title: FL lymph node biopsy, untreated, 581

source_name: FL lymph node biopsy, untreated, 581


title: neocortex control rats biological rep1, technical rep2

status: Public on Mar 29 2015

type: RNA

city: LYON

first: leslie

last: renouard

address: 7 rue Guillaume Paradin

country: France

institute: Inserm U1028 - CNRS UMR5292

description: pool of 6 rats

hyb_protocol: RNAc biotinylated is hybridized on GeneChip rat 230 2.0 with the standard Affymetrix protocol (Expression 10 Analysis Technical Manual, ref 701021 rev.5, Affymetrix, GeneChip Fluidics Station 450).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 and analyzed with Affymetrix GeneChip Operating software (GCOS) version 1.2 using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

data_processing:
For each intergroup comparison, significant expression changes were determined with paired nonparametric test (Microarray Suite 5.0, Affymetrix) using Affymetrix default analysis settings and global scaling. Transcript expression level was considered as modified in the hippocampal formation between two experimental conditions when the three comparisons between the replicas designed them as decreased or increased. Relative measure of the expression level, was computed for each assayed gene.
A weighted mean of probe fluorescence is the signal value (Signal intensity), a relative measure of the expression level, computed for each assayed gene. Global, probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold was used to assign a call of absent present or marginal for each assayed gene (Signal detection). A p-value was calculated to reflect confidence in the detection call (Signal detection p-value).

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: neocortices of rats staying in standard condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Sprague-Dawley rats were housed individually and placed under a constant light/dark cycle (light on from 7:00 AM to 7:00 PM).

extract_protocol: Total RNA was isolated from right neocortex and hippocampal formation of each animal by using RNeasy Lipid Tissue Mini Kit (Qiagen) and RNase-free DNase set (Qiagen) to eliminate DNA contamination according to the manufacturer's instructions. An equal mass amount of total RNA from the right neocortex and hippocampal formation was pooled from two sets of 6 rats for each experimental group (PSC, PSD, PSR; 36 μg/pool).

treatment_protocol: Rats were implanted with electroencephalographic (EEG) and electromyographic (EMG) electrodes. PS deprivation was performed using the flowerpot method. Rats were divided in 3 groups: control, deprived of PS for 78 h and rats allowed to recover for 6 h after such deprivation. After anesthesia, rats were decapitated and the whole brain was removed, right neocortex and hippocampal formation were dissected and stored at -80°C.

tag: group

value: control rat

tag: gender

value: male

tag: number

tag: strain

value: Sprague Dawley (Charles River, L'Arbresle France)

tag: tissue

value: neocortex

tag: weight


title: neocortex control rats biological rep2

description: pool of 6 rats


title: FL lymph node biopsy, untreated, 695

city: Stanford

first: Aaron

middle: M

last: Newman

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine & Division of Oncology, Stanford School of Medicine

country: USA

institute: Stanford University

description: Gene expression data from a surgical lymph node biopsy obtained from an untreated FL patient enrolled in a Phase III clinical trial (NCT00017290)

hyb_protocol: cRNA was hybridized to HGU133 Plus 2.0 microarrays (Affymetrix) according to the manufacturer’s protocol.

scan_protocol: standard Affymetrix protocol

data_processing: MAS5 normalized using the affy package in R/Bioconductor.

organism: Homo sapiens

source_name: FL lymph node biopsy, untreated, 695

label_protocol: standard Affymetrix protocol

extract_protocol: Nucleic acids were extracted from tonsil specimens and PBMCs using AllPrep DNA/RNA Mini kits (Qiagen). For FL lymph node biopsies, total RNA and genomic DNA were prepared and stored using TRIzol and RNeasy Midi Kits (Qiagen, Valencia, CA). Total cellular RNA (at least 300 ng) was assessed for yield (NanoDrop 2000, Thermo Scientific) and quality (2100 Bioanalyzer, Agilent).

value: Lymph node

tag: disease state

value: FL

tag: flow cytometry cell subset proportions

value: CD4 T cells = 7.53%; CD8 T cells = 1.08%; B cells = 91.4%


title: FL lymph node biopsy, untreated, 575

source_name: FL lymph node biopsy, untreated, 575


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA genotyping RepD

type: genomic

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

description: Biological Replicate D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Standard Illumina protocol

label: biotin and dinitrophenyl

molecule: genomic DNA

label_protocol: C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled

growth_protocol: Human Embryonic Stem Cells grew in different subtrates (Feeder Layer and extracellular matrix) and were passaged with different methods (mechanically and enzymatically)

extract_protocol: genomic DNA was extracted using Quiagen DNeasy Blood & Tissue Kit

value: female

tag: growth condition

value: hESCs cultured on mouse feeder layer and enzymatically passagged P41

tag: passage

tag: cell line


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA genotyping RepA

description: Biological Replicate A


title: FL lymph node biopsy, untreated, 1080

source_name: FL lymph node biopsy, untreated, 1080


title: neocortex control rats biological rep1, technical rep1

description: pool of 6 rats


title: PBMCs, post-Rituximab, 4

description: Expression data of PBMCs isolated from a subject following 4 cycles of Rituximab for treatment of FL.

hyb_protocol: Total RNA was linearly amplified (3’ IVT Express, Affymetrix) and cRNA was hybridized to HGU133A microarrays (Affymetrix) according to the manufacturer’s protocol.

source_name: PBMCs

extract_protocol: PBMCs (1.4×106 to 4.0×106 cells per mL) from 6 healthy male adults were isolated and prepared as described in Supplementary Methods and then frozen at -80 °C until use. Total cellular RNA (≥300 ng) was isolated from these 6 subjects along with viably preserved PBMCs from patient 4 (Supplementary Fig. 4c) using RNeasy Mini Kit (Qiagen) and assessed for yield (NanoDrop 2000, Thermo Scientific), and quality (2100 Bioanalyzer, Agilent).

tag: cell type

value: PBMCs

tag: disease status


title: FL lymph node biopsy, untreated, 1063

source_name: FL lymph node biopsy, untreated, 1063


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 mRNA RepA

description: Biological Replicate A

data_processing: The data were filtered for detection pValue <= 0.05 and normalised using robust spline normalisation with lumi in R. Filtering in Genome Studio using the OR clause (it means that even only a sample has a p-value lower  than 0.05 for one specific probe, this probe will be selected).

label: Biotin

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

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

value: mouse feeder layer and mechanically passagged P42


title: PBMCs, C6

description: Expression data of PBMCs collected from a healthy subject.

value: Healthy

value: Tregs = 2.1%


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 mRNA RepD

description: Biological Replicate D


title: hESCs cultured on mouse feeder layer and enzymatically passaged P31 total DNA genotyping RepE

description: Biological Replicate E

value: hESCs cultured on mouse feeder layer and enzymatically passagged P31


title: PBMCs, post-RCHOP, 3

description: Gene expression data from PBMCs, which were isolated from a specimen taken immediately following 6 cycles of RCHOP immunochemotherapy for treatment of DLBCL.

source_name: PBMCs, post-RCHOP, 3

value: DLBCL


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on mouse feeder layer and enzymatically passaged P31 total DNA genotyping RepA

description: Biological Replicate A


title: PBMCs, C5


title: PBMCs, post-RCHOP, 2

description: Gene expression data from PBMCs, which were isolated from a specimen taken immediately following 4 cycles of RCHOP immunochemotherapy for treatment of DLBCL.

source_name: PBMCs, post-RCHOP, 2


title: hESCs cultured on mouse feeder layer and enzymatically passaged P31 total DNA genotyping RepD

description: Biological Replicate D


title: hESCs cultured on mouse feeder layer and enzymatically passaged P31 total DNA genotyping RepF

description: Biological Replicate F


title: hESCs cultured on mouse feeder layer and enzymatically passaged P31 total DNA genotyping RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 mRNA RepE

description: Biological Replicate E

value: mouse feeder layer and mechanically passagged P103


title: hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepE

description: Biological Replicate E

value: mouse feeder layer and mechanically passagged P2


title: hESCs cultured on mouse feeder layer and enzymatically passaged P31 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepD

description: Biological Replicate D


title: PBMCs, pre-Rituximab, 1

description: Gene expression data from peripheral blood mononuclear cells (PBMCs), which were isolated from specimens taken before infusional rituximab monotherapy for extranodal marginal zone lymphoma (EMZL) in a subject without measurable circulating disease.

source_name: PBMCs, pre-Rituximab, 1

value: EMZL


title: PBMCs, post-Rituximab, 1

description: Gene expression data from peripheral blood mononuclear cells (PBMCs), which were isolated from specimens taken after 4 weekly doses of infusional rituximab (375 mg m−2) monotherapy for extranodal marginal zone lymphoma (EMZL) in a subject without measurable circulating disease.

source_name: PBMCs, post-Rituximab, 1


title: PBMCs, C2


title: PBMCs, C3

value: Tregs = 1.9%


title: hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 mRNA RepC

description: Biological Replicate C


title: ExVivo_WT_BMDMs_rep3

status: Public on Mar 28 2015

city: Xi’an

first: Junlong

last: Zhao

state: Shaanxi

address: Chang-Le Xi Street #17

department: Department of Medical Genetics and Developmental Biology

country: China

institute: Fourth Military Medical University

description: miRNA expression in WT mice BMDMs

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4472A) using one color scan setting for 8x15k array slides.

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

organism: Mus musculus

source_name: BMDMs from WT mice, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent's miRNA Complete Labeling and Hyb Kit(p/n 5190-0456) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: BMDMs were isolated from poly(I)-poly(C)-induced MxCre-RBP-Jf/f and MxCre-RBP-Jf/+ mice and stimulated with LPS for 24 h.

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

treatment_protocol: BMDMs were stimulated with LPS for 24 h.

value: bone marrow


title: ExVivo_KO_BMDMs_rep2

description: miRNA expression in Notch deleted mice BMDMs

hyb_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent's miRNA Complete Labeling and Hyb Kit(p/n 5190-0456) according to the manufacturer's instructions.

source_name: BMDMs from KO mice, replicate 2


title: hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepF

description: Biological Replicate F


title: ExVivo_WT_BMDMs_rep2

description: miRNA expression in WT mice BMDMs

source_name: BMDMs from WT mice, replicate 2


title: hESCs cultured on mouse feeder layer and enzymatically passaged P26 total DNA genotyping RepF

description: Biological Replicate F

value: hESCs cultured on mouse feeder layer and enzymatically passagged P26


title: hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepB

description: Biological Replicate B


title: PBMCs, C1


title: ExVivo_KO_BMDMs_rep3

source_name: BMDMs from KO mice, replicate 3


title: ExVivo_KO_BMDMs_rep1

source_name: BMDMs from KO mice, replicate 1


title: hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepA

description: Biological Replicate A


title: hESCs cultured on mouse feeder layer and enzymatically passaged P26 total DNA genotyping RepE

description: Biological Replicate E


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 mRNA RepB

description: Biological Replicate B


title: hESCs cultured on mouse feeder layer and enzymatically passaged P26 total DNA genotyping RepB

description: Biological Replicate B


title: FL lymph node biopsy, untreated, 731

source_name: FL lymph node biopsy, untreated, 731

value: Lymph node


title: hESCs cultured on mouse feeder layer and enzymatically passaged P26 total DNA genotyping RepA

description: Biological Replicate A


title: HSC,18mo,WT,rep4

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Arrays were hybridized overnight with 2.8 ug cDNA using using an Affymetrix hyb station, with hybridization solutions and conditions recommended by the kit manufacturer (Nugen).

scan_protocol: After arrays were washed they were stained with phycoerythrin-streptavidin as recommended by Affymetrix (including anti-SAPE antibody enhancement), and phycoerythrin fluorescence was determined with an Affymetrix scanner. Affymetrix Cammand Console software was used to control the scanner and generate raw image files (DAT) and to consolidate data from individual pixels into array features (CEL files).

data_processing: CEL files were quantile normalized and background subtracted with the Iterplier algorithm of Affymetrix Expression Console.

source_name: hematopoietic stem cells

label_protocol: Biotinylated cDNA was prepared from total RNA with the Nugen WT-Ovation PicoSL Kit.

growth_protocol: Mice were weaned at 3 weeks and fed ad libitum thereafter.

extract_protocol: Mice were killed by carbon dioxide inhalation at 18 months of age. Bone marrow was depleted of Lin+ cells as described by Singh et al. 2009 (Carcinogenesis 30;11-19). SLAM+ HSC were extracted from Lin- cells as described by Kiel et al. 2005 (Cell 121;1109-1121). Selected cells were collected in RNAlater reagent (Ambion) and frozen at -80C until total RNA was extracted with a Micro RNeasy kit (Qiagen).

tag: genotype

value: wild-type Ahr


title: HSC,18mo,AhrKO,rep5

value: Ahr knockout


title: PBMCs, C4

value: Tregs = 2.6%


title: HSC,18mo,AhrKO,rep1


title: HSC,18mo,WT,rep2


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA genotyping RepE

description: Biological Replicate E

value: female

value: hESCs cultured on mouse feeder layer and enzymatically passagged P41


title: HSC,18mo,WT,rep1


title: HSC,18mo,WT,rep3


title: HSC,18mo,AhrKO,rep2


title: flox_011764

city: Glasgow

first: Owen

last: Sansom

address: Garscube Estate

country: United Kingdom

institute: Cancer Research UK Beatson Institute

hyb_protocol: PICR Standard 11uM feature-1 protocol - carried out in the Affymetrix Hybridization Oven 640 according to the manufacturer’s instructions

scan_protocol: PICR Standard 11uM feature-1 protocol - using the Affymetrix GeneChip Scanner 3000 system with Autoloader

data_processing: Data from Affymetrix CEL files (Mouse430_2) were normalized using Robust Multi-array Average (RMA).

source_name: Pancreatic ductal adenocarcinoma

label_protocol: PICR Std Label v 2-0 - utalizing the Enzo BioArray High Yield Transcript Labelling Kit

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

tag: type

value: PDAC (non-metastatic)


title: HSC,18mo,WT,rep5


title: flox_91808


title: flox_91807


title: flox_90593


title: HSC,18mo,AhrKO,rep4


title: HSC,18mo,AhrKO,rep3


title: hESCs cultured on mouse feeder layer and enzymatically passaged P26 total DNA genotyping RepC

description: Biological Replicate C


title: flox_92752


title: ExVivo_WT_BMDMs_rep1

description: miRNA expression in WT mice BMDMs

source_name: BMDMs from WT mice, replicate 1


title: MT_97110

value: PDAC (metastatic)


title: hESCs cultured on mouse feeder layer and enzymatically passaged P11 total DNA genotyping RepE

description: Biological Replicate E

value: hESCs cultured on mouse feeder layer and enzymatically passagged P11


title: MT_88000


title: hESCs cultured on mouse feeder layer and enzymatically passaged P11 total DNA genotyping RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and enzymatically passaged P11 total DNA genotyping RepD

description: Biological Replicate D


title: MT_86119


title: hESCs cultured on mouse feeder layer and enzymatically passaged P11 total DNA genotyping RepB

description: Biological Replicate B


title: SOBC2_2661_1

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description:
Illumina Human HT-12 BeadArray
9344118043_E.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All available data are provided, with no additional filtering.

source_name: PBMC

label_protocol: Standard Illumina target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Primary peripheral blood mononuclear cells were isolated and total RNA was extracted using Qiagen RNEasy.

tag: hedonic

tag: eudaimonic

tag: social

tag: psychological

tag: totalmhcsf

tag: flourishgroup

tag: brownpsychological

tag: brownsocial

tag: age

tag: white

tag: male

tag: bmi

tag: illness

tag: smoke

tag: alcohol

tag: cesd


title: SOBC2_2663_1

description:
Illumina Human HT-12 BeadArray
9344118042_L.AVG_Signal


title: SOBC2_2714_1

description:
Illumina Human HT-12 BeadArray
9344118087_H.AVG_Signal


title: SOBC2_2736_1

description:
Illumina Human HT-12 BeadArray
9344118083_L.AVG_Signal


title: SOBC2_2728_1

description:
Illumina Human HT-12 BeadArray
9344118087_C.AVG_Signal


title: SOBC2_2723_1

description:
Illumina Human HT-12 BeadArray
9344118087_G.AVG_Signal


title: SOBC2_2675_1

description:
Illumina Human HT-12 BeadArray
9344118043_G.AVG_Signal


title: SOBC2_2654_1

description:
Illumina Human HT-12 BeadArray
9344118043_L.AVG_Signal


title: nonMT_01599

tag: genotype

tag: type


title: nonMT_86999


title: SOBC2_2648_1

description:
Illumina Human HT-12 BeadArray
9344118083_F.AVG_Signal

tag: hedonic

tag: eudaimonic


title: MT_80396


title: nonMT_98953


title: nonMT_20647


title: MT_30452


title: nonMT_87978


title: nonMT_84452


title: SOBC2_2647_1

description:
Illumina Human HT-12 BeadArray
9344118043_A.AVG_Signal

tag: social

tag: psychological


title: MT_83330


title: nonMT_83796


title: SOBC2_2659_1

description:
Illumina Human HT-12 BeadArray
9344118047_D.AVG_Signal

tag: totalmhcsf

tag: flourishgroup


title: SOBC2_2644_1

description:
Illumina Human HT-12 BeadArray
9344118047_L.AVG_Signal

tag: brownpsychological

tag: brownsocial


title: SOBC2_2639_1

description:
Illumina Human HT-12 BeadArray
9344118037_A.AVG_Signal

tag: age

tag: white


title: SOBC2_2642_1

description:
Illumina Human HT-12 BeadArray
9344118087_K.AVG_Signal

tag: male

tag: bmi


title: MT_22528


title: hESCs cultured on mouse feeder layer and enzymatically passaged P11 total DNA genotyping RepF

description: Biological Replicate F

tag: gender

tag: growth condition

tag: passage

tag: cell line


title: hESCs cultured on mouse feeder layer and enzymatically passaged P11 total DNA genotyping RepA

description: Biological Replicate A


title: SOBC2_2635_1

description:
Illumina Human HT-12 BeadArray
9344118072_A.AVG_Signal

tag: illness

tag: smoke

tag: alcohol

tag: cesd


title: SOBC2_2616_1

description:
Illumina Human HT-12 BeadArray
9344118083_E.AVG_Signal

tag: hedonic

tag: eudaimonic

tag: social

tag: psychological


title: SOBC2_2597_1

description:
Illumina Human HT-12 BeadArray
9344118037_C.AVG_Signal

tag: totalmhcsf

tag: flourishgroup

tag: brownpsychological

tag: brownsocial


title: SOBC2_2618_1

description:
Illumina Human HT-12 BeadArray
9344118047_J.AVG_Signal

tag: age

tag: white

tag: male

tag: bmi


title: SOBC2_2632_1

description:
Illumina Human HT-12 BeadArray
9344118087_D.AVG_Signal


title: SOBC2_2626_1

description:
Illumina Human HT-12 BeadArray
9344118047_I.AVG_Signal


title: SOBC2_2603_1

description:
Illumina Human HT-12 BeadArray
9344118037_G.AVG_Signal


title: SOBC2_2605_1

description:
Illumina Human HT-12 BeadArray
9344118042_I.AVG_Signal


title: SOBC2_2599_1

description:
Illumina Human HT-12 BeadArray
9344118043_C.AVG_Signal


title: SOBC2_2602_1

description:
Illumina Human HT-12 BeadArray
9344118083_A.AVG_Signal


title: SOBC2_2637_1

description:
Illumina Human HT-12 BeadArray
9344118037_J.AVG_Signal


title: SOBC2_2636_1

description:
Illumina Human HT-12 BeadArray
9344118043_K.AVG_Signal


title: SOBC2_2629_1

description:
Illumina Human HT-12 BeadArray
9344118040_C.AVG_Signal


title: SOBC2_2601_1

description:
Illumina Human HT-12 BeadArray
9344118047_H.AVG_Signal


title: SOBC2_2630_1

description:
Illumina Human HT-12 BeadArray
9344118083_H.AVG_Signal


title: SOBC2_2594_1

description:
Illumina Human HT-12 BeadArray
9344118083_G.AVG_Signal


title: SOBC2_2623_1

description:
Illumina Human HT-12 BeadArray
9344118047_F.AVG_Signal


title: SOBC2_2638_1

description:
Illumina Human HT-12 BeadArray
9344118043_J.AVG_Signal

value: Missing


title: SOBC2_2609_1

description:
Illumina Human HT-12 BeadArray
9344118087_A.AVG_Signal


title: SOBC2_2596_1

description:
Illumina Human HT-12 BeadArray
9344118087_F.AVG_Signal


title: SOBC2_2613_1

description:
Illumina Human HT-12 BeadArray
9344118040_I.AVG_Signal


title: SOBC2_2610_1

description:
Illumina Human HT-12 BeadArray
9344118047_E.AVG_Signal


title: SOBC2_2622_1

description:
Illumina Human HT-12 BeadArray
9344118083_J.AVG_Signal


title: SOBC2_2607_1

description:
Illumina Human HT-12 BeadArray
9344118040_H.AVG_Signal


title: SOBC2_2627_1

description:
Illumina Human HT-12 BeadArray
9344118087_B.AVG_Signal


title: SOBC2_2593_1

description:
Illumina Human HT-12 BeadArray
9344118037_F.AVG_Signal


title: SOBC2_2606_1

description:
Illumina Human HT-12 BeadArray
9344118047_G.AVG_Signal


title: SOBC2_2575_1

description:
Illumina Human HT-12 BeadArray
9344118043_D.AVG_Signal


title: SOBC2_2566_1

description:
Illumina Human HT-12 BeadArray
9344118037_H.AVG_Signal


title: SOBC2_2569_1

description:
Illumina Human HT-12 BeadArray
9344118040_D.AVG_Signal


title: SOBC2_2587_1

description:
Illumina Human HT-12 BeadArray
9344118087_E.AVG_Signal


title: SOBC2_2592_1

description:
Illumina Human HT-12 BeadArray
9344118037_L.AVG_Signal


title: SOBC2_2579_1

description:
Illumina Human HT-12 BeadArray
9344118047_B.AVG_Signal


title: SOBC2_2564_1

description:
Illumina Human HT-12 BeadArray
9344118043_B.AVG_Signal


title: hESCs cultured on mouse feeder layer and enzymatically passaged P26 total DNA genotyping RepD

description: Biological Replicate D

tag: gender

tag: growth condition

tag: passage

tag: cell line


title: SOBC2_2625_1

description:
Illumina Human HT-12 BeadArray
9344118040_G.AVG_Signal

tag: illness

tag: smoke

tag: alcohol

tag: cesd


title: SOBC2_2560_1

description:
Illumina Human HT-12 BeadArray
9344118043_H.AVG_Signal

tag: hedonic

tag: eudaimonic

tag: social

tag: psychological


title: SOBC2_2201_1

description:
Illumina Human HT-12 BeadArray
9344118018_I.AVG_Signal

tag: totalmhcsf

tag: flourishgroup

tag: brownpsychological

tag: brownsocial


title: SOBC2_2586_1

description:
Illumina Human HT-12 BeadArray
9344118037_K.AVG_Signal

tag: age

tag: white

tag: male

tag: bmi


title: SOBC2_2574_1

description:
Illumina Human HT-12 BeadArray
9344118040_L.AVG_Signal


title: SOBC2_2186_1

description:
Illumina Human HT-12 BeadArray
9345724099_D.AVG_Signal


title: SOBC2_2183_1

description:
Illumina Human HT-12 BeadArray
9344118018_J.AVG_Signal


title: SOBC2_2554_1

description:
Illumina Human HT-12 BeadArray
9344118083_D.AVG_Signal


title: SOBC2_2205_1

description:
Illumina Human HT-12 BeadArray
9345724099_I.AVG_Signal


title: SOBC2_2202_1

description:
Illumina Human HT-12 BeadArray
9248833142_E.AVG_Signal


title: SOBC2_2180_1

description:
Illumina Human HT-12 BeadArray
9322957065_C.AVG_Signal


title: SOBC2_2187_1

description:
Illumina Human HT-12 BeadArray
9322957065_G.AVG_Signal


title: SOBC2_2550_1

description:
Illumina Human HT-12 BeadArray
9344118072_C.AVG_Signal


title: SOBC2_2182_1

description:
Illumina Human HT-12 BeadArray
9344118020_G.AVG_Signal


title: SOBC2_2176_1

description:
Illumina Human HT-12 BeadArray
9345724099_C.AVG_Signal


title: SOBC2_2169_1

description:
Illumina Human HT-12 BeadArray
9344118018_B.AVG_Signal


title: SOBC2_2561_1

description:
Illumina Human HT-12 BeadArray
9344118047_K.AVG_Signal


title: SOBC2_2171_1

description:
Illumina Human HT-12 BeadArray
9344118018_A.AVG_Signal


title: SOBC2_2567_1

description:
Illumina Human HT-12 BeadArray
9344118040_E.AVG_Signal


title: SOBC2_2619_1

description:
Illumina Human HT-12 BeadArray
9344118047_C.AVG_Signal


title: SOBC2_2168_1

description:
Illumina Human HT-12 BeadArray
9322957065_I.AVG_Signal


title: SOBC2_2167_1

description:
Illumina Human HT-12 BeadArray
9322957068_E.AVG_Signal


title: SOBC2_2165_1

description:
Illumina Human HT-12 BeadArray
9345724099_F.AVG_Signal


title: SOBC2_2147_1

description:
Illumina Human HT-12 BeadArray
9248833130_D.AVG_Signal


title: SOBC2_2123_1

description:
Illumina Human HT-12 BeadArray
9322957065_D.AVG_Signal


title: SOBC2_2144_1

description:
Illumina Human HT-12 BeadArray
9322957065_B.AVG_Signal


title: SOBC2_2131_1

description:
Illumina Human HT-12 BeadArray
9344118018_E.AVG_Signal


title: SOBC2_2112_1

description:
Illumina Human HT-12 BeadArray
9248833130_A.AVG_Signal


title: SOBC2_2166_1

description:
Illumina Human HT-12 BeadArray
9322957065_L.AVG_Signal


title: SOBC2_2174_1

description:
Illumina Human HT-12 BeadArray
9345724099_G.AVG_Signal


title: SOBC2_2136_1

description:
Illumina Human HT-12 BeadArray
9344118020_K.AVG_Signal


title: SOBC2_2096_1

description:
Illumina Human HT-12 BeadArray
9322957065_J.AVG_Signal


title: SOBC2_2092_1

description:
Illumina Human HT-12 BeadArray
9344118020_A.AVG_Signal


title: SOBC2_2086_1

description:
Illumina Human HT-12 BeadArray
9248833142_C.AVG_Signal


title: SOBC2_2145_1

description:
Illumina Human HT-12 BeadArray
9344118018_F.AVG_Signal


title: SOBC2_2121_1

description:
Illumina Human HT-12 BeadArray
9248833130_H.AVG_Signal


title: SOBC2_2113_1

description:
Illumina Human HT-12 BeadArray
9322957065_F.AVG_Signal


title: SOBC2_2097_1

description:
Illumina Human HT-12 BeadArray
9345724099_K.AVG_Signal


title: SOBC2_2106_1

description:
Illumina Human HT-12 BeadArray
9344118018_H.AVG_Signal


title: SOBC2_2076_1

description:
Illumina Human HT-12 BeadArray
9248833130_E.AVG_Signal


title: SOBC2_2093_1

description:
Illumina Human HT-12 BeadArray
9248833130_F.AVG_Signal


title: SOBC2_2089_1

description:
Illumina Human HT-12 BeadArray
9248833142_K.AVG_Signal


title: SOBC2_2079_1

description:
Illumina Human HT-12 BeadArray
9344118020_I.AVG_Signal


title: SOBC2_2073_1

description:
Illumina Human HT-12 BeadArray
9248833130_K.AVG_Signal


title: SOBC2_2119_1

description:
Illumina Human HT-12 BeadArray
9322957068_J.AVG_Signal


title: SOBC2_2074_1

description:
Illumina Human HT-12 BeadArray
9248833142_I.AVG_Signal


title: SOBC2_2072_1

description:
Illumina Human HT-12 BeadArray
9248833130_C.AVG_Signal


title: SOBC2_2104_1

description:
Illumina Human HT-12 BeadArray
9248833142_H.AVG_Signal


title: SOBC2_2091_1

description:
Illumina Human HT-12 BeadArray
9248833142_G.AVG_Signal


title: SOBC2_2108_1

description:
Illumina Human HT-12 BeadArray
9345724099_E.AVG_Signal


title: SOBC2_2094_1

description:
Illumina Human HT-12 BeadArray
9345724099_L.AVG_Signal


title: SOBC2_2066_1

description:
Illumina Human HT-12 BeadArray
9344118020_L.AVG_Signal


title: SOBC2_2042_1

description:
Illumina Human HT-12 BeadArray
9322957065_K.AVG_Signal


title: SOBC2_2043_1

description:
Illumina Human HT-12 BeadArray
9344118020_E.AVG_Signal


title: SOBC2_2037_1

description:
Illumina Human HT-12 BeadArray
9248833130_B.AVG_Signal


title: SOBC2_2061_1

description:
Illumina Human HT-12 BeadArray
9344118020_H.AVG_Signal


title: SOBC2_2048_1

description:
Illumina Human HT-12 BeadArray
9248833130_J.AVG_Signal


title: SOBC2_2039_1

description:
Illumina Human HT-12 BeadArray
9322957068_F.AVG_Signal


title: SOBC2_2047_1

description:
Illumina Human HT-12 BeadArray
9322957065_H.AVG_Signal


title: SOBC2_2049_1

description:
Illumina Human HT-12 BeadArray
9322957068_L.AVG_Signal


title: SOBC2_2064_1

description:
Illumina Human HT-12 BeadArray
9344118018_K.AVG_Signal


title: SOBC2_2030_1

description:
Illumina Human HT-12 BeadArray
9322957068_D.AVG_Signal


title: SOBC2_2031_1

description:
Illumina Human HT-12 BeadArray
9322957068_B.AVG_Signal


title: SOBC2_2023_1

description:
Illumina Human HT-12 BeadArray
9248833142_A.AVG_Signal


title: SOBC2_2024_1

description:
Illumina Human HT-12 BeadArray
9344118018_G.AVG_Signal


title: SOBC2_2028_1

description:
Illumina Human HT-12 BeadArray
9322957065_A.AVG_Signal


title: SOBC2_2035_1

description:
Illumina Human HT-12 BeadArray
9344118020_C.AVG_Signal


title: SOBC2_2036_1

description:
Illumina Human HT-12 BeadArray
9322957065_E.AVG_Signal


title: SOBC2_2021_1

description:
Illumina Human HT-12 BeadArray
9322957068_A.AVG_Signal


title: SOBC2_2032_1

description:
Illumina Human HT-12 BeadArray
9322957068_H.AVG_Signal


title: SOBC2_2044_1

description:
Illumina Human HT-12 BeadArray
9248833142_J.AVG_Signal


title: SOBC2_2025_1

description:
Illumina Human HT-12 BeadArray
9344118020_J.AVG_Signal


title: SOBC2_2026_1

description:
Illumina Human HT-12 BeadArray
9344118018_D.AVG_Signal


title: CG-647-V1

source_name: CD14+ peripheral blood leukocytes

label_protocol: Standard Illumina probe synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

tag: participant id

tag: study visit (range 1-4 in 6-mo intervals)

tag: sample group

value: non-stressed control group

tag: gender

tag: ethnicity

value: Non-Caucasian

tag: age (at study entry, in yrs)

tag: waistcm (waist circumfrence in cm)

tag: alcohol (drinks per week)

value: non-smoker

tag: exercise (min per wk of brisk physical activity)

tag: education


title: CG-646-V2

value: Caucasian

tag: smoke


title: CG-644-V2


title: CG-645-V2

value: male


title: CG-647-V2


title: SOBC2_2020_1

description:
Illumina Human HT-12 BeadArray
9248833130_G.AVG_Signal

tag: hedonic

tag: eudaimonic

tag: social

tag: psychological

tag: totalmhcsf

tag: flourishgroup

tag: brownpsychological

tag: illness

tag: alcohol

tag: cesd


title: CG-646-V1

tag: participant id

tag: study visit (range 1-4 in 6-mo intervals)

tag: sample group

tag: gender

tag: ethnicity


title: CG-645-V1

tag: age (at study entry, in yrs)

tag: waistcm (waist circumfrence in cm)

tag: alcohol (drinks per week)

tag: exercise (min per wk of brisk physical activity)

tag: education


title: CG-640-V2

tag: smoke


title: CG-643-V1


title: CG-643-V2


title: CG-640-V4


title: CG-642-V4


title: CG-642-V1


title: CG-638-V2


title: CG-640-V1


title: CG-638-V4


title: CG-637-V3


title: CG-638-V3


title: CG-639-V4


title: CG-637-V4


title: CG-642-V3


title: CG-637-V2


title: CG-644-V1


title: CG-641-V1


title: CG-637-V1


title: CG-635-V4


title: CG-635-V3


title: CG-636-V1


title: CG-636-V2


title: CG-640-V3


title: CG-639-V2


title: CG-632-V4


title: CG-634-V3


title: CG-639-V1


title: CG-633-V1


title: CG-634-V1


title: CG-638-V1


title: CG-636-V3


title: CG-635-V2


title: CG-635-V1


title: CG-633-V4


title: CG-633-V3


title: CG-632-V2


title: CG-633-V2


title: CG-631-V2

value: daily smoker


title: CG-632-V1


title: CG-632-V3


title: CG-629-V2


title: CG-634-V2


title: CG-630-V1


title: CG-631-V3


title: CG-629-V3


title: CG-629-V1


title: CG-631-V4


title: CG-629-V4


title: CG-627-V4


title: CG-628-V3


title: CG-639-V3


title: CG-628-V2


title: CG-628-V1


title: CG-627-V3


title: CG-627-V1


title: CG-628-V4


title: CG-626-V4


title: CG-627-V2


title: CG-626-V2


title: CG-626-V3


title: CG-625-V3


title: CG-626-V1


title: CG-625-V2


title: CG-624-V1


title: CG-623-V2


title: CG-622-V4


title: CG-625-V1


title: CG-622-V1


title: CG-625-V4


title: CG-622-V3


title: CG-623-V4


title: CG-623-V1


title: CG-623-V3


title: CG-621-V2


title: CG-622-V2


title: CG-631-V1


title: CG-620-V4


title: CG-621-V4


title: CG-619-V3


title: CG-620-V1


title: CG-618-V1


title: CG-620-V3


title: CG-621-V3


title: CG-617-V3


title: CG-620-V2


title: CG-619-V2


title: CG-619-V1


title: CG-617-V2


title: CG-621-V1


title: CG-617-V1


title: CG-619-V4


title: CG-617-V4


title: CG-616-V3


title: CG-616-V2


title: CG-616-V4


title: CG-615-V4


title: CG-614-V3


title: CG-616-V1


title: CG-614-V4


title: CG-613-V3


title: CG-615-V2


title: CG-615-V1


title: CG-614-V1


title: CG-612-V1


title: CG-610-V4


title: CG-613-V4


title: CG-611-V2


title: CG-613-V2


title: CG-615-V3


title: CG-611-V4


title: CG-614-V2


title: CG-611-V3


title: CG-610-V1


title: CG-610-V3


title: CG-609-V3


title: CG-610-V2


title: CG-611-V1


title: CG-609-V2


title: CG-609-V4


title: CG-608-V4


title: CG-608-V3


title: CG-613-V1


title: CG-607-V4


title: CG-608-V2


title: CG-607-V3


title: CG-608-V1


title: CG-607-V2


title: CG-606-V4


title: CG-609-V1


title: CG-606-V3


title: CG-606-V2


title: CG-605-V1


title: CG-606-V1


title: CG-604-V4


title: Drosophila_melanogaster_anti-PUM_RIP_RNA_rep3

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: This sample is total RNA isolated from anti-PUM RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates.

hyb_protocol: Hybridization was performed following the protocol described in the NimbleGen Array User’s Guide (Gene Expression Arrays, version 6.0).

scan_protocol: Arrays were scanned with a GenePix4000B microarray scanner system (Molecular Devices, Inc., Sunnyvale, CA, USA), and scanned images were initially quantified using Nimblescan (Roche), following the protocol described in the NimbleGen Array User's Guide (Gene Expression Arrays, version 6.0).

data_processing: The raw data (.pair files) were normalized with ArrayStar 3 (DNASTAR) software using the RMA quantile method, and signal intensities were log2-transformed. For normalization, BRAT RIP samples and PUM RIP samples were each normalized separately with the control RIP samples. Therefore, Samples 1-6 were normalized together as one group, and Samples 7-12 were normalized together as a second group.

organism: Drosophila melanogaster

source_name: anti-PUM RIP from w1118 0-3 hour embryo

label_protocol: Labelling was performed following the protocol described in the NimbleGen Array User’s Guide (Gene Expression Arrays, version 6.0).

growth_protocol: The following fly strains were used: w1118. All stocks were maintained at 25oC.

extract_protocol: Total RNA was extracted using TRIzol according to the manufacturer’s protocol.

tag: developmental stage

value: 0-3 hour embryo

tag: strain


title: Drosophila_melanogaster_anti-PUM_RIP_RNA_rep2

description: This sample is total RNA isolated from anti-PUM RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates.


title: Drosophila_melanogaster_anti-PUM_RIP_RNA_rep1

description: This sample is total RNA isolated from anti-PUM RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates.


title: CG-605-V3


title: CG-604-V1


title: Drosophila_melanogaster_control_RIP_RNA_rep3_normalized_with_BRAT_samples

description: This sample is total RNA isolated from synthetic antibody control RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates. The RNA sample itself is the same as SAMPLE 12, but for data processing SAMPLE 6 was normalized together with Samples 1, 2, 3, 4, and 5.

source_name: synthetic antibody control RIP from w1118 0-3 hour embryo


title: Drosophila_melanogaster_control_RIP_RNA_rep2_normalized_with_PUM_samples

description: This sample is total RNA isolated from synthetic antibody control RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates. The RNA sample itself is the same as SAMPLE 5, but for data processing SAMPLE 11 was normalized together with Samples 7, 8, 9, 10, and 12.


title: CG-604-V2


title: Drosophila_melanogaster_control_RIP_RNA_rep1_normalized_with_PUM_samples

description: This sample is total RNA isolated from synthetic antibody control RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates. The RNA sample itself is the same as SAMPLE 4, but for data processing SAMPLE 10 was normalized together with Samples 7, 8, 9, 11, and 12.


title: CG-603-V4


title: CG-607-V1


title: CG-605-V4


title: CG-603-V1


title: CG-602-V3


title: Drosophila_melanogaster_control_RIP_RNA_rep3_normalized_with_PUM_samples

description: This sample is total RNA isolated from synthetic antibody control RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates. The RNA sample itself is the same as SAMPLE 6, but for data processing SAMPLE 12 was normalized together with Samples 7, 8, 9, 10, and 11.


title: CG-604-V3


title: CG-603-V3


title: Drosophila_melanogaster_control_RIP_RNA_rep2_normalized_with_BRAT_samples

description: This sample is total RNA isolated from synthetic antibody control RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates. The RNA sample itself is the same as SAMPLE 11, but for data processing SAMPLE 5 was normalized together with Samples 1, 2, 3, 4, and 6.


title: Drosophila_melanogaster_control_RIP_RNA_rep1_normalized_with_BRAT_samples

description: This sample is total RNA isolated from synthetic antibody control RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates. The RNA sample itself is the same as SAMPLE 10, but for data processing SAMPLE 4 was normalized together with Samples 1, 2, 3, 5, and 6.


title: CG-603-V2


title: CG-602-V2


title: Drosophila_melanogaster_anti-BRAT_RIP_RNA_rep3

description: This sample is total RNA isolated from anti-BRAT RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates.

source_name: anti-BRAT RIP from w1118 0-3 hour embryo


title: Drosophila_melanogaster_anti-BRAT_RIP_RNA_rep2

description: This sample is total RNA isolated from anti-BRAT RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates.


title: Drosophila_melanogaster_anti-BRAT_RIP_RNA_rep1

description: This sample is total RNA isolated from anti-BRAT RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates.


title: CG-602-V1


title: CG-601-V2


title: CG-032-V1

value: caregiver group


title: CG-031-V1


title: CG-034-V1


title: CG-602-V4


title: CG-033-V1


title: CG-032-V2


title: CG-601-V4


title: CG-601-V3


title: CG-030-V1


title: CG-601-V1


title: CG-030-V2


title: CG-029-V2


title: CG-028-V1


title: CG-027-V4


title: CG-029-V1


title: CG-028-V2


title: CG-026-V3


title: CG-029-V3


title: CG-028-V3


title: CG-027-V2


title: CG-027-V1


title: CG-026-V2


title: CG-026-V1


title: CG-027-V3


title: CG-026-V4


title: CG-024-V3


title: CG-025-V4


title: CG-025-V3


title: CG-025-V2


title: CG-025-V1


title: CG-021-V4


title: CG-022-V2


title: CG-024-V1


title: CG-022-V1


title: CG-024-V2


title: CG-021-V1


title: CG-021-V3


title: CG-020-V2


title: CG-019-V1


title: CG-018-V1


title: CG-021-V2


title: CG-018-V2


title: CG-019-V4


title: CG-019-V3


title: CG-020-V1


title: CG-019-V2


title: CG-017-V2


title: CG-017-V4


title: CG-015-V3


title: CG-017-V1


title: CG-016-V2


title: CG-016-V1


title: CG-014-V4


title: CG-014-V2


title: CG-015-V1


title: CG-015-V2


title: CG-014-V1


title: CG-018-V4


title: CG-017-V3


title: CG-015-V4


title: CG-605-V2


title: CG-014-V3


title: CG-012-V4


title: CG-013-V4


title: CG-012-V3


title: CG-010-V3


title: CG-013-V3


title: CG-013-V1


title: CG-011-V1


title: CG-012-V2


title: CG-009-V2


title: CG-010-V2


title: CG-010-V4


title: CG-009-V3


title: CG-013-V2


title: CG-009-V4


title: CG-012-V1


title: CG-009-V1


title: CG-010-V1


title: CG-007-V2


title: CG-006-V1


title: CG-007-V1


title: CG-007-V4


title: CG-007-V3


title: CG-005-V2


title: CG-008-V1


title: CG-018-V3


title: CG-006-V2


title: CG-004-V1


title: CG-004-V3


title: CG-004-V2


title: CG-004-V4


title: CG-003-V1


title: CG-003-V2


title: CG-005-V3


title: CG-002-V4


title: CG-005-V1


title: CG-001-V4


title: CG-001-V1


title: CG-002-V2


title: CG-001-V3


title: CG-003-V4


title: 246p

description:
6260971066_I.AVG_Signal
Illumina Human HT-12 BeadArray

tag: cell type

value: Primary peripheral blood mononuclear cells

tag: age

tag: male

tag: bmi


title: CG-003-V3

tag: participant id


title: 244c

description:
6260971066_D.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol


title: 243p

description:
6260971066_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 245p

description:
6260971066_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 246c

description:
6260971066_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 241p

description:
6260971075_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 245c

description:
6260971066_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 244p

description:
6260971066_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 240p

description:
6260971075_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 242c

description:
6260971075_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 239c

description:
6260971075_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 243c

description:
6260971066_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 242p

description:
6260971066_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 240c

description:
6260971075_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 238p

description:
6260971075_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: CG-002-V3

tag: study visit (range 1-4 in 6-mo intervals)

tag: sample group


title: 241c

description:
6260971075_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 238c

description:
6260971075_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 235p

description:
6260971077_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 236c

description:
6260971075_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 239p

description:
6260971075_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 236p

description:
6260971075_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 233p

description:
6260971077_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 235c

description:
6260971077_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 237p

description:
6260971075_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 234c

description:
6260971077_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: CG-001-V2

tag: gender

tag: ethnicity


title: 234p

description:
6260971077_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 232p

description:
6260971077_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: CG-002-V1

tag: age (at study entry, in yrs)

tag: waistcm (waist circumfrence in cm)


title: 233c

description:
6260971077_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 230p

description:
6260971077_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 232c

description:
6260971077_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 228p

description:
6260971074_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 229p

description:
6260971077_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 229c

description:
6260971074_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 230c

description:
6260971077_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 231p

description:
6260971077_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 227c

description:
6260971074_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 223p

description:
6260971074_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 222p

description:
6260971074_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 218c

description:
6260971067_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 220p

description:
6260971067_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 225c

description:
6260971074_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 225p

description:
6260971074_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 215c

description:
6260971078_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 211p

description:
6260971078_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 227p

description:
6260971074_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 222c

description:
6260971067_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 224c

description:
6260971074_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 224p

description:
6260971074_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 215p

description:
6260971067_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 228c

description:
6260971074_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 219c

description:
6260971067_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 221p

description:
6260971067_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 217p

description:
6260971067_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 216c

description:
6260971067_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 223c

description:
6260971074_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 217c

description:
6260971067_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 211c

description:
6260971078_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 213p

description:
6260971078_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 216p

description:
6260971067_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 218p

description:
6260971067_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 212p

description:
6260971078_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 212c

description:
6260971078_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 210p

description:
6260971078_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 210c

description:
6260971078_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 219p

description:
6260971067_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 209c

description:
6260971078_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 206p

description:
6303281079_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 206c

description:
6303281079_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 205p

description:
6303281079_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 203c

description:
6303281079_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 201c

description:
6303281091_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 209p

description:
6260971078_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 208p

description:
6260971078_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 207p

description:
6303281079_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 205c

description:
6303281079_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 207c

description:
6303281079_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 200c

description:
6303281091_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 208c

description:
6260971078_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 198c

description:
6303281091_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 204p

description:
6303281079_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 197p

description:
6303281091_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 200p

description:
6303281091_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 204c

description:
6303281079_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 199p

description:
6303281091_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 201p

description:
6303281091_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 198p

description:
6303281091_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 202c

description:
6303281079_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 196p

description:
6303281091_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 203p

description:
6303281079_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 202p

description:
6303281079_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 197c

description:
6303281091_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 194p

description:
6303281102_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 195c

description:
6303281102_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 190p

description:
6303281102_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 195p

description:
6303281091_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 193p

description:
6303281102_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 185p

description:
6303281064_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 194c

description:
6303281102_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 183c

description:
6303281100_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 191c

description:
6303281102_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 189p

description:
6303281102_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 188p

description:
6303281064_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 188c

description:
6303281064_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 187c

description:
6303281064_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 184p

description:
6303281064_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 186c

description:
6303281064_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 187p

description:
6303281064_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 192p

description:
6303281102_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 184c

description:
6303281064_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 185c

description:
6303281064_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 196c

description:
6303281091_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 183p

description:
6303281064_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 190c

description:
6303281102_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 182p

description:
6303281100_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 192c

description:
6303281102_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 182c

description:
6303281100_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 181c

description:
6303281100_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 193c

description:
6303281102_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 191p

description:
6303281102_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 189c

description:
6303281064_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 180c

description:
6303281100_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 181p

description:
6303281100_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 186p

description:
6303281064_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 180p

description:
6303281100_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 179c

description:
6303281100_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 174p

description:
6303230004_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 179p

description:
6303281100_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 172c

description:
6303230004_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 171p

description:
6303230004_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 178p

description:
6303281100_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 168c

description:
6260962003_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 175p

description:
6303230004_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 167p

description:
6260962003_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 167c

description:
6260962003_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 169p

description:
6260962003_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 171c

description:
6303230004_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 177p

description:
6303281100_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 178c

description:
6303281100_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 173c

description:
6303230004_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 177c

description:
6303230004_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 166p

description:
6260962003_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 174c

description:
6303230004_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 175c

description:
6303230004_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 166c

description:
6260962003_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 173p

description:
6303230004_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 172p

description:
6303230004_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 169c

description:
6260962003_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 163p

description:
6260962003_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 163c

description:
6260962004_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 164c

description:
6260962003_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 162p

description:
6260962004_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 165p

description:
6260962003_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 170p

description:
6303230004_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 164p

description:
6260962003_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 170c

description:
6260962003_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 162c

description:
6260962004_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 161p

description:
6260962004_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 158p

description:
6260962004_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 159c

description:
6260962004_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 160c

description:
6260962004_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 152p

description:
6260962009_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 148c

description:
6260962050_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 149p

description:
6260962050_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 156p

description:
6260962009_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 155c

description:
6260962009_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 153p

description:
6260962009_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 148p

description:
6260962050_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 157p

description:
6260962004_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 159p

description:
6260962004_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 154c

description:
6260962009_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 156c

description:
6260962009_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 157c

description:
6260962004_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 150p

description:
6260962009_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 154p

description:
6260962009_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 151c

description:
6260962009_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 152c

description:
6260962009_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 146c

description:
6260962050_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 149c

description:
6260962050_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 145p

description:
6260962050_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 146p

description:
6260962050_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 158c

description:
6260962004_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 147c

description:
6260962050_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 150c

description:
6260962050_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 160p

description:
6260962004_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 147p

description:
6260962050_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 155p

description:
6260962009_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 153c

description:
6260962009_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 142c

description:
6260962041_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 139c

description:
6260962041_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 136p

description:
6260962015_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 141p

description:
6260962041_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 137c

description:
6260962015_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 144p

description:
6260962050_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 145c

description:
6260962050_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 140p

description:
6260962041_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 142p

description:
6260962041_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 138c

description:
6260962015_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 135p

description:
6260962015_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 143p

description:
6260962041_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 139p

description:
6260962041_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 134p

description:
6260962015_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 138p

description:
6260962041_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 135c

description:
6260962015_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 143c

description:
6260962041_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 134c

description:
6260962015_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 141c

description:
6260962041_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 133c

description:
6260962015_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 136c

description:
6260962015_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 140c

description:
6260962041_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 144c

description:
6260962041_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 131c

description:
6116750087_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 131p

description:
6116750087_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 132c

description:
6260962015_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 130c

description:
6116750087_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 133p

description:
6260962015_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 130p

description:
6116750087_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 126p

description:
6116750087_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 129c

description:
6116750087_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 124c

description:
6116750088_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 128p

description:
6116750087_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 128c

description:
6116750087_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 127p

description:
6116750087_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 122p

description:
6116750088_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 125c

description:
6116750087_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 127c

description:
6116750087_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 120c

description:
6116750088_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 126c

description:
6116750087_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 123c

description:
6116750088_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 121p

description:
6116750088_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 118p

description:
6116750088_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 116c

description:
6116750093_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 120p

description:
6116750088_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: 118c

description:
6116750093_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 124p

description:
6116750088_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: 119p

description:
6116750088_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: TBE cells with IL-17

city: Davis

first: Reen

last: Wu

state: CALIFORNIA

address: 451 Health Sciences Dr.

department: Center for Comparative Respiratory Biology and Medicine

institute: University of California Davis

hyb_protocol: This information is not available since the experiments were done more than 10 years ago.

source_name: Human primary epithelial cell cultures treated with IL-17A (10 ng/ml) for 24 hours

growth_protocol: TBE cells were grown and stimutaed with the cytokines indicated.

treatment_protocol: Cells were rinsed with cold PBS and and placed in the Trizol solution.

tag: tissue

value: trachea


title: 116p

description:
6116750093_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: TBE cells with IL-6

scan_protocol: This information is not available since the experiments were done more than 10 years ago.

source_name: Human primary epithelial cell cultures treated with IL-6 (10 ng/ml) for 24 hours


title: TBE cells with RA

data_processing: This information is not available since the experiments were done more than 10 years ago.

source_name: Human primary epithelial cell cultures treated with all-trans-retinoic acid (30 nM)


title: 122c

description:
6116750088_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 117c

description:
6116750093_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 115c

description:
6116750093_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: 115p

description:
6116750093_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: TBE cells No RA

source_name: Human primary epithelial cell cultures used as basal controls

label_protocol: This information is not available since the experiments were done more than 10 years ago.


title: 121c

description:
6116750088_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: C33a/CRPVE2 -dox 48h #1

city: Tuebingen

first: Frank

last: Stubenrauch

address: Elfriede-Aulhorn-Str. 6

department: Institute for Medical Virology

country: Germany

institute: University Hospital Tuebingen

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with the 3000System

data_processing:
Raw data were processed with AGCC (Affymetrix) and the Expression Console (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes ( http://www.r-project.org/).
RMA expression value derived from Expression Console software; core-exon analysis
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: C33a/CRPVE2 -dox 48h

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated fromcells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: plus/minus 1µg/ml doxycyclin for 48h

tag: cell line

value: cervical cancer cell line

tag: genotype/variation

value: carrying the doxycycline-inducible pRTS-CRPV E2 vector

tag: incubated with

value: without 1µg/ml doxycyclin for 48h


title: 114p

description:
6116750093_F.AVG_Signal
Illumina Human HT-12 BeadArray

tag: smoke


title: C33a/CRPVE2 -dox 48h #3

tag: cell type


title: C33a/CRPVE2 -dox 48h #2


title: C33a/CRPVE2 +dox 48h #2

source_name: C33a/CRPVE2 +dox 48h

value: with 1µg/ml doxycyclin for 48h


title: PL 24S-Control

city: Taipei

first: Tsan-Piao

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

country: Taiwan

institute: National Taiwan University

description:
Polysomal RNA
Gene expression at polysomal level in shoots after 24hr incubation under control condition

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C  for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arabidopsis V4 Oligo 4Ã—44K Microarray (Agilent Technologies, USA) at 60 °C for 17 h in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Gene expression data were extracted and calculated by GeneSpring 12.5 (Agilent, Santa Clara, CA) and analyzed as described below. First, probes marked as ‘_s_’ or ‘_x_’, indicating they are less specific, were removed. Second, probe sets had to be marked as ‘present’ or ‘marginal’ in all 32 data sets. Third, the average intensity had to be ≥ 50 in both biological replicates from at least one of the time points examined. For calculating the changes in both steady-state and polysome-bound RNA, the average intensity in all 32 chips was scaled to 500. All measurements with intensity < 0.01 were raised to 0.01. For per-chip normalization, 50th percentile for the chips of steady-state mRNA measurement and the PL% for the chips of polysome-bound mRNAs were used, respectively. For per-gene normalization, ratios of GSH-treated to control samples belonging to the same biological experiment were calculated. The above normalizations were performed with the use of GeneSpring 12.5.

organism: Arabidopsis thaliana

source_name: Polysomal RNA, shoot, 24hr, 0 μM GSH

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

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 was surface sterilized, sown on nylon mesh floating on half-strength liquid MS medium (pH 5.7), and kept at 4 °C in darkness for 3 days for stratification.

extract_protocol: About 0.3 g of frozen tissue powder was extracted with 600 μl of polysome extraction buffer (200mM Tris-HCl, pH 8.5, 50mM KCl, 25mM MgCl2, 100 mg/ml heparin, 50 mg/ml cycloheximide, 400 U/ml RNasin (Promega, Madison, WI), 2% polyoxyethylene 10 tridecyl ether, 1% deoxycholic acid). The resuspended mixture was incubated on ice for 5 min, then spun at 15 000 g for 5 min at 4 ℃. In all, 500 μl supernatant was loaded on a 10-ml continuous sucrose gradient (15-50%) and spun at 210 000 g for 3.5 h at 4 ℃. The distribution of the nucleic acids was examined by a UV254 absorbance profile (model #UV-6, ISCO). For polysome-bound RNA (mRNAPL), RNA from polysomal fractions (PL) was purified with phenol/chloroform extraction, LiCl precipitation and dissolved in RNase-free H2O for further analyses. For total RNA (mRNASS), tissues were directly extracted and purified with phenol/chloroform extraction, LiCl precipitation and dissolved in RNase-free H2O for further analyses. Twenty microliters of 1:5000 diluted spike-in DAP mRNA was added before RNA extraction (GeneChip Eukaryotic Poly-A RNAcontrol kit, Ambion, Foster City, CA). For the detection of changes in ribosome occupancy, the expression of spike-in DAP was used as a control to normalize the efficiency of the RNA purification, cDNA synthesis and PCR process. The RNA quantities of NP and PL fractions were summed and set as 100% for the calculation of the relative percentage of each transcript in the PL fraction.  PL% was used as a calibration factor for ‘Per-Chip’ normalization as described previously (Kawaguchi et al, 2004; Branco-Price et al, 2005). PL% is the percentage of the polysomal RNA relative to the total RNA as calculated by the following formula:  PL% = RNA quantity in PL / (RNA quantity in both NP and PL) × 100%.

treatment_protocol: 10-d-old seedlings grown on nylon mesh were directly transferred to half-strength liquid MS medium with our without 100 μM GSH at 9:00 AM during the day and then incubated for 8 h and 24 h for harvest.

tag: cultivar

value: Shoot

tag: time


title: PL 24R-GSH

description:
Polysomal RNA
Gene expression at polysomal level in roots after 24hr of 100 μM GSH treatment

source_name: Polysomal RNA, root, 24hr, 100 μM GSH

value: Root


title: 113p

description:
6116750093_D.AVG_Signal
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: bmi


title: C33a/CRPVE2 +dox 48h #1


title: 112p

description:
6116750093_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: alcohol


title: 114c

description:
6116750093_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PL 24R-Control

description:
Polysomal RNA
Gene expression at polysomal level in roots after 24hr incubation under control condition

source_name: Polysomal RNA, root, 24hr, 0 μM GSH


title: C33a/CRPVE2 +dox 48h #3


title: PL 8S-GSH

description:
Polysomal RNA
Gene expression at polysomal level in shoots after 8hr of 100 μM GSH treatment

source_name: Polysomal RNA, shoot, 8hr, 100 μM GSH


title: 119c

description:
6116750088_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: 110p

description:
6116741113_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 111p

description:
6116741113_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PL 8R-GSH

description:
Polysomal RNA
Gene expression at polysomal level in roots after 8hr of 100 μM GSH treatment

source_name: Polysomal RNA, root, 8hr, 100 μM GSH


title: 113c

description:
6116750093_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PL 8R-Control

description:
Polysomal RNA
Gene expression at polysomal level in roots after 8hr incubation under control condition

source_name: Polysomal RNA, root, 8hr, 0 μM GSH


title: Total 24R-GSH

description:
Total RNA
Gene expression at steady-state level in roots after 24hr of 100 μM GSH treatment

source_name: Total RNA, root, 24hr, 100 μM GSH


title: 111c

description:
6116741113_K.AVG_Signal
Illumina Human HT-12 BeadArray

source_name: PBMC


title: 112c

description:
6116750093_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PL 8S-Control

description:
Polysomal RNA
Gene expression at polysomal level in shoots after 8hr incubation under control condition

source_name: Polysomal RNA, shoot, 8hr, 0 μM GSH


title: 110c

description:
6116741113_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: Total 24S-Control

description:
Total RNA
Gene expression at steady-state level in shoots after 24hr incubation under control condition

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arabidopsis V4 Oligo 4Ã—44K Microarray (Agilent Technologies, USA) at 60 °C for 17 h in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

source_name: Total RNA, shoot, 24hr, 0 μM GSH


title: Total 8S-Control

description:
Total RNA
Gene expression at steady-state level in shoots after 8hr incubation under control condition

source_name: Total RNA, shoot, 8hr, 0 μM GSH


title: Total 24S-GSH

description:
Total RNA
Gene expression at steady-state level in shoots after 24hr of 100 μM GSH treatment

source_name: Total RNA, shoot, 24hr, 100 μM GSH


title: Total 8S-GSH

description:
Total RNA
Gene expression at steady-state level in shoots after 8hr of 100 μM GSH treatment

source_name: Total RNA, shoot, 8hr, 100 μM GSH


title: 109p

description:
6116741113_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: Total 24R-Control

description:
Total RNA
Gene expression at steady-state level in roots after 24hr incubation under control condition

source_name: Total RNA, root, 24hr, 0 μM GSH


title: Total 8R-Control

description:
Total RNA
Gene expression at steady-state level in roots after 8hr incubation under control condition

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arabidopsis V4 Oligo 4Ã—44K Microarray (Agilent Technologies, USA) at 60 °C for 17 h in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C  GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

source_name: Total RNA, root, 8hr, 0 μM GSH


title: 137p

description:
6260962015_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: 108p

description:
6116741113_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: 108c

description:
6116741113_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: Total 8R-GSH

description:
Total RNA
Gene expression at steady-state level in roots after 8hr of 100 μM GSH treatment

source_name: Total RNA, root, 8hr, 100 μM GSH


title: 109c

description:
6116741113_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: FS8

city: Beijing

first: Yunfeng

last: Yang

address: No.1 Qinghuayuan, Haidian District

department: School of Environment

institute: Tsinghua University

description: GeoChip data for soil sample collected at the deposited site, replicate 2

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Data normalization and analyses of raw data were described previously (Yang et al 2014; PMID: 23985745). We removed genes detected in less than two out of five biological replicates and then logarithmically transformed the values, followed by normalization of the signal intensity of each spot by dividing with total abundance.

organism: uncultured bacterium

source_name: Soil microbes in Inner Mongolia grasslands_soil_deposition

label_protocol: As previously described (Yang et al 2013; PMID: 23504798), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: The experiment was set up in Spring of 2010 with a full factorial design of the grazing effect×soil erosion or deposition effect. Thirty 4×4 m plots were arranged into 6 rows and 5 columns with 2.5 m buffer zone in between. In the present study, we focus on the ungrazed plots to exclude the grazing effect, which is comprised of three treatments of control, soil erosion and deposition, with 5 replicates of each treatment. The positions of these plots were randomly assigned. In the early growing season, 1.5-3.0 cm topsoil was blown using a fan at the soil eroded plots in 2010 and 2011. The topsoil collected from the eroded plots was added to the dust deposition plots.

extract_protocol: Genomic DNA of soil microbial community was extracted from 5 g soil sample by a freeze-grinding procedure as described previously (J Zhou et al 1996). Then crude DNA was purified phenol extraction and low melting agarose gel electrophoresis. DNA quality was measured by the absorbance ratios of A260/280nm and A260/230nm using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA), and DNA concentrations were quantified with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany).

treatment_protocol: Soil samples were collected from all the 15 plots in middle August of 2012. In each plot, four soil cores of 0-10 cm depth were randomly taken using auger of 5 cm diameter, and mixed to obtain a composite sample. After passing through a 2 mm sieve and removal of visible roots and stones by hand, subsamples were stored in icebox and transported to laboratory for microbial analysis.

tag: soil condition

value: soil deposition


title: FS25

description: GeoChip data for soil sample collected at the deposited site, replicate 5


title: FS18

description: GeoChip data for soil sample collected at the deposited site, replicate 3


title: FS29

description: GeoChip data for soil sample collected at the control site, replicate 5

source_name: Soil microbes in Inner Mongolia grasslands_control

value: control


title: FS4

description: GeoChip data for soil sample collected at the deposited site, replicate 1


title: FS20

description: GeoChip data for soil sample collected at the deposited site, replicate 4


title: 106p

description:
6116741113_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: FS3

description: GeoChip data for soil sample collected at the control site, replicate 1


title: FS28

description: GeoChip data for soil sample collected at the eroded site, replicate 5

source_name: Soil microbes in Inner Mongolia grasslands_erosion

value: soil erosion


title: FS24

description: GeoChip data for soil sample collected at the eroded site, replicate 4


title: FS9

description: GeoChip data for soil sample collected at the control site, replicate 2


title: 106c

description:
6116741113_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: 107c

description:
6116741113_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: 105p

description:
6116741111_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: FS19

description: GeoChip data for soil sample collected at the control site, replicate 4


title: FS13

description: GeoChip data for soil sample collected at the control site, replicate 3


title: FS14

description: GeoChip data for soil sample collected at the eroded site, replicate 3


title: FS10

description: GeoChip data for soil sample collected at the eroded site, replicate 2


title: 105c

description:
6116741111_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PL 24S-GSH

description:
Polysomal RNA
Gene expression at polysomal level in shoots after 24hr of 100 μM GSH treatment

source_name: Polysomal RNA, shoot, 24hr, 100 μM GSH


title: FS1

description: GeoChip data for soil sample collected at the eroded site, replicate 1


title: Ethylbenzene exposed worker, EBZ 5

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

country: South Korea

institute: Korea Institute of Science & Technology

description: miRNA expression of Ethylbenzene exposed worker

hyb_protocol: Labeled total RNA samples were dried completely by using speed-vac, and then hybrized with probes on array slides, accorkding to the manufacture. The hybridization lasted for 20 hours inside 55'C hybridization oven (Agilent). After hybridization, arrays were washed with Gene Expression Wash Buffer 1 (Agilent) at room temperature, and then wahsed with Wash Buffer 2 (Agilent) at 37'C. The washed array were dried and processed to scanning step immediately.

scan_protocol: Slides was scanned immediated after washing step on Agilent G2565CA Microarray Scanner System. (Scan Area is 61x21.6 mm; Scan resolution is 3um; Color channel is Green; Green PMT is 100%)

data_processing: Transformed by using Feature Extraction (V.10.7.3.1) software on default setting. (Protocol is miRNA_107_Sep09, Grid is 031181_D_F_20111226). FRelative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. Substandard spots, identified by visual examination of each slide, were flagged and excluded from further analysis. Spots harboring dust artifacts or spatial defects were manually flagged and excluded. In an effort to filter out unreliable data, spots with signal-to-noise (signal-background SD) ratios below 10 were not included in the data analysis. Data applied standard normalization methods for one-channel microarrays: quantile normalization using the GeneSpring GX v11.0 (Agilent technologies). The normalized, and log transformed intensity values were then analyzed. Fold change filters included the requirement that the genes be present in at least 150% of controls for up-regulated genes and lower than 67% of controls for down-regulated genes. The statistical significance of the differences was evaluated by using the ANOVA and t-test tool. Differences with P<0.05 were taken as statistically significant. Hierarchical clustering of log ratios was performed to detect clusters of miRNAs and blood samples. In detail, we applied bottom up complete linkage clustering and used the Pearson correlation linkage. In addition, we carried out a standard principal component analysis (PCA), which is dimensionality reduction technique to analysis high-dimensional gene expression dataset using the GeneSpring GX software. PCA was carried out on log-transformed data, using mean centering and scaling.

source_name: Human Whole blood

label_protocol: 100ng Total RNA from each blood case was labeled with Cyanine 3-pCp by using Agilent miRNA labeling kits according to the manufacturer's instructions. Labeled samples were desalted by using MicroBioSpin 6 Columns (Bio-Rad).

extract_protocol: Total RNA containing miRNA from blood samples was extracted using the PAXgene Blood miRNA Kit, including treatment with DNAse I to prevent genomic DNA contamination, strictly following the manufacturer’s instruction (Qiagen)

value: whole blood


title: 104c

description:
6116741111_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: 103c

description:
6116741111_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: Ethylbenzene exposed worker, EBZ 6


title: Ethylbenzene exposed worker, EBZ 7


title: Ethylbenzene exposed worker, EBZ 2


title: Ethylbenzene exposed worker, EBZ 3


title: 107p

description:
6116741113_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 102p

description:
6116741111_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: Xylene exposed worker, XYL 16

description: miRNA expression of Xylene exposed worker


title: 103p

description:
6116741111_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: 104p

description:
6116741111_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: 102c

description:
6116741111_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: Xylene exposed worker, XYL 12


title: Ethylbenzene exposed worker, EBZ 4


title: 101p

description:
6116741111_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: 101c

description:
6116741111_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: Xylene exposed worker, XYL 8


title: Xylene exposed worker, XYL 14


title: Xylene exposed worker, XYL 17


title: 100p

description:
6116741111_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: Ethylbenzene exposed worker, EBZ 1


title: 100c

description:
6116741111_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: Xylene exposed worker, XYL 15


title: Xylene exposed worker, XYL 11


title: Xylene exposed worker, XYL 10


title: Xylene exposed worker, XYL 7


title: Drosophila_melanogaster_w1118_4.5-6h_embryos_rep2

description: This sample is total RNA isolated from w1118 embryos collected 4.5-6 hours post-egglaying. It is the second of three biological replicates.

data_processing: The raw data (.pair files) were normalized with ArrayStar 12 (DNASTAR) software using the RMA quantile method, and signal intensities were log2-transformed. All samples were normalized together.

source_name: 4.5-6 hour w1118 embryo

growth_protocol: The following fly strains were used: w1118, bratfs1/CyO, Df(2L)TE37C-7/CyO. All stocks were maintained at 25˚C.

extract_protocol: Total RNA was extracted using TRI reagent (Molecular Research Center, Inc., Cincinnati, OH) according to the manufacturer’s protocol.

tag: developmental stage

value: 4.5-6 hour embryo

tag: maternal genotype


title: Drosophila_melanogaster_w1118_3-4.5h_embryos_rep2

description: This sample is total RNA isolated from w1118 embryos collected 3-4.5 hours post-egglaying. It is the second of three biological replicates.

source_name: 3-4.5 hour w1118 embryo

value: 3-4.5 hour embryo


title: Drosophila_melanogaster_w1118_4.5-6h_embryos_rep3

description: This sample is total RNA isolated from w1118 embryos collected 4.5-6 hours post-egglaying. It is the third of three biological replicates.


title: Unexposed control worker, Control 22

description: miRNA expression of unexposed control worker


title: Toluene exposed worker, TOL 4

description: miRNA expression of Toluene exposed worker


title: Drosophila_melanogaster_w1118_3-4.5h_embryos_rep3

description: This sample is total RNA isolated from w1118 embryos collected 3-4.5 hours post-egglaying. It is the third of three biological replicates.


title: Drosophila_melanogaster_w1118_3-4.5h_embryos_rep1

description: This sample is total RNA isolated from w1118 embryos collected 3-4.5 hours post-egglaying. It is the first of three biological replicates.


title: Toluene exposed worker, TOL 3


title: Toluene exposed worker, TOL 2


title: Unexposed control worker, Control 19


title: Toluene exposed worker, TOL 9


title: Drosophila_melanogaster_w1118_1.5-3h_embryos_rep3

description: This sample is total RNA isolated from w1118 embryos collected 1.5-3 hours post-egglaying. It is the third of three biological replicates.

source_name: 1.5-3 hour w1118 embryo

value: 1.5-3 hour embryo


title: Toluene exposed worker, TOL 10


title: Toluene exposed worker, TOL 6


title: Xylene exposed worker, XYL 6


title: Toluene exposed worker, TOL 7


title: Drosophila_melanogaster_w1118_1.5-3h_embryos_rep2

description: This sample is total RNA isolated from w1118 embryos collected 1.5-3 hours post-egglaying. It is the second of three biological replicates.


title: Xylene exposed worker, XYL 4

description: miRNA expression of Xylene exposed worker


title: Unexposed control worker, Control 21


title: Toluene exposed worker, TOL 5


title: Unexposed control worker, Control 20


title: Drosophila_melanogaster_w1118_4.5-6h_embryos_rep1

description: This sample is total RNA isolated from w1118 embryos collected 4.5-6 hours post-egglaying. It is the first of three biological replicates.


title: Unexposed control worker, Control 18


title: Toluene exposed worker, TOL 1


title: Toluene exposed worker, TOL 8


title: Unexposed control worker, Control 17


title: Unexposed control worker, Control 16


title: Drosophila_melanogaster_w1118_0-1.5h_embryos_rep2

description: This sample is total RNA isolated from w1118 embryos collected 0-1.5 hours post-egglaying. It is the second of three biological replicates.

source_name: 0-1.5 hour w1118 embryo

value: 0-1.5 hour embryo


title: Drosophila_melanogaster_w1118_1.5-3h_embryos_rep1

description: This sample is total RNA isolated from w1118 embryos collected 1.5-3 hours post-egglaying. It is the first of three biological replicates.


title: Unexposed control worker, Control 15


title: Unexposed control worker, Control 13


title: Castrated animals plus one high dose of estradiol_rep2

city: Campinas

first: Rafaela

middle: da Rosa

last: Ribeiro

address: Charles Dawin st, bl.N room 10

department: Structural and functional biology department

country: Brazil

institute: State University of Campinas

description: Gene expression data from ventral prostate colected from adult rats that received a combination of both treatments (combined orchiectomy and 17β-estradiol)

hyb_protocol: Following fragmentation, 6.75 ug (27 ul at 25ng/ul) of fragmented and labeled single-straded cDNA were hibridized for 18 hrin 45°C hybridization oven, at 60 rpm. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChip were scanned Affymetrix GeneChip Operating Software v1.3 program.

data_processing: The data were summarized and normalized by Expression Console software (Affymetrix).

source_name: Ventral prostate, castrated animals plus on high dose of 17beta-estradiol, three days

label_protocol: Biotinylated single-straded cDNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, 2009, Affymetrix).

growth_protocol: Male Wistar rats were kept under normal light conditions (12-h light:dark cycle) and received filtered tap water and Purina rodent chow ad libitum

extract_protocol: Ventral prostates were dissected under RNAse-free conditions. Thirty mg of the tissue was used for total RNA extraction. Subsequently, the tissue fragments were extracted using Illustra RNAspin Mini kits (GE Healthcare, Buckinghamshire,UK) according to the manufacturer’s instructions.

treatment_protocol: On the 90th day after birth, the rats were assigned to different treatment groups (n=3): First group were castrated (Cas) by orchiectomy via scrotal incision under ketamine (150 mg/Kg body weight) and xylazin (10 mg/kg body weight) anesthesia; Second group received a 25 mg/Kg body weight dose of 17β-estradiol diluted in corn oil (E2 group);Third group received a combination of both treatments (Cas+E2 group) (combined orchiectomy and 17β-estradiol). In the control group (Ct; normal androgen and estrogen), the animals received only the vehicle.

tag: strain

value: Wistar

value: Ventral prostate

tag: gender

value: Male

value: Adult- 90 days old

tag: protocol

value: Castrated+estrogen


title: Unexposed control worker, Control 14

tag: tissue


title: Drosophila_melanogaster_brat_mutant_4.5-6h_embryos_rep2

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 4.5-6 hours post-egglaying. It is the second of three biological replicates.

source_name: 4.5-6 hour embryo from brat mutant female


title: Unexposed control worker, Control 12


title: Unexposed control worker, Control 11


title: Castrated animals plus one high dose of estradiol_rep1


title: One high dose of 17beta-estradiol_rep3

description: Gene expression data from ventral prostate colected from adult rats three days after received a 25 mg/Kg body weight dose of 17β-estradiol diluted in corn oil

source_name: Ventral prostate, one high dose of 17beta-estradiol, three days

value: Estrogen


title: Unexposed control worker, Control 10


title: Unexposed control worker, Control 9


title: Drosophila_melanogaster_brat_mutant_4.5-6h_embryos_rep3

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 4.5-6 hours post-egglaying. It is the third of three biological replicates.


title: Drosophila_melanogaster_w1118_0-1.5h_embryos_rep1

description: This sample is total RNA isolated from w1118 embryos collected 0-1.5 hours post-egglaying. It is the first of three biological replicates.


title: Castrated animals plus one high dose of estradiol_rep3


title: Unexposed control worker, Control 8


title: Drosophila_melanogaster_brat_mutant_3-4.5h_embryos_rep3

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 3-4.5 hours post-egglaying. It is the third of three biological replicates.

source_name: 3-4.5 hour embryo from brat mutant female


title: Castrated animals_for three days_rep3

description: Gene expression data from ventral prostate colected of adult castrated rats for three days ,that were orchiectomized via scrotal incision under ketamine (150 mg/Kg body weight) and xylazin (10 mg/kg body weight) anesthesia

source_name: Ventral prostate, castrated animals, three days

value: Castrated


title: Drosophila_melanogaster_w1118_0-1.5h_embryos_rep3

description: This sample is total RNA isolated from w1118 embryos collected 0-1.5 hours post-egglaying. It is the third of three biological replicates.


title: One high dose of 17beta-estradiol_rep1


title: Drosophila_melanogaster_brat_mutant_3-4.5h_embryos_rep1

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 3-4.5 hours post-egglaying. It is the first of three biological replicates.


title: Drosophila_melanogaster_brat_mutant_3-4.5h_embryos_rep2

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 3-4.5 hours post-egglaying. It is the second of three biological replicates.


title: Unexposed control worker, Control 7

description: miRNA expression of unexposed control worker


title: Drosophila_melanogaster_brat_mutant_4.5-6h_embryos_rep1

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 4.5-6 hours post-egglaying. It is the first of three biological replicates.


title: One high dose of 17beta-estradiol_rep2


title: Castrated animals_for three days_rep2


title: Castrated animals_for three days_rep1


title: Control animal_only vehicle_rep3

description: Gene expression data from ventral prostate colected of control adult rats that received only estrogen vehicle (corn oil)

source_name: Ventral prostate, no-treatment

value: Control


title: Unexposed control worker, Control 6


title: Drosophila_melanogaster_brat_mutant_1.5-3h_embryos_rep3

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 1.5-3 hours post-egglaying. It is the third of three biological replicates.

source_name: 1.5-3 hour embryo from brat mutant female


title: Control animal_only vehicle_rep2