title: High_680

description: F2 haloperidol response: High


title: High_665

status: Public on May 06 2012

type: RNA

city: Portland

first: Ovidiu

middle: Dan

last: Iancu

state: OR

address: 3181 SW Sam Jackson Road

country: USA

institute: OHSU

description: F2 haloperidol response: High

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: lumi R package quintile normalization

molecule: total RNA

organism: Mus musculus

source_name: mouse striatum

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: tissue

value: striatum

tag: genetic background

tag: haloperidol response

value: High


title: Tobacco +Boron 12h slide4 rep2

status: Public on May 05 2012

city: Kyoto

first: Masaru

last: Kobayashi

state: Kyoto

address: Kitasirakawa Oiwakecho, Sakyo

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 4 of 4, Replicate: 2

hyb_protocol: Before use, the DNA on the spotted microarray slides was immobilized by cross-linking the slides under UV light (energy 50 mJ cm2) and slides were prehybridized for 1 h at 55°C in prehybridization buffer [1% bovine serum albumin (BSA), 5× saline sodium citrate (SSC) and 0.1% sodium dodecyl sulfate (SDS)] as described previously [1,2]. Hybridization of microarrays with Cy-5-labeled sample cDNA and Cy-3-labeled DNA sequence as control was performed in ExpressHyb hybridization solution (Clontech, Palo Alto, CA, USA) at 60°C for 4 h as described previously [1]. The protocol described in [1] was later modified with the use of a Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites of the respective vectors (pGEM-Teasy and pBII KS+), instead of the labeled oligo-DNA that was used previously [2]. The hybridized slides were washed in SSC/SDS buffer solutions at 55°C (final wash in 0.1× SSC and 0.1% SDS) and briefly rinsed in water. Slides were dried by centrifugation. [1]Demura, T., Tashiro, G., Horiguchi, G. et al. (2002) Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc. Natl Acad. Sci. USA, 99, 15794–15799. [2]Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45, 1280–1289.

scan_protocol: The Cy-5 (sample signal) and Cy-3 (control signal) were obtained by scanning with a GenePix 4000A microarray scanner (Molecular Dynamics). The scans were subsequently analyzed by the MicroArray Suite iplab program (Scananalytics, BD Biosciences, Rockville, MD, USA).

data_processing: Raw signal data were first modified by subtraction of respective background values. VALUE means (Cy-5-labeled cDNA signal)/(Cy-3-labeled vector control signal) after background correction.

molecule: polyA RNA

organism: Nicotiana tabacum

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 12 h

label_protocol: polyA mRNA quality was estimated by Bioanalyzer. 1 μg of mRNA was labeled and used for single-slide hybridizations. Samples were spiked with control Kanamycin mRNA (Promega). Labeling was performed using SuperScript II reverse transcriptase (Invitrogen), random 9-mer primers, poly(A)-specific poly (dT) primers, and Cy-3/Cy-5-labeled dCTP nucleotides (Amersham Biosciences) for first-strand cDNA synthesis. Quality of probe was estimated by gel electrophoresis and subsequent fluoroimaging analysis.

extract_protocol: The cells were collected by filtration and snap-frozen in liquid nitrogen. Total RNA was prepared using TRIzol reagent (Invitrogen) as described in the manufacturer’s protocols. The poly(A)-rich RNA fraction was isolated from total RNA using a GenElute mRNA Miniprep Kit (Sigma) in two subsequent runs of purification following the Miniprep Kit protocol.

treatment_protocol: Three-day-old cells were deprived of boron as described (Plant & Cell Physiol 50: 26-36, 2009). Briefly, cells were washed with boron-free culture medium, then cultured in the same medium (boron-deprived; -B cells). Cells washed with and cultured in standard growth medium were used as the control (boron-supplied; +B cells).

tag: cell line

tag: treatment

value: supplied with boron

tag: time

molecule: other

organism: synthetic construct

source_name: vector control

tag: sample type


title: High_673

description: F2 haloperidol response: High


title: Tobacco +Boron 6h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 6 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 6 h

value: 6 h

label_protocol: Labeling was performed using SuperScript II reverse transcriptase (Invitrogen), random 9-mer primers, poly(A)-specific poly (dT) primers, and Cy-3/Cy-5-labeled dCTP nucleotides (Amersham Biosciences) for first-strand cDNA synthesis. Quality of probe was estimated by gel electrophoresis and subsequent fluoroimaging analysis.

extract_protocol: Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites of the respective vectors (pGEM-Teasy and pBII KS+)


title: Tobacco -Boron 12h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 12 h

value: deprived of boron

value: Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites


title: Tobacco +Boron 36h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 36 h


title: Tobacco +Boron 3h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 3 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 3 h

value: 3 h


title: High_649

description: F2 haloperidol response: High


title: High_664

description: F2 haloperidol response: High


title: High_653

description: F2 haloperidol response: High


title: High_650

description: F2 haloperidol response: High


title: High_651

description: F2 haloperidol response: High


title: Tobacco -Boron 36h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 36 h


title: High_652

description: F2 haloperidol response: High


title: Tobacco -Boron 3h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth media, Duration of treatment: 3 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 3 h


title: Tobacco before-treatment slide4 rep2

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, no treatment

value: no treatment


title: Tobacco -Boron 6h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 6 h


title: Tobacco +Boron 1h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 1 h, Slide: 4 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 1 h

value: 1 h


title: Tobacco -Boron 12h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 3 of 4, Replicate: 2


title: Tobacco -Boron 36h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 3 of 4, Replicate: 2


title: Tobacco +Boron 36h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 4 of 4, Replicate: 1


title: Tobacco -Boron 12h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 4 of 4, Replicate: 1


title: Tobacco -Boron 1h slide4 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth media, Duration of treatment: 1 h, Slide: 4 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 1 h


title: Tobacco +Boron 12h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 4 of 4, Replicate: 1


title: Tobacco -Boron 36h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 4 of 4, Replicate: 1


title: Tobacco -Boron 3h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 3 h, Slide: 4 of 4, Replicate: 1


title: Tobacco -Boron 6h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 3 of 4, Replicate: 2


title: Tobacco +Boron 3h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 3 h, Slide: 4 of 4, Replicate: 1


title: Tobacco +Boron 3h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 3 h, Slide: 3 of 4, Replicate: 2


title: Tobacco before-treatment slide4 rep1

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 4 of 4, Replicate: 1


title: Tobacco -Boron 1h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 1 h, Slide: 3 of 4, Replicate: 2


title: Tobacco +Boron 1h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 1 h, Slide: 4 of 4, Replicate: 1


title: Tobacco +Boron 1h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 1 h, Slide: 3 of 4, Replicate: 2


title: Tobacco +Boron 6h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 6 h, Slide: 3 of 4, Replicate: 2


title: Tobacco -Boron 6h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 4 of 4, Replicate: 1


title: Tobacco +Boron 12h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 3 of 4, Replicate: 2


title: Tobacco +Boron 6h slide4 rep1


title: Tobacco before-treatment slide3 rep1

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 3 of 4, Replicate: 1


title: Tobacco -Boron 36h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 3 of 4, Replicate: 1


title: Tobacco +Boron 36h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 3 of 4, Replicate: 1


title: Tobacco -Boron 12h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 3 of 4, Replicate: 1


title: Tobacco -Boron 1h slide4 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 1 h, Slide: 4 of 4, Replicate: 1


title: Cnn1

type: genomic

city: Milan

first: Rodrigo

last: Bermejo

state: Lombardy

address: Via Adamello 16

country: Italy

institute: IFOM-IEO-Campus

description: Cnn1-PK6 cycling

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: TXT results were produced by GCOS using a custom CDF which summarizes probes into sets covering 50 basepairs ranges.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP fraction of Cnn1-PK6

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol

growth_protocol: Cells were grown in YPD.

extract_protocol: Extracton was performed as described in Katou et al., 2003.

treatment_protocol: Exponentially growing cells were collected

tag: strain

tag: phase

value: asynchronous

tag: chip antibody

value: anti-PK (anti-V5)

tag: chip antibody vendor & cat. #

value: AbD Serotec, MCA1360

source_name: SUP fraction of Cnn1-PK6


title: Tobacco -Boron 6h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 3 of 4, Replicate: 1


title: Tobacco +Boron 12h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 3 of 4, Replicate: 1


title: Tobacco -Boron 3h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 3 h, Slide: 3 of 4, Replicate: 1


title: Tobacco -Boron 3h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth media, Duration of treatment: 3 h, Slide: 3 of 4, Replicate: 2


title: Tobacco +Boron 3h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 3 h, Slide: 3 of 4, Replicate: 1


title: Tobacco +Boron 6h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 6 h, Slide: 3 of 4, Replicate: 1


title: Tobacco -Boron 1h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 1 h, Slide: 3 of 4, Replicate: 1


title: 11275.s1

city: Los Angeles

first: Rui

last: Luo

state: CA

address: 2309 Gonda Bldg, 695 Charles E. Young Dr. South

department: Human Genetics

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Outlier samples were first removed followed by  quantile normalisation and combat. All data processing steps were done in R (version 2.14.2).

organism: Homo sapiens

label_protocol: standard Illumina protocol

growth_protocol: The live lymphoblast cell lines (LCLs) of the subjects were grown in RPMI 1640 medium with 2 mM L-glutamine and 25 mM HEPES (Invitrogen, Carlsbad, CA, USA), 10% fetal bovine serum, and 1 × Antibiotic-Antimycotic solution (Invitrogen) at 37°C in a humidified 5% CO2 chamber. Cells were grown to a density of 6 × 10^5/ml.

extract_protocol: A total of 9 × 10^6 of lymphoblasts were seeded in a T-75 flask in 30 ml of fresh medium. After 24 h, total RNA was extracted from the cells using an RNeasy Mini Kit with DNase treatment (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

tag: famid

tag: simons simplex collection id

value: lymphoblast cell lines (LCLs)

tag: cell type

value: lymphoblasts

tag: chip id

tag: project

tag: batch

tag: gender

value: female

tag: age

tag: autism trait

value: Control


title: Xenopus laevis inner ear_ biological rep2

city: Las Cruces

first: Elba

middle: E.

last: Serrano

address: 1200 S. Horseshoe, MSC 3AF

department: Biology

institute: New Mexico State University

hyb_protocol: 20 ug of cRNA after fragmentation were hybridized following the manufacturer’s protocol (Affymetrix).

scan_protocol: Xenopus laevis GeneChips were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Bioconductor packages 'affy' and 'gcrma' were used to read in the CEL files and for preprocessing, respectively. Both packages were implemented in R.

organism: Xenopus laevis

source_name: Xenopus laevis juveniles

label_protocol: Biotinylated cRNA was prepared from each RNA replicate (~ 1 ug total RNA) using the GeneChip® One-Cycle Target Labelling kit following the manufacturer’s protocol (Affymetrix).

growth_protocol: Juvenile Xenopus laevis (n = 21) were approximately 1 month old with an average weight of 2.4 ± 1.0 g and an average length of 2.7 ± 0.3 cm and obtained from Nasco (Fort Atkinson, WI). Animal husbandry and surgical procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) as per Trujillo-Provencio C, Powers T, Sultemeier D, Serrano E: RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning. Methods Mol Biol 2009, 493:3-20.

tag: developmental stage

value: juvenile

value: ~1 month

tag: tissue

value: inner ear


title: Xenopus laevis inner ear_ biological rep3


title: Tobacco +Boron 1h slide3 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 1 h, Slide: 3 of 4, Replicate: 1

tag: cell line

tag: treatment

value: supplied with boron

tag: time


title: 11004.p1

value: male

value: Autism


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title: Xenopus laevis inner ear_ biological rep1


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title: 11495.s1


title: Tobacco before-treatment slide2 rep2

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 2 of 4, Replicate: 2

tag: sample type

value: Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites


title: 11333.s1


title: Tobacco -Boron 36h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 2 of 4, Replicate: 2

value: deprived of boron


title: 11495.p1


title: Tobacco +Boron 36h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 2 of 4, Replicate: 2


title: Tobacco -Boron 6h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 2 of 4, Replicate: 2

value: 6 h


title: Tobacco +Boron 6h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 6 h, Slide: 2 of 4, Replicate: 2


title: Tobacco +Boron 3h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 3 h, Slide: 2 of 4, Replicate: 2

value: 3 h


title: Tobacco +Boron 12h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 2 of 4, Replicate: 2


title: 11177.p1


title: 11947.s1


title: Tobacco -Boron 12h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 2 of 4, Replicate: 2


title: Tobacco +Boron 1h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 1 h, Slide: 2 of 4, Replicate: 2

value: 1 h


title: 11333.p1


title: 11948.p1


title: Tobacco +Boron 36h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 2 of 4, Replicate: 1


title: 11274.p1


title: 11247.p1


title: 11356.p1


title: 11625.s1


title: Tobacco before-treatment slide2 rep1

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 2 of 4, Replicate: 1

value: no treatment


title: Tobacco -Boron 3h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth media, Duration of treatment: 3 h, Slide: 2 of 4, Replicate: 2


title: Tobacco -Boron 1h slide2 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 1 h, Slide: 2 of 4, Replicate: 2


title: 11247.s1


title: 11267.p1


title: 12044.p1


title: 11540.s1


title: Tobacco +Boron 12h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 2 of 4, Replicate: 1


title: Tobacco -Boron 36h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 2 of 4, Replicate: 1


title: 11990.p1


title: 11274.s1


title: 11990.s1


title: Tobacco -Boron 12h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 2 of 4, Replicate: 1


title: 12078.s1


title: 11979.p1


title: Tobacco +Boron 1h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 1 h, Slide: 2 of 4, Replicate: 1


title: Tobacco -Boron 1h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 1 h, Slide: 2 of 4, Replicate: 1


title: Tobacco +Boron 6h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 6 h, Slide: 2 of 4, Replicate: 1


title: Tobacco -Boron 3h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 3 h, Slide: 2 of 4, Replicate: 1


title: 11979.s1


title: 11718.p1


title: 12073.s1


title: 11540.p1


title: 15d_5_2

city: Valencia

first: David

last: Montaner

address: C/ Eduardo Primo Yufera, 3

department: Bioinformatics

country: Spain

institute: CIPF

hyb_protocol: On the basis of the protocol for One-Color Microarray-Based Gene Expression Analysis Version 5.5 (Agilent p/n 5188-5977), 3 μg of labeled cRNA was hybridized with Whole Human Genome Oligo Microarray Kit (Agilent p/n G4112F).

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer's protocol and data extracted using Agilent Feature Extraction Software 9.5.1.

data_processing: Data preprocessing was done using R 2.5.1. limma-Bioconductor package was used to normalize data: the normexp option was used to perform background correction and the quantile method was used for the between array normalization.

label_protocol: Eight hundred ng of total RNA were used to produce cyanine 3-CTP-labeled cRNA using the Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent p/n 5188-5339) according to the manufacturer's instructions.

growth_protocol: Undifferentiated hESC (H9 line passages 35-38) were cultured on extracellular matrix (ECM) from human foreskin fibroblasts under different O2 levels (21%, 5%, and 1% O2) using foreskin-fibroblast conditioned medium composed of the following: DMEM-F12 (Invitrogen, Carlsbad, CA, http://www.invitrogen.com), 100 μM ß-mercaptoethanol (Sigma, St. Louis, http://www.sigmaaldrich.com), 1 mM L-glutamine (Invitrogen), 100 mM nonessential amino acids, and 20% serum replacement (Invitrogen).

extract_protocol: Total RNA was extracted from hESC using the High Pure RNA Isolation kit (Roche Diagnostics, Basel, Switzerland, http://www.roche-applied-science.com) and was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, DE, http://www.nanodrop.com).

treatment_protocol: Colonies were disaggregated to single cells using Acumax (Invitrogen) and labeled with Dil according to manufacturer's recommendations (Invitrogen).

value: undifferentiated human embryonic stem cells (hESC)

tag: passages

tag: oxygen level

value: 5% (hypoxic)

tag: replicate

tag: slide id


title: 12015.s1

tag: famid

tag: simons simplex collection id

value: lymphoblast cell lines (LCLs)

tag: cell type

value: lymphoblasts


title: Tobacco +Boron 3h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 3 h, Slide: 2 of 4, Replicate: 1


title: Tobacco -Boron 6h slide2 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 2 of 4, Replicate: 1


title: 11839.p1

tag: chip id

tag: project

tag: batch


title: 12096.s1

tag: gender

tag: age

tag: autism trait

value: Control


title: 12096.p1

tag: cell line


title: 11998.p1


title: 12073.p1

value: female


title: 12015.p1


title: 12279.s1


title: 11998.s1


title: 5d_5_2


title: 15d_5_1


title: 10d_5_2


title: 12048.p1


title: 15d_21_1

value: 21% (normoxic)


title: 10d_21_1


title: 10d_5_1


title: 12346.s1


title: 5d_21_2


title: 10d_1_1

value: 1% (hypoxic)


title: 12297.s1


title: 12399.p1


title: 11948.s1


title: 5d_5_1


title: 15d_21_2


title: 5d_21_1


title: 12420.s1


title: 12279.p1


title: 5d_1_1


title: 24h_21_2


title: 12420.p1


title: 5d_1_2


title: 12385.p1


title: 24h_5_2


title: 12385.s1


title: 24h_5_1


title: 12327.p1


title: 12184.s1


title: 24h_21_1


title: 12399.s1


title: 24h_1_2


title: 11484.p1


title: 11484.s1


title: 11066.p1


title: 24h_1_1


title: 11254.s1


title: 12h_5_2


title: 12h_1_1


title: 11480.p1


title: 12h_21_1


title: 11066.s1


title: 12h_1_2


title: 12h_21_2


title: 11254.p1


title: 12048.s1


title: ICL006_CA04_0h_1

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description:
Sample name: 251485060074_1_2
Cells infected with A/CA/04/2009 at MOI of 3

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

growth_protocol: Calu-3 cells, a human lung adenocarcinoma cell line, were kindly provided by Dr. Raymond Pickles (University of North Carolina, Chapel Hill, NC) and were maintained in a 1:1 mixture of Dulbecco’s modified Eagle’s medium and Ham’s F12 nutrient medium (DF12; Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum.  Madin-Darby canine kidney (MDCK) cells were maintained in minimum essential medium (MEM) (Invitrogen) containing 5% newborn calf serum.  All cells were grown at 37°C in an atmosphere of 5% CO2, with an antibiotic/antimycotic mixture (Invitrogen).

extract_protocol: At 0,3,7,12,18, 24, 30, 36 and 48 hpi, triplicate wells of mock-infected and A/CA/04/2009 influenza virus-infected Calu-3 monolayers were washed with 5 ml cold phosphate buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen), according to the manufacturer’s recommendation, and resulting lysates were stored at -80°C until further processing.  All TRIzol lysates were processed simultaneously:  they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: For RNA isolation, Calu-3 cells were seeded in 6-well plates (1 x 106 cells/well) two days prior to infection.  Immediately preceding infection, monolayers were washed twice with DMEM/F12 supplemented with 0.3% bovine serum albumin (DF12-BSA), and inoculated with A/CA/04/2009 at a MOI of 3 in DF12-BSA for 50 minutes at 37°C.  Mock-infected controls were inoculated with DF12-BSA only.  Following inoculation, monolayers were washed once with DF12-BSA and incubated in DF12-BSA containing 0.5 μg/ml of TPCK-treated trypsin (Worthington Biochemical Corporation, Lakewood, NJ).

value: Calu-3 lung adenocarcinoma cell line

tag: infection

value: A/CA/04/2009 Influenza virus

tag: time point of sample collection


title: Control2

tag: time


title: 11736.p1

value: male

value: Autism


title: Control1

tag: passages


title: ICL006_CA04_0h_3

description:
Sample name: 251485060176_1_2
Cells infected with A/CA/04/2009 at MOI of 3

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.


title: ICL006_CA04_12h_1

description:
Sample name: 251485060195_1_3
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_12h_2

description:
Sample name: 251485060032_1_4
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_0h_2

description:
Sample name: 251485060072_1_3
Cells infected with A/CA/04/2009 at MOI of 3


title: 11356.s1


title: 11407.s1


title: 11879.p1


title: 11407.p1


title: 11610.p1


title: ICL006_CA04_12h_3

description:
Sample name: 251485060076_1_4
Cells infected with A/CA/04/2009 at MOI of 3


title: 12h_5_1

tag: oxygen level


title: 11610.s1


title: ICL006_CA04_18h_2

description:
Sample name: 251485060031_1_2
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_18h_1

description:
Sample name: 251485060075_1_2
Cells infected with A/CA/04/2009 at MOI of 3


title: 12014.s1


title: ICL006_CA04_24h_1

description:
Sample name: 251485060074_1_3
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_24h_2

description:
Sample name: 251485060076_1_2
Cells infected with A/CA/04/2009 at MOI of 3


title: 12603.s1


title: ICL006_CA04_18h_3

description:
Sample name: 251485060072_1_4
Cells infected with A/CA/04/2009 at MOI of 3


title: 12523.p1


title: ICL006_CA04_30h_1

description:
Sample name: 251485060176_1_4
Cells infected with A/CA/04/2009 at MOI of 3


title: 12523.s1


title: 12014.p1


title: 12603.p1


title: ICL006_CA04_24h_3

description:
Sample name: 251485060072_1_2
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_30h_3

description:
Sample name: 251485060032_1_1
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_30h_2

description:
Sample name: 251485060195_1_2
Cells infected with A/CA/04/2009 at MOI of 3


title: 11868.p1


title: 11868.s1


title: ICL006_CA04_36h_1

description:
Sample name: 251485060195_1_4
Cells infected with A/CA/04/2009 at MOI of 3


title: 12417.p1


title: 12417.mo


title: 12308.p1


title: 12594.p1


title: 12100.p1


title: ICL006_CA04_36h_2

description:
Sample name: 251485060034_1_3
Cells infected with A/CA/04/2009 at MOI of 3


title: 11629.p1


title: 11390.p1


title: 11135.p1


title: 11532.p1


title: ICL006_CA04_48h_2

description:
Sample name: 251485060197_1_2
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_48h_1

description:
Sample name: 251485060196_1_1
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_3h_1

description:
Sample name: 251485060075_1_3
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_7h_1

description:
Sample name: 251485060072_1_1
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_36h_3

description:
Sample name: 251485060031_1_3
Cells infected with A/CA/04/2009 at MOI of 3


title: 11334.p1


title: ICL006_CA04_3h_3

description:
Sample name: 251485060197_1_3
Cells infected with A/CA/04/2009 at MOI of 3


title: 11629.mo


title: 12297.p1


title: 11680.p1


title: 12451.p1


title: ICL006_CA04_7h_3

description:
Sample name: 251485060032_1_2
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_mock_0h_1

description:
Sample name: 251485060196_1_3
mock infected

value: mock


title: ICL006_CA04_7h_2

description:
Sample name: 251485060074_1_4
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_3h_2

description:
Sample name: 251485060025_1_1
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_CA04_48h_3

description:
Sample name: 251485060031_1_1
Cells infected with A/CA/04/2009 at MOI of 3


title: ICL006_mock_0h_2

description:
Sample name: 251485060031_1_4
mock infected


title: 12581.p1


title: ICL006_mock_12h_2

description:
Sample name: 251485060073_1_4
mock infected


title: ICL006_mock_12h_3

description:
Sample name: 251485060033_1_2
mock infected


title: ICL006_mock_0h_3

description:
Sample name: 251485060025_1_2
mock infected


title: 12299.s1


title: ICL006_mock_18h_1

description:
Sample name: 251485060073_1_2
mock infected


title: 12343.p1


title: 12685.p1


title: 12239.p1


title: 11962.p1


title: ICL006_mock_24h_3

description:
Sample name: 251485060073_1_1
mock infected


title: 12383.p1


title: 12339.p1


title: 11962.s1


title: 11343.p1


title: ICL006_mock_18h_3

description:
Sample name: 251485060035_1_1
mock infected


title: 12351.s1


title: ICL006_mock_18h_2

description:
Sample name: 251485060076_1_1
mock infected


title: ICL006_mock_24h_2

description:
Sample name: 251485060034_1_2
mock infected


title: 11689.p1


title: 11824.s1


title: 11809.p1


title: ICL006_mock_30h_1

description:
Sample name: 251485060025_1_4
mock infected


title: ICL006_mock_24h_1

description:
Sample name: 251485060033_1_4
mock infected


title: ICL006_mock_36h_1

description:
Sample name: 251485060076_1_3
mock infected


title: ICL006_mock_36h_3

description:
Sample name: 251485060075_1_4
mock infected


title: ICL006_mock_30h_3

description:
Sample name: 251485060035_1_2
mock infected


title: ICL006_mock_12h_1

description:
Sample name: 251485060074_1_1
mock infected


title: 13195.p1


title: 11387.p1


title: ICL006_mock_30h_2

description:
Sample name: 251485060196_1_4
mock infected


title: ICL006_mock_36h_2

description:
Sample name: 251485060035_1_3
mock infected


title: ICL006_mock_3h_1

description:
Sample name: 251485060034_1_4
mock infected


title: 13128.p1


title: Tobacco +Boron 12h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 1 of 4, Replicate: 2

tag: treatment

value: supplied with boron

tag: sample type

value: Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites


title: ICL006_mock_48h_1

description:
Sample name: 251485060195_1_1
mock infected


title: Tobacco -Boron 36h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 1 of 4, Replicate: 2

value: deprived of boron


title: 12958.p1

tag: famid


title: Tobacco -Boron 12h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 1 of 4, Replicate: 2


title: 11080.p1

tag: simons simplex collection id


title: 12736.p1

tag: cell type


title: Tobacco before-treatment slide1 rep2

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 1 of 4, Replicate: 2

value: no treatment


title: Tobacco +Boron 6h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 6 h, Slide: 1 of 4, Replicate: 2

value: 6 h


title: ICL006_mock_3h_2

description:
Sample name: 251485060032_1_3
mock infected


title: 12435.p1

tag: chip id


title: Tobacco -Boron 6h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 1 of 4, Replicate: 2


title: 11433.p1

tag: project


title: Tobacco +Boron 36h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 1 of 4, Replicate: 2


title: ICL006_mock_7h_2

description:
Sample name: 251485060073_1_3
mock infected


title: ICL006_mock_7h_3

description:
Sample name: 251485060197_1_1
mock infected


title: 12984.p1

tag: batch


title: Neural tube electroporated with NEUROG2AQ-GFP, 6h, biological rep4

city: Toulouse

first: Sophie

middle: Bel

last: Vialar

address: 118 rte de narbonne

country: France

institute: CNRS

description:
SBV_Aq4 Signal (log)
RNA extracted from FACS-sorted GFP cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Chicken Genome arrays (Affimetrix). Each microarray was then washed and stained on a GeneChip® Fluidics Station 450.

scan_protocol: Microarrays were scanned with a GeneChip® Scanner 3000 7G.

data_processing: GeneChip Operating Software (GCOS) version 1.4 (Affymetrix, Santa Clara, CA, USA). CEL files were further processed with the Robust Multi-array Average (RMA) algorithm using the affy package in Bioconductor version release (2.4.1).

label: Biotin

organism: Gallus gallus

source_name: Neural tube, overexpression of NEUROG2-AQ

label_protocol: Biotinylated cRNAs were prepared from 50 ng of total RNA using the Ambion MessageAmpTM Premier RNA Amplification Kit from Applied Biosystems according to the manufacturer's instructions.

growth_protocol: Fertilized eggs were grown at 37°C during about 40 hours in order to reach the HH10 stage (E1.5). All of the embryos used for this study had between 13 and 15 somites developed at the time of the electroporation.

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

treatment_protocol: HH10 embryos were electroporated in ovo in the neural tube with a construct co-expressing the appropriate protein and GFP. Embryos were harvested 6h later, and for each biological replicate, neural tubes from 20 embryos were pooled prior to cell dissociation. Neural tube explants were incubated 10' in and then dissociated mechanically. GFP+ cells were collected in Tri-reagent by FACS sorting.

tag: developmental stage

tag: tissue

value: neural tube

value: NEUROG2-AQ overexpression


title: ICL006_mock_48h_3

description:
Sample name: 251485060176_1_1
mock infected


title: ICL006_mock_48h_2

description:
Sample name: 251485060034_1_1
mock infected


title: ICL006_mock_3h_3

description:
Sample name: 251485060196_1_2
mock infected


title: ICL006_mock_7h_1

description:
Sample name: 251485060033_1_3
mock infected


title: 12647.p1

value: lymphoblast cell lines (LCLs)

value: lymphoblasts

tag: gender

tag: age

tag: autism trait


title: RPE+3

city: Philadelphia

first: Joshua

middle: L.

last: Dunaief

state: PA

address: 422 Curie Blvd, 305 Stellar Chance labs

department: Ophthalmology

institute: University of Pennsylvania

description: Gene expression in light-exposed RPE.

hyb_protocol: Labeled cDNA (3ug) was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: RMA was applied using Partek Genomics Suite v 6.6.

source_name: retina, RPE, light

label_protocol: RNA primer and DNA polymerase (Ovation Pico WTA System, NuGEN Inc., San Carlos CA), and the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Male, 10-week-old Balb/cJ mice (n=8) were obtained from The Jackson Laboratory (Bar Harbor, ME, USA).

extract_protocol: RNA isolation was performed with the RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Mice (n = 4) were exposed to 10,000 lux cool white fluorescent light for 18 hours. The control group (n = 4) was kept on a regular 12-hour light-dark cycle. Mice were sacrificed 4 hours after photic injury ended, and the NSR and isolated RPE were collected for mRNA quantification.

tag: strain

value: Balb/cJ

value: light

value: retinal pigment epithelium (RPE)

tag: mouse identifier


title: Neural tube electroporated with NEUROG2AQ-GFP, 6h, biological rep3

description:
SBV_Aq3 Signal (log)
RNA extracted from FACS-sorted GFP cells.


title: Neural tube electroporated with NEUROG2AQ-GFP, 6h, biological rep2

description:
SBV_Aq2 Signal (log)
RNA extracted from FACS-sorted GFP cells.


title: 11090.p1

tag: cell line


title: 11129.p1

value: female


title: Tobacco -Boron 3h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth media, Duration of treatment: 3 h, Slide: 1 of 4, Replicate: 2

tag: time

value: 3 h


title: Tobacco +Boron 3h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 3 h, Slide: 1 of 4, Replicate: 2

tag: treatment


title: Tobacco +Boron 1h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 1 h, Slide: 1 of 4, Replicate: 2

value: 1 h

tag: sample type


title: 11696.p1

tag: famid

value: male

value: Autism


title: RPE-4

description: Gene expression in control RPE.

source_name: retina, RPE, control

value: control


title: 11555.mo

tag: simons simplex collection id

value: Control


title: 12512.p1

tag: cell type


title: RPE+4

description: Gene expression in light-exposed RPE.


title: 11041.p1

tag: chip id


title: Tobacco -Boron 1h slide1 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 1 h, Slide: 1 of 4, Replicate: 2

value: deprived of boron

source_name: vector control

value: Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites


title: Tobacco before-treatment slide1 rep1

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 1 of 4, Replicate: 1

value: no treatment


title: Neural tube electroporated with NEUROG2-GFP, 6h, biological rep3

description:
SBV_Ngn3 Signal (log)
RNA extracted from FACS-sorted GFP cells.

source_name: Neural tube, overexpression of NEUROG2

value: neural tube

value: NEUROG2 overexpression


title: Neural tube electroporated with NEUROG2AQ-GFP, 6h, biological rep1

description:
SBV_Aq1 Signal (log)
RNA extracted from FACS-sorted GFP cells.

value: NEUROG2-AQ overexpression


title: RPE-2

description: Gene expression in control RPE.


title: 11435.p1

value: lymphoblast cell lines (LCLs)

value: lymphoblasts

tag: project


title: RPE+2

description: Gene expression in light-exposed RPE.

value: Balb/cJ

value: light


title: Neural tube electroporated with NEUROG2-GFP, 6h, biological rep4

description:
SBV_Ngn4 Signal (log)
RNA extracted from FACS-sorted GFP cells.


title: Neural tube electroporated with NEUROG2-GFP, 6h, biological rep1

description:
SBV_Ngn1 Signal (log)
RNA extracted from FACS-sorted GFP cells.


title: Tobacco -Boron 36h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 36 h, Slide: 1 of 4, Replicate: 1


title: RPE-3

description: Gene expression in control RPE.

value: retinal pigment epithelium (RPE)


title: Tobacco +Boron 36h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 1 of 4, Replicate: 1

value: supplied with boron


title: 12295.s1

tag: batch


title: Neural tube electroporated with control-GFP, 6h, biological rep4

description:
SBV_Ctl4 Signal (log)
RNA extracted from FACS-sorted GFP cells.

source_name: Neural tube, control

tag: developmental stage


title: NSR+4

description: Gene expression in light-exposed NSR.

source_name: retina, NSR, light

tag: tissue

value: neurosensory retina (NSR)


title: RPE-1

description: Gene expression in control RPE.

tag: gender

value: male


title: 12457.s1

tag: age


title: Tobacco +Boron 12h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 12 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 12 h


title: NSR+3

description: Gene expression in light-exposed NSR.


title: Tobacco +Boron 6h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 6 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 6 h

value: 6 h


title: NSR+1

description: Gene expression in light-exposed NSR.


title: Tobacco -Boron 12h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 12 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 12 h


title: NSR-3

description: Gene expression in control NSR.

source_name: retina, NSR, control

value: control


title: NSR+2

description: Gene expression in light-exposed NSR.


title: Neural tube electroporated with control-GFP, 6h, biological rep3

description:
SBV_Ctl3 Signal (log)
RNA extracted from FACS-sorted GFP cells.


title: Tobacco -Boron 6h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 6 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 6 h


title: Neural tube electroporated with NEUROG2-GFP, 6h, biological rep2

description:
SBV_Ngn2 Signal (log)
RNA extracted from FACS-sorted GFP cells.


title: NSR-4

description: Gene expression in control NSR.


title: 12032.p1

tag: autism trait

value: Autism


title: 12007.p1

value: female


title: Tobacco -Boron 3h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth medium, Duration of treatment: 3 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 3 h

value: deprived of boron

value: 3 h

value: Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites


title: NSR-2

description: Gene expression in control NSR.

tag: strain


title: Tobacco +Boron 3h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 3 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 3 h


title: Tobacco +Boron 1h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth media, Duration of treatment: 1 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 1 h

value: 1 h


title: 12235.p1


title: 11201.s1

value: Control


title: Neural tube electroporated with control-GFP, 6h, biological rep1

description:
SBV_Ctl1 Signal (log)
RNA extracted from FACS-sorted GFP cells.

value: neural tube


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 3

city: Seoul

first: Jong-Doo

last: Lee

address: 250 seonsan-ro seodaemum-gu

country: South Korea

institute: Yonsei University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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: Five- week- old male C57BL6 mice were randomly divided into two groups (n=3/group) and fed control diet (control group, LabDiet, Brentwood, MO, USA) or moderate restriced carbohydrate diet formula (MCD, Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee.

extract_protocol: Non-tumor liver region was isolated from each mouse liver tissue. Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Following a preliminary feeding of each diet formula for one week, HrasG12V / shp53 / GFP4 gene containing transposon vector were injected into mouse tail vein by hydrodynamic injection method. After 5 weeks of diet supplementation, all mice were sacrificed. Mouse liver tissue was excised for microarray analysis.

value: liver tissue (non-tumor region)

tag: disease model

value: human -HrasG12V / shp53/ GFP4 transposon vector induced transgenic mouse with liver cancer


title: 12117.s1

tag: cell line

value: lymphoblast cell lines (LCLs)

value: lymphoblasts


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 2


title: NSR-1

description: Gene expression in control NSR.

value: Balb/cJ

tag: mouse identifier


title: Control Diet Supplemented  Mouse 3

source_name: Control Diet Supplemented


title: Neural tube electroporated with control-GFP, 6h, biological rep2

description:
SBV_Ctl2 Signal (log)
RNA extracted from FACS-sorted GFP cells.

tag: treatment


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 1


title: Control Diet Supplemented  Mouse 2


title: Control Diet Supplemented  Mouse 1


title: Tobacco -Boron 1h slide1 rep1

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in boron-free growth media, Duration of treatment: 1 h, Slide: 1 of 4, Replicate: 1

source_name: Suspension cultured tobacco BY-2 cells, deprived of boron, 1 h

tag: time

tag: sample type


title: Foxp3+PPARg1+Pio#2

status: Public on May 04 2012

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit.

scan_protocol: Affymetrix GeneChip Scanner.

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization).

source_name: pooled spleen and lymph nodes, T cells, Pparg1, pioglitazone

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: TriZol.

tag: genetic background

tag: genotype

tag: Sex

value: 6 to 8 weeks

value: spleen, lymph nodes

value: T cells

tag: transduction

value: pioglitazone

tag: exclusion markers

tag: phenotype markers

value: CD3+ CD4+

tag: separation method

value: MoFlo double-sorting


title: Tobacco +Boron 36h slide3 rep2

description: tissue: suspension-cultured cells, Treatment: washed with and cultured in standard growth medium, Duration of treatment: 36 h, Slide: 3 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, supplied with boron, 36 h

value: supplied with boron


title: Tobacco before-treatment slide3 rep2

description: tissue: suspension-cultured cells, Treatment: none, Stage: log, Slide: 3 of 4, Replicate: 2

source_name: Suspension cultured tobacco BY-2 cells, no treatment

value: no treatment


title: Foxp3+PPARg1+ROS1#3

source_name: pooled spleen and lymph nodes, T cells, Pparg1, rosiglitazone

value: male

tag: tissue

tag: cell type

value: rosiglitazone


title: Foxp3+PPARg1+Pio#1

tag: age


title: Foxp3+PPARg1+Pio#3


title: Foxp3+PPARg1+GW1929#3

source_name: pooled spleen and lymph nodes, T cells, Pparg1, GW1929


title: Foxp3+PPARg1+GW1929#2


title: Foxp3+PPARg1+ROS1#1


title: Foxp3+PPARg1+GW1929#1


title: 12219.p1

tag: famid

tag: simons simplex collection id

tag: chip id

tag: project

tag: batch

tag: gender

tag: autism trait

value: Autism


title: Foxp3+PPARg1+vehicle(DMSO)#2

source_name: pooled spleen and lymph nodes, T cells, Pparg1, vehicle

tag: genetic background

tag: treatment

value: DMSO vehicle


title: Foxp3+Pio#2

hyb_protocol: Affymetrix GeneChip WT cDNA Synthesis and Amplification Kits.

source_name: pooled spleen and lymph nodes, T cells, pioglitazone

label_protocol: Affymetrix GeneChip WT Sense Target Labeling and Control Reagents.

tag: genotype/variation

tag: Sex


title: Foxp3+Pio#1

tag: transduction

tag: exclusion markers


title: Foxp3+vehicle(DMSO)#3

source_name: pooled spleen and lymph nodes, T cells, vehicle

tag: phenotype markers

tag: separation method


title: Foxp3+PPARg1+vehicle(DMSO)#1

tag: genotype

tag: tissue

tag: cell type


title: Foxp3+vehicle(DMSO)#2

tag: age


title: PPARg2+Foxp3+vehicle(DMSO)#2

source_name: pooled spleen and lymph nodes, T cells, Pparg2, vehicle

value: Foxp3+/- Pparg2


title: Foxp3+PPARg1+vehicle(DMSO)#3


title: Foxp3+Pio#3


title: Foxp3+PPARg1+ROS1#2


title: PPARg2+Foxp3+Pio#3

source_name: pooled spleen and lymph nodes, T cells, Pparg2, pioglitazone


title: PPARg2+Foxp3+Pio#2


title: PPARg2+Foxp3+Pio#1


title: PPARg1+Foxp3+Pio#2

value: Foxp3+/- Pparg1


title: CordBloodCD4+_Th17_72h_rep3

city: Turku

first: Soile

last: Tuomela

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: Th17 polarization was initiated with IL-6 (20 ng/ml, Roche), IL1β (10 ng/ml, R&D Systems) and TGFβ (10 ng/ml, R&D Systems)

hyb_protocol: 0.75 µg each sample was hybridized to Illumina’s Sentrix HumanHT-12 Expression BeadChips, version 3 (cat no BD-103-0603) at 58C overnight (18h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridization was detected with 1 µg/ml Cyanine3-streptavidin, GE Healthcare Limited UK (cat no PA43001).

scan_protocol: Chips were scanned with Illumina BeadArray Reader, BeadScan software version 3.5. The numerical results were extracted with GenomeStudio 2008.1 without any normalization.

data_processing: The data was filtered by choosing only the probes with detection p-value <0.05 at least in one time point, at one cell type. Additionally, only the probes having standard deviation >0.15 over all the samples were used in the analysis. The data was normalized using quantile normalization. For each time point, differentially expressed genes were identified using Bioconductor limma package with moderated t-statistic with false discovery rate (FDR) <0.1.

source_name: Cord blood CD4+ cells 72h after activation and polarization towards Th17

label_protocol: Amplification was started using 100ng total RNA with Ambion's Illumina RNA TotalPrep Amplification kit (cat no AMIL1791). IVT reaction took overnight (16h) and during it cRNA was biotinylated. Both before and after the amplifications the RNA/cRNA concentrations where checked with Nanodrop ND-1000 and RNA/cRNA quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: CD4+ T cells were purified from umbilical cord blood of healthy neonates (Turku University Central Hospital, Finland). Mononuclear cells were isolated (Ficoll-Paque, Amersham Biosciences) after which CD4+ cells were collected (Dynal CD4 Positive Isolation Kit, Invitrogen). Cells were activated with plate-bound αCD3 (750 ng/24w culture plate well, Immunotech, France) and soluble αCD28 (1 µg/ml, Immunotech) in density of 0.5x106 cells/ml of X-vivo 20 serum free medium (Lonza) supplemented with 2 mM L-Glutamine (#G7513, Sigma), 50 U/ml Penicillin and 50 μg/ml Streptomycin (#P0781, Sigma) and neutralizing αIL12 (1 µg/ml) and αIL4 (1 µg/ml), and cultured at 37°C in 5 % CO2.

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) according to manufacturer's instructions. In-column DNase (RNase-Free DNase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.

value: Cord blood

tag: protocol

tag: time

tag: biological replicate

value: biological replicate:3


title: PPARg1+Foxp3+Pio#3


title: PPARg2+Foxp3+vehicle(DMSO)#1


title: CordBloodCD4+_Th17_48h_rep3

source_name: Cord blood CD4+ cells 48h after activation and polarization towards Th17


title: PPARg1+Foxp3+Pio#1


title: Foxp3+vehicle(DMSO)#1


title: CordBloodCD4+_Th17_24h_rep3

source_name: Cord blood CD4+ cells 24h after activation and polarization towards Th17


title: PPARg1+Foxp3+vehicle(DMSO)#1


title: PPARg1+Foxp3+vehicle(DMSO)#3


title: RPE+1

description: Gene expression in light-exposed RPE.

source_name: retina, RPE, light

tag: strain

value: Balb/cJ

tag: gender

value: light

value: retinal pigment epithelium (RPE)

tag: mouse identifier


title: CordBloodCD4+_Th0_24h_rep3

source_name: Cord blood CD4+ cells 24h after activation

value: activation


title: LN.Treg.30w.B6.Treg-Pparg.mut#3

source_name: lymph nodes, Treg, Parg+

tag: genetic background

value: Pparg+

value: 30 weeks

value: lymph nodes

value: regulatory T cells (Tregs)

value: CD3+ CD4+ CD25+YFP+


title: CordBloodCD4+_Th17_12h_rep3

source_name: Cord blood CD4+ cells 12h after activation and polarization towards Th17


title: PPARg2+Foxp3+vehicle(DMSO)#3

tag: genotype/variation

value: male

value: 6 to 8 weeks

value: spleen, lymph nodes

value: T cells

tag: treatment

value: CD3+ CD4+

value: MoFlo double-sorting


title: CordBloodCD4+_Th0_48h_rep3

source_name: Cord blood CD4+ cells 48h after activation

value: Cord blood


title: CordBloodCD4+_Th17_2h_rep3

source_name: Cord blood CD4+ cells 2h after activation and polarization towards Th17

value: biological replicate:3


title: LN.Treg.30w.B6.Treg-Pparg.mut#2

tag: Sex


title: PPARg1+Foxp3+vehicle(DMSO)#2

tag: transduction

value: Foxp3+/- Pparg1

value: DMSO vehicle

tag: exclusion markers


title: LN.Tconv.Retired.B6#3

source_name: lymph nodes, Tconv

value: 30 weeks retired breeder

value: conventional T cells (Tconvs)

tag: phenotype markers

tag: separation method


title: CordBloodCD4+_Th17_1h_rep3

source_name: Cord blood CD4+ cells 1h after activation and polarization towards Th17

tag: tissue


title: LN.Treg.30w.B6.Treg-Pparg.wt#1

source_name: lymph nodes, Treg, Parg-

value: Pparg-

tag: cell type


title: LN.Treg.30w.B6.Treg-Pparg.mut#1

value: Pparg+

tag: age

value: 30 weeks


title: CordBloodCD4+_Th0_12h_rep3

source_name: Cord blood CD4+ cells 12h after activation

tag: protocol

value: activation


title: CordBloodCD4+_Th17_0.5h_rep3

source_name: Cord blood CD4+ cells 0.5h after activation and polarization towards Th17

tag: time


title: LN.Treg.30w.B6.Treg-Pparg.wt#2

value: lymph nodes

value: regulatory T cells (Tregs)

value: CD3+ CD4+ CD25+YFP+


title: LN.Treg.Retired.B6#3

source_name: lymph nodes, Treg

value: male


title: CordBloodCD4+_Th17_4h_rep3

source_name: Cord blood CD4+ cells 4h after activation and polarization towards Th17

tag: biological replicate


title: CordBloodCD4+_Th17_6h_rep3

source_name: Cord blood CD4+ cells 6h after activation and polarization towards Th17


title: LN.Treg.30w.B6.Treg-Pparg.wt#3


title: CordBloodCD4+_Th0_72h_rep3

source_name: Cord blood CD4+ cells 72h after activation


title: LN.Treg.Retired.B6#1


title: VAT.Treg.30w.B6.Treg-Pparg.wt#2

source_name: Epi fat, Treg, Pparg+

value: visceral adipose tissue (VAT)


title: LN.Tconv.Retired.B6#2


title: LN.Tconv.Retired.B6#1


title: CordBloodCD4+_Th0_0.5h_rep3

source_name: Cord blood CD4+ cells 0.5h after activation


title: CordBloodCD4+_Th0_1h_rep3

source_name: Cord blood CD4+ cells 1h after activation


title: CordBloodCD4+_Th0_4h_rep3

source_name: Cord blood CD4+ cells 4h after activation


title: CordBloodCD4+_Th0_6h_rep3

source_name: Cord blood CD4+ cells 6h after activation


title: CordBloodCD4+_Th0_2h_rep3

source_name: Cord blood CD4+ cells 2h after activation


title: CordBloodCD4+_Th17_48h_rep2

source_name: Cord blood CD4+ cells 48h after activation and polarization towards Th17

value: biological replicate:2


title: LN.Treg.Retired.B6#2

value: MoFlo double-sorting


title: VAT.Tconv.Retired.B6#3

source_name: Epi fat, Tconv


title: CordBloodCD4+_Th17_12h_rep2

source_name: Cord blood CD4+ cells 12h after activation and polarization towards Th17

value: Cord blood


title: VAT.Treg.30w.B6.Treg-Pparg.mut#3

source_name: Epi fat, Treg, Pparg-


title: CordBloodCD4+_Th17_72h_rep2

source_name: Cord blood CD4+ cells 72h after activation and polarization towards Th17


title: CordBloodCD4+_Th17_2h_rep2

source_name: Cord blood CD4+ cells 2h after activation and polarization towards Th17


title: VAT.Tconv.Retired.B6#1


title: CordBloodCD4+_Th17_4h_rep2

value: activation and polarization towards Th17


title: CordBloodCD4+_Thp_0h_rep3

source_name: Cord blood CD4+ cells without any treatments

value: no treatments

value: biological replicate:3


title: VAT.Treg.30w.B6.Treg-Pparg.wt#1


title: VAT.Treg.Retired.B6#2

source_name: Epi fat, Treg

value: 30 weeks retired breeder


title: CordBloodCD4+_Th17_6h_rep2


title: VAT.Treg.30w.B6.Treg-Pparg.wt#3


title: VAT.Treg.30w.B6.Treg-Pparg.mut#1


title: VAT.Tconv.Retired.B6#2

value: conventional T cells (Tconvs)


title: VAT.Treg.Retired.B6#3


title: CordBloodCD4+_Th0_24h_rep2

source_name: Cord blood CD4+ cells 24h after activation


title: VAT.Treg.Retired.B6#1


title: CordBloodCD4+_Th17_0.5h_rep2

source_name: Cord blood CD4+ cells 0.5h after activation and polarization towards Th17


title: CordBloodCD4+_Th0_72h_rep2

source_name: Cord blood CD4+ cells 72h after activation


title: CordBloodCD4+_Th0_48h_rep2

source_name: Cord blood CD4+ cells 48h after activation


title: CordBloodCD4+_Th0_4h_rep2


title: CordBloodCD4+_Th0_6h_rep2


title: CordBloodCD4+_Th17_1h_rep2

source_name: Cord blood CD4+ cells 1h after activation and polarization towards Th17


title: CordBloodCD4+_Th0_1h_rep2

source_name: Cord blood CD4+ cells 1h after activation


title: CordBloodCD4+_Th0_12h_rep2

source_name: Cord blood CD4+ cells 12h after activation


title: CordBloodCD4+_Th0_2h_rep2


title: Rescue pancreas, biological rep2

city: West Lafayette

first: Daniel

last: DiRenzo

state: IN

address: 201 South University Street Rm. 213

department: Purdue Center for Cancer Research

institute: Purdue University

description:
SK03M010
Gene expression data from MIST1-null pancreatic RNA with inducible MIST1 transgene 36 hours post-tamoxifen

hyb_protocol: Hybridization was done using Affymetrix standard hybridization protocol for Gene ST 1.0 arrays

scan_protocol: GeneChips were scanned using Affymetrix GCOS

data_processing: Partek was used to generate RMA.RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed.

label_protocol: RNA was labeled using Affymetrix standard WT protocol (non-Ambion) from 100ng total RNA.

extract_protocol: Extraction of total RNA was performed using the Qiagen Rneasy Midi Kit with 20-30 mg of pancreatic tissue according to the manufacturer's instructions.

treatment_protocol: Mice were administered 4mg of 20mg/mL tamoxifen dissolved in corn oil via oral gavage, mice were then sacrificed 36 hours post-tamoxifen administration via CO2 euthanasia.

value: Pancreas

tag: strain

tag: genotype

value: Mist1Cre-ER/Cre-ER; LSL-MIST1myc

value: 8 weeks


title: Rescue pancreas, biological rep3

description:
SK03M011
Gene expression data from MIST1-null pancreatic RNA with inducible MIST1 transgene 36 hours post-tamoxifen


title: MIST1-null pancreas, biological rep3

description:
SK03M007
Gene expression data from MIST1-null pancreatic RNA 36 hours post-tamoxifen


title: CordBloodCD4+_Th0_0.5h_rep2

source_name: Cord blood CD4+ cells 0.5h after activation

value: activation


title: CordBloodCD4+_Thp_0h_rep2


title: Rescue pancreas, biological rep1

description:
SK03M009
Gene expression data from MIST1-null pancreatic RNA with inducible MIST1 transgene 36 hours post-tamoxifen


title: CordBloodCD4+_Th17_2h_rep1

value: biological replicate:1


title: MIST1-null pancreas, biological rep2

description:
SK03M006
Gene expression data from MIST1-null pancreatic RNA 36 hours post-tamoxifen


title: Rescue pancreas, biological rep4

description:
SK03M012
Gene expression data from MIST1-null pancreatic RNA with inducible MIST1 transgene 36 hours post-tamoxifen


title: CordBloodCD4+_Th17_4h_rep1

source_name: Cord blood CD4+ cells 4h after activation and polarization towards Th17


title: CordBloodCD4+_Th17_1h_rep1


title: MIST1-null pancreas, biological rep1

description:
SK03M005
Gene expression data from MIST1-null pancreatic RNA 36 hours post-tamoxifen


title: CordBloodCD4+_Th17_12h_rep1


title: CordBloodCD4+_Th0_48h_rep1


title: CordBloodCD4+_Th17_0.5h_rep1


title: wildtype pancreas, biological rep4

description:
SK03M004
Gene expression data from wildtype pancreatic RNA 36 hours post-tamoxifen

source_name: Wildtype pancreatic RNA 36 hours post-tamoxifen

value: wildtype


title: CordBloodCD4+_Th0_4h_rep1

source_name: Cord blood CD4+ cells 4h after activation


title: CordBloodCD4+_Th0_24h_rep1


title: CordBloodCD4+_Th17_6h_rep1

source_name: Cord blood CD4+ cells 6h after activation and polarization towards Th17


title: wildtype pancreas, biological rep2

description:
SK03M002
Gene expression data from wildtype pancreatic RNA 36 hours post-tamoxifen


title: MIST1-null pancreas, biological rep4

description:
SK03M008
Gene expression data from MIST1-null pancreatic RNA 36 hours post-tamoxifen


title: CordBloodCD4+_Th17_24h_rep1

source_name: Cord blood CD4+ cells 24h after activation and polarization towards Th17


title: CordBloodCD4+_Th17_72h_rep1

source_name: Cord blood CD4+ cells 72h after activation and polarization towards Th17


title: CordBloodCD4+_Th0_6h_rep1

source_name: Cord blood CD4+ cells 6h after activation


title: wildtype pancreas, biological rep3

description:
SK03M003
Gene expression data from wildtype pancreatic RNA 36 hours post-tamoxifen


title: CordBloodCD4+_Th0_72h_rep1


title: CordBloodCD4+_Th0_12h_rep1


title: CordBloodCD4+_Th17_48h_rep1

source_name: Cord blood CD4+ cells 48h after activation and polarization towards Th17


title: CordBloodCD4+_Th0_2h_rep1

source_name: Cord blood CD4+ cells 2h after activation


title: wildtype pancreas, biological rep1

description:
SK03M001
Gene expression data from wildtype pancreatic RNA 36 hours post-tamoxifen


title: cyFBPase mutant Vs. Wild-type (Col-0), rosette tissue, replicate 2

city: Granada

first: Mariam

middle: Sahrawy

last: Barragán

state: Granada

address: Profesor Albareda,

department: Department of biochemistry, cellular and molecular biology of plants

institute: Estación Experimental del Zaidín (EEZ)

description: cyFBPase Vs. WT_rosette_rep2

hyb_protocol: Before hybridization, hydratation and UV cross-linking were realized with the glass slides according to the manufacturer’s recommendations (http://www.ag.arizona.edu/microarray/) . DNA was crosslinked to the slides, using 65 mJ of 254-nm UV-C radiation from a Stratalinker® UV Crosslinker (model 2400, Stratagene, La Jolla, CA, USA). Slides were incubated 2 h at 70°C and pre-hybridized with 1% BSA, 5X SSC buffer, and 0.1% (w/v) SDS for 45 min at 54°C. The hybridization mixture consisted of 500 ng labelled cDNA and 4.5 µg µl–1 of salmon sperm DNA (Invitrogen Life Technologies) in a final volume of 35 µl. This volume was mixed with 35 µl of 2X hybridization buffer (1X formamide, 1X SSC, and 0.04X SDS). The mixture was denatured at 95°C for 2 min and transferred to ice. The hybridization mixture was applied to a microarray slide, transferred immediately to a hybridization chamber (Corning, Inc., Lowell, MA, USA), and incubated overnight (15–17 h) at 42°C. The slide was then washed for 5 min successively in each of 2X SSC, 0.1% (w/v) SDS at 54°C, 1X SSC, and 0.1X SSC at room temperature. Slides were immediately dried by centrifuging at 1000 rpm for 4 min.

scan_protocol: The slides were scanned, using a GenePix 4100A scanner (Axon Molecular Devices). The signal was initially normalized during image scanning to adjust the average ratio between the two channels, using control spots. Spot intensities from scanned slides were quantified, using the GenePix Pro 5.1 software (Axon).

data_processing:
Using the GenePix Pro 5.1 software, local Background Subtraction was carried out. GenePix Pro 5.1 output data files (in Excel) were used to perform the lowest intensity normalization, standard deviation regularization, low intensity filtering, and dye-swap analysis, using the MIDAS computer program. Normalization between different slides was carried out by centring. MIDAS was also used for replicate analysis and dye-swap filtering.
Bootstrap analyses with SAM enabled us to identify the differentially expressed genes, using a cut-off of two and adjusting the delta-delta Ct value, FDR, and FSN to minimize the number of false positives genes.

organism: Arabidopsis thaliana

source_name: cyFBPase  knock-out mutant

label_protocol: Fluorescent-labelled probes were prepared, following the Klenow labelling method (indirect labelling). Briefly, 500 ng of cDNA were labelled, using 1 µl of either Cy3- or Cy5-dUTP (Amersham Pharmacia Biotech, Little Chalfont, UK), 10 U Exonuclease-Free Klenow (USB Corporation, Cleveland, OH, USA), and 3 µg random primers (Invitrogen Life Technologies, Carlsbad, CA, USA), and incubated 2 h at 37°C. Unincorporated nucleotides were removed, using a QIAquick PCR Purification Kit (QIAGEN, Inc.). Cleaned probes were concentrated in a speedvac (Eppendorf® Vacufuge Concentrator 5301, Hamburg, Germany).

growth_protocol: Total RNA was extracted from rosettes of 12-days-old Arabidopsis plants (ecotype Col-0) growing in Murashige and Skoog medium and incubated at 22ºC under long-day conditions (16-h-light/8-hdark) and with photosynthetically active radiation of 140 μmol photons m–2 s–1.s.

extract_protocol: Total RNA extraction and DNase treatment were conducted using the AurumTM Total RNA mini Kit according to the manufacturer’s recommendations (BIO-RAD, Inc.).

value: Rosette

tag: ecotype

value: Columbia

value: 12-days-old plants growing in MS medium

source_name: Wild-type, ecotype Col-0


title: hippo_icr_rep1

city: Bar Harbor

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: hsd:ICR (ICR) mice are an outbred line of mice sold by Harlan Labs (Madison, WI).

hyb_protocol: Samples were hybridized to arrays at 45C for 16 hours following procedures outlined in the GeneChip WT Terminal Labeling and Hybridization Use Manual , Rev. 4.

scan_protocol: Arrays were scanned on the Affymetrix GC3000 G7 scanner, and data were extracted and processed using Affymetrix Command Console v3.1.1.1229.

data_processing: Raw array data were normalized and summarized at the probeset level using Affymetrix Power Tools v1.12.0 with default settings for PLIER with GC-bin background correction.  Summarized data were analyzed using limma for BioConductor v3.6.9.

label_protocol: 400ng of each total RNA sample were labeled with an Ambion GeneChip WT Expression Kit (Ambion, Austin, TX, USA) according to the manufacturer's specifications.

growth_protocol: Madison (MSN) mice were selectively bred to display a manic phenotype; hsd:ICR (ICR) mice are the outbred ancestral strain from which MSN mice were derived.  Each line has been maintained in our lab for many generations.  All mice used were male mice, and all mice were approximately the same age.

extract_protocol: Total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA, USA), which uses a guanidinium thiocyanate-phenol-chloroform extraction followed by a spin column cleanup and purification.  RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was assessed using an RNA Pico Chip on an Agilent BioAnalyzer 2100.

treatment_protocol: Prior to RNA extraction, all mice were euthanized by decapitation under deep isofluorane anaesthesia in accordance with UW-Madison IACUC guidelines, and hippocampi were macrodissected and frozen immediately on dry ice.  Tissue was stored for no more than 12 weeks prior to extraction.

tag: mouse line

value: hsd:ICR (ICR)

tag: gender

value: male

value: adult

value: macrodissected hippocampus

tag: behavioral phenotype

value: normal


title: VAT.Treg.30w.B6.Treg-Pparg.mut#2

source_name: Epi fat, Treg, Pparg-

tag: genetic background

tag: genotype/variation

value: Pparg-

tag: Sex

value: 30 weeks

value: visceral adipose tissue (VAT)

value: regulatory T cells (Tregs)

value: CD3+ CD4+ CD25+YFP+

value: MoFlo double-sorting


title: cyFBPase mutant Vs. Wild-type (Col-0), root tissue, replicate 2

description: cyFBPase Vs. WT_root_rep2

value: Roots


title: hippo_icr_rep6


title: CordBloodCD4+_Th17_24h_rep2

value: Cord blood

value: activation and polarization towards Th17

value: biological replicate:2


title: hippo_icr_rep4


title: cyFBPase mutant Vs. Wild-type (Col-0), root tissue, replicate 1

description: cyFBPase Vs. WT_root_rep1

value: Columbia


title: cpFBPaseI mutant Vs. Wild-type (Col-0), rosette tissue, replicate 3

description: cpFBPaseI Vs. WT_rosette_rep3

source_name: cpFBPaseI  knock-out mutant

value: Rosette

value: 12-days-old plants growing in MS medium


title: hippo_icr_rep2

value: hsd:ICR (ICR)

value: male


title: CordBloodCD4+_Th0_1h_rep1

value: activation

value: biological replicate:1


title: CordBloodCD4+_Thp_0h_rep1

source_name: Cord blood CD4+ cells without any treatments

value: no treatments


title: CordBloodCD4+_Th0_0.5h_rep1


title: cyFBPase mutant Vs. Wild-type (Col-0), rosette tissue, replicate 1

description: cyFBPase Vs. WT_rosette_rep1


title: hippo_icr_rep3

value: adult

value: macrodissected hippocampus

value: normal


title: cpFBPaseI mutant Vs. Wild-type (Col-0), root tissue, replicate 2

description: cpFBPaseI Vs. WT_root_rep2


title: hippo_msn_rep5

description: Madison (MSN) mice are a line derived from the outbred ICR ancestral line that displays a manic phenotype relative to ICR.  MSN mice spend significantly more time moving and significantly less time resting than the ancestral ICR line.

value: Madison (MSN)

value: manic


title: cpFBPaseI mutant Vs. Wild-type (Col-0), root tissue, replicate 3

description: cpFBPaseI Vs. WT_root_rep3

value: Roots


title: cyFBPase mutant Vs. Wild-type (Col-0), rosette tissue, replicate 3

description: cyFBPase Vs. WT_rosette_rep3


title: hippo_msn_rep4


title: hippo_msn_rep6


title: cpFBPaseI mutant Vs. Wild-type (Col-0), root tissue, replicate 1

description: cpFBPaseI Vs. WT_root_rep1


title: siRNA-Jmjd6 HUVEC for 48h (gene level) rep1

city: Frankfurt

first: niels

last: boeckel

address: Theodor-Stern-Kai 7

department: Institut for Cardiovascular Regenration

country: Germany

institute: University Frankfurt

description: Huvec treated with siRNA targeting Jmjd6 for 48h

hyb_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.

data_processing:
Data were processed using the EAA (exon array analyzer, Version 2.2); RMA normalized; gene and exon expression levels from Affymetrix Power Tools
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HUVEC

growth_protocol: HUVECs (Lonza) were grown in EBM medium (Lonza) suppelement with EGM single quots (Lonza) and 10% FCS (Gibco). After the third passage, 300000  cells were seeded into 6 cm dishes.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol. The optional on-column DNA digestion was performed, using the RNase-free DNase Set (Qiagen).

treatment_protocol: After 24 h attchement, cells were transfected with siRNA targeting Jmjd6 or a scrambled siRNA (all Sigma Aldrich) using GeneTrans II (MobiTec), all in a final concentration of 60 nM for 48 h

value: HUVEC

tag: treatment

value: siRNA targeting Jmjd6


title: siRNA-Jmjd6 HUVEC for 48h (gene level) rep3

scan_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.


title: hippo_msn_rep3


title: siRNA-Jmjd6 HUVEC for 48h (gene level) rep2

label_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by ATLAS Biolabs using standard Affymetrix protocols.


title: cpFBPaseI mutant Vs. Wild-type (Col-0), rosette tissue, replicate 2

description: cpFBPaseI Vs. WT_rosette_rep2


title: hippo_icr_rep5


title: siRNA-Scrambled HUVEC for 48h (gene level) rep3

description: Huvec treated with control (SCR) siRNA for 48h

value: control siRNA


title: S. coelicolor M28 (degU+) vs M145 wt REP1

city: Campus de Cantoblanco

first: Sonia

last: Gullón

state: Madrid

address: Darwin 3

institute: CNB-CSIC

description: Biological replicate 1 of 3. Gene expression of S. coelicolor M28 (degU+) versus M145 wt

hyb_protocol: Slides were prehybridized in 6x SSC, 0.5% SDS (w/v), and 1% BSA (w/v) at 42ºC for 30 min, followed by five rinses with milliQ water. Excess water was drained with a 2000-rpm spin for 2 min. 300 pmol of dye of each cDNA labeled with either Cy3 or Cy5 were resuspended in 50% formamide, 3x SSC, 5x Denhardt's, 1% SDS and 5% Dextransulphate. This mix was boiled for 5 min at 95ºC and then added to the prehybridized slide. Hybridization took place overnight at 37ºC in a hybridization chamber. Arrays were then washed for 5 min at 37ºC in 0.5x SSPE, tween20 0.1%, twice for 5 min at room temperature (21ºC) with 0.5x SSPE, tween20 0.1%, three times with 0.5x SSPE at room temperature, and 5 min with 0.1x SSPE. The slides were drained with a 2000-rpm spin for 2 min and stored in darknesss until they were scanned.

scan_protocol: The slides were scanned with a GenePix 4000B scanner and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried-out using the LIMMA package (Smyth, 2003) of Bioconductor project. Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Streptomyces coelicolor

source_name: Streptomyces coelicolor M145 (Wild type)

label_protocol: RNA was labeled with Cy3 or Cy5 by using the SuperScript indirect cDNA labeling system (invitrogen) as described in the instruction manual.

growth_protocol: Transcriptomic analyses were done with cultures grown in liquid NMMP medium. Total RNA was extracted from cell cultures at the late exponential phase of growth.

extract_protocol: Total RNA was isolated from mycelia harvested and stored from liquid cultures using the RNeasy midi Kit from Qiagen largely according to manufacturer’s instructions, but with several modifications. Cells pellets were mixed with glass beads (3.5-4.5 mm diameter) previously freezed with 5 ml (SDS 1%, EDTA 160mM, DEPC-treated H2O). After adding  phenol-chloroform (1ml) samples were vortexed twice resting on ice for 2 minutes between vortex. After addition of RNeasy RLT buffer (4 ml) samples were vortexed again and extracted twice with phenol-chloroform ( 8 ml ). Extracts were then treated with ethanol (2.8 ml) and applied to the RNeasy midi columns for purification according to the manufacturer's protocol.

value: wild type

source_name: Streptomyces coelicolor M28 (degU+)

value: M28 (degU+)


title: cyFBPase mutant Vs. Wild-type (Col-0), root tissue, replicate 3

description: cyFBPase Vs. WT_root_rep3

value: Columbia

value: 12-days-old plants growing in MS medium


title: S. coelicolor I32 (degU-) vs M145 wt REP3

description: Biological replicate 3 of 3. Gene expression of S. coelicolor I32 (degU-) versus M145 wt

source_name: Streptomyces coelicolor I32 (degU-)

value: I32 (degU-)


title: siRNA-Scrambled HUVEC for 48h (gene level) rep2


title: S. coelicolor M28 (degU+) vs M145 wt REP2

description: Biological replicate 2 of 3. Gene expression of S. coelicolor M28 (degU+) versus M145 wt


title: CEN 6

city: Regensburg

first: Sabit

last: Delic

address: Franz-Josef-Strauss-Allee 11

department: Department of Neuropathology

institute: University Hospital Regensburg

description: control

data_processing: miRNA expression was calculated by the StatMiner software (Integromics) and normalized to RNU6B and RNU48 expression. Matrix non-normalized table reports raw CT values. CT values greater 38 were excluded and termed undetermined.  Fold Change table reports INF/CEN ratios.

label: fluorescent reporter

source_name: central tumor region

label_protocol: PCR assays were performed using the Micro Fluidic Card System (Applied Biosystems) following the Manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the Superscript II reverse Transcriptase (Invitrogen). Quantitative real-time PCR was performed (StepOne Plus, Applied Biosystems) with 40 cycles at 97°C for 30 seconds and 59.7°C for 60 seconds.

extract_protocol: Total RNA was extracted by calcium chloride ultracentrifugation.

treatment_protocol: From each patient, matched tissue parts from the peripheral and the central tumor area were snap frozen immediately after operation and stored at -80°C. Tissue specimens were histologically confirmed to represent either the tumor infiltration zone (INF) or cell-rich central tumor areas (CEN) and then subjected to subsequent microdissection.

tag: sample

value: glioma 6

value: male

tag: age (y)

tag: tumor grade

value: GB IV


title: CEN 7

description: control

value: glioma 7

value: female


title: siRNA-Scrambled HUVEC for 48h (gene level) rep1

tag: cell type


title: CEN 5

description: control

value: glioma 5


title: hippo_msn_rep1

value: Madison (MSN)

tag: age

value: adult

tag: tissue

value: macrodissected hippocampus


title: cpFBPaseI mutant Vs. Wild-type (Col-0), rosette tissue, replicate 1

description: cpFBPaseI Vs. WT_rosette_rep1

value: Rosette


title: hippo_msn_rep2

value: manic


title: S. lividans strain deficient in SecG versus Wild Type (TK21), rep3

description:
Gene expression of S. lividans deficient in SecG versus Wild Type strain (TK21).
Biological replicate 3 of 3.

data_processing: Data processing was carried-out using the LIMMA package (Smyth, 2003) of Bioconductor project. Raw intensities were background-subtracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Streptomyces lividans

source_name: Streptomyces lividans, wild type

label_protocol: RNA was labeled with Cy3 or Cy5 by using the SuperScript indirect cDNA labeling system (Invitrogen) as described in the instruction manual.

extract_protocol: Total RNA was isolated from mycelia harvested and stored from liquid cultures using the RNeasy midi Kit from Qiagen largely according to manufacturer’s instructions, but with several modifications. Cells pellets were mixed with glass beads (3.5-4.5 mm diameter) previously freezed with 5 ml (SDS 1%, EDTA 160mM, DEPC-treated H2O). After adding  phenol-chloroform (1ml), samples were vortexed twice resting on ice for 2 minutes between vortex. After addition of RNeasy RLT buffer (4 ml), samples were vortexed again and extracted twice with phenol-chloroform (8 ml). Extracts were then treated with ethanol (2.8 ml) and applied to the RNeasy midi columns for purification according to the manufacturer's protocol.

source_name: Streptomyces lividans, SecG deficient


title: S. coelicolor I32 (degU-) vs M145 wt REP2

description: Biological replicate 2 of 3. Gene expression of S. coelicolor I32 (degU-) versus M145 wt


title: S. coelicolor I32 (degU-) vs M145 wt REP1

description: Biological replicate 1 of 3. Gene expression of S. coelicolor I32 (degU-) versus M145 wt


title: ES1-MSC1-iPS1-MSC1

city: Barcelona

first: Rita

last: Vassena

address: Av. Dr. Aiguader 88

department: Stem Cell Bank

institute: CMRB

hyb_protocol: Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: After quality control of raw data, data were background corrected, quartile- normalized and summarized to a gene level using the robust multi-chip average obtaining a total of 28832 transcript clusters, excluding controls, which roughly correspond to genes. Only transcripts with an intensity signal of more than a 10% of all intensities of the mean of the studied groups and then over 50% of variance from total resting variance were considered for further analysis, which lead to 13 250 transcript clusters. LIMMA was then used to obtain differentially expressed genes between conditions.

source_name: mesenchymal stem cells

label_protocol: 200 ng of total RNA were amplified by Ambion WT Expression Kit and labelled by WT Terminal Labelling Kit

growth_protocol: For embryonic and induced pluripotency stem cells, culture media consisted of: KO-DMEM (Invitrogen), 20% KO serum replacement (Invitrogen), Glutamax (2 mmol/l; Invitrogen), penicillin –streptomycin,non-essential amino acids (Lonza, Verviers, Belgium), 2-mercaptoethanol (0.05 mmol/l, Invitrogen) and bFGF (10 ng/m; Invitrogen) and was changed every 24 h. For mesenchymal stem cells, the culture medium was:   DMEM (Invitrogen, Carlsbad, CA, USA) supplemented with fetal Bovine Serum (15%; Invitrogen)

extract_protocol: Trizol

treatment_protocol: Cell were washed in PBS, trypsinized, briefly centrifuged and the supernatant removed

tag: parentality

value: biparental

value: Secondary mesenchymal stem cells


title: CEN 4

description: control

value: glioma 4

value: AA III


title: pES-MSC1-iPS2-MSC1

value: parthenogenetic


title: ES1-MSC2-iPS1-MSC1


title: CEN 2

description: control

value: glioma 2


title: CEN 3

description: control

value: glioma 3


title: S. lividans strain deficient in SecG versus Wild Type (TK21), rep2

description:
Gene expression of S. lividans deficient in SecG versus Wild Type strain (TK21).
Biological replicate 2 of 3.

tag: strain


title: S. coelicolor M28 (degU+) vs M145 wt REP3

description: Biological replicate 3 of 3. Gene expression of S. coelicolor M28 (degU+) versus M145 wt

value: wild type

value: M28 (degU+)


title: ES1-MSC2-iPS1-MSC2


title: INF 7

description: test

source_name: Infiltration zone

value: glioma 7

value: GB IV


title: INF 6

description: test

value: glioma 6

value: male


title: INF 5

description: test

value: glioma 5


title: S. lividans strain deficient in SipY versus Wild Type (TK21), rep3

description:
Gene expression of S. lividans deficient in SipY versus Wild Type strain (TK21).
Biological replicate 3 of 3.

source_name: Streptomyces lividans, SipY deficient


title: ES1-MSC1-iPS1

source_name: induced pluripotent stem cells

value: female

value: induced pluripotent stem cells


title: INF 4

description: test


title: ES1-MSC1

value: mesenchymal stem cells


title: CEN 1

description: control

value: glioma 1


title: INF 3

description: test


title: INF 2

description: test


title: S. lividans strain deficient in SecG versus Wild Type (TK21), rep1

description:
Gene expression of S. lividans deficient in SecG versus Wild Type strain (TK21).
Biological replicate 1 of 3.


title: INF 1

description: test


title: ES1-MSC2

value: biparental


title: pES-MSC1-iPS1


title: S. lividans strain deficient in SipY versus Wild Type (TK21), rep1

description:
Gene expression of S. lividans deficient in SipY versus Wild Type strain (TK21).
Biological replicate 1 of 3.


title: S. lividans strain deficient in SipY versus Wild Type (TK21), rep2

description:
Gene expression of S. lividans deficient in SipY versus Wild Type strain (TK21).
Biological replicate 2 of 3.


title: pES-MSC2


title: pES-MSC1


title: pES-MSC2-iPS1


title: ES1-MSC2-iPS1


title: ES3

source_name: stem cells

value: embryonic stem cells


title: siRNA-Jmjd6 HUVEC for 48h (exon level) rep2

value: HUVEC

value: siRNA targeting Jmjd6


title: siRNA-Jmjd6 HUVEC for 48h (exon level) rep3


title: pES

value: parthenogenetic


title: ES1


title: ES2