title: 2590T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2590


title: MDA468 37oC rep6

status: Public on Dec 01 2013

type: RNA

city: El Paso

first: Brad

middle: Allen

last: Bryan

state: Texas

address: 5001 El Paso Drive

department: Biomedical Sciences

country: USA

institute: Texas Tech University Health Sciences Center

hyb_protocol: 750 ng of biotinylated aRNA was  briefly heat-denatured and loaded onto expression arrays to hybridize overnight.  Following hybridization, arrays were labeled with Cy3-streptavidin.

scan_protocol: The chips were imaged on the Illumina ISCAN.  Intensity values were transferred to GeneSpring GX microarray analysis software (Agilent).

data_processing: GeneSpring GX microarray analysis software (Agilent) was used to filter data based on quality of each call. Statistical relevance was determined using ANOVA with a Benjamini Hochberg FDR multiple testing correction (p-value < 0.05).

molecule: total RNA

organism: Homo sapiens

source_name: MDA468 37oC

label_protocol: RNA was amplified and biotin-labeled using Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: MCF10A, MCF7, MDA231, and MDA468 cells were maintained at constant 37oC as a control.  For the experimental treatment, prewarmed (45oC) conditioned media was added to each cell line and the cells were incubated for 30 minutes.  The 45oC media was then replaced with 37oC conditioned media.  Cells were allowed to grow for 4 hours and RNA was subsequently extracted.

extract_protocol: Total RNA was collected from each cell line 4 hours after completion of the hyperthermia treatment using the Qiagen RNAeasy mini kit.

tag: cell line

tag: cell type

value: breast cancer cells

tag: treatment

value: 37oC control

tag: replicate


title: 2964N

type: genomic

city: Pittsburgh

first: William

middle: Armand

last: LaFramboise

state: PA

address: 5230 Centre Avenue

department: Pathology

institute: University of Pittsburgh

description: hybridized to SNP6.0

hyb_protocol: Affymetrix 6.0

scan_protocol: Affymetrix 6.0

data_processing:
GCOS to Partek Segmentation
primary data description: SNPs and CNV

label: streptavidin phycoerythrin

molecule: genomic DNA

source_name: Normal tissue from patient 2964

label_protocol: Affymetrix 6.0

extract_protocol: QiaAmp DNA FFPE Tissue Kit

tag: tissue

value: benign lymph node


title: red2∆ 1

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: This sample is of S.pombe that lacks the red2 gene.

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: Schizosaccharomyces pombe

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

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA: 0.5% Yeast extract, 3% glucose, 75mg/L adenine) at 30˚C.

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Applied Biosystems) according manufacturer's instructions.

tag: strain


title: MDA468 37oC rep3


title: MDA468 37oC rep4


title: wild-type 2

description: This sample is of wild-type S.pombe.

value: wild-type


title: 2590N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2590


title: 2582T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2582

value: esophageal adenocarcinoma tumor


title: wild-type 1

description: This sample is of wild-type S.pombe.


title: 11260.p1

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: sample id

tag: gender

value: Male

tag: sentrix id

tag: sentrix position

value: A

tag: experiment

tag: group

tag: family

tag: distribution

value: leukocyte


title: 2582N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2582


title: MDA468 37oC rep1


title: SKNDZ-Negative Control-1

city: Taipei

first: Sheng-Kai

last: Chang

address: NO.1 JEN AI ROAD SECTION 1 TAIPEI 100 TAIWAN R.O.C.

department: Clinical Laboratory Science of Medical Biotechnology

country: Taiwan

institute: NATIONAL TAIWAN UNIVERSITY COLLEGE OF MEDICINE

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArrayR (HOA5.1) with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42℃ 5 mins；Wash Ⅱ 42℃, 5 mins, 25℃, 5 mins; Wash Ⅲ rinse 20 times), and the slides were dried by centrifugation and scanned by an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

scan_protocol: The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing:
The technical repeat data was tested by Pearson correlation coefficient calculation to check the reproducibility (R value > 0.975). The signal intensity of each spot was loaded into Rosetta Resolver SystemR (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver SystemR could remove both systematic and random errors. In brief, spots which ﬂag is less than 0 in all arrays were filtered out.
Spots that passed the criteria were normalized by median scaling normalization method. Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups under Rosetta Resolver error model adjustment. The spots with log2 ratio ≥ 1 or log2 ratio ≤ -1 and p-value < 0.05 are tested for further analysis.

source_name: SKNDZ-Negative Control-1

label_protocol: Fluorescent aRNA targets were prepared from 2.5 μg total RNA samples using OneArrayR Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: A total of 1 x 10^6 SKNDZ cells treated with either scramble shRNA or miR-125b-2 were harvested, and total RNA were extracted by TRIzol® reagent.

value: Neuroblastoma

value: SKNDZ

value: Scramble shRNA


title: 2515T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2515


title: 2515N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2515


title: 11102.p1

hyb_protocol: Followed the manufacturer's (Illumina) specifications

value: C


title: 11300.p1

value: L

tag: site

value: fl

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: white


title: MDA468 37oC rep2

tag: cell line

tag: cell type


title: 2514T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2514


title: 2514N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2514


title: MDA231 45oC rep2

source_name: MDA231 45oC

tag: treatment

value: 45oC hyperthermia shock for 30 minutes

tag: replicate


title: 11168.p1

value: I

value: hv


title: 11271.s1

value: J


title: 2460T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2460

tag: tissue


title: MDA231 45oC rep3

value: breast cancer cells


title: 11026.p1.2

tag: sample id

value: D


title: MDA231 45oC rep1


title: MDA231 37oC rep6

source_name: MDA231 37oC

value: 37oC control


title: 2417T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2417

value: esophageal adenocarcinoma tumor


title: 11102.s1

tag: gender

value: Male


title: 11076.s1

tag: sentrix id

value: K

value: leukocyte


title: 11186.s1

tag: sentrix position

value: F


title: MDA231 37oC rep5


title: 2417N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2417

value: benign lymph node


title: MDA231 37oC rep4


title: 2880N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2880


title: 11014.p1

value: E

tag: experiment


title: 2460N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2460


title: 2411T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2411


title: MDA231 37oC rep1


title: MDA231 37oC rep3


title: MDA231 37oC rep2


title: MCF10A 45oC rep2

source_name: MCF10A 45oC

value: mammary epithelial cells


title: MCF10A 45oC rep3


title: 2411N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2411


title: 11124.p1

source_name: leukocyte

tag: group

value: kr


title: 11293.s1

value: B

tag: family


title: 11579.s1

value: C

tag: distribution


title: 2361T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2361


title: 2368N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2368


title: 2368T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2368


title: MCF10A 45oC rep1

value: 45oC hyperthermia shock for 30 minutes


title: 11053.p1

value: H

tag: site

value: fl

value: white


title: 11186.p1


title: 2361N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2361


title: 2359T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2359


title: MCF10A 37oC rep2

source_name: MCF10A 37oC


title: 11192.p1


title: 11146.p1

value: pb

tag: cpea dx


title: MCF10A 37oC rep3

value: 37oC control


title: 11005.s1.1

value: L


title: 2359N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2359


title: 2339T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2339

value: esophageal adenocarcinoma tumor


title: MCF10A 37oC rep1


title: 11345.p1

value: Male

value: xm

tag: age at collection (months)

value: more-than-one-race


title: 11138.p1

value: A

value: leukocyte


title: 11293.p1

value: J


title: 2339N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2339

value: benign lymph node


title: 11192.s1

value: K


title: Pc

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: gene expression in the hippocampi of 2 month old PNFLX rats which received fluoxetine from P2-P27

hyb_protocol: 600 ng  cy3 labeled samples for 8x15 arrays 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: Scanned on an Agilent Technologies G2505C scanner and Images were quantified using Agilent Feature Extraction Software 10.5.1.1

data_processing: The normalization was done using GeneSpring GX 11 Software. 75th percentile shift normalization was done.

organism: Rattus norvegicus

source_name: hippocampal tissue, PNFLX 3

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the  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.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: pups received either fluoxetine (10mg/kg) or vehicle (5% sucrose solution) from postnatal day 2 (P2) to P21, to give rise to the groups PNFLX and Control respectively.

value: whole hippocampi


title: VGLL4 HUES6 3

city: Santa Clara

first: Adriana

last: Tajonar

state: California

address: 3707 Poinciana Drive

institute: Harvard University

description: lentivirus-transduced

hyb_protocol: Following Illumina instructions

scan_protocol: Following Illumina instructions

data_processing: normalized in BeadStudio using the using the average normalization.

label: biotin

source_name: human embryonic stem cells cultured with mouse embryonic fibroblasts

label_protocol: Following Illumina instructions

growth_protocol: HUES6 were plated on irradiated murine embryonic fibroblasts (MEFs) and grown in media containing KO-DMEM (Invitrogen), 10% Knockout Serum Replacement (KOSR, GIBCO), 10% human plasma fraction (Talecris), 2 mM L-glutamine (Invitrogen), 0.1 mM non-essential amino acids (GIBCO), 0.055 mM β-Mercaptoethanol (GIBCO), and 10 ng/ml bFGF (Invitrogen).

extract_protocol: Cells were trypsinized and RNA was purified from total cultures in quadruplicates (biological replicates) using a Qiagen RNeasy kit and 200 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit.

treatment_protocol: HUES6 VGLL4 were transduced with a lentivirus carrying the human VGLL4 open reading frame.

value: VGLL4 overexpression


title: 2330T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2330


title: VGLL4 HUES6 4

description: lentivirus-transduced


title: VGLL4 HUES6 2

description: lentivirus-transduced


title: 2330N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2330


title: 11026.s1.2

value: H

value: hv

tag: ethnicity


title: 11053.s1.1

value: fl

value: white


title: VGLL4 HUES6 1

description: lentivirus-transduced

tag: cell line


title: Pb

description: gene expression in the hippocampi of 2 month old PNFLX rats which received fluoxetine from P2-P26

source_name: hippocampal tissue, PNFLX 2


title: wildtype HUES6 1

description: control

value: control


title: wildtype HUES6 4

description: control


title: wildtype HUES6 3

description: control


title: Pa

description: gene expression in the hippocampi of 2 month old PNFLX rats which received fluoxetine from P2-P25

source_name: hippocampal tissue, PNFLX 1


title: wildtype HUES6 2

description: control


title: 11063.p1

value: E

value: kr

tag: cell type


title: 11271.p1

value: Male

value: G


title: 11149.s1

value: D


title: Pd

description: gene expression in the hippocampi of 2 month old PNFLX rats which received fluoxetine from P2-P28

source_name: hippocampal tissue, PNFLX 4


title: Cd

description: gene expression in the hippocampi of 2 month old control rats which received vehicle from P2-P24

source_name: hippocampal tissue, control 4


title: Histamine_3

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

description:
Sample name: 101615-06
triplicate

hyb_protocol: HumanHT12 v.4 Expression BeadChip, 750ng of bitinylated cRNA used

scan_protocol: Illumina iScan array scanner

data_processing: Illumina Genomestudio v.2010.1 with default settings.  Normalized and transformed values derived using the lumi package.

source_name: HaCaT

label_protocol: biotinylation of cRNA

growth_protocol: HaCaT cells were grown in DMEM medium (1.5mM Ca), supplemented with 10% FCS, p/s and glu

extract_protocol: Qiagen RNeasy Plus Mini Ki

treatment_protocol: samples were exposed to histamine at 1ug/ml for 24h

value: keratinocyte line HaCaT

tag: agent

value: Histamine


title: 2303T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2303

value: esophageal adenocarcinoma tumor


title: 11349.p1

source_name: leukocyte

value: F

value: asian

value: leukocyte


title: 11260.s1

value: C


title: 2303N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2303

value: benign lymph node


title: 2264N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2264


title: 2257T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2257


title: 2257N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2257


title: Cc

description: gene expression in the hippocampi of 2 month old control rats which received vehicle from P2-P23

source_name: hippocampal tissue, control 3

value: whole hippocampi


title: 2207T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2207


title: Histamine_1

description:
Sample name: 101615-04
triplicate


title: 11346.p1

value: K

value: kc


title: Cb

description: gene expression in the hippocampi of 2 month old control rats which received vehicle from P2-P22

source_name: hippocampal tissue, control 2


title: 11178.p1

value: A

value: fl

value: white


title: miR-139-5p rep 3

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were preprocessed by Bioconductor lumi package (version 2.2.1). It was background adjusted, vst transformed and rsn normalized. Probes that did not have a detection p-value < 0.01 in all of the mock-transfected replicates were excluded from further analysis.

source_name: MCF7 cells

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

growth_protocol: HEK293T cells were grown in DMEM according to ATCC recommendations.

extract_protocol: Cells were harvested  24 hours post transfection, and the miRNAs and their bound targets were isolated using streptavidin myOne C1 Dynabeads. Beads were washed before RNA extraction using an RNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 200pmols of synthetic biotin-labeled miRNA duplexes were transfected into HEK293T cells using HiPerFect Transfection Reagent (Qiagen).

tag: transfection molecule

tag: pull-down

value: pull-down


title: 2194T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2194

tag: tissue


title: 11307.p1

tag: sample id

tag: gender

value: Male

value: J


title: Ca

description: gene expression in the hippocampi of 2 month old control rats which received vehicle from P2-P21

source_name: hippocampal tissue, control 1


title: miR-139-5p input rep 3

description: replicate 3


title: miR-139-5p input rep 2

description: replicate 2


title: Control_2

description:
Sample name: 101698-09
triplicate

value: keratinocyte line HaCaT

value: Control


title: 11402.s1

tag: sentrix id

tag: sentrix position

value: E


title: Hippocampus_8mon 4

city: Ansan

first: Hyemyung

last: Seo

address: Hanyang University

country: South Korea

institute: Hanyang University

description: Gene expression data from hippocampus of AD mutant mouse at 8 months of age

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA

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

data_processing: The data were analyzed with affy package using R.

organism: Mus musculus

source_name: Hippocampus, mutant

label_protocol: standard Affymetrix protocol

growth_protocol: Tg6799 transgenic mice were purchased from The Jackson Laboratory (USA) and were housed under a 12h light-dark cycle with free access to food and water

extract_protocol: RNA samples were isolated fromhippocampus of mouse brain region in TRI-Reagent (Sigma-Aldrich, St. Louis, MO) and total RNA was isolated using a phenol/chloroform protocol (Sigma-Aldrich).

value: Brain Hippocampus

tag: genotype

value: AD mutant

tag: age

value: 8 months

value: femlale

tag: strain


title: 2207N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2207

value: benign lymph node


title: Hippocampus_8mon 2

description: Gene expression data from hippocampus of littermate control at 8 months of age

source_name: Hippocampus, littermate

value: littermate


title: Hippocampus_8mon 1


title: 11026.p1.1

value: G

tag: experiment

tag: group

tag: family

tag: distribution

tag: site

value: hv

value: leukocyte


title: 11256.p1

value: H

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

tag: cell type


title: Hippocampus_4mon 4

description: Gene expression data from hippocampus of AD mutant mouse at 4 months of age

tag: tissue

value: 4 months


title: 11218.p1

tag: sample id

value: F

value: pb

value: white


title: Hippocampus_8mon 3

tag: gender


title: miR-139-5p rep 2

description: replicate 2

tag: cell line

tag: transfection molecule

tag: pull-down

value: pull-down


title: Histamine_2

description:
Sample name: 101615-05
triplicate

value: keratinocyte line HaCaT

tag: agent

value: Histamine


title: Hippocampus_4mon 3

value: Brain Hippocampus

tag: genotype

tag: age

tag: strain


title: Control_1

description:
Sample name: 101698-08
triplicate

value: Control


title: Control_3

description:
Sample name: 101698-10
triplicate


title: 2194N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2194


title: 2160T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2160

value: esophageal adenocarcinoma tumor


title: 2160N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2160


title: 2152T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2152


title: miR-139-5p input rep 1

description: replicate 1


title: 2152N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2152


title: miR-139-5p rep 1

description: replicate 1


title: 2147T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2147


title: 2147N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2147


title: 2131T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2131


title: 2131N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2131


title: 2264T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2264


title: 11459.p1

source_name: leukocyte

value: Male

tag: sentrix id

tag: sentrix position

value: K

tag: experiment

tag: group

tag: family

value: xm


title: 11285.s1.1

value: I

tag: distribution

tag: site

value: oi

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: 11089.p1

tag: sample id

tag: gender

value: C

tag: cell type

value: leukocyte


title: 2108T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2108

tag: tissue


title: Ets2 null fibroblasts with the ErbB oncogene present in epithelial cells

city: Columbus

first: Julie

last: Wallace

state: OH

address: 460 W. 12th Ave 840 BRT

institute: OSUCCC

description: Gene expression data from mammary fibroblasts with Ets2 deletion and the ErbB2 oncogene present in epithelial cells

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45ºC on Mouse Genome 430A 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression levels were estimated from GeneChip® probe intensities using robust multi-array average (RMA) normalization and background-correction algorithms.

label: Biotin

source_name: Fibroblasts isolated from mammary gland with Ets2 deletion in fibroblasts and the ErbB2 oncogene present in epithelial cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Fibroblasts were isolated from mammary gland tissue using a modified protocol for gravity separation.

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

treatment_protocol: Fibroblasts were grown in 10% FBS DMEM in a 37º incubator with 7% CO2.

value: FVB/N

value: 16 Weeks

value: Mammary Gland

value: Fibroblasts

tag: genotype


title: miR-182-iso rep 2

description: replicate 2

source_name: HEK293T cell

tag: cell line

tag: transfection molecule

tag: pull-down

value: pull-down


title: miR-182-iso rep 1

description: replicate 1


title: Hippocampus_4mon 2

description: Gene expression data from hippocampus of littermate control at  4 months of age

value: littermate

tag: age

value: 4 months

value: femlale

tag: strain


title: Ets2 deleted in surrounding fibroblasts with PyMT oncogene expression in epithelial cells_FPE101.4

description: Gene expression data from mammaryendothelial cells with Ets2 deletion in fibroblasts and the PyMT oncogene present in epithelial cells

source_name: Endothelial cells isolated from mammary gland with Ets2 deletion in fibroblasts and the PyMT oncogene present in epithelial cells

label_protocol: Total RNA was amplified using Ovation® RNA Amplification System V2, and afterwards biotinylated cRNA was prepared using Encore™Biotin Module.  Biotinylated cRNA was hybridized to chips according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Endothelial cells were isolated from mammary gland tissue after a short collagenase digestion and florescence activated cell sorting using a CD31 specific antibody.

treatment_protocol: Endothelial cells were placed in Trizol directly after sorting.

value: 9 Weeks

value: Endothelial Cells


title: Hippocampus_4mon 1

description: Gene expression data from hippocampus of littermate control at 4 months of age

value: Brain Hippocampus


title: miR-17-5p rep 1

description: replicate 1


title: 11381.p1

value: Male

tag: sentrix id

tag: sentrix position

value: H

tag: experiment

tag: group

value: kr

value: not-specified


title: VB0123

value: VB

value: F


title: 11366.p1

value: B

tag: family

tag: distribution

tag: site

value: fl

tag: cpea dx

value: white

value: leukocyte


title: 11257.p1

tag: sample id

tag: gender

value: L

value: xm

tag: age at collection (months)

tag: ethnicity


title: miR-27a rep 2

description: replicate 2

tag: cell line

value: pull-down


title: miR-17-5p rep 3

description: replicate 3

tag: transfection molecule


title: Ets2 deleted in surrounding fibroblasts with PyMT oncogene expression in epithelial cells_FPE103.4

value: FVB/N

tag: tissue

value: Mammary Gland

tag: cell type

tag: genotype


title: 11008.s1

tag: sentrix id

value: C

value: sb


title: miR-23b rep 2

description: replicate 2

tag: pull-down


title: miR-17-5p-iso rep 2

description: replicate 2


title: 2108N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2108

value: benign lymph node


title: 2056T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2056

value: esophageal adenocarcinoma tumor


title: 11018.p1

value: Male

tag: sentrix position

value: J

tag: experiment

value: ox


title: 2056N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2056


title: miR-17-5p-iso rep 3

description: replicate 3


title: 11415.p1

tag: group

tag: family


title: 2041T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2041


title: 11437.p1

value: D

tag: distribution

tag: site


title: 11399.p1

tag: sample id

value: A

tag: cpea dx


title: Ets2 null fibroblasts with no oncogene present in epithelial cells

description: Gene expression data from mammary fibroblasts with Ets2 deletion and no oncogene present in epithelial cells

source_name: Fibroblasts isolated from mammary gland with Ets2 deletion in fibroblasts and no oncogene present in epithelial cells

tag: strain

tag: age

value: 16 Weeks

value: Fibroblasts


title: Ets2 present in fibroblasts with no oncogene present in epithelial cells

description: Gene expression data from mammary fibroblasts with Ets2 and no oncogene present in epithelial cells

source_name: Fibroblasts isolated from mammary gland with Ets2 present in fibroblasts and no oncogene present in epithelial cells


title: 2041N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2041


title: Ets2 present in surrounding fibroblasts with PyMT oncogene expression in epithelial cells_FPE106.7

description: Gene expression data from mammary endothelial cells with Ets2 present in fibroblasts and the PyMT oncogene present in epithelial cells

source_name: Endothelial cells isolated from mammary gland with Ets2 present in fibroblasts and no oncogene present in epithelial cells

value: 9 Weeks

value: Endothelial Cells


title: 1980T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 1980


title: miR-27a rep 3

description: replicate 3

tag: cell line


title: 1980N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 1980


title: 191T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 191


title: 11305.p1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

tag: gender

value: I

value: kr

tag: age at collection (months)

tag: ethnicity

value: white

value: leukocyte


title: Ets2 deleted in surrounding fibroblasts with PyMT oncogene expression in epithelial cells_FPE104.14

value: FVB/N

tag: tissue

value: Mammary Gland

tag: cell type

tag: genotype


title: 11452.p1

tag: sentrix id

tag: sentrix position

value: C


title: Jmjd2b_KD_3

city: Shanghai

first: Zhen

last: Shao

address: 320 Yueyang Road

country: China

institute: Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

description: Jmjd2b shRNA KD in mESCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed by dchip and arrays were normalized against the baseline array that has the median brightness.

source_name: Mouse ES cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mESCs were grown in standard mouse ES cells media with LIF

extract_protocol: Total RNA was extracted using RNAeasy plus mini kit according to the manufacturer's instructions.

treatment_protocol: mESCs were collected through trypsinization, washed with PBS twice, followed by RNA extraction

tag: phenotype

value: agouti

value: male

value: ESC

tag: genotype/variation

value: Jmjd2b knockdown


title: miR-27a rep 1

description: replicate 1

tag: transfection molecule

tag: pull-down

value: pull-down


title: H4-II-E-C3_high_rep4

city: Fort Detrick

first: Matthew

last: Permenter

state: MD

address: 568 Doughten Dr

institute: US Army Center for Environmental Health Research

hyb_protocol: Samples were hybridized on the GeneChip Rat Genome 230 2.0 Array using Affymetrix instrumentation according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned on an Affymetrix GeneChip Scanner following the manufacturer's instructions.

data_processing: Microarray data was processed for background adjustment, normalization, and summarization using the Robust Multi-Array Averaging method (RMA) using Partek Genomic Suite (GS) software (Version 6.6, St. Louis, MO).

source_name: H4-II-E-C3 cells exposed to 62 µM CoCl2 for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MH1C1 and H4-II-E-C3 cells (ATCC, Manassas, VA) were grown in Dulbecco's Modified Eagle's Medium (DMEM; Lonza, Walkersville, MD) containing 10% fetal bovine serum (Invitrogen, Carlsbad, CA) and 10 mL Glutamax (Invitrogen) in T75 flasks incubated at 37 °C with 5% carbon dioxide.

treatment_protocol: Exposures of 24 hours in duration were initiated once flasks were confluent using the test chemicals CoCl2.


title: VB0053

source_name: leukocyte

tag: sample id

value: VB

value: Male

value: G

tag: experiment

tag: group


title: miR-17-5p rep 2

description: replicate 2


title: Ets2 present in surrounding fibroblasts with PyMT oncogene expression in epithelial cells_FPE101.1

tag: strain

tag: age

value: 9 Weeks


title: VB0036

tag: gender

value: H


title: miR-17-5p-iso rep 1

description: replicate 1

tag: cell line


title: miR-23b rep 1

description: replicate 1


title: 11052.p1

value: B

tag: family

tag: distribution

tag: site

value: oi

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: 191N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 191

tag: tissue

value: benign lymph node


title: 11009.p1

tag: sentrix id

tag: sentrix position

value: E

value: kr

value: white

tag: cell type

value: leukocyte


title: 11435.p1

tag: sample id

value: F


title: Ets2 present in fibroblasts with the ErbB2 oncogene present in epithelial cells

description: Gene expression data from mammary fibroblasts with Ets2 and the ErbB2 oncogene present in epithelial cells

source_name: Fibroblasts isolated from mammary gland with Ets2 present in fibroblasts and the ErbB2 oncogene present in epithelial cells

value: FVB/N

value: 16 Weeks

value: Mammary Gland

value: Fibroblasts

tag: genotype


title: VB0094

value: VB

value: C

tag: experiment

tag: group


title: Jmjd2b_KD_2

description: Jmjd2b shRNA KD in mESCs

tag: strain

tag: phenotype

value: agouti

value: male

value: ESC

tag: genotype/variation

value: Jmjd2b knockdown


title: H4-II-E-C3_untreated_rep4

source_name: H4-II-E-C3 cells untreated

tag: cell line


title: Jmjd2c_KD_2

description: Jmjd2c shRNA KD in mESCs

tag: gender

value: Jmjd2c knockdown


title: Jmjd2b_KD_1

description: Jmjd2b shRNA KD in mESCs


title: H4-II-E-C3_low_rep4

source_name: H4-II-E-C3 cells exposed to 29 µM CoCl2 for 24 h


title: H4-II-E-C3_high_rep3


title: 180N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 180

value: benign lymph node


title: Ets2 present in surrounding fibroblasts with PyMT oncogene expression in epithelial cells_FPE104.13

tag: age

value: 9 Weeks

value: Endothelial Cells


title: Jmjd2c_KD_1

description: Jmjd2c shRNA KD in mESCs


title: 180T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 180

value: esophageal adenocarcinoma tumor


title: 11013.p1

value: Male

value: K

tag: family

tag: distribution

tag: site

value: xm

tag: cpea dx

value: white

value: leukocyte


title: H4-II-E-C3_low_rep3


title: 163T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 163

tag: tissue


title: Anti-GFP_control KD_3

description: Anti-GFP shRNA KD in mESCs

value: control


title: Anti-GFP_control KD_2

description: Anti-GFP shRNA KD in mESCs


title: H4-II-E-C3_untreated_rep3


title: 11404.p1

tag: sentrix id

tag: sentrix position

value: L

value: xx

tag: age at collection (months)

tag: ethnicity


title: 163N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 163


title: 11370.s1

tag: sample id

value: H

tag: experiment

value: ox

value: more-than-one-race

tag: cell type


title: 175T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 175


title: CH5

value: VB

value: I

tag: group


title: 175N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 175

value: benign lymph node


title: 59T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 59


title: H4-II-E-C3_high_rep2


title: CH4

value: G


title: 59N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 59


title: H4-II-E-C3_high_rep1


title: 11054.p1

value: C

value: hv


title: H4-II-E-C3_untreated_rep1


title: H4-II-E-C3_low_rep2


title: Anti-GFP_control KD_1

description: Anti-GFP shRNA KD in mESCs

tag: strain

tag: phenotype

value: agouti

value: male

value: ESC

tag: genotype/variation


title: 11383.p1

tag: gender

value: Male

value: A

value: white


title: H4-II-E-C3_low_rep1

tag: cell line


title: 11488.p1

value: B

tag: family

tag: distribution

value: leukocyte


title: H4-II-E-C3_untreated_rep2


title: 11296.p1

value: L

tag: site

value: sb

tag: cpea dx


title: Threat 4

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description:
Affymetrix MOE430 2.2
126186-124002.CEL

hyb_protocol: Standard Affymetrix hybridization protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

scan_protocol: Standard Affymetrix scan protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

data_processing: RMA (RMAExpress) processing of Affymetrix .CEL files generated by UCLA DNA Microarray Core.

source_name: CD11b+ splenocytes

label_protocol: Standard Affymetrix probe synthesis for gene expression profiling (carried out in UCLA DNA Microarray Core).

extract_protocol: Primary CD11b+ monocytes were isolated by immunomagnetic positive selection of adherent splenocytes, and total RNA was extracted using Qiagen RNEasy.

tag: stress

value: HighThreat

value: CD11b+ splenocytes


title: 11094.p1

tag: sentrix id

tag: sentrix position

value: K


title: Threat 3

description:
Affymetrix MOE430 2.3
126185-124001.CEL


title: Control pool 3-4

description:
Affymetrix MOE430 2.7
126181-123997.CEL

value: LowThreat


title: MH1C1_high_rep4

source_name: MH1C1 cells exposed to 310 µM CoCl2 for 24 h


title: MH1C1_low_rep4

source_name: MH1C1 cells exposed to 160 µM CoCl2 for 24 h


title: Control pool 5-6

description:
Affymetrix MOE430 2.6
126182-123998.CEL


title: Threat 5

description:
Affymetrix MOE430 2.1
126187-124003.CEL


title: VB0076

value: VB

value: J


title: MH1C1_high_rep3


title: Threat 1

description:
Affymetrix MOE430 2.5
126183-123999.CEL


title: MH1C1_untreated_rep4

source_name: MH1C1 cells untreated


title: Threat 2

description:
Affymetrix MOE430 2.4
126184-124000.CEL


title: Threat 6

description:
Affymetrix MOE430 2.0
126188-124004.CEL


title: Control pool 1-2

description:
Affymetrix MOE430 2.8
126180-123996.CEL


title: Control 3T3 cells C2_B_1

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

institute: National Cancer Center Reseach Institute

description: Gene expression data using Mouse Expression Array 430B

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 ﾟC on GeneChip Mouse Expression Array Set 430. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings by Expression Console ver 1.1.

source_name: BALB 3T3

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: Cells were cultured with MEM Prime medium (Invitrogen) supplemented with 10% fetus calf serum, with or without neomycin depending on cell type, in a humidified C02 incubator.

extract_protocol: RNA was extracted using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Plasmid pTE40, containing mucAB ligated to the mouse metalothionein promoter, was introduced into 3T3 cells using Dharma FECT (Thermo) and selected for neo resistance. Selected clones were confirmed for the presence of full length mucAB.

value: BALB/c

tag: treatment

value: non-treated 3T3 cells


title: 11437.s1

source_name: leukocyte

tag: sample id

value: F

value: xm

tag: age at collection (months)

tag: ethnicity


title: Control 3T3 cells C2_B_2

tag: cell type


title: MH1C1_high_rep2


title: MH1C1_low_rep3


title: 11046.p1

value: Male

tag: experiment

tag: group


title: MH1C1_untreated_rep3


title: VB0070


title: Transformed 3T3 cells by mucAB 72_B_2

tag: strain

value: transformed 3T3 cells by mucAB


title: Transformed 3T3 cells by mucAB 63_B_2


title: MH1C1_low_rep2


title: VB0056

tag: gender

value: I


title: MH1C1_high_rep1

tag: cell line


title: Transformed 3T3 cells by mucAB 72_B_1


title: MH1C1_untreated_rep2


title: VB0008

value: D


title: 11417.p1

tag: family

value: kc

value: asian

value: leukocyte


title: VB0017


title: Transformed 3T3 cells by mucAB 52_B_1


title: Transformed 3T3 cells by mucAB 52_B_2


title: MH1C1_low_rep1


title: Transformed 3T3 cells by mucAB 63_B_1


title: 11201.p1

value: E

tag: distribution

value: hv

value: white


title: MH1C1_untreated_rep1


title: Transformed 3T3 cells by mucAB 12_B_2


title: 11492.p1

value: L


title: Transformed 3T3 cells by mucAB 12_B_1


title: 11398.p1

value: K

tag: site


title: Control 3T3 cells C2_2

description: Gene expression data using Mouse Expression Array 430A


title: Transformed 3T3 cells by mucAB 72_2


title: NGP neuroblastoma NP group biological control rep 2

city: New York

first: Darrell

middle: Jiro

last: Yamashiro

state: NY

address: 1130 St. Nicholas Ave, Room 924A

department: Pediatrics

institute: Columbia University

description:
NP.828-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy

hyb_protocol: 15E-6 g of biotinylated cRNA were hybridized to HG-U133A 2.0 gene chip.

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: The CEL files were normalized and summarized into probe-set values using RMA normalization.

source_name: NGP neuroblastoma_NOTCH1 decoy_control

label_protocol: cRNA was labeled and fragmented using Affymetrix GeneChip 3'IVT express kit according to Affymetrix protocol

growth_protocol: 1 x 106 cells were injected intrarenally into 4-6 week old NCR female nude mice

extract_protocol: Total RNA was isolated from tumors by guanidine thiocyanate method using Qiagen miRNeasy mini kit

treatment_protocol: NGP-LacZ and NGP-Notch1 decoy (N1D) tumor-bearing mice were randomized one week after implantation. At this time, 28 mice in each group were treated with 100 ug mouse albumin (Sigma Aldrich) (placebo), and another 28 with 250 ug bevacizumab (10 mg/kg BV, Genentech) by intraperitoneal injection biweekly until time of sacrifice.

tag: host strain background

value: NCR nude mice

tag: host strain gender

value: female

tag: host strain age

value: 4-6 weeks

tag: tissue

value: NGP neuroblastoma cells

tag: transfected with

value: NGP-Notch1 decoy (N1D)

tag: treated with

value: 100 ug mouse albumin (placebo)


title: Control 3T3 cells C2_1

value: BALB/c

tag: treatment

value: non-treated 3T3 cells


title: NGP neuroblastoma NP group biological control rep 5

description:
NP.832-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy


title: NGP neuroblastoma NP group biological control rep 3

description:
NP.829-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy


title: NGP neuroblastoma NP group biological control rep 4

description:
NP.831-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy


title: 11194.p1

tag: sample id

value: Male

tag: sentrix id

tag: sentrix position

value: G

value: fl

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: 11546.p1

tag: gender

value: H

tag: experiment

tag: group

value: sb

tag: cell type

value: leukocyte


title: Transformed 3T3 cells by mucAB 72_1

tag: strain

value: transformed 3T3 cells by mucAB


title: Transformed 3T3 cells by mucAB  63_2


title: NGP neuroblastoma NP group biological control rep 6

description:
NP.833-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy

tag: host strain background

tag: host strain gender


title: NGP neuroblastoma NP group biological control rep 1

description:
NP.826-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy

tag: host strain age

tag: tissue


title: 11230.p1.1

value: E

tag: family

tag: distribution

tag: site

value: white


title: NGP neuroblastoma NBV group, biological rep 6

description:
NBV.392-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy,  treated with Bevacizumab

value: NCR nude mice

tag: transfected with

tag: treated with

value: 250ug bevacizumab (10 mg/kg BV)


title: VB0106

tag: sample id

value: VB

tag: sentrix id

tag: sentrix position

value: D


title: Transformed 3T3 cells by mucAB  63_1

tag: treatment


title: VB0072

tag: gender

value: C

tag: experiment


title: Transformed 3T3 cells by mucAB  52_2

tag: cell type


title: prostate-RP_AA_27

city: Bronx

first: Alex

last: Pearlman

address: 1300 Morris Park Avenue

department: Pediatrics and Genetics

institute: Albert Einstein College of Medicine

description:
Hybridized to 6.0 chip
SNP/CN data for primary tumors.

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing: Processed using Affy Power Tools (Birdseed v2 algorithm).

source_name: prostate tumor tissue (radical prostatectomy)

label_protocol: Affymetrix standard protocol.

extract_protocol: Gentra genomic DNA isolation kit.

treatment_protocol: Fresh frozen tissue from radical prostatectomy.

tag: race

value: AA


title: NGP neuroblastoma NBV group, biological rep 5

description:
NBV.387-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy,  treated with Bevacizumab

tag: host strain background

value: female

value: 4-6 weeks

value: NGP neuroblastoma cells

value: NGP-Notch1 decoy (N1D)


title: 11429.s1

value: Male

value: J

tag: group

value: kc

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: NGP neuroblastoma NBV group, biological rep 4

description:
NBV.385-H_2
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy,  treated with Bevacizumab

tag: host strain gender

tag: host strain age

tag: tissue


title: 11041.p1

value: B

tag: family

tag: distribution

tag: site

value: ox

value: african-amer

value: leukocyte


title: Transformed 3T3 cells by mucAB 12_2

tag: strain

value: BALB/c

value: transformed 3T3 cells by mucAB


title: NGP neuroblastoma NBV group, biological rep 3

description:
NBV.383-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy,  treated with Bevacizumab

value: NCR nude mice

tag: transfected with

tag: treated with

value: 250ug bevacizumab (10 mg/kg BV)


title: 11462.p1

tag: sample id

tag: gender

tag: sentrix id

tag: sentrix position

tag: experiment

value: white


title: Transformed 3T3 cells by mucAB  52_1

tag: cell type

tag: treatment


title: Transformed 3T3 cells by mucAB 12_1


title: prostate-RP_CA_30

tag: race

value: CA


title: VB0051

value: VB

value: G

tag: group


title: NGP neuroblastoma NBV group, biological rep 2

description:
NBV.367-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy,  treated with Bevacizumab

tag: host strain background

tag: host strain gender

value: female

tag: host strain age

value: 4-6 weeks

value: NGP neuroblastoma cells


title: NGP neuroblastoma NBV group, biological rep 1

description:
NBV.211-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with Notch decoy,  treated with Bevacizumab

tag: tissue

value: NGP-Notch1 decoy (N1D)


title: prostate-RP_AA_25

value: AA


title: 11370.p1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: Male

value: F

tag: family

tag: distribution

tag: site

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: more-than-one-race


title: 11282.p1

tag: sample id

tag: gender

tag: sentrix id

value: I

value: kr

value: leukocyte


title: prostate-RP_CA_26


title: prostate-RP_AA_22


title: NGP neuroblastomaLP group, biological rep 6

description:
LP.774-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ

source_name: NGP neuroblastoma_LacZ_control

value: NCR nude mice

tag: transfected with

value: NGP-LacZ

tag: treated with

value: 100 ug mouse albumin (placebo)


title: Stress, 41°C, 360 min, biol. repl.1

city: Amsterdam

first: Femke

last: Mensonides

address: Nieuwe Achtergracht 166

country: Netherlands

institute: University of Amsterdam

hyb_protocol: The biotin-labeled cRNA samples were hybridized to the Affymetrix GeneChip Yeast Genome S98 Array according to the standard Affymetrix protocol.

scan_protocol: The arrays were scanned with the GeneArray Scanner System on standard settings at 3-µm resolution.

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

organism: Saccharomyces cerevisiae

source_name: Stress at 41°C, t=360 min, biol. repl.1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Aerobic batch cultivation,  500 ml,  28°C,  700 rpm,  and aeration rate of one volume of air per minute, equal to culture volume. YNB medium (0.67 % (w/v) YNB w/o amino acids (Difco) and 2 % (w/v) glucose)  in 100 mM potassium phthalate at pH 5.0. The fermentors were thermostated with water jackets.

extract_protocol: Samples were collected by rapidly spraying 50 ml of culture over ice in a 500 ml bucket, at –5 °C. The mixture was centrifuged for 5 minutes at 5000 rpm at 0 °C. The resulting cell pellets were flash-frozen with liquid nitrogen and stored at –80 °C prior to RNA extraction. Total RNA was extracted by the hot-phenol method of Llinas (DeRisi Lab, 2001,  Total RNA isolation from S. cerevisiae.  http://www.microarrays.org/pdfs/TotalRNAIsolation.pdf).

treatment_protocol: During mid-exponential growth (OD600 of 0.5, t=0 min.), the growth temperature was raised to 41°C, without disturbing the culture in any other way. This was done by switching to a thermostat (water bath) that was initially 5 °C warmer than the desired temperature of 41 °C. The stress temperature was reached within five minutes and care was taken to prevent an overshoot in temperature. Samples of the stressed cells were collected at t = 10, 30, 60, 120, 240, 360 minutes after the temperature increase. Control samples of cells growing at 28 °C were taken at three time points during exponential growth: t = 0 (OD600 = 0.50), 120 minutes (OD600 = 0.88), and 240 minutes (OD600 = 1.5).

tag: strain

tag: stress

tag: time

value: 360 min


title: prostate-RP_AA_28

tag: race


title: 11511.p1

tag: sentrix position

value: E

tag: experiment

tag: group

value: fl

value: white

tag: cell type


title: prostate-RP_AA_24


title: Stress, 41°C, 360 min, biol. repl.2

source_name: Stress at 41°C, t=360 min, biol. repl.2


title: prostate-RP_AA_29


title: prostate-RP_AA_23


title: NGP neuroblastomaLP group, biological rep 5

description:
LP.772-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ

tag: host strain background

tag: host strain gender

value: female

tag: host strain age

value: 4-6 weeks

tag: tissue


title: Stress, 41°C, 360 min, biol. repl.3

source_name: Stress at 41°C, t=360 min, biol. repl.3


title: Stress, 41°C, 240 min, biol. repl.3

source_name: Stress at 41°C, t=240 min, biol. repl.3

value: 240 min


title: NGP neuroblastomaLP group, biological rep 4

description:
LP.770-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ

value: NGP neuroblastoma cells


title: 11484.p1

tag: sample id

value: Male

value: C

tag: family

tag: distribution

tag: site

value: xm

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: Stress, 41°C, 240 min, biol. repl.2

source_name: Stress at 41°C, t=240 min, biol. repl.2

tag: strain

tag: stress

tag: time


title: NGP neuroblastomaLP group, biological rep 3

description:
LP.769-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ

tag: transfected with

tag: treated with


title: prostate-RP_AA_21

tag: race

value: AA


title: prostate-RP_CA_19

value: CA


title: prostate-RP_CA_20


title: prostate-RP_CA_18


title: VB0126

value: VB

tag: gender

tag: sentrix id

tag: sentrix position

value: B

tag: experiment

tag: group

tag: cell type

value: leukocyte


title: Stress, 41°C, 240 min, biol. repl.1

source_name: Stress at 41°C, t=240 min, biol. repl.1


title: Stress, 41°C, 120 min, biol. repl.3

source_name: Stress at 41°C, t=120 min, biol. repl.3

value: 120 min


title: Stress, 41°C, 120 min, biol. repl.2

source_name: Stress at 41°C, t=120 min, biol. repl.2


title: VB0014

tag: sample id

value: I


title: 11318.p1

value: A

tag: family

tag: distribution

tag: site


title: NGP neuroblastoma LBV group biological rep 6

description:
LBV.400-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ,  treated with Bevacizumab

source_name: NGP neuroblastoma_LacZ_Bevacizumab

tag: host strain background

value: NCR nude mice

tag: host strain gender

tag: host strain age

tag: tissue

value: NGP-LacZ

value: 250ug bevacizumab (10 mg/kg BV)


title: prostate-RP_CA_13


title: 11227.p1

value: L

value: hv

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: white


title: NGP neuroblastomaLP group, biological rep 2

description:
LP.767-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ

value: female

value: 4-6 weeks

value: NGP neuroblastoma cells

tag: transfected with

tag: treated with

value: 100 ug mouse albumin (placebo)


title: prostate-RP_CA_16

tag: race

value: CA


title: 11492.s1

tag: gender

value: Male

tag: sentrix id

tag: sentrix position

value: H

tag: experiment


title: NGP neuroblastoma LBV group biological rep 5

description:
LBV.344-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ,  treated with Bevacizumab


title: Stress, 41°C, 120 min, biol. repl.1

source_name: Stress at 41°C, t=120 min, biol. repl.1

tag: strain

tag: stress

tag: time


title: 11131.p1

tag: sample id

value: G

tag: group

tag: family

tag: distribution

tag: site

value: sb

tag: cell type

value: leukocyte


title: NGP neuroblastomaLP group, biological rep 1

description:
LP.547-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ

tag: host strain background

tag: host strain gender

tag: host strain age

tag: tissue


title: prostate-RP_CA_14

tag: race


title: Stress, 41°C, 60 min, biol. repl.3

source_name: Stress at 41°C, t=60 min, biol. repl.3

value: 60 min


title: prostate-RP_CA_12


title: 11298.p1

tag: gender

tag: sentrix id

value: E

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: NGP neuroblastoma LBV group biological rep 3

description:
LBV.326-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ,  treated with Bevacizumab

value: NCR nude mice

tag: transfected with

value: NGP-LacZ

tag: treated with


title: NGP neuroblastoma LBV group biological rep 4

description:
LBV.335-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ,  treated with Bevacizumab

value: 250ug bevacizumab (10 mg/kg BV)


title: Stress, 41°C, 60 min, biol. repl.2

source_name: Stress at 41°C, t=60 min, biol. repl.2

tag: strain

tag: stress

tag: time


title: Stress, 41°C, 60 min, biol. repl.1

source_name: Stress at 41°C, t=60 min, biol. repl.1


title: 11377.p1

source_name: leukocyte

tag: sample id

tag: sentrix position

value: B

tag: experiment

tag: group

tag: family

tag: distribution


title: NGP neuroblastoma LBV group biological rep 2

description:
LBV.321-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ,  treated with Bevacizumab

tag: host strain background

tag: host strain gender

tag: host strain age

tag: tissue


title: VB0124

value: VB

tag: gender

tag: sentrix id

value: A

tag: cell type


title: Stress, 41°C, 30 min, biol. repl.3

source_name: Stress at 41°C, t=30 min, biol. repl.3

value: 30 min


title: prostate-RP_CA_9

description:
Hybridized to 6.0 chip
SNP/CN data for primary tumors.

source_name: prostate tumor tissue (radical prostatectomy)

tag: race


title: prostate-RP_CA_11


title: Stress, 41°C, 30 min, biol. repl.2

source_name: Stress at 41°C, t=30 min, biol. repl.2

tag: strain


title: NGP neuroblastoma LBV group biological rep 1

description:
LBV.302-H
Gene expression profile of NGP neuroblastoma tumor cells transfected with LacZ,  treated with Bevacizumab

value: female

value: 4-6 weeks

value: NGP neuroblastoma cells

tag: transfected with

tag: treated with


title: 6 day biofilm + 24 hr macrophage biological replicate 3

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from 6 day biofilms exposed to Macrophages for 24 hr

hyb_protocol: 3 ug of labeled RNA were hybrized for 16 hr at 45C on a S. aureus Affymetrix GeneChip, following the manufacturer's recommendations for antisense prokaryotic arrays (Affymetrix, Santa Clara, CA).  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

organism: Staphylococcus aureus

source_name: S. aureus 6 day biofilm exposed to macrophages for 24 hr

label_protocol: Total bacterial RNA (75 ng) isolated from each sample was independently amplified using ExpressArt Bacterial mRNA amplification Nano kits (AmpTec GmbH, Germany) and biotinylated using BioArray HighYield RN Transcript Labeling kits (Enzo Life Sciences, Inc., Farmingdale, NY).

growth_protocol: Sterile 2-well glass chamber slides (Nunc, Rochester, NY) were treated with 20% human plasma overnight at 4C.  The following day, plasma coating buffer was removed and each chamber inoculated with S. aureus strain USA300 LAC and incubated at 37C under static conditions for a period of 4 or 6 days to gnerate immature and mature biofilms, respectively.  Medium was replenished every 24 h.

extract_protocol: Biofilm media was removed and replaced with RNAprotect (Qiagen, Hilden, Germany).  Biofilms were collected from the bottom of the chamber slide using a cell scraper, sonicated for 5 min, then pelleted by centrifugation for 5 min.  Cell pellets were resuspended in RLT buffer (Qiagen), transferred to a 2 ml FastPrep lysing tube (MP Biomedicals, Santa Ana, CA) and then lysed in a FastPrep homogenizer (MP Biomedicals) for 20 sec on speed setting 6.  Cell debri was collected by centrifugation.  RNA was isolated from the supernatant using RNeasy mini kits (Qiagen) and contaminating DNA was removed by on-column DNase digestion using RNase-Free DNase (Qiagen).

treatment_protocol: Following biofilm formation macrophages or neutrophils (10^7 and 10^6, respectively) were co-cultured with S. aureus biofilms at 37C for the indicated time period to assess their impact on the biofilm transcriptome.  Mock treatment refers to the addition of RPMI media.

tag: sample

value: Whole cell

tag: biofilm

value: 6 day

tag: exposure time

value: 24 hr

tag: exposure item

value: Macrophages


title: Stress, 41°C, 30 min, biol. repl.1

source_name: Stress at 41°C, t=30 min, biol. repl.1

tag: stress

tag: time


title: VB0035

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

tag: sample id

value: Male

tag: sentrix position

value: K

tag: experiment

tag: group

value: leukocyte


title: 11557.p1.1

tag: gender

value: L

tag: family

tag: distribution

tag: site

value: kc

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: more-than-one-race


title: prostate-RP_CA_10

tag: race

value: CA


title: 6 day biofilm + 24 hr macrophage biological replicate 2

tag: sample

tag: biofilm


title: Stress, 41°C, 10 min, biol. repl.3

source_name: Stress at 41°C, t=10 min, biol. repl.3

tag: strain

value: 10 min


title: VB0099

value: VB

tag: sentrix id

value: I

tag: cell type


title: 11435.s1

tag: sample id

value: H

value: kr

value: white


title: Stress, 41°C, 10 min, biol. repl.1

source_name: Stress at 41°C, t=10 min, biol. repl.1

tag: stress

tag: time


title: 6 day biofilm + 24 hr macrophage biological replicate 1

value: Whole cell

tag: exposure time

tag: exposure item


title: 6 day biofilm + 24 hr mock biological replicate 1

description: Gene expression data from 6 day biofilms exposed to RMPI tissue culture medium for 24 hr

source_name: S. aureus 6 day biofilm exposed to RPMI media for 24 hr

value: 6 day

value: RMPI media


title: prostate-RP_CA_8


title: Stress, 41°C, 10 min, biol. repl.2

source_name: Stress at 41°C, t=10 min, biol. repl.2


title: 11696.p1

tag: gender

tag: sentrix position

value: E

tag: experiment

tag: group

tag: family

value: oi


title: 11580.p1

value: Male

value: D

tag: distribution

tag: site

value: xm

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: 6 day biofilm + 4 hr neutrophil biological replicate 2

description: Gene expression data from 6 day biofilms exposed to Neutrophils for 4 hr

source_name: S. aureus 6 day biofilm exposed to neutrophils for 4 hr

tag: sample

tag: biofilm

value: 4 hr

value: Neutrophils


title: 6 day biofilm + 24 hr mock biological replicate 2

value: 24 hr


title: prostate-RP_CA_6

tag: race

value: CA


title: Control, 28°C, 240 min,  biol. repl. 3

source_name: Control at 28°C, t=240 min,  biol. repl. 3

tag: strain

tag: stress

value: control (28°C)

value: 240 min


title: 11377.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

tag: sample id

tag: sentrix id

value: B

tag: cell type

value: leukocyte


title: 6 day biofilm + 4 hr neutrophil biological replicate 1

tag: exposure time

tag: exposure item


title: Control, 28°C, 240 min,  biol. repl. 2

source_name: Control at 28°C, t=240 min,  biol. repl. 2

tag: time


title: prostate-RP_CA_4


title: Control, 28°C, 240 min,  biol. repl. 1

source_name: Control at 28°C, t=240 min,  biol. repl. 1


title: 6 day biofilm + 4 hr biological replicate 2

description: Gene expression data from 6 day biofilms exposed to RMPI tissue culture medium for 4 hr

source_name: S. aureus 6 day biofilm exposed to RPMI media for 4 hr


title: prostate-RP_CA_7


title: 11108.p1

tag: gender

tag: sentrix position

value: A

tag: experiment

tag: group

tag: family

value: fl

value: white


title: Control, 28°C, 120 min,  biol. repl. 2

source_name: Control at 28°C, t=120 min,  biol. repl. 2

value: 120 min


title: Control, 28°C, 120 min,  biol. repl. 3

source_name: Control at 28°C, t=120 min,  biol. repl. 3


title: prostate-RP_CA_5


title: 11226.p1

source_name: leukocyte

value: F

tag: distribution


title: prostate-RP_CA_1


title: 6 day biofilm + 4 hr biological replicate 1

tag: sample

value: Whole cell

value: 6 day

value: RMPI media


title: 6 day biofilm + 1 hr macrophage biological replicate 2

description: Gene expression data from 6 day biofilms exposed to Macrophages for 1 hr

source_name: S. aureus 6 day biofilm exposed to macrophages for 1 hr

tag: biofilm

value: 1 hr

value: Macrophages


title: 6 day biofilm + 1 hr macrophage biological replicate 1


title: normal_CA_30N

source_name: prostate normal tissue

tag: race


title: Control, 28°C, 120 min,  biol. repl. 1

source_name: Control at 28°C, t= 120 min,  biol. repl. 1

tag: strain


title: 11402.p1

value: Male

value: D


title: prostate-RP_CA_17

source_name: prostate tumor tissue (radical prostatectomy)

value: CA


title: 11011.p1

value: E

tag: site

value: sb

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: 6 day biofilm + 1 hr neutrophil biological replicate 2

source_name: S. aureus 6 day biofilm exposed to neutrophils for 1 hr

tag: exposure time

value: Neutrophils


title: 11028.p1

tag: sample id

tag: sentrix id

value: C

value: other

tag: cell type

value: leukocyte


title: Control, 28°C, 0 min,  biol. repl. 3

source_name: Control at 28°C, t=0 min,  biol. repl. 3

tag: stress

value: control (28°C)

tag: time

value: 0 min


title: normal_AA_27N

value: AA


title: 6 day biofilm + 1 hr biological replicate 4

description: Gene expression data from 6 day biofilms exposed to RMPI tissue culture medium for 1 hr

source_name: S. aureus 6 day biofilm exposed to RPMI media for 1 hr

value: Whole cell

tag: exposure item


title: normal_AA_29N


title: 6 day biofilm + 1 hr neutrophil biological replicate 1

description: Gene expression data from 6 day biofilms exposed to Neutrophils for 1 hr

value: 6 day


title: 11553.s1

tag: gender

tag: sentrix position

value: L

tag: experiment

tag: group

tag: family


title: prostate-RP_AA_3

tag: race


title: prostate-RP_CA_2


title: normal_AA_28N


title: Control, 28°C, 0 min,  biol. repl. 1

source_name: Control at 28°C, t=0 min,  biol. repl. 1

tag: strain


title: normal_CA_26N


title: 6 day biofilm + 1 hr biological replicate 3

tag: sample

tag: biofilm

value: 1 hr

value: RMPI media


title: 11235.p1

value: Male

value: J

tag: distribution

tag: site

value: xm

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: more-than-one-race


title: VB0105

tag: sample id

value: VB

tag: sentrix id

value: K

tag: cell type


title: 6 day biofilm + 1 hr biological replicate 2

tag: exposure time

tag: exposure item


title: Control, 28°C, 0 min,  biol. repl. 2

source_name: Control at 28°C, t=0 min,  biol. repl. 2

tag: stress

tag: time


title: 6 day biofilm + 1 hr biological replicate 1


title: BEAS2B - TMTD - 24 hours - repl. 3

city: Mol

first: Sylvie

last: Remy

state: Antwerp

address: Boeretang 200

country: Belgium

institute: VITO

description: Skin sensitizer TMTD

hyb_protocol: Equal amounts of the exposed and negative control labeled cRNA samples were competitively hybridized onto the arrays in a fully automatic HS 4800 Pro hybridization station (Tecan, Grödig/Salzburg, Austria) for 17 hours.

scan_protocol: The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Raw data feature extraction files were generated using Agilent protocol GE2-v5_95_Feb07.  Standard Agilent Feature Extraction normalization

source_name: BEAS2B, vehicle control, 24 hours

label_protocol: 1 μg of total RNA was used in the Agilent LIRAK PLUS, two-colour Low RNA input Linear Amplification method, according to the manufacturer’s instructions.  cRNAs showing a yield >825 ng and a specific activity of 8-20 pmol/μg cRNA were selected for further processing.

growth_protocol:
BEAS-2B cells were grown in T-75 culture flasks precoated with a mixture of 10 µg/ml human plasma fibronectin (Invitrogen, Paisley, UK), 30 µg/ml PureColTM (Advance Biomatrix, USA), and 10µg/ml bovine serum albumin (Sigma–Aldrich Chemie Gmbh, Steinheim, Germany) dissolved in growth medium (BEGM, Lonza). The mixture was added at a ratio of 0.2 ml/cm2 surface area.
The cells were kept in a humidified atmosphere at 37 °C and 5% CO2. Before reaching 80% confluence, cells were subcultured using 0.25 % trypsin/0.53 mM versene (EDTA) solution (LGC Promochem) containing 0.5% polyvinylpyrrolidone (Sigma–Aldrich Chemie Gmbh). Medium was refreshed every 2–3 days and cells were subcultured every 4-5 days (1500–3000 cells/cm2).

extract_protocol: After exposure time, the supernatants was removed and the cells were lysed in the plates with 99% RLT lysis buffer (Qiagen, Hilden, Germany) and 1% 2-mercaptoethanol (Sigma–Aldrich Chemie Gmbh). Total RNA was isolated using mini RNeasy RNA isolation kits, according to the manufacturer’s specifications (Qiagen).

treatment_protocol:
BEAS-2B cells were seeded in six-well plates (6×105 cells suspended in 4 ml growth medium per well) 24 hours before exposure to the test substance.  Cells were exposed for 6, 10, and 24 hours to the selected chemicals to a concentration yielding 20% cell viability reduction (IC20). This concentration was derived from concentration-response relationships after 24 hours of exposure determined using the neutral red uptake assay.
Except for 4 chemicals (DOP, MeSA, STY, and TMA) which did not induce reduction in cell viability for concentrations ranging up to the highest soluble concentration (solved in growth medium supplemented with maximally 0.05% dimethylsulfoxide (DMSO)). These chemicals were applied at highest soluble concentration

tag: cell line

tag: treatment

value: control

source_name: BEAS2B, Skin sensitizer, 24 hours

value: TMTD

value: 24 hours


title: VB0067

city: Atlanta

first: Benjamin

last: Barwick

institute: Emory University

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

tag: gender

tag: sentrix position

value: F

tag: experiment

tag: group

value: leukocyte


title: VB0029

value: B


title: BEAS2B - TMTD - 24 hours - repl. 2

description: Skin sensitizer TMTD


title: 4 day biofilm + 24 hr macrophage biological replicate 3

description: Gene expression data from 4 day biofilms exposed to Macrophages for 24 hr

source_name: S. aureus 4 day biofilm exposed to macrophages for 24 hr

tag: sample

value: Whole cell

tag: biofilm

value: 4 day

value: 24 hr

value: Macrophages


title: 4 day biofilm + 24 hr macrophage biological replicate 2


title: 11251.p1

value: A

tag: family

tag: distribution

tag: site

value: fl

tag: cpea dx

tag: age at collection (months)

value: white


title: normal_AA_24N

tag: race

value: AA


title: normal_AA_23N


title: normal_AA_25N


title: 11429.p1

tag: sample id

value: Male

tag: sentrix id

value: L

value: kc

tag: ethnicity

tag: cell type


title: normal_AA_22N


title: 4 day biofilm + 24 hr macrophage biological replicate 1

tag: exposure time

tag: exposure item


title: BEAS2B - TMTD - 10 hours - repl. 1

description: Skin sensitizer TMTD

source_name: BEAS2B, vehicle control, 10 hours

tag: cell line

tag: treatment

value: control

source_name: BEAS2B, Skin sensitizer, 10 hours

tag: time

value: 10 hours


title: BEAS2B - TMTD - 24 hours - repl. 1

description: Skin sensitizer TMTD

value: TMTD

value: 24 hours


title: 4 day biofilm + 24 hr mock biological replicate 2

description: Gene expression data from 4 day biofilms exposed to RMPI tissue culture medium for 24 hr

source_name: S. aureus 4 day biofilm exposed to RPMI media for 24 hr

tag: sample

value: RMPI media


title: normal_AA_21N


title: BEAS2B - TMTD - 10 hours - repl. 2

description: Skin sensitizer TMTD


title: normal_CA_19N

value: CA


title: BEAS2B - TMTD - 6 hours - repl. 3

description: Skin sensitizer TMTD

source_name: BEAS2B, vehicle control, 6 hours

source_name: BEAS2B, Skin sensitizer, 6 hours

value: 6 hours


title: 11325.p1

source_name: leukocyte

tag: gender

tag: sentrix position

value: C

tag: experiment

tag: group

value: xx

value: leukocyte


title: 11245.p1

value: J

tag: family

tag: distribution

tag: site

value: kr

tag: cpea dx

value: more-than-one-race


title: 4 day biofilm + 24 hr mock biological replicate 1

value: Whole cell

tag: biofilm

value: 4 day

value: 24 hr


title: normal_CA_20N

source_name: prostate normal tissue

tag: race


title: 11553.p1

tag: sample id

value: Male

tag: sentrix id

value: K

tag: cell type


title: normal_CA_16N


title: BEAS2B - TMTD - 6 hours - repl. 2

description: Skin sensitizer TMTD

tag: cell line

value: control


title: 4 day biofilm + 4 hr neutrophil biological replicate 2

description: Gene expression data from 4 day biofilms exposed to Neutrophils for 4 hr

source_name: S. aureus 4 day biofilm exposed to neutrophils for 4 hr

tag: exposure time

value: 4 hr

tag: exposure item

value: Neutrophils


title: 11242.p1

value: I

tag: age at collection (months)

tag: ethnicity

value: white


title: 11004.p1

tag: gender

tag: sentrix position

value: H

value: oi


title: BEAS2B - TMTD - 6 hours - repl. 1

description: Skin sensitizer TMTD

tag: treatment

value: TMTD

tag: time

value: 6 hours


title: 4 day biofilm + 4 hr neutrophil biological replicate 1

tag: sample


title: normal_CA_13N

value: CA


title: BEAS2B - MBT - 24 hours - repl. 3

description: Skin sensitizer MBT

value: MBT

value: 24 hours


title: 4 day biofilm + 4 hr biological replicate 2

description: Gene expression data from 4 day biofilms exposed to RMPI tissue culture medium for 4 hr

source_name: S. aureus 4 day biofilm exposed to RPMI media for 4 hr

value: Whole cell

value: RMPI media


title: epiF3, biological rep 3

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

description: Gene expression data from msh1 mutant albino plant

hyb_protocol: RNA was hybridized to individual Affymetrix GeneChip oligonucleotide ATH1 array using manufacturers instructions

scan_protocol: GeneChip Operating Software (GCOS) and the GCS 3000 7G scanner for scanning, image acquisition and data processing.

data_processing: Expression data from Affymetrix genechips were normalized using the Robust Multichip Average (RMA) method using Bioconductor’s affy package in the R language

organism: Arabidopsis thaliana

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

growth_protocol: Arabidopsis Col-0 and epiF3 plants were grown in metro mix with 12hr daylight at 22°.

extract_protocol: total RNA was extracted from each plant using TRIzol (Invitrogen) extraction procedure followed by purification on RNeasy columns (Qiagen).

tag: ecotype

tag: tissue

value: aerial part

tag: age

value: 30-day-old old plant


title: 11008.p1

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

hyb_protocol: Followed the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

value: Male

value: F

tag: experiment

tag: group

tag: family

tag: distribution

tag: site

value: sb

tag: cpea dx

value: leukocyte


title: epiF3, biological rep 2


title: VB0066

tag: sample id

value: VB

tag: sentrix id

value: E

tag: cell type


title: normal_CA_18N

tag: race


title: BEAS2B - TMTD - 10 hours - repl. 3

description: Skin sensitizer TMTD

tag: cell line

value: control

value: 10 hours


title: BEAS2B - MBT - 24 hours - repl. 1

description: Skin sensitizer MBT

tag: treatment


title: BEAS2B - MBT - 24 hours - repl. 2

description: Skin sensitizer MBT

tag: time


title: 4 day biofilm + 4 hr biological replicate 1

tag: sample

tag: biofilm

value: 4 day

tag: exposure time

value: 4 hr

tag: exposure item


title: normal_CA_17N

value: CA


title: 11522.p1

tag: gender

tag: sentrix position

value: D

tag: experiment

value: ox

tag: age at collection (months)

tag: ethnicity

value: white


title: normal_CA_12N


title: normal_CA_14N


title: normal_CA_10N


title: 11199.p1

value: B

tag: group

tag: family

tag: distribution

tag: site

value: fl

tag: cpea dx


title: 4 day biofilm + 1 hr macrophage biological replicate 1

description: Gene expression data from 4 day biofilms exposed to Macrophages for 1 hr

source_name: S. aureus 4 day biofilm exposed to macrophages for 1 hr

value: Whole cell

value: 1 hr

value: Macrophages


title: 11597.p1

tag: sample id

value: Male

tag: sentrix id

value: C

value: xm

tag: cell type


title: 4 day biofilm + 1 hr macrophage biological replicate 2

tag: sample


title: normal_CA_8N

tag: race


title: epiF3, biological rep 1

tag: ecotype

tag: tissue

value: aerial part

tag: age

value: 30-day-old old plant


title: normal_CA_11N


title: wild type Col-0, biological rep 1

description: Gene expression data from wild type

source_name: wild type


title: wild type Col-0, biological rep 3

description: Gene expression data from wild type


title: 4 day biofilm + 1 hr neutrophil biological replicate 2

description: Gene expression data from 4 day biofilms exposed to Neutrophils for 1 hr

source_name: S. aureus 4 day biofilm exposed to neutrophils for 1 hr

tag: biofilm

tag: exposure time

tag: exposure item

value: Neutrophils


title: 4 day biofilm + 1 hr biological replicate 5

description: Gene expression data from 4 day biofilms exposed to RMPI tissue culture medium for 1 hr

source_name: S. aureus 4 day biofilm exposed to RPMI media for 1 hr

value: 4 day

value: RMPI media


title: 4 day biofilm + 1 hr neutrophil biological replicate 1


title: wild type Col-0, biological rep 2

description: Gene expression data from wild type


title: 11131.s1

tag: gender

tag: sentrix position

value: K

tag: experiment

value: sb

tag: ethnicity

value: leukocyte


title: BEAS2B - MBT - 10 hours - repl. 1

description: Skin sensitizer MBT

tag: cell line

tag: treatment

value: control

value: MBT

tag: time

value: 10 hours


title: BEAS2B - MBT - 10 hours - repl. 3

description: Skin sensitizer MBT


title: 11441.p1

tag: sample id

tag: sentrix id

value: A

tag: group

tag: family

tag: distribution

tag: site

tag: cpea dx

tag: age at collection (months)

value: more-than-one-race


title: BEAS2B - MBT - 10 hours - repl. 2

description: Skin sensitizer MBT


title: BEAS2B - MBT - 6 hours - repl. 3

description: Skin sensitizer MBT

value: 6 hours


title: anti-mir135b 24h 11

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
anti24.11
anti.mir135b 24h 11
q5535688006_G.AVG_Signal

scan_protocol: Arrays were scanned on Illumina BeadStation 500 (Illumina, San Diego, CA)

data_processing: Genome studio (Illumina, San Diego, CA) was used to generate raw intensity signal without normalization. Data log2 transformation and loess normalization was performed with oneChannelGUI v 1.16.0. Data were filtered using an IQR filter (i.e. only genes characterized by an IQR > 0.25, were retained for further analysis). Detection of differentially expressed transcripts was also performed with oneChannelGUI, using masigpro package with default parameters

source_name: mouse breast cancer cell line

label_protocol: cRNA synthesis and labeling were done using Illumina RNA Amplification Kit (Ambion) following the procedure suggested by the manufacturer.

growth_protocol: BALB-neuT mammary cell lines  were cultured in DMEM with Glutamax 1 (DMEM, Life Technologies) supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen)

extract_protocol: mirVana miRNA isolation kit (Applied Biosystems, Milano, Italy)

treatment_protocol: To obtain BALB-neuT cells silenced or overexpressing miR-135a and miR-135b, cells were plated in 6-well plates at 90% confluency and transfected 24h later using using LipofectamineTM2000 (Invitrogen Life Technologies, Carlsbad, CA) reagent, according to manufacturer’s instruction, with 200 nM of specific miRIDIAN microRNA Hairpin Inhibitor (anti-miR-135b) or Mimics (miR-135b-over)(Thermo Scientific Dharmacon). For each experiments cells were also transfected with miRIDIAN microRNA Hairpin Inhibitor or Mimics negative control (control).

value: TUBO

tag: knockdown


title: BEAS2B - MBT - 6 hours - repl. 2

description: Skin sensitizer MBT


title: normal_CA_7N

description:
Hybridized to 6.0 chip
SNP/CN data for primary tumors.

tag: race

value: CA


title: 4 day biofilm + 1 hr biological replicate 4

tag: sample

value: Whole cell

tag: biofilm

tag: exposure time

value: 1 hr

tag: exposure item


title: anti-mir135b 72h 18

description:
anti72.18
anti.mir135b 72h 18
p5535688006_F.AVG_Signal

tag: cell line


title: VB0059

value: VB

tag: gender

value: Male

tag: sentrix position

value: C

tag: experiment

tag: cell type


title: 4 day biofilm + 1 hr biological replicate 2

value: 4 day

value: RMPI media


title: anti-mir135b 72h 17

description:
anti72.17
anti.mir135b 72h 17
o5535688006_E.AVG_Signal

tag: time


title: 4 day biofilm + 1 hr biological replicate 3


title: BEAS2B - MBT - 6 hours - repl. 1

description: Skin sensitizer MBT

tag: treatment


title: 11156.p1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

tag: sample id

tag: sentrix id

value: D

tag: group

tag: family

tag: distribution

value: pb

tag: ethnicity

value: white


title: anti-mir135b 72h 16

description:
anti72.16
anti.mir135b 72h 16
n5535688006_D.AVG_Signal

tag: knockdown


title: 4 day biofilm + 1 hr biological replicate 1

tag: sample

tag: biofilm


title: 11544.p1

tag: site

value: kc

tag: cpea dx

tag: age at collection (months)

value: other

value: leukocyte


title: BEAS2B - CIN - 24 hours - repl. 3

description: Skin sensitizer CIN

source_name: BEAS2B, vehicle control, 24 hours

tag: cell line

value: control

value: CIN

value: 24 hours


title: anti-mir135b 24h 12

description:
anti24.12
anti.mir135b 24h 12
r5535688006_H.AVG_Signal

value: TUBO


title: 11334.p1

tag: gender

tag: sentrix position

value: I

tag: experiment

value: sb


title: BEAS2B - CIN - 24 hours - repl. 2

description: Skin sensitizer CIN

tag: treatment

source_name: BEAS2B, Skin sensitizer, 24 hours

tag: time


title: BEAS2B - CIN - 24 hours - repl. 1

description: Skin sensitizer CIN


title: normal_AA_3N

tag: race

value: AA


title: normal_CA_9N

value: CA


title: BEAS2B - CIN - 10 hours - repl. 3

description: Skin sensitizer CIN

value: 10 hours


title: Optimal Dose 5

city: Baltimore

first: Yen-Ling

last: Chiu

address: 733 N. Broadway, BRB 615

institute: Johns Hopkins University

description:
OD5
Gene expression.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. The signal intensities were normalized by dividing the intensity values by their median.

source_name: Tetramer-sorted M1-specific T cells, optimal dose

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer.

growth_protocol: CD8+ T cells were stimulated with M1 peptide-pulsed monocyte-derived dendritic cells in complete RPMI media supplemented with T cell growth factor.

extract_protocol: T cells were harvested on D14 and tetramer sorted before Trizol-based RNA extraction.

treatment_protocol: Different peptide doses were used to pulse dendritic cells (optimal dose: 10nM; high dose: 10uM).

tag: cell type

value: CD8+ T cells

value: influenza M1 peptide-pulsed monocyte-derived dendritic cells

tag: peptide dosage

value: optimal


title: normal_CA_6N


title: normal_CA_4N


title: 11584.p1

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: sample id

value: Male

tag: sentrix id

tag: group

tag: family

tag: distribution

value: oi


title: scrambled 72h 9

description:
scr72.9
scrambled 72h 9
m5535688006_C.AVG_Signal

tag: knockdown

value: scrambled


title: normal_CA_5N


title: BEAS2B - CIN - 10 hours - repl. 1

description: Skin sensitizer CIN

source_name: BEAS2B, vehicle control, 10 hours


title: 11252.p1

value: J

tag: site

tag: cpea dx

tag: ethnicity

value: white


title: Optimal Dose 4

description:
OD4
Gene expression.


title: BEAS2B - CIN - 6 hours - repl. 3

description: Skin sensitizer CIN

tag: cell line

value: control

value: 6 hours


title: Optimal Dose 3

description:
OD3
Gene expression.


title: 11197.p1

tag: gender

tag: sentrix position

value: L

value: xx

tag: age at collection (months)

value: leukocyte


title: 11312.p1

value: K

tag: experiment

value: kc

value: other


title: BEAS2B - CIN - 10 hours - repl. 2

description: Skin sensitizer CIN

tag: treatment

source_name: BEAS2B, Skin sensitizer, 10 hours

value: CIN

tag: time

value: 10 hours


title: scrambled 72h 7

description:
scr72.7
scrambled 72h 7
i5535688006_A.AVG_Signal

value: TUBO


title: scrambled 24h 2

description:
scr24.2
scrambled 24h 2
g5535688004_G.AVG_Signal


title: scrambled 72h 8

description:
scr72.8
scrambled 72h 8
l5535688006_B.AVG_Signal


title: normal_CA_2N

tag: race

value: CA


title: 11289.p1

tag: sample id

value: Male

value: H

value: kr

value: asian

tag: cell type


title: scrambled 24h 3

description:
scr24.3
scrambled 24h 3
h5535688004_H.AVG_Signal

value: scrambled


title: Optimal Dose 1

description:
OD1
Gene expression.

value: CD8+ T cells

value: influenza M1 peptide-pulsed monocyte-derived dendritic cells

tag: peptide dosage

value: optimal


title: anti-mir135b 48h 15

description:
anti48.15
anti.mir135b 48h 15
f5535688004_F.AVG_Signal


title: anti-mir135b 48h 14

description:
anti48.14
anti.mir135b 48h 14
e5535688004_E.AVG_Signal


title: High Dose 5

description:
HD5
Gene expression.

source_name: Tetramer-sorted M1-specific T cells, high dose

value: high


title: Optimal Dose 2

description:
OD2
Gene expression.


title: BEAS2B - CIN - 6 hours - repl. 2

description: Skin sensitizer CIN

source_name: BEAS2B, vehicle control, 6 hours

value: control

value: 6 hours


title: 11303.p1

tag: sentrix id

value: G

tag: group

tag: family

value: xx

value: white

value: leukocyte


title: normal_CA_1N


title: 11333.p1

value: D

tag: distribution

tag: site


title: BEAS2B - EPI - 24 hours - repl. 3

description: Non-sensitizing irritant EPI

source_name: BEAS2B, Non-sensitizing irritant, 24 hours

value: EPI

value: 24 hours


title: BEAS2B - CIN - 6 hours - repl. 1

description: Skin sensitizer CIN

source_name: BEAS2B, Skin sensitizer, 6 hours

value: CIN


title: VB0117

source_name: leukocyte

value: VB

value: Male

value: A


title: High Dose 3

description:
HD3
Gene expression.

value: CD8+ T cells


title: scrambled 48h 6

description:
scr48.6
scrambled 48h 6
c5535688004_C.AVG_Signal

value: TUBO

tag: knockdown

value: scrambled


title: BEAS2B - EPI - 24 hours - repl. 2

description: Non-sensitizing irritant EPI

tag: cell line


title: scrambled 48h 5

description:
scr48.5
scrambled 48h 5
b5535688004_B.AVG_Signal


title: High Dose 4

description:
HD4
Gene expression.

value: influenza M1 peptide-pulsed monocyte-derived dendritic cells

value: high


title: VB0062

tag: gender

value: F


title: High Dose 1

description:
HD1
Gene expression.


title: High Dose 2

description:
HD2
Gene expression.


title: 11641.p1

tag: sentrix position

value: K

value: pb

tag: cpea dx

tag: ethnicity


title: BEAS2B - EPI - 10 hours - repl. 2

description: Non-sensitizing irritant EPI

tag: treatment

value: control

source_name: BEAS2B, Non-sensitizing irritant, 10 hours

value: 10 hours


title: anti-mir135b 48h 13

description:
anti48.13
anti.mir135b 48h 13
d5535688004_D.AVG_Signal

tag: time


title: 11075.p1

value: I

tag: experiment

value: hv

tag: age at collection (months)

value: white

value: leukocyte


title: 11226.s1

tag: sample id

value: G

tag: cell type


title: VB0060

value: VB

value: Male

tag: sentrix id

value: E


title: 11378.p1

value: J

tag: group

value: ox

value: asian


title: BEAS2B - EPI - 10 hours - repl. 3

description: Non-sensitizing irritant EPI

value: EPI


title: BEAS2B - EPI - 6 hours - repl. 3

description: Non-sensitizing irritant EPI

source_name: BEAS2B, Non-sensitizing irritant, 6 hours

value: 6 hours


title: HEK293 ALKBH7 induced replicate 3, Illumina HumanWG-6 Expression BeadChip version 3

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

data_processing: The data was quantile normalised in J-express

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

growth_protocol: HEL293 were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Lonza) supplemented with 10 % tetracycline-free fetal bovine serum (FBS) (Clontech), 100 U/ml penicillin (Lonza), 100 U/ml streptomycin (Lonza), 2 mM L-glutamine (Lonza), 15 μg/ml blasticidin-S (Invitrogen) and 200 μg/ml hygromycin B.), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency.

extract_protocol: RNA was isolated using the standard TRIzol procedure (Invitrogen), and further purified with an RNeasy mini column (Qiagen GmbH, Hilden, Germany), according to the manufacturers’ instructions.

treatment_protocol: Ectopic ALKBH expression was induced by addition of 2 μg/mL doxycycline to the medium.

tag: expression

value: ALKBH7 induced

value: Human Embryonic Kidney

tag: provider

value: Life Technologies

tag: catalog number


title: HEK293 ALKBH7 induced replicate 1, Illumina HumanWG-6 Expression BeadChip version 3


title: HEK293 ALKBH7 uninduced replicate 3, Illumina HumanWG-6 Expression BeadChip version 3

value: ALKBH7 uninduced


title: HEK293 ALKBH7 induced replicate 2, Illumina HumanWG-6 Expression BeadChip version 3


title: VB0039

value: B


title: HEK293 ALKBH7 uninduced replicate 2, Illumina HumanWG-6 Expression BeadChip version 3


title: BEAS2B - EPI - 10 hours - repl. 1

description: Non-sensitizing irritant EPI

value: control

value: 10 hours


title: scrambled 48h 4

description:
scr48.4
scrambled 48h 4
a5535688004_A.AVG_Signal

value: TUBO

tag: knockdown

value: scrambled


title: BEAS2B - EPI - 24 hours - repl. 1

description: Non-sensitizing irritant EPI

tag: cell line

value: 24 hours


title: HEK293 ALKBH4 induced replicate 3, Illumina HumanWG-6 Expression BeadChip version 3

value: ALKBH4 induced


title: 11599.p1

tag: gender

value: Male

value: C

tag: family

tag: distribution

tag: site

value: oi

value: white

value: leukocyte