title: gDNA from contaminated site B, campaign 1, well P2 (SBC1P2)

description:
Complex environment.
gDNA extracted from contaminated site B, before ERD (enhanced reductive dechlorination) treatment (C1) in the well P2.

source_name: Chlorinated solvent contaminated site B, campaign 1, well P2


title: Burkitt Lymphoma5, miRNA

status: Public on Apr 03 2012

type: RNA

city: Madrid

first: Lorena

last: Di Lisio

address: C/ Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description:
251643611654_S01_miRNA-v1_95_May07_1_3_BL
Corresponds to GSM568271

hyb_protocol: Hybridization settings: 20 hours, at 55ºC, at 20rpm. Blocking agent, hybridization and washing buffers was performed according to Agilent's recommendations.

scan_protocol: Scan resolution 5um on an Agilent scanner.

data_processing: Limma package was used to import the data. After between-array median normalization by the R program, significant analysis of microarray (SAM) Excel macro was used.

molecule: total RNA

organism: Homo sapiens

source_name: Tumoral sample

label_protocol: 100ng of total RNA were dephosphorylated, denaturalizated, treated with ligase T4 and labelled with Cy3 for 2 hours at 16ºC.

extract_protocol: Total RNA was extracted by Trizol reagent (Invitrogen, Carlsbad, CA, USA).

tag: tissue

value: B-cell lymphoma

tag: tumor type

value: Burkitt lymphoma


title: Burkitt Lymphoma1, miRNA

description:
251643611653_S01_miRNA-v1_95_May07_2_1_BL
Corresponds to GSM568267


title: gDNA from contaminated site B, campaign 1, well P1 (SBC1P1)

type: genomic

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

country: France

institute: CNRS - Blaise Pascal University

description:
Complex environment.
gDNA extracted from contaminated site B, before ERD (enhanced reductive dechlorination) treatment (C1) in the well P1.

hyb_protocol: For each hybridization experiment, labeled gDNA were vacuum dried and resuspended in the NimbleGen Hybridization Buffer. The arrays were hybridized on a 4-bay NimbleGen Hybridization System (Roche NimbleGen) at 42°C for 72 hr. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols.

scan_protocol: Arrays were scanned using a Scanner Innoscan 900AL (Innopsys, Carbonne, France) at 2 μm resolution. Individual array images were acquired independently, adjusting the PMT gain for each image as recommended using the software Mapix® (Innopsys). Then, for each array image, raw expression data was extracted using the NimbleScan software v2.5. (Roche NimbleGen) and feature intensities were exported as .pair files.

data_processing: The background noise was determined using random probes present on the microarrays (5,707 probes in our experiment). This background noise is defined by two components: the background median intensity (Bposition) and its dispersion (Bdispersion). Finally, a modified signal-to-noise ratio called SNR’ and based on the formula of Verdik (Verdick, D., Handran, S. and Pickett, S. (2002) In LLC, D. P. (ed.), In G. Kamberova (ed.), DNA array image analysis: nuts and bolts. Salem, MA., pp. p. 83-98) is calculated as follows in order to reduce-centralize our data: SNR’ = (probe signal intensity - Bposition)/ Bdispersion. However, spatial effect across array surface is a predominant within-slide experimental artifact that needs to be eliminated before any other normalization procedure (Wang, X., He, H., Li, L., Chen, R., Deng, X.W. and Li, S. (2006) NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics, 22, 2955-2957). Thus, for all array images obtained in this work, surface was segmented to 16 sub-squares according to probe position (X, Y) indicated in pair report. A Perl script was developed to calculate local background noise in all sub-squares and the median SNR’ retrieved from the eight replicates of each probe. Finally, another Perl script was implemented to summarize each replicate probe treated and determine the median value between the eight replicates. Positive hybridization was considered significant for probes having an SNR’ > 1.5 (value to avoid all false positives).

molecule: genomic DNA

organism: groundwater metagenome

source_name: Chlorinated solvent contaminated site B, campaign 1, well P1

label_protocol: The BioPrime Total Genomic Labelling System (Invitrogen, Carlsbad, California, USA) was used to label the gDNA with Alexa Fluor 3 or 5 fluorescent dyes. The reactions were performed from 1 µg of gDNA template following the manufacturer's instructions and allowed an increase of at least 6-fold the amount of starting gDNA material.

growth_protocol: Groundwater samples were collected by SITA Remediation Company (Lyon, France) from four contaminated sites (B, F, G and H) by direct pumping in four monitoring wells per site (P1, P2, P3 and P4) drilled in the deep aquifer. P1: well located upstream to the contamination source. P2: well in the contamination source. P3 and P4: wells located downstream to the contamination source. For site B, the monitoring of ERD demonstration was performed through a total of 5 sampling campaigns: C1 (T=0), C2 (T=104 days), C3 (T=231 days), C4 (T=291 days) and C5 (T=378 days). For the three other sites (F, G and H), only one sampling campaign was performed after the treatment.

extract_protocol: Groundwater samples were transferred to the laboratory, filtered under vacuum and collected onto a 47 mm 0.2 µm pore size GTTP filter (Millipore). Filters were then cut in pieces and placed into 900 µL of nucleic extraction buffer (50 mM glucose, 10 mM EDTA, 25 mM Tris-HCl pH 8.0) as described by Vetriani (Vetriani, C., Tran, H.V. and Kerkhof, L.J. (2003) Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea. Appl. Environ. Microbiol., 69, 6481-6488). In this protocol, freeze-thaw cycles were replaced by beat betting 1 min at 30 Hz with 1 g of glass beads of ≤106 μm in diameter (Sigma-Aldrich). gDNA were extracted using a standard phenol-chloroform-isoamyl alcohol (25:24:1) method, followed by a second extraction with an equal volume of chloroform. Nucleic acids were then precipitated, washed in 70% ethanol and resuspended in nuclease-free water.

tag: origin

value: monitoring well from TCE contaminated site

tag: site

value: B

tag: sampling campaign

tag: well

tag: treatment

tag: sample type

value: environmental sample


title: gDNA from contaminated site B, campaign 1, well P4 (SBC1P4)

description:
Complex environment.
gDNA extracted from contaminated site B, before ERD (enhanced reductive dechlorination) treatment (C1) in the well P4.

source_name: Chlorinated solvent contaminated site B, campaign 1, well P4


title: Burkitt Lymphoma5, mRNA

description: US22502553_251485032089_S01_GE2-v5_95_Feb07_1_3-BL

hyb_protocol: Hybridization settings: 17 hours, at 65ºC, at 10rpm. Blocking agent, hybridization and washing buffers was performed according according to Agilent's recommendations.

data_processing: Normalization type: lowess, quantiles, normexp (R program). Analysis: t-test (limma).

label_protocol: 500ng RNA were used for cDNA and fluorescent cRNA synthesis. cRNA was purified and hybridized. All reagents and protocols were performed according to Agilent's recommendations.

extract_protocol: Total RNA was extracted by Trizol reagent, purified by QIAGEN RNeasy columns and treated with DNase enzyme.

tag: tissue type

source_name: Reference pool

value: reference


title: Burkitt Lymphoma3, mRNA

description: US22502553_251485032088_S01_GE2-v5_95_Feb07_1_2-BL


title: SAMPLE 28 Control_Day28

status: Public on Apr 02 2012

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner.

data_processing: The log2 of median signal intensites were cyclic lowess normalized and the technical replicates were averaged using the median.

organism: Mus musculus

source_name: Lung Tissue

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Tech, Mississauga, ON, Canada).

extract_protocol: Total RNA enriched with small RNA was extracted using the miRvana isolation kit (Ambion, Canada)

tag: gender

value: female

tag: strain

value: lung

value: 0.9% NaCl MilliQ water containing 10% v/v acellular BAL

tag: day of sacrifice


title: Burkitt Lymphoma4, mRNA

description: US22502553_251485032088_S01_GE2-v5_95_Feb07_1_4-BL


title: SAMPLE 30 Exposed_Day28

value: 0.162 mg Printex 90 in vehicle


title: SAMPLE 26 Exposed_Day1


title: SAMPLE 29 Exposed_Day1


title: Burkitt Lymphoma2, mRNA

description: US22502553_251485032088_S01_GE2-v5_95_Feb07_1_1-BL


title: SAMPLE 31 Control_Day3


title: SAMPLE 25 Control_Day3


title: SAMPLE 32 Control_Day28


title: SAMPLE 33 Exposed_Day3


title: SAMPLE 23 Exposed_Day28


title: Burkitt Lymphoma1, mRNA

description: US22502553_251485032087_S01_GE2-v5_95_Feb07_1_4-BL


title: Lymph Node3, mRNA

description: US22502553_251485029245_S01_GE2-v5_95_Feb07_1_3_LYMPH-NODE

source_name: Nom-tumoral control

value: lymph node


title: SAMPLE 22 Control_Day28


title: SAMPLE 21 Control_Day3


title: SAMPLE 20 Exposed_Day28


title: SAMPLE 18 Control_Day28


title: SAMPLE 27 Control_Day1


title: SAMPLE 19 Exposed_Day1


title: SAMPLE 17 Control_Day1


title: SAMPLE 14 Control_Day3


title: SAMPLE 13 Control_Day1


title: SAMPLE 16 Exposed_Day3


title: SAMPLE 12 Exposed_Day28


title: SAMPLE 11 Exposed_Day3


title: SAMPLE 24 Control_Day1


title: SAMPLE 10 Control_Day28


title: SAMPLE 9 Control_Day3


title: SAMPLE 8 Exposed_Day28


title: SAMPLE 15 Exposed_Day1


title: SAMPLE 7 Exposed_Day1


title: SAMPLE 6 Control_Day28


title: Exposed 2

source_name: lung tissue

value: 0.268 mg Printex 90


title: SAMPLE 2 Control_Day3


title: SAMPLE 3 Exposed_Day1


title: Exposed 3


title: SAMPLE 1 Control_Day1


title: Control 3

value: nanopure water


title: SAMPLE 5 Control_Day1


title: Control 4


title: Exposed 1


title: Exposed 4


title: Control 1


title: Control 2


title: SAMPLE 4 Exposed_Day3


title: sample.64 Day 28 Dose 18ug

hyb_protocol: Agilent Mouse G4852A  Microarrays (containing approximately 44,000 probes) were hybridized with 300 ng Cy5-labelled liver RNA and 300 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software version 10.7.3.1

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

label_protocol: Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

treatment_protocol: female C57BL/6 mice (Taconic, Denmark) were acquired at 5-6 weeks of age and given food (Altromin no 1324; Christian Petersen, Denmark) and water ad libitum. Printex 90 was suspended by sonication in 0.9% NaCl MilliQ water containing 10% v/v acellular bronchial alveolar lavage fluid from C57BL/6 mice. A 40 µl suspension was instilled followed by 150 μl air.

value: Day 28 Dose 18ug

tag: sampleID

tag: day

tag: dose

value: 18 ug

source_name: universal mouse reference

extract_protocol: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))


title: sample.58 Day 3 Dose 18ug

value: Day 3 Dose 18ug


title: sample.48 Day 3 Dose 162ug

value: Day 3 Dose 162ug


title: sample.71 Day 1 Control

value: Day 1 Control


title: sample.66 Day 3 Dose 162ug


title: sample.62 Day 3 Dose 54ug

value: Day 3 Dose 54ug

value: 54 ug


title: sample.54 Day 3 Control

value: Day 3 Control


title: sample.65 Day 1 Dose 162ug

value: Day 1 Dose 162ug


title: sample.49 Day 28 Control

value: Day 28 Control

value: reference


title: sample.61 Day 1 Dose 54ug

value: Day 1 Dose 54ug

value: female


title: sample.70 Day 28 Control


title: sample.59 Day 28 Dose 18ug


title: sample.55 Day 28 Control


title: sample.57 Day 1 Dose 18ug

value: Day 1 Dose 18ug


title: sample.46 Day 3 Dose 18ug


title: sample.69 Day 3 Control


title: sample.45 Day 3 Control


title: sample.72 Day 3 Dose 18ug


title: sample.56 Day 1 Dose 18ug


title: sample.63 Day 28 Dose 54ug

value: Day 28 Dose 54ug


title: sample.50 Day 28 Dose 18ug


title: sample.53 Day 1 Control


title: sample.60 Day 28 Dose 54ug


title: sample.44 Day 1 Dose 162ug


title: sample.47 Day 3 Dose 54ug


title: sample.42 Day 1 Dose 18ug


title: sample.43 Day 1 Dose 54ug


title: sample.41 Day 1 Control


title: sample.38 Day 28 Dose 18ug


title: sample.39 Day 28 Dose 54ug


title: sample.52 Day 28 Dose 162ug

value: Day 28 Dose 162ug


title: sample.40 Day 28 Dose 162ug


title: sample.34 Day 3 Dose 18ug


title: sample.30 Day 1 Dose 18ug


title: sample.27 Day 28 Dose 162ug


title: sample.37 Day 28 Control


title: sample.35 Day 3 Dose 54ug


title: sample.24 Day 28 Dose 162ug


title: sample.33 Day 3 Control


title: sample.23 Day 28 Dose 54ug


title: sample.25 Day 1 Dose 162ug


title: sample.20 Day 3 Dose 162ug


title: sample.28 Day 1 Dose 54ug


title: sample.29 Day 1 Control


title: sample.19 Day 28 Dose 18ug


title: sample.22 Day 3 Dose 54ug


title: sample.18 Day 3 Dose 18ug


title: sample.36 Day 3 Dose 162ug


title: sample.26 Day 3 Dose 162ug


title: sample.32 Day 1 Dose 162ug


title: sample.21 Day 1 Dose 54ug


title: sample.15 Day 28 Control


title: sample.31 Day 1 Dose 54ug


title: sample.14 Day 3 Control


title: sample.13 Day 1 Control


title: sample.17 Day 1 Dose 18ug


title: 5368138051_F

city: Los Angeles

first: Mete

last: Civelek

state: CA

address: 675 Charles E. Young Dr. S. MRL 3220

department: Medicine

country: USA

institute: University of California Los Angeles

description: Replicate 1

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay (Catalogue Number BD-901-1003)

scan_protocol: Illumina iScan System with default settings

data_processing: 19,306 probes were removed due to (i) lack of mapping to any genomic or transcriptomic location, (ii) mapping to multiple genomic or transcriptomic locations, and (iii) presence of single nucleotide polymorphisms in the probe sequence that may affect hybridization efficiency using the methodology developed by Barbosa-Morais et al. (PMID:19923232). The remaining 29,497 probes were processed using non-parametric background correction followed by quantile normalization with both control and expression probes utilizing the neqc function in the limma package (R v2.13.0) (PMID:20929874).

label: Biotin

source_name: subcutaneous adipose

label_protocol: Ambion TotalPrep -96 RNA Amplification kit (Catalogue Number 4393543)

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

value: subcutaneous adipose

tag: sample id

tag: age


title: 5368138051_C

description: Replicate 1

tag: tissue


title: 5368138051_I

description: Replicate 2


title: 5368138051_D

description: Replicate 1


title: sample.6 Day 3 Dose 18ug


title: sample.112 Day 28 Dose 162ug


title: 5368138051_H

description: Replicate 1


title: 5368138051_E

description: Replicate 1


title: sample.111 Day 28 Dose 54ug


title: 5368138051_J

description: Replicate 2


title: 5368138051_L

description: Replicate 2


title: sample.8 Day 3 Dose 162ug


title: sample.16 Day 1 Dose 162ug


title: 5368138051_B

description: Replicate 1


title: sample.110 Day 28 Dose 18ug

value: Day 28 Dose 18ug


title: 5368138051_K

description: Replicate 2


title: 5368138051_A

description: Replicate 1


title: 5368138050_L

description: Replicate 1


title: 5368138051_G

description: Replicate 1


title: sample.68 Day 3 Dose 54ug


title: Exposed_216

source_name: Hepatic Tissue

value: 0.162 mg Printex 90 carbon black nanoparticles


title: sample.2 Day 1 Dose 18ug

value: 18 ug


title: sample.4 Day 1 Dose 162ug


title: sample.3 Day 1 Dose 54ug


title: Control_598


title: Exposed_212


title: 5368138050_H

description: Replicate 1


title: 5368138050_E

description: Replicate 1


title: 5368138050_F

description: Replicate 1


title: 5368138050_D

description: Replicate 1


title: 5368138050_K

description: Replicate 1


title: Control_574


title: 5368138050_J

description: Replicate 1


title: 5368138050_A

description: Replicate 1


title: sample.5 Day 3 Control


title: Control_599


title: Exposed_194


title: 5368138050_I

description: Replicate 1


title: Exposed_177


title: 5368138050_C

description: Replicate 1


title: 5368138050_B

description: Replicate 1


title: 5368138034_L

description: Replicate 1


title: Control_549


title: Control_575


title: Control_596


title: Control_551


title: Exposed_196


title: 5368138034_K

description: Replicate 1


title: Control_572


title: Exposed_214


title: 5368138034_I

description: Replicate 1


title: Exposed_179


title: 5368138034_H

description: Replicate 1


title: 5368138034_G

description: Replicate 1


title: Control_548


title: Control_552


title: 5368138034_D

description: Replicate 1


title: Exposed_215


title: Exposed_213


title: 5368138034_F

description: Replicate 1


title: 5368138034_J

description: Replicate 1


title: Exposed_195


title: Control_595


title: Exposed_197


title: 5368138034_B

description: Replicate 1


title: Control_570


title: HS_15

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

description: childhood adrenocortical tumor

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: Proteinase K method. The detailed protocol can be found in PMID:18786438.

value: France

value: M

tag: age (months)

tag: histological type

value: carcinoma

tag: tnm staging

tag: Stage

value: II

tag: tp53 mutation

value: wt

tag: virilization

value: Y

tag: cushing syndrome

value: N

value: surgical resection only

tag: follow-up (months)

value: Alive (9)


title: 5368138008_L

description: Replicate 1


title: 5368138034_A

description: Replicate 1


title: 5368138034_E

description: Replicate 1


title: Control_600

tag: treatment

tag: gender

value: female

tag: sample type

value: reference


title: Exposed_176

tag: strain


title: Control_550


title: 5368138034_C

description: Replicate 1


title: 5368138008_I

description: Replicate 1


title: Exposed_193


title: 5368138008_H

description: Replicate 1


title: 5368138008_K

description: Replicate 1


title: Exposed_180


title: 5368138008_J

description: Replicate 1


title: 5368138008_E

description: Replicate 1


title: 5368138008_G

description: Replicate 1


title: Control_547


title: Control_573


title: 5368138008_D

description: Replicate 1


title: 5368138008_F

description: Replicate 1


title: 5368138008_A

description: Replicate 1


title: 5368138008_C

description: Replicate 1


title: 5368138050_G

description: Replicate 1


title: 5368138007_L

description: Replicate 1


title: Control 0-5 Male

hyb_protocol: In brief, samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Agilent Technologies Inc., Mississauga, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase, purified by RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada) and were hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) at 60ºC overnight.

scan_protocol: Following a final wash, arrays were scanned on an Agilent G2505B scanner. Data were acquired from microarray images using Agilent Feature Extraction software version 9.5.3.1.

data_processing: A reference design (Kerr 2003; Kerr and Churchill 2007) was used to analyse gene expression microarray data. The background fluorescence was measured using the (-)3xSLv1 probes; probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent (within the background signal). Data were normalized using LOWESS in R (2004).

source_name: Stratagene Universal Reference RNA

label_protocol: Individual total RNA (250 ng) samples from five male and female newborns per treatment group (control or exposed in utero to high dose only) and universal reference total RNA (Stratagene, Mississauga, ON, Canada) was used to synthesize double-stranded cDNA and cyanine labelled cRNA according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies Inc., Mississauga, ON, Canada).

extract_protocol: Total RNA was isolated from the liver tissues of PND2 offspring (n=5/group) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada). RNA quality was confirmed using a nanodrop. RNA samples showing A260/280 ratios between 2.0 - 2.1 and A260/230 ratios between 1.8 - 2.3 were further analysed for RNA integrity using an Agilent bioanalyzer (Agilent Technologies, Inc., Mississauga, ON, Canada). Samples with RNA integrity numbers (RIN) between 7.0 and 9 were used to carry out microarray analysis and RT-PCR validation.

treatment_protocol: Eighty time-mated, nulliparous, young adult mice (C57BL/6BomTac, Taconic Europe, Ejby, DK) were received on gestation day three (GD 3). Mice were distributed in cages of five or six and assigned to four experimental groups: controls (24 mice weighing 23.0±1.3 g), low dose of 11 µg/animal CB (17 mice weighing 22.4±1.2 g), medium dose of 54 µg/animal CB (17 mice 22.6±1.0 g), and high dose of 268 µg/animal CB (22 mice weighing 22.9±0.9 g). Mice were housed in white polypropylene (type III) cages with bedding (Jeluxyl HW 300/500, JELU-Werk J. Ehrler GmbH & Co.KG, Rosenberg, Germany). Soft paper wool (Enviro-Dri) was added for nest building and cages were enriched with mini rodent tunnels and small aspen wood blocks (all from Lillico, Betchworth, UK). Enrichment was removed during lactation. Environmental conditions were controlled (12 hour light from 6.00 a.m., temperature 21 ± 2°C, humidity 50 ± 5%, ventilation 13 air changes per hour). Tap water and food (Altomin1324, Altromin GmbH, Lage, Germany) were available ad libitum. On GD 4 and 7, dams were weighed and their health condition was checked. No animals were eliminated from the study as moribund or with obvious health concerns. The body weight of each dam was also recorded on GD 10, 13, 15 and 18 immediately before the exposures. All the procedures complied with the EC Directive 86/609/EEC and the Danish law regulating experiments on animals (The Danish Ministry of Justice, Animal Experiments Inspectorate, Permit 2006/561-1123).

tag: reference

value: Stratagene Universal Reference RNA

molecule: polyA RNA

source_name: Control 0-5 Male

value: male

value: liver

value: control

value: postnatal day 2


title: 5368138007_I

description: Replicate 1

value: subcutaneous adipose


title: 5368138008_B

description: Replicate 1


title: 5368138007_J

description: Replicate 1


title: 5368138007_E

description: Replicate 1


title: 5368138007_G

description: Replicate 1


title: Control 0-8 Female

source_name: Control 0-8 Female

tag: dose


title: 5368138007_K

description: Replicate 1

tag: sample id


title: Hi 3-13 Female

source_name: Hi 3-13 Female

value: high

tag: age


title: Hi 3-9 Male

source_name: Hi 3-9 Male

tag: tissue


title: Control 0-4 Female

source_name: Control 0-4 Female


title: Hi 3-5 Male

source_name: Hi 3-5 Male


title: 5368138007_C

description: Replicate 1


title: Hi 3-8 Female

source_name: Hi 3-8 Female


title: 5368138007_H

description: Replicate 1


title: Hi 3-7 Male

source_name: Hi 3-7 Male


title: Hi 3-6 Female

source_name: Hi 3-6 Female


title: 5368138007_F

description: Replicate 1


title: Control 0-6 Male

source_name: Control 0-6 Male


title: Control 0-9 Female

source_name: Control 0-9 Female


title: Control 0-3 Male

source_name: Control 0-3 Male


title: 5368138007_B

description: Replicate 1


title: Control 0-2 Female

source_name: Control 0-2 Female


title: Control 0-1 Male

source_name: Control 0-1 Male


title: Hi 3-4 Female

source_name: Hi 3-4 Female


title: 5368138006_L

description: Replicate 1

source_name: subcutaneous adipose


title: 5368138007_A

description: Replicate 1


title: Hi 3-14 Male

source_name: Stratagene Universal Reference RNA

source_name: Hi 3-14 Male


title: Control 0-11 Female

source_name: Control 0-11 Female


title: 5368138006_K

description: Replicate 1


title: 5368138006_I

description: Replicate 1


title: 5368138006_J

description: Replicate 1


title: Control 0-7 Male

source_name: Control 0-7 Male


title: Medium 50

data_processing:
A reference design (Kerr 2003; Kerr and Churchill 2007) was used to analyse gene expression microarray data. The background fluorescence was measured using the (-)3xSLv1 probes; probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent (within the background signal). Data were normalized using LOWESS in R (2004).
RawCy5 and RawCy3 are the median signal intensities for the Cy5 and Cy3 channels on each microarray. NormCy5 and NormCy3 are the loess normalized signal intensities for the Cy5 and Cy3 channels within each array; this is a within-array normalization performed separately for each array. Flag indicates whether the median signal intensity falls in the background, i.e below threshold calculated from the negative controls (mean plus three standard deviations of the negative controls.) Log.Ratio is calculated as log2(NormCy5/NormCy3)

label_protocol: Individual total RNA (250 ng) samples from 5 dams per treatment group (control or exposed to low, medium and high dose) and universal reference total RNA (Stratagene, Mississauga, ON, Canada) were used to synthesize double-stranded cDNA and cyanine labelled cRNA (Agilent Linear Amplification Kits, Agilent Technologies Inc., Mississauga, ON, Canada) as described in {Halappanavar, 2011 #48}. In brief, samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Agilent Technologies Inc., Mississauga, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase, purified by RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada) and were hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) at 60ºC overnight. Following a final wash, arrays were scanned on an Agilent G2505B scanner. Data were acquired from microarray images using Agilent Feature Extraction software version 9.5.3.1.

extract_protocol: Total RNA was isolated from the lung tissues of dams (n=5/group) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada). RNA quality was confirmed using a nanodrop. RNA samples showing A260/280 ratios between 2.0 - 2.1 and A260/230 ratios between 1.8 - 2.3 were further analysed for RNA integrity using an Agilent bioanalyzer (Agilent Technologies, Inc., Mississauga, ON, Canada). Samples with RNA integrity numbers (RIN) between 7.0 and 9 were used to carry out microarray analysis and RT-PCR validation.

source_name: Time-mated mice lung tissue

value: medium

value: lung


title: High 65

hyb_protocol: In brief, samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Agilent Technologies Inc., Mississauga, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase, purified by RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada) and were hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) at 60ºC overnight. Following a final wash, arrays were scanned on an Agilent G2505B scanner. Data were acquired from microarray images using Agilent Feature Extraction software version 9.5.3.1.


title: 5368138006_H

description: Replicate 1


title: 5368138006_E

description: Replicate 1


title: 5368138006_G

description: Replicate 1


title: Medium 49


title: Low 36

value: low


title: 5368138006_B

description: Replicate 1


title: 5368138006_D

description: Replicate 1


title: 5368138006_F

description: Replicate 1


title: Low 31


title: High 63


title: Control 18


title: Control 15


title: 5368138006_C

description: Replicate 1


title: Medium 48


title: 5361198030_L

description: Replicate 1


title: 5361198030_J

description: Replicate 1


title: 5361198030_K

description: Replicate 1


title: High 64


title: 5361198030_H

description: Replicate 1


title: High 62


title: Low 28


title: 5361198030_G

description: Replicate 1


title: Control 7


title: 5361198030_I

description: Replicate 1


title: Low 27


title: Control 14


title: 5368138006_A

description: Replicate 1


title: Medium 47


title: 5361198030_F

description: Replicate 1


title: 5368138007_D

description: Replicate 1


title: 5361198030_D

description: Replicate 1


title: Control 4


title: Medium 46


title: High 60


title: 5361198028_H

description: Replicate 1


title: B5_90_6, rep5

description:
V65
Sampled immediately post-treatment.

hyb_protocol: Labelled cRNA was hybridized to Agilent 22K mouse development microarrays (~20,000 unique 60-mer oligonucleotides; Agilent Technologies Inc., USA) at 60ºC overnight.

scan_protocol: Arrays were scanned on a ScanArray Express (Perkin-Elmer Life Sciences), and data were acquired with ImaGene 5.5 (BioDiscovery Inc.).

data_processing: Non-background-subtracted median signal intensities were Lowess normalized in R using the transform.madata function of the maanova library.

source_name: MutaMouse FE1 pulmonary cell line, 90 ug/ml of CSC from Brand 5, harvested immediately after exposure

label_protocol: Total RNA samples from 5 independent replicates from each treatment group and time point were analyzed alongside matched solvent-exposed controls. A reference sample (Stratagene Universal Mouse Reference RNA) was hybridized to each microarray as an internal control and for normalization. Double-stranded cDNA and Cyanine-labelled cRNA were generated according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies). Experimental samples were labelled with Cyanine 3-CTP, and reference RNA with Cyanine 5-CTP (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada). T7 RNA polymerase was used to transcribe Cyanine-labelled cRNA targets, followed by purification with RNeasy Mini Kits (Qiagen).

growth_protocol: The FE1 cell line, which was derived from Muta™Mouse lung epithelial cells, was cultured as described in White et al. Environ Mol Mutagen 42 (2003) 166-184.Briefly, cells were cultured in 1:1 DMEM:F12 nutrient mixture supplemented with 2% FBS, 2 mM glutamine, 100 U/ml penicillin G, 100 ug/ml streptomycin sulphate, and 1 ng/ml murine epidermal growth factor (Invitrogen Life Technologies, Canada). Incubations were conducted at 37˚C, 95% humidity, and 5% CO2. Confluence (%) was determined using a replicate plate. Cells on replicate plates were trypsinized and aliquots used to assess cell numbers using a Coulter Particle Counter (Beckman Coulter, USA). This measurement was compared with a pre-determined cell count for a completely confluent plate (100%).

extract_protocol: RNA was isolated using TRIzol® LS Reagent (Invitrogen Life Technologies, Canada) and RNeasy Mini columns (Qiagen, Canada). RNA quality was verified using an Agilent Bioanalyzer (Agilent Technologies, USA). RNA quality was determined acceptable by a 28S:18S ratio of at least 1.7 and an Absorbance 260/280 minimum of 1.8 using a UV spectrophotometer.

treatment_protocol: The combustion of the cigarettes and preparation of the cigarette smoke condensate (CSC) samples was conducted by Labstat International Inc. (Kitchener, Ontario). The cigarettes were smoked using a Borgwaldt 20 port rotary smoking machine following International Organization for Standardization (ISO) standard 3308 (i.e., puff volume of 35 mL, puff duration of 2 s, puff interval of 60 s). The smoke was passed through a 92 mm glass fibre filter disk for particulate matter collection according to the Health Canada official test method. To prepare condensate samples, filter pads were placed in a flask containing dimethyl sulfoxide (DMSO) (ACS spectrophotometric grade, >99.9%) and shaken on a wrist-action shaker (model 3589, Barnstead International, Melrose Park, IL) for 20 min. Each sample was standardized to a concentration of 30mg TPM per mL of DMSO. For microarray analysis, FE1 cells were propagated from one vial of cryopreserved stock from passage # 19. Cells were exposed to CSC from 3 brands: Brand #1 Full Flavor; Brand #3 – Regular; Brand #5 – Light King Size. Experiments were performed on 5 replicates per condition (i.e., n=5 per group). Cells were exposed at 70% confluence in 150 mm plates to either 45 µg/ml or 90 µg/ml CSC alongside cells exposed to 1% DMSO (Sigma-Alderich, Canada) in 1:1 DMEM:F12 (without FBS). Cells were exposed to CSC for 6 hours and then either: (a) immediately harvested, or (b) washed in PBS and cultured for another 4 hours in fresh media. The two time points were called 6 hours or 10 hours (6 hours exposure, 4 hours recovery for the latter). Cells were harvested with TRIzol (Invitrogen) and stored at -80oC.

value: MutaMouse

tag: cell line

tag: cell type

value: immortalized pulmonary epithelial cells

value: 90 ug/ml of CSC from Brand 5

tag: treatment duration

value: 6 hours

tag: sampling time

value: 6 hours (harvested immediately after exposure)

source_name: Universal Mouse Reference RNA

extract_protocol: Stratagene Universal Mouse Reference RNA (Catalog #740100; Stratagene, La Jolla, CA, USA).

value: reference derived from 11 mouse cell lines


title: 5361198028_K

description: Replicate 1


title: 5361198030_B

description: Replicate 1


title: 5361198030_C

description: Replicate 1


title: Low 25

value: female


title: 5361198028_L

description: Replicate 1


title: B5_90_6, rep1

description:
V9
Sampled immediately post-treatment.


title: B3_45_6, rep1

description:
V7
Sampled immediately post-treatment.

source_name: MutaMouse FE1 pulmonary cell line, 45 ug/ml of CSC from Brand 3, harvested immediately after exposure

value: 45 ug/ml of CSC from Brand 3


title: 5361198030_A

description: Replicate 1


title: 5361198028_J

description: Replicate 1


title: B3_90_6, rep1

description:
V8
Sampled immediately post-treatment.

source_name: MutaMouse FE1 pulmonary cell line, 90 ug/ml of CSC from Brand 3, harvested immediately after exposure

value: 90 ug/ml of CSC from Brand 3


title: 5361198028_I

description: Replicate 1


title: B5_45_6, rep5

description:
V64
Sampled immediately post-treatment.

source_name: MutaMouse FE1 pulmonary cell line, 45 ug/ml of CSC from Brand 5, harvested immediately after exposure

value: 45 ug/ml of CSC from Brand 5


title: 5361198030_E

description: Replicate 1


title: B3_90_6, rep5

description:
V63
Sampled immediately post-treatment.


title: B1_90_6, rep4

description:
V60
Sampled immediately post-treatment.

source_name: MutaMouse FE1 pulmonary cell line, 90 ug/ml of CSC from Brand 1, harvested immediately after exposure

value: 90 ug/ml of CSC from Brand 1


title: B1_45_6, rep5

description:
V66
Sampled immediately post-treatment.

source_name: MutaMouse FE1 pulmonary cell line, 45 ug/ml of CSC from Brand 1, harvested immediately after exposure

value: 45 ug/ml of CSC from Brand 1


title: B1_45_6, rep1

description:
V6
Sampled immediately post-treatment.


title: DMSO_6, rep4

description:
V61
Sampled immediately post-treatment.

source_name: MutaMouse FE1 pulmonary cell line, 1% DMSO, harvested immediately after exposure

value: 1% DMSO


title: 5361198028_E

description: Replicate 1

value: subcutaneous adipose


title: 5361198028_B

description: Replicate 1


title: 5361198028_D

description: Replicate 1


title: B5_90_10, rep5

description:
V55
Following treatment, cells were put in fresh media and sampled 4 hours later.

source_name: MutaMouse FE1 pulmonary cell line, 90 ug/ml of CSC from Brand 5, harvested after 4-hour recovery

value: 10 hours (harvested after 4-hour recovery)


title: 5361198023_L

description: Replicate 1


title: B1_90_10, rep5

description:
V57
Following treatment, cells were put in fresh media and sampled 4 hours later.

source_name: MutaMouse FE1 pulmonary cell line, 90 ug/ml of CSC from Brand 1, harvested after 4-hour recovery


title: B3_45_6, rep5

description:
V62
Sampled immediately post-treatment.


title: B5_45_6, rep4

description:
V52
Sampled immediately post-treatment.


title: B3_90_10, rep4

description:
V53
Following treatment, cells were put in fresh media and sampled 4 hours later.

source_name: MutaMouse FE1 pulmonary cell line, 90 ug/ml of CSC from Brand 3, harvested after 4-hour recovery


title: B3_45_10, rep5

description:
V59
Following treatment, cells were put in fresh media and sampled 4 hours later.

source_name: MutaMouse FE1 pulmonary cell line, 45 ug/ml of CSC from Brand 3, harvested after 4-hour recovery


title: 5361198028_G

description: Replicate 1

source_name: subcutaneous adipose


title: B5_90_6, rep4

description:
V51
Sampled immediately post-treatment.


title: 5361198028_C

description: Replicate 1


title: DMSO_10, rep5

description:
V58
Following treatment, cells were put in fresh media and sampled 4 hours later.

source_name: MutaMouse FE1 pulmonary cell line, 1% DMSO, harvested after 4-hour recovery


title: B5_45_10, rep4

description:
V54
Following treatment, cells were put in fresh media and sampled 4 hours later.

source_name: MutaMouse FE1 pulmonary cell line, 45 ug/ml of CSC from Brand 5, harvested after 4-hour recovery


title: 5361198023_D

description: Replicate 1


title: B5_90_10, rep1

description:
V5
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198023_J

description: Replicate 1


title: B1_45_10, rep5

description:
V56
Following treatment, cells were put in fresh media and sampled 4 hours later.

source_name: MutaMouse FE1 pulmonary cell line, 45 ug/ml of CSC from Brand 1, harvested after 4-hour recovery


title: B3_45_6, rep4

description:
V50
Sampled immediately post-treatment.


title: 5361198023_F

description: Replicate 1


title: 5361198028_A

description: Replicate 1


title: 5361198023_H

description: Replicate 1


title: DMSO_6, rep3

description:
V48
Sampled immediately post-treatment.


title: 5361198023_E

description: Replicate 1


title: 5361198023_I

description: Replicate 1


title: 5361198023_K

description: Replicate 1


title: 5361198023_G

description: Replicate 1


title: B3_90_6, rep4

description:
V49
Sampled immediately post-treatment.


title: 5361198023_C

description: Replicate 1


title: 5361198028_F

description: Replicate 1


title: B1_45_6, rep4

description:
V47
Sampled immediately post-treatment.


title: B1_90_6, rep3

description:
V46
Sampled immediately post-treatment.


title: B1_45_6, rep3

description:
V45
Sampled immediately post-treatment.


title: 5361198022_J

description: Replicate 1


title: B1_90_6, rep2

description:
V42
Sampled immediately post-treatment.


title: 5361198022_H

description: Replicate 1


title: 5361198022_L

description: Replicate 1


title: 5361198023_B

description: Replicate 1


title: DMSO_6, rep2

description:
V43
Sampled immediately post-treatment.


title: B5_90_6, rep3

description:
V41
Sampled immediately post-treatment.


title: B3_45_10, rep1

description:
V4
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198022_I

description: Replicate 1


title: 5361198022_K

description: Replicate 1


title: B3_45_6, rep3

description:
V44
Sampled immediately post-treatment.


title: B5_45_6, rep3

description:
V40
Sampled immediately post-treatment.


title: B3_90_6, rep3

description:
V39
Sampled immediately post-treatment.


title: 5361198022_D

description: Replicate 1


title: 5361198022_B

description: Replicate 1


title: 5361198022_C

description: Replicate 1


title: B5_90_10, rep4

description:
V37
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B3_90_10, rep3

description:
V35
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B5_45_10, rep3

description:
V36
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B3_45_10, rep4

description:
V34
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B1_45_10, rep4

description:
V38
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198022_F

description: Replicate 1


title: 5361198022_A

description: Replicate 1


title: 5361198022_E

description: Replicate 1


title: DMSO_10, rep4

description:
V33
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198021_L

description: Replicate 1


title: B1_90_10, rep4

description:
V32
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198021_K

description: Replicate 1


title: 5361198021_J

description: Replicate 1


title: B3_45_10, rep3

description:
V30
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B1_90_10, rep3

description:
V28
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: DMSO_10, rep1

description:
V3
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B3_90_10, rep2

description:
V31
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198021_I

description: Replicate 1


title: 5361198021_G

description: Replicate 1


title: DMSO_10, rep3

description:
V29
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198021_H

description: Replicate 1


title: 5361198021_F

description: Replicate 1


title: 5361198023_A

description: Replicate 1


title: 5361198021_E

description: Replicate 1


title: B1_45_10, rep3

description:
V27
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B1_90_6, rep1

description:
V23
Sampled immediately post-treatment.


title: B5_45_10, rep2

description:
V25
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198021_A

description: Replicate 1


title: 5361198020_K

description: Replicate 1


title: B1_45_6, rep2

description:
V22
Sampled immediately post-treatment.


title: 5361198021_D

description: Replicate 1


title: B5_90_6, rep2

description:
V21
Sampled immediately post-treatment.


title: 5361198021_B

description: Replicate 1


title: 5361198021_C

description: Replicate 1


title: DMSO_6, rep1

description:
V24
Sampled immediately post-treatment.


title: B5_90_10, rep3

description:
V26
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B5_45_6, rep2

description:
V20
Sampled immediately post-treatment.


title: B3_90_6, rep2

description:
V19
Sampled immediately post-treatment.


title: B1_90_10, rep1

description:
V2
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198020_J

description: Replicate 1


title: B3_45_6, rep2

description:
V18
Sampled immediately post-treatment.


title: 5361198020_L

description: Replicate 1


title: 5361198020_I

description: Replicate 1


title: 5361198020_F

description: Replicate 1


title: 5361198020_H

description: Replicate 1


title: DMSO_10, rep2

description:
V17
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198020_D

description: Replicate 1


title: B1_90_10, rep2

description:
V16
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B5_45_6, rep1

description:
V10
Sampled immediately post-treatment.


title: B5_45_10, rep1

description:
V11
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198009_J

description: Replicate 1


title: 5361198020_E

description: Replicate 1


title: B1_45_10, rep2

description:
V15
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198020_A

description: Replicate 1


title: 5361198020_C

description: Replicate 1


title: 5361198022_G

description: Replicate 1


title: B1_45_10, rep1

description:
V1
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: B5_90_10, rep2

description:
V12
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198009_I

description: Replicate 1


title: 5361198009_K

description: Replicate 1


title: B3_45_10, rep2

description:
V13
Following treatment, cells were put in fresh media and sampled 4 hours later.


title: 5361198009_H

description: Replicate 1


title: 5361198009_L

description: Replicate 1


title: 5361198009_F

description: Replicate 1


title: 5361198009_G

description: Replicate 1


title: 5361198009_D

description: Replicate 1


title: 5361198020_G

description: Replicate 1


title: 5361198009_E

description: Replicate 1


title: Thymus_p53KO

city: Milano

first: Simone

middle: Paolo

last: Minardi

state: Italy

address: Via Adamello

department: Microarray and NGS Unit

country: Italy

institute: Cogentech

description: pool of RNA (4 mice)

hyb_protocol: Following fragmentation,10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430 2.0 array. GeneChip arrays were  washed and stained in the Affymetrix Fluidic Station 450.

scan_protocol: GeneChip array images were scanned using the Affymetrix GeneChip Scanner 30007G instrument.

data_processing: The data were analyzed with Partek Genomics Suite v 6.5 using RMA algorithm.

label: biotin

source_name: Thymus p53 knock-out (p53-/-)

label_protocol: Biotinylated cRNA were prepared according to Affymetrix OneCycle amplification protocol from 3000 ng total RNA, and labeled using  the IVT Labeling Kit

growth_protocol: Total RNA was extracted from  freshly isolated thymus, liver, heart and lung of two months old mice (pool of four mice for each genotype)

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

value: 2 months old

value: thymus

tag: genotype

value: p53 knock-out (p53-/-)


title: Lung_p66KO

description: pool of RNA (4 mice)

source_name: Lung p66 knock-out (p66-/-)

value: lung

value: p66 knock-out (p66-/-)


title: Heart_p53KO

description: pool of RNA (4 mice)

source_name: Heart p53 knock-out (p53-/-)

value: heart


title: Liver_p53KO

description: pool of RNA (4 mice)

source_name: Liver p53 knock-out (p53-/-)

value: liver


title: B3_90_10, rep1

description:
V14
Following treatment, cells were put in fresh media and sampled 4 hours later.

value: MutaMouse

value: immortalized pulmonary epithelial cells

value: 6 hours

source_name: Universal Mouse Reference RNA

value: reference derived from 11 mouse cell lines


title: 5361198020_B

description: Replicate 1


title: Lung_p53KO

description: pool of RNA (4 mice)

source_name: Lung p53 knock-out (p53-/-)


title: Thymus_p66KO

description: pool of RNA (4 mice)

source_name: Thymus p66 knock-out (p66-/-)


title: 5361198009_C

description: Replicate 1


title: Heart_p66KO

description: pool of RNA (4 mice)

source_name: Heart p66 knock-out (p66-/-)


title: Lung_WT

description: pool of RNA (4 mice)

source_name: Lung Wild type

value: Wild type


title: Liver_p66KO

description: pool of RNA (4 mice)

source_name: Liver p66 knock-out (p66-/-)


title: MEFS p53KO H2O2 induced,biological rep2

description:
Gene expression data from MEFs passage 2
GeneChip MOE430PM strip arrays on Affymetrix GeneAtlas instrument

hyb_protocol: Following fragmentation,6 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MOE430PM strip array. GeneChip strip was washed and stained in the Affymetrix GeneAtlas instrument .

scan_protocol: GeneChip strip images were acquired using the GeneAtlas Imaging Station.

source_name: MEFS p53KO H2O2 induced

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix 3' IVTprotocol from 100 ng total RNA.

growth_protocol: Primary murine embryonic fibroblasts (MEFs) were isolated from 13.5-day-old embryos according to standard procedures from WT, p53KO and p66ShcKO mice. MEFs were cultured in DMEM supplemented with 10% fetal bovine calf serum, 100µg/ml streptomycin, 100 µg/ml penicillin FBS, L-glutamine (2 mM) and incubated at 37°C in a humidified atmosphere containing 5% CO2 and normal oxygen tension (20%). For all the experiments MEFs at early passages (p.2) were used. Treatment: Early passage (p.2-5) MEFs were washed twice with PBS1X solution, and then incubated in DMEM media containing 400 μM of H2O2 or 0.25μg/ml of Doxorubicin (SIGMA) at 37°C for four hours.

treatment_protocol: Early passage (p.2) MEFs were washed twice with PBS1X solution, and then incubated in DMEM media containing 400 μM of H2O2 or 0.25μg/ml of Doxorubicin (SIGMA) at 37°C for four hours.

value: 13.5-day-old embryos


title: MEFS p53KO at Basal,biological rep3

source_name: MEFS p53KO at Basal

value: Primary murine embryonic fibroblasts (MEFs)


title: MEFS p53KO at Basal,biological rep4


title: MEFS p53KO H2O2 induced,biological rep4


title: Thymus_WT

description: pool of RNA (4 mice)

source_name: Thymus Wild type


title: MEFS p53KO H2O2 induced,biological rep1


title: 5361198009_A

description: Replicate 1

source_name: subcutaneous adipose


title: Liver_WT

description: pool of RNA (4 mice)

source_name: Liver Wild type


title: MEFS p53KO H2O2 induced,biological rep3


title: MEFS p53KO at Basal,biological rep1


title: MEFS p66KO DOXO induced,biological rep2

source_name: MEFS p66KO DOXO induced


title: 5361198008_L

description: Replicate 1


title: 5361198008_J

description: Replicate 1


title: 5361198008_K

description: Replicate 1


title: MEFS p66KO H2O2 induced,biological rep4

source_name: MEFS p66KO H2O2 induced


title: 5361198008_I

description: Replicate 1


title: MEFS p66KO DOXO induced,biological rep1


title: MEFS p66KO at Basal,biological rep1

source_name: MEFS p66KO at Basal


title: 5361198008_D

description: Replicate 1


title: MEFS p66KO H2O2 induced,biological rep1


title: Heart_WT

description: pool of RNA (4 mice)

source_name: Heart Wild type


title: MEFS p66KO H2O2 induced,biological rep2


title: MEFS p66KO H2O2 induced,biological rep3


title: MEFS p66KO at Basal,biological rep4


title: 5361198008_H

description: Replicate 1


title: 5361198008_A

description: Replicate 1


title: MEFS WT DOXO induced,biological rep1

source_name: MEFS WT DOXO induced


title: 5361198008_E

description: Replicate 1


title: 5361198008_B

description: Replicate 1


title: 5361198007_K

description: Replicate 1


title: 5361198008_G

description: Replicate 1


title: 5361198008_F

description: Replicate 1


title: MEFS p66KO at Basal,biological rep2


title: MEFS p53KO at Basal,biological rep2


title: MEFS WT DOXO induced,biological rep2


title: MEFS p66KO at Basal,biological rep3


title: 5361198008_C

description: Replicate 1


title: 5361198007_L

description: Replicate 1


title: MEFS WT H2O2 induced,biological rep4

source_name: MEFS WT H2O2 induced


title: 5361198007_J

description: Replicate 1


title: MEFS WT H2O2 induced,biological rep3


title: MEFS WT at Basal,biological rep1

source_name: MEFS WT at Basal


title: rin mutant mature green rep3

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

country: Japan

institute: National Food Research Institute

description:
PK353G1
Tomatoes were harvested at the period corresponding to the normal mature green stage

hyb_protocol: The Cy3-labelled cRNA (1.65 ug) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture. The reaction mixture (40 ul) was used for hybridization with Agilent-022270 Tomato Gene Expression Microarray 44K slides (platform ID: GPL10570) (44K x 4 pack) for 17 hours at 65°C in an oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technoligies Microarray Scanner at a resolution of 5 um. Signal intensities of spots for the probes were monitored using the feature extraction software ver. 10.5.1.1 (Agilent).

data_processing: Raw data were subjected to per chip normalization to 75th percentile using Genespring ver.10.0 software (Agilent).

organism: Solanum lycopersicum

source_name: whole tomato at the mature green stage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. The Cy3-labeled cRNA was purified with RNAeasy mini spin columns (QIAGEN, Valencia, CA).

growth_protocol: Plants were grown in a glasshouse, and the fruits were harvested at two maturation stages: mature green (G), pink colouring (P; about 4 days after breaker stage). The fruits of the rin mutant line were harvested at the G stage and at the stages corresponding to the wild type at the P stage (about 5 days after the fruit skin started to show a yellow colour). [See Kitagawa et al. (2005) PHYSIOLOGIA PLANTARUM 123: 331–338.]

extract_protocol: The frozen fruits were powdered with electric mill, moter and pestle. Total RNA was extracted and purified from 0.2 mg of the powder with RNeasy plus mini kit (Qiagen, Hilden, Germany).

treatment_protocol: The harvested fruits were immediately frozen in liquid nitrogen and stored at -80°C.

tag: cultivar

value: ripening inhibitor (rin) mutant

tag: developmental stage

value: mature green stage

value: whole tomato


title: MEFS WT H2O2 induced,biological rep2


title: MEFS WT H2O2 induced,biological rep1


title: rin mutant pink coloring rep3

description:
PK353P1
Tomatoes were harvested at the period corresponding to the normal pink coloring stage

source_name: whole tomato at the pink coloring stage

value: pink coloring stage


title: ESRD-RCC case65 atypical cyst

city: Yufu-City, Oita

first: Toru

last: Inoue

address: Hasama-machi 1-1

department: Department of Molecular Pathology

institute: Faculty of medicineOita University

description: Non-neoplastic tissues in the other 12 patients were used as the source of control DNA

hyb_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

scan_protocol: standard Agilent protocol

data_processing: Microarray images were analyzed by using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies).Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). The log2ratio of Cy5 (tumor) to Cy3 (Control) was normalized by the Centralization Algorithm in DNA Analytics. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 12.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.263034, maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.263034 to detect regions showing a change in the averaged copy number equal to or more than 1.2-fold (log2(1.2)=0.263034).

source_name: ESRD-RCC : FFPE sample

label_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 24 h

extract_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

treatment_protocol: standard proteinase K-digestion method

tag: phenotype

value: atypical cyst

value: Male

tag: disease state

value: ESRD-RCC

value: RCC tumor

tag: individual

value: case 65

source_name: control : FFPE sample

value: various non-neoplastic tissues from 12 patients

value: control


title: MEFS WT at Basal,biological rep3


title: MEFS WT at Basal,biological rep2


title: 5361198007_H

description: Replicate 1

value: subcutaneous adipose


title: MEFS WT at Basal,biological rep4


title: 5361198007_I

description: Replicate 1


title: ESRD-RCC case61 simple cyst

value: simple cyst

tag: gender

value: case 61


title: 5361198007_E

description: Replicate 1


title: 5361198007_F

description: Replicate 1


title: ESRD-RCC case63 simple cyst

value: case 63


title: ESRD-RCC case59 simple cyst

value: case 59


title: ESRD-RCC case56 atypical cyst

value: case 56


title: 5361198007_D

description: Replicate 1


title: ESRD-RCC case60 simple cyst

value: Female

value: case 60


title: 5361198007_B

description: Replicate 1


title: 5361198007_G

description: Replicate 1


title: 5361198007_C

description: Replicate 1


title: 5361198009_B

description: Replicate 1


title: ESRD-RCC case13 atypical cyst

value: case 13


title: ESRD-RCC case53 simple cyst

value: case 53


title: ESRD-RCC case53 atypical cyst

value: atypical cyst


title: ESRD-RCC case54 simple cyst

value: Male

value: case 54


title: rin mutant mature green rep2

description: Tomatoes were harvested at the period corresponding to the normal mature green stage

value: ripening inhibitor (rin) mutant

value: mature green stage

value: whole tomato


title: ESRD-RCC case52 simple cyst

value: ESRD-RCC

value: RCC tumor

value: case 52

value: various non-neoplastic tissues from 12 patients

value: control


title: normal pink coloring rep1

description: Tomatoes were harvested at the pink coloring stage

value: wild type

value: pink coloring stage


title: rin mutant pink coloring rep1

description: Tomatoes were harvested at the period corresponding to the normal pink coloring stage


title: 5361198001_H

description: Replicate 1

value: subcutaneous adipose


title: 5361198001_L

description: Replicate 1


title: 5361198001_K

description: Replicate 1


title: rin mutant pink coloring rep2


title: 5361198001_J

description: Replicate 1


title: ESRD-RCC case54 atypical cyst


title: rin mutant mature green rep1


title: normal pink coloring rep3

description:
PK331P3
Tomatoes were harvested at the pink coloring stage


title: normal mature green rep3

description:
PK331G3
Tomatoes were harvested at the mature green stage


title: ESRD-RCC case11 simple cyst

value: simple cyst

value: case 11


title: normal mature green rep1

description: Tomatoes were harvested at the mature green stage


title: 5361198001_G

description: Replicate 1


title: normal mature green rep2


title: 5361198001_F

description: Replicate 1


title: ESRD-RCC case9 atypical cyst

value: case 9


title: Dissected Peripheral cells 5

city: Bethesda

first: Tsutomu

last: Matsubara

state: MD

address: 9000 Rockville Pike

institute: NCI

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). And, Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Peripheral area of mouse thyroid cells after partial thyroidectomy

label_protocol: antisense RNA amplified with RiboAmp PLUS amplification kit and and laveled with Arcturus Turbo Labeling kit

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

treatment_protocol: Collected cells from frozen tissue section using leaser chapture microdissection

tag: strain

value: Thyroid

source_name: Ambion Mouse Assorted Total RNA

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: Dissected Peripheral cells 4

value: Male


title: ESRD-RCC case9 simple cyst


title: Dissected Peripheral cells 3


title: 5361198007_A

description: Replicate 1


title: 5361198001_E

description: Replicate 1


title: 5361198001_C

description: Replicate 1


title: ESRD-RCC case5 simple cyst

value: Female

value: case 5


title: 5361198001_I

description: Replicate 1


title: 5361198001_D

description: Replicate 1


title: HS_76

description: childhood adrenocortical tumor

tag: origin

value: USA

value: M

tag: age (months)

tag: histological type

value: carcinoma

tag: tnm staging

tag: Stage

value: IV

tag: tp53 mutation

value: hdel

tag: virilization

value: N

tag: cushing syndrome

value: Y

tag: treatment

value: surgical resection plus chemotherapy

tag: follow-up (months)

value: Alive (15)


title: normal pink coloring rep2

tag: cultivar

tag: genotype

value: wild type

value: pink coloring stage

tag: tissue

value: whole tomato


title: HS_75

description: childhood adrenocortical tumor

tag: sample id

value: III

value: surgical resection only

value: Alive (18)


title: ESRD-RCC case8 simple cyst

tag: phenotype

value: simple cyst

value: Male

tag: disease state

value: ESRD-RCC

value: RCC tumor

tag: individual

value: case 8

value: various non-neoplastic tissues from 12 patients

value: control


title: Dissected Peripheral cells 2

tag: gender

tag: strain

value: Thyroid

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: ESRD-RCC case4 atypical cyst

value: atypical cyst

value: Female

value: case 4


title: Dissected Peripheral cells 1


title: Dissected Central cells 5

source_name: Central area of mouse thyroid cells after partial thyroidectomy


title: 5361198001_A

description: Replicate 1

value: subcutaneous adipose

tag: age


title: ESRD-RCC case1 simple cyst

value: case 1


title: 5361198001_B

description: Replicate 1


title: 5298416059_L

description: Replicate 1


title: MDEbiorep2techrep2

city: Seattle

first: Janet

middle: M.

last: Young

state: WA

address: 1100 Fairview Avenue N., C3-168,  P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Pre-hybridized arrays were treated following Schott’s protocol for the Nexterion’s SLIDE-E surface. Experimental and reference samples were combined and resuspended in 200 μl of 1x miRCURY hybridization buffer (Exiqon, Inc., Woburn, MA), incubated for 5 minutes at 95°C, and subsequently centrifuged for 5 minutes at 14,000xg. Combined sample pairs were co-hybridized to each array using the SureHyb Microarray Hybridization System (Agilent Technologies , Santa Clara, CA).  Hybridization chambers were rotated at 4 rpm at 60°C for 16-18 hours using a Robbins Scientific 400 Hybridization Incubator (SciGene Corporation, Sunnyville, CA).  Post-hybridized arrays were washed for 2 minutes in 2XSSC + 0.2% SDS at 60°C, followed by 2x washes in 1xSSC at RT for 2 min each, and finishing with a final wash in 0.2XSSC at RT for 2 min.  Slides were dried by centrifugation at 200xg for 5 min.

scan_protocol: Slides were scanned at 10um resolution using a GenePix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA).  Image quantification was performed using GenePix Pro 6.0 Microarray Image Analysis software (Molecular Devices Corporation, Sunnyvale, CA).

data_processing: For each array, we took log2 ratios of the green and red signals at each spot.  As a form of normalization, we calculated the mean ratio for four probes representing U6 snRNA, which should not change on MD~E introduction, and subtracted the mean U6 log2 ratio from all other log ratios on the same array. We then averaged the log ratios between dye-swap replicates. Signals on these arrays were generally weak and somewhat inconsistent across dye-swaps and replicates, making it very difficult to use more sophisticated normalization methods. We used these arrays only to choose the most obviously changed miRNAs: any findings important to our publication were verified independently using miRNA Northern blots. These array results are not of high enough quality to make general statements about expression changes across the full repertoire of human miRNAs.

source_name: RD cells transduced with empty vector pCLBabe

label_protocol: miRNAs were labeled using Exiqon’s miRCURY LNA labeling kit

growth_protocol: RD cells were obtained from ATCC (American Type Culture Collection) in approximately 1990, and all analyses have been performed on cells that originated from low passage number frozen aliquots. Cells were maintained in DMEM with 10% bovine calf serum and 1% Pen-Strep (Gibco). Low-serum differentiation media consisted of DMEM with 1% horse serum, 1% Pen-Strep and 10 ug/mL insulin and transferrin.

extract_protocol: RNA was isolated using Trizol and acid-phenol purification

treatment_protocol: RD cells were transduced with either MD~E or empty vector pCLBabe retroviruses, selected with puromycin for 48 hours and differentiated for 24 hours with selection

tag: cell type

value: RD cells

value: transduced with empty vector pCLBabe

source_name: RD cells transduced with MD~E forced dimer

value: transduced with MD~E forced dimer


title: HS_77

description: childhood adrenocortical tumor

tag: origin

value: USA

value: F

tag: age (months)

tag: histological type

value: ND

tag: tnm staging

tag: Stage

value: I

value: Y

value: surgical resection only

value: Alive (21)


title: MDEbiorep1techrep2

tag: treatment


title: Dissected Central cells 4

value: Male

value: Thyroid

value: Swiss Webster


title: MDEbiorep1techrep1


title: 5298416059_K

description: Replicate 1

source_name: subcutaneous adipose


title: 5298416059_G

description: Replicate 1


title: 5298416059_J

description: Replicate 1


title: Dissected Central cells 2

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: Sample 7 Liver 8a Dexamethasone+GW3965

first: Tomoshige

last: Kino

address: 10 Center Drive MSC 1109

department: Program in Reproductive and Adult Endocrinology

institute: National Institute of Child Health & Human Development

description: Sample 7 Liver 8a Dexamethasone + GW3965.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Rat Genome 230 2.0 Arrays. 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 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.

organism: Rattus norvegicus

source_name: Liver 8a Dexamethasone + GW3965

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: Sprague-Dawley

tag: orally gavaged (for 3 days)

tag: on the third day

value: Dexamethasone + GW3965

tag: intra-muscular injection (on the third day)

value: Dexamethasone

value: liver


title: 5298416059_I

description: Replicate 1

tag: tissue

value: subcutaneous adipose

tag: sample id


title: Dissected Central cells 3


title: Dissected Central cells 1


title: Normal Peripheral cells 2

source_name: Peripheral area of mouse thyroid cells w/o partial thyroidectomy


title: Normal Peripheral cells 1


title: Sample 8 Liver 8b Dexamethasone+GW3965

description: Sample 8 Liver 8b Dexamethasone + GW3965.CEL

source_name: Liver 8b Dexamethasone + GW3965


title: Sample 6 Liver 6b GW3965

description: Sample 6 Liver 6b GW3965.CEL

source_name: Liver 6b GW3965

value: vehicle


title: 5298416059_H

description: Replicate 1


title: Normal Peripheral cells 3


title: Sample 5 Liver 6a GW3965

description: Sample 5 Liver 6a GW3965.CEL

source_name: Liver 6a GW3965


title: Sample 4 Liver 4b Dexamethasone

description: Sample 4 Liver 4b Dexamethasone.CEL

source_name: Liver 4b Dexamethasone


title: 5298416059_F

description: Replicate 1


title: HS_68

description: childhood adrenocortical tumor

value: The Netherlands

value: M

value: carcinoma

tag: tp53 mutation

tag: virilization

tag: cushing syndrome

value: N

tag: follow-up (months)

value: Alive (68)


title: 5298416059_E

description: Replicate 1

tag: age


title: Normal Central cells 5

source_name: Central area of mouse thyroid cells w/o partial thyroidectomy

tag: gender

tag: strain


title: Sample 3 Liver 4a Dexamethasone

description: Sample 3 Liver 4a Dexamethasone.CEL

source_name: Liver 4a Dexamethasone


title: 5298416059_D

description: Replicate 1


title: HS_67

description: childhood adrenocortical tumor

tag: origin

value: F

tag: age (months)

value: adenoma

value: I

value: Y

value: surgical resection only

value: Alive (26)


title: Normal Central cells 2

value: Male

value: Thyroid

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: 5298416059_C

description: Replicate 1

value: subcutaneous adipose


title: Sample 2 Liver 1b vehicle

description: Sample 2 Liver 1b vehicle.CEL

source_name: Liver 1b vehicle

value: Sprague-Dawley

value: vehicle

value: liver


title: Normal Central cells 3


title: HS_46

description: childhood adrenocortical tumor

value: Switzerland

value: M

tag: histological type

value: carcinoma

tag: tnm staging

value: ND

value: DFP (5)


title: Normal Central cells 4


title: HS_73

description: childhood adrenocortical tumor

value: USA

value: F

tag: Stage

value: I

value: wt

value: N

tag: treatment

value: Alive (0)


title: 5298416059_B

description: Replicate 1


title: 5298416059_A

description: Replicate 1


title: HS_74

description: childhood adrenocortical tumor

value: II

value: Y

value: surgical resection plus chemotherapy

value: Alive (2)


title: Sample 1 Liver 1a vehicle

description: Sample 1 Liver 1a vehicle.CEL

source_name: Liver 1a vehicle

value: Sprague-Dawley

tag: orally gavaged (for 3 days)

value: vehicle

tag: on the third day


title: HS_70

description: childhood adrenocortical tumor

value: The Netherlands

value: adenoma

value: surgical resection only

value: Alive (38)


title: N2 vs. CB4856, T3, rep3

status: Public on Apr 01 2012

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

country: United Kingdom

institute: King's College London

hyb_protocol: Microarrays were hybridized following the Genisphere Array 900 HS protocol with modifications.

scan_protocol: A Perkin Elmer scanner was used to extract the raw intensities.

data_processing: Preprocessing and normalization was done in the R software (http://www.r-project.org/) using Limma package. Loess method was used for normalization within arrays and normalization between arrays was done using aquantile method, both of them included in limma package.

organism: Caenorhabditis elegans

source_name: N2, 214 hours

label_protocol: Labeled cDNA was produced with the Array 900 HS kit from Genisphere and Superscript II from Invitrogen. The Nucleospin kit was used to clean the cDNA samples in order to reduce unspecific binding to the arrays.

growth_protocol: Two C. elegans wild types, N2 and CB4856, were used to generate gene expression data at three different ages. The nematodes were cultured on standard nematode growth medium (NGM) with E. coli OP50 as food source and a constant temperature of 24ºC. Populations were started with nonmated hermaphrodites and screened regularly to remove any occurring males.

extract_protocol: RNA from nematodes was extracted following the Trizol method, followed by the RNeasy Micro kit (Quiagen, Valencia, CA, USA) to clean up the samples.

treatment_protocol: Reproductive nematodes from N2 and CB4856 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect age-synchronized eggs which were inoculated in 24 dishes (t0). After 40 hours (H1), nematodes from 6 dishes were collected in late L3 stage, frozen in liquid nitrogen and kept at -80ºC until the RNA extraction procedure. The remaining 18 dishes were kept in culture until hour 41 when the nematodes were transferred to fresh NGM dishes (with E. coli OP50) treated with 0.05-0.01 mg/ml of FUDR in order to avoid reproduction. After 30 hours in dishes with FUDR and when the reproductive period was about to finish, nematodes were transferred to fresh dishes without FUDR to prevent starvation. After 23 hours, 96 hours of total culture time (H2), nematodes from 6 dishes were collected and frozen in liquid nitrogen prior to RNA extraction. The remaining 12 dishes were kept at constant temperature until 214 hours of culture (H3), when they were harvested and frozen in liquid nitrogen. All the dishes were visually inspected before the harvest. Any population with contamination, more than one generation (reproduction) or starving nematodes (lacking bacteria) were discarded.

tag: genotype

value: wild type

value: 214 hours

tag: developmental stage

value: old (senescent)

tag: temperature


title: CB4856 vs. N2, T3, rep1


title: N2 vs. CB4856, T3, rep1


title: N2 vs. CB4856, T2, rep3

source_name: N2, 96 hours

value: 96 hours

value: reproductive

source_name: CB4856, 96 hours


title: CB4856 vs. N2, T3, rep2


title: MDEbiorep2techrep1

tag: cell type

value: RD cells

value: transduced with empty vector pCLBabe

value: transduced with MD~E forced dimer


title: N2 vs. CB4856, T2, rep1


title: Normal Central cells 1

value: Male

tag: tissue

value: Thyroid

source_name: Ambion Mouse Assorted Total RNA

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: CB4856 vs. N2, T2, rep1


title: N2 vs. CB4856, T1, rep3

source_name: N2, 40 hours

value: 40 hours

value: late L3 (juvenile)

source_name: CB4856, 40 hours


title: N2 vs. CB4856, T2, rep2


title: N2 vs. CB4856, T3, rep2


title: CB4856 vs. N2, T1, rep1


title: N2 vs. CB4856, T1, rep2


title: N2 vs. CB4856, T1, rep1


title: CB4856 vs. N2, T1, rep2


title: HS_72

description: childhood adrenocortical tumor

tag: sample id

value: USA

value: M

value: carcinoma

value: III

tag: tp53 mutation

tag: virilization

value: N

tag: cushing syndrome

value: surgical resection plus chemotherapy

tag: follow-up (months)

value: Alive (3)


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL11

city: Kita-gun

first: Saeko

last: Konishi-Sugita

state: Kagawa

address: 2393, Ikenobe, Miki-cho

department: Faculty of Agriculture

institute: Kagawa University

hyb_protocol: 400ng 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. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

label_protocol: 2 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 Cy3(or Cy5) CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Qiagen RNeasy mini kit.

growth_protocol: Rice plants were grown in a greenhouse under normal conditions. Developing panicles and flowers of various stages were collected.

extract_protocol: Total RNAs were extracted from LM cells with a PicoPure™ RNA isolation kit (Molecular Devices). Total RNA was quantified with a Quant-iT™ RiboGreen RNA reagent and kit (Invitrogen, San Diego, CA, USA).

treatment_protocol: The samples were fixed in FAA fixative overnight at 4°C. Dehydration and paraffin embedding were performed as described by Inada and Wildermuth (2005) by using a microwave processor. Paraffin-embedded sections were cut to a thickness of 16μm and mounted on PEN membrane glass slides (Molecular Devices, Ontario, Canada) for LM. To remove the paraffin, slides were immersed in 100% xylene (twice), 50% xylene/50% ethanol and 100% ethanol (v/v) for 5min each, and then air-dried completely at room temperature. Three or four individual flowers were used for each LM experiment. LM was performed using the Veritas Laser Microdissection System LCC1704 (Molecular Devices). Selected areas were captured by an infrared laser (IR laser) onto CapSure Macro LCM Caps (Molecular Devices), and were subsequently cut by a UV laser. The target cells that fused to the LCM cap were collected by removing the cap from the tissue section.

tag: variety

value: young panicle

tag: panicle length

tag: flower length

tag: region

value: abscission layer

source_name: lower region of abscission layer at the base of flower in rice, NIL(qSH1)

value: lower region of abscission layer


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL9

source_name: abscission layer at the base of flower in rice, NIL(qSH1)


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL10

source_name: upper region of abscission layer at the base of flower in rice, NIL(qSH1)

value: upper region of abscission layer


title: P65 KO Air 1

city: Homburg (Saar)

first: Christoph

last: Beisswenger

address: Kirrbergerstrasse

department: Department of Internal Medicine V – Pulmonology, Allergology and Respiratory Critical Care Medicine

country: Germany

institute: Saarland University Medical Center

hyb_protocol: Affymetrix Whole Transcript (WT) Sense Target Hybridization Protocol

scan_protocol: Affymetrix Whole Transcript (WT) Sense Target Scan Protocol

data_processing: Affymetrix Command Console; Affymetrix Expression Console; Bioconductor RMA

source_name: Lung

label_protocol: Affymetrix Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: RNeasy Kit (Qiagen, Germany, silica-based membrane)

tag: gender

value: female

tag: genotype/variation

value: RelA/p65  deficient

tag: strain

value: Lewis lung carcinoma cells resected from lungs

tag: treatment/exposure

value: exposed to air


title: P65 KO Smoke 1

value: exposed to smoke


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL6

source_name: abscission layer at the base of flower in rice, Nipponbare

value: Nipponbare

value: 3 mm


title: Wildtype Smoke 3

value: wild type


title: P65 KO Air 2


title: P65 KO Smoke 2


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL5


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL2

value: 8 mm

value: abscission layerm


title: Wildtype Smoke 2


title: Wildtype Smoke 1


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL1


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL7


title: Homozygote biol rep 1

city: Philadelphia

first: Mitchell

middle: J

last: Weiss

state: PA

address: 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Philadelphia

description:
Th3_homozygous_1
Gene expression data from Th3/Th3 E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts

hyb_protocol: Affymetrix standard protocol

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

data_processing: Affymetrix Command Console was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features using the MAS5.0 algorithm. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average feature signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All signal values from one microarray were then multiplied by the appropriate scaling factor

label_protocol: 35ng of RNA was amplify with the WT-Ovation Pico RNA amplification System from NuGen, ST -cDNA generation was performed with the WT-Ovation Exon Module starting 4ug of cDNA, 5 ug of ST -cDNA was fragmented and labeled with the Encore Biotin Module.

growth_protocol: E14.5 fetal livers from Th3/+ x Th3/+ crosses were disaggregated, and CD71+Ter119+FSChigh cells purified by FACS

extract_protocol: Trizo lLS RNA samples were prepared using Qiagen miRNAeasy kit according to manufacturer instructions

tag: strain background

value: 129SV background and backcrossed onto C57BL/6 for 9 generations

tag: developmental stage

value: Th3/Th3 homozygote

value: fetal liver


title: Homozygote biol rep 3

description:
Th3_homozygous_3
Gene expression data from Th3/Th3 E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts

tag: cell type


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL8

tag: tissue

value: young panicle


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL4

value: 38 mm

value: abscission layer

value: 35 mm


title: Homozygote biol rep 2

description:
Th3_homozygous_2
Gene expression data from Th3/Th3 E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts


title: Wildtype Air 1

value: female


title: P65 KO Smoke 3

value: RelA/p65  deficient


title: P65 KO Air 3

value: Lewis lung carcinoma cells resected from lungs


title: Wildtype Air 2

value: exposed to air


title: TAF7 KO CD4+ T cells

first: Dinah

last: Singer

state: Maryland

department: Experimental Immunology Branch

institute: National Cancer Institute

hyb_protocol: Microarrays were hybridized overnight with 5 ug biotin-labelled ss-DNA, and washed in fluidics station wash protocol: FS450_0001.

scan_protocol: GeneChip scanner 3000 7G was used.

data_processing: Exon array data were analyzed with Affymetrix Expression Console SoftwareTM (version 1.1). The Robust Multi-array Analysis (RMA) algorithm was used for gene intensity analysis. Only genes in the “core” set, which represents RefSeq and full-length GenBank mRNAs, were included in the analysis.

source_name: CD4+ T cells, Taf7 -/-

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual.

extract_protocol: Total RNA is extracted using shredders and the Qiagen RNeasy mini kit. Their quality was assayed before using for hybridization.

tag: background strain

value: C57/BL6 and 129 mix

value: CD4+ T cell

tag: genotype


title: Heterozygote biol rep 3

description:
Th3_het_3
Gene expression data from Th3/+ E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts

value: Th3/+ heterozygote


title: Heterozygote biol rep 2

description:
Th3_het_2
Gene expression data from Th3/+ E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts


title: Mouse liver, cotrol animal, biological replicate 1

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

description: The liver samples were collected from transgenic mice as well as from control animals at the age of 4 weeks

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for normalization, BRB Array Tools for statistical analysis

source_name: Wild type mouse

extract_protocol: RNA was purified from frozen liver samples kept in RNAlater (Qiagen) by RNAeasy mini kit (Qiagen) according to manufacturer's instruction.

value: liver

value: wild type

tag: genetic background

value: C57BL/6 and NMRI mixed, backcrossed at least 4-times to C57BL/6 background


title: Wild type biol rep 1

description:
Wild_type_1
Gene expression data from +/+ E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts

value: 129SV background and backcrossed onto C57BL/6 for 9 generations


title: Mouse liver, cotrol animal, biological replicate 2

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: Mouse liver, constitutively active IKK2, biological replicate 1

source_name: Trangenic mouse, biol. Replicate 1

value: constitutively active IKK2 transgenic


title: Heterozygote biol rep 1

description:
Th3_het_1
Gene expression data from Th3/+ E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts

value: fetal liver


title: Mouse liver, constitutively active IKK2, biological replicate 4

source_name: Trangenic mouse, biol. Replicate 4


title: Wild type biol rep 3

description:
Wild_type_3
Gene expression data from +/+ E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts


title: TAF7 HET CD4+ T cells

source_name: CD4+ T cells, Taf7 +/-


title: Wild type biol rep 2

description:
Wild_type_2
Gene expression data from +/+ E14.5 fetal liver CD71+Ter119+FSChigh erythroblasts


title: T3-M

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

hyb_protocol: Standard Affymetrix hybridisation protocol

scan_protocol: Standard Affymetrix Scanning protocol with a Affymetrix Scanner 3000 7G System

data_processing: RMA Normalisation with PARTEK software 6.5

label: biotin-Streptavidin-PE

source_name: T-ALL - mouse passage

label_protocol: Standard Affymetrix labeling protocol

growth_protocol: intravenous injection into immune-permissive mice

extract_protocol: Qiagen RNAeasy Mini Kit Isolation

value: human leukemia cells from bone marrow

tag: donor

value: T-ALL Donor 3

tag: treatment

value: passaged in mouse


title: Mouse liver, cotrol animal, biological replicate 3


title: Mouse liver, constitutively active IKK2, biological replicate 2

source_name: Trangenic mouse, biol. Replicate 2


title: Brain TAMs_human glioblastoma-conditioned_rep3

city: Tokyo

first: Yurai

last: Okaji

address: Bunkyo-ku, Hongo 7-3-1

institute: The University of Tokyo

description: Gene expression data from murine TAMs, induced by human glioblastoma cells in vitro.

hyb_protocol: Labeled cDNA was hybridized on GeneChip Mouse Gene 1.0 ST Array for 17 hr at 450C in Affymetrix Hybridization Oven 640. Subsequent washing and staining of arrays was done in Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GCS3000 Scanner and Affymetrix Genechip Command Console (AGCC) 2.0 software.

data_processing: Data were normalized and annotated with Expression Console Ver.1.1 using Affymetrix default settings for gene level analysis (RMA-Sketch).

source_name: Murine spleen monocytes, cultured in human glioblastoma cell line-conditioned medium, 8-40h

label_protocol: Biotinylated cDNA was prepared from 150 ng total large RNA according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay, Rev. 5, 2009, Affymetrix).

growth_protocol: Spleens were excised, peripheral blood mononuclear cells isolated by gradient centrifugation, and cultured for overnight on 10 cm dishes.

extract_protocol: Total RNA (>200nt) was extracted according to the manufacturer's instructions using the miRNeasy Mini Kit (QIAgen; #217004) and RNeasy MinElute Cleanup Kit (QIAgen; #74204).

treatment_protocol: Unadhered cells (lymphocytes) were washed out, and firmly adhered cells (monocytes) cultured in control medium or tumour cell-conditioned medium for 8-40h.

value: BALB/cA Jcl-nu/nu

tag: sex

tag: age

value: 8w old

value: spleen

value: monocytes, tumor associated macrophages

tag: tumour cell line used for conditioning medium

value: human glioblastoma U-87MG


title: Brain TAMs_human glioblastoma-conditioned_rep2

value: female


title: Mouse liver, cotrol animal, biological replicate 4


title: Mouse liver, constitutively active IKK2, biological replicate 3

source_name: Trangenic mouse, biol. Replicate 3


title: HS_71

description: childhood adrenocortical tumor

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label_protocol: standard Illumina protocol

extract_protocol: Proteinase K method. The detailed protocol can be found in PMID:18786438.

tag: sample id

tag: origin

value: The Netherlands

value: F

tag: age (months)

tag: histological type

value: carcinoma

tag: tnm staging

tag: Stage

value: IV

tag: tp53 mutation

tag: virilization

value: Y

tag: cushing syndrome

value: surgical resection plus chemotherapy

tag: follow-up (months)


title: Colon TAMs_human colorectal adenocarcinoma-conditioned_rep3

description: Gene expression data from murine TAMs, induced by human colorectal adenocarcinoma cells in vitro.

source_name: Murine spleen monocytes, cultured in human colorectal adenocarcinoma cell line-conditioned medium, 8-40h

tag: strain

tag: tissue

tag: cell type

value: human colorectal adenocarcninoma HT-29


title: Control macrophage_unconditoned_rep1

description: Gene expression data from murine control Mø, induced by tumour cell-free culture in vitro.

source_name: Murine spleen monocytes, cultured in control medium, 8-40h

value: monocytes, macrophages


title: Control macrophage_unconditoned_rep3


title: T2-M

value: human leukemia cells from bone marrow

tag: donor

value: T-ALL Donor 2

tag: treatment


title: Colon TAMs_human colorectal adenocarcinoma-conditioned_rep1

tag: sex

tag: age


title: T1-M

value: T-ALL Donor 1

value: passaged in mouse


title: Brain TAMs_human glioblastoma-conditioned_rep1

value: BALB/cA Jcl-nu/nu

value: 8w old

tag: tumour cell line used for conditioning medium


title: A3-M

source_name: AML - mouse passage

value: AML Donor 3


title: surgical resection HC19

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description: Gene expression data from combined hepatocellular-cholangiocarcinoma

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Affymetrix expression console was used to check the scaned data and RMA on R programm  was used as the normalisation method.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was extracted from clinical and pathologic records from patient in agreement with French laws and ethical guidelines related to the protection of the patient

tag: tissue type

tag: gender


title: A2-M

value: AML Donor 2


title: Colon TAMs_human colorectal adenocarcinoma-conditioned_rep2

value: female

value: spleen

value: monocytes, tumor associated macrophages


title: surgical resection HC18


title: Control macrophage_unconditoned_rep2


title: surgical resection HC20


title: T3-BM

source_name: T-ALL - no passage

value: T-ALL Donor 3


title: T2-BM


title: 382546A09_Ki3_R2_T1

city: Saint Paul

first: Nathan

middle: M

last: Springer

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

hyb_protocol: Per sample, ~20μg of Cy3- or Cy5-labeled RNAs were hybridized for 16-20 hours at 42°C using the NimbleGen Hybridization System.  Post hybridization, slides were washed (NimbleGen Wash Buffer Kit) and dried for two minutes by centrifugation.

scan_protocol: Slides were immediately scanned using the GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer protocol.

data_processing: Array images and data were processed using NimbleScan software.  Briefly, images from each slide were separated into 12 subarrays and aligned to a grid to extract signal intensity for each feature on the array.  Experimental integrity was verified by evaluation of the signal intensities of the sample tracking control features for each subarray.  In addition, metrics reports were produced for each array to report the signal uniformity across the array and the intensity of known empty features, random probes and experimental probes.  Signal-to-noise ratios were estimated by dividing the average signal intensity of the experimental gene probes (signal) by the average signal intensity of the random sequence control probes (noise).  Only slides with a signal-to-noise ratio ≤ 2 were retained. NimbleScan was used to generate RMA-normalized (Irizarry et al. 2003) gene expression values from the spatially-corrected probe signal intensities on a per probe and per gene basis.  Normalized gene expression values across multiple replications (technical or biological) of the same genotype were averaged, when possible. Comparisons of the distributions of signal intensity for the random sequence controls to the experimental gene probes on each array (Figure SM2) were used to determine a reasonable signal threshold for positive expression across all slides.  The plots demonstrate that in most cases, the random sequence control log2 signal intensity is ≤ 10 suggesting that signals above that threshold are true signal.  Hence, genes with average probe log2 signals of  >10 in at least three arrays were retained as expressed (N=19,792 expressed genes).  Since genetic polymorphisms could contribute to differences in hybridization between transcripts from some genotypes and probes developed based on the B73 reference sequence we further filtered the probeset based on a previous comparative genomic hybridization dataset developed using many of the same genotypes and the same array platform (Swanson-Wagner et al., 2010).  Any probes that exhibit substantially reduced CGH values for at least three genotypes (26,937 probes) were removed resulting in a set of 46,167 probes that detect expression of 18,242 genes with one to four probes per gene.   This dataset of N=18,242 expressed genes detected by probes without substantial evidence for polymorphisms was used for all analyses.

organism: Zea mays

source_name: Ki3, above ground seedling tissue

label_protocol: Purified RNAs (10ug per sample) were reverse transcribed and labeled according to the array manufacturer protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis v3.2).

growth_protocol: Maize seeds were grown in a greenhouse with 50% field soil and 50% Metromix with a 16hour light and 8 hour dark treatment

extract_protocol: RNAs were isolated using the commercial TRIzol (Invitrogen, Carlsbad, CA; cat# 15596026) from above-ground tissue.  RNAs were purified by Lithium Chloride treatment followed by 3M sodium acetate (0.1 vol) and 95% ethanol (2.5 vol) precipitation.

treatment_protocol: No treatments

tag: pooling type

value: pooled multiple seedlings

tag: genotype

tag: classification


title: Laser micro-dissection sample of abscission layer at the base of flower in rice, LM-AL3

tag: variety

value: Nipponbare

value: young panicle

tag: panicle length

value: 7 mm

tag: region

value: abscission layer

source_name: abscission layer at the base of flower in rice, NIL(qSH1)

value: 10 mm


title: surgical resection HC9


title: T1-BM

value: human leukemia cells from bone marrow


title: surgical resection HC8

value: male


title: A1-M

value: AML Donor 1

value: passaged in mouse


title: 382546A10_Il14H_R2_T1

source_name: Il14H, above ground seedling tissue


title: Wildtype Air 3

source_name: Lung

tag: genotype/variation

value: wild type

value: Lewis lung carcinoma cells resected from lungs

tag: treatment/exposure

value: exposed to air


title: A3-BM

source_name: AML - no passage

value: AML Donor 3


title: surgical resection HC17

value: female


title: A2-BM

value: AML Donor 2


title: surgical resection HC6


title: surgical resection HC15


title: surgical resection HC16