title: tumor cell line GC424 established from the antrum of tumor bearing CEA424-Tag mice, separate culture 2, rep1

description: tumor cell line


title: Choroid plexus 1 day Control Rats MT38, MT39, MT83

status: Public on Aug 02 2012

type: RNA

city: Jefferson

first: John

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

country: USA

institute: National Center for Toxicological Research FDA

hyb_protocol: 1.65 µg cRNA was fragmented and hybridized onto an Agilent 4x44K oligonucleotide microarray in a hybridization oven at 65°C for 17 hr using the Agilent Gene Expression Hybridization Kit (5188-5281).  The hybridized microarrays were disassembled at room temperature in Gene Expression Wash Buffer 1 (5188-5325), and then washed in Gene Expression Wash Buffer 1 at room temperature for 1 min.  This was followed by a wash for 1 min in Gene Expression Wash Buffer 2 (5188-5326) at an elevated temperature (≈31°C) and air dried.  To preserve the fluorescent signal intensity and prevent Cy3 degradation to environmental ozone, the entire procedure with the final drying step and scanning conducted was done inside a low-ozone biobubble (<1 ppb ozone).

scan_protocol: The arrays were scanned on an Axon 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA)

data_processing:
Initially processing used GenePix Pro 6.0 software (Molecular Devices) and background was (determined from median dark corners) subtracted from probe/gene signals
The working microarray dataset was obtained through, background correction, logbase2 (log2) transformation, and normalization. Probes/ID REFs were filtered to include only those genes with official NCBI gene symbols. We included in our analysis each probe for genes with less than 4 probes/ID REFs. For genes with 4 or more probes/ID REFs, we used the signal intensity after for all the probes/ID REFs except for the ones with the minimum and maximum values. Raw expression data was corrected for background signal. To symmetrize the distribution of background-corrected intensity values and stabilize the variance, we transformed gene expression data using log2 transformation and applied quantile normalization (Bolstad et al., 2003).

molecule: total RNA

organism: Rattus norvegicus

source_name: choroid plexus  EIH 1 day post

label_protocol: 500 ng of total RNA was used in the Agilent Quick Amp Labeling Kit according to the manufacturer's instructions.  The cRNA was fluorescently labeled by incorporation of cyanine (Cy)3-CTP.  After purification, using the RNeasy mini kit (Qiagen), cRNA yield and Cy3 incorporation efficiency (specific activity) into the cRNA were determined using a NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies).  All cRNAs had a yield >5 µg and a specific activity of 8–15 pmol/µg

growth_protocol: Animals used in these experiments were NCTR strain of Sprague-Dawley rat kept on a 12hour light cycle 6:00am to 6:00pm

extract_protocol: Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).

treatment_protocol: Tissues (trunk blood collected by decapitation and choroid plexus of the brain) were extracted from 3 month old Sprague-Dawley rats (NCTR strain) at 3 hr or 1 day after saline, environmental hyperthermia or amphetamine exposure after.

tag: tissue

value: choroid plexus from 3 rats

tag: gender

value: male

tag: age

value: 3 months

tag: treatment

value: environmentally induced hyperthermia

tag: time

value: 1 day post

tag: strain

value: Sprague-Dawley


title: Choroid plexus 1 day Control Rats MT71, MT39, MT85


title: tumor cell line GC424 established from the antrum of tumor bearing CEA424-Tag mice, separate culture 1

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

country: Germany

institute: University of Bonn

description: tumor cell line

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using R Statistical language and packages from the Bioconductor project. The given data were normalized in a context of additional arrays, which are not displayed here.

label: biotin

organism: Mus musculus

source_name: antrum of the stomach

label_protocol: Biotinylated cRNA was prepared with the  Illumina® TotalPrep™ RNA Amplification Kit (Applied Biosystems, Darmstadt, Germany).

extract_protocol: RNA was extracted with Nucleospin extraction kit  according to the manufacturer´s protocol ((Machery&Nagel, Düren, Germany). Quality control was performed with denaturing gel electrophoresis and UV measurement.

tag: genetic background

value: 2-6 months

tag: cell line

tag: transfection


title: Choroid plexus 1 day AMPH Rats MT16, MT19, MT47

source_name: choroid plexus  AMPH 1 day post

value: amphetamine toxicity


title: Choroid plexus 1 day AMPH Rats MT55, MT58, MT76


title: 60_TCDD_2 [exiqon]

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

description: Universal Reference RNA is a pool of individual RNA samples

hyb_protocol: Hybridization and washing steps were carried out using Tecan hybridization stations.

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays.

data_processing: The data was normalized by Exiqon using LOESS method and log2 transformation. Depending on the experimental setup and the size of the project customized data analysis is provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA). The "1_Exiqon_" raw data files correspond to the Hy3-labelled test RNA, while the "0_Exiqon_" raw data files correspond to the Hy5-labelled reference RNA.

organism: Danio rerio

source_name: zebrafish embryos,60 hours post-fertilization

label_protocol: miRCURY™ LNA Array Power labeling kit was used.

extract_protocol: Total RNA was isolated using QIAGEN miRNeasy kit. Total RNA was assessed for quality using Bioanalyzer.

treatment_protocol: Zebrafish embryos at 30 hours post-fertilization were exposed to DMSO or TCDD for 1 hour and sampled at 36 hpf and 60 hpf for miRNA expression profiling

value: wildtype TL strain

value: zebrafish embryos

tag: developmental stage

value: 60 hours post-fertilization

value: TCDD

source_name: Universal Reference RNA

tag: reference

value: pool of individual RNA samples


title: 60_TCDD_3 [exiqon]


title: 36_TCDD_1 [exiqon]

source_name: zebrafish embryos,36 hours post-fertilization

value: 36 hours post-fertilization


title: 36_TCDD_2 [exiqon]


title: 36_TCDD_3 [exiqon]


title: 60_DMSO_1 [exiqon]

value: DMSO


title: 60_TCDD_1 [exiqon]


title: 60_DMSO_2 [exiqon]


title: 36_DMSO_3 [exiqon]


title: Choroid plexus 3 hr AMPH Rats MT5, MT6, MT17

source_name: choroid plexus  AMPH 3 hr post

value: 3 hr post


title: Choroid plexus 3 hr AMPH Rats MT18, MT20, MT83


title: Choroid plexus 3 hr EIH Rats MT12, MT13, MT14

source_name: choroid plexus  EIH 3 hr post


title: 36_DMSO_2 [exiqon]


title: Blood 3 hr EIH Rat MT86

source_name: Blood EIH 3 hr post

value: blood from striatum (brain region)


title: Choroid plexus 1 day Control Rats MT11, MT21, MT22

value: choroid plexus from 3 rats


title: 60_DMSO_3 [exiqon]


title: Choroid plexus 1 day AMPH Rats MT7, MT9, MT10

value: male


title: 36_DMSO_1 [exiqon]


title: Choroid plexus 1 day Control Rats MT23, MT25, MT38

value: 3 months


title: Choroid plexus 3 hr EIH Rats MT71, MT82, MT86

value: environmentally induced hyperthermia


title: Choroid plexus 3 hr AMPH Rats MT26, MT75, MT78


title: Choroid plexus 3 hr Control Rats MT34, MT46 & MT47

source_name: choroid plexus  saline 3 hr post

value: saline


title: Choroid plexus 3 hr EIH Rats MT37, MT70, MT72

value: Sprague-Dawley


title: Choroid plexus 3 hr Control Rats MT63, MT64 & MT65


title: Choroid plexus 3 hr Control Rats MT3, MT4 & MT33


title: Choroid plexus 3 hr Control Rats MT1, MT2 & MT31


title: Dhcr7 knockout liver, F300

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 10 µg of purified cRNA was fragmented to uniform size and applied to CodeLink Mouse Whole Genome Microarrays in hybridization buffer. Arrays were hybridized at 37°C for 18 hrs. in a temperature-controlled shaking incubator, washed at 46°C for 1 hr, and stained with Cy5-Streptavidin dye conjugate for 30 min.

scan_protocol: Rinsed and dried arrays were scanned with an Axon GenePix 4000B Microarray Scanner at 5 µm resolution.

data_processing: CodeLink software was used to process the scanned images from arrays (gridding and feature intensity extraction), and the data generated for each probe on the array was analyzed with GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Intensity values were normalized to the 75th percentile intensity of each array.

source_name: Liver, Dhcr7 knockout

label_protocol: Biotin-labelled cRNA was prepared by linear amplification of the poly(A)+ RNA population within the total RNA sample. Briefly, 2 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.

extract_protocol: Total RNA was extracted and purified using RiboPure RNA Isolation (Ambion). Total RNA samples were quantitated by UV spectrophotometry. Quality of total RNA was assessed using an Agilent Bioanalyzer.

tag: strain/background

tag: genotype

value: Dhcr7 knockout

value: embryo E18.5

value: liver


title: Choroid plexus 3 hr EIH Rats MT24, MT40, MT69


title: 60_TCDD_3 [agilent]

description: miRNA expression profiling at 60 hpf, after 1h exposure to DMSO or TCDD at 30 hpf.

hyb_protocol: Hybridization was done at 55 degrees for 18 hours.

scan_protocol: Scanning of the slides was done using Genepix 4000B (Molecular devices)

data_processing: Data was extracted using Agilent Feature Extraction software 9.5. and statistical analysis was conducted using AgiMicroRna package in R (Bioconductor package)

label_protocol: Labeling of RNA was done following Agilent hydridization kit following manufacturer's guidelines

value: wildtype TL strain

value: zebrafish embryos


title: Dhcr7 knockout lung, F300

source_name: Lung, Dhcr7 knockout

value: lung


title: 60_TCDD_2 [agilent]

value: 60 hours post-fertilization

value: TCDD


title: 60_TCDD_1 [agilent]


title: LacZ_siTCONS_0004057

city: Sapporo

first: Masashi

last: Idogawa

country: Japan

institute: Sapporo Medical University

description: Gene expression after the transfection of siTCONS_00004057 and Ad-LacZ infection

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction. The VALUEs in the data matrix were calculated by Limma (R package) for the normalization.

organism: Homo sapiens

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: Hep3B cells were cultured in RPMI1640 with 10% FCS.

extract_protocol: 24h after second transfection, total RNA was extracted by RNeasy mini kit (QIAGEN) according to manufacturer's protocol. RNA was quantified using the NanoDrop spectrophotometer.

treatment_protocol: Hep3B cells were transfected with siRNAs targeting the indicated lincRNAs or negative control. 4h after the transfection, these cells were infected with adenovirus expressing p53 (Ad-p53) or LacZ (Ad-LacZ) as control at 100 moi. 24h after the infection, siRNAs were transfected into cells again.

tag: infection

value: Ad-LacZ


title: Choroid plexus 1 day AMPH Rats MT51, MT53, MT54

value: amphetamine toxicity

value: 1 day post


title: Dhcr7 knockout lung, F297


title: Dhcr7 knockout lung, F299


title: Dhcr7 knockout liver, F297


title: p53_siTCONS_00022563

description: Gene expression after the transfection of siTCONS_00022563 and Ad-p53 infection


title: Dhcr7 knockout brain, F299

source_name: Brain, Dhcr7 knockout

value: brain


title: Dhcr7 knockout brain, F300


title: 60_DMSO_3 [agilent]

value: DMSO


title: p53_siTCONS_0004057

description: Gene expression after the transfection of siTCONS_00004057 and Ad-p53 infection


title: p53_siControl

description: Gene expression after the transfection of siControl and Ad-p53 infection

value: siControl


title: Dhcr7 knockout brain, F297


title: Dhcr7 knockout liver, F299


title: LacZ_siTCONS_00020760

description: Gene expression after the transfection of siTCONS_00020760 and Ad-LacZ infection


title: LacZ_siTCONS_00022563

description: Gene expression after the transfection of siTCONS_00022563 and Ad-LacZ infection


title: LacZ_siControl

description: Gene expression after the transfection of siControl and Ad-LacZ infection


title: p53_siTCONS_00020760

description: Gene expression after the transfection of siTCONS_00020760 and Ad-p53 infection


title: Serie A, HepG2 exposed to BaP for 12h, biological rep 3

city: Maastricht

first: Christina

last: Magkoufopoulou

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Trizol extraction was performed using the miRNAeasy kit from qiagen accoding to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO, 0.5% EtOH or PBS)

tag: compound, dose

value: BaP


title: Wild-type liver, F295

source_name: Liver, wild-type

value: wild-type


title: 60_DMSO_2 [agilent]


title: Choroid plexus 3 hr AMPH Rats MT48, MT49, MT52

value: choroid plexus from 3 rats

value: male

value: 3 months

value: 3 hr post

value: Sprague-Dawley


title: Wild-type brain, F295

source_name: Brain, wild-type

value: embryo E18.5


title: NHDF_1408 c1_rep2

city: Strasbourg

first: Frédéric

last: Schramm

address: 3, rue Koeberlé

country: France

institute: EA4438 Physiopathologie et médecine translationnelle, Groupe borréliose de Lyme

description: Biological replicate 2 of 2 for  1408 c1 stimulation of NHDF cells

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQOR (TM) Skin Microarrays Human Antisense using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized PIQOR (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR (TM) microarrays was done using ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Lowess method. For normalisation only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.  All data were further inter-array normalized by median-normalization using BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html).

source_name: NHDF cells, 1408 c1-stimulated

label_protocol: 1 µg of the respective T7-amplified RNA was labeled by reverse transcription either with Cy3-dCTPs or Cy5-dCTPs as described elsewhere (PMID: 8800675)

extract_protocol: RNA was isolated using a standard Trizol extraction protocol

tag: strain origin

value: 1408 c1  isolated from skin biopsy of acrodermatitis chronica atrophians

source_name: NHDF cells, unstimulated control

tag: cell references


title: 36_TCDD_2 [agilent]

description: miRNA expression profiling at 36hpf, after 1h exposure to DMSO or TCDD at 30 hpf.

value: wildtype TL strain

tag: tissue

value: zebrafish embryos

value: 36 hours post-fertilization


title: NHDF_1408 c1_rep1

description: Biological replicate 1 of 2 for 1408 c1 stimulation of NHDF cells


title: 36_TCDD_3 [agilent]

value: TCDD


title: 60_DMSO_1 [agilent]

value: 60 hours post-fertilization


title: 36_TCDD_1 [agilent]


title: Wild-type lung, F295

source_name: Lung, wild-type

value: lung


title: NHDF_Pbre c4_rep2

description: Biological replicate 2 of 2 for  Pbre c4 stimulation of NHDF cells

source_name: NHDF cells, Pbre c4-stimulated

value: Pbre c4  isolated from skin biopsy of erythema migrans


title: NHDF_Pbre c4_rep1

description: Biological replicate 1 of 2 for Pbre c4 stimulation of NHDF cells


title: Wild-type liver, F294

value: liver


title: NHDF_N40_rep1

description: Biological replicate 1 of 2 for N40 stimulation of NHDF cells

source_name: NHDF cells, N40-stimulated

value: N40 isolated from a tick


title: 36_DMSO_2 [agilent]

value: DMSO


title: NHDF_N40_rep2

description: Biological replicate 2 of 2 for N40 stimulation of NHDF cells


title: 36_DMSO_3 [agilent]


title: Wild-type lung, F294

value: wild-type


title: Wild-type liver, F293


title: 36_DMSO_1 [agilent]


title: 28591-31B

status: Public on Aug 01 2012

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: CD68 and NOS2 were measured by qRT-PCR and dichotomized as high/low based on median expression levels Crohn's disease and Ulcerative Colitis separately.  Missing values were dropped from analysis.

hyb_protocol: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing: The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 2.0). Intensities of each spot were the median intensities of foreground. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. Each microRNA oligo is represented by quadruplicate spots on these arrays as two distant pairs of two adjacent spots. If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package and all replicate spots were averaged. Batch effects caused by day to day variability was removed using Partek Genomics Suite.

label: Biotin

source_name: Colon Tissue from patient with Ulcerative Colitis

label_protocol: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.

tag: disease

value: Ulcerative Colitis

tag: dategroup of array

value: E

tag: cd68 expression

value: High

tag: nos2 expression


title: 28588-32A


title: 28589-32B


title: 28590-31A

value: Low


title: Wild-type brain, F294

value: embryo E18.5

value: brain


title: 28567-30B

source_name: Colon Tissue from patient with Crohn's disease

value: Chron's Disease


title: 28574-29A


title: 28575-29B


title: 28563-30A


title: 28593-28B


title: 28592-28A


title: 28581-26B


title: 28580-26A


title: Wild-type lung, F293


title: 21596-15B


title: Wild-type brain, F293


title: 28582-23A

value: D


title: 21595-15A


title: 21582-14A


title: 21464-14B


title: 28583-23B


title: 28584-25A

value: F


title: 28586-21A


title: 21448-19A


title: 21449-19B


title: 21594-18B


title: 21473-18A


title: 21585-17A


title: 21586-17B


title: 21444-10B


title: 19697-11A


title: 21465-13B


title: 21467-12B


title: 28585-25B


title: 21584-12A


title: 21466-13A


title: 21576-10A


title: 19695-09A


title: 19696-09B


title: 21457-08B


title: 21456-08A


title: 28587-21B


title: 19700-11B


title: 19702-07A


title: 19703-07B


title: 19692-06B

value: C


title: 21575-04B


title: 19691-06A


title: 19693-05A


title: 19705-03B


title: 21443-01B


title: 21455-02B


title: 21442-01A


title: 27747-50N


title: 21557-02A


title: 27744-49F


title: 27746-50F


title: 27745-49N


title: 24951-47N


title: 27256-48F


title: 24950-47F


title: 19694-05B


title: 19704-03A


title: 23287-45N


title: 23286-45F


title: 27257-48N


title: 21636 41F

value: B


title: 21637 41N


title: 22214-44F


title: 22215-44N


title: 21633 40N


title: 21632 40F


title: 21629 38N


title: 21628 38F


title: 21623 37N


title: 21631 39N


title: 21630 39F


title: 21622 37F


title: 21574-04A


title: 21604 32F


title: 21606 33F


title: 21603 31N


title: 21602 31F


title: 21601 30N


title: 21614 36F


title: 21610 34N


title: 21598 29N


title: 21607 33N


title: 21605 32N


title: 21615 36N


title: 21523-25F

value: A


title: 21600 30F


title: 21524-25N


title: 21597 29F


title: 21462-23N


title: 21460-23F


title: 21451-22F


title: 21454-22N


title: 16549-12N


title: 16550-12F


title: 21609 34F


title: 16509-11N


title: 19067-19N


title: 21445-21F


title: 16508-11F


title: 16491-08N


title: 19068-19F


title: 16490-08F


title: 21446-21N


title: 16467-01F


title: 16470-02N


title: 16469-02F


title: 16482-04N


title: 16487-06N


title: 16481-04F


title: 16486-06F


title: CRS019

type: genomic

city: San Francisco

first: Susan

last: Lynch

state: CA

address: 513 Parnassus Ave, S357D

department: Medicine

institute: University of California at San Francisco

description: 16S ribosomal RNA gene is amplified for phylogenetic profiling.

hyb_protocol: Hybridization solution contained 100 mM MES (N-morpholinoethanesulfonic acid), 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20, pH 6.6 (referred to as 1× MES). In addition, the solution contained 0.1 mg of herring sperm DNA (Promega)/ml, 0.5 mg of acetylated bovine serum albumin (BSA; Invitrogen)/ml, and 50 pM control oligonucleotide B2 (Affymetrix). Hybridization was carried out at 45°C for 16 h with mixing on a rotary mixer at 60 rpm. Following hybridization, the sample solution was removed and the array was washed and stained in a GeneChip Fluidics Station (Affymetrix). In brief, to enhance the signals, 10 μg of streptavidin (Vector Laboratories)/ml and 2 mg of BSA/ml in 1× MES were used as the first staining solution. After the streptavidin solution was removed, an antibody mix was added as the second stain, containing 0.1 mg of goat immunoglobulin G (Sigma-Aldrich)/ml, 5 μg of biotinylated anti-streptavidin antibody (Vector Laboratories)/ml, and 2 mg of BSA/ml in 1× MES. Nucleic acid was fluorescently labeled by incubation with 10 μg of streptavidin R-phycoerythrin conjugate (Molecular Probes)/ml and 2 mg of BSA/ml in 1× MES.

scan_protocol: The arrays were scanned at 570 nm with a resolution of 3 μm with a GeneChip Scanner 3000 (GCS 3000; Affymetrix).

data_processing: Fluorescence intensities were normalized to the spike-in control oligonucleotides using a custom Perl script.

molecule: genomic DNA

organism: human nasopharyngeal metagenome

source_name: mucosal brushing, healthy

label_protocol: DNA was resuspended in 96 μl of 30 mM MOPS (morpholinepropanesulfonic acid, pH 7.5), and 4 μl of a 50 mM polyethylene oxide-iodoacetyl biotin (Pierce Chemical) solution was added to introduce the biotin label. The reaction mixture was incubated at 37°C for 1 h, and the labeled DNA was subsequently ethanol precipitated and washed twice with 70% ethanol to remove unreacted biotin compounds.

extract_protocol: Mucosal brushings were transferred to Lysis Matrix B (MP Biomedicals, OH)  tubes containing 600ul RLT buffer (Qiagen). Samples were subjected to 30 seconds of bead beating at 5.5 m/second, followed by centrifugation for one minute at 2000 rpm. Supernatant was transferred to the AllPrep DNA spin column and nucleic acid purification was carried out according to the manufacturer’s instructions (Qiagen). Nucleic acid concentrations were determined using a NanoDrop spectophotometer (Thermo Scientific).

treatment_protocol: Sinus brushings were obtained during functional endoscopic sinus surgery (FESS) of CRS patients, or surgery for non-CRS complaints, e.g. obstructive sleep apnea or post-traumatic malocclusion, in healthy subjects. Endoscopically-guided brush samples of mucosal surfaces of the lateral, central, and medial portions of the maxillary sinus were obtained and pooled together in 1 ml of RNALater and placed at 4 °C for 24 hours prior to storage at -80 °C until processed for analysis.

value: mucosal brushing of the maxillary sinus

tag: disease status

value: healthy


title: CRS020


title: CRS008

source_name: mucosal brushing, CRS

value: chronic rhinosinusitis (CRS)


title: CRS018


title: CRS014


title: CRS013


title: CRS010


title: CRS017


title: CRS011


title: 16468-01N


title: CRS002


title: CRS004


title: CRS006


title: CRS009


title: CRS007


title: M199 culture, biological rep 4

city: Dublin

first: Graham

middle: P

last: Pidgeon

address: St. James' Hospital

country: Ireland

institute: Trinity College Dublin

description:
OE33_control_4
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with M199 medium.

hyb_protocol: Affymetrix hybridization manual One-Cycle Kit using commercial HWS reagent (#900720)

scan_protocol: Affymetrix 3000G scanner

data_processing: The data were quality checked and analyzed using the R programming language.  The GCRMA algorithm was used for background correction and normalization [the gcrma library (version 2.22.0) for R (version 2.12.2)].

source_name: OE33 following 24 hour culture with M199 medium

label_protocol: Affymetrix One-Cycle Labeling Kit

growth_protocol: OE33 was maintained in RPMI medium supplemented with penicillin, streptomycin and foetal bovine serum (FBS) (10%). OE33 was used at 70% confluency and serum starved (0.5% FBS) for 16 hours prior to treatment.

extract_protocol: RNA was extracted from OE33 using Qiagen Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: OE33 was seeded at 50,000 cells per insert in a non-contact transwell system. Visceral adipose tissue (1 g)  or M199 medium were placed in well beneath the insert. OE33 were co-cultured for 24 hours prior to RNA extraction.

tag: cell type

value: oesophageal adenocarcinoma tumour cells


title: adipocyte co-culture, biological rep 4

description:
OE33_adipocyte_4
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes.

source_name: OE33 following 24 hour co-culture with adipocytes from patient

treatment_protocol: OE33 was seeded at 50,000 cells per insert in a non-contact transwell system.  Adipocytes (250,000) or M199 medium were placed in well beneath the insert. OE33 were co-cultured for 24 hours prior to RNA extraction.

tag: cell line

tag: co-cultured with

value: adipocytes from patient 4


title: M199 culture, biological rep 3

description:
OE33_control_3
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with M199 medium.


title: adipose tissue co-culture, biological rep 6

description:
OE33_adipose tissue_6
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants.

source_name: OE33 following 24 hour co-culture with visceral adipose tissue from patient

value: visceral adipose tissue from patient 6


title: adipose tissue co-culture, biological rep 4

description:
OE33_adipose tissue_4
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants.

value: visceral adipose tissue from patient 4


title: R.decussatus gills non infected by Perkinsus olseni (C1)

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: gills RNA of Ruditapes decussatus (Perkinsus sp. free)

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization  of gPRocessed signalusing R2.6.1 statistical software

organism: Ruditapes decussatus

source_name: C1  R.decussatus sampled in Perkinsus olseni free gills , collected during August 2009 in the Ria Formosa, Portugal

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted using Trizol reagent and after purified with according to QiAgen RNeasy MiniKit protocol for RNA purification

tag: geographical location

value: R. decussatus sampled in Ria Formosa

value: non-infected

value: gills


title: M199 culture, biological rep 4 (re-analysis)


title: R.decussatus gills infected by Perkinsus olseni (5INF)

description: Perkinsus olseni infected gills RNA of Ruditapes decussatus

source_name: 5INF R.decussatus sampled in Perkinsus olseni infected gills, collected during August 2009 in the Ria Formosa, Portugal

value: infected with P. olseni


title: M199 culture, biological rep 1

description:
OE33_control_1
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with M199 medium.


title: adipose tissue co-culture, biological rep 1

description:
OE33_adipose tissue_1
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants.

value: visceral adipose tissue from patient 1


title: IMR+OHT si cdhl/IMR+OHT si control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: S635 Median column as Red signal and S532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: IMR+OHT si control

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: IMR90-ER:RAS cells were cultured in DME supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using TRIZOL according to the manufacturer's instructions.

treatment_protocol: IMR-90-ER:Ras cells were cultured for 6 days  with or without 4-hydroxytamoxifen (OHT) and were subsequently subjected to transfection with siRNA oligos against fzr1/cdh1 or control for three times (at 2 day intervals).

value: Human lung embryonic fibroblast

tag: strain

tag: sample type

value: senescent cells

source_name: IMR+OHT si cdhl

value: fzr1/cdh1 depleted senescent cells


title: R.decussatus gills non infected by Perkinsus olseni (C6)

source_name: C6  R.decussatus sampled in Perkinsus olseni free gills , collected during August 2009 in the Ria Formosa, Portugal


title: M199 culture, biological rep 2

description:
OE33_control_2
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with M199 medium.


title: adipocyte co-culture, biological rep 1

description:
OE33_adipocyte_1
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes.

value: adipocytes from patient 1


title: adipocyte co-culture, biological rep 3

description:
OE33_adipocyte_3
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes.

value: adipocytes from patient 3


title: R.decussatus gills non infected by Perkinsus olseni (C2)

source_name: C2  R.decussatus sampled in Perkinsus olseni free gills , collected during August 2009 in the Ria Formosa, Portugal


title: adipocyte co-culture, biological rep 6

description:
OE33_adipocyte_6
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes.

value: adipocytes from patient 6


title: adipose tissue co-culture, biological rep 5

description:
OE33_adipose tissue_5
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants.

value: visceral adipose tissue from patient 5


title: adipose tissue co-culture, biological rep 3

description:
OE33_adipose tissue_3
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants.

value: visceral adipose tissue from patient 3


title: adipocyte co-culture, biological rep 2

description:
OE33_adipocyte_2
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes.

value: oesophageal adenocarcinoma tumour cells

value: adipocytes from patient 2


title: IMR si control2/IMR+OHT si control

source_name: IMR si control2

value: proliferating cells


title: R.decussatus gills infected by Perkinsus olseni (1INF)

source_name: 1INF R.decussatus sampled in Perkinsus olseni infected gills, collected during August 2009 in the Ria Formosa, Portugal


title: R.decussatus gills infected by Perkinsus olseni (2INF)

source_name: 2INF R.decussatus sampled in Perkinsus olseni infected gills, collected during August 2009 in the Ria Formosa, Portugal


title: R.decussatus gills infected by Perkinsus olseni (20INF)

source_name: 20INF R.decussatus sampled in Perkinsus olseni infected gills collected during August 2009 in the Ria Formosa, Portugal


title: R.decussatus gills non infected by Perkinsus olseni (C22)

source_name: C22  R.decussatus sampled in Perkinsus olseni free gills , collected during August 2009 in the Ria Formosa, Portugal


title: adipocyte co-culture, biological rep 5

description:
OE33_adipocyte_5
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes.

value: adipocytes from patient 5


title: M199 culture, biological rep 1 (re-analysis)


title: adipose tissue co-culture, biological rep 2

description:
OE33_adipose tissue_2
Gene expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants.

value: visceral adipose tissue from patient 2


title: M199 culture, biological rep 2 (re-analysis)


title: M199 culture, biological rep 3 (re-analysis)


title: GSY2168-ScerCEN.PK-SbayCBS7001-Hybrid

city: Stanford

first: Barbara

last: Dunn

department: Genetics

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84276.gif

hyb_protocol: not provided

scan_protocol: Agilent methods

data_processing: Agilent lowess-normalized

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng

label_protocol: not provided

extract_protocol: not provided

tag: reference

organism: Saccharomyces bayanus x Saccharomyces cerevisiae

source_name: GSY2168 genomic DNA, HaeIII-cut, 100 ng

tag: genotype

value: GSY2168 S. cerevisiae-S. bayanus interspecific hybrid

tag: condition

value: Control


title: EtOH400gen-V4-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95327.gif

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 350 ng each

source_name: GCEP EtOH400gen-V4-2 HaeIII-cut genomic DNA 600 ng

value: clone b (batch 4 at generation 400)

value: EtOH


title: T500-Ba-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86352.gif

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng each

source_name: T500-Ba-New genomic DNA, HAEIII-cut, 100ng

value: clone a repl (batch 2 at generation 500)

value: High Temperature


title: T500-Ac

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84288.gif

value: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng

source_name: T500-Ac genomic DNA, HAEIII-cut, 100ng

value: clone c (batch 1 at generation 500)


title: GSY2160-Scerevisiae-CEN.PK

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84286.gif

organism: Saccharomyces cerevisiae

source_name: GSY2160 genomic DNA, HAEIII-cut, 100ng

value: GSY2160 S. cerevisiae CEN.PK parent


title: Slide17-SelfControl

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84283.gif

value: self-self control(mix of dna from parental cerevisiae and bayanus strains)


title: T500-Ab-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86349.gif

value: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng each

source_name: T500-Ab-New genomic DNA, HAEIII-cut, 100ng

value: clone b repl (batch 1 at generation 500)


title: FounderHybrid-F2a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84282.gif

source_name: Founder Hybrid F2a genomic DNA, HaeIII-cut, 100 ng

value: Viable F2 spore


title: T500-Ba

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84277.gif

source_name: T500-Ba genomic DNA, HaeIII-cut, 100 ng

value: clone a (batch 2 at generation 500)


title: CI25E delta Cot1 replicate 3

city: Toulouse

first: Laurent

last: Benbadis

address: 135 Av de Rangueil

institute: LISBP INSA CNRS UMR5504

description: CI25E delta Cot1 harvested in exponential phase biological replicate 3

hyb_protocol: Hybridation was carried out in an automatic hybridization chamber ( Discovery from Ventana Medical System) for 10h at 42°C. After hybridization, slides were washed in 2xSSC/0,2%(v/v)SDS, immersed briefly in iso-propanol and then dried under a stream of air.

scan_protocol: The hybridization signal were detected by scanning using GenePix 4000B laser Scanner (Axon Instruments) and transformed to numerical values using the integrated GenePix software version 3.01

data_processing: R computing environnement was used for background subtraction and weighted global median and quantile normalization was performed

source_name: Total RNA from CI25E delta Cot1 exponential phase

label_protocol: Incorporation of cyanine-3 and cyanine-5 was performed during reverse transcription of total RNA using label star reverse transcriptase (quiagen). Labelled cDNA from the microarray experiment was purified on minElute spin columns (quiagen).

growth_protocol: Microarray analysis was performed on wt and cobalt resistant mutants. These cultures were grown in three replicates on 100ml YMM at 500 ml flask to their exponential phase DO600=3 ; 3 107 cells/ml

extract_protocol: Total RNA from three independant cultures were extracted using the SV Total RNA isolation System (promega)

tag: genetic variant

value: CI25E delta Cot1


title: FounderHybrid-F2c

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84279.gif

source_name: Founder Hybrid F2c genomic DNA, HaeIII-cut, 100 ng


title: EtOH400gen-V6-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95333.gif

value: S.cerevisae and S. bayanus sonicated genomic DNA 350 ng each

source_name: GCEP EtOH400gen-V6-4 HaeIII-cut genomic DNA 600 ng

value: clone d (batch 6 at generation 400)


title: T500-Aa

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84290.gif

source_name: T500-Aa genomic DNA, HAEIII-cut, 100ng

value: clone a (batch 1 at generation 500)


title: T500-Cc-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86356.gif

source_name: T500-Cc-New genomic DNA, HAEIII-cut, 100ng

value: clone c repl (batch 3 at generation 500)


title: T500-Bc

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84278.gif

source_name: T500-Bc genomic DNA, HaeIII-cut, 100 ng

value: clone c (batch 2 at generation 500)


title: CI25E delta Cot1 replicate 2

description: CI25E delta Cot1harvested in exponential phase biological replicate 2


title: T500-Ca-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86353.gif

source_name: T500-Ca-New genomic DNA, HAEIII-cut, 100ng

value: clone a repl (batch 3 at generation 500)


title: T500-Ab

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84280.gif

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng

source_name: T500-Ab genomic DNA, HaeIII-cut, 100 ng

value: clone b (batch 1 at generation 500)


title: FounderHybrid-F2b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84287.gif

source_name: Founder Hybrid F2b genomic DNA, HAEIII-cut, 100ng

value: Control


title: WT replicate 3

description: WT harvested in exponential phase biological replicate 3

source_name: Total RNA from WT CEN-PK exponential phase

value: WT CEN-PK


title: WT replicate 2

description: WT harvested in exponential phase biological replicate 2


title: CI25E delta Cot1 replicate 1

description: CI25E delta Cot1 harvested in exponential phase biological replicate 1

source_name: Total RNA from CI25E deltaCot1 exponential phase


title: T500-Bb

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84291.gif

value: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng

source_name: T500-Bb genomic DNA, HAEIII-cut, 100ng

value: clone b (batch 2 at generation 500)

value: High Temperature


title: T500-Cb

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84285.gif

source_name: T500-Cb genomic DNA, HAEIII-cut, 100ng

value: clone b (batch 3 at generation 500)


title: T500-Bb-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86354.gif

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng each

source_name: T500-Bb-New genomic DNA, HAEIII-cut, 100ng

value: clone b repl (batch 2 at generation 500)


title: GSY2161-Sbayanus-CBS7001

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84289.gif

organism: Saccharomyces bayanus

source_name: GSY2161 genomic DNA, HAEIII-cut, 100ng

value: GSY2161 S. bayanus CBS7001 parent


title: T500-Ca

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84284.gif

source_name: T500-Ca genomic DNA, HAEIII-cut, 100ng

value: clone a (batch 3 at generation 500)


title: EtOH400gen-V5-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95330.gif

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 350 ng each

source_name: GCEP EtOH400gen-V5-3 HaeIII-cut genomic DNA 600 ng

value: clone c (batch 5 at generation 400)

value: EtOH


title: T500-Aa-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86355.gif

value: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng each

source_name: T500-Aa-New genomic DNA, HAEIII-cut, 100ng

value: clone a repl (batch 1 at generation 500)


title: GSY2168-ScerCEN.PK-SbayCBS7001-Hybrid-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95332.gif

value: S.cerevisae and S. bayanus sonicated genomic DNA 350 ng each

source_name: GCEP Parent F1 Hybrid HaeIII-cut genomic DNA 600 ng

value: GSY2168 S. cerevisiae-S. bayanus interspecific hybrid-rep1


title: T500-Cb-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86350.gif

source_name: T500-Cb-New genomic DNA, HAEIII-cut, 100ng

value: clone b repl (batch 3 at generation 500)


title: Slide24-SelfControl

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89610.gif

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 250 ng each

value: self-self control(mix of dna from parental cerevisiae and bayanus strains)


title: CI25E replicate 3

description: CI25E harvested in exponential phase biological replicate 3

source_name: Total RNA from CI25E exponential phase


title: T500-Bc-New

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86351.gif

source_name: T500-Bc-New genomic DNA, HAEIII-cut, 100ng

value: clone c repl (batch 2 at generation 500)


title: T500-Cc

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-07/84281.gif

source_name: S.cerevisae and S. bayanus sonicated genomic DNA 100 ng

source_name: T500-Cc genomic DNA, HaeIII-cut, 100 ng

value: clone c (batch 3 at generation 500)


title: CI25E replicate 1

description: CI25E harvested in exponential phase biological replicate 1


title: 14286621 - 8days 1G R1 vs 8days microgravity R1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Action of microgravity on root development

hyb_protocol: 8days microgravity R1 Cy5 / 8days 1G R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: 8days microgravity R1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - Media=MS10 hygrometry=100% Temperature=25+/- 2°C Light=70µE m-2s-1

extract_protocol: 8days microgravity R1:15ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:simulated microgravity 8days - environmental treatment - microgravity,microgravity:time 8day . Seeds of Arabidopsis were sterilized then placed on solid Murashige and Skoog Medium supplemented with 10% sucrose. Arabidopsis were grown on horizontal or vertical clinostat for 4, 8 or 12 days. Seedlings on horizontal clinostat were in simulated microgravity and seedlings on vertical clinostat are considered as a control. Plants were placed in a plant growth chamber under a 16h photoperiod at 25+/- 2 °C with 70 µE m-2s-1.

tag: ecotype

value: Columbia

tag: age

tag: developmental stage

value: (Boyes et al. Plant Cell 2001):boyes:0.5

source_name: 8days 1G R1

extract_protocol: 8days 1G R1:15ug. (Qiagen_RNeasy.pdf)

value: 8day a


title: WT replicate 1

description: WT harvested in exponential phase biological replicate 1

source_name: Total RNA from WT CEN-PK exponential phase

value: WT CEN-PK


title: 14286620 - 4days microgravity R2 vs 4days 1G R2

hyb_protocol: 4days 1G R2 Cy5 / 4days microgravity R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4days 1G R2

extract_protocol: 4days 1G R2:15ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:simulated microgravity 4days - environmental treatment - microgravity,microgravity:time 4day . Seeds of Arabidopsis were sterilized then placed on solid Murashige and Skoog Medium supplemented with 10% sucrose. Arabidopsis were grown on horizontal or vertical clinostat for 4, 8 or 12 days. Seedlings on horizontal clinostat were in simulated microgravity and seedlings on vertical clinostat are considered as a control. Plants were placed in a plant growth chamber under a 16h photoperiod at 25+/- 2 °C with 70 µE m-2s-1.

source_name: 4days microgravity R2

extract_protocol: 4days microgravity R2:15ug. (Qiagen_RNeasy.pdf)

value: 4day a


title: 14286622 - 8days microgravity R1 vs 8days 1G R1

hyb_protocol: 8days 1G R1 Cy5 / 8days microgravity R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286624 - 8days microgravity R2 vs 8days 1G R2

hyb_protocol: 8days 1G R2 Cy5 / 8days microgravity R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 8days 1G R2

extract_protocol: 8days 1G R2:15ug. (Qiagen_RNeasy.pdf)

source_name: 8days microgravity R2

extract_protocol: 8days microgravity R2:15ug. (Qiagen_RNeasy.pdf)


title: 14286619 - 4days 1G R2 vs 4days microgravity R2

hyb_protocol: 4days microgravity R2 Cy5 / 4days 1G R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286626 - 12days microgravity R1 vs 12days 1G R1

hyb_protocol: 12days 1G R1 Cy5 / 12days microgravity R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 12days 1G R1

extract_protocol: 12days 1G R1:15ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:simulated microgravity 12days - environmental treatment - microgravity,microgravity:time 12day . Seeds of Arabidopsis were sterilized then placed on solid Murashige and Skoog Medium supplemented with 10% sucrose. Arabidopsis were grown on horizontal or vertical clinostat for 4, 8 or 12 days. Seedlings on horizontal clinostat were in simulated microgravity and seedlings on vertical clinostat are considered as a control. Plants were placed in a plant growth chamber under a 16h photoperiod at 25+/- 2 °C with 70 µE m-2s-1.

source_name: 12days microgravity R1

extract_protocol: 12days microgravity R1:15ug. (Qiagen_RNeasy.pdf)

value: 12day a


title: 14286623 - 8days 1G R2 vs 8days microgravity R2

hyb_protocol: 8days microgravity R2 Cy5 / 8days 1G R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286617 - 4days microgravity R1 vs 4days 1G R1

hyb_protocol: 4days 1G R1 Cy5 / 4days microgravity R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4days 1G R1

extract_protocol: 4days 1G R1:15ug. (Qiagen_RNeasy.pdf)

source_name: 4days microgravity R1

extract_protocol: 4days microgravity R1:15ug. (Qiagen_RNeasy.pdf)


title: 14286625 - 12days 1G R1 vs 12days microgravity R1

hyb_protocol: 12days microgravity R1 Cy5 / 12days 1G R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286614 - 12days 1G R2 vs 12days microgravity R2

hyb_protocol: 12days microgravity R2 Cy5 / 12days 1G R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 12days microgravity R2

extract_protocol: 12days microgravity R2:15ug. (Qiagen_RNeasy.pdf)

source_name: 12days 1G R2

extract_protocol: 12days 1G R2:15ug. (Qiagen_RNeasy.pdf)


title: 14286616 - 4days 1G R1 vs 4days microgravity R1

hyb_protocol: 4days microgravity R1 Cy5 / 4days 1G R1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286615 - 12days microgravity R2 vs 12days 1G R2

hyb_protocol: 12days 1G R2 Cy5 / 12days microgravity R2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CI25E replicate 2

description: CI25E harvested in exponential phase biological replicate 2

source_name: Total RNA from CI25E exponential phase


title: ROSE cells treated with scrambled siRNA

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

description:
Rose 199 cells ( Adams and Auersperg, 1985)
ROSE cells treated with Scrambled siRNA

hyb_protocol: Samples were hybridized accordingly to the manufacturer’s protocol using Hybridization Wash and Stain Kit (Affymetrix). The hybridization at 45°C and 60 rpm for 16hrs, the staining and washing were carried out as recommended by Affymetrix (Affymetrix).

scan_protocol: GeneChipScanner 3000 G7 system (Affymetrix)

data_processing:
CEL files were analysed using bioconductor oligo package in  R, normalisation was done using rma with target probeset.
pd.ragene.1.0.st.v1
pd.ragene.1.0.st.v1

label_protocol: 5.5 μg of the single-strand DNA was enzymatically fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and biotinylated using the WT terminal labeling kit (Affymetrix).

growth_protocol: RAS-ROSE abd ROSE cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) supplemented with 10 % fetal calf serum (FCS) (Sigma-Aldrich), 2 mM Ultraglutamine 1 (Lonza, BioWhittaker), and 100 units/ml penicillin/streptomycin (Biochrom AG) (standard medium). The medium was supplemented with G418 (400 μg/μl).  45000 RAS-ROSE cells were seeded into 6-well plates (BD Falcon) in standard medium 24 h prior to transient transfection of siRNA.

extract_protocol: Total RNA extraction were prepared using TRIZOL reagent (Invitrogen) according to the manufacturer’s instructions. CDNA synthesis was performed using the Ambion® WT Expression Kit (Ambion).

treatment_protocol: Cells were transfected twice with an interval of 24 h using Oligofectamine (Invitrogen), serum-free OptiMEM (Invitrogen) and a final siRNA concentration of 1 nM according to the manufacturer's specifications. After 4 h of incubation, FCS was added to the medium at a final concentration of 10 %.

value: Rose 199 cells

tag: treatment

value: with Scrambled siRNA


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with JunB siRNA 1

growth_protocol: RAS-ROSE cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) supplemented with 10 % fetal calf serum (FCS) (Sigma-Aldrich), 2 mM Ultraglutamine 1 (Lonza, BioWhittaker), and 100 units/ml penicillin/streptomycin (Biochrom AG) (standard medium). The medium was supplemented with G418 (400 μg/μl).  45000 RAS-ROSE cells were seeded into 6-well plates (BD Falcon) in standard medium 24 h prior to transient transfection of siRNA.

value: RAS-ROSE:KRAS-transformed Rose 199 cells

value: with JunB siRNA 1


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Fosl1 siRNA 2

value: with Fosl1 siRNA 2


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Hmga2 siRNA 2

value: with Hmga2 siRNA 2


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Hmga2 siRNA 1

value: with Hmga2 siRNA 1


title: lung cancer patient after chemotherapy-17

city: Kaohsiung

first: yungche

last: chen

address: 123, Ta-Pei Rd. Niao-Sung Dist.

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: PBMC

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: All the cancer patients received first line chemotherapy with CDDP (mean dose 70 mg/m2) on day 1 plus GEM (GEMZAR®; EliLilly and Company, Indianapolis, IN; mean dose 1000 mg/m2) on day 1, 8, and 15 of a 28-day cycle. Treatment was planned for a maximum of six cycles (median 4, range 1-6) unless discontinued because of progressive disease, stable disease, unacceptable toxicity, or death.

tag: tissue

value: PBMC

value: after chemotherapy

tag: tumor stage

tag: Sex

value: male

tag: treatment response

value: partial response


title: lung cancer patient after chemotherapy-16

value: female

value: stable disease


title: lung cancer patient after chemotherapy-14


title: RAS-ROSE cells treated with scrambled siRNA

description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Scrambled siRNA

tag: cell line


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Otx1 siRNA 1

value: with Otx1 siRNA 1


title: lung cancer patient after chemotherapy-15


title: lung cancer patient after chemotherapy-11


title: lung cancer patient after chemotherapy-10


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with JunB siRNA 2

value: with JunB siRNA 2


title: lung cancer patient after chemotherapy-12


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Gfi1 siRNA 1

value: with Gfi1 siRNA 1


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Gfi1 siRNA 2

value: with Gfi1 siRNA 2


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Klf6 siRNA 2

value: with Klf6 siRNA 2


title: RAS-ROSE cells treated with Scrambled siRNA

source_name: scramble

value: with Scrambled siRNA


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Klf6 siRNA 1

value: RAS-ROSE:KRAS-transformed Rose 199 cells

value: with Klf6 siRNA 1


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with RelA siRNA 2

value: with RelA siRNA 2


title: lung cancer patient after chemotherapy-09


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Otx1 siRNA 2

value: with Otx1 siRNA 2


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with RelA siRNA 1

value: with RelA siRNA 1


title: lung cancer patient before chemotherapy-27

value: PBMC

value: before chemotherapy


title: lung cancer patient after chemotherapy-08

value: after chemotherapy

value: male


title: lung cancer patient before chemotherapy-28

value: female


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with transfection reagents only

source_name: Mock

value: with transfection reagents only


title: lung cancer patient before chemotherapy-32

value: progressive disease


description:
RAS-ROSE: KRAS-transformed Rose 199 cells (Tchernitsa et al., 2004; Adams and Auersperg, 1985)
RAS-ROSE cells treated with Fosl1 siRNA 1

value: with Fosl1 siRNA 1


title: lung cancer patient before chemotherapy-31

value: partial response


title: healthy subject-19

value: healthy


title: lung cancer patient before chemotherapy-29

value: stable disease


title: healthy subject-15


title: healthy subject-16


title: healthy subject-20


title: healthy subject-17


title: healthy subject-18


title: lung cancer patient before chemotherapy-30


title: healthy subject-11


title: healthy subject-10


title: healthy subject-14


title: healthy subject-12


title: healthy subject-09


title: lung cancer patient before chemotherapy-23


title: lung cancer patient before chemotherapy-21


title: lung cancer patient before chemotherapy-22


title: lung cancer patient before chemotherapy-24


title: lung cancer patient before chemotherapy-25


title: lung cancer patient before chemotherapy-19


title: lung cancer patient before chemotherapy-26


title: lung cancer patient before chemotherapy-18


title: healthy subject-07


title: healthy subject-05


title: lung cancer patient before chemotherapy-17


title: lung cancer patient before chemotherapy-16


title: lung cancer patient before chemotherapy-13


title: healthy subject-02


title: healthy subject-01


title: lung cancer patient before chemotherapy-14


title: healthy subject-03


title: lung cancer patient before chemotherapy-15


title: lung cancer patient before chemotherapy-12


title: healthy subject-13


title: healthy subject-08


title: lung cancer patient before chemotherapy-11


title: healthy subject-06


title: lung cancer patient before chemotherapy-20


title: healthy subject-04


title: lung cancer patient after chemotherapy-07


title: lung cancer patient after chemotherapy-05


title: lung cancer patient after chemotherapy-03


title: lung cancer patient after chemotherapy-04


title: lung cancer patient after chemotherapy-01


title: lung cancer patient before chemotherapy-07


title: lung cancer patient before chemotherapy-10


title: lung cancer patient after chemotherapy-06


title: lung cancer patient before chemotherapy-08


title: lung cancer patient after chemotherapy-02


title: lung cancer patient before chemotherapy-09


title: lung cancer patient before chemotherapy-03


title: lung cancer patient before chemotherapy-06


title: lung cancer patient before chemotherapy-05


title: lung cancer patient after chemotherapy-13


title: CM3p

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

institute: Goethe-University Frankfurt

description: Polysomal RNA from MCF7 cells treated for 4h with supernatant of TPA-activated U937 monocyte derived macrophages (replicate 3).

data_processing: Statistical analysis was done with the statistical computing environment R (version 2.8.1). Additional software packages were taken from the Bioconductor project.

source_name: MCF7 cells

extract_protocol: RNA was extracted with NaAce/Isopranol, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: MCF7 cells

tag: rna

value: Polysomal RNA

tag: conditioned medium

value: supernatants of U937 monocytes


title: Ctr2p

description: Polysomal RNA from MCF7 cells treated for 4h with supernatant of U937 monocytes (replicate 2).

value: supernatants of TPA-activated U937 monocyte-derived macrophages


title: lung cancer patient before chemotherapy-01


title: CM3t

description: Total RNA from MCF7 cells treated for 4h with supernatant of TPA-activated U937 monocyte derived macrophages (replicate 3).

value: Total RNA


title: lung cancer patient before chemotherapy-02


title: CM1t

description: Total RNA from MCF7 cells treated for 4h with supernatant of TPA-activated U937 monocyte derived macrophages (replicate 1).


title: Ctr2t

description: Total RNA from MCF7 cells treated for 4h with supernatant of U937 monocytes (replicate 2).


title: CM2p

description: Polysomal RNA from MCF7 cells treated for 4h with supernatant of TPA-activated U937 monocyte derived macrophages (replicate 2).


title: Ctr3t

description: Total RNA from MCF7 cells treated for 4h with supernatant of U937 monocytes (replicate 3).


title: CM2t

description: Total RNA from MCF7 cells treated for 4h with supernatant of TPA-activated U937 monocyte derived macrophages (replicate 2).


title: Ctr3p

description: Polysomal RNA from MCF7 cells treated for 4h with supernatant of U937 monocytes (replicate 3).


title: Ctr1t

description: Total RNA from MCF7 cells treated for 4h with supernatant of U937 monocytes (replicate 1).


title: CM1p

description: Polysomal RNA from MCF7 cells treated for 4h with supernatant of TPA-activated U937 monocyte derived macrophages (replicate 1).


title: Ctr1p

description: Polysomal RNA from MCF7 cells treated for 4h with supernatant of U937 monocytes (replicate 1).


title: lung cancer patient before chemotherapy-04


title: Splenic Marginal Zone Lymphoma P69

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

country: Spain

institute: Center for Applied Medical Research (Cima)

hyb_protocol: Hybridization methods and analytical procedures have been described elsewhere: Snijder AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001;29:263-264.

scan_protocol: Images of the arrays were captured using a custom-built CCD camera

data_processing: UCSF SPOT software was used to analyze the images

source_name: Splenic Marginal Zone Lymphoma P69

label_protocol: genomic DNA from SMZL samples and reference genomic DNA were labeled by random priming using Cy3 and Cy5, respectively

extract_protocol: genomic DNA were extracted from mononuclear cells of Splenic Mariginal Zone Lymphoma patients obtained from spleen, peripheral blood or bone marrow using standard methods

tag: disease state

value: Splenic Marginal Zone Lymphoma

source_name: reference genomic DNA

value: reference


title: Splenic Marginal Zone Lymphoma P71

source_name: Splenic Marginal Zone Lymphoma P71

tag: sample type


title: Splenic Marginal Zone Lymphoma P74

source_name: Splenic Marginal Zone Lymphoma P74


title: Splenic Marginal Zone Lymphoma P67

source_name: Splenic Marginal Zone Lymphoma P67


title: Splenic Marginal Zone Lymphoma P68

source_name: Splenic Marginal Zone Lymphoma P68


title: Splenic Marginal Zone Lymphoma P72

source_name: Splenic Marginal Zone Lymphoma P72


title: Splenic Marginal Zone Lymphoma P75

source_name: Splenic Marginal Zone Lymphoma P75


title: Splenic Marginal Zone Lymphoma P73

source_name: Splenic Marginal Zone Lymphoma P73


title: Splenic Marginal Zone Lymphoma P66

source_name: Splenic Marginal Zone Lymphoma P66


title: Splenic Marginal Zone Lymphoma P62

source_name: Splenic Marginal Zone Lymphoma P62


title: Splenic Marginal Zone Lymphoma P65

source_name: Splenic Marginal Zone Lymphoma P65


title: Splenic Marginal Zone Lymphoma P58

source_name: Splenic Marginal Zone Lymphoma P58


title: Splenic Marginal Zone Lymphoma P63

source_name: Splenic Marginal Zone Lymphoma P63


title: Splenic Marginal Zone Lymphoma P61

source_name: Splenic Marginal Zone Lymphoma P61


title: Splenic Marginal Zone Lymphoma P56

source_name: Splenic Marginal Zone Lymphoma P56


title: Splenic Marginal Zone Lymphoma P59

source_name: Splenic Marginal Zone Lymphoma P59


title: Splenic Marginal Zone Lymphoma P60

source_name: Splenic Marginal Zone Lymphoma P60


title: Splenic Marginal Zone Lymphoma P53

source_name: Splenic Marginal Zone Lymphoma P53

source_name: reference genomic DNA


title: Splenic Marginal Zone Lymphoma P55

source_name: Splenic Marginal Zone Lymphoma P55


title: Splenic Marginal Zone Lymphoma P54

source_name: Splenic Marginal Zone Lymphoma P54


title: Splenic Marginal Zone Lymphoma P48

source_name: Splenic Marginal Zone Lymphoma P48


title: Splenic Marginal Zone Lymphoma P49

source_name: Splenic Marginal Zone Lymphoma P49


title: Splenic Marginal Zone Lymphoma P51

source_name: Splenic Marginal Zone Lymphoma P51


title: Splenic Marginal Zone Lymphoma P52

source_name: Splenic Marginal Zone Lymphoma P52


title: Splenic Marginal Zone Lymphoma P50

source_name: Splenic Marginal Zone Lymphoma P50


title: Splenic Marginal Zone Lymphoma P46

source_name: Splenic Marginal Zone Lymphoma P46


title: Splenic Marginal Zone Lymphoma P45

source_name: Splenic Marginal Zone Lymphoma P45


title: Splenic Marginal Zone Lymphoma P43

source_name: Splenic Marginal Zone Lymphoma P43


title: Splenic Marginal Zone Lymphoma P41

source_name: Splenic Marginal Zone Lymphoma P41


title: Splenic Marginal Zone Lymphoma P34

source_name: Splenic Marginal Zone Lymphoma P34


title: Splenic Marginal Zone Lymphoma P36

source_name: Splenic Marginal Zone Lymphoma P36


title: Splenic Marginal Zone Lymphoma P35

source_name: Splenic Marginal Zone Lymphoma P35


title: Splenic Marginal Zone Lymphoma P44

source_name: Splenic Marginal Zone Lymphoma P44


title: Splenic Marginal Zone Lymphoma P38

source_name: Splenic Marginal Zone Lymphoma P38


title: Splenic Marginal Zone Lymphoma P39

source_name: Splenic Marginal Zone Lymphoma P39

source_name: reference genomic DNA


title: Splenic Marginal Zone Lymphoma P40

source_name: Splenic Marginal Zone Lymphoma P40


title: Splenic Marginal Zone Lymphoma P33

source_name: Splenic Marginal Zone Lymphoma P33


title: Splenic Marginal Zone Lymphoma P32

source_name: Splenic Marginal Zone Lymphoma P32


title: Splenic Marginal Zone Lymphoma P47

source_name: Splenic Marginal Zone Lymphoma P47


title: Splenic Marginal Zone Lymphoma P37

source_name: Splenic Marginal Zone Lymphoma P37


title: Splenic Marginal Zone Lymphoma P29

source_name: Splenic Marginal Zone Lymphoma P29


title: Splenic Marginal Zone Lymphoma P31

source_name: Splenic Marginal Zone Lymphoma P31


title: Splenic Marginal Zone Lymphoma P30

source_name: Splenic Marginal Zone Lymphoma P30


title: Splenic Marginal Zone Lymphoma P19

source_name: Splenic Marginal Zone Lymphoma P19


title: Splenic Marginal Zone Lymphoma P21

source_name: Splenic Marginal Zone Lymphoma P21


title: Splenic Marginal Zone Lymphoma P20

source_name: Splenic Marginal Zone Lymphoma P20


title: Splenic Marginal Zone Lymphoma P22

source_name: Splenic Marginal Zone Lymphoma P22


title: Splenic Marginal Zone Lymphoma P17

source_name: Splenic Marginal Zone Lymphoma P17


title: Splenic Marginal Zone Lymphoma P9

source_name: Splenic Marginal Zone Lymphoma P9


title: Splenic Marginal Zone Lymphoma P25

source_name: Splenic Marginal Zone Lymphoma P25


title: Splenic Marginal Zone Lymphoma P26

source_name: Splenic Marginal Zone Lymphoma P28


title: Splenic Marginal Zone Lymphoma P11

source_name: Splenic Marginal Zone Lymphoma P11

source_name: reference genomic DNA


title: Splenic Marginal Zone Lymphoma P28


title: Splenic Marginal Zone Lymphoma P8

source_name: Splenic Marginal Zone Lymphoma P8


title: Splenic Marginal Zone Lymphoma P15

source_name: Splenic Marginal Zone Lymphoma P15


title: Splenic Marginal Zone Lymphoma P24

source_name: Splenic Marginal Zone Lymphoma P24


title: Splenic Marginal Zone Lymphoma P6

source_name: Splenic Marginal Zone Lymphoma P6


title: Splenic Marginal Zone Lymphoma P7

source_name: Splenic Marginal Zone Lymphoma P7


title: Splenic Marginal Zone Lymphoma P16

source_name: Splenic Marginal Zone Lymphoma P16


title: Splenic Marginal Zone Lymphoma P13

source_name: Splenic Marginal Zone Lymphoma P13


title: Splenic Marginal Zone Lymphoma P4

source_name: Splenic Marginal Zone Lymphoma P4


title: Splenic Marginal Zone Lymphoma P14

source_name: Splenic Marginal Zone Lymphoma P14


title: Splenic Marginal Zone Lymphoma P5

source_name: Splenic Marginal Zone Lymphoma P5


title: Splenic Marginal Zone Lymphoma P18

source_name: Splenic Marginal Zone Lymphoma P18


title: Splenic Marginal Zone Lymphoma P1

source_name: Splenic Marginal Zone Lymphoma P1


title: Splenic Marginal Zone Lymphoma P3

source_name: Splenic Marginal Zone Lymphoma P3


title: Splenic Marginal Zone Lymphoma P10

source_name: Splenic Marginal Zone Lymphoma P10


title: Splenic Marginal Zone Lymphoma P12

source_name: Splenic Marginal Zone Lymphoma P12


title: arcA strain to H2O2 rep4

city: Hangzhou

first: haichun

last: gao

address: 388 Yuhangtang Rd.

country: China

institute: Zhejiang University

description: Biological replicate 4 of 4

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

organism: Shewanella oneidensis

source_name: 5 min H2O2 treated cells

growth_protocol: Grow in LB to Mid-log phase

treatment_protocol: 200uM H2O2 (final concentration) was added to cultures

value: arcA mutant

source_name: untreated cells

value: untreated


title: arcA strain to H2O2 rep2

description: Biological replicate 2 of 4


title: arcA strain to H2O2 rep3

description: Biological replicate 3 of 4


title: arcA strain to H2O2 rep1

description: Biological replicate 1 of 4


title: Splenic Marginal Zone Lymphoma P2

source_name: Splenic Marginal Zone Lymphoma P2

source_name: reference genomic DNA


title: wild type to H2O2 rep4

description: Biological replicate 4 of 4

value: Wild type


title: D5_basal_ganglia_HIV infected_w/HAD_w/ HIVE

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

description:
72G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Human U133 2.0 plus GeneChips were washed and stained.

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

data_processing: The data were analyzed with Affy package for R programming.

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

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

tag: race

value: Hispanic

tag: gender

value: male

tag: phenotype

value: HIV Infected with HAD and encephalitis

value: Basal ganglia


title: D3_basal_ganglia_HIV infected_w/HAD_w/ HIVE

description:
70G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain

value: White


title: D2_basal_ganglia_HIV infected_w/HAD_w/ HIVE

description:
69G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: wild type to H2O2 rep2

description: Biological replicate 2 of 4

tag: genotype


title: D1_basal_ganglia_HIV infected_w/HAD_w/ HIVE

description:
68G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: wild type to H2O2 rep3

description: Biological replicate 3 of 4


title: MSC/KDM6Bsh BMP 4hr

city: Los Angeles

first: Bo

last: Yu

address: CHS 33-030, 10833 Le Conte Ave,

institute: UCLA School of Dentistry

description: Gene expression data from KDM6B knockdown MSCs after 4hr of BMP4/7 treatment.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: hmesenchymal stem cells; KDM6B knockdown, BMP 4hr

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

growth_protocol: Cells were grown in a humidified 5% CO2 incubator in MEM alpha modified Eagle's medium supplemented with 15% fetal bovine serum

extract_protocol: Rneasy Kit (QiaGen) extraction of total RNA was performed according to the manufacturer's protocol

treatment_protocol: BMP4/7 (150ng/ul) for 4hrs

tag: cell type

value: bone marrow derived mesenchymal stem cells

tag: knockdown

tag: time


title: wild type to H2O2 rep1

description: Biological replicate 1 of 4

tag: treatment


title: C7_basal_ganglia_HIV infected_w/HAD_w/o HIVE

description:
67G757.CEL
Gene expression data from the white matter of HIV infected HAD human brain

tag: age

value: HIV Infected with HAD

tag: tissue


title: C6_basal_ganglia_HIV infected_w/HAD_w/o HIVE

description:
66G759.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: MSC/KDM4Bsh BMP 24hr

description: Gene expression data from KDM4B knockdown MSCs after 24hr of BMP4/7 treatment.

source_name: hmesenchymal stem cells; KDM4B knockdown, BMP 24hr

treatment_protocol: BMP4/7 (150ng/ul) for 24hrs


title: MSC/Scrsh, BMP 4hr

description: Gene expression data from control MSCs after 4hr of BMP4/7 treatment.

source_name: hmesenchymal stem cells, Scramble shRNA control, BMP4/7 4hr

value: Scramble shRNA


title: C5_basal_ganglia_HIV infected_w/HAD_w/o HIVE

description:
65G759.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: C1_basal_ganglia_HIV infected_w/HAD_w/o HIVE

description:
61G759.CEL
Gene expression data from the white matter of HIV infected HAD human brain

value: Black


title: C4_basal_ganglia_HIV infected_w/HAD_w/o HIVE

description:
64G759.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: B4_basal_ganglia_HIV infected

description:
58G759.CEL
Gene expression data from the white matter of HIV infected human brain

value: HIV Infected


title: C3_basal_ganglia_HIV infected_w/HAD_w/o HIVE

description:
63G759.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: MSC/Scrsh, BMP 24hr

description: Gene expression data from control MSCs after 24hr of BMP4/7 treatment.

source_name: hmesenchymal stem cells, Scramble shRNA control, BMP4/7 24hr


title: B3_basal_ganglia_HIV infected

description:
57G759.CEL
Gene expression data from the white matter of HIV infected human brain


title: MSC/Scrsh, BMP 0hr

description: Gene expression data from control MSCs after 0hr of BMP4/7 treatment.

source_name: Scramble shRNA control, BMP4/7 0hr


title: MSC/KDM6Bsh BMP 0hr

description: Gene expression data from KDM6B knockdown MSCs after 0hr of BMP4/7 treatment.

source_name: hmesenchymal stem cells; KDM6B knockdown, BMP 0hr


title: MSC/KDM4Bsh BMP 0hr

description: Gene expression data from KDM4B knockdown MSCs after 0hr of BMP4/7 treatment.

source_name: hmesenchymal stem cells; KDM4B knockdown, BMP 0hr


title: MSC/KDM6Bsh BMP 24hr

description: Gene expression data from KDM6B knockdown MSCs after 24hr of BMP4/7 treatment.

source_name: hmesenchymal stem cells; KDM6B knockdown, BMP 24hr


title: D4_basal_ganglia_HIV infected_w/HAD_w/ HIVE

description:
71G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: B5_basal_ganglia_HIV infected

description:
59G759.CEL
Gene expression data from the white matter of HIV infected human brain


title: C2_basal_ganglia_HIV infected_w/HAD_w/o HIVE

description:
62G759.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: MSC/KDM4Bsh BMP 4hr

description: Gene expression data from KDM4B knockdown MSCs after 4hr of BMP4/7 treatment.

source_name: hmesenchymal stem cells; KDM4B knockdown, BMP 4hr


title: B2_basal_ganglia_HIV infected

description:
56G759.CEL
Gene expression data from the white matter of HIV infected human brain


title: B1_basal_ganglia_HIV infected

description:
55G759.CEL
Gene expression data from the white matter of HIV infected human brain


title: A2_basal_ganglia_Control

description:
50G759.CEL
Gene expression data from the white matter of control human brain

value: normal (control)


title: A5_basal_ganglia_Control

description:
53G759.CEL
Gene expression data from the white matter of control human brain


title: C5_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE

description:
41G758.CEL
Gene expression data from the white matter of HIV infected HAD human brain

value: HIV Infected with neurocognitive impairment (HAD:HIV-associated dementia)

value: Frontal cortex


title: D3_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE

description:
46G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain

value: HIV Infected with HAD and HIV encephalitis (HIVE)


title: A1_basal_ganglia_Control

description:
49G759.CEL
Gene expression data from the white matter of control human brain


title: A3_basal_ganglia_Control

description:
51G759.CEL
Gene expression data from the white matter of control human brain


title: C3_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE

description:
39G758.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: B4_Frontal_Cortex_HIV infected

description:
34G758.CEL
Gene expression data from the white matter of HIV infected human brain


title: C1_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE

description:
37G758.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: B3_Frontal_Cortex_HIV infected

description:
33G758.CEL
Gene expression data from the white matter of HIV infected human brain


title: B2_Frontal_Cortex_HIV infected

description:
32G758.CEL
Gene expression data from the white matter of HIV infected human brain


title: C6_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE

description:
42G758.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: D4_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE

description:
47G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: C7_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE

description:
43G757.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: D5_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE

description:
48G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: C2_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE

description:
38G758.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: C4_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE

description:
40G758.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: D2_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE

description:
45G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain