title: PrEC control-2

description: MeDIP-chip PrEC control

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 3

tag: cell line


title: PrEC control-1

status: Public on Jan 01 2014

type: genomic

city: Corvallis

first: Carmen

last: Wong

state: OR

address: 103 Milam Hall

department: Biological and Population Health Sciences

country: USA

institute: Oregon State University

description: MeDIP-chip PrEC control

hyb_protocol: Sample hybridization were done using Nimblegen Hybridization System 4 (Roche)

scan_protocol: Array scanning were done using Axon GenePix Pro 4200A (Molecular Device)

data_processing: Arrays were processed using Nimblegen's standard default protocol for Nimblescan data extraction. Attached .gff files with scaled, log2 (ChIP/Input) ratio.

molecule: genomic DNA

organism: Homo sapiens

source_name: MeDIP DNA from PrEC control

label_protocol: MeDIP and input DNA were labeled using NimbleGen Dual-Color DNA Labeling Kit per manufacturer's protocol.  MeDIP DNA was labeled with Cy5, input DNA was labeled with Cy3

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 2

extract_protocol: Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen), and fragmented using MseI restriction enzyme digestion to yield DNA fragments between 200 to 1,000 bp.  Methylated DNA was enriched using methyl-DNA immunoprecipitation (MeDIP) according to manufacturer’s protocol.  MeDIP-enriched DNA as well as input DNA was amplified with GenomePlex Complete Whole Genome Amplification kit (Sigma).

treatment_protocol: Cells were treated with vehicle control

value: PrEC

source_name: Input DNA from PrEC control


title: T1954A

type: RNA

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

institute: Moffitt Cancer Center

description:
Formalin-Fixed, Paraffin-Embedded colon tissue
TaqMan® Array Human MicroRNA Panel v1.0
miRNA

data_processing: Any raw Ct value above 32 was considered as undetectable (i.e., no expression). The endogenous gene, RNU44, showed the least variation in expression among the endogenous control genes and was used to calculate average delta-Ct by subtraction. Since delta-Ct value is reverse of the log scale of the miRNA amount, we converted the value to the log scale of the amount of miRNA by subtraction of the maximum of delta-Ct value to each delta-Ct value (i.e., miRNA expression value=maximum (delta-Ct) - delta-Ct).

label: FAM

molecule: total RNA

extract_protocol: RNA was extracted from FFPE material using the RecoverAllTM  Total Nucleic Acid Isolation kit-optimized for FFPE samples (Ambion Inc., Austin, TX

tag: corresponding to gse17536

tag: gender

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: T1102A

source_name: Formalin-Fixed, Paraffin-Embedded colon tissue

value: MALE

value: POORLY DIFF

value: dead

value: recurrence


title: T1213A


title: T251A


title: T2549C


title: RNA mixture control sample 1, batch 1, nugen

city: Toronto

first: Rui

last: Yan

address: 101 College Street

department: Informatics and Bio-computing Platform

country: Canada

institute: Ontario Institute for Cancer Research

description: Nugen

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: All analyses were performed in R (v2.15.2). Data processing was performed for each sample using RMA (affy package, v1.36.0 ) for pre-processing and updated Entrez GeneID annotation(hgu133plus2hsentrezgcdf package, v15.0.0).

label: biotin

source_name: RNA mixture control sample [Michigan reference RNA]

label_protocol: 50ng of total RNA was reverse transcribed into double-stranded cDNA and linearly amplified using the WT-Ovation Pico Kit (NuGEN Technologies, San Carlos, CA). The cDNA was fragmented and biotin labeled using the FL-Ovation cDNA biotin Module v2 (NuGEN). 200ng of total RNA was reverse transcribed into double-stranded cDNA with the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and linearly amplified using the GeneChip 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was isolated from flash-frozen cervix tissues embedded in Optimal Cutting Temperature (OCT) storage medium using the Norgen Total RNA Purification Kit (Norgen Biotek, Thorold, ON), according to manufacturer's instructions.

tag: tissue

value: control

tag: disease type

value: normal

tag: batch

tag: protocol

value: Nugen


title: T2130A

tag: corresponding to gse17536


title: kidney sample 1, batch 1, nugen

description: Nugen

source_name: normal kidney sample

value: Kidney

tag: gender


title: kidney sample 2, batch 1, nugen

description: Nugen


title: kidney sample 2, batch 1, affy_express

description: Affymetrix Express

value: Affymetrix Express


title: SKNBE2 siJMJD2B, biological rep1

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method.

source_name: Cells treated with JMJD2B siRNA for 72h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol starting with 100 ng of total RNA (GeneChip 3' IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FCS, 1% L-glutamine, 1% penicillin–streptomycin.

extract_protocol: RNeasy mini kit

treatment_protocol: Cells were transfected with 20 nM of siRNA oligos for 72 hours.

tag: cell line

tag: myc status

value: N-Myc

tag: sirna


title: kidney sample 1, batch 1, affy_express

description: Affymetrix Express


title: cervical tumour sample 86, batch3, nugen,rep2

description: Nugen

source_name: squamous cell carcinoma of the cervix

value: Cervix

value: squamous cell carcinoma

value: Female


title: cervical tumour sample 58, batch3, nugen,rep2

description: Nugen


title: cervical tumour sample 67, batch3, nugen, rep2

description: Nugen


title: T3025B1

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: MOD DIFF

value: Stage 4


title: T3702A

value: MALE

value: no; 1:metastasis):0

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: N

tag: overall survival (os)

value: alive

value: no recurrence


title: RNA mixture control sample 1, batch 1, affy_express

description: Affymetrix Express

tag: tissue

value: control

value: normal


title: T4956A1

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event

value: recurrence


title: T5102A1

tag: corresponding to gse17536

value: dead


title: T3216A

tag: gender

value: Stage 3


title: cervical tumour sample 57, batch3, nugen,rep2

description: Nugen

value: Cervix

tag: disease type

value: squamous cell carcinoma

value: Female

tag: batch

tag: protocol

value: Nugen


title: cervical tumour sample 44, batch1, nugen,rep2

description: Nugen


title: cervical tumour sample 45, batch1, nugen,rep2

description: Nugen


title: normal cervix sample 3926, batch3, nugen,rep2

description: Nugen

source_name: normal cervical epithelium


title: T2875A1

tag: t stage

value: MOD DIFF


title: T3701A1

value: MALE

tag: n stage

value: POORLY DIFF


title: LnCAP control-2

description: MeDIP-chip LnCAP control

source_name: MeDIP DNA from LnCAP control

growth_protocol: LnCAP cells were passaged in RPMI media containing 10% fetal bovine serum

tag: cell line

value: LnCAP

source_name: Input DNA from LnCAP control


title: 592 Tumor - Infiltrating component

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: Netherlands

institute: Genentech

hyb_protocol: Labelled DNA was hybridized on a 720K Nimblegen CGH array (human CGH 3x720k whole-genome tiling v3.1 arrays: GPL14965 and GPL15436), containing 719690 unique in situ synthesized 60-mer oligonucleotides, according to manufacturer’s protocol (Roche Nimblegen, Madison, USA).

scan_protocol: Slides of the arrays were scanned using a G2505C microarray scanner (Agilent Technologies).

data_processing: Data was processed using the NimbleScan sorftware provided by the vendor. The RATIO_CORRECTED value, a background corrected log2 ratio of the two color channels, was used in all subsequent analyses.

source_name: Patient 592 Tumor - Infiltrating component DNA

label_protocol: Labeling was performed using the Enzo Genomic DNA Labeling kit according to the manufacturer's instructions (Enzo Life Sciences). Briefly, 500 ng genomic DNA was combined with a mixture of primers and reaction buffer to a final volume of 39 μl. The DNA was denatured at 99°C for 10 min, and placed on ice. While on ice, 10 μl cyanine 3-dUTP and cyanine 5-dUTP nucleotide mixture was added to the test and reference DNA, respectively, and finally 1 μl Klenow DNA polymerase was added to each sample to extend the primers. After 4 hr incubation at 37°C, 5 μl stop buffer was added to stop the reaction. Label was purified using the QIAquick PCR Purification Kit (Qiagen, Westburg, Leusden, NL).

extract_protocol: Genomic DNA was isolated from 10 10 m-thick paraffin-embedded tissue sections. Sections were deparaffinated twice for 5 min in xylene, rehydrated in 100, 96 and 70% ethanol for 30 s each, stained with haematoxylin for 30 s, rinsed with water and incubated overnight in 1 m NaSCN at 37°C to remove crosslinks. Slides were rinsed twice 10 min in 1  PBS at room temperature, and completely air-dried. Tumour tissue was scraped from the glass with a scalpel to obtain at least 70% tumour cells in 200 l Qiagen ATL buffer (QIAamp® DNA extraction kit cat. 51306), transferred to eppendorf tubes and incubated with 27 l proteinase-K (20 mg/ml stock) at 450 rpm (Eppendorf® Thermomixer R) at 55°C. Three more aliquots of 27 l proteinase-K were added at 4, 20 and 28 h. After a total protK incubation of 44 h, DNA isolation proceeded as in the manufacturer's protocol (Qiagen, Cat. 51306). Samples of isolated genomic DNA were analysed by 0.8% agarose gel electrophoresis to visualise DNA concentration and size distribution. In case of tumour tissue, we scraped regions containing at least 70% tumour as indicated by an experienced breast cancer pathologist.

tag: patient

value: Tumor (Infiltrating component)

tag: molecular subtype

value: luminal

tag: age

tag: previoustreatment

value: HighDensityTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: Grade I

tag: recurrencefreesurvival

tag: overalstatus

value: death

tag: overallsurvival

source_name: Megapool reference DNA female, EA-100F

extract_protocol: aCGH reference DNA was isolated from peripheral blood lymphocytes from six apparently healthy female individuals. It was pooled and sonicated until its median fragment length was similar to that of the test samples.

tag: sample type


title: 456 LN

source_name: Patient 456 LN DNA

tag: tissue

value: LN

tag: gender

value: Grade II

value: alive

value: control


title: 425 Tumor

source_name: Patient 425 Tumor DNA

value: Tumor

value: Triple Negative


title: normal cervix sample 3856, batch1, nugen,rep2

description: Nugen

value: Cervix

tag: disease type

value: normal

value: Female

tag: batch

tag: protocol


title: cervical tumour sample 50, batch1, nugen,rep2

description: Nugen

value: squamous cell carcinoma

value: Nugen


title: 592 Tumor - Expansive component

source_name: Patient 592 Tumor - Expansive component DNA

value: Tumor (Expansive component)


title: 355 LN

source_name: Patient 355 LN DNA

value: ConventionalTreatment

value: Grade III


title: T3254B

tag: corresponding to gse17536

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: dead

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: cervical tumour sample 38, batch1, nugen, rep2

description: Nugen

tag: tissue


title: T4088A

tag: gender

value: MALE

value: POORLY DIFF

value: Y

value: alive


title: 396 LN

source_name: Patient 396 LN DNA

tag: patient

value: LN

tag: molecular subtype

value: Triple Negative

value: Female

tag: age

tag: previoustreatment

value: HighDensityTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

tag: recurrencefreesurvival

tag: overalstatus

tag: overallsurvival

tag: sample type

value: control


title: 456 Tumor

source_name: Patient 456 Tumor DNA

value: Tumor

value: luminal

value: Grade II


title: cervical tumour sample 18, batch3, nugen,rep2

description: Nugen

value: Cervix

tag: disease type

value: squamous cell carcinoma

tag: batch

tag: protocol

value: Nugen


title: Prep1deltaSM_P90

city: Nuthetal

first: Timo

last: Kanzleiter

address: Arthur-Scheunert-Alle 114

department: Experimental Diabetology

country: Germany

institute: DIfE

description:
P90
RNA from tibialis muscle of Prep1deltaSM mice.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014868 Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: tibialis anterior muscle, Prep1deltaSM

label_protocol: Cy3-labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using TRIzol reagent according to the manufacturer's instruction. RNA was subjected to DNase digestion to remove genomic DNA. Quantification of RNA was performed on a Nanodrop-1000 and RNA integrity was measured on Agilents Bioanalyzer.

tag: strain/background

tag: genotype/variation

value: male

value: 8 weeks

value: tibialis anterior muscle


title: cervical tumour sample 1, batch3, nugen, rep2

description: Nugen

tag: tissue

tag: gender


title: T5513A1.1

source_name: Formalin-Fixed, Paraffin-Embedded colon tissue

tag: corresponding to gse17536

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: POORLY DIFF

tag: ajcc staging

value: Stage 4

tag: adjuvant chemo

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event

value: recurrence


title: cervical tumour sample 14, batch3, nugen, rep2

description: Nugen

tag: disease type

value: Female

tag: batch

tag: protocol


title: 592 LN

source_name: Patient 592 LN DNA

tag: patient

tag: tissue

value: LN

tag: molecular subtype

tag: age

tag: previoustreatment

value: HighDensityTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: Grade I

tag: recurrencefreesurvival

tag: overalstatus

value: death

tag: overallsurvival

tag: sample type

value: control


title: Prep1deltaSM_P58

description:
P58
RNA from tibialis muscle of Prep1deltaSM mice.

tag: strain/background

tag: genotype/variation

tag: gender


title: 592 Tumor

source_name: Patient 592 Tumor DNA

value: Tumor

value: luminal


title: 322 LN

source_name: Patient 322 LN DNA

value: Triple Negative

value: ConventionalTreatment

value: Grade II


title: cervical tumour sample 67, batch2, affy_express, rep1

description: Affymetrix Express

source_name: squamous cell carcinoma of the cervix

value: Cervix

tag: disease type

value: squamous cell carcinoma

tag: batch

value: Affymetrix Express


title: 355 Tumor

source_name: Patient 355 Tumor DNA

tag: patient

value: Grade III


title: 841 Tumor

source_name: Patient 841 Tumor DNA

tag: tissue


title: Prep1deltaSM_P54

description:
P54
RNA from tibialis muscle of Prep1deltaSM mice.

value: male

value: 8 weeks

value: tibialis anterior muscle


title: 322 Tumor

source_name: Patient 322 Tumor DNA

tag: molecular subtype

value: Female


title: 881 LN

source_name: Patient 881 LN DNA

value: LN

tag: age

value: HighDensityTreatment


title: 881 Tumor

source_name: Patient 881 Tumor DNA

tag: previoustreatment

value: death

source_name: Megapool reference DNA female, EA-100F


title: cervical tumour sample 86, batch2, affy_express,rep1

description: Affymetrix Express

tag: protocol


title: Prep1f/+_P66

description:
P66
RNA from tibialis muscle of Prep1f/+ mice.

source_name: tibialis anterior muscle, Prep1f/+


title: Prep1f/+_P86

description:
P86
RNA from tibialis muscle of Prep1f/+ mice.


title: 245 LN

source_name: Patient 245 LN DNA

tag: numberpositivelymphnodes

tag: tumorstage

value: control


title: cervical tumour sample 58, batch1, affy_express,rep1

description: Affymetrix Express


title: 841 LN

source_name: Patient 841 LN DNA

tag: grade

tag: recurrencefreesurvival


title: 795 LN

source_name: Patient 795 LN DNA

tag: overalstatus

value: alive

tag: overallsurvival


title: AML-blast cell sample-7330

city: Rotterdam

first: Maarten

last: Fornerod

address: Dr. Molewaterplein 50

department: Cell Biology

institute: ErasmusMC

description: Test

data_processing: Raw Ct-values were analyzed, summarized and exported per plate using SDS 2.3 (Applied Biosystems). Baseline was manually set at 0.15 for all plates. All data mining and analyses were done in R 2.11.1.4 Per card type, Ct-values were imported (readCtData) into a qPCR-set using the package HTqPCR.5 The average cycle threshold (Ct) value was used to calculate microRNA expression levels relative to the expression level of the small reference RNAs (mean of (mean) Mamm-U6, RNU44 and RNU48) by use of the comparative cycle time (ΔCt) method. Non detected miRNAs were substituted by an artificial low level of expression of -25.

label: SYBR Green

source_name: AML blast cells

label_protocol: MicroRNA expression was measured on Taqman® Array MicroRNA Cards v2.0 using Taqman technology in the 7900 HT Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) according to the manufacturers' protocol.

growth_protocol: Viably frozen diagnostic bone marrow or peripheral blood samples from a selection of 90 de novo pediatric AML cases were provided by the Dutch Childhood Oncology Group (DCOG), the AML ‘Berlin-Frankfurt-Münster’ Study Group (AML-BFM-SG), the Czech Pediatric Hematology Group (CPH), and the St. Louis Hospital in Paris, France.

extract_protocol: Total cellular RNA was isolated using Trizol reagent (Invitrogen, Breda, The Netherlands) as previously described (Van Vlierberghe P, van Grotel M, Beverloo HB, Lee C, Helgason T, Buijs-Gladdines J, et al. The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia. Blood 2006;108:3520–9.).

tag: tumor stage

value: Initial

tag: genetic aberration

value: MLL-rearranged


title: Prep1deltaSM_P70

description:
P70
RNA from tibialis muscle of Prep1deltaSM mice.

source_name: tibialis anterior muscle, Prep1deltaSM

tag: strain/background

tag: genotype/variation

tag: gender


title: cervical tumour sample 57, batch1, affy_express,rep1

description: Affymetrix Express

tag: disease type

tag: batch


title: cervical tumour sample 27, batch1, nugen,rep2

description: Nugen

tag: tissue

value: Nugen


title: AML-blast cell sample-7326

description: Test


title: AML-blast cell sample-7194

description: Test


title: cervical tumour sample 50, batch1, affy_express,rep1

description: Affymetrix Express


title: Prep1f/+_P62

description:
P62
RNA from tibialis muscle of Prep1f/+ mice.

tag: age


title: ChIP-chip profile of Khd1-RNase cells

city: Boston

first: Suzanne

last: Komili

state: MA

address: 44 Binney St.

institute: Harvard University

hyb_protocol: Labeled cDNA was centrifuged, washed once with 75% ethanol, and air-dried in the dark.  Pellets were resuspended in 10μL ddH20 and combined.  We then added 2.73μL 10mg/mL salmon sperm DNA (pre-boiled), 2.73μL 10mg/mL yeast tRNA (Sigma), and 54.5μL DIG Easy Hybe solution and incubated at 65oC for 2 minutes.  Samples were applied to arrays by pipetting along the lifterslip coverslip (Erie Scientific) and incubated for 16 hours at 37oC.  Arrays were disassembled in 1xSSC, washed three times at 50oC for ten minutes each in 1xSSC, 0.1% SDS, rinsed briefly in 1xSSC, and centrifuged for 5 minutes at 1000rpm to dry.

scan_protocol: Image scanning hardware and software:  Genepix 4.0

data_processing: Normalization and transformation performed by Rosetta Resolver.

label: Cy5/Cy3 (fluors were swapped on alternate replicates)

organism: Saccharomyces cerevisiae

source_name: Khd1 IP'd DNA

label_protocol: The amplified chromatin was labeled with either Cy3 or Cy5-dUTP using one round of PCR with Klenow and random primers.

growth_protocol: Cultures were grown to early log phase (OD260 0.4-0.6) at 30oC.

extract_protocol: 50mL cultures of Loc1-myc9, Khd1-myc9, and Puf6-myc9 cultures were grown to log phase (OD600 0.4 – 0.6) in YPD, crosslinked by the addition of 1.4mLs of 30% formaldehyde and incubated at 30oC for 5 minutes.  Cells were lysed in 50mM HEPES-KOH ph 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM phenylmethylsulphonyl fluoride, 3 ng/ml each: pepstatin, leupeptin, aprotinin, antipain, and chymostatin (“lysis buffer” hereafter) with glass beads.  We pelleted the chromatin and sonicated to ~400bp resolution, extracted the soluble fraction.  The soluble fraction was either incubated with dynal beads pre-incubated with myc 9E11 or with no beads or antibody overnight at 4oC.  Beads were either treated with 33uL of an RNase coctail (Ambion) for 30 minutes at room temperature or incubated without RNase treatment for the same time at room temperature.  Beads were then washed and the protein was eluted and de-crosslinked, then degraded by Proteinase K digestion.  DNA was precipitated, RNAse-treated, and amplified by ligation-mediated PCR.

tag: sample type

value: Khd1 IP

value: Khd1-myc9 in W303 cells

tag: treatment

value: RNAase for 30 minutes

label: Cy5/Cy3 (fluors were swapped on certain replicates)

source_name: Khd1 whole-cell extract DNA

value: input DNA


title: cervical tumour sample 45, batch2, affy_express,rep1

description: Affymetrix Express

value: Cervix

value: squamous cell carcinoma

tag: protocol

value: Affymetrix Express


title: AML-blast cell sample-7190

description: Test


title: ChIP-chip profile of Puf6-RNase cells

source_name: Puf6 IP'd DNA

value: Puf6 IP

value: Puf6-myc9 in W303 cells

source_name: Puf6 whole-cell extract DNA


title: P12_5

city: Cambridge

first: Tsute

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

description:
Sample_44
RNA expression signals in POD12 Wound infected with Pa

hyb_protocol: Labeling and hybridization was performed according to standard Agilent recommended protocols.

scan_protocol: Scanning was performed according to standard Agilent recommended protocols.

data_processing: Data preprocessing was performed using the Bioconductor Agi4x44PreProcess package.The Agilent Feature Extraction (AFE) algorithm was used for image analysis and background correction. Quantile normalization was then used to correct for the non-biological variations across arrays.

label: total RNA

organism: Oryctolagus cuniculus

source_name: POD12 Wound infected with Pa

label_protocol: Total RNA were labeled with the One-Color Quick-Amp Labeling Kit (Agilent Technologies

extract_protocol: Total RNA was isolated according to the manufacturer’s protocol. Contaminating genomic DNA during RNA preparation was removed using the Turbo DNA-free kit (Ambion, Austin, TX). In general, 1 µg of RNA was obtained from each wound. The quantity and quality (Absorbance 260/Absorbance 280 ratio, 28s/18s RNA ratio, RNA integrity number) of the extracted RNA was determined using a NanoDrop 2000C UV-Vis Spectrophotometer (Thermo Scientific, Wilmington, DE) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.

treatment_protocol: The dermal layer on the dorsal side of the ear wound was removed and the wound bed was punched out and samples of all wounds were frozen in RNAlater (Ambion, Austin, TX) at -80oC for molecular analysis. Wound samples were homogenized using a Mini-bead beater-8 (Biospec Products Inc, Bartlesville, OK) using Zirconia beads (2.0 mm diameter, Biospec Products Inc) in the presence of Trizol Reagent (Sigma-Aldrich, St. Louis, MO)

tag: condition id

tag: rabbit id

value: Pseudo 2

value: Pseudo POD12

tag: wound id

tag: array id


title: ChIP-chip profile of Loc1-RNase cells

source_name: Loc1 IP'd DNA

value: Loc1 IP

value: Loc1-myc9 in W303 cells

source_name: Loc1 whole-cell extract DNA


title: cervical tumour sample 44, batch1, affy_express,rep1

description: Affymetrix Express

source_name: squamous cell carcinoma of the cervix

value: Female


title: AML-blast cell sample-7183

description: Test

value: Initial


title: P12_4

description:
Sample_43
RNA expression signals in POD12 Wound infected with Pa


title: 788 LN

source_name: Patient 788 LN DNA

tag: patient

value: LN

tag: molecular subtype

value: Triple Negative

tag: previoustreatment

value: HighDensityTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: Grade III

tag: recurrencefreesurvival

tag: overalstatus

value: alive

tag: overallsurvival

value: control


title: 788 Tumor

source_name: Patient 788 Tumor DNA

tag: tissue

value: Tumor

tag: gender

tag: age


title: normal cervix sample 3926, batch2, affy_express,rep1

description: Affymetrix Express

source_name: normal cervical epithelium

value: Cervix

tag: disease type

value: normal

tag: batch

tag: protocol


title: 524 Tumor

source_name: Patient 524 Tumor DNA

value: luminal

value: Grade II

value: death

source_name: Megapool reference DNA female, EA-100F

tag: sample type


title: ChIP-chip profile of Puf6+RNase cells

value: Puf6 IP

tag: genotype/variation

value: Puf6-myc9 in W303 cells

tag: treatment

value: RNAase for 30 minutes

value: input DNA


title: P12_2

description:
Sample_41
RNA expression signals in POD12 Wound infected with Pa

tag: condition id

tag: rabbit id

value: Pseudo 2

value: Pseudo POD12

tag: wound id

tag: array id


title: P12_3

description:
Sample_42
RNA expression signals in POD12 Wound infected with Pa


title: normal cervix sample 3856, batch2, affy_express,rep1

description: Affymetrix Express

value: Female

value: Affymetrix Express


title: AML-blast cell sample-672

description: Test

tag: tumor stage

value: Initial

tag: genetic aberration


title: AML-blast cell sample-7153

description: Test

value: MLL-rearranged


title: 229 LN

source_name: Patient 229 LN DNA

tag: patient

value: LN

tag: molecular subtype

tag: previoustreatment

value: ConventionalTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: Grade III

tag: recurrencefreesurvival

tag: overalstatus

value: control


title: Prep1f/+_P286

description:
P286
RNA from tibialis muscle of Prep1f/+ mice.

source_name: tibialis anterior muscle, Prep1f/+

tag: strain/background

tag: gender

value: male

tag: age

value: 8 weeks

tag: tissue

value: tibialis anterior muscle


title: ChIP-chip profile of Loc1+RNase cells

tag: sample type

value: Loc1 IP

tag: genotype/variation

value: Loc1-myc9 in W303 cells

tag: treatment


title: 104 LN

source_name: Patient 104 LN DNA

value: luminal

value: Grade I

value: alive

tag: overallsurvival


title: 565 LN

source_name: Patient 565 LN DNA

value: Grade II

value: death


title: K12_5

description:
Sample_39
RNA expression signals in POD12 Wound infected with Kp

source_name: POD12 Wound infected with Kp

tag: condition id

tag: rabbit id

value: Kleb 1

value: Kleb POD12

tag: wound id

tag: array id


title: AML-blast cell sample-5644

description: Test

source_name: AML blast cells

tag: tumor stage

value: Initial

tag: genetic aberration


title: AML-blast cell sample-5237

description: Test


title: cervical tumour sample 27, batch1, affy_express,rep1

description: Affymetrix Express

value: Cervix

tag: disease type

value: squamous cell carcinoma

value: Female

tag: batch

tag: protocol

value: Affymetrix Express


title: ChIP-chip profile of Khd1 cells

source_name: Khd1 IP'd DNA

extract_protocol: 50mL cultures of Loc1-myc9, Khd1-myc9, and Puf6-myc9 cultures were grown to log phase (OD600 0.4 – 0.6) in YPD, crosslinked by the addition of 1.4mLs of 30% formaldehyde and incubated at 30oC for 20 minutes.  Cells were lysed in 50mM HEPES-KOH ph 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM phenylmethylsulphonyl fluoride, 3 ng/ml each: pepstatin, leupeptin, aprotinin, antipain, and chymostatin (“lysis buffer” hereafter) with glass beads.  We pelleted the chromatin and sonicated to ~400bp resolution, extracted the soluble fraction.  The soluble fraction was either incubated with dynal beads pre-incubated with myc 9E11 or with no beads or antibody overnight at 4oC.  Beads were washed and the protein was eluted and de-crosslinked, then degraded by Proteinase K digestion.  DNA was precipitated, RNAse-treated, and amplified by ligation-mediated PCR.

value: Khd1 IP

value: Khd1-myc9 in W303 cells

source_name: Khd1 whole-cell extract DNA

value: input DNA


title: cervical tumour sample 18, batch2, affy_express,rep1

description: Affymetrix Express


title: AML-blast cell sample-5236

description: Test


title: K12_4

description:
Sample_38
RNA expression signals in POD12 Wound infected with Kp


title: ChIP-chip profile of Loc1 cells

value: Loc1 IP


title: K12_3

description:
Sample_37
RNA expression signals in POD12 Wound infected with Kp


title: 229 Tumor

source_name: Patient 229 Tumor DNA

tag: patient

value: Tumor

tag: molecular subtype

tag: previoustreatment

value: ConventionalTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: Grade III

tag: recurrencefreesurvival

tag: overalstatus

value: control


title: 524 LN

source_name: Patient 524 LN DNA

tag: tissue

value: LN

value: luminal

tag: gender

tag: age

value: HighDensityTreatment

value: Grade II

tag: overallsurvival

tag: sample type


title: C4_4

description:
Sample_36
RNA expression signals in POD4 Wound Control

source_name: POD4 Wound Control

tag: condition id

tag: rabbit id

value: Control 2?

tag: treatment

value: Ctrl POD4

tag: wound id

tag: array id


title: cervical tumour sample 1, batch2, affy_express, rep1

description: Affymetrix Express

source_name: squamous cell carcinoma of the cervix

value: Cervix

tag: disease type

value: squamous cell carcinoma

tag: batch

tag: protocol


title: ChIP-chip profile of Puf6 cells

source_name: Puf6 IP'd DNA

treatment_protocol: Strain: Puf6-myc9 in W303 cells

value: Puf6 IP

tag: genotype/variation

value: Puf6-myc9 in W303 cells

source_name: Puf6 whole-cell extract DNA


title: 565 Tumor

source_name: Patient 565 Tumor DNA

tag: patient

tag: molecular subtype

value: Female

tag: previoustreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: death


title: C4_3

description:
Sample_35
RNA expression signals in POD4 Wound Control

value: Control 2


title: 782 Tumor

source_name: Patient 782 Tumor DNA

tag: tissue

value: Tumor

tag: gender

tag: age

tag: recurrencefreesurvival

tag: overalstatus

tag: overallsurvival


title: AML-blast cell sample-5179

description: Test

tag: tumor stage

value: Initial

tag: genetic aberration


title: ChIP-chip profile of Khd1+RNase cells

tag: sample type

value: Khd1 IP

value: Khd1-myc9 in W303 cells

tag: treatment

value: RNAase for 30 minutes

value: input DNA


title: AML-blast cell sample-5178

description: Test


title: Transcriptional profile of khd1- cells

source_name: Khd1- cells

growth_protocol: Cultures were grown to early log phase (OD260 0.2-0.4) at 30oC.

extract_protocol: 50mL cultures were grown in YPD to early log phase (OD260 0.2-0.4) at 30oC, centrifuged at room temperature and flash-frozen using liquid nitrogen.  mRNA was extracted from cell pellets using the hot phenol method and precipitated overnight in ethanol.  The mRNA was reverse-transcribed using a poly-T oligo and Superscript III Reverse Transcriptase, and the resulting cDNA was labeled with either Cy3 or Cy5-dUTP using one round of PCR with Klenow and random primers.  Labeled cDNA was hybridized to microarrays containing all yeast ORFs.

tag: genotype/variation

tag: background strain

source_name: Wild-type

value: Wild-type


title: A_lipoferum_4B_nipponbare_roots_rep1

city: Villeurbanne

first: Benoît

last: DROGUE

state: Rhône-Alpes

address: Boulevard du 11 novembre

department: Université Lyon 1

country: France

institute: Université de Lyon

description: This sample is the first replicate of Azospirillum lipoferum 4B cells recovered from Nipponbare roots incubated 7 day in growth chamber

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

scan_protocol: Scanner model is GenePix 4000B.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) using a quantile normalization (Bolstad et al. Bioinformatics 19(2):185) for RMA background correction and (ii) a median polish summarization to summarize probe data into gene level signal values. The median value was used for the replicate method.

organism: Azospirillum lipoferum 4B

source_name: A. lipoferum 4B nipponbare roots

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

growth_protocol: Before inoculation, Azospirillum lipoferum 4B cells were grown overnight in Nfbm medium (Vial et al. J. Bacteriol. 108:5364-75). Bacterial cells were harvested in the late-exponential phase (at OD580 around 1.2), centrifuged and resuspended in a defined volume of 0.8% NaCl to obtain 2 x109 cells mL-1. Then, 109 cells were mixed with 50 ml plant agar (8 g l-1) and introduced into 120 × 120 × 17 mm square plates.All the plates were incubated vertically, for 7 d in a growth chamber (MLR350, SANYO, UK) with a photoperiod of 16 h at 28°C (light 150 μE m-2 s-1), and 8 h at 22°C in the dark.

extract_protocol: For each condition, the bacterial cell pellet was resuspended in 960 µl of suspension buffer (Environ. Microbiol. 14:2645-2660) and transferred in 1.5 ml tubes containing 400 mg of glass beads (Sigma). Cell lysis was realized by shaking twice for 1 min with the TissueLyser II equipment (Qiagen); after a centrifugation of 5 min, at 4°C, 13,000 rpm, the aqueous phase containing ribonucleic acids was taken, and 1 ml of TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA) was added. After incubation of 5 min at room temperature, 100 µl of phenol/chloroform/isoamyl alcohol (25:24:1) were added, the samples were homogenized, incubated during 5 min at room temperature and centrifuged for 10 min, at 4°C, 13,000 rpm. A second phenol/chloroform/isoamyl alcohol extraction (200 µl) was done and ribonucleic acids were precipitated overnight at -20°C in a solution containing 2 volumes of 100 % ethanol, 0.1 volume of 7.5 M ammonium acetate and 0.01 volume of 5 mg ml-1 glycogen. Samples were centrifuged during 15 min, at 4°C, 13,000 rpm and the pellets were rinsed twice with 70 % ethanol before resuspension. PCR (16S rrna) on all samples confirmed that the DNase I (Invitrogen) treatment had removed all remaining DNA. RNA integrity was assessed using Agilent RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and the Agilent 2100 Bioanalyzer (Agilent Technologies) device.

tag: lifestyle

value: Sessile associated to Nipponbare roots

tag: daypostinoculation


title: A_lipoferum_4B_cigalon_roots_rep2

description: This sample is the second replicate of Azospirillum lipoferum 4B cells recovered from Cigalon roots incubated 7 day in growth chamber

source_name: A. lipoferum 4B cigalon roots

value: Sessile associated to Cigalon roots


title: AML-blast cell sample-5175

description: Test


title: AML-blast cell sample-5170

description: Test


title: 61 LN

source_name: Patient 61 LN DNA

tag: patient

value: LN

tag: molecular subtype

value: Triple Negative

tag: previoustreatment

value: ConventionalTreatment

tag: numberpositivelymphnodes

value: Grade II

source_name: Megapool reference DNA female, EA-100F

value: control


title: C4_2

description:
Sample_34
RNA expression signals in POD4 Wound Control

tag: condition id

tag: rabbit id

value: Ctrl POD4

tag: wound id

tag: array id


title: RNA IP/Whole-cell extract for Loc1

source_name: Loc1 IP'd RNA

label_protocol: The resulting cDNA was labeled with either Cy3 or Cy5-dUTP using one round of PCR with Klenow and random primers.

extract_protocol: 500mL cultures of PSY2546 (Loc1-myc6/loc1Δ) and PSY2547 (Loc1/loc1Δ) cultures were grown to early-log phase (1-2×107 cells/ml) in YPD and lysed in phosphate-buffered saline with 2mM MgCl2, 1mM ethylenediamine tetra-acetic acid, 0.2% Triton X-100, 1mM phenylmethylsulphonyl fluoride, 3 ng/ml each: pepstatin, leupeptin, aprotinin, and chymostatin; 2 U/ml RNasein (Promega) and 1 U/ml SuperRNasin (Ambion) (“lysis buffer” hereafter) with glass beads.  We diluted the lysates to 10mg/ml total protein, combined them with c-myc (9E10) agarose conjugate beads (1mL lysate and 250μL of a 50% bead slurry in lysis buffer) and 1000U RNase-free DNase I (Roche), and incubated at 4oC for 4H.  The beads were washed five times with lysis buffer and the resulting protein was eluted by a 10 minute incubation at 65oC in RNase-free solution containing 10mM Tris-Cl, 10mM EDTA, and 0.5% SDS.  Whole-cell extracts were given identical treatments as the immunoprecipitations except for the addition of beads and subsequent wash and elution steps.  RNA was isolated from all samples by Trizol extraction and ethanol precipitation.  Reverse-transcription and cDNA amplification were performed using Clontech’s SMART PCR kit.

value: Loc1 IP

value: PSY2546 (Loc1-myc6/loc1delta)

source_name: Loc1 whole-cell extract RNA

value: PSY2547 (Loc1/loc1delta)


title: Whole-cell extract for Loc1-myc6/Whole-cell extract for Loc1

source_name: Loc1-myc Whole-cell Extract RNA


title: cervical tumour sample 14, batch2, affy_express, rep1

description: Affymetrix Express

tag: tissue

value: Cervix

tag: disease type

value: squamous cell carcinoma

tag: gender

value: Female

tag: batch

tag: protocol

value: Affymetrix Express


title: RNA IP/mock IP for Loc1

tag: sample type

value: IP

tag: genotype/variation

source_name: Loc1 mock IP

extract_protocol: 500mL cultures of PSY2546 (Loc1-myc6/loc1?) and PSY2547 (Loc1/loc1?) cultures were grown to early-log phase (1-2×107 cells/ml) in YPD and lysed in phosphate-buffered saline with 2mM MgCl2, 1mM ethylenediamine tetra-acetic acid, 0.2% Triton X-100, 1mM phenylmethylsulphonyl fluoride, 3 ng/ml each: pepstatin, leupeptin, aprotinin, and chymostatin; 2 U/ml RNasein (Promega) and 1 U/ml SuperRNasin (Ambion) (?lysis buffer? hereafter) with glass beads. We diluted the lysates to 10mg/ml total protein, combined them with c-myc (9E10) agarose conjugate beads (1mL lysate and 250?L of a 50% bead slurry in lysis buffer) and 1000U RNase-free DNase I (Roche), and incubated at 4oC for 4H. The beads were washed five times with lysis buffer and the resulting protein was eluted by a 10 minute incubation at 65oC in RNase-free solution containing 10mM Tris-Cl, 10mM EDTA, and 0.5% SDS. Whole-cell extracts were given identical treatments as the immunoprecipitations except for the addition of beads and subsequent wash and elution steps. RNA was isolated from all samples by Trizol extraction and ethanol precipitation. Reverse-transcription and cDNA amplification were performed using Clontech's SMART PCR kit.


title: AML-blast cell sample-5165

description: Test

source_name: AML blast cells

tag: tumor stage

value: Initial

tag: genetic aberration

value: MLL-rearranged


title: K12_1

description:
Sample_31
RNA expression signals in POD12 Wound infected with Kp

source_name: POD12 Wound infected with Kp

value: Kleb 1

tag: treatment

value: Kleb POD12


title: A_lipoferum_4B_artificial_roots_rep2

description: This sample is the second replicate of Azospirillum lipoferum 4B cells recovered from cellulose acetate filters incubated 7 day in growth chamber

source_name: A. lipoferum 4B artificial roots

tag: lifestyle

value: Sessile associated to Artificial roots

tag: daypostinoculation


title: C4_1

description:
Sample_33
RNA expression signals in POD4 Wound Control

source_name: POD4 Wound Control

value: Control 1


title: Transcriptional profile of puf6- cells

source_name: Puf6- cells

label_protocol: The mRNA was reverse-transcribed using a poly-T oligo and Superscript III Reverse Transcriptase, and the resulting cDNA was labeled with either Cy3 or Cy5-dUTP using one round of PCR with Klenow and random primers.

tag: background strain

value: wild type


title: AML-blast cell sample-7171

description: Test


title: A_lipoferum_4B_cigalon_roots_rep1

description: This sample is the first replicate of Azospirillum lipoferum 4B cells recovered from Cigalon roots incubated 7 day in growth chamber

value: Sessile associated to Cigalon roots


title: A_lipoferum_4B_nipponbare_roots_rep2

description: This sample is the second replicate of Azospirillum lipoferum 4B cells recovered from Nipponbare roots incubated 7 day in growth chamber

value: Sessile associated to Nipponbare roots


title: A_lipoferum_4B_artificial_roots_rep1

description: This sample is the first replicate of Azospirillum lipoferum 4B cells recovered from cellulose acetate filters incubated 7 day in growth chamber


title: AML-blast cell sample-5183

description: Test


title: C12_5

description:
Sample_30
RNA expression signals in POD12 Wound Control

source_name: POD12 Wound Control

tag: condition id

value: Ctrl POD12


title: C12_4

description:
Sample_29
RNA expression signals in POD12 Wound Control

tag: rabbit id


title: AML-blast cell sample-5156

description: Test


title: AML-blast cell sample-5154

description: Test


title: A_lipoferum_4B_liquid_culture_rep2

description: This sample is the second replicate of late exponential phase Azospirillum lipoferum 4B liquid culture in Nfbm medium

source_name: A. lipoferum 4B liquid culture

value: Planktonic


title: AML-blast cell sample-5152

description: Test


title: AML-blast cell sample-5157

description: Test


title: AML-blast cell sample-5148

description: Test


title: AML-blast cell sample-5146

description: Test


title: AML-blast cell sample-5147

description: Test


title: V583 with vancomycin at 30 min_TCR0040

city: Oeiras

first: Neuza

last: Teixeira

address: Av. da República, Estação Agronómica Nacional

country: Portugal

institute: ITQB

description: Gene expression data from E. faecalis V583 after 30 minutes of vancomycin addition.

hyb_protocol: Samples were hybridized to a previously described custom E. faecalis Affymetrix GeneChip.

scan_protocol: GeneChips were scanned at the University of Iowa DNA Core Facility.

data_processing: Data was analyzed using Affymetrix GeneChip Operating Software, which identifies probe sets with statistically significant hybridization over background (i.e. presence versus absence calls) and among those, identifies probe sets for which hybridization is significantly increased or decreased in pairwise comparisons of microarray experiments. Signal log ratios for differentially expressed probe sets were averaged and converted to fold change values.

organism: Enterococcus faecalis V583

source_name: E. faecalis V583 with vancomycin at 30 min

label_protocol: Biotinylated cRNA were prepared with the BioArray Terminal Labeling Kit (Enzo Life Sciences).

growth_protocol: E. faecalis strains were grown in BHI, at 37ºC, until 0.4 OD (600nm). At this point, purified GBAP was added to a final concentration of 10nM in the culture. For others samples we did the same protocol but without GBAP.

extract_protocol: RNA was stabilized with RNA protect (Qiagen) and RNA was isolated with RNeasy columns per the manufacturer's instructions (Qiagen). Samples were treated with RNase-free DNase I (Roche) to remove contaminating DNA

tag: agent

value: vancomycin

tag: time

value: 30 min


title: AML-blast cell sample-5153

description: Test


title: V583 without vancomycin at 30 min_TCR0038

description: Gene expression data from E. faecalis V583 after 30 minutes without vancomycin.

source_name: E. faecalis V583 without vancomycin at 30 min

value: without vancomycin


title: C12_2

description:
Sample_27
RNA expression signals in POD12 Wound Control

tag: wound id

tag: array id


title: V583 with vancomycin at 10 min_TCR0035

description: Gene expression data from E. faecalis V583 after  10 minutes of vancomycin addition.

source_name: E. faecalis V583 with vancomycin at 10 min

value: 10 min


title: cervical tumour sample 38, batch1, affy_express, rep1

description: Affymetrix Express

source_name: squamous cell carcinoma of the cervix

tag: tissue

value: Cervix

tag: disease type

value: squamous cell carcinoma

tag: gender

value: Female

value: Affymetrix Express


title: C12_3

description:
Sample_28
RNA expression signals in POD12 Wound Control


title: V583 with vancomycin at 10 min_TCR0039


title: P6_5

description:
Sample_25
RNA expression signals in POD6 Wound infected with Pa

source_name: POD6 Wound infected with Pa

value: Pseudo 1

value: Pseudo POD6


title: P6_2

description:
Sample_22
RNA expression signals in POD6 Wound infected with Pa


title: AML-blast cell sample-5145

description: Test

value: Initial


title: AML-blast cell sample-5143

description: Test


title: V583 without vancomycin at 30 min_TCR0034


title: P6_1

description:
Sample_21
RNA expression signals in POD6 Wound infected with Pa


title: C12_1

description:
Sample_26
RNA expression signals in POD12 Wound Control

value: Control 1


title: K6_2

description:
Sample_18
RNA expression signals in POD6 Wound infected with Kp

source_name: POD6 Wound infected with Kp

value: Kleb 2

value: Kleb POD6


title: V583 with vancomycin at 30 min_TCR0036


title: V583 without vancomycin at 10 min_TCR0037

description: Gene expression data from E. faecalis V583 after 10 minutes without vancomycin.

source_name: E. faecalis V583 without vancomycin at 10 min


title: AML-blast cell sample-5115

description: Test

value: MLL-rearranged


title: V583 without vancomycin at 10 min_TCR0033


title: K6_4

description:
Sample_19
RNA expression signals in POD6 Wound infected with Kp


title: K6_5

description:
Sample_20
RNA expression signals in POD6 Wound infected with Kp


title: P6_3

description:
Sample_23
RNA expression signals in POD6 Wound infected with Pa


title: K6_3

description:
Sample_17
RNA expression signals in POD6 Wound infected with Kp


title: A_lipoferum_4B_liquid_culture_rep1

description: This sample is the first replicate of late exponential phase Azospirillum lipoferum 4B liquid culture in Nfbm medium


title: AML-blast cell sample-5023

description: Test


title: whole blood_xen29 injection_24 h_rep3

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: 1X108 bacteria in 100 ul PBS and injection subcutaneouly in the back of mice via Fr. 25 needle

hyb_protocol: The pre-hybridization of MRmiOA v4 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on MRmiOA v4 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 520 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The data processing was processed by R program (2.12.1). Import Foreground value of each miRNA probes in triplicates from GPR files. Filter out probes that ﬂag <0 in all samples. Combined repeated probes within one chip by median then normalized them by 75% media scaling between arrays.

source_name: whole blood

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy5, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

growth_protocol: No growth protocol

extract_protocol: RNA extraction by RNeasy Protect Animal Blood Kit (QIAGEN Cat. no. 73224). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧5).

treatment_protocol: The recombinant specific Gram negative pathogens Escherichia coli (xen14) and Gram positive pathogens Staphyllococcus aureus (xen29) were purchased from the Caliper (Caliper, Princeton, NJ, USA). 1×108 Escherichia coli or Staphyllococcus aureus pathogen in 100 μl PBS was injected subcutaneously with Fr. 25 needle into the back of the mice to cause bacterial infection of the mice. An extra group of animals was inoculated with PBS to serve as a negative control. The mice had access to food and water ad libitum both before and after bacteria injection. The mice were killed at the indicated time points (4, 8, and 24 h) after the bacteria injection, and whole blood was drawn.

tag: strain

tag: treatment injection

value: xen29 in 100 ul PBS

tag: kill time


title: whole blood_xen29 injection_24 h_rep2


title: K6_1

description:
Sample_16
RNA expression signals in POD6 Wound infected with Kp

value: Kleb 1


title: AML-blast cell sample-5017

description: Test

tag: tumor stage

tag: genetic aberration


title: AML-blast cell sample-4770

description: Test


title: AML-blast cell sample-4769

description: Test


title: AML-blast cell sample-4745

description: Test


title: whole blood_xen29 injection_8 h_rep1


title: AML-blast cell sample-4742

description: Test


title: whole blood_xen29 injection_8 h_rep3


title: whole blood_xen29 injection_8 h_rep2


title: whole blood_xen14 injection_24 h_rep3

value: xen14 in 100 ul PBS


title: whole blood_xen29 injection_24 h_rep1


title: C6_3

description:
Sample_13
RNA expression signals in POD6 Wound Control

source_name: POD6 Wound Control

tag: treatment

value: Ctrl POD6


title: C6_5

description:
Sample_15
RNA expression signals in POD6 Wound Control


title: C6_4

description:
Sample_14
RNA expression signals in POD6 Wound Control


title: C6_2

description:
Sample_12
RNA expression signals in POD6 Wound Control


title: P4_2

description:
Sample_08
RNA expression signals in POD4 Wound infected with Pa

source_name: POD4 Wound infected with Pa

value: Pseudo 2

value: Pseudo POD4


title: P4_4

description:
Sample_10
RNA expression signals in POD4 Wound infected with Pa


title: AML-blast cell sample-4720

description: Test

source_name: AML blast cells


title: C6_1

description:
Sample_11
RNA expression signals in POD6 Wound Control


title: whole blood_xen14 injection_24 h_rep2


title: AML-blast cell sample-4740

description: Test


title: whole blood_xen14 injection_24 h_rep1


title: whole blood_xen14 injection_8 h_rep3


title: P4_3

description:
Sample_09
RNA expression signals in POD4 Wound infected with Pa


title: NHNP 2d

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: The labeled input DNA was precipitated with 11.5 µl 5M NaCl and 1 volume isopropanol, and hybridized in 14.4 µl HybridizationMix containing 2x Hybridization buffer, Hybridization Component A and alignment oligos together with 5.6 µl sample tracking control. Arrays were hybridized in Maui hybridization stations for 40-48h h at 42C, and then washed in wash-buffer I, II, III containing 0,1 % 1M DTT.Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf)

scan_protocol: Arrays were scanned on an nimblegen MS2000 scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.6 ChIP data extraction. Spatial correction is applied to the raw signal intensities. Cy3 and cy5 signal intensities are normalized to one another using qspline normalization (Workmann C et al., 2002). These conversions were made using the software Roche NimbleGen SignalMap v1.9. The processed data files contain the log2-intensity values for each feature for the 532nm and 635nm channel and the ratio of the two channels.

source_name: 2d differentiated NHNP cells

label_protocol: 1 µg input DNA was directly labeled by Klenow (nimblegen) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

extract_protocol: Genomic DNA was isolated using NaCl/chloroform extraction.

treatment_protocol: differentiated for 2d

tag: cell type

value: normal neural progenitor cells

source_name: peripheral blood

tag: sample type

value: mixed genomic DNA from male and female lymphocytes


title: AML-blast cell sample-4717

description: Test


title: AML-blast cell sample-4713

description: Test


title: AML-blast cell sample-4718

description: Test


title: whole blood_xen14 injection_8 h_rep2


title: T00_006J

city: Philadelphia

first: Daria

last: Babushok

state: PA

address: 3615 Civic Center Blvd, ARC 302

institute: University of Pennsylvania

description: Genomic DNA extracted from bone marrow aspirates was genotyped using Infinium Human Quad610 Genotyping Beadchips (Illumina).

hyb_protocol: a high-throughput Illumina BeadLab Genotyping System that uses standard operating procedures based on

scan_protocol: the manufacturer’s specifications.

data_processing:
SNP Array genotyping methods have been previously described in Hakonarsson et al. Nature 448, 591-594 (2 August 2007)
Image data was analyzed using Illumina GenomeStudio Software.

label: C-Bio and A-DNP

source_name: genomic DNA_BMF

label_protocol: Samples were processed by the Center for Applied Genomics at Children’s Hospital, which operates  the Center for Applied Genomics at  Children’s Hospital, which operates  a high-throughput Illumina BeadLab  Genotyping System that uses customized  standard operating procedures based on  the manufacturer’s specifications (Peiffer  et al. 2006; Hakonarson et al. 2007; Maris  et al. 2008).

extract_protocol: DNA was extracted from bone marrow aspirates using Qiagen Blood DNA Mini Kit according to the manufacturer's instructions.

value: Bone Marrow Aspirate

value: Male

tag: disease state

value: NeutropeniaNOS


title: whole blood_xen14 injection_8 h_rep1


title: T00_311J

value: Female

value: SCN


title: AML-blast cell sample-4708

description: Test

value: Initial


title: AML-blast cell sample-4710

description: Test


title: AML-blast cell sample-4706

description: Test


title: NHNP 5d

source_name: 5d differentiated NHNP cells

treatment_protocol: differentiated for 5d


title: AML-blast cell sample-4704

description: Test


title: whole blood_xen29 injection_4 h_rep2


title: whole blood_xen29 injection_4 h_rep1


title: P4_1

description:
Sample_07
RNA expression signals in POD4 Wound infected with Pa

tag: condition id

tag: rabbit id

value: Pseudo 1


title: 245 Tumor

source_name: Patient 245 Tumor DNA

tag: patient

value: Tumor

tag: molecular subtype

value: luminal

tag: age

tag: previoustreatment

value: HighDensityTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: Grade II

tag: recurrencefreesurvival

tag: overalstatus

value: death

tag: overallsurvival

source_name: Megapool reference DNA female, EA-100F

value: control


title: K4_2

description:
Sample_02
RNA expression signals in POD4 Wound infected with Kp

source_name: POD4 Wound infected with Kp

value: Kleb 1

value: Kleb POD4

tag: wound id

tag: array id


title: K4_5

description:
Sample_05
RNA expression signals in POD4 Wound infected with Kp

value: Kleb 2

tag: treatment


title: K4_4

description:
Sample_04
RNA expression signals in POD4 Wound infected with Kp


title: K4_1

description:
Sample_01
RNA expression signals in POD4 Wound infected with Kp


title: whole blood_xen29 injection_4 h_rep3

tag: strain

tag: treatment injection

value: xen29 in 100 ul PBS

tag: kill time


title: K4_3

description:
Sample_03
RNA expression signals in POD4 Wound infected with Kp

tag: condition id

tag: rabbit id


title: AML-blast cell sample-4703

description: Test

tag: tumor stage

tag: genetic aberration


title: T06_297E

tag: tissue

value: Bone Marrow Aspirate

tag: gender

tag: disease state

value: SDS


title: whole blood_xen14 injection_4 h_rep3

description: 1X108 bacteria in 100 ul PBS and injection subcutaneouly in the back of mice via Fr. 25 needle

value: xen14 in 100 ul PBS


title: T06_297F

value: Male


title: NHNP

source_name: undifferentiated NHNP cells

tag: cell type

value: normal neural progenitor cells

tag: sample type

value: mixed genomic DNA from male and female lymphocytes


title: NHNP 24h

source_name: 24h differentiated NHNP cells

treatment_protocol: differentiated for 24h


title: T07_160D

value: Female

value: AnemiaNOS


title: T07_021D

value: NeutropeniaNOS


title: T03_074B

value: DBA


title: T07_246B

value: MDS


title: AML-blast cell sample-4536

description: Test

value: Initial


title: AML-blast cell sample-4698

description: Test


title: AML-blast cell sample-4567

description: Test


title: AML-blast cell sample-4555

description: Test

value: MLL-rearranged


title: T08_221B


title: whole blood_control_4 h_rep3

description: 100 ul PBS injection subcutaneouly in the back of mice via Fr. 25 needle

value: 100 ul PBS


title: AML-blast cell sample-4533

description: Test


title: whole blood_xen14 injection_4 h_rep1


title: whole blood_control_4 h_rep2


title: AML-blast cell sample-4531

description: Test


title: T09_056E

value: AA


title: T08_275B

value: Other


title: whole blood_control_4 h_rep1


title: T09_148B


title: T09_148C


title: AML-blast cell sample-4530

description: Test


title: AML-blast cell sample-4508

description: Test


title: T09_301


title: AML-blast cell sample-4501

description: Test


title: AML-blast cell sample-4500

description: Test


title: T09_301B


title: T10_023


title: T09_354


title: AML-blast cell sample-4450

description: Test


title: T10_029B


title: T10_023B


title: whole blood_xen14 injection_4 h_rep2


title: T10_029C


title: AML-blast cell sample-4525

description: Test


title: AML-blast cell sample-4420

description: Test


title: AML-blast cell sample-4425

description: Test


title: AML-blast cell sample-4444

description: Test


title: AML-blast cell sample-4448

description: Test


title: T10_092


title: AML-blast cell sample-4409

description: Test


title: AML-blast cell sample-4391

description: Test


title: AML-blast cell sample-4416

description: Test


title: T10_092B


title: AML-blast cell sample-4382

description: Test


title: CLL_Immobilized_rep16

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

hyb_protocol: Cy3-labeled RNA was hybridized to the Human microRNA microarray Version 3 from the Sanger database v12.0 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized signal intensities provided in Series supplementary file miRNA_processed_data.txt.

source_name: CLL

label_protocol: Single-color hybridization microarray experiments for miRome were performed with 100 ng total RNA/sample labeled with Cyanine(Cy)-3 dye using the microRNA Complete Labeling System & Hyb Kit (Agilent Technologies).

growth_protocol: Freshly isolated CLL cells cultured (1 × 107 cells/ml) in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate (Life Technologies, Carlsbad, CA, USA). CLL cells (n = 49/76) were also co-stimulated for 20h with 1 × 107/mL Dynabeads M-450 Epoxy (Life Technologies) coated with 10 μg goat anti-human IgM (immobilized anti-IgM) (SouthernBiotech, Birmingham, AL).27, 28 The coating procedure was done according to the manufacturer's instructions (Life Technologies).

extract_protocol: Total RNA was extracted from purified CLL cells and normal peripheral blood B cells of healthy donors using the TRIZOL Reagent (Life Technologies) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: In selected experiments, CLL cells  co-stimulated with immobilized anti-IgM were cultured in the presence or not of R406 4mM (Axon Medchem, The Netherlands). CLL cells  were also cultured in the presence or not of 7.5 μg/ml phosphorothioate CpG-ODN oligonucleotide 2006 (5′-TCG TCG TTT TGT CGT TTT GTC GTT-3′; CpG-ODN2006) (Life Technologies, CA) for 20 hours, as previously reported.27, 28

value: Peripheral blood

value: male

value: B-CLL

value: co-stimulated with immobilized anti-IgM


title: T10_114

value: Bone Marrow Aspirate


title: T10_116

value: Male

value: BMFNOS


title: CLL_Immobilized_rep15


title: CLL_Untreated_rep16

value: untreated


title: CLL_Untreated_rep15


title: AML-blast cell sample-4372

description: Test


title: AML-blast cell sample-4370

description: Test


title: SMZL#26_F-CTRL

city: Pierre Benite

first: Laurent

last: JALLADES

address: 165 Chemin du Grand Revoyet

institute: Hospices Civils de Lyon

description: Patient SMZL#26 versus female reference (dye-swap)

hyb_protocol: Each tumour samples (SMZL) were combined either with the female reference DNA or with the male reference DNA using a dye swap methodology to obtain a sex-matched and a sex-mismatch CGH profile. After denaturation, probes were pre-annealed with 50 µg of human Cot-1 DNA (Invitrogen, California, USA) and hybridization was performed at 65°C for 24 hours.

scan_protocol: The arrays were scanned on an Agilent G2565AA scanner.

data_processing: Microarray images were analyzed using Agilent Feature Extraction Software (version 9.5.3.1) for background subtraction and normalization.

label_protocol: Digested DNA products were labeled using random priming with either Alexa-5-dUTP or Alexa-3-dUTP using the Bioprime Total Genomic Labeling System (Invitrogen, California, USA) according to the manufacturer’s instructions.

growth_protocol: Spleen tumour cell suspensions were collected from patients that had undergone therapeutic splenectomy between 1999-2009 and were stored in the Biological Resource Centre of the Hospices Civils de Lyon, France.

extract_protocol: Total high quality genomic DNA was isolated according to the manufacturer’s instructions (Qiagen, Germantown, MD, USA) from frozen tumour spleen samples containing more than 60% of malignant B cells based on flow cytometry immunophenotyping or from control samples.

treatment_protocol: Spleen tumour cell suspensions were collected before any specific chemotherapy or immunotherapy.

value: female

value: spleen tumor

tag: disease

value: splenic marginal zone lymphoma

source_name: F-CTRL

value: blood

value: healthy


title: T10_195

value: Female


title: SMZL#27_F-CTRL

description: Patient SMZL#27 versus female reference (dye-swap)


title: M-CTRL_SMZL#27

description: Patient SMZL#27 versus male reference

source_name: M-CTRL


title: AML-blast cell sample-4217

description: Test

value: Initial

value: MLL-rearranged


title: CLL_Immobilized_rep13


title: AML-blast cell sample-4216

description: Test


title: AML-blast cell sample-4090

description: Test


title: SMZL#24_F-CTRL

description: Patient SMZL#24 versus female reference (dye-swap)


title: CLL_Immobilized_rep14


title: M-CTRL_SMZL#26

description: Patient SMZL#26 versus male reference


title: F-CTRL_SMZL#25

description: Patient SMZL#25 versus female reference


title: T10_206

value: SDS


title: SMZL#25_M-CTRL

description: Patient SMZL#25 versus male reference (dye-swap)


title: T10_253

value: Other


title: CLL_Untreated_rep14

value: Peripheral blood

value: male


title: M-CTRL_SMZL#24

description: Patient SMZL#24 versus male reference


title: T10_253B


title: CLL_Untreated_rep13

value: B-CLL


title: AML-blast cell sample-4087

description: Test


title: CLL_Untreated_rep12


title: 782 LN

source_name: Patient 782 LN DNA

extract_protocol: Genomic DNA was isolated from 10 10 m-thick paraffin-embedded tissue sections. Sections were deparaffinated twice for 5 min in xylene, rehydrated in 100, 96 and 70% ethanol for 30 s each, stained with haematoxylin for 30 s, rinsed with water and incubated overnight in 1 m NaSCN at 37°C to remove crosslinks. Slides were rinsed twice 10 min in 1  PBS at room temperature, and completely air-dried. Tumour tissue was scraped from the glass with a scalpel to obtain at least 70% tumour cells in 200 l Qiagen ATL buffer (QIAamp® DNA extraction kit cat. 51306), transferred to eppendorf tubes and incubated with 27 l proteinase-K (20 mg/ml stock) at 450 rpm (Eppendorf® Thermomixer R) at 55°C. Three more aliquots of 27 l proteinase-K were added at 4, 20 and 28 h. After a total protK incubation of 44 h, DNA isolation proceeded as in the manufacturer's protocol (Qiagen, Cat. 51306). Samples of isolated genomic DNA were analysed by 0.8% agarose gel electrophoresis to visualise DNA concentration and size distribution. In case of tumour tissue, we scraped regions containing at least 70% tumour as indicated by an experienced breast cancer pathologist.

tag: patient

value: LN

tag: molecular subtype

value: luminal

tag: age

tag: previoustreatment

value: ConventionalTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: Grade III

tag: recurrencefreesurvival

tag: overalstatus

value: death

tag: overallsurvival

value: control


title: SMZL#23_M-CTRL

description: Patient SMZL#23 versus male reference (dye-swap)

value: spleen tumor

value: splenic marginal zone lymphoma


title: CLL_Untreated_rep11

tag: treatment

value: untreated


title: 425 LN

source_name: Patient 425 LN DNA

tag: tissue

value: Triple Negative

value: Female

value: HighDensityTreatment

value: alive

extract_protocol: aCGH reference DNA was isolated from peripheral blood lymphocytes from six apparently healthy female individuals. It was pooled and sonicated until its median fragment length was similar to that of the test samples.


title: T10_282B

value: Bone Marrow Aspirate

tag: gender

value: Male

value: AA


title: 396 Tumor

source_name: Patient 396 Tumor DNA

value: Tumor


title: T10_116C

tag: disease state

value: BMFNOS


title: T10_282


title: AML-blast cell sample-3494

description: Test

tag: tumor stage

value: Initial

tag: genetic aberration

value: MLL-rearranged


title: CLL_Immobilized_rep12

value: Peripheral blood

value: male

tag: cell type

value: B-CLL

value: co-stimulated with immobilized anti-IgM


title: T10_259

value: NeutropeniaNOS


title: CLL_Immobilized_rep11


title: T10_298


title: AML-blast cell sample-4079

description: Test


title: AML-blast cell sample-3492

description: Test


title: SMZL#01_SMZL#22

description: Patient SMZL#22 versus patient SMZL#01

value: female

value: spleen tumor

tag: disease

value: splenic marginal zone lymphoma


title: 120 LN

source_name: Patient 120 LN DNA

tag: patient

value: LN

tag: molecular subtype

value: Triple Negative

value: Female

value: ConventionalTreatment

value: Grade III

value: death

tag: sample type

value: control


title: 795 Tumor

source_name: Patient 795 Tumor DNA

value: Tumor

tag: age

tag: previoustreatment

value: HighDensityTreatment

tag: numberpositivelymphnodes

value: alive


title: F-CTRL_SMZL#23

description: Patient SMZL#23 versus female reference

value: blood

value: healthy

value: male


title: CLL_Untreated_rep10

value: Peripheral blood

value: B-CLL

value: untreated


title: T10_345

value: Bone Marrow Aspirate

value: AA


title: AML-blast cell sample-3447

description: Test

source_name: AML blast cells

value: Initial


title: CLL_Immobilized_rep10

value: co-stimulated with immobilized anti-IgM


title: AML-blast cell sample-4084

description: Test


title: 44 LN

source_name: Patient 44 LN DNA

value: LN

value: luminal

value: Female

tag: tumorstage

tag: grade

value: Grade II

tag: recurrencefreesurvival


title: SMZL#22_M-CTRL

description: Patient SMZL#22 versus male reference (dye-swap)

value: spleen tumor

value: splenic marginal zone lymphoma


title: SMZL#21_M-CTRL

description: Patient SMZL#21 versus male reference (dye-swap)


title: 104 Tumor

source_name: Patient 104 Tumor DNA

value: Tumor

value: ConventionalTreatment

value: Grade I

tag: overalstatus

value: alive

tag: overallsurvival

value: control


title: CLL_Untreated_rep9

tag: tissue

value: Peripheral blood

tag: gender

value: male

value: B-CLL

tag: treatment


title: T10_328

source_name: genomic DNA_BMF

value: Bone Marrow Aspirate

value: Male

tag: disease state

value: JMML


title: T10_397

value: BMFNOS


title: 120 Tumor

source_name: Patient 120 Tumor DNA

value: Triple Negative

value: Grade III

value: death


title: CLL_Immobilized_rep9

tag: cell type

value: co-stimulated with immobilized anti-IgM


title: 122 LN

source_name: Patient 122 LN DNA

value: LN

value: luminal

value: Female

source_name: Megapool reference DNA female, EA-100F


title: T10_397B


title: AML-blast cell sample-3443

description: Test

tag: tumor stage

value: Initial

tag: genetic aberration

value: MLL-rearranged


title: AML-blast cell sample-3446

description: Test


title: T10_401

value: NeutropeniaNOS


title: CLL_Untreated_rep8

value: Peripheral blood

value: untreated


title: AML-blast cell sample-3442

description: Test


title: T10_402

value: AA


title: CLL_Immobilized_rep8

value: male

value: B-CLL


title: CLL_Untreated_rep7


title: CLL_Immobilized_rep7


title: T10_402C (BM)

value: Bone Marrow Aspirate

value: Male


title: CLL_Untreated_rep6


title: AML-blast cell sample-3436

description: Test


title: AML-blast cell sample-3435

description: Test


title: T10_402C (PB)

value: Peripheral Blood


title: AML-blast cell sample-3420

description: Test


title: AML-blast cell sample-3433

description: Test


title: 122 Tumor

source_name: Patient 122 Tumor DNA

tag: patient

value: Tumor

tag: molecular subtype

value: ConventionalTreatment

value: Grade III

value: control


title: CLL_Immobilized_rep6

value: co-stimulated with immobilized anti-IgM


title: F-CTRL_SMZL#21

description: Patient SMZL#21 versus female reference

value: female

value: blood

tag: disease

value: healthy

value: spleen tumor

value: splenic marginal zone lymphoma


title: T10_406

value: Other


title: 44 Tumor

source_name: Patient 44 Tumor DNA

value: luminal

value: Female

tag: age

tag: previoustreatment

value: HighDensityTreatment

value: Grade II

value: alive

tag: sample type


title: AML-blast cell sample-3415

description: Test

value: Initial

value: MLL-rearranged


title: AML-blast cell sample-3414

description: Test


title: F-CTRL_SMZL#20

description: Patient SMZL#20 versus female reference

value: male


title: SMZL#19_F-CTRL

description: Patient SMZL#19 versus female reference (dye-swap)


title: T10_402B

description: Genomic DNA extracted from bone marrow aspirates was genotyped using Infinium Human Quad610 Genotyping Beadchips (Illumina).

value: Bone Marrow Aspirate

value: Male

value: AA


title: 61 Tumor

source_name: Patient 61 Tumor DNA

value: Tumor

value: Triple Negative

value: ConventionalTreatment

tag: numberpositivelymphnodes

tag: tumorstage

tag: grade

value: death

value: control


title: T10_410

value: DC


title: SMZL#20_M-CTRL

description: Patient SMZL#20 versus male reference (dye-swap)

value: spleen tumor

value: splenic marginal zone lymphoma

value: blood

value: healthy


title: AML-blast cell sample-3410

description: Test


title: CLL_Untreated_rep5

source_name: CLL

value: Peripheral blood

value: B-CLL

value: untreated


title: T11_090

value: Female

value: NeutropeniaNOS


title: CLL_Immobilized_rep5

value: male

value: co-stimulated with immobilized anti-IgM


title: T11_111

value: Bone Marrow Aspirate

value: AAPNH


title: SMZL#18_M-CTRL

description: Patient SMZL#18 versus male reference (dye-swap)

value: female

source_name: M-CTRL


title: CLL_Untreated_rep4


title: M-CTRL_SMZL#19

description: Patient SMZL#19 versus male reference


title: F-CTRL_SMZL#18

description: Patient SMZL#18 versus female reference

source_name: F-CTRL


title: SMZL#17_F-CTRL

description: Patient SMZL#17 versus female reference (dye-swap)


title: SMZL#16_M-CTRL

description: Patient SMZL#16 versus male reference (dye-swap)


title: F-CTRL_SMZL#16

description: Patient SMZL#16 versus female reference


title: AML-blast cell sample-3400

description: Test

value: Initial

value: MLL-rearranged


title: CLL_Immobilized_rep4


title: AML-blast cell sample-2771

description: Test


title: T11_115

value: MDS


title: CLL_Untreated_rep3


title: T11_115B


title: CLL_Immobilized_rep3


title: AML-blast cell sample-1583

description: Test


title: AML-blast cell sample-1732

description: Test


title: T11_139

value: SDS


title: T11_139B


title: T11_147

value: Male

value: BMFNOS


title: CLL_Immobilized_rep2


title: AML-blast cell sample-1311

description: Test


title: CLL_Untreated_rep1


title: CLL_Untreated_rep2


title: M-CTRL_SMZL#17

description: Patient SMZL#17 versus male reference

value: blood

value: healthy

value: spleen tumor

value: splenic marginal zone lymphoma


title: CLL_Immobilized_rep1

value: Peripheral blood

value: B-CLL


title: T11_242

value: FA


title: M-CTRL_SMZL#15

description: Patient SMZL#15 versus male reference

value: male


title: SMZL#14_M-CTRL

description: Patient SMZL#14 versus male reference (dye-swap)


title: SMZL#15_F-CTRL

description: Patient SMZL#15 versus female reference (dye-swap)


title: T11_243

value: Bone Marrow Aspirate


title: F-CTRL_SMZL#13

description: Patient SMZL#13 versus female reference


title: T11_257

value: Female

value: AAPNH


title: T11_260


title: SMZL#12_F-CTRL

description: Patient SMZL#12 versus female reference (dye-swap)

value: female


title: T11_270

value: AnemiaNOS


title: F-CTRL_SMZL#14

description: Patient SMZL#14 versus female reference


title: SMZL#13_M-CTRL

description: Patient SMZL#13 versus male reference (dye-swap)


title: T11_280

value: Other


title: M-CTRL_SMZL#12

description: Patient SMZL#12 versus male reference


title: T11_319

value: MDS


title: SMZL#10_M-CTRL

description: Patient SMZL#10 versus male reference (dye-swap)


title: T11_323


title: Human NPC replicate 2

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Human NPC replicate 2

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs for each sample was hybridized to The Affymetrix Human Genome ST 2.0 GeneChip.  Hybridization of samples occured over two separate batches.  The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin(Vector Laboratories, Burlingame, CA).

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using Affymetrix AGCC software.

data_processing: Gene expression intensities were summarized and normalized using the Affymetrix Expression Console with the RMA Sketch option selected (Affymetrix, Inc).  Resulting normalized intensities for samples hybridized as part of batch 2 were then baseline subtracted using the mean difference between cell types with those samples hybridized as part of batch 1.

label: Biotin

source_name: Human NPC replicate 2

label_protocol: Samples were prepared according to Affymetrix protocols (Affymetrix, Inc). RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively. Per RNA labeling, 200 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 2.0 ST chips.

growth_protocol: Purified adult peripheral CD34 cells were growed in complete StemSpan Serum-Free Expansion Medium for 7 days before collection; iPS and iNS were generated by transfecting CD34+ cells with Sendai virus constructs for SOX-2,Klf-4, OCT3/4 and C-MYC (Invitrogen) at MOI of 20. After 5 days, floating cells were collected and transfered to 6 well plates coated with Cellstart (Invitrogen) in  stem cell media for 20 days, with daily media change. iPS colonies were collected and expended in the same culture conditions. For iNS generation, 5 days after transfection, adherent cells were collected by pipetting and transfered to noncoating plates in NPC media for neural stem cell selection. When reaching 60% confluence, the cells were subcultured in neural stem cell media (Invitrogen). To generate NSC from iPS, iPS were collected and replated in non-coating 6 well plates in neural stem cell media for neural stem cell induction. Attached cells were collected after reaching 60% confluence. Primary human NPC were cultured on poly-D-lysine coated 6 well-plates in NPC media.

extract_protocol: RNA extraction was performed using the Total RNA purification kit (Norgen Biotek, Canada) following the manufacturer’s instructions.

treatment_protocol: No treatment was applied to the cells.

value: NPC

tag: source sample

tag: hybridization batch


title: Human NPC replicate 3

description: Human NPC replicate 3

source_name: Human NPC replicate 3


title: Human NPC replicate 4

description: Human NPC replicate 4

source_name: Human NPC replicate 4


title: Human iNS derived from iPSC replicate 2

description: Human iNS derived from iPSC replicate 2

source_name: Human iNS derived from iPSC replicate 2

value: iNS derived from iPSC


title: T11_353

tag: tissue

tag: gender

value: Male

value: NeutropeniaNOS


title: SMZL#11_F-CTRL

description: Patient SMZL#11 versus female reference (dye-swap)

value: spleen tumor

value: blood

value: healthy


title: F-CTRL_SMZL#09

description: Patient SMZL#09 versus female reference

value: splenic marginal zone lymphoma


title: F-CTRL_SMZL#10

description: Patient SMZL#10 versus female reference


title: M-CTRL_SMZL#11

description: Patient SMZL#11 versus male reference


title: Human iNS derived from iPSC replicate 1

description: Human iNS derived from iPSC replicate 1

source_name: Human iNS derived from iPSC replicate 1


title: SMZL#09_M-CTRL

description: Patient SMZL#09 versus male reference (dye-swap)


title: T11_354

tag: disease state

value: AA


title: T09_342B

value: BMFNOS


title: SMZL#08_M-CTRL

description: Patient SMZL#08 versus male reference (dye-swap)

value: male


title: F-CTRL_SMZL#08

description: Patient SMZL#08 versus female reference


title: Human NPC replicate 1

description: Human NPC replicate 1

source_name: Human NPC replicate 1

tag: cell type


title: T06_336B

value: Bone Marrow Aspirate

value: Female


title: T11_357


title: Human iNS replicate 3

description: Human iNS replicate 3

source_name: Human iNS replicate 3

value: iNS


title: Human iNS replicate 1

description: Human iNS replicate 1

source_name: Human iNS replicate 1


title: SMZL#07_F-CTRL

description: Patient SMZL#07 versus female reference (dye-swap)

value: female


title: Human iNS replicate 2

description: Human iNS replicate 2

source_name: Human iNS replicate 2


title: Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells, rep2'

city: Powai, Mumbai

first: Sarika

last: Mehra

state: MH

address: IIT Bombay

department: Chemical Engineering

country: India

institute: IIT Bombay

description: Biological replicate2'/3:Total RNA isolated from Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C

hyb_protocol: Hybridazation and washing of array was carried out using TIGR protocol

scan_protocol: Scanned on an Perkin Elmer Scanner scannarryGX.

data_processing: Images were quantified using Perkin Elmer Scannarry Express Software

label: Alexa 647

organism: Streptomyces coelicolor

source_name: S. coelioclor cells Ciprofloxacin treated

label_protocol: 10 µg of total RNA were primed with 9 µg of Random primers at 65°C for 15 min, then reversed transcribed by incubation at 25°C for 5 min, 37°Cfor 10 min and 50°Cfor 1 h 45 min in the presence of 400 U SuperScript III RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dUTP, 25 µM Cy3-labe

growth_protocol: Cell cultured to exponetial phase in SMM media

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

treatment_protocol: Cells with OD ~1 were exposed to 10 µg/ml ciprofloxacin for one hour with parallel controls.

tag: strain

tag: growth phase

value: Exponential phase

tag: genotype

value: Wild type

label: Alexa 555

source_name: S. coelioclor cells control:untreated

growth_protocol: For exponential phase cultures, the spores were pre-germinated in 2xYT media  and then inoculated into liquid SMM  in baffled flasks with stainless steel (SS) springs. The cultures were shaken at a speed of 250 rpm at 30°C


title: Human CD34 replicate 2

description: Human CD34 replicate 2

source_name: Human CD34 replicate 2


title: 9741242830

source_name: genomic DNA_BMF

value: DBA


title: M-CTRL_SMZL#06

description: Patient SMZL#06 versus male reference


title: M-CTRL_SMZL#07

description: Patient SMZL#07 versus male reference


title: Human CD34 replicate 1

description: Human CD34 replicate 1

source_name: Human CD34 replicate 1


title: SMZL#06_F-CTRL

description: Patient SMZL#06 versus female reference (dye-swap)


title: Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells, rep2

description: Biological replicate2/3:Total RNA isolated from Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C


title: Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells, rep3

description: Biological replicate3/3:Total RNA isolated from Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C


title: SMZL#05_F-CTRL

description: Patient SMZL#05 versus female reference (dye-swap)


title: siEWS 3 (exon)

city: Rome

first: Maria Paola

last: Paronetto

address: Piazza Lauro de Bosis, 6

department: Department of Health Sciences

institute: University of Rome "Foro Italico"

description: HeLa cells transfected with siEWS oligonuclleotides

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps

source_name: EWS -/-

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HeLa cells were grown in complete medium (DMEM, 10% FBS, Penicillin/Strptomycin). Before transfection, cells were plated 24 hours before transfection at 40000 per well in 35mm plates in DMEM 10&FBS without antibiotics

extract_protocol: Total RNA was extracted using Rneasy mini kit (Qiagen, cat. N.

treatment_protocol: HeLa cells were plated 24 hours before transfection in 35mm plates in DMEM 10%FBS without antibiotics and transfected with 150pmol of a scrambled or EWS siRNA oligonucleotides using lipofectamine RNAiMAX (Cat. N. 13778-150, Invitrogen) in Optimem Medium (Invitrogen). Five hours after transfection, the medium was removed and replaced with fresh DMEM /10% FBS/Penicillin/Strptomycin). The transfection was repeated for three days in a row, and the fourth days cells were harvested for RNA extraction.

value: Female cervix adenocarcinoma

tag: cell line

value: HeLa

tag: transfection

value: siEWS oligonucleotides


title: Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells, rep1

description: Biological replicate1/3:Total RNA isolated from Ciprofloxacin treated cells and its corresponding control. During treatment the cultures were  sheken at 250 rpm at 30°C


title: Scrambled 2 (exon)

description: HeLa cells transfected with scrambled oligonuclleotides

source_name: scrambled

value: scrambled oligonucleotides


title: T11_234

description: Genomic DNA extracted from bone marrow aspirates was genotyped using Infinium Human Quad610 Genotyping Beadchips (Illumina).

value: Male


title: M-CTRL_SMZL#05

description: Patient SMZL#05 versus male reference

source_name: M-CTRL

value: blood

tag: disease

value: healthy

value: spleen tumor


title: SMZL#03_F-CTRL

description: Patient SMZL#03 versus female reference (dye-swap)

value: splenic marginal zone lymphoma

source_name: F-CTRL


title: siEWS 1 (exon)


title: SMZL#04_M-CTRL

description: Patient SMZL#04 versus male reference (dye-swap)

value: male


title: siEWS 2 (exon)


title: Scrambled 1 (exon)


title: AFYZ22_MousePreg

first: Alexey

last: Fedulov

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA Express

source_name: Mouse BAL macrophages

label_protocol: Affy/Nugen

growth_protocol: RPMI supplemented with FBS, penn-strep, L-glutamine and HEPES

extract_protocol: Qiagen RNEasy with DNAse digestion

treatment_protocol: Estradiol 1 ug/mL overnight

tag: group

value: Pregnant


title: M-CTRL_SMZL#04

description: Patient SMZL#04 versus male reference


title: Scrambled 3 (exon)

tag: sample type


title: AFYZ20_MousePreg


title: SMZL#02_F-CTRL

description: Patient SMZL#02 versus female reference (dye-swap)


title: AFYZ19_MouseCtrl

value: Control


title: AFYZ21_MousePreg


title: M-CTRL_SMZL#01

description: Patient SMZL#01 versus male reference (dye-swap)


title: F-CTRL_SMZL#03

description: Patient SMZL#03 versus female reference


title: AFYZ17_MouseCtrl


title: AFYZ15_RAWestr

value: Estradiol


title: F-CTRL_SMZL#02

description: Patient SMZL#02 versus female reference

value: female


title: pvcA mutant vs normal 3

city: Lubbock

first: Uzma

last: Qaisar

state: TX

institute: Texas Tech University

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Pseudomonas aeruginosa

source_name: pvcA mutant

label_protocol: total RNA were primed with 1 µl of 100 µM random primer at 70°C for 10 min, then reversed transcribed and labeled using Fairplay III microarray labelling kit (Agilent Technologies) according to manufacturer instructions.

growth_protocol: Bacterial strains were grown in 5ml of LB media in 4 separate 125ml conical flasks for 8hr and 3 ml culture was mixed with RNA protact bacterial reagent (Qiagen). Samples were processed according to manufacturer's instructions.

extract_protocol: Total RNA extracted using RNAeasy mini kit following manufacturer's instructions

tag: genotype/variation

value: pvcA mutant


title: AFYZ14_RAWestr


title: Sca-E(spl)m3-HLH_2

city: Paris

first: francois

last: schweisguth

address: 25 rue du Dr Roux

institute: Institut Pasteur

description: LM-PCR amplified gDNA (DamID - see Choksi et al., 2006). DamID experiment to map E(spl)m3HLH binding in the proneural clusters.

hyb_protocol: Hybridisation performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Scanning performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP-Chip data extraction.

organism: Drosophila melanogaster

source_name: DamID processed gDNA from Sca-Gal4 UAS-Dam-E(spl)HLHm3 wing imaginal discs

label_protocol: Labelling performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Grown at 25°C and shifted at 29°C 14hours before dissection

extract_protocol: gDNA was extracted from embryos using the Qiagen DNeasy kit, 2.5ug of gDNA was precipitated and then digested with DpnI O/N. DpnI-digested DNA was ligated to an adaptor and then digested with DpnII. DpnII-digested DNA was PCR amplified and purified using a Qiagen PCR purification kit. For more info on specifics of DamID, please see http://research.nki.nl/vansteensellab/damid.htm or Choksi et al., 2006.

treatment_protocol: gDNA was extracted from 3rd instar wing imaginal discs, DpnI digested and amplified using LM-PCR.

tag: developmental stage

value: 3rd instar larvae

value: wing imaginal discs

source_name: DamID processed gDNA from Sca-Gal4 UAS-Dam wing imaginal discs

value: Sca-Gal4, Tub-Gal80ts, UAS-Dam


title: pvcA mutant vs normal 4

description: Dye swap


title: pvcA mutant vs normal 2


title: pvcA mutant vs normal 1


title: AFYZ13_RAWestr


title: AFYZ12_RAWctrl

value: Unstimulated


title: Neur-Sens_2

description: LM-PCR amplified gDNA (DamID - see Choksi et al., 2006). DamID experiment to map Senseless binding in the Sensory Organ Precursor cells.

source_name: DamID processed gDNA from Neur-Gal4 UAS-Dam-Sens wing imaginal discs

value: Neur-Gal4, Tub-Gal80ts, UAS-Dam-Sens

source_name: DamID processed gDNA from Neur-Gal4 UAS-Dam wing imaginal discs

value: Neur-Gal4, Tub-Gal80ts, UAS-Dam


title: S-SiO2-NW 2

status: Public on Dec 31 2013

city: Gaithersburg

first: Leona

middle: Dance

last: Scanlan

address: 100 Bureau Dr

institute: NIST

scan_protocol: 16-bit GenePix 4000B microarray scanner with 5-micron resolution and features, edited with GenePix Pro 6.0

data_processing: Regression analysis in GenePixPro, subsequent analysis as in Loguinov 2004, with a “Treatment vs. Control”  design.

organism: Daphnia magna

source_name: short silica silver nanowire exposed

label_protocol: as per Agilent Quick-Amp one-color array kit and protocol. 300 ng total RNA starting material.

growth_protocol: Grew daphnids in COMBO growth medium. Fed and changed media three times per week; 8 hours dark and 16 hours light per day.

extract_protocol: Phenol and chloroform extraction (Trizol) with handheld homogenizer

treatment_protocol: Exposed to 1/10 LC50 concentrations of AgNW or Ag+ for 24 hours.

value: whole organism


title: S-SiO2-NW 3

hyb_protocol: as per Agilent Quick-Amp one-color array kit and protocol.


title: AFYZ11_RAWctrl


title: AFYZ18_MouseCtrl


title: AFYZ10_RAWctrl


title: S-SiO2-NW 4


title: Neur-Sens_1


title: S-SiO2-NW 1


title: S-PVP-NW 3

source_name: short PVP silver nanowire exposed


title: Neur-Achaete_2

description: LM-PCR amplified gDNA (DamID - see Choksi et al., 2006). DamID experiment to map Achaete binding in the Sensory Organ Precursor cells.

source_name: DamID processed gDNA from Neur-Gal4 UAS-Dam-Ac wing imaginal discs

value: Neur-Gal4, Tub-Gal80ts, UAS-Dam-Ac


title: Sca-E(spl)m3-HLH_1


title: S-PVP-NW 4


title: Sca-Achaete_2

description: LM-PCR amplified gDNA (DamID - see Choksi et al., 2006). DamID experiment to map Achaete binding in the proneural clusters.

source_name: DamID processed gDNA from Sca-Gal4 UAS-Dam-Ac wing imaginal discs

value: Sca-Gal4, Tub-Gal80ts, UAS-Dam-Ac


title: T09_056B

value: Bone Marrow Aspirate

value: Male

value: AA


title: L-SiO2-NW 3

source_name: long silica silver nanowire exposed


title: L-SiO2-NW 2


title: S-PVP-NW 2


title: L-SiO2-NW 4


title: S-PVP-NW 1


title: L-SiO2-NW 1


title: L-PVP-NW D

source_name: long PVP silver nanowire exposed


title: Neur-Asense_2

description: LM-PCR amplified gDNA (DamID - see Choksi et al., 2006). DamID experiment to map Asense binding in the Sensory Organ Precursor cells.

source_name: DamID processed gDNA from Neur-Gal4 UAS-Dam-Ase wing imaginal discs

value: Neur-Gal4, Tub-Gal80ts, UAS-Dam-Ase

source_name: DamID processed gDNA fromNeur-Gal4 UAS-Dam wing imaginal discs


title: Neur-Achaete_1


title: Ag+ 1

source_name: ionic silver exposed


title: Ag+ 2


title: L-PVP-NW A


title: Ag+ 3


title: L-PVP-NW B


title: Control 4

source_name: media control


title: Sca-Achaete_1


title: Ag+ 4


title: Control 2


title: Control 1


title: L-PVP-NW C


title: Control 3


title: Gene expression in Pten::Keap1-Alb::Nrf2

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

country: Japan

institute: Tohoku University

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Data was obtained using the Agilent Feature Extraction software (v10.1), using default for all parameters.  The data were analyzed using GeneSpring GX software (v11.5) (Agilent).

source_name: Pten flox/flox::Keap1 flox/flox::Albumin-Cre::Nrf2–/– (P15, female) livers

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole livers using Isogen (Nippon Gene).

value: mixed (mainly C57BL/6J, and probably included 129sv and DBA/2)

value: liver


title: Gene expression in Pten::Keap1-Alb

description: Gene expression in Pten::Keap1-Alb

source_name: Pten flox/flox::Keap1 flox/flox::Albumin-Cre (P15, female) livers


title: Gene expression in Pten-Alb

description: Gene expression in Pten-Alb

source_name: Pten flox/flox::Albumin-Cre (P15, female) livers

value: Pten-Alb


title: Sca-Asense_2

description: LM-PCR amplified gDNA (DamID - see Choksi et al., 2006). DamID experiment to map Asense binding in the proneural clusters.

source_name: DamID processed gDNA from Sca-Gal4 UAS-Dam-Ase wing imaginal discs

value: Sca-Gal4, Tub-Gal80ts, UAS-Dam-Ase


title: Neur-Asense_1

value: 3rd instar larvae


title: Gene expression in Keap1-Alb

description: Gene expression in Keap1-Alb

source_name: Keap1 flox/flox::Albumin-Cre (P15, female) livers


title: Sca-Asense_1

value: wing imaginal discs

source_name: DamID processed gDNA from Sca-Gal4 UAS-Dam wing imaginal discs