title: Wild-type ESCs Rep3

city: Columbus

first: Christopher

last: Phiel

state: OH

address: 700 Children's Drive W432

institute: The Research Institute at Nationwide Children's Hospital

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.

source_name: Total RNA from WT ESCs

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.

extract_protocol: Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).

tag: genotype/variation

value: Wild-type (E14K)


title: SMC TGF-B Rx Donor 3 rep1

status: Public on Jun 16 2011

type: RNA

city: New Haven

first: Amir

middle: Hossein

last: Lebastchi

state: CT

address: 10 Amistad

department: Surgery

country: USA

institute: Yale University

scan_protocol: The stained chips were read and analyzed with GeneChip Scanner 3000 (Affymetrix)

data_processing: Standard Protocols for Affymetrix Human Genechip 1.0 ST Array. Expressionintensities were quantified and compared using Partek Genomics Suite v6.4 with Robust Multi-Array Average for normalization and fold change calculations.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Smooth Muscle Cell TGF-B Rx (1 ng/ml)

growth_protocol: Smooth Muscle Cells were cultured from 4 different donors, deprived of serum in M199 medium for 48hr.

extract_protocol: Total human RNA was extracted from cultured smooth muscle cells using Rneasy Mini kits (Qiagen)

treatment_protocol: After culturing the cells in serum deprived medium for 48 hr the cells either remained untreated for 6 hr or were treated with 1ng/ml TGF-B for 6 hr.

tag: gender

value: female

tag: tissue

value: smooth muscle cell from aorta

tag: treatment

value: TGF-B Rx (1 ng/ml)


title: MP4 DNA Methylome

type: genomic

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description: DNA methylation profiling of an iPS clone.

hyb_protocol: Bisulphite-converted (EZ DNA methylation kit) DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

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

data_processing: Background-subtracted beta values (M/(M+U)), corrected for presence through the detection p-value.

label: Cy5, Cy3

molecule: genomic DNA

source_name: MP4 iPS

label_protocol: Standard Illumina protocol.

growth_protocol: As described in PMID 20841480.

extract_protocol: Phenol-chloroform extraction.

tag: cell line

tag: cell type

value: induced pluripotent stem cells (iPS)


title: SMC TGF-B Rx Donor 4 rep1

hyb_protocol: Standard Protocols for Affymetrix Human Genechip 1.0 ST Array

value: male


title: p53 shRNA 0 Gy rep3

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

description:
Replicate 3.
p53_shRNA_0_Gy_rep3

hyb_protocol: Hybridization was performed at the Yale Microarray Facility. After quality control assessment, 1.5 µg of cRNA was mixed with the hybridization controls and hybridized to the array. The array was hybridized for 16 hours in a hybridization oven with a rocking platform at 58°C. The array chip then was subjected to a series of washes before it was stained with streptavidin-Cy3. After the staining, it went through a final wash and drying.

scan_protocol: The standard Illumina scanning protocol was performed using an iScan system at the Yale Microarray Facility.

data_processing: Data were background corrected, variance stabilizing transformed and quantile normalized using the lumi software package (version 1.14.0) for the R programming environment (version 2.11.0).

source_name: U2OS cells, p53, 0 Gy

label_protocol: Labeling was performed at the Yale Microarray Facility. Single-stranded cDNA was synthesized by reverse transcription using T7 oligo(dT) primers. The single-stranded cDNA was then converted into double-stranded cDNA and purified using the Ambion Illumina TotalPrep RNA Amplification Kit. An in vitro transcription (IVT) reaction was then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double-stranded cDNA. The cRNA from the IVT reaction was purified using the same Amplification Kit.

growth_protocol: U2OS cells (ATCC) were maintained in DMEM supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and L-glutamate.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit using the manufacturer's following the optional DNAse treatment steps.

treatment_protocol: U2OS cells were infected with NFBD1 and/or p53 shRNA-expressing retroviruses.  Two days later, cells were irradiated with a Shepherd Mark I 137Cs irradiator with a dose of 5 Gy or mock irradiated.  Four hours later RNA was isolated.

tag: array #

value: osteosarcoma

tag: shRNA-expressing retrovirus

value: pSIREN p53

tag: ionizing radiation

value: 0 Gy


title: Wild-type ESCs Rep2

organism: Mus musculus

value: embryonic stem cells


title: Gsk-3a-/-; Gsk-3b-/- ESCs Rep3

source_name: Total RNA from Gsk-3a-/-; Gsk-3b-/- ESCs


title: HCT116 DNA Methylome

description: DNA methylation profiling of HCT116 colorectal cancer cell line.

source_name: HCT116 colorectal cancer cell line

value: colorectal cancer cells


title: MP2 DNA Methylome

source_name: MP2 iPS


title: Gsk-3a-/-; Gsk-3b-/- ESCs Rep2


title: Gsk-3a-/-; Gsk-3b-/- ESCs Rep1


title: Wild-type ESCs Rep1


title: SMC TGF-B Rx Donor 2 rep1

label_protocol: Standard Protocols for Affymetrix Human Genechip 1.0 ST Array


title: SMC TGF-B Rx Donor 1 rep1


title: Conjunctival fornix_PN20_sample_3

status: Public on Jun 15 2011

city: Pittsburgh

first: Shivalingappa

middle: Kottur

last: Swamynathan

state: PA

address: 203 Lothrop Street Room 1025

department: Ophthalmology

institute: University of Pittsburgh

hyb_protocol: Hybridization controls (900454) were added, and each sample was hybridized overnight to a Mouse Genome 430 2.0 Array (900495).

scan_protocol: The chips were washed, developed and scanned in an Agilent ChipScanner (Affymetrix Inc., Santa Clara, CA).

data_processing: Raw data were processed and analyzed using Affymetrix GeneChip Operating System (GCOS) v1.4 software. GCOS was used to assess the presence or absence of the target sequence of each panel, its expression level, and then to make all relevant pair-wise statistical comparisons among samples. Unscaled 2% trimmed means (159 ± 52 mean ± SD, n=12) were scaled to 150. Processed data was sorted and inspected in the Microsoft Excel spreadsheet program (Microsoft, Redmond, WA) and further analyzed using BRB-Array Tools software (Biometric Research Branch, NCI, NIH, Bethesda, MD (www.nci.nih.gov/brb-arraytools.html/)).   The Mouse Genome 430 2.0 chip contains 45,101 panels, each targeting a specific transcript sequence. Approximately 22,000 (21,996) transcripts identified by Entrez Gene numbers are redundantly targeted by 41,429 panels: the remaining 3,672 panels target products that currently have no Entrez Gene number. Panels showing consistent, GCOS-validated changes were submitted to Ingenuity Pathways Analysis (https://analysis.ingenuity.com) for classifying the genes according to Gene Ontology groups, functional interactive networks, or canonical pathways.   The following conditions were used to designate genes as differentially expressed between any two groups of samples: (a) all three samples in the high-expression group have detectable transcripts (called Present), (b) of the nine pair-wise comparisons made by the GCOS software, at least 6 show valid differences, (c) group values do not overlap, i.e., the lowest value of the high-expression group is higher than the highest value of the low expression group, and (d) the average value of the high-expression group is >2 fold greater than the average value of the low-expression group.

label_protocol: Between 20 and 120 ng of total RNA was subjected to two cycles of transcriptional amplification using appropriate Affymetrix products (cited as catalog numbers) as follows. Eukaryote Poly A RNA internal standards (900433) were added to the samples, and the poly A containing mRNA component was reverse-transcribed in the presence of a T7-(dT)24 primer (900432). The resulting cDNA was extracted (900371) and subjected to transcriptional amplification using a MEGAscript T7 kit from Ambion (Austin, TX). The amplified cRNA product was extracted (900371) and copied back to cDNA using random primers (900432). Extracted cDNA was again transcribed in vitro, in the presence of biotin-labeled ribonucleotides (900449). The biotinylated cRNA product (107 ± 37 µg, mean ± SD, n = 11 with one outlier of 27 µg) was extracted and 20 μg was fragmented (900371: for 35 minutes at 94°C).

extract_protocol: Epithelial layer of mouse conjunctival fornix isolated by laser capture microscopy.

tag: developmental stage

value: Post-natal day 20

value: wild type

tag: strain

value: mixed background


title: control brain, biological rep1

city: Oklahoma City

first: Lorin

last: Olson

state: Oklahoma

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

description: Gene expression data from brain microvessels expressing wild type PDGFRb in pericytes

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

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

data_processing: The data were analyzed with GCRMA normalization

source_name: Microvascular fragments from P1 brain, PDGFRb wild type

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

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

value: brain microvessels

tag: genotype

tag: age

value: postnatal day 1

tag: genetic background

value: 129S/J mixed


title: Conjunctival fornix_PN14_Klf4CN_sample_2

source_name: Epithelial layer of mouse conjunctival fornix

value: Post-natal day 14

value: KLf4 conditional knockout


title: mutant brain, biological rep4

description: Gene expression data from brain microvessels expressing constitutively active PDGFRb in pericytes

source_name: Microvascular fragments from P1 brain, PDGFRb mutant

value: PDGFRb (D849V)


title: mutant brain, biological rep3


title: control brain, biological rep2


title: control brain, biological rep3


title: Conjunctival fornix_PN9_sample_2

value: Post-natal day 9


title: control brain, biological rep4


title: Conjunctival fornix_PN20_sample_1


title: Conjunctival fornix_PN14_Klf4CN_sample_3


title: mutant brain, biological rep1


title: Conjunctival fornix_PN14_sample_3


title: Conjunctival fornix_PN14_sample_2


title: Conjunctival fornix_PN20_sample_2


title: Conjunctival fornix_PN14_sample_1


title: mutant brain, biological rep2


title: Conjunctival fornix_PN14_Klf4CN_sample_1


title: Conjunctival fornix_PN9_sample_3


title: Conjunctival fornix_PN9_sample_1


title: hLCR knock-in fetal liver expression replicate 1

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: Hybridization was performed according to Affymetrix protocol

scan_protocol: Scanning was performed according to Affymetrix protocol

data_processing: Data was normalized using rma in the affy Bioconductor package

molecule: polyA RNA

source_name: hLCR knock-in fetal liver expression

label_protocol: Labeling was performed according to Affymetrix protocol

extract_protocol: affymetrix one-cycle cDNA synthesis protocol was used

value: FVB

value: fetal liver

value: hLCR knock-in


title: WT fetal liver expression replicate 3

source_name: WT fetal liver expression


title: WT fetal liver expression replicate 1


title: hLCR knock-in fetal liver expression replicate 3


title: hLCR knock-in fetal liver expression replicate 2


title: WT fetal liver expression replicate 2


title: Prostate cancer sample number 295

city: Sao Paulo

first: Yuri

middle: Barros

last: Moreira

state: SP

address: Av. Prof. Lineu Prestes 748 sala 1200

department: Biochemistry

country: Brazil

institute: Universidade de Sao Paulo

description: Prostate cancer tissue specimens  obtained from patient undergoing radical prostatectomy at Hospital Sirio-Libanes in Sao Paulo. Samples was collected between with informed consent from patients submitted to radical prostatectomy.

hyb_protocol: Each patient sample Cy3- and Cy5-labeled cRNA replicates (750 ng cRNA per sample) were co-hybridized (self-self hybridization) for 17 h at 60°C according to Agilent's In Situ Hybridization Kit Plus protocol. Arrays were washed with Agilent SSPE wash protocol v. 2.1

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Images were quantified using Agilent Feature Extraction Software (version A.9.0)

data_processing: Only valid features in at least 90 per cent of the recurrent set and/or non-recurrent set were used. Log scaled geometric mean of Cy3 and Cy5 replicates of the same sample were used as intensity value for each sample. These values were normalized via quantile normalization, available in the affy package through Bioconductor project.  Empirical Bayes method was used to adjust for the batch effect between experiments. The method is available at http://statistics.byu.edu/johnson/ComBat/Abstract.html

source_name: prostate cancer tumor number 295

label_protocol: mRNA amplification and labeling were performed with in vitro transcription using 300 ng total RNA and the T7-poly-dT based Low RNA Input Fluorescent Linear Amplification Kit (Agilent)

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen) and purified with the RNeasy mini-kit (Qiagen) plus a DNase treatment using Qiagen DNA-free kit.

tag: recurrence within the 60-months follow-up

tag: age (yr-old)

tag: gleason score

tag: psa before surgery

tag: clinical stage

tag: tumor size (%)

tag: capsule

tag: extra

tag: vs

tag: ln

tag: pathological stage

tag: surgery date

tag: follow-up (months)

tag: psa at recurrence

tag: experimental batch number

tag: tumor size (cm3)


title: Prostate cancer sample number 189

source_name: prostate cancer tumor number 189


title: Prostate cancer sample number 212

source_name: prostate cancer tumor number 212


title: Prostate cancer sample number 217

source_name: prostate cancer tumor number 217


title: Prostate cancer sample number 182

source_name: prostate cancer tumor number 182


title: Canonical pool

type: other

city: Seattle

first: Muneesh

last: Tewari

state: WA

address: 1100 Fairview Ave, N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Replicate 1

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions.  For each assay, a high-density scan (600 fields of view) was performed.

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls. The sum of the positive controls for a given sample was divided by the mean sum of the positive controls across all samples to yield a normalization factor.  Multiplication of this normalization factor by the raw counts yielded normalized counts.

molecule: other

organism: synthetic construct

source_name: Synthetic oligo pool

extract_protocol: Synthetic oligos were synethesized by IDT. We assayed two pools of synthetic RNA oligonucleotides representing canonical or variant forms of 14 miRNAs of interest, with each miRNA at a concentration of 30 pmol.

tag: assay

value: canonical


title: Prostate cancer sample number 176

source_name: prostate cancer tumor number 176

tag: recurrence within the 60-months follow-up


title: Prostate cancer sample number 187

source_name: prostate cancer tumor number 187

tag: age (yr-old)


title: Prostate cancer sample number 68

source_name: prostate cancer tumor number 68

tag: gleason score


title: Prostate cancer sample number 148

source_name: prostate cancer tumor number 148

tag: psa before surgery


title: Prostate cancer sample number 171

source_name: prostate cancer tumor number 171

tag: clinical stage


title: Prostate cancer sample number 121

source_name: prostate cancer tumor number 121

tag: tumor size (%)


title: Variant pool

description: Replicate 1

value: variant


title: Prostate cancer sample number 122

source_name: prostate cancer tumor number 122

tag: capsule


title: Prostate cancer sample number 84

source_name: prostate cancer tumor number 84

tag: extra


title: Prostate cancer sample number 28

source_name: prostate cancer tumor number 28

tag: vs


title: Prostate cancer sample number 71

source_name: prostate cancer tumor number 71

tag: ln


title: Prostate cancer sample number 36

source_name: prostate cancer tumor number 36

tag: pathological stage


title: Prostate cancer sample number 55

source_name: prostate cancer tumor number 55

tag: surgery date


title: Prostate cancer sample number 155

source_name: prostate cancer tumor number 155

tag: follow-up (months)


title: T23 cell line

city: Milan

first: Paola

last: Pittoni

state: Italy

address: Via Amadeo, 42

department: Dept. Experimental Oncology

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio Gene Expression Module v3

source_name: Prostate tumor from TRAMP mouse

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina RNA TotalPrep amplification kit

extract_protocol: RNA was extracted using the guanidinium thiocyanate/cesium chloride gradient method, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: genotype/variation

value: TRAMP

tag: age

value: 30 wks

tag: tissue origin

value: Prostate

tag: tissue type

value: tumor cell line

tag: cell line


title: Prostate cancer sample number 35

source_name: prostate cancer tumor number 35

tag: recurrence within the 60-months follow-up

tag: age (yr-old)

tag: gleason score

tag: psa at recurrence

tag: experimental batch number

tag: tumor size (cm3)


title: wt prost rep 1

description: replicate 1

value: WT

value: 18 wks

value: normal


title: Prostate cancer sample number 100

source_name: prostate cancer tumor number 100

tag: psa before surgery

tag: clinical stage

tag: tumor size (%)

tag: capsule

tag: extra

tag: vs


title: Prostate cancer sample number 73

source_name: prostate cancer tumor number 73

tag: ln

tag: pathological stage

tag: surgery date

tag: follow-up (months)


title: Prostate cancer sample number 75

source_name: prostate cancer tumor number 75


title: wt prost rep 2

description: replicate 2

tag: strain

tag: genotype/variation

tag: age

tag: tissue origin

tag: tissue type


title: HCT-116 si ZCCHC11 replicate 1 canonical assay

description:
Canonical
Replicate 1

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using the vsn R package

source_name: HCT-116 cells

growth_protocol: HCT-116 cells grown in McCoy's media with 10% FBS

extract_protocol: RNA was isolated using the miRNeasy RNA isolation kit from Qiagen. 400 ng of RNA was used as input for the nCounter sample prep reaction.

treatment_protocol: Treated with 30 nM Dharmacon SMARTpool siRNAs against enzyme of interest or Cyclophilin B as a negative control

tag: cell type

tag: transfection

value: si ZCCHC11


title: HCT-116 si ZCCHC11 replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: HCT-116 si ZCCHC11 replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: T1525 cell line

description: replicate 1

tag: cell line


title: Prostate cancer sample number 455

source_name: prostate cancer tumor number 455

tag: recurrence within the 60-months follow-up

tag: age (yr-old)

tag: gleason score

tag: psa before surgery

tag: clinical stage:

tag: psa at recurrence

tag: experimental batch number

tag: tumor size (cm3)


title: Prostate cancer sample number 421

source_name: prostate cancer tumor number 421

tag: clinical stage

tag: tumor size (%)

tag: capsule

tag: extra

tag: vs

tag: ln

tag: pathological stage

tag: surgery date

tag: follow-up (months)


title: Prostate cancer sample number 320

source_name: prostate cancer tumor number 320

tag: recurrence within the 60-months follow-up


title: HCT-116 si TUT1 replicate 2 variant 2 assay

description:
Variant 2
Replicate 2

tag: cell type

tag: transfection

value: si TUT1


title: HCT-116 si TUT1 replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: HCT-116 si TUT1 replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: HCT-116 si TUT1 replicate 2 canonical assay

description:
Canonical
Replicate 2


title: HCT-116 si TUT1 replicate 1 canonical assay

description:
Canonical
Replicate 1


title: HCT-116 si TUT1 replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: HCT-116 si TRNT1 replicate 2 variant 2 assay

description:
Variant 2
Replicate 2

value: si TRNT1


title: HCT-116 si TRNT1 replicate 2 canonical assay

description:
Canonical
Replicate 2


title: HCT-116 si TRNT1 replicate 1 canonical assay

description:
Canonical
Replicate 1


title: Prostate cancer sample number 463

source_name: prostate cancer tumor number 463

tag: age (yr-old)

tag: gleason score

tag: psa before surgery


title: HCT-116 si TRNT1 replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: HCT-116 si TRNT1 replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: HCT-116 si TRNT1 replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: Prostate cancer sample number 461

source_name: prostate cancer tumor number 461

tag: psa at recurrence

tag: experimental batch number


title: Prostate cancer sample number 459

source_name: prostate cancer tumor number 459

tag: clinical stage:

tag: tumor size (cm3)


title: Prostate cancer sample number 240

source_name: prostate cancer tumor number 240

tag: clinical stage

tag: tumor size (%)

tag: capsule


title: Prostate cancer sample number 339

source_name: prostate cancer tumor number 339

tag: extra

tag: vs

tag: ln


title: Prostate cancer sample number 297

source_name: prostate cancer tumor number 297

tag: pathological stage

tag: surgery date

tag: follow-up (months)


title: Prostate cancer sample number 273

source_name: prostate cancer tumor number 273

tag: recurrence within the 60-months follow-up


title: Prostate cancer sample number 422

source_name: prostate cancer tumor number 422

tag: age (yr-old)


title: Prostate cancer sample number 469

source_name: prostate cancer tumor number 469

tag: gleason score


title: Prostate cancer sample number 340

source_name: prostate cancer tumor number 340

tag: psa before surgery


title: Prostate cancer sample number 385

source_name: prostate cancer tumor number 385

tag: psa at recurrence


title: Prostate cancer sample number 453

source_name: prostate cancer tumor number 453

tag: experimental batch number


title: HCT-116 si PAPOLG replicate 2 canonical assay

description:
Canonical
Replicate 2

tag: cell type

tag: transfection

value: si PAPOLG


title: Prostate cancer sample number 108

source_name: prostate cancer tumor number 108

tag: clinical stage

tag: tumor size (cm3)


title: HCT-116 si PAPOLG replicate 2 variant 1 assay

description:
Variant 1
Replicate 2

source_name: HCT-116 cells


title: HCT-116 si PAPOLG replicate 2 variant 2 assay

description:
Variant 2
Replicate 2


title: HCT-116 si PAPOLG replicate 1 canonical assay

description:
Canonical
Replicate 1


title: HCT-116 si PAPD5 replicate 2 canonical assay

description:
Canonical
Replicate 2

value: si PAPD5


title: HCT-116 si PAPOLG replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: HCT-116 si PAPOLG replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: HCT-116 si PAPD5 replicate 2 variant 2 assay

description:
Variant 2
Replicate 2


title: HCT-116 si PAPD5 replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: Prostate cancer sample number 202

source_name: prostate cancer tumor number 202

tag: tumor size (%)

tag: capsule


title: HCT-116 si PAPD5 replicate 1 canonical assay

description:
Canonical
Replicate 1


title: HCT-116 si PAPD5 replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: HCT-116 si PAPD5 replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: Prostate cancer sample number 426

source_name: prostate cancer tumor number 426

tag: extra

tag: vs


title: Prostate cancer sample number 62

source_name: prostate cancer tumor number 62

tag: ln

tag: pathological stage


title: Prostate cancer sample number 437

source_name: prostate cancer tumor number 437

tag: surgery date

tag: follow-up (months)


title: Prostate cancer sample number 293

source_name: prostate cancer tumor number 293

tag: recurrence within the 60-months follow-up

tag: age (yr-old)


title: Prostate cancer sample number 131

source_name: prostate cancer tumor number 131

tag: gleason score

tag: psa before surgery


title: Prostate cancer sample number 321

source_name: prostate cancer tumor number 321

tag: psa at recurrence

tag: experimental batch number


title: HCT-116 si PAPD4 replicate 2 canonical assay

description:
Canonical
Replicate 2

tag: cell type

tag: transfection

value: si PAPD4


title: Prostate cancer sample number 277

source_name: prostate cancer tumor number 277

tag: clinical stage

tag: tumor size (cm3)


title: Prostate cancer sample number 303

source_name: prostate cancer tumor number 303

tag: tumor size (%)

tag: capsule


title: HCT-116 si PAPD4 replicate 2 variant 2 assay

description:
Variant 2
Replicate 2


title: HCT-116 si PAPD4 replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: Prostate cancer sample number 201

source_name: prostate cancer tumor number 201

tag: extra

tag: vs


title: HCT-116 si PAPD4 replicate 1 canonical assay

description:
Canonical
Replicate 1


title: HCT-116 si PAPD4 replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: HCT-116 si PAPD1 replicate 2 canonical assay

description:
Canonical
Replicate 2

value: si PAPD1


title: Prostate cancer sample number 261

source_name: prostate cancer tumor number 261

tag: ln

tag: pathological stage


title: Prostate cancer sample number 250

source_name: prostate cancer tumor number 250

tag: surgery date

tag: follow-up (months)


title: HCT-116 si PAPD4 replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: HCT-116 si PAPD1 replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: HCT-116 si PAPD1 replicate 1 canonical assay

description:
Canonical
Replicate 1


title: HCT-116 si PAPD1 replicate 2 variant 2 assay

description:
Variant 2
Replicate 2


title: Prostate cancer sample number 284

source_name: prostate cancer tumor number 284

tag: recurrence within the 60-months follow-up

tag: age (yr-old)


title: Prostate cancer sample number 183

source_name: prostate cancer tumor number 183

tag: gleason score

tag: psa before surgery


title: Prostate cancer sample number 254

source_name: prostate cancer tumor number 254

tag: psa at recurrence

tag: experimental batch number


title: Prostate cancer sample number 102

source_name: prostate cancer tumor number 102


title: Prostate cancer sample number 125

source_name: prostate cancer tumor number 125


title: HCT-116 si ZCCHC11 replicate 1 variant 1 assay

description:
Variant 1
Replicate 1

source_name: HCT-116 cells

tag: cell type

tag: transfection


title: HCT-116 si Cyclophilin B replicate 4 canonical assay

description:
Canonical
Replicate 4

value: si Cyclophilin B


title: HCT-116 si PAPD1 replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: HCT-116 si PAPD1 replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: HCT-116 si Cyclophilin B replicate 4 variant 2 assay

description:
Variant 2
Replicate 4


title: HCT-116 si Cyclophilin B replicate 4 variant 1 assay

description:
Variant 1
Replicate 4


title: Ovarian cancer sample 61

city: boston

first: panagiotis

last: konstantinopoulos

state: MA

address: 330 brookline av

department: hem/onc

institute: bidmc

hyb_protocol: The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: dChip

source_name: Ovarian cancer

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.

extract_protocol: RNA was isolated using the trizol protocol

tag: survival in months

tag: event indicator

value: censored


title: HCT-116 si Cyclophilin B replicate 3 canonical assay

description:
Canonical
Replicate 3


title: Ovarian cancer sample 60


title: Ovarian cancer sample 59


title: Ovarian cancer sample 58


title: HCT-116 si Cyclophilin B replicate 3 variant 1 assay

description:
Variant 1
Replicate 3


title: Prostate cancer sample number 50

source_name: prostate cancer tumor number 50

tag: clinical stage

tag: tumor size (%)

tag: capsule

tag: tumor size (cm3)


title: Prostate cancer sample number 454

source_name: prostate cancer tumor number 454

tag: extra

tag: vs

tag: ln

tag: pathological stage


title: Prostate cancer sample number 54

source_name: prostate cancer tumor number 54

tag: recurrence within the 60-months follow-up

tag: age (yr-old)

tag: surgery date

tag: follow-up (months)


title: Ovarian cancer sample 57


title: Ovarian cancer sample 55

value: event


title: Ovarian cancer sample 56


title: HCT-116 si Cyclophilin B replicate 2 canonical assay

description:
Canonical
Replicate 2


title: Prostate cancer sample number 425

source_name: prostate cancer tumor number 425

tag: gleason score

tag: psa before surgery

tag: psa at recurrence

tag: experimental batch number


title: HCT-116 si Cyclophilin B replicate 2 variant 2 assay

description:
Variant 2
Replicate 2

tag: cell type

tag: transfection


title: HCT-116 si Cyclophilin B replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: Prostate cancer sample number 334

source_name: prostate cancer tumor number 334

tag: clinical stage

tag: tumor size (%)


title: Ovarian cancer sample 53

tag: survival in months

tag: event indicator


title: HCT-116 siCyclophilin B replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: HCT-116 siCyclophilin B replicate 1 canonical assay

description:
Canonical
Replicate 1


title: Ovarian cancer sample 54


title: Ovarian cancer sample 52


title: Differentiated H1 Cells V2 Assay 5

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization.

source_name: H1 hESC

growth_protocol: H1 human embryonic stem cells were cultured and differentiated as previously described (Bar et al., 2008)

extract_protocol: RNA isolation was performed as described in (Bar et al., 2008)

value: Differentiated H1 hESC


title: Ovarian cancer sample 51


title: HCT-116 siCyclophilin B replicate 1 variant 2 assay

description:
Variant 2
Replicate 1


title: Ovarian cancer sample 49


title: Ovarian cancer sample 50


title: Differentiated H1 Cells V2 Assay 3


title: Differentiated H1 Cells V2 Assay 4


title: Ovarian cancer sample 48


title: Ovarian cancer sample 47


title: Prostate cancer sample number 223

source_name: prostate cancer tumor number 223

tag: capsule

tag: extra

tag: vs

tag: tumor size (cm3)


title: Prostate cancer sample number 221

source_name: prostate cancer tumor number 221

tag: recurrence within the 60-months follow-up

tag: age (yr-old)

tag: ln

tag: pathological stage


title: Differentiated H1 Cells V2 Assay 2


title: Differentiated H1 Cells V2 Assay 1


title: Prostate cancer sample number 471

source_name: prostate cancer tumor number 471

tag: gleason score

tag: psa before surgery

tag: surgery date

tag: follow-up (months)


title: Ovarian cancer sample 45


title: Ovarian cancer sample 44


title: Ovarian cancer sample 43


title: Ovarian cancer sample 46


title: Differentiated H1 Cells Canonical Assay 3

tag: cell type


title: HCT-116 si Cyclophilin B replicate 3 variant 2 assay

description:
Variant 2
Replicate 3

tag: transfection


title: Ovarian cancer sample 38


title: Ovarian cancer sample 39


title: Ovarian cancer sample 41


title: Ovarian cancer sample 35


title: Ovarian cancer sample 40


title: Ovarian cancer sample 42


title: Ovarian cancer sample 36


title: Differentiated H1 Cells V1 Assay 2


title: Differentiated H1 Cells Canonical Assay 4


title: Differentiated H1 Cells V1 Assay 3


title: Differentiated H1 Cells V1 Assay 5


title: Differentiated H1 Cells V1 Assay 4


title: Differentiated H1 Cells V1 Assay 6


title: Differentiated H1 Cells V1 Assay 1


title: Differentiated H1 Cells Canonical Assay 2


title: Ovarian cancer sample 37


title: Differentiated H1 Cells Canonical Assay 1


title: Undifferentiated H1 Cells Variant 2 Assay 5

value: Undifferentiated H1 hESC


title: Undifferentiated H1 Cells Variant 2 Assay 4


title: Undifferentiated H1 Cells Variant 2 Assay 3


title: Undifferentiated H1 Cells Variant 2 Assay 2


title: Mixed pool rep2

description: Replicate 2

source_name: Synthetic oligo pool

extract_protocol: Synthetic oligos were synethesized by IDT and Qiagen. We assayed three pools of synthetic RNA oligonucleotides representing canonical, variant 1, and variant 2 versions of 5 miRNAs (miR-15a, miR-15b, miR-125a-5p, miR-143 and miR-221), with each miRNA at a concentration of 30 pmol. We also assayed a mixed pool containing 60% canonical, 30% Variant 1, and 10% Variant 2 for each of the 5 miRNAs listed above.

tag: assay

value: mixed


title: Mixed pool rep3

description: Replicate 3


title: Mixed pool rep1

description: Replicate 1


title: Undifferentiated H1 Cells Variant 1 Assay 5


title: Ovarian cancer sample 31

tag: survival in months


title: Ovarian cancer sample 33

tag: event indicator


title: Ovarian cancer sample 32


title: Ovarian cancer sample 34


title: Variant 2 pool rep3

description: Replicate 3

value: variant 2


title: Ovarian cancer sample 22


title: Ovarian cancer sample 19


title: Ovarian cancer sample 20


title: Ovarian cancer sample 24


title: Ovarian cancer sample 25


title: Ovarian cancer sample 27


title: Ovarian cancer sample 23


title: Ovarian cancer sample 26


title: Ovarian cancer sample 30


title: Ovarian cancer sample 28


title: Ovarian cancer sample 29


title: Ovarian cancer sample 18


title: Ovarian cancer sample 21


title: Ovarian cancer sample 17


title: Variant 2 pool rep2

description: Replicate 2


title: Undifferentiated H1 Cells Variant 1 Assay 4


title: Undifferentiated H1 Cells Variant 2 Assay 1


title: Prostate cancer sample number 195

source_name: prostate cancer tumor number 195

tag: clinical stage

tag: tumor size (%)

tag: capsule

tag: psa at recurrence

tag: experimental batch number


title: Undifferentiated H1 Cells Variant 1 Assay 3


title: Ovarian cancer sample 16


title: Ovarian cancer sample 15


title: Variant 1 pool rep3

description: Replicate 3

value: variant 1


title: Variant 2 pool rep1

description: Replicate 1


title: Canonical pool rep2

description: Replicate 2

value: canonical


title: Ovarian cancer sample 12


title: Ovarian cancer sample 13


title: Ovarian cancer sample 14


title: Ovarian cancer sample 11


title: Variant 1 pool rep2

description: Replicate 2


title: Canonical pool rep3

description: Replicate 3


title: Undifferentiated H1 Cells Canonical Assay 5


title: Undifferentiated H1 Cells Variant 1 Assay 1


title: Variant 1 pool rep1

description: Replicate 1


title: Undifferentiated H1 Cells Canonical Assay 4


title: Undifferentiated H1 Cells Canonical Assay 3


title: Undifferentiated H1 Cells Variant 1 Assay 2


title: Undifferentiated H1 Cells Canonical Assay 2


title: Ovarian cancer sample 10


title: Undifferentiated H1 Cells Canonical Assay 1


title: Canonical pool rep1

description: Replicate 1


title: Ovarian cancer sample 8


title: Ovarian cancer sample 9


title: HCT-116 si ZCCHC6 replicate 2 variant 2 assay

description:
Variant 2
Replicate 2

value: si ZCCHC6


title: HCT-116 si ZCCHC6 replicate 2 canonical assay

description:
Canonical
Replicate 2


title: Ovarian cancer sample 7


title: HCT-116 si ZCCHC6 replicate 1 canonical assay

description:
Canonical
Replicate 1


title: PPK1-PPX double mutant

city: Santiago

first: Francisco

last: Chavez

address: 3425, Las Palmeras

country: Chile

institute: Universidad de Chile

description:
experimental sample: Δppk-ppx
cohybridization: wt vs ppk-ppx double mutant
4,239 E. coli K12 specific oligonucleotide probes represent the complete Escherichia coli (K12)genome.

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution HybIT2 (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

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 Alexa555 and Alexa647 density mean value and the Alexa555 and Alexa647 background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing:
Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data is from the mean.
zi = (Ri – mean(R)) / sd(R), where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

label: Alexa555, Alexa647

organism: Escherichia coli K-12

source_name: double mutant (PPK1 and PPX)

label_protocol: 10 mg of total RNA were used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647, employing the SuperScript Plus direct labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm and 647 respectively.

extract_protocol: Briefly, total RNA were isolated from cell culture with Total RNA Extraction Kit (RBC Bioscience) according to manufacturer's specifications. DNA was degraded by DNAse (Promega).

tag: genotype/variation

value: null polyphosphate metabolism

source_name: control

value: wild type (control)


title: HCT-116 si ZCCHC6 replicate 2 variant 1 assay

description:
Variant 1
Replicate 2


title: polyphosphate kinase 1 (PPK1) mutant

description:
experimental sample: Δppk
cohybridization: wt vs ppk mutant
4,239 E. coli K12 specific oligonucleotide probes represent the complete Escherichia coli (K12)genome.

source_name: single mutant in polyphosphate kinase 1 (PPK1)

value: polyphosphate depleted levels


title: Ovarian cancer sample 6


title: Ovarian cancer sample 5


title: exopolyphosphatase (PPX) mutant

description:
experimental sample: Δppx
cohybridization: wt vs ppx mutant
4,239 E. coli K12 specific oligonucleotide probes represent the complete Escherichia coli (K12)genome.

source_name: single mutant in exopolyphosphatase (PPX)

value: polyphosphate accumulation


title: Experiment-8-M1-SDHHBtail vs wild-type

first: Vijay

last: Pancholi

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

description: Comparison of gene expression in the M1-SDHHBtail mutant vs the parental strain M1-SF370

hyb_protocol: Hybridization protocol The labeled cDNA-probes (wild-type and mutant strains) were combined and purified using QIAquickTM PCR spin columns (Qiagen). The labeled cDNA was hybridized with the array slide in the hybridization buffer (3xSSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C overnight using hybridization chamber (HybrChambTm, GeneMachines). The hybridized array slides were washed consecutively with 1 x SSC, 0.2 x SSC and 0.05 x SSC each with 0.03% SDS.

scan_protocol: Scan protocol Signals of the bound reagents on the microarray spots in terms of relative fluorescence values were measured and quantified by a laser scanner (GenePix 4100 ) at 10um/pixel resolution. The resulting images were processed using Gene Pix Pro software (version 4.0, Axon instruments).

data_processing: The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data. All raw data (in the form of *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signals was applied and within microarray normalization was achieved using the Lowess method. Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were termed as "null" (kept empty). The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. This package employs the moderated t-statistics from the LIMMA package (liner models for micro array data) based on bayesian Significantly differentially expressed genes were those showing log2 values > 1.0( up regulated) and Log2 values < 1 (down-regulated), Bioconductors Multtest package provided suitable method (e.g. Benjamini and Hochberg) adjust P values according to multiple hypothesis testing problems.

label: Alexafluor 647

organism: Streptococcus pyogenes

source_name: M1-SDHHBtail mutant

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

growth_protocol: Todd-Hewitt broth late log phase

extract_protocol: Washed streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).

treatment_protocol: Streptococus pyogenes M-Hbtail mutant was derived from the wild type strain. Total RNA was isolated from this mutant strain strain. ( Boel et al [2005] Infect. Immun.73:6237.)

tag: strain

label: AlexaFluor 555

source_name: M1-SF370 wild-type

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

growth_protocol: Todd-Hewitt broth-late log phase culture

treatment_protocol: Streptococus pyogenes parent strain type M1 SF370 was obtained from ATCC and grown to late log phase culture. Total RNA was isolated from this wild-type strain


title: Experiment-6-M1-SDHHBtail vs wild-type


title: Experiment-5-M1-SDHHBtail vs wild-type


title: Experiment-7-M1-SDHHBtail vs wild-type


title: HCT-116 si ZCCHC6 replicate 1 variant 2 assay

description:
Variant 2
Replicate 1

source_name: HCT-116 cells


title: Experiment-4-M1-SDHHBtail vs wild-type

description: Comparison of gene expression in the M1-SDHHBtail mutant vs the parental strain M1 SF370

data_processing: The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data. All raw data (in the form of *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signals was applied and within microarray normalization was achieved using the Lowess method. Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were termed as "null" (kept empty). The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. This package employs the moderated t-statistics from the LIMMA package (liner models for micro array data) based on bayesian Significantly differentially expressed genes were those showing log2 values > 1.0( up regualted) and Log2 values < 1 (down-regulated), Bioconductors Multtest package provided suitable method (e.g. Benjamini and Hochberg) adjust P values according to multiple hypothesis testing problems.


title: HCT-116 si ZCCHC6 replicate 1 variant 1 assay

description:
Variant 1
Replicate 1


title: Ovarian cancer sample 4

source_name: Ovarian cancer


title: HCT-116 si ZCCHC11 replicate 2 canonical assay

description:
Canonical
Replicate 2

value: si ZCCHC11


title: TRAMP Cromolyn rep 2

description: replicate 2

source_name: TRAMP Cromolyn

tag: background strain

value: TRAMP

tag: age

value: 24 wks

tag: tissue origin

value: Prostate

tag: tissue type

value: tumor


title: Ovarian cancer sample 3

value: event


title: TRAMP Cromolyn rep 3

description: replicate 3


title: HCT-116 si ZCCHC11 replicate 2 variant 2 assay

description:
Variant 2
Replicate 2


title: Ovarian cancer sample 2

value: censored


title: Ovarian cancer sample 1


title: TRAMP KitWsh rep 1

description: replicate 1

source_name: TRAMP KitWsh

value: TRAMP KitW-sh


title: TRAMP Cromolyn rep 1

description: replicate 1


title: Experiment-2-M1-SDHHBtail vs wild-type


title: TRAMP 30wk rep 1

description: replicate 1

source_name: TRAMP 30wk

value: 30 wks


title: Experiment-3-M1-SDHHBtail vs wild-type

source_name: M1SDHHbtail-total RNA


title: TRAMP 30wk rep 2

description: replicate 2


title: Experiment-1-M1-SDHHBtail vs wild-type

data_processing: The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data. All raw data (in the form of *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signals was applied and within microarray normalization was achieved using the Lowess method. Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were termed as "null". The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. This package employs the moderated t-statistics from the LIMMA package (liner models for micro array data) based on bayesian Significantly differentially expressed genes were those showing log2 values > 1.0( up regualted) and Log2 values < 1 (down-regulated), Bioconductors Multtest package provided suitable method (e.g. Benjamini and Hochberg) adjust P values according to multiple hypothesis testing problems.

growth_protocol: Todd-Hewitt broth

treatment_protocol: Streptococus pyogenes parent strain type M1 SF370 was obtained from ATCC and grown to late log phase culture. Total RNA was isolated from this wild-type strain.

growth_protocol: Todd-Hewitt broth_late log phase culture


title: wt prost rep 1

description: replicate 1

source_name: wt prost

value: wild type

value: non-tumor


title: Bi1iDC

status: Public on Jun 14 2011

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: Immature Dendritic Cell, No LPS. rep 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v3 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: Immature Dendritic Cell, No LPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA using MessageAmp™ II aRNA Kit from Ambion

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

value: Immature dendritic cells

tag: disease state

value: healthy


title: Bm7IL10mDC

description: IL-10 mature Dendritic cells, with LPS. rep 1

source_name: IL-10 mature Dendritic cells, with LPS

tag: cell type

value: IL-10 mature dendritic cells


title: Am6mDC

description: Mature Dendritic Cell, No LPS. rep 1

source_name: Mature Dendritic Cell, No LPS

value: Mature dendritic cells


title: Bi2IL10iDC

description: Immature Dendritic cells, No LPS. rep 3


title: Ai5imMACRO

description: Immature macrophage, No LPS. rep 2

source_name: Immature macrophage, No LPS

value: Immature macrophage


title: Bm6mDC

description: Mature Dendritic Cell, with LPS. rep 1

source_name: Mature Dendritic Cell, with LPS


title: Ai1iDC

description: Immature Dendritic Cell, No LPS. rep 2


title: Bi4VITD3iDC

description: Vitamin D3 immature Dendritic cells, No LPS. rep 1

value: Vitamin D3 immature dendritic cells


title: Bm10mMACRO

description: Mature macrophage, with LPS. rep 2

source_name: Mature macrophage, with LPS

value: Mature macrophage


title: Am9VITD3mDC

description: Vitamin D3 mature Dendritic cells, No LPS. rep 1

value: Vitamin D3 mature dendritic cells


title: Ai4VITD3iDC

description: Vitamin D3 immature Dendritic cells, No LPS. rep 2


title: Bm9VITD3mDC

description: Vitamin D3 mature Dendritic cells, with LPS. rep 1


title: v5

city: Philadelphia

first: Tamas

last: Dolinay

address: 220 S. 33rd St., Towne building, Room 390

department: Bioengineering

institute: University of Pennsylvania

description: replicate 1

data_processing: Microarray expression profiles were generated using Illumina REF8 mouse arrays according to the manufacturer’s protocol. The data were normalised using quantile normalisation with IlluminaGUI in R.  For statistical analysis we applied Welch's two-sample t-tests to find genes with significant expression changes. The P values from the t-tests were adjusted for multiple testing using the false discovery rate (FDR) controlling procedure of Benjamini. Genes which have the adjusted P values less than 0.05 were considered significantly changed .

source_name: ventilation 5

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

extract_protocol: Total RNA was extracted from lung tissues with Trizol (Invitrogen). RNA clean-up and DNase I treatment was performed with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: NOD/shi

value: 6-12 weeks

tag: tissue

value: whole lung

tag: ventilation

value: yes


title: Am10mMACRO

description: Mature macrophage, No LPS. rep 1

source_name: Mature macrophage, No LPS


title: v1

description: replicate 1

source_name: ventilation 1


title: Bm8DEXmDC

description: Dexamethason mature Dendritic cells, with LPS. rep 1

value: Dexamethason mature dendritic cells


title: v4

description: replicate 1

source_name: ventilation 4


title: Ai2IL10iDC

description: IL-10 immature Dendritic cells, No LPS. rep 1

source_name: IL-10 immature Dendritic cells, No LPS

value: IL-10 immature dendritic cells


title: Am7IL10mDC

description: IL-10 mature Dendritic cells, No LPS. rep 1

source_name: IL-10 mature Dendritic cells, No LPS


title: Bi5imMACRO

description: Immature macrophage, No LPS. rep 1


title: c3

description: replicate 1

source_name: control 3 (no ventilation)

value: no


title: v3

description: replicate 1

source_name: ventilation 3


title: 4C WT mice Rad23a fetal liver replicate 2

hyb_protocol: Details on the protocol can be found on http://www.nimblegen.com/technology/index.html

data_processing: Data were normalized using the 'lowess' method using standard settings (see Smyth & Speed, 2003, Methods 31, 265-273 (2003)

source_name: Rad23a 4C fetal liver, digested with HindIII and DpnII

extract_protocol: 4C was performed as described before in Simonis et al. 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 38(11):1348-54

tag: sample type

tag: genetic background

value: FVB

value: fetal liver

tag: genotype

value: wild type

source_name: WT genomic DNA fetal liver, digested with HindIII and DpnII


title: 4C hLCR-knock-in mice fetal liver replicate 2

scan_protocol: Details on the protocol can be found on http://www.nimblegen.com/technology/index.html

source_name: integrated hLCR genomic DNA fetal liver, digested with HindIII and DpnII

value: hLCR knock-in

source_name: integrated hLCR 4C material fetal liver, digested with HindIII and DpnII


title: v2

description: replicate 1

source_name: ventilation 2


title: Am8DEXmDC

description: Dexamethason mature Dendritic cells, No LPS. rep 1

value: healthy


title: c2

description: replicate 1

source_name: control 2 (no ventilation)


title: c1

description: replicate 1

source_name: control 1 (no ventilation)


title: wt prost rep 2

description: replicate 2

source_name: wt prost

value: 30 wks

value: Prostate

value: non-tumor


title: Bi3DEXiDC

description: Dexamethason immature Dendritic cells, No LPS. rep 1

value: Dexamethason immature dendritic cells


title: 11EXP2: Experiment 2, condition 2, triplicate #2

source_name: Ishikawa cells grown on glass with steroids: estradiol (E2 at 10exp -8M) and medroxyprogesterone acetate (MPA at 10 exp -7M)): 24h with E2, followed by E2+MPA for 72h

value: Ishikawa


title: 10EXP2: Experiment 2, condition 2, triplicate #1


title: Ai3DEXiDC

description: Dexamethason immature Dendritic cells, No LPS. rep 2


title: 9CON2: Control, condition 2, triplicate #3

source_name: Ishikawa cells grown on glass without steroids


title: 8CON2: Control, condition 2, triplicate #2


title: 7CON2: Control, condition 2, triplicate #1


title: 4C hLCR-knock-in mice fetal liver replicate 1

label_protocol: Details on the protocol can be found on http://www.nimblegen.com/technology/index.html

value: integrated hLCR 4C material fetal liver, digested with HindIII and DpnII

value: integrated hLCR genomic DNA fetal liver, digested with HindIII and DpnII


title: 6EXP1: Experiment 1, condition 1, triplicate #3

source_name: Ishikawa cells on plastic with steroids: estradiol (E2 at 10exp -8M) and medroxyprogesterone acetate (MPA at 10 exp -7M)): 24h with E2, followed by E2+MPA for 72h


title: 2CON1: Control, condition 1, triplicate #2

source_name: Ishikawa cells grown on plastic without steroids


title: 31CON1: Control, condition 1, triplicate #3


title: 1CON1: Control, condition 1, triplicate #1


title: 1MACROINF24HRS

description: Macrophages #1, with HIV-1 infection, 24-hrs, triplicate #1.

source_name: Primary Macrophages, with HIV-1 infection, 24-hrs

value: Primary Macrophages


title: 12EXP2: Experiment 2, condition 2, triplicate #3


title: 3MACRO7DAYS

description: Macrophages #3, no HIV-1 infection, 7-days, triplicate #3.

source_name: Primary Macrophages, no HIV-1 infection, 7-days


title: 1MACROINF7DAYS

description: Macrophages #1, with HIV-1 infection, 7-days, triplicate #1.

source_name: Primary Macrophages, with HIV-1 infection, 7-days


title: 3MACROINF24HRS

description: Macrophages #3, with HIV-1 infection, 24-hrs, triplicate #3.


title: 2MACROINF7DAYS

description: Macrophages #2, with HIV-1 infection, 7-days, triplicate #2.


title: 3MACROINF7DAYS

description: Macrophages #3, with HIV-1 infection, 7-days, triplicate #3.


title: 4EXP1: Experiment 1, condition 1, triplicate #1


title: 2MACROINF24HRS

description: Macrophages #2, with HIV-1 infection, 24-hrs, triplicate #2.


title: 5EXP1: Experiment 1, condition 1, triplicate #2


title: 2MACRO7DAYS

description: Macrophages #2, no HIV-1 infection, 7-days, triplicate #2.


title: 1MACRO7DAYS

description: Macrophages #1, no HIV-1 infection, 7-days, triplicate #1.


title: 2MACRO24HRS

description: Macrophages #2, no HIV-1 infection, 24-hrs, triplicate #2.

source_name: Primary Macrophages, no HIV-1 infection, 24-hrs


title: 1MACRO24HRS

description: Macrophages #1, no HIV-1 infection, 24-hrs, triplicate #1.


title: 3MACRO24HRS

description: Macrophages #3, no HIV-1 infection, 24-hrs, triplicate #3.


title: 3CD4TINF7DAYS

description: CD4+T-cells #3, with HIV-1 infection, 7-days, triplicate #3.

source_name: Primary CD4+T-cells, with HIV-1 infection, 7-days

value: Primary CD4+T-cells


title: 4C WT mice Rad23a fetal liver replicate 1

value: WT genomic DNA fetal liver, digested with HindIII and DpnII

source_name: Rad23a 4C fetal liver, digested with HindIII and DpnII


title: 2CD4TINF7DAYS

description: CD4+T-cells #2, with HIV-1 infection, 7-days, triplicate #2.


title: 3CD4TINF24HRS

description: CD4+T-cells #3, with HIV-1 infection, 24-hrs, triplicate #3.

source_name: Primary CD4+T-cells, with HIV-1 infection, 24-hrs


title: 2CD4TINF24HRS

description: CD4+T-cells #2, with HIV-1 infection, 24-hrs, triplicate #2.


title: 1CD4TINF24HRS

description: CD4+T-cells #1, with HIV-1 infection, 24-hrs, triplicate #1.


title: 3CD4T7DAYS

description: CD4+T-cells #3, no HIV-1 infection, 7-days, triplicate #3.

source_name: Primary CD4+T-cells, no HIV-1 infection, 7-days


title: 2CD4T24HRS

description: CD4+T-cells #2, no HIV-1 infection, 24-hours, triplicate #2.

source_name: Primary CD4+T-cells, no HIV-1 infection, 24-hours


title: 2ASTROINF6HRS

description: Astrocytes #2, with HIV-1 infection, 6-hours, triplicate #2.

source_name: Primary Astrocytes, with HIV-1 infection, 6-hours

value: Primary Astrocytes


title: 1CD4T24HRS

description: CD4+T-cells #1, no HIV-1 infection, 24-hours, triplicate #1.


title: 3ASTROINF6HRS

description: Astrocytes #3, with HIV-1 infection, 6-hours, triplicate #3.


title: 1CD4T7DAYS

description: CD4+T-cells #1, no HIV-1 infection, 7-days, triplicate #1.


title: 1ASTROINF6HRS

description: Astrocytes #1, with HIV-1 infection, 6-hours, triplicate #1.


title: 3CD4T24HRS

description: CD4+T-cells #3, no HIV-1 infection, 24-hours, triplicate #3.


title: 1ASTROINF24HRS

description: Astrocytes #1, with HIV-1 infection, 24-hours, triplicate #1.

source_name: Primary Astrocytes, with HIV-1 infection, 24-hours


title: 3ASTRO6HRS

description: Astrocytes #3, NO HIV-1 infection, 6-hours, triplicate #3.

source_name: Primary Astrocytes , NO HIV-1 infection, 6-hours


title: 2ASTRO24HRS

description: Astrocytes #2, NO HIV-1 infection, 24-hours, triplicate #2.

source_name: Primary Astrocytes , NO HIV-1 infection, 24-hours


title: 2ASTRO6HRS

description: Astrocytes #2, NO HIV-1 infection, 6-hours, triplicate #2.


title: 1ASTRO6HRS

description: Astrocytes #1, NO HIV-1 infection, 6-hours, triplicate #1.


title: 3ASTRO24HRS

description: Astrocytes #3, NO HIV-1 infection, 24-hours, triplicate #3.


title: 2ASTROINF24HRS

description: Astrocytes #2, with HIV-1 infection, 24-hours, triplicate #2.


title: 1ASTRO24HRS

description: Astrocytes #1, NO HIV-1 infection, 24-hours, triplicate #1.


title: 12TLE

description: 12TLE: Tumid (TLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #1.

value: Tumid (TLE) Non-Lesional dermis

value: Cutaneous lupus erythematosus


title: 1CD4TINF7DAYS

description: CD4+T-cells #1, with HIV-1 infection, 7-days, triplicate #1.


title: 53TLE31

description: 53TLE31: Tumid (TLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #1.

value: Tumid (TLE) Lesional dermis


title: 32TLE

description: 32TLE: Tumid (TLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #3.


title: 50TLE90

description: 50TLE90: Tumid (TLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #4.


title: 13TLE13

description: 13TLE13: Tumid (TLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #2.


title: 2CD4T7DAYS

description: CD4+T-cells #2, no HIV-1 infection, 7-days, triplicate #2.


title: 49TLE90

description: 49TLE90: Tumid (TLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #4.


title: 6SCLE

description: 6SCLE: Subacute cutaneous (SCLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #1.


title: 14TLE13

description: 14TLE13: Tumid (TLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #2.


title: 45SCLE101

description: 45SCLE101: Subacute cutaneous (SCLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #4.


title: 31TLE103

description: 31TLE103: Tumid (TLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #3.


title: 41SCLE95A

description: 41SCLE95A: Subacute cutaneous (SCLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #3.


title: 20SCLE

description: 20SCLE: Subacute cutaneous (SCLE) Non-Lesional dermis Cutaneous lupus erythematosus (CLE) patients, replicate #1.

source_name: Subacute cutaneous (SCLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients


title: 3ASTROINF24HRS

description: Astrocytes #3, with HIV-1 infection, 24-hours, triplicate #3.


title: 15DLE46

description: 15DLE46: Discoid (DLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #1.

value: Discoid (DLE) Lesional dermis


title: 43DLE001

description: 43DLE001: Discoid (DLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #3.


title: 23DLE

description: 23DLE: Discoid (DLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #2.


title: 44DLE001

description: 44DLE001: Discoid (DLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #3.

value: Discoid (DLE) Non-Lesional dermis


title: 24DLE

description: 24DLE: Discoid (DLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #2.


title: 46SCLE101

description: 46SCLE101: Subacute cutaneous (SCLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #4.


title: 42SCLE95

description: 42SCLE95: Subacute cutaneous (SCLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #3.


title: CON3

description: CON3: Control dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #1.

value: Control dermis


title: CON4

description: CON4: Control dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #2.


title: 51DLE002

description: 51DLE002: Discoid (DLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #4.


title: 21SCLE

description: 21SCLE: Subacute cutaneous (SCLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #2.


title: 48CON1B

description: 48CON1B: Control dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #4.


title: 16DLE

description: 16DLE: Discoid (DLE) Non-Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #1.


title: 9SCLE

description: 9SCLE: Subacute cutaneous (SCLE) Lesional dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #2.


title: AT55

description: AT55: GM Medium - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with macrophages (GM-CSF alone, GM), replicate #1.


title: AT61

description: AT61: GM LPS 18h - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with macrophages (GM-CSF alone, GM), stimulated with LPS for 18 hours, replicate #2.

source_name: GM LPS 18h - human monocyte-derived dendritic cells (MDDC), stimulated with LPS for 18 hours


title: AT57

description: AT57: GM LPS 18h - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with macrophages (GM-CSF alone, GM), stimulated with LPS for 18 hours, replicate #1.


title: AT60

description: AT60: GM Medium - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with macrophages (GM-CSF alone, GM), replicate #2.


title: AT65

description: AT65: Human monocyte-derived dendritic cells (MDDC), replicate #3.

value: human monocyte-derived dendritic cells (MDDC)


title: AT79

description: AT79: GM Medium - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with macrophages (GM-CSF alone, GM), replicate #3.


title: AT50

description: AT50: Human monocyte-derived dendritic cells (MDDC), replicate #2


title: AT48

description: AT48: Human monocyte-derived dendritic cells (MDDC), replicate #1.


title: 5CON5

description: 5CON5: Control dermis from Cutaneous lupus erythematosus (CLE) patients, replicate #3.


title: AT80

description: AT80: G4 Medium - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with GM-CSF+IL-4 (G4), replicate #3.


title: AT56

description: AT56: G4 Medium - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with GM-CSF+IL-4 (G4), replicate #1.


title: AT59

description: AT59: G4 Medium - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with GM-CSF+IL-4 (G4), replicate #2.


title: AT58

description: AT58: G4 LPS 18h - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with GM-CSF+IL-4 (G4), stimulated with LPS for 18 hours, replicate #1.

source_name: G4 LPS 18h - human monocyte-derived dendritic cells (MDDC), stimulated with LPS for 18 hours


title: AT81

description: AT81: G4 LPS 18h - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with GM-CSF+IL-4 (G4), stimulated with LPS for 18 hours, replicate #3.


title: HT29KO2: Cell line derived from colon carcinoma, replicate #2.

source_name: HT29: colon carcinoma cell line; media only

tag: cell line

value: colon carcinoma

value: Human Cancer


title: HT29S1: Cell lines derived from colon carcinoma, Triplicate #1.

source_name: HT29: colon carcinoma cell line; treated with glycodendrimers containing GlcNAc


title: HT29S2: Cell lines derived from colon carcinoma, Triplicate #2.


title: HT29KO3: Cell line derived from colon carcinoma, replicate #3.


title: AT78

description: AT78: GM LPS 18h - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with macrophages (GM-CSF alone, GM), stimulated with LPS for 18 hours, replicate #3.


title: K562KO2: Cell line derived from chronic myeloid leukemia, triplicate #2.

source_name: K562:chronic myeloid leukemia cell line; media only

value: myeloid leukemia


title: K562KO1: Cell line derived from chronic myeloid leukemia, triplicate #1.


title: HT29S3: Cell lines derived from colon carcinoma, Triplicate #3.


title: AT62

description: AT62: G4 LPS 18h - human monocyte-derived dendritic cells (MDDC) obtained by differentiation with GM-CSF+IL-4 (G4), stimulated with LPS for 18 hours, replicate #2.


title: NK92K02: Cell lines derived from multiple myeloma, triplicate #2.

source_name: NK92:multiple myeloma cell line, media only

value: multiple myeloma


title: NK92K01: Cell lines derived from multiple myeloma, triplicate #1.


title: NK92S03: Cell lines derived from multiple myeloma, triplicate #3.

source_name: NK92:multiple myeloma cell line, treated with glycodendrimers containing GlcNAc .


title: NK92S01: Cell lines derived from multiple myeloma, triplicate #1.


title: K562S1: Cell line derived from chronic myeloid leukemia, triplicate #1.

source_name: K562:chronic myeloid leukemia cell line; treated with glycodendrimers containing GlcNAc


title: K562S2: Cell line derived from chronic myeloid leukemia, triplicate #2.


title: K562KO3: Cell line derived from chronic myeloid leukemia, triplicate #3.


title: NK92S02: Cell lines derived from multiple myeloma, triplicate #2.


title: 1DNEG

description: 1DNEG: Caco2 cells with no B. infantis and no HMO (negative control), replicate #1.

source_name: Caco2 cells with no B. infantis and no human milk oligosacharides

tag: Sex

value: female

value: healthy


title: K562S3: Cell line derived from chronic myeloid leukemia, triplicate #3.


title: 4DNEG

description: 4DNEG: Caco2 cells with no B. infantis and no HMO (negative control), replicate #3.

value: Caco2 cells with no B. infantis and no human milk oligosacharides


title: 2DNEG

description: 2DNEG: Caco2 cells with no B. infantis and no HMO (negative control), replicate #2.


title: 5DNEG

description: 5DNEG: Caco2 cells with no B. infantis and no HMO (negative control), replicate #4.


title: 2DPLUS

description: 2DPLUS: Caco2 cells exposed to HMO, replicate #1.

source_name: Caco2 cells exposed to human milk oligosacharides


title: HT29KO1: Cell line derived from colon carcinoma, replicate #1.


title: NK92K03: Cell lines derived from multiple myeloma, triplicate #3.


title: 3DPLUS

description: 3DPLUS: Caco2 cells exposed to HMO, replicate #2.

value: Caco2 cells exposed to human milk oligosacharides


title: 4BNEG

description: 4BNEG: Caco2 cells exposed to B. infantis pre-grown on lactose, replicate #4.

source_name: Caco2 cells exposed to B. infantis pre-grown on lactose.


title: 6DPLUS

description: 6DPLUS: Caco2 cells exposed to HMO, replicate #4.


title: 5DPLUS

description: 5DPLUS: Caco2 cells exposed to HMO, replicate #3.


title: 3BNEG

description: 3BNEG: Caco2 cells exposed to B. infantis pre-grown on lactose, replicate #3.

value: Caco2 cells exposed to B. infantis pre-grown on lactose.


title: 2BNEG

description: 2BNEG: Caco2 cells exposed to B. infantis pre-grown on lactose, replicate #2.


title: 1BNEG

description: 1BNEG: Caco2 cells exposed to B. infantis pre-grown on lactose, replicate #1.


title: 2BPLUS

description: 2BPLUS: Caco2 cells exposed to HMO and to B. infantis pre-grown on HMO, replicate #2.

source_name: Caco2 cells exposed to human milk oligosacharides and to B. infantis pre-grown on HMO.


title: 1BPLUS

description: 1BPLUS: Caco2 cells exposed to HMO and to B. infantis pre-grown on HMO, replicate #1.

value: Caco2 cells exposed to human milk oligosacharides and to B. infantis pre-grown on HMO.


title: 5BPLUS

description: 5BPLUS: Caco2 cells exposed to HMO and to B. infantis pre-grown on HMO, replicate #4.


title: 4BPLUS

description: 3BPLUS: Caco2 cells exposed to HMO and to B. infantis pre-grown on HMO, replicate #3.


title: JYPLUS05

description: JYPLUS05: HSB-2(human B lymphoma) cells expressing PEN5, replicate #2.

source_name: JY cells expressing PEN5

value: JY

value: cells expressing PEN6

value: Lymphoma


title: JYPLUS06

description: JYPLUS06: HSB-2(human B lymphoma) cells expressing PEN5, replicate #3.

value: cells expressing PEN7


title: JYNEG06

description: JYNEG06: HSB-2(Human B lymphoma) cells NOT expressing PEN5, replicate #3.

source_name: JY cells NOT expressing PEN5

value: cells NOT expressing PEN5


title: JYNEG05

description: JYNEG05: HSB-2(Human B lymphoma) cells NOT expressing PEN5, replicate #2.


title: JYPLUS04

description: JYPLUS04: HSB-2(human B lymphoma) cells expressing PEN5, replicate #1.

value: cells expressing PEN5


title: PF3: Hela PF replicate #2.

source_name: Hela PF cell line

value: Hela PF


title: PF4: Hela PF replicate #1.


title: PFB: Hela PF replicate #3.


title: JYNEG04

description: JYNEG04: HSB-2(Human B lymphoma) cells NOT expressing PEN5, replicate #1.


title: HPLUS05

description: HPLUS05: HSB-2(Human T-leukemia) cells expressing PEN5, replicate #2.

source_name: HSB-2 cells expressing PEN5

value: Leukemia


title: FMVECTNF203

description: FMVECTNF203: Stimulated, FMVEC cells nr. 50 were from passage 11, replicate 1

source_name: TNF Stimulated, FMVEC cells from passage 11.

value: male

value: FMVEC (human promary microvascular endothelial cells isolated from foreskins)


title: HNEG05

description: HNEG05: HSB-2(Human T-leukemia) cells NOT expressing PEN5, replicate #2.

source_name: HSB-2 cells NOT expressing PEN5


title: Lymphatic endothilial cells, stimulated with TNF

value: unknown

value: primary human lymphatic endothelial cells (LEC)


title: Lymphatic endothilial cells, resting

source_name: Lymphatic endothilial cells, resting


title: hcMECTNF2

description: hcMECTNF2: Stimulated, hcMEC cells were from passage nr. 32 and 33, replicate 2

source_name: TNF Stimulated, hcMEC cells were from passage nr. 32 and 33.

value: female

value: hcMEC/D3 (human brain endothelial cells line)


title: FMVECTNF50

description: FMVECTNF50: Stimulated, FMVEC cells nr. 50 were from passage 11, replicate 2


title: hcMECTNF3

description: hcMECTNF3: Stimulated, hcMEC cells were from passage nr. 32 and 33, replicate 1


title: hcMECCON2

description: hcMECCON2: Control, hcMEC cells were from passage nr. 32 and 33,replicate 2

source_name: Control, hcMEC cells were from passage nr. 32 and 33.


title: hcMECCON3

description: hcMECCON3: Control, hcMEC cells were from passage nr. 32 and 33, replicate 3


title: FMVECCON50

description: FMVECCON50: Control, FMVEC cells nr. 50 were from passage 11, replicate 1

source_name: Control, FMVEC cells from passage 11.


title: HNEG06

description: HNEG06: HSB-2(Human T-leukemia) cells NOT expressing PEN5, replicate #3.


title: hcMECCON1

description: hcMECCON1: Control, hcMEC cells were from passage nr. 32 and 33, replicate 1


title: HNEG04

description: HNEG04: HSB-2(Human T-leukemia) cells NOT expressing PEN5, replicate #1.


title: FMVECCON203

description: FMVECCON203: Control, FMVEC cells nr. 203 were from passage 11, replicate 2


title: HPLUS06

description: HPLUS06: HSB-2(Human T-leukemia) cells expressing PEN5, replicate #3.


title: HPLUS04

description: HPLUS04: HSB-2(Human T-leukemia) cells expressing PEN5, replicate #1.


title: hcMECTNF1

description: hcMECTNF1: Stimulated, hcMEC cells were from passage nr. 32 and 33, replicate 3


title: EV23: Hela EV2 cells replicate #1.

source_name: Hela EV2 cell line

value: Hela EV2


title: EV2B: Hela EV2 cells replicate #2.


title: EV233: Hela EV2 cells replicate #3.


title: CEM_2

description: Human CEM cell line RNA  Replicate #2

source_name: Human CEM cell line


title: T7: tumor lung, SCC, replicate #7.

source_name: tumor, squamous cell carcinoma

value: lung tumor

value: squamous cell carcinoma


title: T3: tumor lung, SCC, replicate #3.


title: iDCC

description: Immature Dendritic Cells, replicate #2.

organism: unidentified

source_name: Immature Dendritic Cells

value: Immature Dendritic Cells


title: moC

description: Monocytes, replicate #2.

source_name: Monocytes

value: Monocytes


title: iDCB

description: Immature Dendritic Cells, replicate #1.


title: T8: tumor lung, SCC, replicate #8.


title: T6: tumor lung, SCC, replicate #6.


title: N7: non-tumor lung, normal, replicate #7.

source_name: non-tumor lung, normal

value: normal lung

value: normal


title: N10: non-tumor lung, normal, replicate #10.


title: T2: tumor lung, SCC, replicate #2.


title: T1: tumor lung, SCC, replicate #1.


title: mDCA

description: Mature dendritic cells, replicate #1.

source_name: Mature dendritic cells

value: Mature dendritic cells


title: N5: non tumor lung, normal, replicate #5.


title: CEM_1

description: Human CEM cell line  Replicate #1


title: N9: non-tumor lung, normal, replicate #9.


title: N6: non-tumor lung, normal, replicate #6.


title: N8: non-tumor lung, normal, replicate #8.


title: N4: non tumor lung, normal, replicate #4.


title: mDCC

description: Mature Dendritic Cells, replicate #2.


title: N1: non tumor lung, normal, replicate #1.


title: N2: non tumor lung, normal, replicate #2.


title: T4: tumor lung, SCC, replicate #4.


title: T9: tumor lung, SCC, replicate #9.


title: moA

description: Monocytes, replicate #1.


title: T5: tumor lung, SCC, replicate #5.


title: N3: non tumor lung, normal, replicate #3.


title: T10: tumor lung, SCC, replicate #10.


title: 293_1

description: Human HEK 293 cell line RNA  Replicate #1

source_name: Human HEK 293 cell line


title: 293_2

description: Human HEK 293 cell line RNA  Replicate #2


title: 450A

description: Breast cancer cells MDA-MB-231 treated with 50uM But4ManNAc.  Replicate #1.

value: Metastatic breast cancer


title: 4125B

description: Breast cancer cells MDA-MB-231 treated with 125uM But4ManNAc.  Replicate #2.


title: 5125C

description: Breast cancer cells MDA-MB-231 treated with 125uM But5Man.  Replicate #3


title: D2: CD8 T cells, weak antigenic signal, triplicate #2.

description: D2: weak antigenic signal (deletion conditions) with cognate antigen, triplicate #2.

source_name: CD8+ T cells; weak antigenic signal (deletion conditions) with cognate antigen

value: CD8+ T cells


title: A1: CD8 T cells, strong antigenic signal, triplicate #1.

description: A1: purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) with cognate antigen, triplicate #1.

source_name: CD8+ T cells; purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) with cognate antigen.


title: A2: CD8 T cells, strong antigenic signal, triplicate #2.

description: A2: purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) with cognate antigen, triplicate #2.


title: EC

description: Breast cancer cells MDA-MB-231, Ethanol treated control.  Replicate #3


title: EA

description: Breast cancer cells MDA-MB-231, Ethanol treated control.  Replicate #1


title: D3: CD8 T cells, weak antigenic signal, triplicate #3.

description: D3: weak antigenic signal (deletion conditions) with cognate antigen, triplicate #3.


title: EB

description: Breast cancer cells MDA-MB-231, Ethanol treated control.  Replicate #2


title: 450B

description: Breast cancer cells MDA-MB-231 treated with 50uM But4ManNAc.  Replicate #2.


title: N3: Control, naive transgenic CD8 cells, triplicate #3.

source_name: CD8+ T cells; Control, naive transgenic CD8 cells


title: CON2: Control WEHI-231 cells, replicate #2.

source_name: Control WEHI-231 cells

value: Normal B cell


title: CON1: Control WEHI-231 cells, replicate #1.


title: 550A

description: Breast cancer cells MDA-MB-231 treated with 50uM But5Man.  Replicate #1


title: 5125B

description: Breast cancer cells MDA-MB-231 treated with 125uM But5Man.  Replicate #2


title: 550B

description: Breast cancer cells MDA-MB-231 treated with 50uM But5Man.  Replicate #2


title: APP1: Apoptotic WEJI-231 cells, replicate #1.

source_name: Apoptotic WEJI-231 cells

value: Apoptotic B cell


title: D1: CD8 T cells, weak antigenic signal, triplicate #1.

description: D1: weak antigenic signal (deletion conditions) with cognate antigen, triplicate #1.


title: 4125C

description: Breast cancer cells MDA-MB-231 treated with 125uM But4ManNAc.  Replicate #3.


title: CON3: Control WEHI-231 cells, replicate #3.


title: APP2: Apoptotic WEJI-231 cells, replicate #2.


title: APP3: Apoptotic WEJI-231 cells, replicate #3.


title: 4125A

description: Breast cancer cells MDA-MB-231 treated with 125uM But4ManNAc.  Replicate #1.


title: 450C

description: Breast cancer cells MDA-MB-231 treated with 50uM But4ManNAc.  Replicate #3.


title: 5125A

description: Breast cancer cells MDA-MB-231 treated with 125uM But5Man.  Replicate #1


title: 550C

description: Breast cancer cells MDA-MB-231 treated with 50uM But5Man.  Replicate #3


title: N1: Control, naive transgenic CD8 cells, triplicate #1.


title: A3: CD8 T cells, strong antigenic signal, triplicate #3.

description: A3: purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) with cognate antigen, triplicate #3.


title: N2: Control, naive transgenic CD8 cells, triplicate #2.


title: Day11E

description: Mouse ES scraped cells, with feeders, extensively washed in PBS to remove growth media containing FCS and LIF.    Cells are passage #25  Replicate #1

source_name: Mouse ES scraped cells, with feeders, extensively washed in PBS to remove growth media containing FCS and LIF. Passage #25

value: male

value: embryonic stem (ES)


title: Day31E

description: Mouse ES scraped cells, with feeders, extensively washed in PBS to remove growth media containing FCS and LIF.    Cells are passage #25  Replicate #3


title: Day23E

description: Mouse ES Trypsinized cells, pre-plated. Very little fibroblast (about 1 percent).    Cells are passage #25  Replicate #2

source_name: Mouse ES Trypsinized cells, pre-plated. Very little fibroblast (about 1 percent). Passage #25


title: Day13E

description: Mouse ES Trypsinized cells, pre-plated. Very little fibroblast (about 1 percent).    Cells are passage #25  Replicate #1


title: Day22E

description: Mouse ES Trypsinized cells, no pre-plating.  Same amount of fibroblasts as in scraped cells.    Cells are passage #25  Replicate #1

source_name: Mouse ES Trypsinized cells, no pre-plating.  Same amount of fibroblasts as in scraped cells. Passage #25


title: Day32E

description: Mouse ES Trypsinized cells, no pre-plating.  Same amount of fibroblasts as in scraped cells.    Cells are passage #25  Replicate #2


title: Day33E

description: Mouse ES Trypsinized cells, pre-plated. Very little fibroblast (about 1 percent).    Cells are passage #25  Replicate #3


title: P5325

description: P5325: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBhigh (naïve) populations (CD4+CD25-CD45RBhigh), replicate #3.

source_name: Naïve female C57BL/6 mice flow sorted into CD45RBhigh (naïve) populations (CD4+CD25-CD45RBhigh)


title: P541

description: P541: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBhigh (naïve) populations (CD4+CD25-CD45RBhigh), replicate #4.


title: P61112

description: P61112: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBlow (activated/memory) populations (CD4+CD25-CD45RBlow), replicate #1.

source_name: Naïve female C57BL/6 mice flow sorted into CD45RBlow (activated/memory) populations (CD4+CD25-CD45RBlow)


title: P61312

description: P61312: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBlow (activated/memory) populations (CD4+CD25-CD45RBlow), replicate #2.


title: P6325

description: P6325: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBlow (activated/memory) populations (CD4+CD25-CD45RBlow), replicate #3.


title: Day21E

description: Mouse ES scraped cells, with feeders, extensively washed in PBS to remove growth media containing FCS and LIF.    Cells are passage #25  Replicate #2


title: P51112

description: P51112: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBhigh (naïve) populations (CD4+CD25-CD45RBhigh), replicate #1.


title: purR deletion mutant, M9 minimal medium with 100 μg/ml adenine, 2

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

institute: UCSD

description: E. coli K12 MG1655, ∆purR strain in M9 minimal media with 100 μg/ml adenine, biological replicate 2

hyb_protocol: Hybridization was performed by UCSD GeneChip Core, following affymetrix standard operating protocol. See www.affymetrix.com.

scan_protocol: Scan was performed with an Affymetrix 7G scanner by UCSD GeneChip Core, following affymetrix standard operating protocol. See www.affymetrix.com.

data_processing: The raw data (.CEL file) was normalized using GC RMA from the affy R package.

organism: Escherichia coli str. K-12 substr. MG1655

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

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal medium supplemented with 2 g/L glucose and cultured overnight at 37 oC with constant agitation. The cultures were inoculated into 100 mL of the fresh M9 minimal medium in either the presence or absence of 100 μg/ml adenine and continued to culture at 37 oC with constant agitation to mid-log phase.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Thermo NanoDrop 1000.

value: ∆purR

tag: growth condition

value: M9 minimal media with 100 μg/ml adenine

tag: biological replicate


title: P641

description: P641: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBlow (activated/memory) populations (CD4+CD25-CD45RBlow), replicate #4.

value: female


title: Wild type, M9 minimal medium with with 100 μg/ml adenine, 2

description: E. coli K12 MG1655, wild type cells in M9 minimal medium with 100 μg/ml adenine, biological replicate 2

treatment_protocol: The cultures were inoculated into 100 mL of the fresh M9 minimal medium in either the presence or absence of 100 μg/ml adenine and continued to culture at 37 oC with constant agitation to mid-log phase.

value: Wild type


title: P81112

description: P81112: CD4+CD25+(CD45RBlow) Treg population, replicate #1.

source_name: CD4+CD25+(CD45RBlow) Treg population


title: P8325

description: P8325: CD4+CD25+(CD45RBlow) Treg population, replicate #3.


title: Wild type, M9 minimal medium with with 100 μg/ml adenine, 1

description: E. coli K12 MG1655, wild type cells in M9 minimal medium with 100 μg/ml adenine, biological replicate 1


title: P81312

description: P81312: CD4+CD25+(CD45RBlow) Treg population, replicate #2.


title: human tumor xenograft in mouse MDA-MB-435-L1Mic-GFP polymetastasis rep 4

city: Chicago

first: Xinan

middle: "Holly"

last: Yang

state: IL

institute: universty of Chicago

description: human tumor xenograft in mouse

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 1.5 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custom designed Agilent Whole Human Genome Oligo Microarrays (GPL10749) 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.  Scan slides on GenePix 4000B at 5μm using GenePix 6.0 pro software.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 023265_D_F_20090315) to obtain background subtracted and spatially detrended gProcessed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism:
Homo sapiens
Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200-1000 ng RNA using the One-Color Agilent Quick Amp Kit  according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop software.

growth_protocol: The tail vein experimental lung colonization assay was performed to model the development of MDA-MB-435-GFP oligometastatic or polymetastatic phenotype in the lung and other organs in vivo.

extract_protocol: Total RNA from four lungs of oligometastatic animals’ tail-vein injected with L1 MDA-MB-435-GFP cells, or of polymetastatic animals receiving L1Mic MDA-MB-435-GFP cells were extracted and purified using TRIzol (Gibco/BRL) according to manufacturer’s instructions. Lung tissues were snap frozen immediately in liquid nitrogen upon resection and stored at -80 degree C.

tag: classifier

value: polymetastasis

value: lung metastases

tag: sample id

value: metastatic lung tumor in mice orginating from human MDA-MB-435-L1Mic-GFP cells

tag: source cell line

tag: mouse strain

value: nude


title: human tumor xenograft in mouse  MDA-MB-435-GFP oligometastasis rep 1

description: human tumor xenograft in mouse

value: oligometastasis

value: metastatic lung tumor in mice orginatingfrom human MDA-MB-435-GFP cells


title: human tumor xenograft in mouse  MDA-MB-435-GFP oligometastasis rep 3

description: human tumor xenograft in mouse


title: purR deletion mutant, M9 minimal medium with 100 μg/ml adenine, 1

description: E. coli K12 MG1655, ∆purR strain in M9 minimal media with 100 μg/ml adenine, biological replicate 1


title: purR deletion mutant, M9 minimal medium, 1

description: E. coli K12 MG1655, ∆purR strain in M9 minimal media, biological replicate 1

value: M9 minimal media


title: Wild type, M9 minimal medium, 2

description: E. coli K12 MG1655, wild type cells in M9 minimal medium, biological replicate 2

value: M9 minimal medium


title: P841

description: P841: CD4+CD25+(CD45RBlow) Treg population, replicate #4.

tag: strain


title: P51312

description: P51312: The splendic CD4+CD25-T cell fraction of four to six week old, naïve female C57BL/6 mice flow sorted into CD45RBhigh (naïve) populations (CD4+CD25-CD45RBhigh), replicate #2.


title: human tumor xenograft in mouse MDA-MB-435-L1Mic-GFP polymetastasis rep 2

description: human tumor xenograft in mouse


title: human tumor xenograft in mouse  MDA-MB-435-GFP oligometastasis rep 4

description: human tumor xenograft in mouse


title: human tumor xenograft in mouse MDA-MB-435-L1Mic-GFP polymetastasis rep 1

description: human tumor xenograft in mouse


title: Wild type, M9 minimal medium, 1

description: E. coli K12 MG1655, wild type cells in M9 minimal medium, biological replicate 1


title: human tumor xenograft in mouse  MDA-MB-435-GFP oligometastasis rep 2

description: human tumor xenograft in mouse


title: human tumor xenograft in mouse MDA-MB-435-L1Mic-GFP polymetastasis rep 3

description: human tumor xenograft in mouse


title: purR deletion mutant, M9 minimal medium, 2

description: E. coli K12 MG1655, ∆purR strain in M9 minimal media, biological replicate 2


title: MDA-MB-435-L1Mic (Poly-like) cell line rep 4

description: Injection of MDA-MB-435-GFP cancer cells into the mammary pat pad to develop oligo- or poly-metastasis in lung.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 1.5 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (012391) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scan slides on GenePix 4000B at 5μm using GenePix 6.0 pro software

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1_V5-95-Feb07 and Grid: 014850_D_F_20090315) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Agilent Quick Amp Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop software.

growth_protocol: All animal work was conducted in accordance with an approved protocol. Age and weight-matched NCI athymic female mice were used for all experiments. Lungs were perfused through the trachea with 2-3 ml of PBS, excised and then fixed in 10% formalin for 12 hours. Paraffin embedding, sectioning and H&E staining were performed.  A total of 5 lungs from each treatment group were examined.

extract_protocol: Total RNA from cell lines extracted and purified using TRIzol (Gibco/BRL) according to manufacturer’s instructions.

tag: cell label

value: GFP labeled


title: ActBcell

description: Mouse spleen B cell, stimulated in vitro with antiCD40, plus CpG and IL4 for 5 days    This is the only replicate

value: spleen

tag: disease state

value: healthy

value: B cells


title: RestBcell

description: Mouse B cells, resting.    This is the only replicate.

source_name: Mouse B cells, resting

tag: cell type


title: MDA-MB-435-L1Mic (Poly-like) cell line rep 3


title: MDA-MB-435-L1Mic (Poly-like) cell line rep 2


title: MCF10A_miR_221_222_mimic_3

city: South San Francisco

first: Peng

last: Yue

address: 1 DNA Way

institute: Genentech Inc

hyb_protocol: According to the manufacturer’s instruction

data_processing: Expression was normalized and estimated using RMA (bioconductor package)

extract_protocol: total cellular RNA were extracted with mirVanaTM miRNA Isolation Kit (Ambion, Austin, TX).

treatment_protocol: Three biological replicates of MCF10A cell lines transfected with either miR-221/222 or miR-control

tag: treatment


title: MCF10A_miR_control_3

scan_protocol: According to the manufacturer’s instruction

value: miR-control


title: MCF10A_miR_control_1

label_protocol: According to the manufacturer’s instruction


title: MCF10A_miR_221_222_mimic_1


title: MDA-MB-435-L1-GFP (Ol-like) cell line rep 4


title: MCF10A_miR_221_222_mimic_2