title: 557228A12 - crl-homozygote_BR2 vs crl-heterozygote_BR2

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: crl mutants and CDT1-RNAi lines have very similar macroscopic phenotypes as well as identical defects in plastid division and biogenesis. Our goal wwas to determine how much of these similarities originated from similar alterations of gene expression.

hyb_protocol: crl-heterozygote_BR2 Cy5 / crl-homozygote_BR2 Cy3 : 30pmol.

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

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

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: seedling - Media=MS1/2 hygrometry=60% Temperature=20°C Light=16h

treatment_protocol: no treatment

tag: ecotype

value: columbia

value: crl-heterozygote mutant

tag: dev.stage (boyes et al. plant cell 2001)

value: crl-homozygote mutant


title: CGH_ESCC_118

status: Public on Sep 01 2013

type: genomic

city: beppu

first: sawada

last: genta

address: tsurumihara

country: Japan

institute: kyushu university

hyb_protocol: Hybridization of genomic DNA onto the Agilent-014693 Human Genome Microarray Kit 244K (Agilent Technologies) was performed according to Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol.

scan_protocol: Arrays were analyzed using the Agilent DNA microarray scanner according to Agilent's user manual.

data_processing: The raw signal intensities were measured and transformed into log ratio to reference DNA with 'Feature Extraction' software (version 9.1) from Agilent Technologies. The log ratio was thereafter used as the signal intensity of each probe.

molecule: genomic DNA

organism: Homo sapiens

source_name: esophageal squamous cell carcinoma

label_protocol: Labeling was performed according to the manufacturer's instructions.

extract_protocol: Total DNA was extracted from tumor tissue with QIAamp DNA Micro Kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: Laser micro-dissection.

tag: disease status

value: esophageal squamous cell carcinoma (ESCC)

tag: tissue

value: ESCC tumor

tag: gender

value: male

tag: age

tag: his type

value: well

tag: depth

tag: lymph node metastasis

value: negative

source_name: reference DNA

tag: sample type

value: reference


title: TH_control_exposure_0hrs_rep2

type: RNA

city: Notre Dame

first: Erliang

last: Zeng

state: IN

address: 384 Fitzpatrick Hall

country: USA

institute: University of Notre Dame

description: SAMPLE 11

hyb_protocol: One μg of cDNA was labeled with Cy3-random nonamers (Roche NimbleGen) for microarray hybridization.

scan_protocol: After extensive washing, the arrays were dried and then scanned using a NimbleGen MS 200 Microarray Scanner.

data_processing: Array data was extracted and analyzed using NimbleSan software v2.5 (Roche NimbleGen, Inc.). The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5.

molecule: total RNA

organism: Streptococcus pyogenes

label_protocol: Double-stranded cDNA was synthesized from 10 μg of total RNA using random hexamer primers with the SuperScript cDNA synthesis kit (Invitrogen).

extract_protocol: Total RNA extraction and purification from the bacterial pellets were performed using the RNeasy isolation kit per manufacturer's instructions (Qiagen). RNA sample integrity was confirmed on an Agilent Bioanalyzer (Agilent Technologies) and RNA concentration was measured with a NanoDrop analyzer.

treatment_protocol: For SLS exposure conditions, bacterial pellets containing GAS ∆SagA mutants were incubated with 1. supernatants containing wtSLS; 2. supernatants containing SLS S39A isoform; or 3. sterile TH media with 10mg/ml of BSA. The bacteria pellets were quickly resuspended after which the bacterial pellets were recollected for RNA isolation.  A total of three exposure timepoints were used: 0h (immediately after exposure to SLS-containing supernatants) 3h post-exposure, and 6h post-exposure. The pellets were frozen at -80C until used for RNA extraction.

tag: strain

value: Group A Streptococcus (GAS)

tag: genotype/variation

value: ∆SagA mutant

tag: incubated with

value: 10mg/ml of BSA for 0 hr

value: Bacterial pellets


title: E40_4H_1 with array type rice from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description:
oryza sativa (nipponbare)  - dev.stage (boyes et al. plant cell 2001): mature seed
One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.

hyb_protocol: labelled extract quantity: 15ug

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: Oryza sativa

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: embryonic axis - Controlled deterioration treatment: • 3 days at 85% relative hygrometry and 25°C • 14 days at 85% relative hygrometry and 40°C • 3 days at 32% relative hygrometry and 25°C

treatment_protocol: Name:40°C - growth conditions - temperature,temperature:time 14day .

value: seed

tag: cultivar

value: nipponbare

tag: treatment


title: 557228A09 - crl-heterozygote_BR1 vs crl-homozygote_BR1

hyb_protocol: crl-homozygote_BR1 Cy5 / crl-heterozygote_BR1 Cy3 : 30pmol.


title: CGH_ESCC_117


title: 557228A11 - crl-heterozygote_BR2 vs crl-homozygote_BR2

hyb_protocol: crl-homozygote_BR2 Cy5 / crl-heterozygote_BR2 Cy3 : 30pmol.


title: 557228A10 - crl-homozygote_BR1 vs crl-heterozygote_BR1

hyb_protocol: crl-heterozygote_BR1 Cy5 / crl-homozygote_BR1 Cy3 : 30pmol.


title: TH_control_exposure_0hrs_rep1

description: SAMPLE 10


title: E25_4H_2 with array type rice from Affymetrix

growth_protocol: embryonic axis - Controlled deterioration treatment: • 3 days at 85% relative hygrometry and 25°C • 14 days at 85% relative hygrometry and 25°C • 3 days at 32% relative hygrometry and 25°C

treatment_protocol: Name:25°C - growth conditions - temperature,temperature:time 14day .


title: CGH_ESCC_114

value: positive


title: CGH_ESCC_116

value: poor


title: 557183A03 - WS_BR2 vs CDT1-RNAi_BR2

hyb_protocol: CDT1-RNAi_BR2 Cy5 / WS_BR2 Cy3 : 30pmol.

value: wassilewskija (Ws)

value: mutant (CDT1-RNAi line)

extract_protocol: WS_BR2:5ug. (NucleoSpinRNAPlant.pdf)

value: wild type


title: CGH_ESCC_115

value: esophageal squamous cell carcinoma (ESCC)


title: E25_4H_3 with array type rice from Affymetrix


title: S39A_mutant_exposure_6hrs_rep3

description: SAMPLE 9

value: supernatants containing SLS S39A isoform for 6 hrs


title: S39A_mutant_exposure_6hrs_rep2

description: SAMPLE 8


title: 557183A04 - CDT1-RNAi_BR2 vs WS_BR2

hyb_protocol: WS_BR2 Cy5 / CDT1-RNAi_BR2 Cy3 : 30pmol.


title: E25_4H_1 with array type rice from Affymetrix


title: CGH_ESCC_113

value: ESCC tumor

value: female

value: moderate


title: S39A_mutant_exposure_6hrs_rep1

description: SAMPLE 7


title: 557183A02 - CDT1-RNAi_BR1 vs WS_BR1

hyb_protocol: WS_BR1 Cy5 / CDT1-RNAi_BR1 Cy3 : 30pmol.

extract_protocol: WS_BR1:5ug. (NucleoSpinRNAPlant.pdf)


title: E25OH_3 with array type rice from Affymetrix

treatment_protocol: Name:CONTROL - control - control,temperature:time 14day . TREATMENT DATE 06/08/12 FACTOR VALUE 25 °


title: 557183A01 - WS_BR1 vs CDT1-RNAi_BR1

hyb_protocol: CDT1-RNAi_BR1 Cy5 / WS_BR1 Cy3 : 30pmol.


title: E25OH_2 with array type rice from Affymetrix


title: S39A_mutant_exposure_3hrs_rep3

description: SAMPLE 6

value: supernatants containing SLS S39A isoform for 3 hrs


title: CGH_ESCC_112

value: male

value: negative

value: reference


title: E25OH_1 with array type rice from Affymetrix


title: S39A_mutant_exposure_3hrs_rep2

description: SAMPLE 5

value: Group A Streptococcus (GAS)

value: ∆SagA mutant

value: Bacterial pellets


title: 557228A06 - U73343_BR2 vs U73122_BR2

description: What are the genes that are regulated by basal PI-PLC?

growth_protocol: cell culture/primary cell - Media=Gamborg hygrometry=100% Temperature=22°C Light=100 microEnstein, continuous

treatment_protocol: Name:U73122 - compound based treatment - compound addition,u73122:quantity 60mM time 4hour . Chemicals were added to 5-day old suspensin cells (7 mL cerca 1 g cells). 4 hr later cells were harvested.

value: columbia

tag: harvest date

treatment_protocol: Name:U73343 - compound based treatment - compound addition,u73343:quantity 60mM time 4hour . Chemicals were added to 5-day old suspensin cells (7 mL cerca 1 g cells). 4 hr later cells were harvested.


title: CGH_ESCC_111

value: well

value: positive


title: S39A_mutant_exposure_0hrs_rep3

description: SAMPLE 3

value: supernatants containing SLS S39A isoform for 0 hr


title: 557228A08 - U73122_BR2 vs ctrl_BR2

hyb_protocol: ctrl_BR2 Cy5 / U73122_BR2 Cy3 : 30pmol.

treatment_protocol: Name:ter-ButOH/DMSO, 2/1, v/v - compound based treatment - compound addition,dmso:time 4hour . Chemicals were added to 5-day old suspensin cells (7 mL cerca 1 g cells). 4 hr later cells were harvested.


title: 557228A07 - ctrl_BR2 vs U73122_BR2

hyb_protocol: U73122_BR2 Cy5 / ctrl_BR2 Cy3 : 30pmol.


title: S39A_mutant_exposure_3hrs_rep1

description: SAMPLE 4


title: E45_3 with array type rice from Affymetrix

label_protocol: labelling Biotin direct, amplification=yes, total RNA 50 ng.

growth_protocol: embryonic axis - Controlled deterioration treatment: • 3 days at 85% relative hygrometry and 25°C • 14 days at 85% relative hygrometry and 45°C • 3 days at 32% relative hygrometry and 25°C

treatment_protocol: Name:45°C - growth conditions - temperature,temperature:time 14day .

value: seed

value: nipponbare


title: CGH_ESCC_110

value: esophageal squamous cell carcinoma (ESCC)


title: S39A_mutant_exposure_0hrs_rep2

description: SAMPLE 2


title: CGH_ESCC_107

value: ESCC tumor


title: 557228A05 - U73122_BR2 vs U73343_BR2


title: E45_2 with array type rice from Affymetrix


title: E45_1 with array type rice from Affymetrix


title: CGH_ESCC_109


title: S39A_mutant_exposure_0hrs_rep1

description: SAMPLE 1


title: 557228A02 - U73343_BR1 vs U73122_BR1


title: E40_2 with array type rice from Affymetrix


title: 557228A04 - U73122_BR1 vs ctrl_BR1

hyb_protocol: ctrl_BR1 Cy5 / U73122_BR1 Cy3 : 30pmol.


title: E40_3 with array type rice from Affymetrix


title: 557228A03 - ctrl_BR1 vs U73122_BR1

hyb_protocol: U73122_BR1 Cy5 / ctrl_BR1 Cy3 : 30pmol.


title: CGH_ESCC_106

value: female


title: Soybean ZH24-CK-root

status: Public on Aug 31 2013

city: Guangzhou

first: Xiaolong

last: Fang

address: NO. 483 Wushan Road Tianhe District

country: China

institute: College of Agriculture, South China Agricultural University

description: Cd sensitive and high accumulating cultivar

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Glycine max

source_name: soybean root

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

growth_protocol: Seeds of each cultivar were sown in sterile quartz sand and left for 4 days (d) to germinate. Then, seedlings were transferred into 1/2 full-strength nutrient solution containing 2.5 mM KNO3, 2.5 mM Ca(NO3)2.4H2O, 0.082 mM Fe(III)-EDTA, 4.57 μM MnCl2.4H2O, 0.25 mM K2SO4, 1.0 mM MgSO4.7H2O, 0.38 μM ZnSO4.7H2O, 1.57 mM CuSO4.5H2O, 0.09 μM (NH4)6MO7O2.4H2O, 23.13 μM H3BO3 and 0.5mM KH2PO4, and then were cultured in a growth chamber with the following settings: 70% relative humidity, 28 °C / 25 °C and a light regime of 14 h light / 10 h dark

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacture's instructions

treatment_protocol: Two days after transplant, stress with different Cd concentrations (0 μM and 22 μM Cd added in culture solution) was carried out. The culture solutions, with or without Cd, were changed every two days. Roots were harvested at 6, 12, 24, 48, 96 and 144 h after the initiation of Cd treatment

value: root

value: ZH24 (Cd-sensitive)


title: CGH_ESCC_105

value: male

value: moderate


title: Soybean ZH24-Cd-root


title: E40_4H_2 with array type rice from Affymetrix


title: Soybean HX3-CK-root

description: Cd resistant and low accumulating cultivar

value: HX3 (Cd-tolerant)


title: Soybean HX3-Cd-root


title: CGH_ESCC_104

value: reference


title: 557228A01 - U73122_BR1 vs U73343_BR1


title: CGH_ESCC_103

value: negative


title: Myometrium_Asoprisnil_10_21

status: Public on Aug 23 2013

city: Edinburgh

first: Hilary

last: Critchley

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

description: Myometrium

hyb_protocol: Chapter 3 in http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf Table 3.2 Array format 49 = 200ul volume. Step 11  hybridise for 16 hrs, proceed to 'GeneChip Expression Wash, Stain and Scan User Manual' P/N 702731: http://media.affymetrix.com/support/downloads/manuals/wash_stain_scan_cartridge_arrays_manual.pdf Chapter 1. Fluidics station 450. Table 1.1  49 format = 250ul volume. Fluidics protocol FS450_0001.

data_processing: 1. RMA normalisation, 2. Removal of sample Endo_50Rex for quality reasons, 3. Non-specific filtering by variation (gene's Inter-Quartile-Range has to be above Inter-Quartile-Range median of all genes), 4. Statistical testing through eBayes moderated t tests between placebo group and each of the Asoprisnil dose groups. P-value adjustment for multiple testing was done with Benjamini-Yekutieli method. Software: R/Bioconductor

label: biotin

label_protocol: Biotin-labelled cRNA was synthesised from 10 ug total RNA. cDNA synthesis, second strand synthesis, in-vitro transcription amplification, biotin-labelling and purification were performed according to the Affymetrix Gene Chip Expression 'Eukaryotic Sample and Array Processing' manual.

extract_protocol: RNA was extracted from endometrial samples, collected from women exposed to asoprisnil, as previously described (Henderson et al 2003; J. Clin. Endocrinol. Metab. 88: 440-449). Quality and integrity of each RNA sample was checked with the Agilent 2100 Bioanalyser (Agilent Inc, Santa Clara, CA, USA) according to manufacturer's instructions and the RNA Integrity Number (RIN) determined. Only samples with a RIN > 8.5 were processed for further analysis. Prior to full array analysis, RNA was subjected to the Affymetrix Test3 Array (Affymetrix Inc, Santa Clara, CA, USA) to exclude degraded samples with insufficient target.

value: Myometrium

value: Female


title: Fibroid_Asoprisnil_10_17

description: Fibroid

value: Fibroid


title: Myometrium_Placebo_15

description: Myometrium


title: Myometrium_Asoprisnil_25_20

description: Myometrium


title: CGH_ESCC_102

value: well

value: positive


title: Myometrium_Asoprisnil_10_17

description: Myometrium


title: Myometrium_Asoprisnil_10_13

description: Myometrium


title: Fibroid_Asoprisnil_25_14

description: Fibroid


title: Fibroid_Placebo_15

description: Fibroid


title: Endometrium_Asoprisnil_10_8a

description: Endometrium, asoprisnil-exposed

value: Endometrium


title: E40_1 with array type rice from Affymetrix

value: seed

value: nipponbare


title: Myometrium_Asoprisnil_25_14

description: Myometrium


title: Myometrium_Asoprisnil_25_22

description: Myometrium


title: Endometrium_Asoprisnil_25_7a

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_10_35

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_25_36

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_10_38

description: Endometrium, asoprisnil-exposed


title: Endometrium_50Rex

description:
Sample TAP_ENDO_50Rex included in normalisation but excluded from analysis due to clinical considerations
Endometrium, asoprisnil-exposed


title: Endometrium_Placebo_49

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_25_33

description: Endometrium, asoprisnil-exposed


title: CGH_ESCC_101

value: esophageal squamous cell carcinoma (ESCC)

value: ESCC tumor

value: poor


title: Endometrium_Placebo_9a

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_10_31a

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_25_29

description: Endometrium, asoprisnil-exposed


title: Myometrium_Placebo_34

description: Myometrium


title: Endometrium_Asoprisnil_25_27

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_10_25

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_10_28a#2

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_25_22

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_10_21a

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_10_23

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep24

status: Public on Aug 09 2013

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.

source_name: kidney tubules-HK171-MspI

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: 1mm x 1mm biopsy tissues were placed under an Olympus model SZX12 stereomicroscope using 90x magnification. The biopsy tissue was manually microdissected at 4°C for glomerular and tubular compartments using fine tip forceps. The corresponding tubulointerstitial and vascular compartment was used for genomic DNA extraction.For easier designation we called this component tubules. Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

value: kidney tubule

tag: restriction enzyme

source_name: kidney tubules-HK171-HpaII

value: HpaII


title: KidneyTubules, biological rep25

source_name: kidney tubules-HK169-MspI

source_name: kidney tubules-HK169-HpaII


title: Endometrium_Placebo_18

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep23

source_name: kidney tubules-HK177-MspI

source_name: kidney tubules-HK177-HpaII


title: Endometrium_Asoprisnil_25_20

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep22

source_name: kidney tubules-HK179-MspI

source_name: kidney tubules-HK179-HpaII


title: KidneyTubules, biological rep21

source_name: kidney tubules-HK181-MspI

source_name: kidney tubules-HK181-HpaII


title: Endometrium_Asoprisnil_25_16

description: Endometrium, asoprisnil-exposed


title: Endometrium_Placebo_15

description: Endometrium, asoprisnil-exposed


title: Endometrium_Asoprisnil_25_14

description: Endometrium, asoprisnil-exposed


title: Endometrium_Placebo_26a

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep20

source_name: kidney tubules-HK188-MspI

source_name: kidney tubules-HK188-HpaII


title: KidneyTubules, biological rep18

source_name: kidney tubules-HK53-MspI

source_name: kidney tubules-HK53-HpaII


title: KidneyTubules, biological rep19

source_name: kidney tubules-HK37-MspI

source_name: kidney tubules-HK37-HpaII


title: KidneyTubules, biological rep16

source_name: kidney tubules-HK64-MspI

source_name: kidney tubules-HK64-HpaII


title: KidneyTubules, biological rep17

source_name: kidney tubules-HK56-MspI

source_name: kidney tubules-HK56-HpaII


title: Endometrium_Asoprisnil_10_11a

description: Endometrium, asoprisnil-exposed


title: Endometrium_Placebo_12a

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep26

source_name: kidney tubules-HK158-MspI

source_name: kidney tubules-HK158-HpaII


title: Endometrium_Asoprisnil_10_17

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep12

source_name: kidney tubules-HK146-MspI

source_name: kidney tubules-HK146-HpaII


title: Endometrium_Asoprisnil_10_13

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep13

source_name: kidney tubules-HK79-MspI

source_name: kidney tubules-HK79-HpaII


title: CGH_ESCC_108

hyb_protocol: Hybridization of genomic DNA onto the Agilent-014693 Human Genome Microarray Kit 244K (Agilent Technologies) was performed according to Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol.

source_name: esophageal squamous cell carcinoma

value: male

value: moderate

source_name: reference DNA


title: KidneyTubules, biological rep9

source_name: kidney tubules-HK168-MspI

source_name: kidney tubules-HK168-HpaII


title: KidneyTubules, biological rep10

source_name: kidney tubules-HK164-MspI

source_name: kidney tubules-HK164-HpaII


title: KidneyTubules, biological rep8

source_name: kidney tubules-HK178-MspI

source_name: kidney tubules-HK178-HpaII


title: KidneyTubules, biological rep7

source_name: kidney tubules-HK182-MspI

source_name: kidney tubules-HK182-HpaII


title: KidneyTubules, biological rep14

source_name: kidney tubules-HK70-MspI

source_name: kidney tubules-HK70-HpaII


title: KidneyTubules, biological rep3

source_name: kidney tubules-HK67-MspI

source_name: kidney tubules-HK67-HpaII


title: Endometrium_Asoprisnil_25_55

description: Endometrium, asoprisnil-exposed


title: KidneyTubules, biological rep1

source_name: kidney tubules-HK74-MspI

source_name: kidney tubules-HK74-HpaII


title: KidneyTubules, biological rep5

source_name: kidney tubules-HK187-MspI

source_name: kidney tubules-HK187-HpaII


title: KidneyTubules, biological rep15

source_name: kidney tubules-HK65-MspI

source_name: kidney tubules-HK65-HpaII


title: AML 5676

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: Arrays were hybridized overnight at 60°C in microarray hybridization chambers (Corning, Corning, NY, USA). Hybridization and wash buffers from the miRCURY LNA microRNA Array Kit (Exiqon) were used according to the manufacturer’s instructions.

scan_protocol: GenePix 4100A Microarray Scanner

data_processing: Primary data analysis was performed using ArrayNorm (Pieler et al, 2004). Features were filtered for low quality spots, local background was subtracted, spots were normalized to the global mean, and the ratios between the sample of interest and the common reference were log2 transformed. Only miRNAs with positive human annotation and which were expressed in at least 5 samples (n=143) were considered for further analyses.

source_name: AML

label_protocol: miRCURY™ LNA microRNA array labelling kit (Exiqon)

extract_protocol: Trizol

tag: disease state

value: AML

tag: Sex

value: m

tag: fab/who

value: secondary AML post MDS

tag: de novo/sec

value: secondary

tag: white blood cell count

tag: % blasts

value: peripheral blood

source_name: Pooled AML samples

value: pooled reference


title: KidneyTubules, biological rep11

source_name: kidney tubules-HK148-MspI

tag: tissue

source_name: kidney tubules-HK148-HpaII


title: AML 5329

tag: age


title: AML 5209

value: f

value: secondary AML post MDS/AML multilineage dysplasia


title: AML 5038

value: t-AML


title: AML 4945


title: AML 5318


title: AML 4705


title: AML 4677


title: AML 4816

value: M1/secondary AML post MDS


title: KidneyTubules, biological rep2

source_name: kidney tubules-HK72-MspI

source_name: kidney tubules-HK72-HpaII


title: AML 4547


title: KidneyTubules, biological rep6

source_name: kidney tubules-HK186-MspI

source_name: kidney tubules-HK186-HpaII


title: AML 4430


title: AML 2028

value: M0/secondary AML post MDS


title: AML 5678

value: de novo


title: AML 3205


title: AML 5652


title: KidneyTubules, biological rep4

source_name: kidney tubules-HK58-MspI

source_name: kidney tubules-HK58-HpaII


title: AML 4535


title: AML 5589


title: AML 5390

value: sek AML post OMF


title: AML 5554


title: AML 5550


title: AML 5431


title: AML 5311


title: AML 5316


title: AML 5536

value: M4/recurrent abnormalities


title: AML 5301

value: M4/not otherwise categorized


title: AML 5344


title: AML 5224


title: AML 5256

value: M0/not otherwise categorized


title: AML 5160

value: M1/AML multilineage dysplasia


title: AML 5153

value: AML


title: AML 5286

value: m

value: M1/not otherwise categorized


title: AML 4950


title: AML 5081


title: AML 5082


title: AML 4855


title: AML 4963

value: M4 Eo


title: AML 5053

value: peripheral blood


title: AML 4893

value: pooled reference


title: AML 4851

value: f


title: AML 4780


title: AML 4842


title: AML 4736


title: AML 4774


title: AML 4690

value: M3/recurrent abnormalities


title: AML 4532


title: AML 4687


title: AML 4626


title: AML 4606


title: AML 4385


title: AML 4618


title: Healthy donor, CD34 positive cells CD34+3271A

source_name: Healthy donor, CD34 positive cells

value: healthy

tag: cell type

value: CD34 positive cells


title: Healthy donor, CD34 positive cells CD34+3210A

tag: sample type


title: Healthy donor, CD34 positive cells CD34+2598A


title: AML 4381


title: Healthy donor, bone marrow BM_D

source_name: Healthy donor, bone marrow

value: bone marrow


title: Healthy donor, bone marrow BM_C


title: Healthy donor, bone marrow BM_A


title: Healthy donor, bone marrow BM_0


title: Healthy donor, peripheral blood PB_T

source_name: Healthy donor, peripheral blood


title: Healthy donor, bone marrow BM_E


title: Healthy donor, peripheral blood PB_B


title: Healthy donor, peripheral blood PB_R


title: Healthy donor, peripheral blood PB_F


title: AML 4357

value: de novo


title: Healthy donor, peripheral blood PB_K


title: Heart failure ISACHC class 3 Patient 9

status: Public on Jul 20 2013

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C US10353831 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: whole blood

extract_protocol: Total RNA extracted using Rneasy Protect Animal Blood Kit following manufacturer's instructions (Qiagen, USA)

treatment_protocol: Blood collection into Rneasy Protect Animal Blood Tubes  (Qiagen, USA).

tag: breed

value: Dachshund

value: whole blood drawn from the cephalic or jugular veins and collected into Rneasy Protect Animal Blood Tubes (Qiagen, USA)

value: Heart failure ISACHC class 3

source_name: common reference sample compsed of total RNAs isolated from whole blood from 10 healthy dogs


title: Heart failure ISACHC class 3 Patient 1

label_protocol: according to the manufacturer's protocol


title: Heart failure ISACHC class 3 Patient 8


title: Heart failure ISACHC class 3 Patient 2


title: Heart failure ISACHC class 3 Patient 6


title: Heart failure ISACHC class 2 Patient 11

value: Cocker Spaniel

value: Heart failure ISACHC class 2


title: Heart failure ISACHC class 2 Patient 13


title: Heart failure ISACHC class 3 Patient 5


title: Heart failure ISACHC class 2 Patient 10


title: Heart failure ISACHC class 2 Patient 12


title: Heart failure ISACHC class 3 Patient 12


title: Heart failure ISACHC class 3 Patient 11


title: Heart failure ISACHC class 3 Patient 3


title: Heart failure ISACHC class 2 Patient 8


title: Heart failure ISACHC class 2 Patient 9


title: Heart failure ISACHC class 3 Patient 7


title: Heart failure ISACHC class 2 Patient 4


title: Heart failure ISACHC class 3 Patient 10


title: Heart failure ISACHC class 3 Patient 4


title: Heart failure ISACHC class 2 Patient 6

value: Airedale Terrier


title: Heart failure ISACHC class 2 Patient 7


title: Heart failure ISACHC class 2 Patient 3


title: Heart failure ISACHC class 2 Patient 1


title: Heart failure ISACHC class 2 Patient 5


title: Heart failure ISACHC class 1 Patient 12

value: Heart failure ISACHC class 1


title: Heart failure ISACHC class 1 Patient 11

value: Miniature Poodle


title: Heart failure ISACHC class 2 Patient 2

value: Schnauzer


title: Heart failure ISACHC class 1 Patient 9


title: Heart failure ISACHC class 1 Patient 10

value: Labrador


title: Heart failure ISACHC class 1 Patient 7


title: Heart failure ISACHC class 1 Patient 8


title: Heart failure ISACHC class 1 Patient 13


title: Heart failure ISACHC class 1 Patient 4


title: Heart failure ISACHC class 1 Patient 6


title: Healthy Dog Patient 14

value: German Shepherd

value: Healthy


title: Heart failure ISACHC class 1 Patient 2


title: Healthy Dog Patient 11


title: Healthy Dog Patient 8


title: Healthy Dog Patient 13


title: Heart failure ISACHC class 1 Patient 1


title: Healthy Dog Patient 12


title: Healthy Dog Patient 10


title: Heart failure ISACHC class 1 Patient 5


title: Healthy Dog Patient 9


title: Healthy Dog Patient 7


title: Heart failure ISACHC class 1 Patient 3


title: Healthy Dog Patient 6

value: Rottweiler


title: Healthy Dog Patient 2

value: healthy


title: Healthy Dog Patient 1


title: Healthy Dog Patient 5

value: German Pointer


title: Healthy Dog Patient 4


title: Kidney Tubules biological rep24

status: Public on Jul 18 2013

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

scan_protocol: The data were scanned using a GeneChip scanner in accordance with the Affymetrix protocol.

data_processing: Data were normalized in GeneSpring software using the RMA16 summarization algorithm. Baseline is the median of all samples.

source_name: Kidney Tubules

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: 1mm x 1mm biopsy tissues were placed under an Olympus model SZX12 stereomicroscope using 90x magnification. The biopsy tissue was manually microdissected at 4°C in RNALater for glomerular and tubular compartments using fine tip forceps. The corresponding tubulointerstitial and vascular compartment was placed into RLT solution. For easier designation we called this component tubules. Dissected tissue was homogenized using a Powergen125 (Fisher) homogenizer and stored at -80°C. RNA was prepared using RNAeasy mini columns (Qiagen) according to manufacturer's instructions. RNA quality and quantity was determined using a Lab-on-Chip Total RNA PicoKit (Agilent BioAnalyzer). Only samples without evidence of degradation were used.

value: microdissected kidney tubule


title: Healthy Dog Patient 3


title: Kidney Tubules biological rep25


title: Kidney Tubules biological rep20


title: Kidney Tubules biological rep19


title: Kidney Tubules biological rep22


title: Kidney Tubules biological rep21


title: Kidney Tubules biological rep18


title: Kidney Tubules biological rep23


title: Kidney Tubules biological rep16


title: Kidney Tubules biological rep15


title: Kidney Tubules biological rep14


title: Kidney Tubules biological rep9


title: Kidney Tubules biological rep17


title: KidneyTubules, biological rep3


title: Kidney Tubules biological rep13


title: Kidney Tubules biological rep10


title: Kidney Tubules biological rep2


title: Kidney Tubules biological rep7


title: Kidney Tubules biological rep6


title: Kidney Tubules biological rep1


title: ZKam-OVX-08

status: Public on May 24 2013

city: Baltimore

first: Jerry

last: Guintivano

state: MD

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

description:
100k probes generated in silico
Used the normalized M-values from the E2 data (GSE43460) to generate normalized M-values for 40 simulated arrays (see GSE43462-linked file)

hyb_protocol: Enriched unmethylated fractions were hybridized according to manfacturer's manual

scan_protocol: according to manfacturer's manual

data_processing: Here we report the simulated quantile normalized M-values for 40 arrays. Quantile normalized M-values from a previous experiment (GSE43460) were used to generate this simulated dataset. This simulated dataset of 40 arrays was generated using the "rnorm" function in R to create probe-wise distributions with the same mean and variance as the M-values in the experimentally measured dataset (GSE43460). We limited the simulation dataset to 100,000 probes. We subsequently generated DMRs with effect sizes ranging from 0.1 to 2 fold DNA methylation difference and inserted them randomly into the matrix, retaining the positions of the “hidden DMRs” for follow up analysis. DMRs were generated over variable probe lengths using the “rnorm” function separately for the case and control groups. For the case group, the mean of the distribution per probe was increased by the effect size such that the middle probe in the specified DMR represented the maximum value and the mean effect across probes approximated the simulated effect size. The probe specific variation was retained throughout this process.  In total, 1,456 hidden DMRs were generated.

organism: Mus musculus

source_name: Vehicle 30 days

label_protocol: Standard Affymetrix protocol

extract_protocol: All genomic DNA was isolated from hippocampal tissue with the MasterPure DNA Purification Kit (Epicentre Biotechnologies) according to manufacturer's instructions.

treatment_protocol: C57BL/6J mice were ovariectomized at eight weeks of age. At the time of surgery mice were randomized to receive (s.c. implantation) a Silastic™ capsule (i.d. 1.02 mm; o.d. 2.16 mm) containing 5 mm of dry packed 17β-estradiol (n=5/group/timepoint). Controls received an empty capsule.

tag: strain

value: hyppocampus


title: ZKam-OVX-09

source_name: Estradiol 30 days


title: Kidney Tubules biological rep4


title: ZKam-OVX-07


title: ZKam-OVX-10


title: ZKam-OVX-06


title: ZKam-OVX-05


title: ZKam-OVX-04


title: Kidney Tubules biological rep5


title: Arabidopsis thaliana (Col-0) infested with Pseudomonas syringae DC3000: replica 3

status: Public on Jun 01 2013

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

description: Two color microarray. Biological replicas are dye-swaped between slides.

hyb_protocol: Hybridizations were performed in a Slide Booster Hybridization Station (Advalytix, Brunnthal, Germany), and the slides were washed according to the manufacturers’ descriptions (Genisphere and Advalytix).

scan_protocol: The slides were scanned at 10 mm resolution on a G2505B Agilent DNA microarray scanner (Agilent Technologies,Palo Alto, CA, USA). The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).

data_processing: Spots identified as not found or which were manually flagged out as bad were filtered out. The data sets were log-transformed and normalized using the printtip-loess approach. Within-array replicated measurements for the same gene were merged by taking the average between the replicates. The data were then scaled so that all array data sets had the same median absolute deviation. No background normalization was done. The differentially expressed genes were identified using the Limma software package. The p-values were then used to compute the q-values (Storey 2002). References: Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3 (2004); Storey J.D. A direct approach to false discovery rates. Journal of the Royal Statistical Society. Series B-Statistical Methodology 64, 479–498 (2002).

source_name: Arabidopsis thaliana (Col-0) rosette leaves infested with Pseudomonas syringae DC3000 (biological replica 3)

label_protocol: Total RNA (15 mg) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction.  Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.

growth_protocol: Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers Vötsch VB 1514 (Vötch Industrietechnik GmbH, Germany) with a 8/16 h (light/dark) photoperiod at 22/18 °C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity.

extract_protocol: Total RNA was isolated with the Spectrum Plant Total RNA Kit (Sigma, St. Louis,MO,USA) and was quantified with NanodropND 1000 (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Pseudomonas syringae pv. tomato strain DC3000 culture was grown overnight in 10 ml of Kings B solution supplemented with antibiotics rifampicin (50 μg ml−1) and kanamycin (25 μg ml−1). Overnight culture was washed once in 10 mM MgCl2 and final cell densities were adjusted to approximately 0.20 at 600 nm (approximately 1.5 × 108 cfu ml−1) in 10 mM MgCl2. Plants were mock-challenged with 10 mM MgCl2 or inoculated with DC3000 strain, 3-4 leaves were infiltrated on the abaxial surface with a needleless 1-ml syringe.

tag: ecotype

value: rosette leaves

source_name: Rosette leaves from mock-infected Arabidopsis thaliana (Col-0) plants (biological replica 3)

value: mock-infected


title: ZKam-OVX-02


title: ZKam-OVX-03


title: Arabidopsis thaliana (Col-0) infested with Pseudomonas syringae DC3000: replica 1

source_name: Arabidopsis thaliana (Col-0) rosette leaves infested with Pseudomonas syringae DC3000 (biological replica 1)

source_name: Rosette leaves from mock-infected Arabidopsis thaliana (Col-0) plants (biological replica 1)


title: Kidney Tubules biological rep11


title: Arabidopsis thaliana (Col-0) infested with Pseudomonas syringae DC3000: replica 2

description: Two color microarray. Biological replicas are dye-swaped between slides

source_name: Rosette leaves from mock-infected Arabidopsis thaliana (Col-0) plants (biological replica 2)

source_name: Arabidopsis thaliana (Col-0) rosette leaves infested with Pseudomonas syringae DC3000 (biological replica 2)


title: ZKam-OVX-01


title: Kidney Tubules biological rep12


title: Arabidopsis thaliana (Col-0) plants exposed to Brevicoryne Brassicae: replica 4

source_name: Rosette leaves from untreated Arabidopsis thaliana (Col-0) plants (biological replica 4)

growth_protocol: Arabidopsis seedlings were grown in 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite), 3 plants per pot. Plants were kept in growth chambers Vötsch VB 1514 (Vötsch Industrietechnik GmbH, Germany) under the following conditions: a 16/8 h (light/dark)) photoperiod at 22°C/18°C, 40%/70% relative humidity, and 70/0 μmol m-2s-1 light intensity

treatment_protocol: Each plant was infested with 32 wingless aphids (4 per leaf), which were transferred to leaves with a fine paintbrush. Infested plants and aphid-free control plants were kept in plexiglass cylinders.

value: untreated

source_name: Arabidopsis thaliana (Col-0) rosette leaves exposed to Brevicoryne Brassicae (biological replica 4)

value: exposed to Brevicoryne Brassicae


title: Arabidopsis thaliana (Col-0) infested with Pseudomonas syringae DC3000: replica 4

source_name: Rosette leaves from mock-infected Arabidopsis thaliana (Col-0) plants (biological replica 4)

source_name: Arabidopsis thaliana (Col-0) rosette leaves infested with Pseudomonas syringae DC3000 (biological replica 4)


title: Arabidopsis thaliana (Col-0) plants exposed to Brevicoryne Brassicae: replica 3

source_name: Arabidopsis thaliana (Col-0) rosette leaves exposed to Brevicoryne Brassicae (biological replica 3)

source_name: Rosette leaves from untreated Arabidopsis thaliana (Col-0) plants (biological replica 3)


title: Arabidopsis thaliana (Col-0) plants exposed to Brevicoryne Brassicae: replica 2

source_name: Rosette leaves from untreated Arabidopsis thaliana (Col-0) plants (biological replica 2)

source_name: Arabidopsis thaliana (Col-0) rosette leaves exposed to Brevicoryne Brassicae (biological replica 2)


title: Arabidopsis thaliana (Col-0) plants exposed to Brevicoryne Brassicae: replica 1

source_name: Arabidopsis thaliana (Col-0) rosette leaves exposed to Brevicoryne Brassicae (biological replica 1)

source_name: Rosette leaves from untreated Arabidopsis thaliana (Col-0) plants (biological replica 1)


title: Mouse mandibular molar 7

status: Public on Mar 31 2013

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

description: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.

hyb_protocol: 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix)

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: Mouse mandibular molar

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

growth_protocol: Pregnant female mice (C57Bl6 genetic background) were euthanized at 14.5 days of gestation (E14.5), embryos were collected and tooth samples (lower incisors, mandibular and maxillary first molars) were microdissected

extract_protocol: Total RNA was extracted with the RNAeasy micro Kit (Qiagen) from pools of 4 tooth germs to obtain enough RNA for subsequent microarray hybridization.

value: mandibular molar

tag: genetic background


title: isolated blood vessels from normal bladder; patient 21

status: Public on Mar 08 2013

city: Zurich

first: Filip

last: Roudnicky

address: Langwiesstrasse 25

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Cocktails were heated at 99°C for 2 minutes, then 42° C for 5 minutes, then centrifuged at max speed for 5 minute. Afterwards, 200μl of hybridization solution was transferred to each array. Arrays were hybridized for 18 h at 45°C at 60rpm. Arrays were then washed using an Affymetrix Fluidics Station 450  FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled target. Affymetrix GeneChip Command Console (AGCC) was used for image processing.

data_processing:
Raw data were RMA16-normalized and log transformed by using Genespring GX 12. Only core probes were used for the analysis.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na32.hg19.core.csv

source_name: Laser capture microdissected blood vessels from matched normal tissue

label_protocol: Samples were enzymatically fragmented and biotinylated using the Encore biotin module (Nugen).

extract_protocol: LCM was performed on frozen sections. Up to 1 mm2 of immunostained blood vessels were isolated per sample and immediately lysed in Buffer RLT Plus (Qiagen) containing 3% β-mercaptoethanol (Fluka). RNA was isolated using the RNeasy Plus Micro Kit (Qiagen), amplified and converted to cDNA using the whole transcriptome amplification kit Ovation Pico WTA System (Nugen). Then, cDNA was purified using the QIAquick PCR purification kit (Qiagen).

value: m

tag: age (y)


title: isolated blood vessels from normal bladder; patient 14


title: non-AD_TC, biological rep17

status: Public on Apr 17 2013

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.

source_name: Temporal cortex of non-AD brain

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: We examined postmortem human brains donated for the Hisayama study.

extract_protocol: Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

treatment_protocol: During autopsy dissection, parts of the frontal cortex, temporal cortex and hippocampus were cut out from each brain, and preserved at –80°C until RNA preparation.

value: Temporal cortex

value: M


title: Mouse mandibular molar 2


title: Mouse mandibular molar 6


title: isolated blood vessels from normal bladder; patient 7


title: Mouse mandibular molar 5


title: non-AD_TC, biological rep16

value: F


title: Mouse mandibular molar 3


title: isolated blood vessels from bladder cancer; patient 14

source_name: Laser capture microdissected blood vessels from bladder cancer

tag: Stage

tag: grade


title: isolated blood vessels from bladder cancer; patient 6


title: non-AD_FC, biological rep18

source_name: Frontal cortex of non-AD brain

value: Frontal cortex


title: isolated blood vessels from bladder cancer; patient 16


title: non-AD_TC, biological rep18


title: Mouse mandibular molar 8


title: isolated blood vessels from bladder cancer; patient 7


title: Mouse mandibular molar 4


title: Mouse mandibular molar 1


title: non-AD_HI, biological rep10

source_name: Hippocampus of of non-AD brain

value: Hippocampus


title: isolated blood vessels from bladder cancer; patient 12


title: isolated blood vessels from normal bladder; patient 6


title: isolated blood vessels from normal bladder; patient 12


title: Kidney Tubules biological rep8

source_name: Kidney Tubules


title: mandible_at_E10.5_M_embryo rep2

status: Public on Jul 13 2012

city: Tokyo

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

department: Pathology

institute: The Nippon Dental University

description:
Mus_E10.5_MA_M-2
Gene expression data from 40 embryos

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Microarray (Mouse expression 430 2.0, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The expression value and detection calls were computed from the raw data with Affymetrix® Expression Console  1.1 software (v.1.1).

source_name: Medial region Mandibular arch from E10.5 mouse embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: Timed-pregnant ICR mice were kept under a 12-h light-dark cycle and were given standard laboratory fodder and water ad libitum.

extract_protocol: Total RNA was extracted from the sample using RNeasy Micro Kit (QIAGEN) according to the manufacturer's instruction.

treatment_protocol: Dams were sacrificed by cervical dislocation and the uteri dissected out were placed in Hanks’ balanced salt solution (HBSS) at 4C. Embryos were rinsed with fresh HBSS to remove amniotic fluid and blood. Mandibular arches were collected from the embryos.

value: ICR

tag: developmental stage

value: Mandibular arches

tag: region

value: Medial


title: PC3 siMYC+siMYCLo-6-2

status: Public on Jul 04 2012

city: Columbus

first: Taewan

last: Kim

state: OH

institute: The Ohio State University

description:
raw data file: GSE39077_PC3_MYC_and_MYCLo-456.txt
nCounter Virtual Cell Cycle Gene Set

hyb_protocol: Hybridization reactions were performed according to manufacturer's instructions with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h.

scan_protocol: A high-density scan (600 fields of view) was performed.

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by Nanostring Technologies.

source_name: Prostate cancer-derived PC3 cell line

growth_protocol: Cells were grown in 37 degree humidified incubator with 5% CO2.

extract_protocol: Total RNA samples were prepared using TRIZOL (Invitrogen) in accordance with manufacturer's instruction

treatment_protocol: Cells were transfected with siRNA (Final concentration: 50nM for HCT116 and 100nM for PC3) by using Lipofectamine RNAiMAX from Invitrogen as the instruction of manufacturer.

tag: cell line

value: Prostate cancer-derived PC3 cell line

tag: treatment

value: siRNA targeting CARLo-1 v2


title: PC3 siMYC+siMYCLo-6-3


title: Aug_25_2009_at_5:00_transplanted_on_May_19_rep2

status: Public on Dec 07 2012

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

hyb_protocol: 825ng of labeled cRNA were used for hybridization according to manufacturer's protocol. Open-lab in rgrc in NIAS was used.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

source_name: rice,leaf,in the field

label_protocol: 400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using NTP and 400 µM Cy5 (or Cy3) CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.

growth_protocol: Rice plants were grown in a paddy field in Tsukuba, Japan on 2009 using a typical cultivation method. Transplanting dates were May 19, June 19, July 16 and July 31 to obtain RNA from plants at different developmental stage on the sampling date.

extract_protocol: Total RNA extracted using QIAGEN RNeasy Plant Mini Kit following manufacturer's instructions

treatment_protocol: Rice leaves were sampled at the paddy field. Cut leaves were frozen using liquid N imeditately after sampling.

tag: cultivar

value: Norin 8

tag: sampling time

value: transplanted on May 19

tag: genotype

value: osgi


title: Oct_8_2009_at_11:00_transplanted_on_July_31_rep4

value: transplanted on July 31


title: PC3 siMYC+siMYCLo-5-3


title: PC3 siMYC+siMYCLo-5-2


title: HCT116 siMYC-3

description:
raw data file: GSE39077_HCT116_MYC_and_MYCLo-123.txt
nCounter Virtual Cell Cycle Gene Set

source_name: Colorectal cancer-derived HCT116 cell line

value: siRNA targeting CARLo-5


title: PC3 siMYC+siMYCLo-4-3


title: PC3 siMYC+siCTRL-3


title: PC3 siMYC+siCTRL-2


title: PC3 siMYC+siMYCLo-4-2


title: mandible_at_E10.5_M_embryo rep1

description:
Mus_E10.5_MA_M-1
Gene expression data from 40 embryos

tag: tissue


title: PC3 siMYC+siMYCLo-4-1


title: mandible_at_E9.7_M_embryo

description:
Mus_E9.7_MA_M
Gene expression data from 40 embryos

source_name: Medial region Mandibular arch from E9.7 mouse embryos


title: mandible_at_E9.7_L_embryo

description:
Mus_E9.7_MA_L
Gene expression data from 40 embryos

source_name: Lateral region Mandibular arch from E9.7 mouse embryos

value: Lateral


title: mandible_at_E10.5_L_embryo rep1

description:
Mus_E10.5_MA_L-1
Gene expression data from 40 embryos

source_name: Lateral region Mandibular arch from E10.5 mouse embryos


title: mandible_at_E10.5_L_embryo rep2

description:
Mus_E10.5_MA_L-2
Gene expression data from 40 embryos


title: mandible_at_E10.5_M_embryo rep3

description:
Mus_E10.5_MA_M-3
Gene expression data from 40 embryos


title: PC3 siMYC+siMYCLo-6-1


title: mandible_at_E11.5_M_embryo rep2

description:
Mus_E11.5_MA_M-2
Gene expression data from 40 embryos

source_name: Medial region Mandibular arch from E11.5 mouse embryos


title: HCT116 siMYC-2

value: Colorectal cancer-derived HCT116 cell line


title: mandible_at_E11.5_M_embryo rep1

description:
Mus_E11.5_MA_M-1
Gene expression data from 40 embryos


title: mandible_at_E10.5_L_embryo rep3

description:
Mus_E10.5_MA_L-3
Gene expression data from 40 embryos


title: HCT116 siMYC-1


title: PC3 siMYC+siCTRL-1


title: HCT116 siMYCLo-3-3

value: siRNA targeting CARLo-4


title: PC3 siMYC+siMYCLo-5-1


title: HCT116 siMYCLo-3-2


title: HCT116 siMYCLo-3-1


title: HCT116 siMYCLo-1-3

value: siRNA targeting CARLo-1 v3


title: HCT116 siMYCLo-1-1


title: HCT116 siMYCLo-2-1

value: siRNA targeting CARLo-3


title: HCT116 siMYCLo-2-2


title: HCT116 siMYCLo-1-2


title: HCT116 siMYCLo-2-3


title: Npy expressing, Embryonic derived N_46 cell line from hypothalamus_3

status: Public on Jun 01 2012

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

description: Gene expression data from Npy expressing embryonic hypothalamus derived cell line

hyb_protocol: 15ug of biotinylated cRNA was fragmented  hybridized for 17 hr at 45C on the Mouse 430_2 genechip array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Genespring Version 11.0.1 and summarized using the RMA quantile algorithm [raw_RMA] followed by a per-probe median centered normalization

label_protocol: Biotinylated cRNA were prepared according to the manufacturers kit (Enzo IVT) from 5 ug of starting total RNA

growth_protocol: Cell lines were grown to 70% confluence in 5% FBS DMEM in triplicate plates for each of either the adult or embryonic line origin.

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

treatment_protocol: Cells were collected using standard protocols and RNA was harvested.

tag: cell line tissue source

value: embyronic hypothalamus

tag: genotype/variation

value: expressing Npy (neuropeptide y)


title: WT littermate 4

status: Public on Apr 11 2012

city: Ann Arbor

first: Jaime

last: D'Agostino

state: MI

address: 2025 S huron Parkway apt 102

institute: University of Michigan

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45°C in a GeneChip hybrization oven with constant rotation. Arrays were then stained and washed using the antibody and staining protocol from Affymetrix in a GeneChip Fluidics Station 400.

scan_protocol: The expression data were collected with a gene array scanner using Affymetrix Microarray Suite Version 5.0 (MAS 5.0)

data_processing: The experimental data sets were normalized using GCRMA program in GeneSpring 10.0. The data from the WT littermates was used as the baseline. Probe sets with raw intensity below the 20th percentile in all eight samples were eliminated. Analysis for signifigance was performed using the unpaired t-test.

source_name: enterocytes isolated from mouse small intestine

label_protocol: 5 micrograms of total RNA were used for synthesis of biotinylated antisense RNA with MESSAGEAMP aRNA kit from Ambion.

growth_protocol: Animals were maintained at 22°C with a 12-h light on, 12-h light off cycle and were allowed free access to water and a standard laboratory diet.

extract_protocol: Total RNA was prepared from enterocytes using TRIzol and the samples were further purified using Rneasy mini columns.

treatment_protocol: Animals were sacrificed by CO. The small intestine was dissected and enterocytes were isolated following the procedure of Zhang et al., Drug Metab. Dispos., 31:1346-1351, 2003.

value: Wildtype

tag: gender

value: male

value: small intestine

tag: age


title: IE-Cpr-Null 2

value: IE-Cpr-Null

tag: strain


title: WT littermate 3


title: IE-Cpr-Null 3


title: PDAC_Patient:GEO-PC-085_rep1

status: Public on Mar 31 2012

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: Amplified cRNA (750ng) was hybridized onto Illumina human HT-12 arrays (V4) as per manufacturer's instructions.

scan_protocol: Arrays were scanned on a Bead Array Reader (Illumina)

data_processing: Expression measurements were extracted using the GenomeStudio (version 2009.1) software, using no background correction or normalisation, and exported in two batches. This unnormalised data from two separate genome studio files were combined, retaining the 47215 probes in common, followed by variance-stabilising transformation (vst) and robust spline normalisation (rsn) using lumi (v2.4.0) in R (v 2.13.1)/Bioconductor (v2.8). Note that the vst-scale is very similar to the log2-scale for high levels (see Lin et al, NAR 36:e11). To obtain natural scale data, use inverseVST from lumi in R/Bioconductor. The 2 replicates from Patient ICGC-PC-027 were then averaged.

source_name: PDAC tumour RNA

label_protocol: mRNA samples (150ng/sample) were amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) as per manufacturer’s instructions. Amplified RNA was quantified using a NanoDrop (Thermo Scientific) and distribution of the amplified material was analysed in an 2100 Bioanalyzer (Agilent)

growth_protocol: Pancreas tissue was surgically removed from PDAC patients undergoing Whipple surgical resection.

extract_protocol: RNA was extracted from primary tissue using the Qiagen Allprep kit in accordance with the manufacturers instructions.

treatment_protocol: Tissue was immediately snap frozen in liquid nitrogen (for full protocol see APGI website: http://www.pancreaticcancer.net.au/).

value: Pancreas

tag: disease

value: PDAC (pancreatic ductal adenocarcinoma)


title: Npy expressing, Adult derived A_212 cell line from hypothalamus_3

description: Gene expression data from Npy expressing adult hypothalamus derived cell line

value: adult hypothalamus


title: IE-Cpr-Null 1


title: PDAC_Patient:GEO-PC-090_rep1


title: Npy expressing, Embryonic derived N_46 cell line from hypothalamus_2


title: Npy expressing, Adult derived A_212 cell line from hypothalamus_1


title: PDAC_Patient:GEO-PC-088_rep1


title: PDAC_Patient:GEO-PC-087_rep1


title: IE-Cpr-Null 4


title: PDAC_Patient:GEO-PC-079_rep1


title: Npy expressing, Adult derived A_212 cell line from hypothalamus_2


title: PDAC_Patient:GEO-PC-083_rep1


title: WT littermate 2


title: PDAC_Patient:GEO-PC-086_rep1


title: Npy expressing, Embryonic derived N_46 cell line from hypothalamus_1


title: PDAC_Patient:GEO-PC-089_rep1


title: PDAC_Patient:GEO-PC-082_rep1


title: PDAC_Patient:GEO-PC-081_rep1


title: PDAC_Patient:GEO-PC-084_rep1


title: WT littermate 1


title: PDAC_Patient:GEO-PC-080_rep1


title: PDAC_Patient:GEO-PC-076_rep1


title: PDAC_Patient:GEO-PC-077_rep1


title: PDAC_Patient:GEO-PC-078_rep1


title: PDAC_Patient:GEO-PC-072_rep1


title: PDAC_Patient:GEO-PC-074_rep1


title: PDAC_Patient:GEO-PC-075_rep1


title: PDAC_Patient:GEO-PC-067_rep1


title: PDAC_Patient:GEO-PC-071_rep1


title: PDAC_Patient:GEO-PC-069_rep1


title: PDAC_Patient:GEO-PC-066_rep1


title: PDAC_Patient:GEO-PC-068_rep1


title: PDAC_Patient:GEO-PC-073_rep1


title: PDAC_Patient:GEO-PC-061_rep1


title: PDAC_Patient:GEO-PC-054_rep1


title: PDAC_Patient:GEO-PC-056_rep1


title: PDAC_Patient:GEO-PC-065_rep1


title: PDAC_Patient:GEO-PC-055_rep1


title: PDAC_Patient:GEO-PC-057_rep1


title: PDAC_Patient:GEO-PC-053_rep1


title: PDAC_Patient:GEO-PC-058_rep1


title: PDAC_Patient:GEO-PC-059_rep1


title: PDAC_Patient:GEO-PC-062_rep1


title: PDAC_Patient:GEO-PC-046_rep1


title: PDAC_Patient:GEO-PC-051_rep1


title: PDAC_Patient:GEO-PC-049_rep1


title: PDAC_Patient:GEO-PC-064_rep1


title: PDAC_Patient:GEO-PC-048_rep1


title: PDAC_Patient:GEO-PC-050_rep1


title: PDAC_Patient:GEO-PC-047_rep1


title: PDAC_Patient:GEO-PC-052_rep1


title: PDAC_Patient:GEO-PC-060_rep1


title: PDAC_Patient:GEO-PC-036_rep1


title: PDAC_Patient:GEO-PC-063_rep1


title: PDAC_Patient:GEO-PC-034_rep1


title: PDAC_Patient:GEO-PC-038_rep1


title: PDAC_Patient:GEO-PC-032_rep1


title: PDAC_Patient:GEO-PC-033_rep1


title: PDAC_Patient:GEO-PC-045_rep1


title: PDAC_Patient:GEO-PC-026_rep1


title: PDAC_Patient:GEO-PC-039_rep1


title: PDAC_Patient:GEO-PC-043_rep1


title: PDAC_Patient:GEO-PC-044_rep1


title: PDAC_Patient:GEO-PC-022_rep1


title: PDAC_Patient:GEO-PC-040_rep1


title: PDAC_Patient:GEO-PC-023_rep1


title: PDAC_Patient:GEO-PC-027_rep1


title: PDAC_Patient:GEO-PC-028_rep1


title: PDAC_Patient:GEO-PC-042_rep1


title: PDAC_Patient:GEO-PC-025_rep1


title: PDAC_Patient:GEO-PC-020_rep1


title: PDAC_Patient:GEO-PC-021_rep1


title: PDAC_Patient:GEO-PC-024_rep1


title: PDAC_Patient:GEO-PC-035_rep1


title: PDAC_Patient:GEO-PC-031_rep1


title: PDAC_Patient:GEO-PC-018_rep1


title: PDAC_Patient:GEO-PC-030_rep1


title: PDAC_Patient:GEO-PC-037_rep1


title: PDAC_Patient:GEO-PC-008_rep1


title: PDAC_Patient:GEO-PC-005_rep1


title: PDAC_Patient:GEO-PC-001_rep1


title: PDAC_Patient:GEO-PC-011_rep1


title: PDAC_Patient:GEO-PC-010_rep1


title: PDAC_Patient:GEO-PC-015_rep1


title: PDAC_Patient:GEO-PC-003_rep1


title: PDAC_Patient:GEO-PC-012_rep1


title: PDAC_Patient:GEO-PC-014_rep1


title: PDAC_Patient:GEO-PC-006_rep1


title: PDAC_Patient:GEO-PC-017_rep1


title: PDAC_Patient:GEO-PC-019_rep1


title: PDAC_Patient:GEO-PC-004_rep1


title: PDAC_Patient:GEO-PC-016_rep1


title: PDAC_Patient:GEO-PC-007_rep1


title: PDAC_Patient:GEO-PC-013_rep1


title: PDAC_Patient:GEO-PC-041_rep1


title: primary human: blood; FACS-sorted CD3+ cells (CLL175N_CD3)

status: Public on Nov 29 2011

first: Sami

middle: N

last: Malek

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix CEL files for each DNA sample were analyzed using Affymetrix's Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to determine final call rates and quality. Call rates for the entire group of CD19+ samples included in this report were between 95.06% and 99.63%, with a mean call rate of 98.53%. Corresponding call rates for CD3+ or buccal DNA were between 93.14% and 99.66%, with a mean call rate of 98.49%. Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip adapted to operate in a 64-bit environment.
dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using the software's median-smoothing algorithm.

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol: Purification_protocol: Cryopreserved CLL cells were washed and stained with phycoerythrin (PE)–conjugated anti-CD19 and fluorescein isothiocyanate (FITC)–conjugated anti-CD3 antibodies (eBioscience, San Diego, CA). Propidium iodide was added to a concentration of 1 μg/mL to discriminate dead cells, and viable CD19+ and CD3+ single-positive cells were sorted on a high-speed FACSAria cell sorter (Becton Dickinson, Mountain View, CA).  Buccal swabs were used as normal controls in eleven cases.

treatment_protocol: Not applicable

tag: normal vs tumor

value: normal


title: primary human: blood; FACS-sorted CD3+ cells (CLL176N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL236N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL168N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL239N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL240N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL237N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL238N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL174N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL140N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL159N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL156N_CD3_092809)


title: primary human: blood; FACS-sorted CD3+ cells (CLL235N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL155N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL157N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL173N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL139N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL153N_CD3_092809)


title: primary human: blood; FACS-sorted CD3+ cells (CLL152N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL146N_CD3_062410)


title: primary human: blood; FACS-sorted CD3+ cells (CLL144N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL158N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL165N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL170N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL145N_CD3_062410)


title: primary human: blood; FACS-sorted CD3+ cells (CLL142N_CD3_092809)


title: primary human: blood; FACS-sorted CD3+ cells (CLL150N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL149N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL147N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL136N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL119N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL125N_CD3_062410)


title: primary human: blood; FACS-sorted CD3+ cells (CLL117N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL111N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL126N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL113N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL134N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL123N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL110N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL106N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL107N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL102N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL129N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL112N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL099N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL105N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL132N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL092N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL109N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL128N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL118N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL115N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL130N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL094N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL135N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL121N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL114N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL093N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL098N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL131N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL090N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL083N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL088N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL087N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL085N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL068N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL077N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL046N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL047N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL086N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL062N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL079N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL067N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL060N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL059N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL070N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL055N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL069N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL048N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL045N_CD3_062410)


title: primary human: blood; FACS-sorted CD3+ cells (CLL050N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL089N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL075N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL052N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL040N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL042N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL057N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL043N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL053N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL041N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL066N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL039N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL080N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL036N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL034N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL038N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL033N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL030N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL027N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL025N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL029N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL032N_CD3)


title: CD44 Low T-cell lymphoma, replicate 2

status: Public on Nov 01 2011

city: Boston

first: Xi

last: Wang

state: Massachusetts

address: 44 Binney Street, M654

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

hyb_protocol: The cRNA is hybridized to a microarray chip. The bound cRNA is stained with fluorescent streptavidin.

scan_protocol: The microarray chip is then scanned using a laser, and the positions and intensities of the fluorescent emissions are captured. These measurements provide the basis of subsequent biostatistical analysis.

data_processing: Data was analyzed using the Gene Pattern software. RMA normalization.

source_name: CD44lo cells purified from stable mouse Snf5-deficient T cell lymphoma cell lines

label_protocol: RNA of interest is converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA.

extract_protocol: Total RNA was isolated from MEF and Lymphoma samples using RNA Trizol per the manufacturer’s protocol and Qiagen RNAeasy purification. RNA was hybridized to Affymetrix Mouse 430A 2.0 arrays, and CEL files were preprocessed using Robust Multichip Average (RMA).

tag: subpopulation


title: CD44 Low T-cell lymphoma, replicate 3


title: CD44 Low T-cell lymphoma, replicate 1


title: CD44 Low T-cell lymphoma, replicate 4


title: CD44 Hi T-cell lymphoma, replicate 4

source_name: CD44hicells purified from stable mouse Snf5-deficient T cell lymphoma cell lines


title: primary human: blood; FACS-sorted CD3+ cells (CLL024N)


title: CD44 Hi T-cell lymphoma, replicate 2


title: primary human: blood; FACS-sorted CD3+ cells (CLL011N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL019N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL035N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL017N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL018N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL016N)


title: CD44 Hi T-cell lymphoma, replicate 1


title: Control 3_new

status: Public on Oct 13 2011

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

description: Gene expression of control white matter

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 values were used to normalize the Agilent one-colour microarray signals. BEFORE 2013: Noramlization was done over all the cases included in each comparion (e.g. all 4 controls vs all 3 NAWMs)and log2fold changes were calculated with those normalized data. The log2fold change data matrix for each comparison [Control vs EL (=innate lesion), Control vs LL (=early demyelinated lesion), Control vs NAWM] is provided as a supplementary file on the Series records. Each file is a combination of the 7 Samples for each of the three comparisons described in the manuscript Fischer et al., 2012. UPDATE in 2013: Normalization was done over all 16 arrays.

source_name: Control white matter

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 (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: White matter

tag: disease state

value: control white matter


title: primary human: blood; FACS-sorted CD3+ cells (CLL008N_CD3)


title: Control 1_new

description: Gene expression of control white matter


title: Control 4_new

description: Gene expression of control white matter


title: primary human: blood; FACS-sorted CD3+ cells (CLL010N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL013N_CD3)


title: CD44 Hi T-cell lymphoma, replicate 3


title: Control 2_new

description: Gene expression of control white matter


title: primary human: blood; FACS-sorted CD3+ cells (CLL026N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL006N)


title: Multiple Sclerosis 3_2

description: Gene expression of initial lesion

source_name: Initial lesion

value: initial lesion


title: primary human: buccal swab (CLL005N)

source_name: primary human: buccal swab


title: primary human: blood; FACS-sorted CD3+ cells (CLL007N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL004N_CD3)


title: Multiple Sclerosis 1_2

description: Gene expression of early demyelinated lesion

source_name: Early demyelinated lesion

value: early demyelinated lesion


title: primary human: blood; FACS-sorted CD3+ cells (CLL009N_CD3)


title: Multiple Sclerosis 2_3


title: Multiple Sclerosis 1_1

description: Gene expression of normal appearing white matter

source_name: Normal appearing white matter

value: normal appearing white matter


title: Multiple Sclerosis 3_1


title: primary human: buccal swab (CLL002N)


title: Multiple Sclerosis 3_3


title: Multiple Sclerosis 2_2

description: Gene expression of initial lesion


title: Multiple Sclerosis 2_1


title: primary human: blood; FACS-sorted CD3+ cells (CLL020N_CD3)


title: PGL primary tumor 08T160

status: Public on Dec 31 2010

city: Madrid

first: Elena

middle: López

last: Jiménez

address: Melchor Fernandez Almagro nº3

department: Human Cancer Genetics

country: Spain

institute: Spanish National Cancer Centre

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to a established protocol by Agilent Technologies (Santa Clara, CA, USA)

scan_protocol: Images were scanned using Agilent scanner, G2565BA

data_processing: The data were normalized using the method  normexp in order to eliminate the background (Herrero et al.,Nucleic Acids Research, 2003) and limma library by Bioconductor ( Performing loess for intra-array correction and quantiles for inter-array correction)[Smyth et al., Bioinformatics, 2005]. Merged replicates (median) with GEPAS package (Herrero J et al., Nucleic Acids Research, 2003).

source_name: RNA extracted from primary tumors

label_protocol: 0.5 ug of tumoral amplified RNA was labeled with Cy5 and the same amount of the reference (Universal reference RNA from Stratagene) was labeled with Cy3

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Amplified RNA - MMLV-RT.

tag: tissue type

value: PGL primary tumor

source_name: Universal Human Reference RNA (Stratagene)

value: Pool of 10 cel lines (Adenocarcinoma, mammary gland Hepatoblastoma, liver Adenocarcinoma, cervix Embryonal carcinoma, testis Glioblastoma, brain Melanoma Liposarcoma Histiocytic lymphoma; macrophase; histocyte Lymphoblastic leukemiaPlasmacytoma; myeloma; B lymphocyte )


title: PCC primary tumor 08T157

value: PCC primary tumor


title: PGL primary tumor 08T152


title: PGL primary tumor 09T65


title: PCC primary tumor 08T161


title: PCC primary tumor 08T79


title: PCC primary tumor 08T155


title: PCC primary tumor #96


title: primary human: blood; FACS-sorted CD3+ cells (CLL022N_CD3)


title: PCC primary tumor #36


title: primary human: blood; FACS-sorted CD3+ cells (CLL061N_CD3)


title: PCC primary tumor #24


title: PCC primary tumor 146


title: PCC primary tumor #49


title: PCC primary tumor #2


title: PCC primary tumor 08T156


title: PCC primary tumor 08T154


title: PCC primary tumor 142


title: Small RNAs from Chlamydomonas reinhardtii under phosphate starvation

status: Public on Sep 30 2011

type: SRA

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

description:
CRE7
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

library_source: transcriptomic

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artefacts.

organism: Chlamydomonas reinhardtii

source_name: Phosphate starvation

extract_protocol: Total RNA was extracted  with the TriReagent (Molecular Research Center). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).

tag: growth protocol

value: culture

tag: stress

value: Phosphate starvation


title: PGL primary tumor JRSC

description: JRSC


title: PCC primary tumor 165


title: PCC primary tumor 166


title: PCC primary tumor PANIGALI

description: PANIGALI


title: PCC primary tumor 152


title: PCC primary tumor COLOM

description: COLOM


title: PCC primary tumor #7


title: PGL primary tumor CLAU

description: CLAU


title: PCC primary tumor 168


title: PGL primary tumor 230


title: Small RNAs from Chlamydomonas reinhardtii control

description:
CRE6
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

source_name: Control

value: Control


title: PCC primary tumor 09T43


title: PCC primary tumor 08T64


title: PCC primary tumor 07T204


title: PCC primary tumor 07T203


title: PCC primary tumor 124


title: PCC primary tumor 07T202


title: PCC primary tumor 07T205


title: Small RNAs from Volvox carteri under phosphate starvation

description:
VCA6
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

organism: Volvox carteri

source_name: Sulphate starvation


title: PCC primary tumor 122


title: PGL primary tumor 09T42


title: PCC primary tumor 245


title: Small RNAs from Chlamydomonas reinhardtii under sulphate starvation

description:
CRE8
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: Sulphate starvation


title: PGL primary tumor 07T126


title: PCC primary tumor 075


title: PCC primary tumor 07T177


title: PCC primary tumor 074


title: PGL primary tumor 07T157


title: PGL primary tumor 06T69


title: PCC primary tumor 060


title: PCC primary tumor 07T169


title: PCC primary tumor 06T367


title: PGL primary tumor 05T120


title: Small RNAs from Volvox carteri under sulphate starvation

description:
VCA5
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.


title: Small RNAs from Chara corallina thallus grown under no-phosphate conditions

status: Public on Apr 30 2011

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artifacts.

organism: Chara corallina

source_name: Thallus, no phosphate

growth_protocol:
Control: detached and incubated in culture medium.
No phosphate: detached and incubated in a culture medium with 1 mM each of CaCl2, MgCl2, KCl, and NaCl, pH 7.5.
No phosphate and salt stressed: detached and incubated in a culture medium with 1 mM each of CaCl2, MgCl2 and KCl as well as 65mMolal NaCl, about -3bar, pH 7.5.

extract_protocol: Total RNA was extracted with the Plant RNA Purification Reagent (Invitrogen). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000). Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: thallus

tag: condition

value: no phosphate


title: PCC primary tumor 07T158


title: PGL primary tumor 06T105


title: Small RNAs from Volvox carteri control

description:
VCA4
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.


title: PCC primary tumor 05T296


title: PGL primary tumor 08T57


title: PCC primary tumor 055


title: Small RNAs from Chara corallina thallus grown under no-phosphate and salt-stressed conditions

source_name: Thallus, no phosphate and salt stressed

value: no phosphate and salt stressed


title: PCC primary tumor 04T40


title: PCC primary tumor 04T282


title: PGL primary tumor 04T182


title: PGL primary tumor 04T321


title: PCC primary tumor 04T191


title: PCC primary tumor 03T345


title: PGL primary tumor 03T7


title: PGL primary tumor 03T343


title: PCC primary tumor 03T30


title: PCC primary tumor 04T152


title: PGL primary tumor 03T56


title: PCC primary tumor 03T23


title: PCC primary tumor 03T33


title: PCC primary tumor 03T32


title: PCC primary tumor 03T62


title: Small RNAs from Chara corallina thallus grown under control conditions

source_name: Thallus, control

value: control


title: PCC primary tumor 078


title: PCC primary tumor 01T168


title: PGL primary tumor 03T154


title: PCC primary tumor 03T29


title: PCC primary tumor 04T412


title: PCC primary tumor 03T151


title: PCC primary tumor 04T283


title: PCC primary tumor 03T246


title: PCC primary tumor 07T147


title: PCC primary tumor 04T192


title: PGL primary tumor 03T155


title: 5 dpl laser captured CCP replicate 3

status: Public on Oct 22 2010

city: Cambridge

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

institute: Cambridge University

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

data_processing: Data were filtered, removing any non expressed probes according to the detection p-value, then variance stabilization was applied and finally the data were normalised using quantile normalization.

organism: Rattus norvegicus

source_name: Rat caudal cerebellar peduncle

label_protocol: Standard Illumina hybridisation protocol

extract_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

treatment_protocol: Rat caudal cerebellar peduncles (CCP) were demyelinated using 0.1 % ethidium bromide.  The lesioned CCPs were selectively isolated from frozen brains using laser capture microdissections at 5, 14 and 28 days postlesion before RNA extraction and microarray analysis.

value: Sprague Dawley

value: 12 weeks at 0 dpl (days post lesion)

value: caudal cerebellar peduncles

tag: time

value: 5 dpl (days post lesion)


title: PZ_U133A_2_10-1187

status: Public on Sep 15 2010

first: Lakshmanan

middle: K

last: Iyer

state: MA

address: 136 Harrison Ave

department: Neuroscience

institute: Tufts University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to manufactuer's instructions on U133A 2 Array. GeneChips were washed and stained as per manufacturer's instructions.

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: bone marrow

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

tag: cell type

value: CD138-selected plasma cells

tag: cyclin d1 expression level

value: high


title: PZ_U133A_2_6-1001-rep


title: PZ_U133A_2_6_1304

value: low


title: PZ_U133A_2_3_1033


title: PGL primary tumor 04T292

value: PGL primary tumor

value: Pool of 10 cel lines (Adenocarcinoma, mammary gland Hepatoblastoma, liver Adenocarcinoma, cervix Embryonal carcinoma, testis Glioblastoma, brain Melanoma Liposarcoma Histiocytic lymphoma; macrophase; histocyte Lymphoblastic leukemiaPlasmacytoma; myeloma; B lymphocyte )


title: PZ_U133A_2_5_1169


title: PZ_U133A_2_8-1195


title: PZ_U133A_2__1_783NR


title: PZ_U133A_2_8_1392


title: 14 dpl laser captured CCP replicate 1

tag: tissue

value: 14 dpl (days post lesion)


title: PZ_U133A_2_4_1137


title: 5 dpl laser captured CCP replicate 1


title: PCC primary tumor 005

value: PCC primary tumor


title: 14 dpl laser captured CCP replicate 3


title: PZ_U133A_2_2_934


title: 5 dpl laser captured CCP replicate 2


title: PZ_U133A_2_7_1348


title: PZ_U133A_2_3-1003


title: PZ_U133A_2_9_1426


title: PZ_U133A_2_9-898


title: PZ_U133A_2_4-795