title: Pt1_poor_recovery

value: 31 years


title: Pt2_poor_recovery

value: 36 years


title: mESCs 40 hours after differentiation start


title: mESCs 44 hours after differentiation start


title: undifferentiated mESCs

description: undifferentiated mESCs


title: mESCs 24 hours after differentiation start


title: Pt5_poor_recovery

value: 52 years


title: Pt16_poor_recovery

value: PI


title: mESCs 18 hours after differentiation start


title: mESCs 12 hours after differentiation start


title: mESCs 48 hours after differentiation start


title: mESCs 52 hours after differentiation start


title: Pt24_good_recovery

value: 27 years


title: ExVivoBlood_24hr_5Gy_rep5

status: Public on Jul 01 2008

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

description: Gene expression after 24hr in 5Gy-irradiated human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/g cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded, and only features flagged as Positive and Significant (above background) were included.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 g RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer’s recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 3 ml aliquots of blood were exposed at a rate of 0.82 Gy per minute to 0, 0.5, 2, 5 or 8 Gy g-rays using a Gammacell-40 137Cs irradiator, then incubated as above for 6 or 24 hours prior to RNA extraction.

tag: Gender

value: female

tag: Age

value: 23 years


title: ExVivoBlood_24hr_0.5Gy_rep4

description: Gene expression after 24hr in 0.5Gy-irradiated human blood

value: 46 years


title: ExVivoBlood_24hr_8Gy_rep5

description: Gene expression after 24hr in 8Gy-irradiated human blood


title: ExVivoBlood_24hr_5Gy_rep2

value: male

value: 47 years


title: ExVivoBlood_24hr_5Gy_rep3

value: 30 years


title: ExVivoBlood_24hr_8Gy_rep2


title: ExVivoBlood_24hr_0Gy_rep5

description: Gene expression after 24hr in un-irradiated human blood


title: ExVivoBlood_24hr_0Gy_rep4


title: ExVivoBlood_24hr_8Gy_rep3


title: Control_ L6E9_rat_myoblast_cell_line_rep1

status: Public on Sep 23 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
l6e9 rat myogenic neonatal cell line (nadal-ginard b. cell. 1978 15(3): 855-64). Infection: Trypanosoma cruzi, Brazil (TCI); Y, CL and Tulahuen (TC II) strains
Determine and compare the transcriptomic alteration induced by infection with various strains of the parasite T. cruzi

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-labeled biological replica overnight at 50°C on a Duke Operon Rat 27k V3.0 printed oligonucleotide array V3.0  (GPL9207). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.

label: Alexa Fluor®_647

source_name: Control_ L6E9_rat_myoblast_cell_line

label_protocol: 20ug total RNA extracted from the culture dish was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: The L6E9 rat myoblast cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin/Streptomycin at 37°C with 5% CO2 atmosphere. Cells were dissociated with Trypsin/EDTA solution (Gibco) and 1mil cells were plated in 100mm cell culture dishes. After 24 hours of plating, cells were washed with PBS containing Ca2+ and Mg2+ (Gibco) and infected with 2x106 trypomastigote forms of T. cruzi in DMEM.

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: After 24 hours of plating in 100mm cell culture dishes, myoblasts were washed with PBS containing Ca2+ and Mg2+ (Gibco). 4 dishes were kept as control and 16 dishes were infected with 2mil trypomastigote forms of the Y, CL, Tulahuen or Brazil Trypanosoma cruzi strains (4 dishes for each strain). Forty eight hours post-infection cells were washed twice with Ca2+/Mg2+ PBS to remove free trypomastigotes in the supernatant and re-fed with fresh supplemented DMEM. Total RNA was harvested at 72 hours post infection using TRIZOL reagent (Invitrogen) following the protocol indicated by the manufacturer when at least 25% of the cultured cells were infected, presenting only intracellular amastigotes and no release of trypomastigotes (which would lead to reinfection of culture)

value: l6e9 rat myogenic neonatal cell line (nadal-ginard b. cell. 1978 15(3):855-64).

tag: infection

value: control


title: ExVivoBlood_24hr_5Gy_rep4


title: ExVivoBlood_24hr_2Gy_rep4

description: Gene expression after 24hr in 2Gy-irradiated human blood


title: ExVivoBlood_24hr_2Gy_rep2


title: ExVivoBlood_24hr_0Gy_rep3


title: ExVivoBlood_24hr_8Gy_rep4


title: ExVivoBlood_24hr_0.5Gy_rep5


title: ExVivoBlood_24hr_2Gy_rep3


title: ExVivoBlood_24hr_0.5Gy_rep3


title: ExVivoBlood_24hr_2Gy_rep5


title: ExVivoBlood_24hr_0.5Gy_rep2


title: Pt7_good_recovery

value: PBMC

value: Male

value: 24 years

value: African American

value: NNRTI


title: mESCs 56 hours after differentiation start


title: mESCs 36 hours after differentiation start


title: ExVivoBlood_24hr_0Gy_rep2


title: ExVivoBlood_24hr_8Gy_rep1

value: 38 years


title: ExVivoBlood_24hr_0.5Gy_rep1


title: ExVivoBlood_24hr_5Gy_rep1


title: ExVivoBlood_24hr_2Gy_rep1


title: ExVivoBlood_24hr_0Gy_rep1


title: ExVivoBlood_6hr_0Gy_rep5

description: Gene expression after 6hr in un-irradiated human blood

value: 36 years


title: ExVivoBlood_6hr_5Gy_rep4

description: Gene expression after 6hr in 5Gy-irradiated human blood

value: 35 years


title: ExVivoBlood_6hr_2Gy_rep4

description: Gene expression after 6hr in 2Gy-irradiated human blood


title: ExVivoBlood_6hr_2Gy_rep5


title: ExVivoBlood_6hr_5Gy_rep5


title: ExVivoBlood_6hr_0Gy_rep3

value: 53 years


title: ExVivoBlood_6hr_8Gy_rep2

description: Gene expression after 6hr in 8Gy-irradiated human blood

value: female

value: 20 years


title: ExVivoBlood_6hr_5Gy_rep3


title: ExVivoBlood_6hr_8Gy_rep5


title: ExVivoBlood_6hr_0.5Gy_rep5

description: Gene expression after 6hr in 0.5Gy-irradiated human blood


title: ExVivoBlood_6hr_5Gy_rep2


title: ExVivoBlood_6hr_2Gy_rep3


title: ExVivoBlood_6hr_0.5Gy_rep4


title: ExVivoBlood_6hr_8Gy_rep4


title: ExVivoBlood_6hr_0.5Gy_rep3


title: ExVivoBlood_6hr_2Gy_rep2


title: ExVivoBlood_6hr_8Gy_rep3


title: ExVivoBlood_6hr_2Gy_rep1

value: 39 years


title: ExVivoBlood_6hr_0.5Gy_rep1

value: male


title: ExVivoBlood_6hr_5Gy_rep1


title: ExVivoBlood_6hr_0Gy_rep4


title: ExVivoBlood_6hr_0Gy_rep2


title: ExVivoBlood_6hr_0Gy_rep1


title: ExVivoBlood_6hr_8Gy_rep1


title: ExVivoBlood_6hr_0.5Gy_rep2


title: MPI-245

status: Public on Jun 07 2006

first: Michael

last: Hummel

address: Hindenburgdamm 30

institute: Universitätsmedizin Berlin, Campus Benjamin Franklin

description: Mature aggressive B-cell lymphoma

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

source_name: Frozen tissue

tag: Relapse

value: unk

tag: Sex

value: DLBCL

value: present

value: absent

value: IG-MYC

tag: Lesions

tag: Radiotherapy

tag: RITUXIMAB

tag: Chemotherapy

value: intermediate

value: ABC

value: Training

value: no


title: MPI-222

description: Mature aggressive B-cell lymphoma

value: I

value: nodal

value: dead

value: yes

value: CR

value: CHOP-like

value: unclassified

value: Test


title: MPI-210

description: Mature aggressive B-cell lymphoma

value: female

value: III

value: other

value: non-mBL


title: MPI-248

description: Mature aggressive B-cell lymphoma

value: unk

value: male

value: DLBCL

value: present

value: absent

value: non-IG-MYC

value: GCB


title: MPI-070

description: Mature aggressive B-cell lymphoma

value: no

value: nodal + extranodal

value: dead

value: intermediate

value: ABC


title: MPI-094

description: Mature aggressive B-cell lymphoma

value: Training


title: MPI-161

description: Mature aggressive B-cell lymphoma

value: IG-MYC

value: IV

value: nodal

value: yes

value: NC

value: CHOP-like


title: MPI-051

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: I

value: extranodal

value: other

value: Test


title: MPI-121

description: Mature aggressive B-cell lymphoma

value: unk

value: male

value: present

value: absent

value: non-IG-MYC

value: GCB

value: no


title: MPI-060

description: Mature aggressive B-cell lymphoma

value: IG-MYC

value: III

value: nodal + extranodal

value: dead

value: PR

value: intermediate

value: Training


title: MPI-072

description: Mature aggressive B-cell lymphoma

value: DLBCL


title: MPI-061

description: Mature aggressive B-cell lymphoma

value: female

value: II

value: nodal

value: CR

value: other

value: ABC


title: MPI-165

description: Mature aggressive B-cell lymphoma

value: present

value: absent

value: non-IG-MYC

value: I

value: extranodal

value: Test


title: MPI-074

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: dead

value: non-mBL


title: MPI-169

description: Mature aggressive B-cell lymphoma

value: unk

value: atypical BL

value: intermediate

value: unclassified

value: Training


title: MPI-099

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: III

value: nodal

value: other

value: GCB


title: MPI-168

description: Mature aggressive B-cell lymphoma

value: absent

value: present

value: IG-MYC

value: CHOP-like

value: ABC


title: MPI-037

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: non-IG-MYC

value: IV

value: dead

value: Progress

value: Test


title: MPI-026

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: intermediate


title: MPI-190

description: Mature aggressive B-cell lymphoma

value: non-mBL


title: MPI-038

description: Mature aggressive B-cell lymphoma

value: nodal

value: CR

value: other

value: unclassified

value: Training


title: MPI-031

description: Mature aggressive B-cell lymphoma

value: present

value: absent

value: III

value: alive

value: ABC


title: mESCs 66 hours after differentiation start