title: 2101_plant_s_3 with array type SUNFLOWER from Affymetrix


title: L63-1

status: Public on Sep 01 2012

type: genomic

city: College Park

first: Juan

last: Luo

state: MD

address: RM1122, BLDG142, Animal & Avian Sciences

department: Animal & Avian Sciences

country: USA

institute: University of Maryland

description: CGH in L63-1

data_processing: The hybridization, normalization and segmentation analysis were performed by NimbleGen Systems Inc. (Madison, USA). A detailed description of their technical specifics can be found on http://www.nimblegen.com/products/lit/lit.html.Briefly, the segments with five or more probes having a mean log2 ratio greater than ±0.5 (0.5_5) were chosen as candidate CNVs.

molecule: genomic DNA

organism: Gallus gallus

source_name: Genomic DNA from L63 red blood cells

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

extract_protocol: Genomic DNA from 20μl red blood cells was extracted using the DNeasy bBlood & Tissue Mini Kit (Qiagen, USA).

tag: cell line

value: L63, highly resistant to MD

tag: cell type

value: red blood cells

source_name: Genomic DNA from Red Junglefowl red blood cells

tag: reference

value: DNA from Red Junglefowl


title: HD, biological replicate 1

type: RNA

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

description: messenger RNA

hyb_protocol: Followed manufacturer's instructions.

scan_protocol: Followed manufacturer's instructions.

data_processing: The probe cell intensity data from the Affymetrix GeneChips was normalized and annotated following previously published methods (Pacheco, Houseman et al. 2011 (PMID 21674046)). The linear models of microarray analysis (LIMMA) procedure (Smyth, Yang et al. 2003) (R package limma) was used to fit a linear regression model for each transcript on the Affymetrix GeneChip Array for each pair of treatment and controls. The p-values were adjusted for multiple comparisons with the qvalue package in R (Storey 2002) and the log2 expression ratios were transformed into fold change values.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: sperm, HD

label_protocol: Followed manufacturer's instructions.

extract_protocol:
Sperm isolation protocol: The cauda epididymides were punctured repeatedly with 30 or 26 gauge needles and put into micro-centrifuge tubes containing 1 mL phosphate-buffered saline (PBS). The samples were incubated in a water bath at 37°C for 10 minutes to aid sperm diffusion from the tissue. The tubes were spun for 3 minutes at 300 xg to pellet the epididymal pieces and the supernatant containing sperm were put into a new tube. The tube was spun for an additional 5 minutes at 2000 xg to pellet the sperm and the supernatant was removed. One mL of lysis buffer (0.15 M ammonium chloride, 10 mM potassium bicarbonate, 0.1 mM EDTA) was added to the sperm pellet, incubated on the bench top for 30 seconds and spun at 16,100 xg for 1 minute. The pellet was washed with 1 mL of PBS and spun at 16,100 xg for 1 minute.

RNA was extracted from the fresh sperm using the mirVana miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA), which separated the RNA into large and small fractions, per manufacturer’s instructions.

tag: strain

value: Fischer 344

tag: tissue

value: sperm

tag: treatment

tag: recovery

value: no


title: M1+IL6 H3K4me1

city: Bethesda

first: Junfang

last: Zhang

address: 37 Convent Dr.

department: NCI-CCR

institute: NIH

description: M1 cells treated with IL-6 for 5 days

hyb_protocol: A total of 3 µg of labeled ChIP and input DNA was cohybridized to the chip for 40 hours at 65°C

scan_protocol: scanned on an Agilent Scanner with Agilent Scan Control 7.0 software

data_processing: Data was extracted with Feature Extraction 9.1 software and analyzed using ChIP Analytics 1.3 software (Agilent).

organism: Mus musculus

source_name: M1+IL6 H3K4me1

label_protocol: A total of 2.5 µg of amplified DNA was labeled with Cy3 (input) or Cy5 (IP) dUTP (PerkinElmer Life and Analytical Sciences) using the CGH labeling kit (Invitrogen).

growth_protocol:
M1cells were seeded in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum and treated with interleukin-6 (IL-6) for5 days
M1cells were seeded in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum and treated with interleukin-6 (IL-6) for5 days
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

extract_protocol: Chromatin immunoprecipitation assays was conducted as previously described (Paul, Bies et al. 2010). Cells were fixed in 0.8% formaldehyde for 6 minutes at room temperature. After lysis, samples were sonicated to a size range of 200 to 1000 bp. Chromatin (150-200 µg) was immunoprecipitated with antibodies for H3K4me3 (Abcam, ab8580), H3K4me1 (Abcam, ab8895), H3K9/14Ac (Upstate, 06-599), CTCF (Abcam, ab70303), H3K9me3 (Abcam, ab8898), H3K27me3 (Upstate,17-622),or rabbit IgG (Sigma-Aldrich, 15006). A 10% aliquot was removed as an input fraction. ChIP DNA and input DNA were amplified using WGA2 kit (Sigma-Aldrich).

treatment_protocol: For cell differentiation, M1 cells were seeded at a density of 1-2 x 105 cells / ml in medium containing interleukin-6 (IL-6) for 4-5 days.

tag: c-myb expression

value: No

tag: antibody

source_name: M1+IL6 Input


title: biological replicate 2: 72h DFO 20µM+FAC 20µM

city: RENNES

first: DOYARD

last: Mathilde

address: rue Henri Le Guilloux

country: France

institute: INSERM

description:
gene expression after 72h of DFO 20µM+FAC 20µM treatment
265_2.txt
DFO+FAC_2

hyb_protocol: 1,65μg of each sample cRNA were hybridized using in situ Gene Expression Hybridization kit on Agilent Human Whole Genome Microarrays 4 × 44 K at 60°C, during 17h at 10rpm in the dark.

scan_protocol: Slides were scanned with the dynamic autofocus G2565BA Agilent scanner. Probe feature information was extracted using the Agilent Feature Extraction software v.10.7.

data_processing: Raw intensities were log2-transformed and normalized (median centering within and between arrays) with GeneSpring GX software v11.5.

label: Cy 3

organism: Homo sapiens

label_protocol: Total RNA (350ng) were amplified and labelled using a One Color Agilent’s low RNA Imput Linear Amplification Kit PLUS according to the manufacturer protocol (Agilent).

growth_protocol: The osteoblast-like MG-63 cells were maintained in minimum essential medium supplemented with 10% fetal bovine serum, 2mM L-Glutamine, 1% non essential amino acids and 1% penicillin/streptomycin.

extract_protocol: Total RNAs were extracted using the SV Total RNA Isolation System (Promega®).

treatment_protocol: Ferric Ammonium Citrate and/or Desferioxamine were added or not during three days each day when cells reached confluence.

value: MG-63 osteoblastic cell line


title: 2515_plant_i_3 with array type SUNFLOWER from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: The aim of this project is to assess the possibility of implementing transcriptomic studies on sunflower plants grown in field assays. Data obtained from plants under drought in the glasshouse have already obtained. We intend to use these results as a template and see if the field offers the possibility of carrying these studies. In order to do so, treatment-effect as well as intra and inter-plot variability will be assessed.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: caulin leaf - - Plants were grown at INRA in Auzeville (Haute Garonne, France). They were sown on 7th May 2009 and the tissue used for the chip hybridizations was harvested on 30th July 2009, that is 85-day-long cultivation.

treatment_protocol: Name:IRRIGATION - environmental treatment - hydrometry,tr_m,water:quantity 1 time 30day .  TR_M. Il correspond au ratio entre levapotranspiration réelle et levapotrnaspiration maximale. En étant un ratio, il ny a pas dunités. On nutilise pas water donc, en tant que facteur.

tag: harvest date

tag: age

tag: developmental stage

value: flowering stage (Boyes et al. Plant Cell 2001)

tag: condition

value: irrigation


title: 3006_plant_s_1 with array type SUNFLOWER from Affymetrix


title: biological replicate 5: 72h DFO 20µM

description:
gene expression after 72h of DFO 20µM treatment
266_4.txt
DFO_5

source_name: biological replicate 5: 72h DFO 20µM


title: biological replicate 4: 72h DFO 20µM

description:
gene expression after 72h of DFO 20µM treatment
127_1.txt
DFO_4

source_name: biological replicate 4: 72h DFO 20µM


title: biological replicate 1: 72h DFO 20µM+FAC 20µM

description:
gene expression after 72h of DFO 20µM+FAC 20µM treatment
127_4.txt
DFO+FAC_1


title: WMG300 ETIC-2

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description:
ETIC replicate 4
5773678003_F

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

label: streptavidin Cy3

source_name: epithelial tumor initiating cell culture

label_protocol: As suggested by illumina

extract_protocol: RNA was extracted with the Macherey-Nagel  NucleoSpin RNA II kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: monolayer cultured cell in presence of ROCK inhbitor


title: WMG300-902-2

description:
902 replicate 2
5773678003_H


title: WMG300-902-1

description:
902 replicate 1
5773678003_G


title: 0806_pool_s_1 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:ABSENCE OF IRRIGATION - environmental treatment - abiotic stress,water:time 30day .

value: absence of irrigation


title: M1 H3K4me1

description: untreated myeloblastic M1 cells

source_name: M1 H3K4me1

growth_protocol:
M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum
M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

value: Myeloid M1

value: Yes

source_name: M1 Input


title: 1612_pool_i_2 with array type SUNFLOWER from Affymetrix


title: biological replicate 3: 72h DFO 20µM

description:
gene expression after 72h of DFO 20µM treatment
315_3.txt
DFO_3

source_name: biological replicate 3: 72h DFO 20µM


title: biological replicate 2: 72h DFO 20µM

description:
gene expression after 72h of DFO 20µM treatment
314_2.txt
DFO_2

source_name: biological replicate 2: 72h DFO 20µM


title: Stage3 vs Stage1

city: Bunkyo-ku

first: Saneyuki

last: Kawabata

state: Tokyo

address: 1-1-1 Yayoi

country: Japan

institute: University of Tokyo

hyb_protocol: Microarray hybridizations and labeling were performed using the 3DNA array 50 kit ver. 2 (Genisphere, USA) according to the manufacturer’s instructions. cDNA hybridisations were performed using the formamide buffer supplied in the kit for 16-17 hours at 45C. The 3DNA probe hybridization was performed at 45C for 3-4 hours.

scan_protocol: Images were quantified using Agilent Feature Extraction Software ver. 10.7.3.1

data_processing: Background corrections were not performed. When the spot signal intensity was lower than 1.5 times the intensity of the background in more than 5 arrays out of 8 arrays, signal data for that spot was removed. M values (log2-transformed ratio of the signals for both channels) were calculated and normalised spatially within the arrays using the rlowess function of the R package ‘maanova’ (Wu et al., 2003). Between-array normalization and statistical analysis were performed using the ‘limma’ R package (Smyth, 2004, 2005; Smyth and Speed, 2003). To compare expression changes during the four developmental stages, three contrasts of log-transformed microarray signal intensities, i.e., Stage2-Stage1, Stage3-Stage1, and Stage4-Stage1, were calculated as log10 ratios (M values)['log10_three_stage_comparison.txt available on Series record].

organism: Eustoma russellianum

label_protocol: RNA was reverse-transcribed using SuperScript III Reverse Transcriptase (Invitrogen) at 45C for 2 hours.

growth_protocol: Seedlings of Eustoma grandiflorum ‘Azuma no Murasaki’ were grown on peat moss-based media at 20-25˚C. Two months after germination, the seedlings were transplanted to a 1:2 mixture of peat-based Soil Mix (Sakata, Yokohama, Japan) and granulated soil Engei Baido (Kureha, Tokyo, Japan) and grown in growth room maintained at 25ºC with a 14/10 hr light/dark cycle at 10,000 lx supplied with metal halide lamps (ECO-CERA II, GS-Yuasa).

extract_protocol: Total RNA was extracted according to a CTAB protocol. Three-gram samples were ground into powder in liquid nitrogen, mixed with 30 ml of 2X CTAB solution (1.4 M NaCl, 0.1 M Tris-HCl pH 9.5, 20 mM EDTA, 2% CTAB, and 1% 2-mercaptoethanol), and incubated at 65C for 10 min. The solution was centrifuged at 5,000 rpm for 10 min at room temperature. The supernatant was collected and extracted with a 25:25:1 mixture of phenol/chloroform/isoamyl alcohol (PCI). RNA was precipitated by the addition of propanol. The precipitate was resuspended in 2.0 ml of water and precipitated with 2 M LiCl, followed by a series of PCI and chloroform extractions. Finally, the sample was collected by ethanol precipitation and resolved in 50 μl of water.

treatment_protocol: Petal samples were collected at the end of the light period for the four flower developmental stages defined as follows: Stage 1 - closed buds 1.8 ± 1 mm in length and 7 ± 1 mm in width; Stage 2 - closed buds 3.5 ± 1 mm in length and 11 ± 1 mm in width; Stage 3 - unfolding has begun, partially pigmented; and Stage 4 - fully open corolla, stamen and pistils matured, and pigmentation completed. Petal samples from three separate flowers at the same developmental stage were combined as one biological replicate, and four replicates were prepared for microarray hybridization.

tag: cultivar

value: Azuma no Murasaki

value: petal

value: 3:unfolding has begun, partially pigmented

value: 1:closed buds 1.8±1 mm in length and 7±1 mm in width


title: WMG316 ETIC-2

description:
ETIC replicate 2
5773678003_D


title: Stage4 vs Stage2

value: 4:fully open corolla, stamen and pistils matured, and pigmentation completed

value: 2:closed buds 3.5±1 mm in length and 11±1 mm in width


title: 0712_pool_i_1 with array type SUNFLOWER from Affymetrix


title: 1706_pool_s_2 with array type SUNFLOWER from Affymetrix


title: biological replicate 1: 72h DFO 20µM

description:
gene expression after 72h of DFO 20µM treatment
262_3.txt
DFO_1

source_name: biological replicate 1: 72h DFO 20µM


title: WMG300 ETIC-1

description:
ETIC replicate 3
5773678003_E


title: biological replicate 5: 72h FAC 20µM

description:
gene expression after 72h of FAC 20µM treatment
316_4.txt
FAC20_5

source_name: biological replicate 5: 72h FAC 20µM


title: 2515_pool_i_3 with array type SUNFLOWER from Affymetrix


title: Stage2 vs Stage3


title: WMG316 ETIC-1

description:
ETIC replicate 1
5773678003_C


title: 3006_pool_s_4 with array type SUNFLOWER from Affymetrix


title: biological replicate 4: 72h FAC 20µM

description:
gene expression after 72h of FAC 20µM treatment
262_4.txt
FAC20_4

source_name: biological replicate 4: 72h FAC 20µM


title: WMG300 MTIC-2

description:
MTIC replicate 2
5773678003_B

source_name: mesodermal tumor initiating cell culture

value: monolayer cultured cells


title: Stage1 vs Stage3


title: 2915_plant_i_1 with array type SUNFLOWER from Affymetrix


title: Stage2 vs Stage4


title: Stage3 vs Stage4


title: 2915_plant_i_3 with array type SUNFLOWER from Affymetrix


title: thymic tumor biological gene rep 3

city: Madison

first: Bruce

last: Bagley

state: WI

address: 777 Highland Ave.

department: Pharmacy

institute: University of Wisconsin - Madison

description: three whole thymic tumor samples pooled

hyb_protocol: Samples were hybridized to Mouse Exon 1.0 ST arrays at 45°C for 16 hours following all procedures outlined in the GeneChip Whole Transcript Sense Target Labeling Assay Manual for Mouse Exon 1.0 ST Arrays.

scan_protocol: GeneChips scanned on the GC3000 G7 Scanner

data_processing:
The data were normalized using rma as implemented in the xps system, available at Bioconductor (www.bioconductor.org).
pd.moex.1.0.st.v1
pd.moex.1.0.st.v1
Signal estimates normalized using Bioconductor (http://www.bioconductor.org/biocLite.R)

source_name: thymic tumor

label_protocol: RNA was fragmented and labeled with the GeneChip® WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mouse whole thymus at 21 days of age, or thymic tumors extracted when moribund.

extract_protocol: Mice were genotyped at 14 days of age using tail clip DNA.  All thymuses and thymic tumors were dissected and snap frozen immediately in liquid nitrogen.  Samples were later thawed,  RNA was extracted using Trizol (Invitrogen), and cleaned up using an RNeasy kit (Qiagen).  Amplified sense-strand cDNA was generated using the Ambion® WT expression kit (Applied Biosciences).

value: thymic tumor

tag: Sex

value: female

tag: genotype

value: moribund

tag: model

value: sdl


title: WMG300 MTIC-1

description:
MTIC replicate 1
5222622051_A


title: Stage1 vs Stage2


title: Stage4 vs Stage1


title: 2915_plant_i_4 with array type SUNFLOWER from Affymetrix

value: flowering stage (Boyes et al. Plant Cell 2001)


title: biological replicate 1: 72h FAC 20µM

description:
gene expression after 72h of FAC 20µM treatment
315_4.txt
FAC20_1

source_name: biological replicate 1: 72h FAC 20µM

tag: cell line

value: MG-63 osteoblastic cell line


title: biological replicate 2: 72h FAC 20µM

description:
gene expression after 72h of FAC 20µM treatment
126_4.txt
FAC20_2

source_name: biological replicate 2: 72h FAC 20µM


title: thymic tumor biological gene rep 4

description: three whole thymic tumor samples pooled


title: thymic tumor biological gene rep 1

description: three whole thymic tumor samples pooled


title: biological replicate 3: 72h FAC 20µM

description:
gene expression after 72h of FAC 20µM treatment
267_4.txt
FAC20_3

source_name: biological replicate 3: 72h FAC 20µM


title: 2515_plant_i_4 with array type SUNFLOWER from Affymetrix

value: irrigation


title: thymic tumor biological gene rep 2

description: three whole thymic tumor samples pooled


title: biological replicate 5: 72h FAC 5µM

description:
gene expression after 72h of FAC 5µM treatment
128_3.txt
FAC5_5

source_name: biological replicate 5: 72h FAC 5µM


title: biological replicate 4: 72h FAC 5µM

description:
gene expression after 72h of FAC 5µM treatment
313_2.txt
FAC5_4

source_name: biological replicate 4: 72h FAC 5µM


title: biological replicate 2: 72h FAC 5µM

description:
gene expression after 72h of FAC 5µM treatment
265_4.txt
FAC5_2

source_name: biological replicate 2: 72h FAC 5µM


title: 3006_plant_s_4 with array type SUNFLOWER from Affymetrix

value: absence of irrigation


title: 2915_plant_i_2 with array type SUNFLOWER from Affymetrix


title: biological replicate 3: 72h FAC 5µM

description:
gene expression after 72h of FAC 5µM treatment
264_1.txt
FAC5_3

source_name: biological replicate 3: 72h FAC 5µM


title: pre-leukemic whole thymus biological gene rep 4

description: three whole thymus samples pooled

source_name: pre-leukemic thymus

value: pre-leukemic thymus

value: 21 days


title: 2101_plant_s_4 with array type SUNFLOWER from Affymetrix


title: 2515_plant_i_2 with array type SUNFLOWER from Affymetrix


title: pre-leukemic whole thymus biological gene rep 3

description: three whole thymus samples pooled


title: pre-leukemic whole thymus biological gene rep 1

description: three whole thymus samples pooled


title: pre-leukemic whole thymus biological gene rep 2

description: three whole thymus samples pooled


title: biological replicate 5: Control (FAC 0µM)

description:
gene expression after 72h of FAC 0µM treatment (negative control)
267_2.txt
FAC0_5


title: wild-type whole thymus biological gene rep 4

description: three whole thymus samples pooled

source_name: wild-type thymus

value: wild-type thymus


title: 3006_plant_s_3 with array type SUNFLOWER from Affymetrix

description: The aim of this project is to assess the possibility of implementing transcriptomic studies on sunflower plants grown in field assays. Data obtained from plants under drought in the glasshouse have already obtained. We intend to use these results as a template and see if the field offers the possibility of carrying these studies. In order to do so, treatment-effect as well as intra and inter-plot variability will be assessed.


title: 2101_plant_s_1 with array type SUNFLOWER from Affymetrix


title: biological replicate 3: Control (FAC 0µM)

description:
gene expression after 72h of FAC 0µM treatment (negative control)
126_2.txt
FAC0_3


title: wild-type whole thymus biological gene rep 3

description: three whole thymus samples pooled


title: biological replicate 4: Control (FAC 0µM)

description:
gene expression after 72h of FAC 0µM treatment (negative control)
127_3.txt
FAC0_4


title: biological replicate 2: Control (FAC 0µM)

description:
gene expression after 72h of FAC 0µM treatment (negative control)
314_1.txt
FAC0_2


title: biological replicate 1: 72h FAC 5µM

description:
gene expression after 72h of FAC 5µM treatment
128_2.txt
FAC5_1

source_name: biological replicate 1: 72h FAC 5µM


title: MDS-L_DAC_1

city: Tsukuba

first: Akira

last: Yokoi

state: Ibaraki

address: Tokodai 5-1-3

department: Oncology PCU

institute: Eisai Co., Ltd

description: Gene expression after 7 days in 4nM decitabine treated MDS-L cells

hyb_protocol: 600 ng of Cyanine 3-labeled fragmented cRNA was hybridized to a SurePrint G3 Human GE 8x60K Microarray Kit (Agilent Technologies Inc.) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on a High-Resolution Microarray Scanner (Agilent Technologies Inc.) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies Inc.) using default parameters (Protocol: GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MDS-L, 7 days, decitabine 4nM, replicate 1

label_protocol: Purified 100 ng of total RNA was amplified with a Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies Inc.) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen).

growth_protocol: The MDS-L cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum, 50μM 2-mercaptoethanol, 2.0mM L-glutamine and 100U/ml IL-3.

extract_protocol: Total RNA was extracted with a TRIZOL LS Reagent (Invitrogen) and cleaned up with an RNeasy MinElute Cleanup Kit (Qiagen)

treatment_protocol: The MDS-L cells were treated with DMSO or 4 nM decitabine for 7 days.

value: bone marrow of a patient with MDS

tag: cell line name

value: MDS-L


title: 3006_plant_s_2 with array type SUNFLOWER from Affymetrix


title: 2515_plant_i_1 with array type SUNFLOWER from Affymetrix


title: biological replicate 1: Control (FAC 0µM)

description:
gene expression after 72h of FAC 0µM treatment (negative control)
262_1.txt
FAC0_1


title: MDS-L_DAC_3

source_name: MDS-L, 7 days, decitabine 4nM, replicate 3


title: wild-type whole thymus biological gene rep 2

description: three whole thymus samples pooled


title: MDS-L_Control_2

description: Gene expression after 7 days in DMSO treated MDS-L cells

source_name: MDS-L, 7 days, DMSO, replicate 2


title: wild-type whole thymus biological gene rep 1

description: three whole thymus samples pooled


title: Pool_KO_Sample_17_09_08_14_15_16_11_12_18

status: Public on Aug 31 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of all 9 KO animals

hyb_protocol: Hybridization was performed in the hybridization oven (Agilent Technologies, 17h, 10 rpm, 65˚C)

scan_protocol: Cy3 intensities were detected by a one-color microarray scanner (G2505C, Agilent Technologies) at 5 µm resolution

data_processing: Data were quantile normalized and log2 transformed using R (2.13.0) and Bioconductor package limma (3.8.2)

source_name: hippocampus, CA1 subfield KO

label_protocol: For each array 200 ng RNA was processed and Cy3 labeled by the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: animals were housed at the central animal facility of the University Medical Center Göttingen

extract_protocol: mRNA was isolated from acute hippocampal tissue slices after microdissection of the CA1 subfield. Tissue samples were transferred into trizol buffer, homogenized and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer´s instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf)

value: hippocampus, CA1 subfield

tag: gender

value: male

tag: average age (days after birth)


title: 2101_plant_s_2 with array type SUNFLOWER from Affymetrix


title: 2.0_Sample_17_09_08_KO_1.2

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of 3 KO animals

tag: strain

tag: tissue


title: 1.3_Sample_10_13_23_WT_2.4

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of yet another 3 WT animals

source_name: hippocampus, CA1 subfield WT


title: MDS-L_Control_3

source_name: MDS-L, 7 days, DMSO, replicate 3


title: 2.1_Sample_14_15_16_KO_2.3

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of another 3 KO animals


title: Albumin-Cre E2f8loxp/loxp liver 3w 8KO 4 (Affymetrix)

city: Columbus

first: Madhu

last: Ouseph

state: Ohio

address: 460w 12th Ave

institute: The Ohio State University

description: liver 3 weeks gene expression

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430.2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene Chips were scanned using the Affy GeneChip Scanner 3000.

data_processing: The data were analyzed with RMAExpress (version 1.0 beta 4) and normalized using Quantile Normalization. Robust mean analysis (RMA) was performed with default parameter settings and the output was log transformed.

source_name: liver 3 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA.

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

treatment_protocol: Adult liver tissues were collected at described time.

value: liver

value: 3 weeks

value: Albumin-Cre E2f8loxp/loxp

tag: genetic background

value: FVB


title: MDS-L_DAC_2

source_name: MDS-L, 7 days, decitabine 4nM, replicate 2


title: Albumin-Cre E2f8loxp/loxp liver 3w 8KO 1 (Affymetrix)

description: liver 3 weeks gene expression


title: Wild type control liver 3w WT 2 (Affymetrix)

description: liver 3 weeks gene expression

value: Wild type control


title: Wild type control liver 3w WT 3 (Affymetrix)

description: liver 3 weeks gene expression


title: MDS-L_Control_1

source_name: MDS-L, 7 days, DMSO, replicate 1


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 3w 78KO 3 (Affymetrix)

description: liver 3 weeks gene expression

value: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp


title: Albumin-Cre E2f7loxp/loxp liver 3w 7KO 2 (Affymetrix)

description: liver 3 weeks gene expression

value: Albumin-Cre E2f7loxp/loxp


title: Albumin-Cre E2f8loxp/loxp liver 3w 8KO 2 (Affymetrix)

description: liver 3 weeks gene expression


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 3w 78KO 1 (Affymetrix)

description: liver 3 weeks gene expression


title: Wild type control liver 3w WT 1 (Affymetrix)

description: liver 3 weeks gene expression


title: Albumin-Cre E2f7loxp/loxp liver 3w 7KO 1 (Affymetrix)

description: liver 3 weeks gene expression


title: Albumin-Cre E2f7loxp/loxp liver 3w 7KO 4 (Affymetrix)

description: liver 3 weeks gene expression


title: 1.0_Sample_25_22_21_WT_1.1

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of 3 WT animals


title: Pool_WT_Sample_25_22_21_19_20_24_10_13_23

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of all 9 WT animals


title: 2.2_Sample_11_12_18_KO_2.1

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of yet another 3 KO animals


title: Albumin-Cre E2f7loxp/loxp liver 3w 7KO 3 (Affymetrix)

description: liver 3 weeks gene expression


title: Wild type control liver 2m WT 5 (Affymetrix)

description: liver 2 months gene expression

source_name: liver 2 months

value: 2 months


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 3w 78KO 2 (Affymetrix)

description: liver 3 weeks gene expression


title: 1.1_Sample_19_20_24_WT_1.4

description: mRNA hippocampus, CA1 subfield, adult mouse, pooled mRNA of another 3 WT animals


title: Albumin-Cre E2f8loxp/loxp liver 3w 8KO 3 (Affymetrix)

description: liver 3 weeks gene expression


title: Mx1-Cre E2f1-/- E2f2-/- E2f3loxp/loxp liver 2m 123KO 2 (Affymetrix)

description: liver 2 months gene expression

value: Mx1-Cre E2f1-/- E2f2-/- E2f3loxp/loxp

value: mixed C57B/L6 and FVB


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 2m 78KO 2 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 3w 78KO 4 (Affymetrix)

description: liver 3 weeks gene expression


title: Mx1-Cre E2f1-/- E2f2-/- E2f3loxp/loxp liver 2m 123KO 3 (Affymetrix)

description: liver 2 months gene expression


title: Wild type control liver 2m WT 3 (Affymetrix)

description: liver 2 months gene expression


title: Wild type control liver 2m WT 4 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 2m 78KO 1 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 2m 78KO 4 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f7loxp/loxp liver 2m 7KO 3 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f8loxp/loxp liver 2m 8KO 3 (Affymetrix)

description: liver 2 months gene expression


title: Mx1-Cre E2f1-/- E2f2-/- E2f3loxp/loxp liver 2m 123KO 1 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f8loxp/loxp liver 2m 8KO 4 (Affymetrix)

description: liver 2 months gene expression


title: E2f3a+/+;E2f7+/+;E2f8+/+ placenta WT 1

description: Placenta E10.5 Gene expression data

source_name: Placenta E10.5

treatment_protocol: Embryos and placentas were collected from timed pregnancies at 10.5 days post coitum.

value: Placenta

value: mixed 129SvEv, C57BL/6NTac and FVB/Ntac


title: Albumin-Cre E2f7loxp/loxp liver 2m 7KO 1 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f7loxp/loxp liver 2m 7KO 4 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f8loxp/loxp liver 2m 8KO 2 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f7loxp/loxp E2f8loxp/loxp liver 2m 78KO 3 (Affymetrix)

description: liver 2 months gene expression


title: Albumin-Cre E2f7loxp/loxp liver 2m 7KO 2 (Affymetrix)

description: liver 2 months gene expression


title: Wild type control liver 2m WT 1 (Affymetrix)

description: liver 2 months gene expression


title: E2f3a+/+;E2f7+/+;E2f8+/+ placenta WT 3

description: Placenta E10.5 Gene expression data


title: Wild type control liver 2m WT 2 (Affymetrix)

description: liver 2 months gene expression


title: Sox2Cre+;E2f7F/-;E2f8F/- placenta sox2 4

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ placenta WT 5

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ placenta WT 6

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ placenta WT 4

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ placenta WT 2

description: Placenta E10.5 Gene expression data


title: Albumin-Cre E2f8loxp/loxp liver 2m 8KO 1 (Affymetrix)

description: liver 2 months gene expression


title: Sox2Cre+;E2f7F/-;E2f8F/- placenta sox2 1

description: Placenta E10.5 Gene expression data


title: Sox2Cre+;E2f7F/-;E2f8F/- placenta sox2 3

description: Placenta E10.5 Gene expression data


title: Sox2Cre+;E2f7F/-;E2f8F/- placenta sox2 2

description: Placenta E10.5 Gene expression data


title: Cyp19Cre+;E2f7F/F;E2f8F/F placenta Cyp19 1

description: Placenta E10.5 Gene expression data


title: Cyp19Cre+;E2f7F/F;E2f8F/F placenta Cyp19 2

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- placenta 78KO 4

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- placenta 78KO 1

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- placenta 78KO 2

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- placenta 78KO 3

description: Placenta E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ placenta 3KO 2

description: Placenta E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- placenta 3a78KO 4

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ embryo WT 6

description: Embryo E10.5 Gene expression data

source_name: Embryo E10.5

value: Embryo


title: E2f3a+/+;E2f7+/+;E2f8+/+ embryo WT 3

description: Embryo E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ embryo WT 2

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- placenta 3a78KO 5

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ embryo WT 5

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- placenta 3a78KO 2

description: Placenta E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ placenta 3KO 4

description: Placenta E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- placenta 3a78KO 3

description: Placenta E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ placenta 3KO 1

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ embryo WT 1

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- placenta 3a78KO 1

description: Placenta E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ placenta 3KO 3

description: Placenta E10.5 Gene expression data


title: Cyp19Cre+;E2f7F/F;E2f8F/F placenta cyp 19 3

description: Placenta E10.5 Gene expression data


title: E2f3a+/+;E2f7+/+;E2f8+/+ embryo WT 4

description: Embryo E10.5 Gene expression data


title: Sox2Cre+;E2f7F/-;E2f8F/- embryo sox2 3

description: Embryo E10.5 Gene expression data


title: Sox2Cre+;E2f7F/-;E2f8F/- embryo sox2 4

description: Embryo E10.5 Gene expression data


title: Cyp19Cre+;E2f7F/F;E2f8F/F embryo Cyp19 2

description: Embryo E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- embryo 78KO 1

description: Embryo E10.5 Gene expression data


title: Cyp19Cre+;E2f7F/F;E2f8F/F embryo Cyp19 3

description: Embryo E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- embryo 78KO 4

description: Embryo E10.5 Gene expression data


title: Sox2Cre+;E2f7F/-;E2f8F/- embryo Sox2 1

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ embryo 3KO 2

description: Embryo E10.5 Gene expression data


title: Cyp19Cre+;E2f7F/F;E2f8F/F embryo Cyp19 1

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ embryo 3KO 1

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ embryo 3KO 3

description: Embryo E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- embryo 78KO 3

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7+/+;E2f8+/+ embryo 3KO 4

description: Embryo E10.5 Gene expression data


title: E2f3a+/+;E2f7-/-;E2f8-/- embryo 78KO 2

description: Embryo E10.5 Gene expression data


title: Sox2Cre+;E2f7F/-;E2f8F/- embryo sox2 2

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- embryo 3a78KO 5

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- embryo 3a78KO 4

description: Embryo E10.5 Gene expression data


title: E2f3a-/-;E2f7-/-;E2f8-/- embryo 3a78KO 3

description: Embryo E10.5 Gene expression data


title: ATRA treated aortic heart valve at post natal day 1, biological replicate 3

city: Milwaukee

first: Joy

last: Lincoln

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
atRA-c
ATRA-treated aortic heart valves from 5-6 pups, pooled

hyb_protocol: Biotinylated cDNA (5 ug/samples) was diluted in hybridization buffer along with hybridization controls and control oligo. The mixture was denatured for 2 minutes at 99C and then loaded on to the surface of Affmetrix Gene ST 1.0 GeneChips and hybridized for 16-18 hours at 45C under constant rotation in a Affymetrix Model 640 hybridization oven.

scan_protocol: The Affymetrix 3000 7G Plus Scanner controlled by Affymetrix AGCC software was used for data acquisition.

data_processing:
Expression Console Version 1.1 software was used to generate probe set intensities using  .CEL files. Specifically the RMA algorithm was used for background adjustment, quantile normalization, and probe set summarization; then untransformed probe set intensities were outputted for presentation and archiving. Log2-transformed probe intensities were outputted for purposes of statistical analysis.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: ATRA_aortic heart valve at post natal day 1

label_protocol: Total RNA samples were converted to amplified cDNA using the Nugen (San Carlos, CA) Ovation Pico WTA amplification kit. Sense strand cDNA was generated using the Nugen Ovation Exon Module. The cDNA was fragmented and labeled using the Nugen Encore Biotin Module kit.

growth_protocol: Pooled valves were cultured on floating filters in DMEM media (cellgro) supplememted with 1% penicillin/Streptomycin, 4mM L-glutamine and 10% FBS.

extract_protocol: Explants were removed from filter and homogenized in Trizol and total RNA was isolated.

treatment_protocol: 1umol/L all-trans retinoic acid in DMSO or DMSO alone (0.001% final concentration) was added to the culture media and incubated for 48 hours

tag: strain background

value: post natal day 1

tag: treated with

value: 1umol/L all-trans retinoic acid for 48hr

value: Aortic valve


title: E2f3a-/-;E2f7-/-;E2f8-/- embryo 3a78KO 1

description: Embryo E10.5 Gene expression data


title: LE540 treated aortic heart valve at post natal day 1, biological replicate 1

description:
le540-a
LE540-treated aortic heart valves from 5-6 pups, pooled

source_name: LE540_aortic heart valve at post natal day 1

value: retinoic acid receptor antagonist (LE540) for 48hr


title: ATRA treated aortic heart valve at post natal day 1, biological replicate 2

description:
atRA-b
ATRA-treated aortic heart valves from 5-6 pups, pooled


title: E2f3a-/-;E2f7-/-;E2f8-/- embryo 3a78KO 2

description: Embryo E10.5 Gene expression data


title: LE540 treated aortic heart valve at post natal day 1, biological replicate 3

description:
le540-c
LE540-treated aortic heart valves from 5-6 pups, pooled


title: DMSO treated aortic heart valve at post natal day 1, biological replicate 3

description:
DMSO-c
DMSO-treated aortic heart valves from 5-6 pups, pooled

source_name: DMSO_aortic heart valve at post natal day 1

value: DMSO at 0.001% final conc. for 48hr


title: ATRA treated aortic heart valve at post natal day 1, biological replicate 1

description:
atRA-a
ATRA-treated aortic heart valves from 5-6 pups, pooled


title: W8 biological replicate 1

status: Public on Aug 16 2012

city: Peoria

first: Eric

last: Johnson

state: IL

address: 1815 N. University St.

department: Crop Bioprotection Research

institute: USDA ARS

description: parent 2 inbred

hyb_protocol: 40 µL of probe (40 pmol of Cy5 labeled cDNA, 40 pmol of Cy3 labeled cDNA, 25 µg of yeast tRNA, and 12 µg of salmon sperm DNA) was added to a sealed hybridization chamber containing the microarray slide. Pre-hybridization and hybridization for ~16 hours was completed as described (Hedge et al. 2000, Biotechniques 29:548) with the exception of an additional high stringency wash at room temperature.

scan_protocol: Microarray slides were scanned at 10 µm resolution with an Axon GenePix 4100A scanner using GenePix Pro software. Photomultiplier tube levels were adjusted using the Auto-PMT feature. Each image was visually scanned for aberrant signals and flagged for removal.

data_processing:
For each slide, the data was normalized so that the mean of the ratio of medians of all the features was equal to one (completed using GenePix software).
Each set (one set has 4 replicates) of signal intensities (mean signal intensity minus background) for one inbred was scaled to the one replicate with the highest mean intensity. The normalized intensity values were converted to log2 values.

organism: Zea mays

source_name: third visible leaf

label_protocol: 10 µg of total RNA was converted to cDNA with amino allyl dUTP by Superscript III reverse transcriptase. Cy5 or Cy3 dye was coupled to the modified cDNA and then purified. Details of the procedure are available in the accompanying publication.

growth_protocol: Plants were grown in a controlled environment room at 50 ± 10% relative humidity, 14:10 light:dark cycle, with a day temperature of 24 ± 1 deg. C and a night temperature of 18 ± 1 deg. C. Lighting was supplied by alternating 1000 W sodium and halide bulbs. Plants were grown in soil mix #3 (Dowd et al. 2007, J. Ag. Food Chem. 55:3421)

extract_protocol: Total RNA was extracted from powdered tissue using Trizol as previously described (Johnson et al. 2011, Mol Gen. Genom. 285:517)

treatment_protocol: Leaf samples were cut off the plant together with leaf disc samples (from the same leaf) that were used in insect bioassays to determine mean resistance levels (see accompanying publication for details).

value: 7 leaf plant

value: third visible leaf

tag: line


title: W8 biological replicate 4

description: parent 2 inbred

tag: age


title: human islets, ID30

status: Public on Jul 05 2012

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

description: Gene expression data from human pancreatic islets

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized onto the GeneChip® Human Gene 1.0 ST whole transcript based assay overnight in the GeneChip® Hybridization oven 6400 using standard procedures. The arrays were washed and stained in a GeneChip® Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing: The array data was summarized and normalized with Robust Multi-array Analysis (RMA) method using the software “Expression Console” (Affymetrix).

source_name: Islets from cadaver donor ID30

label_protocol: Briefly, 100-200 ng total RNA was processed as indicated by GeneChip® Expression 3’-Amplification Reagents Onecycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) was used to produce double-stranded cDNA. This was used as a template to generate biotintargeted cRNA following the manufacturer’s specifications.

extract_protocol: Total RNA was isolated with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were measured using an Agilent 2100 bioanalyzer (Bio-Rad, Hercules, CA, USA) and a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1–9 days prior to RNA preparation.

value: pancreatic islets

value: Male

tag: bmi

tag: status

value: non-diabetic donors


title: LE540 treated aortic heart valve at post natal day 1, biological replicate 2

description:
le540-b
LE540-treated aortic heart valves from 5-6 pups, pooled


title: R. sphaeroides pRPcrZ vs. R. sphaeroides pR4352 replicate 2

status: Public on Aug 15 2012

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description: pooled biological sample 4-6

hyb_protocol: The RNA of three independent experiments of Rhodobacter sphaeroides pR4352 and the PcrZ over-expression (pRPcrZ) were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: R with Limma package was used for data evaluation. LOWESS normalized and background subtracted.

organism: Cereibacter sphaeroides

source_name: R. sphaeroides PcrZ total cells

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

growth_protocol: R. sphaeroides strains grown under low oxygen conditions (0,5 mg/L O2).

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

tag: sample type

value: total RNA isolates of R. sphaeroides pRPcrZ

value: pRPcrZ

tag: growth condition

value: low oxygen (0.5 mg/L O2)

source_name: R. sphaeroides 2.4.1 pR4352 total cells

value: total RNA isolates of R. sphaeroides pR4352


title: W8 biological replicate 2

description: parent 2 inbred


title: human islets, ID19

source_name: Islets from cadaver donor ID19

tag: Sex


title: DMSO treated aortic heart valve at post natal day 1, biological replicate 1

description:
DMSO-a
DMSO-treated aortic heart valves from 5-6 pups, pooled


title: Oh43 biological replicate 4

description: progeny inbred


title: Oh40B biological replicate 3

description: parent 1 inbred


title: R. sphaeroides pRPcrZ vs. R. sphaeroides pR4352 replicate 1

description: pooled biological sample 1-3


title: Oh43 biological replicate 2

description: progeny inbred


title: Oh40B biological replicate 2

description: parent 1 inbred


title: Oh43 biological replicate 3

description: progeny inbred


title: DMSO treated aortic heart valve at post natal day 1, biological replicate 2

description:
DMSO-b
DMSO-treated aortic heart valves from 5-6 pups, pooled


title: Oh43 biological replicate 1

description: progeny inbred


title: exposure to AB for AB-Zn and AB-Cu dataset

status: Public on May 02 2012

city: Padua

first: Karina

last: Fincati

address: V.le G. Colombo, 3

department: Department of Biology, University of Padua

country: Italy

institute: CNR-Institute for Biomedical Technologies

description: In all hybridizations SH-SY5Y  cell  culture was used as control for direct comparison to the experimental  conditions: expoure to AB

hyb_protocol: Labeled aRNA was dissolved in 90 ul of hybridization buffer, denaturated at 90ºC for 3 min and applied directly to microarray slides. Microarray hybridization was carried out in an ArrayBooster Hybridization Station. The reaction was carried out overnight at 42ºC. Posthybridization washing was performed according to the microarray slides manufacturer’s instructions.

scan_protocol: The microarrays slides were scanned using a GenePix 4000B laser scanner  and images were processed using Genepix 6.0 software.

data_processing: Data analysis  were performed using Acuity 4.0 software. Initial results were normalized using Lowess algorithm and filtered to exclude extreme outliers and flags. We also excluded any spots that had no detectable response on all slides. The log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected intensity medians of red dye over green dye intensities. In order to obtain a single expression value for each gene, the internal replicates (1 to 14) were plotted versus the technical replicates (6 for exposure to AB and 2 for exposure to AB-metal complex and metal). The X-Y scatterplot confirmed that the data were generally reproducible but we observed the presence of extreme outliers values. Then we excluded the outliers and the values of spots replicates within and among arrays were averaged using a trimmed mean. We excluded any spot that had no detectable response in all three treatments.

label: Alexa Fluor 555, Alexa Fluor 647

source_name: human neuroblastoma cells culture

label_protocol: 1 ug of total RNA was amplified following the SuperscriptTM Indirect RNA Amplification System Kit (InvitrogenTM): total RNA was reverse transcribed into single-stranded complementary DNA (cDNA) using oligo(dT) primer containing a T7 promoter and Superscript III reverse transcriptase. RNase H was then added together with E. coli DNA polymerase I and E. coli DNA ligase, followed by a short incubation in order to achieve synthesis of the second-strand cDNA. The purified double-strand cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase. This step generated antisense RNA (aRNA) molecules complementary to the original mRNA targets, incorporating amino-allyl UTP (aa-UTP) into the aRNA. 10 ug of purified aRNA was coupled with Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen) according to the manufacturer’s instructions.

growth_protocol: SH-SY5Y human neuroblastoma cells were purchased from ECACC. SH-SY5Y human neuroblastoma cells were maintained in Dulbecco’s modified Eagle’s medium (1: 1) with L-Glutamine and 15 mM Hepes at 37 °C with 5% CO2 in a humidified atmosphere (90 % humidity). The medium was replaced every 2 days. Penicillin (100 units/ml) and streptomycin (100 ug/ml), 15 % fetal bovine serum, and MEM non-essential amino acids (100x) were added to the medium. 0.25% Trypsin-EDTA solution and phosphate buffered saline (PBS) were obtained from Sigma Aldrich. SHSY5Y cells were plated onto 6-well plates.

extract_protocol: Total RNA of SH-SY5Y human neuroblastoma cells exposed to AB,  AB-metal complexes (AB-Cu or AB-Zn) and Cu or Zn was isolated using the Qiagen RNA/DNA Mini Kit following the manufacturer’s instructions.

treatment_protocol: The day after this plating, the culture medium was replaced with the same medium with 2 % FBS containing AB or AB-metal complexes at 0.5 uM peptide concentration. The cells were incubated with different AB or AB-metal complexes for 24h. The cell treatment was also performed in the presence of metals (Cu or Zn) at a concentration 10-fold higher than the peptide concentration.

tag: treatment

value: AB

source_name: human neuroblastoma cells exposed to AB

value: control


title: W8 biological replicate 3

description: parent 2 inbred


title: Oh40B biological replicate 1

description: parent 1 inbred


title: mutant tongue at E13.5, biological rep4

status: Public on Feb 03 2012

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, cRNA was hybridized  Affymetrix GeneChip Mouse Genome 430 2.0 Arrays, according to manufacturer's recommended protocols. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to manufacturer's recommended protocols.

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

data_processing: We used WebArray software  (www.webarraydb.org/) to generate scaled log2 transformed gene expression values based on the RMA algorithm.

source_name: Tongue from mouse embryos at day E13.5 of development

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All animals were maintained at the University of Southern California.

extract_protocol: Total RNA was extracted using RNeasy Mini Kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: RNA was isolated from tongue primordia at day 13.5 of development using RNeasy Mini Kits (Qiagen) and the manufacturer's recommended protocols.

value: tongue

tag: genotype


title: Oh40B biological replicate 4

description: parent 1 inbred


title: mutant tongue at E13.5, biological rep3


title: mutant tongue at E13.5, biological rep5


title: control tongue at E13.5, biological rep4


title: mutant tongue at E13.5, biological rep6


title: control tongue at E13.5, biological rep5


title: control tongue at E13.5, biological rep2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: mutant tongue at E13.5, biological rep1


title: control tongue at E13.5, biological rep6


title: ScglnK-3-F172-F455-50 h

status: Public on Dec 31 2011

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description: Medium F172

hyb_protocol: 3 µg of cDNA were hybridized for 16 hr at 50°C on Array Platform GPL9471. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA (Bolstad, 2002) as implemented in the affy package of Bioconductor.

organism: Streptomyces coelicolor

label_protocol: Biotinylated cDNA were prepared after fragmentation according to the standard Affymetrix protocol from 3 µg total RNA (Prokaryotic Sample and Array Processing, Technical Manual 701030 Rev. 5, 2004, Affymetrix).

growth_protocol: Fermentations were performed using the SCglnK-3 mutant strain. As described previously (Nieselt et al., 2010), 5x108 CFU/l of germinated spores were used to inoculate 1.8 L of growth medium in 3-liter Applikon fermenters. The growth medium led to glutamate depletion after about 34 h of cultivation, with all other components remaining in excess until the end of the fermentation trials. Neutral pH (7.0) was maintained in the culture by the automatic addition of 2 M HCl (before glutamate depletion) and 2 M NaOH (after glutamate depletion). Dissolved oxygen levels were maintained at a minimum of 50 % by the automatic adjustment of agitation (minimal stirrer speed 325 rpm) at a constant aeration rate of 0.5 l/l-min sterile air. The medium is referred to as F172.

extract_protocol: Total RNA isolation was performed via phenol extraction and RNeasy Midi Kit (Qiagen, 2001) according to manufacturer's instruction.

tag: genotype/variation

value: mutant


title: mutant tongue at E13.5, biological rep2


title: control tongue at E13.5, biological rep3


title: control tongue at E13.5, biological rep1


title: ScglnK-3-F172-F455-42 h

description: Medium F172


title: ScglnK-3-F172-F455-46 h

description: Medium F172


title: ScglnK-3-F172-F455-40 h

description: Medium F172


title: ScglnK-3-F172-F455-48 h

description: Medium F172


title: ScglnK-3-F172-F455-38 h

description: Medium F172


title: ScglnK-3-F172-F455-39 h

description: Medium F172


title: ScglnK-3-F172-F455-35 h

description: Medium F172


title: ScglnK-3-F172-F455-44 h

description: Medium F172


title: ScglnK-3-F172-F455-36 h

description: Medium F172


title: ScglnK-3-F172-F455-34 h

description: Medium F172


title: ScglnK-3-F172-F455-29 h

description: Medium F172


title: ScglnK-3-F172-F455-37 h

description: Medium F172


title: ScglnK-3-F172-F455-33 h

description: Medium F172


title: M145E-F172-F357-46 h

description: Medium F172

growth_protocol: Fermentations were performed using the S. coelicolor M145 (Kieser et al., 2000) strain. As described previously (Nieselt et al., 2010), 5x108 CFU/l of germinated spores were used to inoculate 1.8 L of growth medium in 3-liter Applikon fermenters. The growth medium led to glutamate depletion after about 34 h of cultivation, with all other components remaining in excess until the end of the fermentation trials. Neutral pH (7.0) was maintained in the culture by the automatic addition of 2 M HCl (before glutamate depletion) and 2 M NaOH (after glutamate depletion). Dissolved oxygen levels were maintained at a minimum of 50 % by the automatic adjustment of agitation (minimal stirrer speed 325 rpm) at a constant aeration rate of 0.5 l/l-min sterile air. The medium is referred to as F172.

value: wild type


title: M145E-F172-F357-58 h

description: Medium F172


title: M145E-F172-F357-38.5 h

description: Medium F172


title: M145E-F172-F357-40 h

description: Medium F172


title: M145E-F172-F357-41 h

description: Medium F172


title: SCglnK-3-F172-F455-21 h

description: Medium F172


title: ScglnK-3-F172-F455-25 h

description: Medium F172


title: M145E-F172-F357-54 h

description: Medium F172


title: M145E-F172-F357-44 h

description: Medium F172


title: M145E-F172-F357-42 h

description: Medium F172


title: M145E-F172-F357-39 h

description: Medium F172


title: M145E-F172-F357-38 h

description: Medium F172


title: M145E-F172-F357-35 h

description: Medium F172


title: M145E-F172-F357-34.5 h

description: Medium F172


title: M145E-F172-F357-36.5 h

description: Medium F172


title: M145E-F172-F357-37.5 h

description: Medium F172


title: M145E-F172-F357-31 h

description: Medium F172


title: M145E-F172-F357-35.5 h

description: Medium F172


title: M145E-F172-F357-36 h

description: Medium F172


title: M145E-F172-F357-32 h

description: Medium F172


title: M145E-F172-F357-30 h

description: Medium F172


title: M145E-F172-F357-39.5 h

description: Medium F172


title: M145E-F172-F357-33.5 h

description: Medium F172


title: M145E-F172-F357-37 h

description: Medium F172


title: M145E-F172-F357-33 h

description: Medium F172


title: M145E-F172-F357-32.5 h

description: Medium F172


title: M145E-F172-F357-28 h

description: Medium F172


title: M145E-F172-F357-27 h

description: Medium F172


title: M145E-F172-F357-26 h

description: Medium F172


title: R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 2

status: Public on Nov 09 2011

description: biological sample 4-6 pooled

hyb_protocol: The RNA of three independent experiments of Rhodobacter sphaeroides wild type and the irr deletion mutant (Δ3179) were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides Δirr (total cells)

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentatio.n

growth_protocol: Cells grown to an OD660=0.4 under microaerobic (30 µM oxygen) conditions

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy MinElute spin columns (Qiagen) following the manufacturer's instructions.

value: irr deletion mutant (Δirr)

source_name: R. sphaeroides 2.4.1 (total cells)


title: R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 1

description: biological sample 1-3 pooled


title: M145E-F172-F357-20 h

description: Medium F172


title: R. sphaeroides blue light delta-cryB vs. R. sphaeroides 2.4.1 replicate 2

description: biological sample 4-6

hyb_protocol: The RNA of three independent experiments of Rhodobacter sphaeroides wild type and the cryB deletion mutant (delta-3077) were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

source_name: R. sphaeroides delta-cryB total cells

growth_protocol: R. sphaeroides strains grown semiaerobically (90 µM) under blue light illumination (20 µmol m-2 s-1).

value: delta-CryB

value: blue light + semi-aerobic

source_name: R. sphaeroides 2.4.1 total cells


title: M145E-F172-F357-24 h

description: Medium F172


title: R. sphaeroides photo-oxidation delta-cryB vs. R. sphaeroides 2.4.1 replicate 1

description: biological sample 1-3

growth_protocol: R. sphaeroides strains grown aerobically (180 µM) under 20 minutes high white light intensities (800 W m-2) and addition of methylene blue (final conc. 0.2 µM) to generate 1O2.

value: delta-cryB

value: photo-oxidative stress


title: R. sphaeroides blue light delta-cryB vs. R. sphaeroides 2.4.1 replicate 1

description: biological sample 1-3


title: Δirr -Fe vs. Δirr +Fe - microaerobic conditions - replicate 1

description: biological sample 1-3 pooled

hyb_protocol: The RNA of three independent experiments of the Rhodobacter sphaeroides irr deletion mutant (Δ3179) under normal iron (+Fe) and iron limitation (-Fe) were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

source_name: Δirr - Fe (total cells)

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation.

growth_protocol: R. sphaeroides strains grown microaerobically (30 µM oxygen) to an OD660 = 0.4  either under normal iron conditions or under iron limitation conditions.

value: -Fe (iron limited)

source_name: Δirr + Fe (total cells)

value: +Fe (normal)


title: Δirr -Fe vs. Δirr +Fe - microaerobic conditions - replicate 2

description: biological sample 4-6 pooled


title: R. sphaeroides delta-CryB vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 2

description: Biologial sample 4-6

hyb_protocol: A total of three arrays were hybridized to RNA from a total of nine 2.4.1 cultures. In the same way three arrays were hybridized to RNA from a total of nine 2.4.1delta-CryB cultures. 2 µg of the pooled RNA were incubated with Cy3 dye (2.4.1delta-CryB) or Cy5 dye (2.4.1) for 15 min at 85°C in the dark. Labeled RNAs were purified using KREApure columns, and the dye incorporation was measured using the nanodrop. Equal quantities of Cy3/Cy5 incorporated RNAs were mixed and incubated with fragmentation buffer for 30 min at 60°C. The samples were mixed with hybridization buffer (Agilent), hybridized onto microarray glass slides, and incubated overnight (17 hrs) at 65°C in a hybridization oven.

scan_protocol: Scanned on an Genepix 3100 scanner. Images were quantified using GenePix Pro 7 Acquisition and Analysis Microarray Software.

data_processing: R with the LIMMA package was used for data evaluation. LOWESS normalized, background subtracted.

source_name: R. sphaeroides delta-CryB (total cells)

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, Netherlands) was used for RNA labeling and fragmentation. 2 µg of the pooled RNA were incubated with Cy3 dye (2.4.1delta-CryB) or Cy5 dye (2.4.1) for 15 min at 85°C in the dark. Labeled RNAs were purified using KREApure columns, and the dye incorporation was measured using the nanodrop.

growth_protocol: Cells grown to an OD660=0,8 under microaerobic (30 µM) conditions and isolated with hot phenol

extract_protocol: Total RNA was extracted by the hot phenol method (Gabain et al., 1983; Janzon et al., 1986). Genomic DNA contamination from RNA samples was removed by DNaseI treatment (Invitrogen, Carlsbad, USA). After DNA digestion, RNA was purified on RNeasy® MinElute™ spin columns (QIAGEN, Hilden, Germany).

value: microaerobic

source_name: R. sphaeroides 2.4.1


title: R. sphaeroides delta-CryB vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 1

description: Biologial sample 1-3


title: R. sphaeroides delta-CryB vs. R. sphaeroides 2.4.1 - microaerobic conditions - replicate 3

description: Biologial sample 7-9


title: Meningitis Tuberculosis 1

status: Public on Oct 06 2011

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Gene expression of cortical lesion

hyb_protocol: The Hybridization Mix was prepared using the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) and hybridized to the Arrays using the Agilent Microarray Hybridzation Chamber Kit (G2534A). After the hybridization, the Arrays were washed using the Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326). The Hybridization was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

scan_protocol: The scanning was done with the Agilent Microarray Scanner (Agilent p/n G2565BA). Information from scan data was processed using the Agilent’s Scan Control software, version A.7.0.1 and data were extracted with the Agilent Feature Extraction Software 9.5.1. The scanning as well as the feature extraction was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

data_processing: The 75th percentile signal value was used to normalize the Agilent one-colour microarray signals for inter-array comparisons.

source_name: Cortical lesion

label_protocol: For the labeling, theLow RNA Input Linear Amplification Kit, PLUS, One colour was used (Agilent p/n 5188-5339). The labelled cRNA was purified using Quiagen’s RNeasy spin colums (RNeasy Mini Kit, Quiagen p/n 74104) and quantified using a NanoDrop ND-1000 Spectrophotometer. Labeling was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

extract_protocol: Sections from formaldehyde-fixed, paraffin-embedded (FFPE) tissue were used. Consecutively cut sections of 6-10 µm were mounted on glass slides in RNAse-free conditions. The localization of interest was marked in the Klüver-Barrera stained slide which was used as template for the scratching with a scalpel from the unstained slices. The scratched FFPE material was collected, each region of interest to a separate Eppendorf tube. The scratched material in the Eppendorf tubes was deparaffinated with Xylol, afterwards total RNA was isolated using the Roche High Pure FFPE RNA Micro Kit. The mRNA in the isolate was then transcribed to the cDNA using the Paradise® Reagent System (Arcturus, USA). Two rounds of linear amplification were performed and the obtained purified aRNA was then sent to Imagenes (Source BioScience imaGenes GmbH, D-13125 Berlin, www.imagenes-bio.de) where the RNA was Cy 3 labeled and hybridized to human whole genome 4x44K Agilent platforms. The Roche High Pure FFPE RNA Micro Kit as well as the Paradise® Reagent System was used according to the instructions of the manufacturer.

tag: brain tissue

value: cortex

tag: disease state

value: meningitis tuberculosis


title: Alzheimers disease 1

description: Gene expression of cortex

source_name: Cortex

value: alzheimers


title: Alzheimers disease 2

description: Gene expression of cortex


title: Meningitis Tuberculosis 2

description: Gene expression of cortical lesion


title: Multiple Sclerosis 1

description: Gene expression of cortical lesion

value: multiple sclerosis


title: Control 1

description: Gene expression of cortex


title: Control 2

description: Gene expression of cortex


title: Control 3

description: Gene expression of cortex


title: Multiple Sclerosis 3

description: Gene expression of cortical lesion


title: Alzheimers disease 3

description: Gene expression of cortex


title: Meningitis Tuberculosis 3

description: Gene expression of cortical lesion


title: S298_cohort 2

status: Public on Jun 30 2010

city: Bordeaux

first: fred

last: chibon

address: 229 cours de l'argonne

department: Pathology

institute: Institut Bergonie

hyb_protocol: Samples were then analyzed on Human Genome U133 Plus 2.0 array (Affymetrix®), according to the manufacturer’s procedures.

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

data_processing: All microarray data were simultaneously normalized using the GCRMA algorithm using dChip 2008 (5/8/08)

source_name: Internal trunk

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol  (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: RNA extracted from frozen tissue of the untreated primary tumor

tag: cohort

value: cohort 2

value: Internal trunk

tag: cinsarc group

tag: metastasis

value: no

tag: time

tag: diagnosis

value: Liposarcoma - dedifferentiated


title: Multiple Sclerosis 2

description: Gene expression of cortical lesion


title: S304_cohort 2

source_name: Extremities

tag: tissue

value: Extremities

value: yes

value: Undifferentiated sarcoma


title: S303_cohort 2


title: Tissue_F38_JBI_PLUS2

status: Public on Aug 13 2010

city: Woburn

first: Christos

last: Hatzis

state: MA

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

description: F38 Plus.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A or Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html). MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.

source_name: tissue from breast tumor excision

label_protocol: A single-round of T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA was used for cRNA synthesis.

extract_protocol: Total RNA was extracted from fresh frozen breast cancer tissue using Qiagen RNeasy columns.

tag: patient id

tag: lab

value: JBI

tag: array platform_id


title: S307_cohort 2


title: S306_cohort 2


title: S302_cohort 2

value: Leiomyosarcoma


title: S309_cohort 2


title: S297_cohort 2


title: S305_cohort 2


title: exposure to AB

status: Public on Feb 10 2011

description: In all hybridizations SH-SY5Y  cell  culture was used as control for direct comparison to the experimental  conditions: expoure to AB, AB-Aal or Al

data_processing: Data analysis  were performed using Acuity 4.0 software. Initial results were normalized using Lowess algorithm and filtered to exclude extreme outliers and flags. We also excluded any spots that had no detectable response on all slides. The log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected intensity medians of red dye over green dye intensities. In order to obtain a single expression value for each gene, the internal replicates (1 to 14) were plotted versus the technical replicates (6 for exposure to AB and 2 for exposure to Al and AB-Al complex). The X-Y scatterplot confirmed that the data were generally reproducible but we observed the presence of extreme outliers values. Then we excluded the outliers and the values of spots replicates within and among arrays were averaged using a trimmed mean. We excluded any spot that had no detectable response in all three treatments.

extract_protocol: Total RNA of SH-SY5Y human neuroblastoma cells exposed to AB,  AB-metal complexes (AB-Al) and Al was isolated using the Qiagen RNA/DNA Mini Kit following the manufacturer’s instructions.

treatment_protocol: The day after this plating, the culture medium was replaced with the same medium with 2 % FBS containing AB or AB-metal complexes at 0.5 uM peptide concentration. The cells were incubated with different AB or AB-metal complexes for 24h. The cell treatment was also performed in the presence of metals (Al) at a concentration 10-fold higher than the peptide concentration.

tag: cell line

value: B-amyloid

value: untreated


title: S310_cohort 2


title: S308_cohort 2


title: S295_cohort 2


title: S300_cohort 2


title: S299_cohort 2


title: S301_cohort 2


title: S296_cohort 2

source_name: Trunk wall

value: Trunk wall


title: S294_cohort 2


title: S293_cohort 2

value: Other


title: S292_cohort 2


title: S288_cohort 2


title: S291_cohort 2


title: S289_cohort 2


title: S287_cohort 2


title: S285_cohort 2


title: S286_cohort 2


title: S284_cohort 2


title: S290_cohort 2


title: S275_cohort 2


title: S280_cohort 2


title: S272_cohort 2


title: S269_cohort 2


title: S283_cohort 2


title: S270_cohort 2


title: S271_cohort 2


title: S282_cohort 2


title: S279_cohort 2


title: S276_cohort 2


title: S281_cohort 2


title: S278_cohort 2


title: M145E-F172-F357-25 h

description: Medium F172

tag: strain

value: wild type


title: S277_cohort 2


title: R. sphaeroides photo-oxidation delta-cryB vs. R. sphaeroides 2.4.1 replicate 2

description: biological sample 4-6

value: delta-cryB

value: photo-oxidative stress


title: S274_cohort 2


title: S267_cohort 2


title: S266_cohort 2


title: S257_cohort 2


title: S273_cohort 2


title: S264_cohort 2


title: S247_cohort 2


title: S260_cohort 2


title: S268_cohort 2


title: S254_cohort 2


title: S262_cohort 2


title: S246_cohort 2


title: S263_cohort 2


title: S261_cohort 2


title: S251_cohort 2


title: S256_cohort 2


title: S259_cohort 2


title: S244_cohort 2


title: S255_cohort 2


title: S265_cohort 2


title: S241_cohort 2


title: S253_cohort 2


title: S242_cohort 2


title: S243_cohort 2


title: S258_cohort 2


title: S250_cohort 2


title: S248_cohort 2


title: S240_cohort 2


title: S249_cohort 2


title: S237_cohort 2


title: S245_cohort 2


title: S238_cohort 2


title: S233_cohort 2


title: S239_cohort 2


title: S252_cohort 2


title: S234_cohort 2


title: S235_cohort 2


title: S230_cohort 2


title: S228_cohort 2

source_name: Head and neck

value: Head and neck


title: S232_cohort 2

value: cohort 2


title: S226_cohort 2


title: S223_cohort 2

value: Internal trunk


title: S225_cohort 2


title: S221_cohort 2

value: no


title: S227_cohort 2


title: S231_cohort 2


title: S236_cohort 2


title: S229_cohort 2


title: S222_cohort 2


title: S224_cohort 2


title: S214_cohort 2


title: S217_cohort 2


title: S213_cohort 2


title: S207_cohort 2


title: S219_cohort 2


title: S211_cohort 2


title: S206_cohort 2


title: S208_cohort 2


title: S204_cohort 2


title: S215_cohort 2


title: S218_cohort 2


title: S201_cohort 2


title: S198_cohort 2


title: S203_cohort 2


title: S205_cohort 2


title: S209_cohort 2


title: S200_cohort 2


title: S216_cohort 2


title: S212_cohort 2


title: S195_cohort 2


title: S193_cohort 2


title: S210_cohort 2


title: S194_cohort 2


title: S196_cohort 2


title: S199_cohort 2


title: S197_cohort 2


title: S202_cohort 2


title: S192_cohort 2


title: S191_cohort 2


title: S185_cohort 2


title: S190_cohort 2


title: S187_cohort 2


title: S97_cohort 1

value: cohort 1


title: S188_cohort 2

value: Extremities


title: S184_cohort 2

value: Liposarcoma - dedifferentiated


title: S92_cohort 1


title: S98_cohort 1

value: Undifferentiated sarcoma


title: S93_cohort 1

value: yes


title: S89_cohort 1

value: Leiomyosarcoma


title: S189_cohort 2


title: S90_cohort 1


title: S91_cohort 1


title: S94_cohort 1


title: S82_cohort 1


title: S88_cohort 1


title: S99_cohort 1


title: S84_cohort 1


title: S87_cohort 1


title: S95_cohort 1


title: S86_cohort 1


title: S85_cohort 1


title: S83_cohort 1


title: S186_cohort 2


title: S9_cohort 1


title: S81_cohort 1


title: S79_cohort 1


title: S78_cohort 1


title: S8_cohort 1


title: S73_cohort 1


title: S75_cohort 1


title: S80_cohort 1


title: S77_cohort 1


title: S68_cohort 1


title: S7_cohort 1


title: S70_cohort 1


title: S74_cohort 1


title: S71_cohort 1


title: S69_cohort 1


title: S76_cohort 1


title: S220_cohort 2


title: S65_cohort 1


title: S72_cohort 1


title: S64_cohort 1


title: S61_cohort 1


title: S67_cohort 1


title: S62_cohort 1


title: S56_cohort 1


title: S66_cohort 1


title: S59_cohort 1


title: S60_cohort 1


title: S6_cohort 1


title: S57_cohort 1


title: S55_cohort 1


title: S54_cohort 1


title: S58_cohort 1


title: S63_cohort 1


title: S53_cohort 1


title: S52_cohort 1


title: S51_cohort 1


title: S50_cohort 1


title: S96_cohort 1


title: S5_cohort 1


title: S49_cohort 1


title: S47_cohort 1


title: S45_cohort 1


title: S43_cohort 1


title: S44_cohort 1


title: S41_cohort 1


title: S42_cohort 1


title: S48_cohort 1


title: S46_cohort 1


title: S4_cohort 1


title: S39_cohort 1


title: S36_cohort 1


title: S30_cohort 1


title: S37_cohort 1


title: S40_cohort 1


title: S34_cohort 1


title: S32_cohort 1


title: S23_cohort 1


title: S24_cohort 1


title: S38_cohort 1


title: S33_cohort 1


title: S27_cohort 1


title: S31_cohort 1


title: S3_cohort 1


title: S22_cohort 1


title: S35_cohort 1


title: S25_cohort 1


title: S29_cohort 1


title: S21_cohort 1


title: S183_cohort 1


title: S28_cohort 1


title: S178_cohort 1


title: S181_cohort 1


title: S19_cohort 1


title: S18_cohort 1


title: S179_cohort 1


title: S20_cohort 1


title: S180_cohort 1


title: S2_cohort 1


title: S177_cohort 1


title: S175_cohort 1


title: S26_cohort 1


title: S172_cohort 1


title: S176_cohort 1


title: S174_cohort 1


title: S182_cohort 1


title: S17_cohort 1


title: S167_cohort 1


title: S166_cohort 1


title: S170_cohort 1


title: S168_cohort 1


title: S164_cohort 1


title: S173_cohort 1


title: S165_cohort 1


title: S163_cohort 1


title: S169_cohort 1


title: S171_cohort 1


title: S161_cohort 1


title: S160_cohort 1


title: S162_cohort 1


title: S156_cohort 1


title: S155_cohort 1


title: S152_cohort 1


title: S158_cohort 1


title: S159_cohort 1


title: S15_cohort 1


title: S154_cohort 1


title: S153_cohort 1


title: S147_cohort 1


title: S157_cohort 1


title: S16_cohort 1


title: S148_cohort 1


title: S151_cohort 1


title: S149_cohort 1


title: S150_cohort 1


title: S141_cohort 1


title: S145_cohort 1


title: S144_cohort 1


title: S142_cohort 1


title: S138_cohort 1


title: S14_cohort 1


title: S135_cohort 1


title: S146_cohort 1


title: S136_cohort 1


title: S134_cohort 1


title: S140_cohort 1


title: S133_cohort 1


title: S139_cohort 1


title: S143_cohort 1


title: S137_cohort 1


title: S132_cohort 1


title: S120_cohort 1


title: S131_cohort 1


title: S129_cohort 1


title: S126_cohort 1


title: S114_cohort 1


title: S123_cohort 1


title: S121_cohort 1


title: S12_cohort 1


title: S128_cohort 1


title: S125_cohort 1


title: S110_cohort 1


title: S13_cohort 1


title: S117_cohort 1


title: S127_cohort 1


title: S115_cohort 1


title: S124_cohort 1


title: S118_cohort 1


title: S116_cohort 1


title: S106_cohort 1


title: S109_cohort 1


title: S111_cohort 1


title: S130_cohort 1


title: S113_cohort 1


title: S107_cohort 1


title: S11_cohort 1


title: S122_cohort 1


title: S112_cohort 1


title: S119_cohort 1


title: S108_cohort 1


title: S102_cohort 1


title: S104_cohort 1


title: S101_cohort 1


title: S100_cohort 1


title: S105_cohort 1


title: S103_cohort 1


title: S10_cohort 1


title: S1_cohort 1


title: liver-LnA-cornoil-19h rep1

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: liver, LnA, COil, 19 hours

hyb_protocol: Manufacturer's protocol

scan_protocol: Manufacturer's protocol

data_processing: Array data were loaded into the R statistical environment (v2.6.1) using the affy package (v1.12.0) of the BioConductor open-source library (Gentleman et al., 2004).  The array data were pre-processed with the GCRMA algorithm (v2.10.0, (Irizarry et al., 2003)).

source_name: liver, LnA, COil, 19 hours

label_protocol: Manufacturer's protocol

growth_protocol: Three rat strains/lines harbouring wildtype AHR were selected: Sprague-Dawley (SD), Long-Evans (LE), and Line-C (LnC). Two rat strains/lines harbouring mutant AHR were selected: Han/Wistar(Kuopio) (HW) and Line-A (LnA). Four animals of each strain were obtained from the breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland; they were fed and housed under identical conditions in this facility. All animals were males 10-12 weeks old.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer's instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver was harvested between 8:30 and 11:00 from rats treated by gavage with corn oil vehicle for 19 hours.


title: ULL-D-066

status: Public on Jan 06 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24792.gif
Scanner Make: Axon
name: 24792_Scanner Make

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Reference, amplified total RNA

tag: cell type

value: primary breast carcinoma

tag: ID


title: ULL-D-214

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24821.gif
Scanner Make: Axon
name: 24821_Scanner Make


title: ULL-L-024

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27245.gif

source_name: Stratagene Reference, ampl. totRNA

source_name: ULL-T-024, ampl. totRNA


title: ULL-L-014

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27432.gif

source_name: ULL-T-014, ampl. totRNA


title: ULL-D-087

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24803.gif
Scanner Make: Axon
name: 24803_Scanner Make


title: ULL-L-088

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24804.gif
Scanner Make: Axon
name: 24804_Scanner Make


title: ULL-L-028

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25303.gif

source_name: Stratagene, amplified totRNA

source_name: ULL-T-028, amplified totRNA


title: ULL-D-002

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25978.gif

source_name: Stratagene Reference aRNA

source_name: ULL-T-002 aRNA


title: ULL-D-169

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27243.gif

source_name: ULL-T-169, ampl. totRNA


title: ULL-D-122

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24808.gif
Scanner Make: Axon
name: 24808_Scanner Make


title: ULL-D-216

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24824.gif
Scanner Make: Axon
name: 24824_Scanner Make


title: ULL-D-201

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24816.gif
Scanner Make: Axon
name: 24816_Scanner Make


title: ULL-L-111

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24807.gif
Scanner Make: Axon
name: 24807_Scanner Make


title: ULL-D-026

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26065.gif

source_name: ULL-T-026, ampl. totRNA


title: ULL-D-020

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26066.gif

source_name: ULL-T-020, ampl. totRNA


title: ULL-L-031

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35559.gif

source_name: ULL-L-031, ampl. totRNA


title: ULL-L-181

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35561.gif

source_name: ULL-L-181, ampl. totRNA


title: ULL-L-168

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24810.gif
Scanner Make: Axon
name: 24810_Scanner Make


title: ULL-D-177

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27246.gif

source_name: ULL-T-177, ampl. totRNA


title: ULL-D-056

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24785.gif
Scanner Make: Axon
name: 24785_Scanner Make


title: ULL-L-105

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35566.gif

source_name: ULL-L-105, ampl. totRNA


title: ULL-D-202

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24819.gif
Scanner Make: Axon
name: 24819_Scanner Make


title: ULL-D-080

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24800.gif
Scanner Make: Axon
name: 24800_Scanner Make


title: ULL-D-011

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27429.gif

source_name: ULL-T-011, ampl. totRNA


title: ULL-L-097

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24805.gif
Scanner Make: Axon
name: 24805_Scanner Make


title: ULL-L-069

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35560.gif

source_name: ULL-L-069, ampl. totRNA


title: ULL-L-019

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35558.gif

source_name: ULL-L-019, ampl. totRNA


title: ULL-D-023

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26911.gif
Scanner Make: Axon
name: 26911_Scanner Make


title: ULL-L-112

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35562.gif

source_name: Stratagene Reference, ampl. totRNA

source_name: ULL-L-112, ampl. totRNA