title: Glioma Stem Cells GSC13


title: Glioma Stem Cells GSC46

status: Public on Aug 15 2013

type: RNA

city: Austin

first: Brian

middle: D

last: Vaillant

state: TX

department: Neurology

country: USA

institute: Seton Brain and Spine Institute

hyb_protocol: standard Affymetrix protocol, Performed by Expression Analysis (Durham, NC)

data_processing:
Affymetrix data processed in R using a custom CDF from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/ensg.download/hgu133a2hsensgcdf_16.0.0.tar.gz
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/ensg.download/hgu133a2hsensgcdf_16.0.0.tar.gz

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Glioma Stem Cells isolated from glioblastoma

growth_protocol: Neural basal media supplemented with bFGF and EGF

extract_protocol: Whole RNA extraction kit from ABI

tag: cell type

tag: tissue

value: brain


title: Glioma Stem Cells GSC23

scan_protocol: standard Affymetrix protocol, Performed by Expression Analysis (Durham, NC)

value: Glioma Stem Cells isolated from glioblastoma


title: Glioma Stem Cells GSC37

label_protocol: standard Affymetrix protocol, Performed by Expression Analysis (Durham, NC)


title: Glioma Stem Cells GSC35


title: Glioma Stem Cells GSC7-2


title: Glioma Stem Cells GSC38


title: Glioma Stem Cells GSC16


title: Glioma Stem Cells GSC6-27


title: Glioma Stem Cells GSC30


title: Blister blight test

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
48 years
SA-6

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Camellia sinensis 4x44K designed by Genotypic Technology Private Limited. (AMADID: 043117) 1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Feature extracted data was analyzed using GeneSpring GX version 11.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift Normalization

organism: Camellia sinensis

source_name: Blister blight test

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Blister blight and Gery blight spores were collected and infected to healthy tea plants and incubated in controlled condition for expression of respective diseases

extract_protocol: RNA extraction was done using RNAqueous kit from Ambion (Cat. No. AM1912) following the manufacturer's recommendations.

treatment_protocol: One healthy and one control potted plants were maintained in glass house in 3 replicates

value: Whole leaf


title: Grey blight test

description:
51 years
UPASI – 10

source_name: Grey blight test


title: Blister blight control

description:
48 years
SA-6

source_name: Blister blight control


title: Grey blight control

description:
51 years
UPASI – 10

source_name: Grey blight control


title: Normal liver, 1 (U133A)

city: London

first: Claude

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

country: United Kingdom

institute: Barts & The London School of Medicine (QMUL)

description:
Gene expression data from Normal Liver.
NORMLIVER_A

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Robust multi-array analysis (RMA) using R.

source_name: Normal liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Freshly frozen PDACs, metastatic liver and normal pancreas samples were obtained with full ethical approval from the host institutions.

extract_protocol: Total RNA was extracted from tissues with TRIzol Reagent (Invitrogen Life Technologies) according to the manufacturer’s protocol. Total RNA from normal liver was purchased from Ambion (Invitrogen).

value: liver


title: Liver metastasis, 1 (U133A)

description:
Gene expression data from Liver Metastasis.
LIVERMETA_A

source_name: Liver metastasis

value: liver metastasis


title: Liver metastasis, 4 (U133A)

description:
Gene expression data from Liver Metastasis.
14m_a


title: Normal liver, 2 (U133A)

description:
Gene expression data from Normal Liver.
CNL2_A


title: Normal pancreas, 2 (U133A)

description:
Gene expression data from Normal Pancreas.
NpaGA

source_name: Normal pancreas

value: pancreas


title: Normal pancreas, 3 (U133A)

description:
Gene expression data from Normal Pancreas.
NpaVA


title: Liver metastasis, 5 (U133A)

description:
Gene expression data from Liver Metastasis.
9B_O_A


title: Primary PDAC, 2 (U133A)

description:
Gene expression data from Primary PDAC.
205a

source_name: Primary PDAC

value: primary pancreatic ductal adenocarcinoma


title: Primary PDAC, 3 (U133A)

description:
Gene expression data from Primary PDAC.
fta


title: Liver metastasis, 2 (U133A)

description:
Gene expression data from Liver Metastasis.
22m_a


title: Primary PDAC, 4 (U133A)

description:
Gene expression data from Primary PDAC.
pa


title: BS1 rep3

city: München

first: Florian

last: Reisinger

address: Schneckenburgerstr. 8

country: Germany

institute: Helmholtz-Zentrum München

description: Gene expression data from BS1-treated HepaRG cells

hyb_protocol: The amplified and fragmented biotinylated complementary RNA was hybridized to Affymetrix Human Gene 1.0 ST Arrays (HuGene-1_0-st-v1, 33297 probe sets) using standard procedures.

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

data_processing: The array data were analyzed using tools in Expression consol software (Affymetrix). The Robust Multi-array Analysis (RMA) algorithm was used for probeset (gene-level) intensity normalization. The data were analyzed for differential gene expression using an empirical Bayes moderated t-test, implemented in the Bioconductor package Linear Models for Microarray Data LIMMA. The results were sorted by the adjusted p-value and exported in tab-delimited format

source_name: HepaRG

label_protocol: Total RNA was amplified and labeled using WT Expression Kit (Ambion) and Terminal labeling Kit (Affymetrix) according to the manufacturer’s recommendations.

growth_protocol: HepaRG cells were cultured, differentiated for 4 weeks and infected with HBV as already described in Lucifora et al., Journal of Hepatology, 2011

extract_protocol: Total RNA was extracted from cells using RNeasy RNA-extraction kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Cells were not treated (mock) or treated with lymphotoxin-beta receptor agonist (BS1) at 0.5 ug/mL 24h before infection and until the end of the experiment 4 days after infection

tag: agent

value: lymphotoxin-beta receptor agonist (BS1)

tag: state

value: differentiated


title: Mock rep2

description: Gene expression data from mock-treated HepaRG cells

value: mock


title: Normal pancreas, 1 (U133A)

description:
Gene expression data from Normal Pancreas.
NpaA


title: Normal liver, 3 (U133A)

description:
Gene expression data from Normal Liver.
CNL_A


title: BS1 rep1


title: BS1 rep4


title: Primary PDAC, 1 (U133A)

description:
Gene expression data from Primary PDAC.
194bA


title: Mock rep4


title: BS1 rep2


title: Mock rep3


title: TN88

city: Heidelberg

first: Robert

middle: A

last: Lindner

state: BW

address: INF 364

institute: University of Heidelberg

description: TNBC sample TN88   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

hyb_protocol: standard as recommended by illumina (WG-DASL)

scan_protocol: Scanned with BeadArray Reader (Illumina) and processed with BeadStudio software (Illumina)

data_processing: The data was preprocessed by Bioconductor lumi package. It was log2 transformed and quantile normalized. Samples with less than 30 % detectable probes and probes that were detectable in less than 10 % of the samples were discarded.

source_name: FFPE core from TNBC patient 278

extract_protocol: 1.5mm core from FFPE block, area of invasive disease indicated by study pathologist based on H&E staining. RecoverAll Total Nucleic Acid Isolation kit (Applied Biosystems) following the manufacturer's protocol

tag: race

value: African American

tag: diagnosis age

tag: Stage

tag: nodes

value: Negative

tag: mva


title: TN90

description: TNBC sample TN90   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 280

label_protocol: standard as recommended by illumina (WG-DASL)

value: European American


title: TN87

description: TNBC sample TN87   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 277


title: TN92

description: TNBC sample TN92   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 282


title: TN96

description: TNBC sample TN96   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 285


title: Mock rep1


title: TN91

description: TNBC sample TN91   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 281


title: TN89

description: TNBC sample TN89   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 279


title: TN86

description: TNBC sample TN86   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 276


title: TN83

description: TNBC sample TN83   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 274


title: TN85

description: TNBC sample TN85   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 275

value: Hispanic


title: TN82

description: TNBC sample TN82   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 273


title: TN80

description: TNBC sample TN80   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 271


title: TN66

description: TNBC sample TN66   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 268


title: Cryptococcus neoformans grown in DMEM for 6hr

type: SAGE

anchor: NlaIII

city: Vancouver

first: Emma

last: Griffiths

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: Cryptococcus neoformans H99

data_processing: Tag detection and counting was carried out using PHRED and CrossMatch software (University of Oklahoma’s Advanced Center for Genome Technology, http://www.genome.ou.edu/cneo.html)

molecule: polyA RNA

organism: Cryptococcus neoformans H99

source_name: Cryptococcus neoformans H99

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated fetal calf serum (FBS), 1% nonessential amino acids, 100 µg mL-1 penicillin-streptomycin, and 4 mM L-glutamine (Invitrogen) for 6hr at 37oC.

extract_protocol: polyA mRNA was extracted using standard TRIZOL procedures and libraries were prepared using the NlaIII anchoring enzyme and the I-Long SAGE kit (Invitrogen).

treatment_protocol: untreated

tag: mating type

value: alpha

tag: isolate

value: human isolate

tag: pathogen

value: human pathogenic basidomycete yeast


title: TN54

description: TNBC sample TN54   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 254


title: LPS-Induced Mouse 1

city: Queens

first: Sandra

middle: Eve

last: Reznik

state: NY

address: 8000 Utopia Parkway

department: Pharmaceutical Sciences

institute: St. John's University

description: Biological replicate 1 of 5.  Mouse induced to PTL with LPS

hyb_protocol: Equimolar amounts of Cy3 and Cy5 labeled aRNA were combined in one tube.

scan_protocol: GenePix 4000A microarray scanner (Axon Instruments, Foster City, Calif.) at the cDNA Microarray Facility, AECOM. UHR Cy3 Cy5 images were acquired with GenePix Pro 6.0 Software.

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

organism: Mus musculus

source_name: total placental RNA

label_protocol: 1 mg of total RNA was mixed with 1 ml T7 Oligo(dT) Primer, and the volume was adjusted to 12 ml

extract_protocol: Total RNA extracted, using Rneasy Minikit (Qiagen, Inc.)

treatment_protocol: RNA, amplified and labeled by using an Amino Allyl MesageAmpTM II aRNA Amplification Kit (AmbionÒ , USA)

value: placenta

tag: treatment

value: injected with ip LPS

tag: embryonic stage

tag: strain

source_name: Total RNA from pooled placentas

value: injected with IP PBS


title: Cryptococcus neoformans H99 extracted from J774A.1 macrophage-like cells

description: Cryptococcus neoformans H99

growth_protocol: Murine macrophage-like cell line J774A.1 was grown at 37°C in 10% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated fetal calf serum (FBS), 1% nonessential amino acids, penicillin-streptomycin, and L-glutamine (Invitrogen). Cryptococcus cells were opsonized with monoclonal antibody 18B7 against capsule and macrophages were treated with recombinant mouse gamma interferon (IFN-gamma) and lipopolysaccharide (LPS) prior to co-incubation at a multiplicity of infection (MOI) of 1:1. Macrophages were inoculated with H99 cells and washed after 1 h of inoculation to remove unattached, extracellular fungal cells. After 6 h of incubation, sterile, ice-cold distilled H2O was applied to each well to lyse the macrophages, and the fungal cells (4 x 107) were harvested by centrifugation.

extract_protocol: polyA RNA was extracted using standard TRIZOL procedures and libraries were constructed using the NlaIII anchoring enzyme and the I-Long SAGE kit (Invitrogen).

tag: incubation partner

value: J774A.1 murine macrophage-like cell line


title: LPS-Induced Mouse 5

description: Biological replicate 5 of 5.  Mouse induced to PTL with LPS


title: TN53

description: TNBC sample TN53   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 253

value: Positive


title: TN59

description: TNBC sample TN59   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 252


title: TN32

description: TNBC sample TN32   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 242


title: TN29

description: TNBC sample TN29   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 244


title: LPS-Induced Mouse 2

description: Biological replicate 2 of 5.  Mouse induced to PTL with LPS


title: TN19

description: TNBC sample TN19   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 243


title: LPS-Induced Mouse 4

description: Biological replicate 4 of 5.  Mouse induced to PTL with LPS


title: LPS-Induced Mouse 3

description: Biological replicate 3 of 5.  Mouse induced to PTL with LPS


title: TN20

description: TNBC sample TN20   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 249


title: TN25

description: TNBC sample TN25   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 245


title: TN12

description: TNBC sample TN12   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 241


title: TN11

description: TNBC sample TN11   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 239


title: TN36

description: TNBC sample TN36   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 248


title: TN18

description: TNBC sample TN18   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 247


title: P69 Rep 1

city: Richmond

first: William

middle: Thomas

last: Budd

state: VA

address: 401 College Street Room 1-112

department: Department of Biochemistry and Molecular Biology

institute: Virginia Commonwealth University

data_processing: After calibrating the plates to one another using the GeneEX software supplied by Exiqon, Raw CT values were normalized to the global mean of all miRNAs (delta CT) and the delta delta CT was calculated for each probe by subtracting the dCT of M12 from dCT of P69.

label: SYBR Green

source_name: prostate cancer cell line P69

label_protocol: SYBR Green labeling performed using the microRNA Ready-to-Use PCR human panel I+II (Exiqon, Demark) following the Manufacturer’s instructions.

growth_protocol: Cells grown in RPMI1640 with 5% FBS, 5ug/ml insulin, 5ug/ml transferrin, 5 ug/ml of selenium, and Gentamycin (0.05mg/ml) at 37 degrees Celsius with 5% CO2 in humdified einvironment. All cells were extracted during log phase of growth.

extract_protocol: RNA was extracted from frozen cell pellets using the miRVANA kit from Ambion following the manufacturer's instructions.

tag: cell line

tag: tumorgenicity

value: Poorly tumorigenic, non-metastatic variant

tag: input rna

value: 25 ng


title: P69 Rep2

value: 50 ng


title: M12-T11 P4 Rep 2

source_name: prostate cancer cell line M12

value: Highly tumorigenic, metastatic


title: TN57

description: TNBC sample TN57   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 238


title: TN17

description: TNBC sample TN17   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 209


title: M12-T11 P4 Rep 1


title: Tg-WD-Liver-1

city: Rootstown

first: John

last: Chiang

state: OH

address: 4209 State Route 44

department: Biochemistry and Molecular Pathology

institute: Northeast Ohio Medical University

hyb_protocol: cRNA was quantified using a nanodrop spectrophotometer and the cRNA quality (size distribution) was further analyzed on a 1% agarose gel. cRNA was hybridized to the Illumina MouseRef8 v2 Expression BeadChip using standard protocols (provided by Illumina, San Diego, CA). Individual hybridizations were performed on each sample, and no pooling of samples took place.

scan_protocol: Scan and Imaging procedures adhered strictly to standard protocols provided by Illumina, San Diego, CA.

data_processing: The summarized data from the raw microarray data were log2 transformed after background correction and quantile normalized. Quality control analyses were applied to detect the outlier samples.

label: Biotin

source_name: Mouse liver total RNA

label_protocol: Label protocol 250 ng of RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) following manufacturer's protocol.

treatment_protocol: Male Cyp7a1 transgenic mice (littermates) at age of 12-14 weeks were housed in individual cages under a normal light-dark cycle (lights on between 6am-6pm) and were fed a standard Western diet (Harlan Teklad #88137 containing 42% fat calories and 0.2% cholesterol) for 4 month. At the end point, mice were fasted overnight for ~16 hr (5pm-9am) and liver tissues were collected.

tag: geonotype/variation

value: Tg

tag: diet

value: WD

tag: gender

value: male

tag: age

value: 6 month

tag: tissue

value: liver


title: TN15

description: TNBC sample TN15   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 208

tag: race

value: African American

tag: diagnosis age

tag: Stage

tag: nodes

value: Negative


title: Liver metastasis, 3 (U133A)

description:
Gene expression data from Liver Metastasis.
21m_a

source_name: Liver metastasis

value: liver metastasis


title: Tg-WD-Liver-2

hyb_protocol: cRNA was quantified using a nanodrop spectrophotometer and the cRNA quality (size distribution) was further analyzed on a 1% agarose gel. cRNA was hybridized to the Illumina MouseRefseq8 v2 Expression BeadChip using standard protocols (provided by Illumina, San Diego, CA). Individual hybridizations were performed on each sample, and no pooling of samples took place.

scan_protocol: Scan and Imaging procedures adhered strictly to standard protocols provided by Illumina, San Diego, CA

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) following manufacturer's protocol


title: Tg-WD-Liver-4

label_protocol: 250 ng of RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).


title: WT-WD-Liver-2

treatment_protocol: Male wild type mice at age of 12-14 weeks were housed in individual cages under a normal light-dark cycle (lights on between 6am-6pm) and were fed a standard Western diet (Harlan Teklad #88137 containing 42% fat calories and 0.2% cholesterol) for 4 month. At the end point, mice were fasted overnight for ~16 hr (5pm-9am) and liver tissues were collected.

value: WT


title: Sorted calcein AM efflux low

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Matlab

source_name: HL60 cell line

label_protocol: Standard Illumina label protocol

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

value: Sorted calcein AM efflux low


title: TN47

description: TNBC sample TN47   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 227

tag: mva


title: TN35

description: TNBC sample TN35   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 220

value: European American


title: TN27

description: TNBC sample TN27   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 218


title: TN69

description: TNBC sample TN69   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 236


title: WT-WD-Liver-4


title: Mock sorted, untreated

description: replicate 1

tag: treatment

value: Mock sorted, untreated


title: Mock sorted, treated

description: replicate 1

value: Mock sorted, treated


title: Tg-Chow-Liver-2

treatment_protocol: Male Cyp7a1 transgenic mice (littermates) at age of 12-14 weeks were housed in individual cages under a normal light-dark cycle (lights on between 6am-6pm) and were fed a standard laboratory chow diet for 4 month. At the end point, mice were fasted overnight for ~16 hr (5pm-9am) and liver tissues were collected.

value: Chow


title: Tg-Chow-Liver-3


title: TN60

description: TNBC sample TN60   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 233


title: TN13

description: TNBC sample TN13   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 240


title: TN81

description: TNBC sample TN81   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 272

value: Positive


title: TN33

description: TNBC sample TN33   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 222


title: Sorted calcein AM efflux high

description: replicate 1

value: Sorted calcein AM efflux high


title: WT-WD-Liver-3


title: Tg-WD-Liver-3


title: WT-WD-Liver-1


title: Tg-Chow-Liver-4


title: MP32

description: TNBC sample MP32   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 369


title: TN44

description: TNBC sample TN44   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 210


title: TN39

description: TNBC sample TN39   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 213


title: TN21

description: TNBC sample TN21   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 219


title: Tg-Chow-Liver-1


title: Human saliva microbiota from caries-active adult_C221

type: genomic

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

hyb_protocol: DNA was suspended in hybridization buffer and then kept at 65°C until hybridization. Hybridizations were performed at 42°C for 10 h using a Tecan HS4800 Pro hybridization station

scan_protocol: Arrays were scanned with a ScanArray 500 microarray scanner  at 633 nm using a laser power of 90% and a photomultiplier tube (PMT) gain of 75%.

data_processing:
The data processing and analysis was carried out by the IEG microarray manager available at http://ieg.ou.edu/microarray/, which is a data analysis pipeline specifically designed for functional gene arrays such as GeoChip and HuMiChip etc.
Data was filtered by SNR<=2, minimal signal intensity>=1000, resulting incomplete/subset data matrix (Probes which did not meet these criteria were not considered as detected in the study).
Signal intensity were normalized by CORS universal standard probes (Liang et. al 2010 AEM), probes with SNR<2 are removed, all data was log transformed and mean ratio was calculated for further statistical analysis
We used minimal signal intensity of 1000 and SNR (Signal to Noise Ratio) cutoff of 2 for positive callings of the presence of a gene

molecule: genomic DNA

organism: human oral metagenome

source_name: Human saliva microbiota_caries-active

label_protocol: DNA was labeled with the fluorescent dye Cy5 (GE Healthcare) by random priming

extract_protocol: Two milliliters of saliva were collected from each human-host individual into a tube containing an equal volume of lysis buffer and followed by DNA extraction

tag: dmft index


title: Human saliva microbiota from caries-active adult_C219


title: Human saliva microbiota from caries-active adult_C220


title: Human saliva microbiota from caries-active adult_C222


title: Human saliva microbiota from caries-active adult_C217


title: Human saliva microbiota from caries-active adult_C211


title: Liver metastasis, 5 (U133B)

description:
Gene expression data from Liver Metastasis.
9B_O_B

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133B Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: Human saliva microbiota from caries-active adult_C212


title: Liver metastasis, 1 (U133B)

description:
Gene expression data from Liver Metastasis.
LIVERMETA_B


title: Human saliva microbiota from caries-active adult_C207

value: female


title: Human saliva microbiota from caries-active adult_C206


title: Liver metastasis, 4 (U133B)

description:
Gene expression data from Liver Metastasis.
14m_b


title: WT-Chow-Liver-4

source_name: Mouse liver total RNA

treatment_protocol: Male wild type at age of 12-14 weeks were housed in individual cages under a normal light-dark cycle (lights on between 6am-6pm) and were fed a standard laboratory chow diet for 4 month. At the end point, mice were fasted overnight for ~16 hr (5pm-9am) and liver tissues were collected.

tag: strain


title: TN37

description: TNBC sample TN37   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 237


title: WT-Chow-Liver-2

data_processing: The summarized data from the raw microarray data were log2 transformed after force positive background correction and quantile normalized. Quality control analyses were applied to detect the outlier samples.

treatment_protocol: Male wild type at age of 12-14 weeks were housed in individual cage under a normal light-dark cycle (lights on between 6am-6pm) and were fed a standard laboratory chow diet for 4 month. At the end point, mice were fasted overnight for ~16 hr (5pm-9am) and liver tissues were collected.


title: TN68

description: TNBC sample TN68   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 235


title: WT-Chow-Liver-3


title: Human saliva microbiota from caries-active adult_C204


title: WT-Chow-Liver-1

source_name: mouse liver total RNA


title: TN4

description: TNBC sample TN4   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 205


title: TN30

description: TNBC sample TN30   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 226


title: TN16

description: TNBC sample TN16   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 229


title: Human saliva microbiota from healthy adult_H122

source_name: Human saliva microbiota_healthy


title: TN45

description: TNBC sample TN45   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 206


title: TN46

description: TNBC sample TN46   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 223

value: Hispanic


title: TN67

description: TNBC sample TN67   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 234


title: TN9

description: TNBC sample TN9   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 212


title: TN31

description: TNBC sample TN31   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 225


title: Liver metastasis, 3 (U133B)

description:
Gene expression data from Liver Metastasis.
21m_b

source_name: Liver metastasis


title: Liver metastasis, 2 (U133B)

description:
Gene expression data from Liver Metastasis.
22m_b


title: Normal liver, 3 (U133B)

description:
Gene expression data from Normal Liver.
CNL_B

source_name: Normal liver


title: TN10

description: TNBC sample TN10   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 204


title: Human saliva microbiota from healthy adult_H121


title: Normal liver, 2 (U133B)

description:
Gene expression data from Normal Liver.
CNL2_B


title: Human saliva microbiota from healthy adult_H118


title: Primary PDAC, 4 (U133B)

description:
Gene expression data from Primary PDAC.
pb

source_name: Primary PDAC

value: primary pancreatic ductal adenocarcinoma


title: TN14

description: TNBC sample TN14   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 207


title: Human saliva microbiota from healthy adult_H117


title: Human saliva microbiota from healthy adult_H106

value: male


title: Human saliva microbiota from healthy adult_H107


title: Human saliva microbiota from healthy adult_H111


title: Primary PDAC, 3 (U133B)

description:
Gene expression data from Primary PDAC.
ftb


title: Normal liver, 1 (U133B)

description:
Gene expression data from Normal Liver.
NORMLIVER_B


title: Human saliva microbiota from healthy adult_H102


title: Primary PDAC, 2 (U133B)

description:
Gene expression data from Primary PDAC.
205b


title: Normal pancreas, 1 (U133B)

description:
Gene expression data from Normal Pancreas.
NpaB

source_name: Normal pancreas

value: pancreas


title: TN5

description: TNBC sample TN5   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 203


title: Normal pancreas, 2 (U133B)

description:
Gene expression data from Normal Pancreas.
NpaGB


title: Normal pancreas, 3 (U133B)

description:
Gene expression data from Normal Pancreas.
NpaVB


title: TN43

description: TNBC sample TN43   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 215


title: TN22

description: TNBC sample TN22   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 221


title: TN62

description: TNBC sample TN62   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 231


title: TN64

description: TNBC sample TN64   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 230


title: TN26

description: TNBC sample TN26   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 217


title: Human saliva microbiota from healthy adult_H112

source_name: Human saliva microbiota_healthy


title: Human saliva microbiota from healthy adult_H116


title: TN42

description: TNBC sample TN42   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 214


title: TN7

description: TNBC sample TN7   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 201


title: Vector control clone V1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Vector control clone V1

growth_protocol: Panc1 stable cell lines were maintained in DMEM with 10% FBS.

extract_protocol: Extraction of total RNA was performed using the Ambion RNAqueous kit according to the manufacturer's instructions.

treatment_protocol: Cells were grown to 70-80% confluence before RNA extraction.

tag: cell type

value: pancreatic cancer

tag: vector

value: control


title: ts.H.NO3.M3.X30703

city: Livermore

first: Anu

last: Chakicherla

address: 7000 East Avenue, Mail Stop: L-446

institute: Lawrence Livermore National Lab

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30703_532

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Thiobacillus denitrificans ATCC 25259

source_name: thiosulfate.H2.NO3.Batch M3

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

growth_protocol: Wild-type T. denitrificans (ATCC strain 25259) was cultivated at 30oC under strictly anaerobic conditions with exposure conditions described in (Beller et al, 2013).

extract_protocol: Total RNA was extracted using the MasterPure Complete DNA and RNA Purification Kit (EpiCentre) using a modified protocol and RNAprotect (Qiagen).

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group VII.


title: TN23

description: TNBC sample TN23   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 216

value: African American

value: Negative


title: ts.H.NO3.M3.X32386

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
32386_532


title: ts.H.NO3.M3.X30645

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30645_532


title: synUO2.H.NO3.M3.X32365

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
32365_532

source_name: synUO2.H2.NO3.Batch M3

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group VI.


title: Vector control clone V3, b

source_name: Vector control clone V3

tag: cell line


title: TN6

description: TNBC sample TN6   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 202


title: bioUO2.H.NO3.M3.X32428

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
32428_532

source_name: bioUO2.H2.NO3.Batch M3


title: mosaic larval eye-antennal discs RasACT bskDN overexpressing scrib mutant 2

city: East Melbourne

first: Helena

middle: Elizabeth

last: Richardson

state: Victoria

address: 7 St Andrew's place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Center

description: tumours

hyb_protocol: Hybridization was carried out following standard Affymetrix protocols

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 following Affymetrix protocols.

data_processing: The data was gcrma normalised using the R Bioconductor package gcrma.

organism: Drosophila melanogaster

source_name: RasV12  bskDN (dominant negative) expressing scrib mutant Drosophila larval mosaic eye-antennal discs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Larvae were incubated at 25oC and grown on standard fly media

extract_protocol: Samples were prepared in triplicate, and the RNA isolated using TRIZOL, before being column purified (Qiagen).

treatment_protocol: eye-annennal disc were dissected from 3rd instar larvae at day 5 after egg deposition.

value: larval mosaic eye-antennal discs

tag: genotype

tag: developmental stage

value: 3rd instar larvae

tag: genetic background


title: bioUO2.H.NO3.M3.X30938

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30938_532


title: TN140

description: TNBC sample TN140   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 315


title: feco3.H.NO3.M3.X30661

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30661_532

source_name: FeCO3.H2.NO3.Batch M3

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group V.


title: MP5

description: TNBC sample MP5   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 379


title: TN136

description: TNBC sample TN136   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 309


title: TN132

description: TNBC sample TN132   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 324

value: European American


title: S100P overexpressing clone 1, b

source_name: S100P overexpressing clone 1

value: S100P overexpressing


title: S100P overexpressing clone 5, a

source_name: S100P overexpressing clone 5


title: TN131

description: TNBC sample TN131   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 313


title: Vector control clone V3, a


title: bioUO2.H.NO3.M3.X32385

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
32385_532


title: mosaic larval eye-antennal discs RasACT bskDN overexpressing scrib mutant 1

description: tumours

value: RasV12  bskDN (dominant negative) expressing scrib mutant


title: feco3.H.NO3.M3.X32363

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
32363_532


title: S100P overexpressing clone 5, b


title: TN134

description: TNBC sample TN134   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 303


title: Primary PDAC, 1 (U133B)

description:
Gene expression data from Primary PDAC.
194bB

source_name: Primary PDAC


title: mosaic larval eye-antennal discs RasACT overexpressing scrib mutant 3

description: tumours

source_name: RasV12 expressing scrib mutant Drosophila larval mosaic eye-antennal discs

value: RasV12 expressing scrib mutant


title: ts.H.NO3.M2.X30828

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30828_532

source_name: thiosulfate.H2.NO3.Batch M2

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group III.


title: feco3.H.NO3.M3.X30630

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30630_532


title: TN135

description: TNBC sample TN135   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 326


title: mosaic larval eye-antennal discs RasACT overexpressing scrib mutant 2

description: tumours


title: S100P overexpressing clone 1, a


title: TN137

description: TNBC sample TN137   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 316


title: TN129

description: TNBC sample TN129   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 306


title: ts.H.NO3.M2.X30800

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30800_532


title: mosaic larval eye-antennal discs RasACT bskDN overexpressing scrib mutant 3

description: tumours


title: solfe.H.NO3.M2.X30793

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30793_532

source_name: soluble Fe2.H2.NO3.Batch M2

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group II.


title: mosaic larval eye-antennal discs RasACT overexpressing scrib mutant 1

description: tumours


title: ts.H.NO3.M2.X30796

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30796_532


title: TN125

description: TNBC sample TN125   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 314


title: solfe.H.NO3.M2.X30764

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30764_532


title: mosaic larval eye-antennal discs NotchACT bskDN overexpressing scrib mutant B

description: tumours

source_name: NotchICD bskDN (dominant negative) expressingscrib mutant Drosophila larval mosaic eye-antennal discs

value: NotchICD bskDN (dominant negative) expressing scrib mutant


title: mosaic larval eye-antennal discs NotchACT overexpressing scrib mutant A

description: tumours

source_name: NotchICD expressing scrib mutant Drosophila larval mosaic eye-antennal discs

value: NotchICD expressing scrib mutant


title: mosaic larval eye-antennal discs NotchACT bskDN overexpressing scrib mutant A

description: tumours


title: mosaic larval eye-antennal discs NotchACT overexpressing scrib mutant 2

description: tumours


title: TN123

description: TNBC sample TN123   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 307

value: Positive


title: feco3.noH.NO3.M1.X30697

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30697_532

source_name: FeCO3.no H2.NO3.Batch M1

treatment_protocol: Exposure conditions are shown in Table 1 (Beller et al 2013), Group I.


title: TN126

description: TNBC sample TN126   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 308


title: feco3.noH.NO3.M1.X30687

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30687_532


title: TN127

description: TNBC sample TN127   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 302


title: solfe.H.NO3.M2.X30789

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30789_532


title: TN124

description: TNBC sample TN124   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 310


title: mosaic larval eye-antennal discs NotchACT overexpressing scrib mutant 1

description: tumours


title: mosaic larval eye-antennal discs NotchACT bskDN overexpressing scrib mutant 1

description: tumours


title: TN122

description: TNBC sample TN122   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 325


title: TN121

description: TNBC sample TN121   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 323


title: mosaic larval eye-antennal discs FRT control 3

description: no tumours

source_name: control Drosophila larval mosaic eye-antennal discs


title: Fetus from pregnant ewe exposed to 110 days of hypoxia at high altitude 4

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

description: Transcriptome analysis

hyb_protocol: One µg of purified cRNA was fragmented to uniform size and applied to Agilent Sheep Gene Expression Microarray, 8 x 15K (Design ID 019921, Agilent Technologies) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a shaking incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with Gene Spring GX v7.3.1 software (Agilent Technologies).  Annotations are based on the Agilent eArray annotation file dated January, 2010.

organism: Ovis aries

source_name: Carotid Arteries, hypoxia

label_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 1 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the labeled cRNA was assayed by spectrophotometry and the Agilent Bioanalyzer.

extract_protocol: Tissue samples were lysed in Tri-reagent (Ambion, Austin, TX) and total RNA was isolated using phenol/chloroform extraction, followed by purification over spin columns (Ambion).  The concentration and purity of total RNA was measured by spectrophotometry at OD260/280, and the quality of the total RNA sample was assessed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies).

treatment_protocol:
For the hypoxia study, at 30 days gestation, ewes were transported to the Barcroft Laboratory, White Mountain Research Station (WMRS, CA; elevation 3,801 m, barometric pressure -480 Torr), where they were kept until 135 days gestation. They were maintained in an sheltered outdoor pen that was sheltered and were fed with alfalfa pellets ad libitum. Sheep in both groups were kept in natural day-night conditions.
For control (normoxic) group, sheep were maintained at the suppliers ranch (a 300 m elevation) on alfalfa pellets ad libitum.

tag: maternal treatment

value: hypoxia

tag: gestation

value: fetal carotid arteries


title: TN120

description: TNBC sample TN120   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 317


title: mosaic larval eye-antennal discs FRT control 1

description: no tumours

tag: tissue


title: Fetus from pregnant ewe exposed to 110 days of hypoxia at high altitude 3

description: Transcriptome analysis


title: TN113

description: TNBC sample TN113   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 269

tag: race

value: Hispanic


title: TN112

description: TNBC sample TN112   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 296

tag: diagnosis age


title: feco3.noH.NO3.M1.X30643

description:
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
30643_532


title: mosaic larval eye-antennal discs Abrupt overexpressing scrib mutant 3

description: tumours

source_name: Abrupt expressing scrib mutant Drosophila larval mosaic eye-antennal discs

value: Abrupt expressing scrib mutant


title: TN119

description: TNBC sample TN119   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 319

tag: Stage


title: Fetus from pregnant ewe exposed to 110 days of hypoxia at high altitude 1

description: Transcriptome analysis


title: TN117

description: TNBC sample TN117   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 299

tag: nodes


title: mosaic larval eye-antennal discs FRT control 2

description: no tumours


title: TN108

description: TNBC sample TN108   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 293

tag: mva


title: Fetus sea level control 4

description: Transcriptome analysis

source_name: Carotid Arteries, control

value: control (normoxia)


title: mosaic larval eye-antennal discs Abrupt overexpressing scrib mutant 1

description: tumours


title: Fetus sea level control 3

description: Transcriptome analysis


title: mosaic larval eye-antennal discs Abrupt overexpressing 3

description: no tumours

source_name: Abrupt expressing Drosophila larval mosaic eye-antennal discs

value: Abrupt expressing


title: WT iron x ∆fur iron- rep2

city: Sao Paulo

first: Rogerio

last: Lourenco

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Bioquimica

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: Standard Agilent protocol  Agilent protocol  Agilent protocol  Agilent protocol

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excel and the log10 values extracted with no additional processing or filtering

organism: Caulobacter vibrioides NA1000

source_name: WT- iron

label_protocol: Standard Cy3-dCTP and Cy5-dCTP incorporations

growth_protocol: overnight C. crescentus cultures were diluted to an optical density at 600 nm (OD600) of 0.1 in 35 ml of PYE medium and grown until midlog phase (OD600 ~ 0.5)

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

treatment_protocol: cultures were divided and treated with 100 µM FeSO4 (iron sufficiency) or 100 µM 2,2-dipyridyl (iron limitation)

tag: genotype/variation

value: WT

tag: growth protocol (iron conditions)

value: NA1000 cells under iron sufficiency

source_name: ∆fur- iron

value: fur mutant


title: TN106

description: TNBC sample TN106   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 291

value: African American


title: Fetus sea level control 2

description: Transcriptome analysis


title: WT iron x ∆fur iron- rep1

scan_protocol: Standard Agilent protocol  Agilent protocol


title: TN73

description: TNBC sample TN73   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 262

value: Negative


title: mosaic larval eye-antennal discs Abrupt overexpressing scrib mutant 2

description: tumours

value: larval mosaic eye-antennal discs

value: 3rd instar larvae


title: Fetus sea level control 1

description: Transcriptome analysis


title: WT iron x WT DP- rep1

source_name: WT- 2,2-dipyridyl

value: NA1000 cells under iron limitation


title: mosaic larval eye-antennal discs Abrupt overexpressing 1

description: no tumours


title: mosaic larval eye-antennal discs Abrupt overexpressing 2

description: no tumours


title: WT iron x WT DP- rep2


title: TN76

description: TNBC sample TN76   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 266


title: TN72

description: TNBC sample TN72   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 261

value: European American


title: TN70

description: TNBC sample TN70   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 259


title: TN101

description: TNBC sample TN101   MVA: Normalized microvessel area measured by AQUA. Method is published: pubmed 18799189

source_name: FFPE core from TNBC patient 256


title: dentate gyrus, stimulated, 7 days, biological rep3

status: Public on Aug 14 2013

city: Warsaw

first: Katarzyna

last: Lukasiuk

address: 3 Pasteur Street

department: Department of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology Polish Academy of Sciences

description: Gene expression data from the left dentate gyrus from stimulated rats sacrificed after 7 days after electrical stimulation of amygdala

hyb_protocol: Affymetrix guidelines for GeneAtlas instrument

scan_protocol: Affymetrix GeneAtlas System

data_processing: R/Bioconductor RMA algorithm implemented in oligo package ver 1.22.0

organism: Rattus norvegicus

source_name: Left dentate gyrus from stimulated animal sacrificed after 7 days after electrical stimulation of amygdala

label_protocol: 100 ng of total mRNA was used for cDNA synthesis using Ambion WT Expression Kit (Life Technologies #4411974).

extract_protocol: Total RNA including miRNA was isolated from the left dentate gyrus region from hippocampi isolated on ice and placed in RNAlater solution (Ambion, AM7024) and stored at -20C until use. Isolation from dissected left dentate gyrus was performed by miRNease Mini kit (QIAGEN, 217004), according to the manufacturer's instructions.

treatment_protocol: Amygdala electrical stimulation model of temporal lobe epilepsy.

value: Sprague-Dawley

value: dentate gyrus

tag: days after stimulation

tag: treatment

value: electrical stimulation of amygdala


title: RNA from Immunoprecipitation with IgG Antibody

city: Montreal

first: Imed

last: Gallouzi

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

description: RNA from immunoprecipitation using proliferating C2C12 extract and anti-IgG antibody

hyb_protocol: Hy3™-labeled immunoprecipitated RNA and Hy5™-labeled reference RNA were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station. Hybridized slides were stored in an ozone-free environment (ozone levels below 2.0 ppb)

scan_protocol: Scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technoliges, Inc., USA) in an ozone-free environment

data_processing: Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc.,USA). The quantified signals were background corrected (Normexp with offset value 10 according to the convolution method described by Ritchie ME, Bioinformatics (2007), Vol. 23, no. 20, pages 2700-2707. The signals were further normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Proliferating C2C12

label_protocol: The miRCURY™ LNA Array power labelling kit was used to label 600 - 1000ng of RNA isolated from immunoprecipitation with Hy3 and reference samples from total RNA with Hy5.

growth_protocol: Proliferating C2C12 muscle cells were grown in DMEM supplemented with 20% FBS and 1% Pen/Strep. At 80% confluency, cells were collected.

extract_protocol: RNA was extracted with phenol/chloroform from proliferating C2C12 cell extracts that were subject to immunoprecipitation with an antibody that recognized either HuR or IgG. Total RNA was isolated from proliferating C2C12 using TRIzol reagent and used as reference sample.

treatment_protocol: No treatments

tag: antibody

value: IgG

source_name: Common Reference Pool


title: RNA from Immunoprecipitation with HuR Antibody

description: RNA from immunoprecipitation using proliferating C2C12 extract and anti-HuR antibody

value: HuR

tag: cell line


title: dentate gyrus, stimulated, 30 days, biological rep1

description: Gene expression data from the left dentate gyrus from stimulated rats sacrificed after 30 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from stimulated animal sacrificed after 30 days after electrical stimulation of amygdala

tag: genotype


title: dentate gyrus, stimulated, 30 days, biological rep4


title: crypt

city: Osaka

first: Toshio

last: Takahashi

address: 1-1-1 Wakayamadai

country: Japan

institute: Suntory Foundation for Life Sciences

description: wild tyle

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (4x44K V2) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: crypt

label_protocol: 40 ng total RNA from sample o- organoid and 20 ng total RNA from all other samples was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: AGPC metnod for preparation of RNA extraction

tag: strain


title: dentate gyrus, stimulated, 7 days, biological rep2


title: dentate gyrus, sham operated, 30 days, biological rep2

description: Gene expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 30 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from sham operated animal, time matched control for stimulated animal sacrificed after 30 days after electrical stimulation of amygdala

value: sham operated


title: dentate gyrus, stimulated, 30 days, biological rep2


title: dentate gyrus, stimulated, 7 days, biological rep1


title: y- organoid

description: wild tyle

source_name: crypt-villus organoid


title: o- organoid

description: wild tyle


title: dentate gyrus, stimulated, 30 days, biological rep3


title: dentate gyrus, stimulated, 30 days, biological rep5


title: dentate gyrus, sham operated, 30 days, biological rep3


title: dentate gyrus, sham operated, 30 days, biological rep4


title: dentate gyrus, stimulated, 7 days, biological rep4


title: dentate gyrus, sham operated, 7 days, biological rep3

description: Gene expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 7 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from sham operated animal, time matched control for stimulated animal sacrificed after 7 days after electrical stimulation of amygdala


title: dentate gyrus, sham operated, 7 days, biological rep1


title: dentate gyrus, sham operated, 30 days, biological rep1


title: dentate gyrus, sham operated, 7 days, biological rep5


title: dentate gyrus, stimulated, 7 days, biological rep5


title: intestine

description: wild tyle

source_name: whole intestine


title: dentate gyrus, stimulated, 90 days, biological rep5

description: MiRNA expression data from the left dentate gyrus from stimulated rats sacrificed after 90 days after electrical stimulation of amygdala

hyb_protocol: The hybridization was performed according to the miRCURY LNATM microRNA Array Instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria). [Service conducted at Exiqon Services, Denmark.]

scan_protocol: The microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).  [Service conducted at Exiqon Services, Denmark.]

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using quantile normalization method. [Service conducted at Exiqon Services, Denmark.]

source_name: Left dentate gyrus from stimulated animal sacrificed after 90 days after electrical stimulation of amygdala

label_protocol: 750 ng total RNA from sample was labeled with Hy3TM fluorescent label, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3TM-labeled samples were hybridized to the miRCURY LNATM microRNA Array 7'th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. [Service conducted at Exiqon Services, Denmark.]


title: dentate gyrus, sham operated, 30 days, biological rep5


title: dentate gyrus, sham operated, 7 days, biological rep4


title: dentate gyrus, stimulated, 90 days, biological rep3


title: dentate gyrus, stimulated, 90 days, biological rep4


title: dentate gyrus, sham operated, 90 days, biological rep4

description: MiRNA expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 90 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from sham operated animal, time matched control for stimulated animal sacrificed after 90 days after electrical stimulation of amygdala


title: dentate gyrus, stimulated, 90 days, biological rep2


title: dentate gyrus, sham operated, 90 days, biological rep5


title: dentate gyrus, stimulated, 90 days, biological rep1


title: dentate gyrus, sham operated, 90 days, biological rep3


title: dentate gyrus, sham operated, 90 days, biological rep2


title: dentate gyrus, stimulated, 30 days, biological rep5

description: MiRNA expression data from the left dentate gyrus from stimulated rats sacrificed after 30 days after electrical stimulation of amygdala


title: dentate gyrus, stimulated, 30 days, biological rep4


title: dentate gyrus, stimulated, 30 days, biological rep3


description: MiRNA expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 30 days after electrical stimulation of amygdala


title: dentate gyrus, stimulated, 30 days, biological rep1


title: dentate gyrus, stimulated, 30 days, biological rep2


title: Recovery V-372/Susceptible variety root tissue 42nd day after sowing, biological rep1

city: new delhi

first: Nepolean

last: Thirunavukkarasu

state: Delhi

address: IARI PUSA

department: Division of Genetics

institute: Indian Agricultural Research Institute

description:
VPRa
Gene expression data from V-372/Susceptible variety root tissue collected on 42nd day after drainage of excess water on 35th day of sowing.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000.

data_processing: The background correction, normalization and probe set summarization of data was done using the GCRMA package of R.

organism: Zea mays

source_name: Zea mays V-372/Susceptible variety root tissue 42nd day after sowing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® 3' IVT Express Kit, 2008-2010 , Affymetrix).

growth_protocol: The genotypes were sown in plastic pots filled with loam soil with sandy texture. The plants were watered daily to soil capacity until the application of stress at 28 days after sowing.

extract_protocol: Total RNA was isolated and purified from root samples (50mg) using the RNeasy mini kit (Qiagen, Hilden, Germany) after grinding the tissues in liquid nitrogen, following the manufacturer's guidelines.

treatment_protocol: To impose waterlogging condition, the perforation in the bottom of the pots (35 cm in height) was sealed on the 29th day post-sowing and the stress treatment was given by watering the pots (5 cm standing water) for seven continuous days. To allow for recovery from stress, the perforations of the pots were unsealed for proper drainage of excess water.

tag: inbred line

tag: phenotype

value: susceptible

value: root

value: waterlogging

tag: time point

value: 42 days after sowing

tag: treatment stage

value: post-stress recovery


title: Severe V-372/Susceptible variety root tissue 35th day after sowing, biological rep1

description:
VPSa
Gene expression data from V-372/Susceptible variety root tissue collected on 35th day of sowing after providing 7 days of waterlogging condition.

source_name: Zea mays V-372/Susceptible variety root tissue 35th day after sowing

tag: tissue

value: 35 days after sowing

value: severe stress


title: 3_9_15 pool

city: Dresden

first: Manja

last: Wobus

address: Fetscherstr. 74

department: Hematology/Oncology

institute: University Hospital Dresden

description: gene expression after 2 days in control medium

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files.

source_name: SCP-1, day 2, control medium, 3 replicates

label_protocol: 1 µg of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was prepared using standard RNA extraction protocols (Trizol). Quality was checked via the Agilent 2100 Bioanalyzer platform.

treatment_protocol: Human immortalized mesenchymal stromal cells (SCP-1) were incubated with conditioned medium of the breast carcinoma cell line MCF-7 for 24, 48, and 72 hours at 37 ºC in a humidified incubator with 5% CO2.

value: mesenchymal stromal cells

tag: co-cultured medium

value: control

tag: sample day


title: 4_10_16 pool

description: gene expression after 2 days in MCF-7 medium

source_name: SCP-1, day 2, MCF-7 medium, 3 replicates

value: MCF-7 medium


title: dentate gyrus, sham operated, 90 days, biological rep1


title: Severe V-372/Susceptible variety root tissue 35th day after sowing, biological rep2

description:
VPSb
Gene expression data from V-372/Susceptible variety root tissue collected on 35th day of sowing after providing 7 days of waterlogging condition.


title: Fetus from pregnant ewe exposed to 110 days of hypoxia at high altitude 2

description: Transcriptome analysis

source_name: Carotid Arteries, hypoxia

tag: maternal treatment

value: hypoxia

tag: gestation

value: fetal carotid arteries


title: 6_12_18 pool

description: gene expression after 3 days in MCF-7 medium

source_name: SCP-1, day 3, MCF-7 medium, 3 replicates


title: Severe HKI1105/Tolerant variety root tissue 35th day after sowing, biological rep2

description:
HPRSb
Gene expression data from HKI1105/Tolerant variety root tissue collected on 35th day of sowing after providing 7 days of waterlogging condition.

source_name: Zea mays HKI1105/Tolerant variety root tissue 35th day after sowing

value: tolerant


title: dentate gyrus, sham operated, 30 days, biological rep4

value: Sprague-Dawley

value: dentate gyrus


title: Recovery V-372/Susceptible variety root tissue 42nd day after sowing, biological rep2

description:
VPRb
Gene expression data from V-372/Susceptible variety root tissue collected on 42nd day after drainage of excess water on 35th day of sowing.


title: dentate gyrus, sham operated, 30 days, biological rep3


title: 5_11_17 pool

description: gene expression after 3 days in control medium

source_name: SCP-1, day 3, control medium, 3 replicates


title: Moderate V-372/Susceptible variety root tissue 32nd day after sowing, biological rep1

description:
VPMa
Gene expression data from V-372/Susceptible variety root tissue collected on 32nd day of sowing after providing 4 days of waterlogging condition.

source_name: Zea mays V-372/Susceptible variety root tissue 32nd day after sowing

value: 32 days after sowing

value: moderate stress


title: Moderate V-372/Susceptible variety root tissue 32nd day after sowing, biological rep2

description:
VPMb
Gene expression data from V-372/Susceptible variety root tissue collected on 32nd day of sowing after providing 4 days of waterlogging condition.

value: susceptible


title: Control V-372/Susceptible variety root tissue 28th day after sowing, biological rep2

description:
VPCb
Gene expression data from V-372/Susceptible variety root tissue collected on 28th day of sowing.

source_name: Zea mays V-372/Susceptible variety root tissue 28th day after sowing

value: root

value: 28 days after sowing


title: dentate gyrus, sham operated, 30 days, biological rep2

value: sham operated


title: dentate gyrus, sham operated, 30 days, biological rep1


title: 1_7_13 pool

description: gene expression after 1 day in control medium

source_name: SCP-1, day 1, control medium, 3 replicates


title: Control V-372/Susceptible variety root tissue 28th day after sowing, biological rep1

description:
VPCa
Gene expression data from V-372/Susceptible variety root tissue collected on 28th day of sowing.


title: Severe HKI1105/Tolerant variety root tissue 35th day after sowing, biological rep1

description:
HPRSa
Gene expression data from HKI1105/Tolerant variety root tissue collected on 35th day of sowing after providing 7 days of waterlogging condition.

value: waterlogging


title: dentate gyrus, sham operated, 7 days, biological rep2

description: Gene expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 7 days after electrical stimulation of amygdala


title: 2_8_14 pool

description: gene expression after 1 day in MCF-7 medium

source_name: SCP-1, day 1, MCF-7 medium, 3 replicates


title: dentate gyrus, stimulated, 14 days, biological rep5

description: MiRNA expression data from the left dentate gyrus from stimulated rats sacrificed after 14 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from stimulated animal sacrificed after 14 days after electrical stimulation of amygdala

value: electrical stimulation of amygdala


title: dentate gyrus, stimulated, 14 days, biological rep4


title: dentate gyrus, stimulated, 14 days, biological rep3


title: dentate gyrus, stimulated, 14 days, biological rep2


title: Moderate HKI1105/Tolerant variety root tissue 32nd day after sowing, biological rep2

description:
HPRMb
Gene expression data from HKI1105/Tolerant variety root tissue collected on 32nd day of sowing after providing 4 days of waterlogging condition.

source_name: Zea mays HKI1105/Tolerant variety root tissue 32nd day after sowing


title: dentate gyrus, sham operated, 14 days, biological rep5

description: MiRNA expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 14 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from sham operated animal, time matched control for stimulated animal sacrificed after 14 days after electrical stimulation of amygdala


title: BMM_uninfected_9hr_rep2

city: Ithaca

first: Helene

last: Marquis

address: Vet Medical Center, Room C5-169

department: Microbiology & Immunology

institute: Cornell University

description:
9C2
Gene expression after 9 hr without infection

hyb_protocol: A total of 825 ng per sample of Cy3-labelled cRNA was fragmented, blocked, hybridized to Agilent Whole Mouse Genome Microarray 4x44K (G4122F), and washed according to manufacturer’s instructions.

scan_protocol: The slides were then scanned using the one-color scan setting for 4x44 array slides (scan area 61 x 21.6 mm, scan resolution 5um, dye channel set to red and green, and PMT 100%) using the Agilent DNA Microarray Scanner (G2505B).  Feature Extraction Software 9.1 (Agilent) analyzed the scanned images for background, subtracted and spatially detrended processed signal intensities, and excluded non-uniform outliers flagged in feature extraction (protocol GE1-105_DEC8 and Grid: 012391_D_20060331).

data_processing: Data was analyzed using GeneSpring11.5 (Agilent Technologies), threshold to raw signal was set 1.0, shifted to 75.0 percentile, and baseline set to median of all samples.  Experimental groupings were created by dividing the samples into conditions (a) wild-type infected (triplicate),(b) plcB∆pro mutant (triplicate), and (c) uninfected (duplicate).  Interpretations were created using the average replicates in condition, non-numeric, continuous parameters, and including detected, not detected, and compromised flags.  Statistical analysis was then performed between conditions (a)/(c) & (b)/(c), unpaired T-test, no correction, p-value <0.05.  We then performed functional annotation using our significant gene lists through the Database for Annotation, Visualization and Integrated Discovery (DAVID 6.7, National Institute of Allergy and Infectious Diseases – National Institutes of Health) to find pathways significantly affected by up- or down-regulated genes

source_name: BMMs_no infection_9hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng - 1 ug total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bone marrow cells were collected from BALB/C mice and macrophages were differentiated in medium containing 50% DMEM, 30% Fetal Bovine Serum (FBS), 20% L-cell conditioned medium, 1% 100 U/ml Penicillin G,100 μg/ml Streptomycin, 1mM Sodium pyruvate, and 2mM L-glutamine.  Differentiated macrophages were seeded at a concentration of 3.6 x 106 cells in 100 mm petri dishes containing four 12 mm glass cover slips, and incubated overnight at 37°C, 5% CO2.  Bacteria were grown overnight in BHI at 30°C, passaged 1/10 or 1/100 in BHI and incubated at 30°C, 200 rpm until reaching an OD600 of 0.6-0.8.

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Kit (Qiagen) per manufacturer’s instructions.  RNA sample purity was assessed using Agilent 2100 Bioanalyzer RNA 6000 Nano LabChip (Agilent Technologies).  All samples were >9.1 RIN (RNA Integrity Number).

treatment_protocol: Macrophages were infected with either wild-type L. monocytogenes or L. monocytogenes plcB∆pro at an MOI of 1.  Cells were washed in PBS at 30 min post infection and tissue culture medium was added to dishes.  At one hour post-infection, gentamicin was added at a final concentration of 50 μg/ml.  At three hours post-infection, the medium was replaced with antibiotic-free medium to prevent intracellular bacterial killing as the mutant affects membrane permeability.   Samples were collected at 3, 6, and 9 hr p.i. for RNA purification.  Cover slips were collected at the same time points to determine bacteria counts.

tag: strain background

value: BALB/C

tag: cell type

value: bone marrow derived macrophages (BMMs)

tag: infected with

value: none (uninfected control)

tag: timepoint

value: 9 hours

tag: replicate


title: Recovery HKI1105/Tolerant variety root tissue 42nd day after sowing, biological rep2

description:
HPRRb
Gene expression data from HKI1105/Tolerant variety root tissue collected on 42nd day after drainage of excess water on 35th day of sowing.

source_name: Zea mays HKI1105/Tolerant variety root tissue 42nd day after sowing

tag: treatment

value: 42 days after sowing

value: post-stress recovery


title: BMM_uninfected_9hr_rep1

description:
9C1
Gene expression after 9 hr without infection


title: BMM_mutLm_9hr_rep3

description:
9B3
Gene expression after 9 hr infection with mutant L. monocytogenes

source_name: BMMs_mutant Listeria monocytogenes_9hr

value: L. monocytogenes plcB∆pro mutant strain


title: BMM_mutLm_9hr_rep2

description:
9B2
Gene expression after 9 hr infection with mutant L. monocytogenes


title: RNA from Immunoprecipitation with HuR antibody and C2C12 extract from proliferating (exp) cells

hyb_protocol: RNA was denatured with NaOH and spotted onto S&S Nytran SuperCharge nylon membranes. Twenty-four 384-well plates were printed using a BioRobotics MicroGrid Arrayer.

scan_protocol: the submiitter has not supplied the information

data_processing: Array Pro software was used to calculate differences in signal intensities and to normalize by Z-score transformation

label_protocol: RNA was reverse transcribed in the presence of [α-33P]dCTP.

extract_protocol: RNA was extracted with phenol/chloroform from C2C12 cell extracts that were subject to immunoprecipitation with an antibody that recognized either HuR or IgG.

treatment_protocol: No treatment

tag: antibody

value: HuR

tag: cell line


title: RAG1KO H3K4me2

first: Eugene

middle: M

last: Oltz

state: MO

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

description: Chip-chip Rag1KO DN cells -H3K4me2

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: H3K4me2 DNA from Rag1-/ DN cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 5 million cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 400 bp using a BiorupterTM sonicator (Diagenode). 5 µg of antibody was incubated with Dynabeads ProteinA beads (Invitrogen at 4C for 2-4 hours . The chromatin (from 5 million cells) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and added to the anitbody conugated to the Dynabeads overnight at 4C. After incubation, the immune complexes were collected by centrifugation and washed with the following buffers each for 3 min at 4C;low salt (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and TE (10 mM Tris pH8.0, 1 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 100 mM NaHCO3) at 65C overnight followed by the addition of proteinaseK to 500 µg/ml and incubaton at 56C for 1 hour. Genomic DNA was isolated using QIAquick PCR purification column and subject to whole genome amplication (Sigma).

treatment_protocol: Rag1KO DN cells were obtained from thymus of 3-4 week old mice.

tag: genotype

value: DN cells

tag: strain

tag: chip antibody

source_name: Input DNA from Rag1KO DN cells

value: none, input DNA


title: Moderate HKI1105/Tolerant variety root tissue 32nd day after sowing, biological rep1

description:
HPRMa
Gene expression data from HKI1105/Tolerant variety root tissue collected on 32nd day of sowing after providing 4 days of waterlogging condition.

tag: inbred line

tag: phenotype

value: tolerant

tag: time point

value: 32 days after sowing

tag: treatment stage

value: moderate stress


title: BMM_mutLm_9hr_rep1

description:
9B1
Gene expression after 9 hr infection with mutant L. monocytogenes


title: Recovery HKI1105/Tolerant variety root tissue 42nd day after sowing, biological rep1

description:
HPRRa
Gene expression data from HKI1105/Tolerant variety root tissue collected on 42nd day after drainage of excess water on 35th day of sowing.

tag: tissue

value: root


title: dentate gyrus, sham operated, 14 days, biological rep4

value: Sprague-Dawley

value: dentate gyrus

tag: days after stimulation

value: sham operated


title: BMM_wtLm_9hr_rep3

description:
9A3
Gene expression after 9 hr infection with wild type L. monocytogenes

source_name: BMMs_wild type Listeria monocytogenes_9hr

tag: strain background

value: BALB/C

value: L. monocytogenes wild-type strain


title: dentate gyrus, stimulated, 14 days, biological rep1

value: electrical stimulation of amygdala


title: BMM_uninfected_6hr_rep2

description:
6C2
Gene expression after 6 hr without infection

source_name: BMMs_no infection_6hr

tag: cell type

value: bone marrow derived macrophages (BMMs)

value: none (uninfected control)

value: 6 hours


title: Control HKI1105/Tolerant variety root tissue 28th day after sowing, biological rep1

description:
HPRCa
Gene expression data from HKI1105/Tolerant variety root tissue collected on 28th day of sowing.

source_name: Zea mays HKI1105/Tolerant variety root tissue 28th day after sowing

value: 28 days after sowing

value: control


title: BMM_wtLm_9hr_rep2

description:
9A2
Gene expression after 9 hr infection with wild type L. monocytogenes

tag: infected with

value: 9 hours


title: BMM_wtLm_9hr_rep1

description:
9A1
Gene expression after 9 hr infection with wild type L. monocytogenes

tag: timepoint


title: Germinating wheat seed at P4_biological rep3

city: Beijing

first: Yonglong

last: Yu

address: 105 Xisanhuan North Road

country: China

institute: College of Life Science, Capital Normal University

description:
Wheat seed_P4-3
Gene expression data from Wheat seed_48 hours after imbibition

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

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

organism: Triticum aestivum

source_name: Wheat seed_48 hours after imbibition

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

growth_protocol: The collection of germinating seed which germinated naturally according to the different germinating phases (P0-P4).

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

treatment_protocol: Sterile wheat seeds were completely steeped in sterile pure water for 12 hours first, then homogeneously put them into the sterile petri dish which contain moderate sterile pure water for the following germination. The collected seeds of different phases were placed in -80℃ condition for the subsequent experiments.

tag: cultivar

value: Jimai 20

value: germinating seeds


title: dentate gyrus, sham operated, 14 days, biological rep3

tag: treatment


title: RNA from Immunoprecipitation with IgG antibody and C2C12 extract from proliferating (exp) cells

tag: antibody

value: IgG


title: Germinating wheat seed at P4_biological rep2

description:
Wheat seed_P4-2
Gene expression data from Wheat seed_48 hours after imbibition


title: Control HKI1105/Tolerant variety root tissue 28th day after sowing, biological rep2

description:
HPRCb
Gene expression data from HKI1105/Tolerant variety root tissue collected on 28th day of sowing.

value: tolerant


title: Germinating wheat seed at P4_biological rep1

description:
Wheat seed_P4-1
Gene expression data from Wheat seed_48 hours after imbibition


title: dentate gyrus, sham operated, 14 days, biological rep1

description: MiRNA expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 14 days after electrical stimulation of amygdala


title: BMM_uninfected_6hr_rep1

description:
6C1
Gene expression after 6 hr without infection

tag: replicate


title: dentate gyrus, sham operated, 14 days, biological rep2

tag: genotype


title: Germinating wheat seed at P3_biological rep3

description:
Wheat seed_P3-3
Gene expression data from Wheat seed_36 hours after imbibition

source_name: Wheat seed_36 hours after imbibition


title: DTF2  85˚C replicate 1

city: Sanda

first: Ryota

last: Hidese

state: Hyogo

address: Gakuen 2-1

department: School of Science and Technology

institute: Kwansei-Gakuin University

description:
Technical replicate 1 of 2. DTF2 grown at 85˚C
DTF2-85-rep1

hyb_protocol: The labeled cDNA was dissolved in hybridization buffer (30 µl) containing 6×SSC (1×SSC is 0.1 M NaCl, 0.015 M sodium citrate), 0.2% Sodium lauryl sulfate, 5×Denhard's solution (Sigma-Aldrich), and 0.1 mg/ml denatured salmon sperm DNA. Hybridization was perfomed under a coverslip (Spaced cover glass XL, Takara bio) in a humidity chamber at 65˚C for 15 h. After hybridiztion, the microarray plates were washed four times with 2×SSC and 0.2% SDS at 55˚C for 5 min, rinsed in 0.05×SSC, and dried by centrifugation.

scan_protocol: The intensities of the Cy3 and Cy5 dyes were measured by using an Affymetrix 428 array scanner (Affymetrix)

data_processing: The microarray images were analyzed using ImaGene version 5.5 software (Biodiscovery) using a local background correction. For normalization of data, global intensity normalization was performed.

organism: Thermococcus kodakarensis

label_protocol: 10 µg of total RNA was annealed with random hexamers, and reverse transcription was performed in solutions containing CyDye-labeled dUTP (GE Healthcare). RNA was subsequently degraded with RNase H, and the labeled cDNA was purified by using a QiaQuick PCR purification kit (Qiagen).

growth_protocol: KU216, DTF1, and DTF2 strains were individually cultivated at 60°C, 85°C, and 93°C in the rich media supplemented with elemental sulfur. Cells were harvested in the late-logarithmic phase.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen).

treatment_protocol: The grown cells were freezed at -80˚C prior to RNA extraction.

tag: genotype/variation

value: ∆tk2287, ∆pyrF

tag: growth tempature

value: ∆pyrF

tag: growth temperature


title: dentate gyrus, stimulated, 7 days, biological rep4

description: MiRNA expression data from the left dentate gyrus from stimulated rats sacrificed after 7 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from stimulated animal sacrificed after 7 days after electrical stimulation of amygdala

value: Sprague-Dawley

value: dentate gyrus


title: BMM_mutLm_6hr_rep3

description:
6B3
Gene expression after 6 hr infection with mutant L. monocytogenes

source_name: BMMs_mutant Listeria monocytogenes_6hr

value: BALB/C

value: L. monocytogenes plcB∆pro mutant strain


title: DTF2  93˚C replicate 1

description:
Technical replicate 1 of 2. DTF2 grown at 93˚C
DTF2-93-rep1


title: DTF2  93˚C replicate 2

description:
Technical replicate 2 of 2. DTF2 grown at 93˚C
DTF2-93-rep2


title: BMM_wtLm_6hr_rep2

description:
6A2
Gene expression after 6 hr infection with wild type L. monocytogenes

source_name: BMMs_wild type Listeria monocytogenes_6hr

value: L. monocytogenes wild-type strain


title: dentate gyrus, stimulated, 7 days, biological rep3

value: electrical stimulation of amygdala


title: DTF2  60˚C replicate 2

description:
Technical replicate 2 of 2. DTF2 grown at 60˚C
DTF2-60-rep2


title: BMM_mutLm_6hr_rep2

description:
6B2
Gene expression after 6 hr infection with mutant L. monocytogenes

value: bone marrow derived macrophages (BMMs)


title: Germinating wheat seed at P3_biological rep1

description:
Wheat seed_P3-1
Gene expression data from Wheat seed_36 hours after imbibition


title: BMM_wtLm_6hr_rep1

description:
6A1
Gene expression after 6 hr infection with wild type L. monocytogenes

value: 6 hours


title: BMM_mutLm_6hr_rep1

description:
6B1
Gene expression after 6 hr infection with mutant L. monocytogenes


title: Germinating wheat seed at P3_biological rep2

description:
Wheat seed_P3-2
Gene expression data from Wheat seed_36 hours after imbibition


title: DTF2  60˚C replicate 1

description:
Technical replicate 1 of 2. DTF2 grown at 60˚C
DTF2-60-rep1


title: BMM_wtLm_6hr_rep3

description:
6A3
Gene expression after 6 hr infection with wild type L. monocytogenes


title: DTF2  85˚C replicate 2

description:
Technical replicate 2 of 2. DTF2 grown at 85˚C
DTF2-85-rep2


title: dentate gyrus, stimulated, 7 days, biological rep5


title: Germinating wheat seed at P2_biological rep3

description:
Wheat seed_P2-3
Gene expression data from Wheat seed_24 hours after imbibition

source_name: Wheat seed_24 hours after imbibition


title: Germinating wheat seed at P2_biological rep2

description:
Wheat seed_P2-2
Gene expression data from Wheat seed_24 hours after imbibition


title: dentate gyrus, stimulated, 7 days, biological rep1


title: dentate gyrus, stimulated, 7 days, biological rep2


title: DTF1  93˚C replicate 2

description:
Technical replicate 2 of 2. DTF1 grown at 93˚C
DTF1-93-rep2

value: ∆tk1280, ∆pyrF


title: dentate gyrus, sham operated, 7 days, biological rep5

description: MiRNA expression data from the left dentate gyrus from sham operated rats – time match control for stimulated animal sacrificed after 7 days after electrical stimulation of amygdala

source_name: Left dentate gyrus from sham operated animal, time matched control for stimulated animal sacrificed after 7 days after electrical stimulation of amygdala

value: sham operated


title: dentate gyrus, sham operated, 7 days, biological rep4


title: DTF1  93˚C replicate 1

description:
Technical replicate 1 of 2. DTF1 grown at 93˚C
DTF1-93-rep1


title: Germinating wheat seed at P2_biological rep1

description:
Wheat seed_P2-1
Gene expression data from Wheat seed_24 hours after imbibition


title: DTF1  85˚C replicate 2

description:
Technical replicate 2 of 2. DTF1 grown at 85˚C
DTF1-85-rep2


title: dentate gyrus, sham operated, 7 days, biological rep3


title: DTF1  85˚C replicate 1

description:
Technical replicate 1 of 2. DTF1 grown at 85˚C
DTF1-85-rep1


title: BMM_uninfected_3hr_rep2

description:
3C2
Gene expression after 3 hr without infection

source_name: BMMs_no infection_3hr

value: none (uninfected control)

value: 3 hours


title: dentate gyrus, sham operated, 7 days, biological rep2


title: DTF1  60˚C replicate 2

description:
Technical replicate 2 of 2. DTF1 grown at 60˚C
DTF1-60-rep2


title: Germinating wheat seed at P1_biological rep3

description:
Wheat seed_P1-3
Gene expression data from Wheat seed_12 hours after imbibition

source_name: Wheat seed_12 hours after imbibition

value: Jimai 20

value: germinating seeds


title: DTF1  60˚C replicate 1

description:
Technical replicate 1 of 2. DTF1 grown at 60˚C
DTF1-60-rep1


title: dentate gyrus, sham operated, 7 days, biological rep1


title: Germinating wheat seed at P1_biological rep1

description:
Wheat seed_P1-1
Gene expression data from Wheat seed_12 hours after imbibition


title: Germinating wheat seed at P1_biological rep2

description:
Wheat seed_P1-2
Gene expression data from Wheat seed_12 hours after imbibition


title: Germinating wheat seed at P0_biological rep3

description:
Wheat seed_P0-3
Gene expression data from Wheat seed_before imbibition (0 hour)

source_name: Wheat seed_before imbibition (0 hour)


title: BMM_mutLm_3hr_rep1

description:
3B1
Gene expression after 3 hr infection with mutant L. monocytogenes

source_name: BMMs_mutant Listeria monocytogenes_3hr


title: Germinating wheat seed at P0_biological rep2

description:
Wheat seed_P0-2
Gene expression data from Wheat seed_before imbibition (0 hour)


title: BMM_uninfected_3hr_rep1

description:
3C1
Gene expression after 3 hr without infection


title: BMM_wtLm_3hr_rep3

description:
3A3
Gene expression after 3 hr infection with wild type L. monocytogenes

source_name: BMMs_wild type Listeria monocytogenes_3hr


title: BMM_wtLm_3hr_rep1

description:
3A1
Gene expression after 3 hr infection with wild type L. monocytogenes