title: transcriptional effects of LMP3 in MSC_Adψ5_replicate3

status: Public on Dec 31 2010

type: RNA

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

description: Hybridizations were carried out independently for each condition using three biological replicates, according to the “minimum information about a microarray experiment” (MIAME) guidelines.

hyb_protocol: Hybridization was performed at 45° for 16h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix Genechip Fluidics Station.

scan_protocol: Fluorescence intensities were scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Data analysis were performed using BRB ArrayTools. Probe level summaries were generated using robust multi-array average (RMA) analysis. The normalized probe intensity values were then compiled, or summarized, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log (base 2) transformed.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

label_protocol: The syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). Biotinylated, fragmented cRNA probes were hybridized to the Human Focus Array (Affymetrix).

extract_protocol: RNA was isolated from cells using using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. In order to avoid genomic DNA in samples, RNA was digested with amplification grade DNase I (Qiagen). The yield of RNA isolation was determined using spectrophotometry (Beckman DU800, Beckman Coulter, Inc., Fullerton, CA). The quality and integrity of total RNA were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: cells treated with Adψ5

tag: gender

value: male

tag: tissue

value: bone marrow

tag: cell type

value: mesenchymal stem cells


title: transcriptional effects of LMP3 in MSC_LMP3_replicate1

treatment_protocol: cells treated with AdLMP3


title: transcriptional effects of LMP3 in MSC_LMP3_replicate2


title: transcriptional effects of LMP3 in MSC_Adψ5_replicate1


title: transcriptional effects of LMP3 in MSC_LMP3_replicate3


title: transcriptional effects of LMP3 in MSC_control2

treatment_protocol: untreated cells


title: transcriptional effects of LMP3 in MSC_Adψ5_replicate2


title: transcriptional effects of LMP3 in MSC_control3


title: transcriptional effects of LMP3 in MSC_control1


title: narco_9

hyb_protocol: Hybridization was performed at 45°C for 16 h in a hybridization oven (Affymetrix). The Genechips were then automatically washed and stained with streptavidin–phycoerythrin conjugate using the Genechip Fluidics Station (Affymetrix).

data_processing:
CEL files were imported using the default BRB Array tools normalization parameters.  Probe-level data were pre-processed, including background correction, normalization,  and summarization , using robust multi-array average (RMA) analysis; subsequent  data normalization was performed across all arrays using quantile normalization.
The normalized probe intensity values were then compiled, or summarized, within each probe set, using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.

source_name: blood

label_protocol: the syntheses of cDNA and biotinylated cRNA were performed according to the protocols provided by Affymetrix

extract_protocol: A blood specimen of 2,5 ml was collected from each subject using PAXgene Blood RNA tubes and total RNA was isolated using PAXgene Blood RNA Kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s protocols. Total RNA was quantified using spectrophotometry (Beckman). Quality of total RNA was checked using 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

value: whole blood

tag: sex

tag: disease status

value: narcolepsy patient


title: narco_11


title: narco_6


title: narco_5


title: contr_11

value: healthy control


title: contr_17

value: female


title: contr_9


title: narco_2


title: contr_13


title: narco_1


title: narco_8


title: narco_3


title: contr_14


title: narco_12


title: contr_12


title: narco_4


title: contr_16


title: contr_5


title: contr_7


title: contr_6


title: 19 day old, blood feed, biological rep3

city: Irvine

first: Mei-Hui

last: Wang

state: CA

address: 3501B Hewitt Hall UCI

country: USA

institute: UC irvine

description: Female adult, 19 day old, Blood feed

hyb_protocol: 2.2 μg of the resulting fragmented, biotin-tagged cDNA  was placed into a hybridization cocktail (220 μL), with 200 μL actually hybridized at 45°C with rotation for 18 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix array (GeneChip® Plasmodium/Anopheles Genome Array). The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450 using the FS450_0004 fluidics protocol

scan_protocol: Scanning on an Affymetrix GeneChip 3000 Scanner 7G

data_processing: Results were quantified and analyzed using Expression Console ver.1.1 software (Affymetrix, Inc.) using the PLIER Algorithm default values (Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

label: Biotin

organism: Anopheles gambiae

source_name: Female adult, 19 day old, Blood feed

label_protocol: 3.75 μg of the resulting amplified cDNA material for each sample was first fragmented and subsequently end-labeled using the NuGEN FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos CA)

growth_protocol: There were 250 adult (male:female=1:1) for each cage. Mosquito colonies were maintained by blood feeding on anesthetized rabbits every five days.

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

treatment_protocol: Female mosquitoes were collected at Day 1, Day 4, Day 10, Day 19 and Day 28. All the females were split into two sets. One set of mosquitoes were not blood fed and the other set of mosquitoes were blood fed every five days. Blood-fed females only collected at Day 10, Day 19, and Day 28.

value: whole body

tag: genotype

tag: age

value: 19 day


title: 28 day old, blood feed, biological rep4

description: Female adult, 28 day old, Blood feed

source_name: Female adult, 28 day old, Blood feed

value: 28 day


title: 28 day old, blood feed, biological rep2

description: Female adult, 28 day old, Blood feed


title: 19 day old, blood feed, biological rep1

description: Female adult, 19 day old, Blood feed


title: 10 day old, blood feed, biological rep4

description: Female adult, 10 day old, Blood feed

source_name: Female adult, 10 day old, Blood feed

value: 10 day


title: 10 day old, blood feed, biological rep3

description: Female adult, 10 day old, Blood feed


title: 28 day old, blood feed, biological rep1

description: Female adult, 28 day old, Blood feed


title: 19 day old, blood feed, biological rep4

description: Female adult, 19 day old, Blood feed


title: 28 day old, Non blood feed, biological rep3

description: Female adult, 28 day old, Non blood feed

growth_protocol: There were 250 adult (male:female=1:1) for each cage. Adults had access to raisins and cotton balls saturated with dd-water.


title: 19 day old, blood feed, biological rep2

description: Female adult, 19 day old, Blood feed


title: 28 day old, blood feed, biological rep3

description: Female adult, 28 day old, Blood feed


title: 28 day old, Non blood feed, biological rep2

source_name: Female adult, 28 day old, Non blood feed


title: 10 day old, Non blood feed, biological rep1

description: Female adult, 10 day old, Non blood feed


title: 10 day old, Non blood feed, biological rep2

source_name: Female adult, 10 day old, Non blood feed


title: 19 day old, Non blood feed, biological rep1

description: Female adult, 19 day old, Non blood feed


title: 10 day old, Non blood feed, biological rep4


title: 28 day old, Non blood feed, biological rep1


title: 19 day old, Non blood feed, biological rep2

source_name: Female adult, 19 day old, Non blood feed


title: 10 day old, blood feed, biological rep2

description: Female adult, 10 day old, Blood feed


title: 19 day old, Non blood feed, biological rep4


title: 4 day old, Non blood feed, biological rep1

description: Female adult, 4 day old, Non blood feed

source_name: Female adult, 4 day old, Non blood feed

value: 4 day


title: 10 day old, blood feed, biological rep1

description: Female adult, 10 day old, Blood feed


title: 1 day old, Non blood feed, biological rep4

description: Female adult, 1 day old, Non blood feed

source_name: Female adult, 1 day old, Non blood feed

value: 1 day


title: 4 day old, Non blood feed, biological rep3

description: Female adult, 4 day old, Non blood feed


title: 1 day old, Non blood feed, biological rep2

description: Female adult, 1 day old, Non blood feed


title: 19 day old, Non blood feed, biological rep3


title: 10 day old, Non blood feed, biological rep3


title: 4 day old, Non blood feed, biological rep2

description: Female adult, 4 day old, Non blood feed


title: 4 day old, Non blood feed, biological rep4

description: Female adult, 4 day old, Non blood feed


title: 1 day old, Non blood feed, biological rep1

description: Female adult, 1 day old, Non blood feed


title: 1 day old, Non blood feed, biological rep3

description: Female adult, 1 day old, Non blood feed


title: CGH: HCC1937

type: genomic

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: Hybridization was performed as described previously (Nat Genet. 2004 Mar;36(3):299-303) for 40 hours.

scan_protocol: Slides were scanned at 10uM resolution on a Perkin Elmer ScanArray Express.

data_processing: Data were extracted from images using SoftWorx Tracker software.  Systematic biases were removed from Log2 ratios (Cy3/Cy5) using CGHNorm (BMC Bioinformatics. 2005 Nov 18;6:274).  Only clones with SD<=0.075 and SNR>3 (for both channels) were used for further work.

molecule: genomic DNA

label_protocol: Labeling was performed as described previously (Nat Genet. 2004 Mar;36(3):299-303).  Briefly, tumors were labeled with cy3 dUTP using random primers and Klenow fragment.  Diploid reference was labeled with cy5 dUTP.

tag: cell line

tag: catalog number

value: ATCC# CRL-2336

source_name: diploid male reference

tag: sample type

value: diploid male reference


title: Liver, hydrogen-saturated water administrated for 4weeks #1

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

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.

organism: Rattus norvegicus

source_name: Liver, administrated hydrogen-saturated water for 4 weeks

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using ISOGEN (Nippon Gene Co., Ltd., Toyama, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

tag: strain

value: Sprague-Dawley (SD)

value: 8 weeks

value: liver


title: CGH: HCC1599

value: ATCC# CRL-2331


title: CGH: HCC1143

value: ATCC# CRL-2321


title: Liver, hydrogen-saturated water administrated for 4weeks #2

value: male


title: Liver, hydrogen-saturated water administrated for 4weeks #3


title: Liver, Control (sterilized distilled water administrated for 4 weeks) #3

source_name: Liver, administrated control sterilized distilled water for 4 weeks


title: Liver, Control (sterilized distilled water administrated for 4 weeks) #4


title: CGH: HCC38

value: ATCC# CRL-2314


title: Liver, hydrogen-saturated water administrated for 4weeks #4


title: Liver, Control (sterilized distilled water administrated for 4 weeks) #1


title: CGH: HCC1395

value: ATCC# CRL-2324


title: CGH: HCC1008

value: ATCC# CRL-2320


title: Liver, Control (sterilized distilled water administrated for 4 weeks) #2


title: CGH: HCC2218

value: ATCC# CRL-2343


title: Allelic status: MCF7

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
MCF7

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Analyzed using dChip with the reference genotypes of sixty individuals obtained from the dChip website

label: standard Affymetrix protocol

source_name: DNA from breast cancer cell line

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

treatment_protocol: standard Affymetrix protocol

value: ATCC# HTB-22


title: Spleen_normal_rep2

city: Gaithersburg

first: Joseph

last: Briggs

state: MD

address: 37 Convent Drive

department: Pediatric Oncology Branch

institute: National Cancer Institute

hyb_protocol: Samples were hybridized to Canine Genome Version 2.0 Affymetrix oligonucleotide arrays according to manufacturer's instructions (Affymetrix, Santa Clara, CA) at the NCI Microarray Core Facility (Frederick, MD).

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner 3000.  Data were collected using Affymetrix GCOS software.

data_processing: Affymetrix .CEL files containing the raw, probe-level signal intensities were analyzed using Partek® software, version 6.4 (build 6.09.0310, Copyright 1993-2009, Partek Inc. Partek and all other Partek Inc. product or service names are registered trademarks or trademarks of Partek Inc., St. Louis, MO, USA.).  Robust multichip averaging (RMA) was used for pre-processing of probe-level data (using only interrogating probes) including pre-background adjustment for GC content and probe sequence followed by RMA background correction.  All chips underwent quantile normalization and probeset summaries were median polished (Bolstad, Irizarry, Astrand and Speed 2003).

organism: Canis lupus familiaris

label_protocol: Five micrograms of purified RNA was reverse transcribed and used to make biotinylated cRNA according to standard Affymetrix protocol.

extract_protocol: RNA was extracted from all samples using TRIzol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).  Samples were then further purified using Qiagen miniprep RNA clean up (Qiagen, Valencia, CA) as per Affymetrix protocols for array preparation.  Samples were quantified and assessed for quality using a Bioanalyzer 2100 instrument (Agilent Technologies, Palo Alto, CA).

value: Spleen

tag: disease

value: normal


title: Allelic status: BT474

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
BT474

value: ATCC# HTB-20


title: SkeletalMuscle_normal_rep4

value: Skeletal Muscle


title: SkeletalMuscle_normal_rep3


title: Allelic status: HCC1599

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1599


title: Spleen_normal_rep3


title: SkeletalMuscle_normal_rep2


title: Allelic status: HCC2218

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC2218


title: Spleen_normal_rep4


title: Spleen_normal_rep1


title: Allelic status: HCC1395

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1395


title: Allelic status: HCC1143

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1143


title: Allelic status: HCC1008

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1008


title: Allelic status: HCC38

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC38


title: Pancreas_normal_rep3

value: Pancreas


title: SkeletalMuscle_normal_rep1


title: Lung_normal_rep4

value: Lung


title: Kidney_normal_rep4

value: Kidney


title: LymphNode_normal_rep3

value: Lymph Node


title: Pancreas_normal_rep1


title: Liver_normal_rep4

value: Liver


title: LymphNode_normal_rep4


title: Lung_normal_rep2


title: Lung_normal_rep1


title: Lung_normal_rep3


title: Liver_normal_rep3


title: Kidney_normal_rep2


title: Liver_normal_rep2


title: Jejunum_normal_rep4

value: Jejunum


title: Kidney_normal_rep3


title: Liver_normal_rep1


title: Jejunum_normal_rep1


title: Jejunum_normal_rep2


title: Jejunum_normal_rep3


title: Kidney_normal_rep1


title: Heart_normal_rep3

value: Heart


title: Heart_normal_rep4


title: Heart_normal_rep2


title: Heart_normal_rep1


title: Brain_normal_rep4

value: Brain (cerebrum)


title: Brain_normal_rep3


title: Brain_normal_rep2


title: Brain_normal_rep1


title: LymphNode_normal_rep2


title: Scotch salmon W_L_SF_267_HH008_003, Lower river mort

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

institute: University of British Columbia

hyb_protocol: Each fish examined in the array experiments was run on a single slide against a reference control that was a pool of all of the fish used in the experiment.  Microarray data were expressed in terms of normalized (background corrected) log2 ratios between each fish and the reference control.  All slides were processed on Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland). All steps from washing, hybridization, denaturation, and slide drying were carried out automatically.

scan_protocol: Fluorescent images were scanned using a Perkin Elmer ScanArray Express (Perkin Elmer, Boston, MA), adjusting the PMT gain for optimized visualization of each image.  The images were quantified using Imagene (BioDiscovery, El Segundo, CA, www.biodiscovery.com).

data_processing: Expression data were managed using a local installation of BASE. BASE was customized slightly to support Imagene two-file formatting. Each slide was normalized in BASE using the print-tip LOESS method. The number of missing values, mean signal-to-noise log-ratio and quality metrics from arrayQualityMetrics and arrayQuality in Bioconductor were used to assess slide quality.  Slides were removed from further experimental analysis if two or more plots were flagged on the arrayQualityMetrics report after data normalization, if more than 40% missing spots were identified by the SNR and missing spots report, if there were more than 30% missing spots and an experimentally low SNR value as identified by the SNR and missing spots report, or if the slide had spatial problems as identified by the plots from the arrayQuality package and substantiated by the spatial plots score of the raw microarray data in the arrayQualityMetrics report.  Based on these criteria, 6% of slides were typically considered low quality and removed. The data for each retained slide was further processed to remove poor-quality spots. Flagged spots were treated as missing, as were spots with a SNR less than 2. In a set of slides considered a single data set, probes with more than 50% missing values were removed prior to statistical analysis. For procedures such as PCA that require matrices without missing values, missing data were imputed using an average of the existing probe intensities. The submitted data includes all probes and imputed data is not included.

label: Alexa 555

organism: Oncorhynchus nerka

source_name: gill

label_protocol: 500 nanograms to 5 micrograms of total RNA was amplified 1x using a MessageAmp(TM) II-96 kit (Ambion, TX, USA), performed manually according to manufacturers instructions.  Five micrograms of aRNA was reverse transcribed into cDNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit, with modifications from the manufacturer's instructions.  Briefly, the cDNA was purified using Zymo-25 Clean-Up columns (Zymo Research, Orange, CA) and eluted using the 2X coupling buffer, supplied by Invitrogen.  During dye labelling, samples were processed individually by first adding DMSO, then cDNA to the Alexa dye tube and incubating for 1h at room temperature.  All individual (experimental) samples were fluorescently tagged with Alexa 555 and references were labelled with Alexa 647.  Samples and references were cleaned up by adding 50 microliters of DNA binding buffer (Zymo) to each Alexa tube and then combining the sample and references for each slide into Zymo-25 Clean-Up columns.  The unbound portion of the labelled cDNA was removed by centrifugation at 13,000 rpm/min. The labelled cDNA was washed three times with DNA wash buffer (Zymo) and eluted in 9 microliters of 1X TE buffer.  Two microlitres of poly dA was added to the targets, which were then denatured for 10 min at 80C, followed by the addition of 125 microliters of pre-warmed SlideHybe3 buffer (Ambion, TX, USA) before loading into the hybridization chamber in Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland)

extract_protocol: Field collected samples were initially stored in a charged liquid nitrogen cryo-shipper and transferred to -80C upon arrival to the lab. Total RNA was purified from individual fish gill using Magmax(TM)-96 for Microarrays Kits (Ambion Inc, Austin, TX, USA) with a Biomek FXP (Beckman-Coulter, Mississauga, ON, Canada) automated liquid-handling instrument.  Two gill filaments per fish were homogenized with stainless steel beads in TRI-reagent (Ambion Inc, Austin, TX, USA) on a MM301 mixer mill (Retsch Inc., Newtown, PA, USA).  One hundred micro liter aliquots of homogenates were pipetted into 96 well plates and extractions were carried out according to the manufacturer's instructions using the No-Spin Procedure on the Biomek FXP.  In the final step, RNA was eluted with RNAase-, DNAase-free water and RNA yield was determined by measuring the A260 of the eluate. Purity was assessed by measuring the A260/A280 ratio of the eluate. Solutions of RNA were stored at -80C until use for cDNA synthesis or quantitative RT-PCR.

value: gill

tag: alternative identifier

tag: Sex

value: F

tag: run

value: Early summer

tag: sampling date

tag: last tracked zone

tag: last tracked date

tag: fate

value: Lower river mort

tag: stock

value: Scotch

label: Alexa 647

source_name: gill from all samples in the series

extract_protocol: to be updated

tag: reference

value: Pooled RNA reference


title: Scotch salmon W_F_SF_92_HH008_246, Fisheries

tag: tissue

value: Fisheries


title: Chilko salmon W_F_CM_363_HH008_130, Fisheries

value: M

value: Summer run

value: Chilko


title: Lower Adams salmon W_S_LAM_332_HH008_063, Survivor

value: Late run

value: Survivor

value: Lower Adams


title: Scotch salmon W_F_SF_165_HH008_013, Fisheries


title: Scotch salmon W_F_SM_364_HH008_262, Lower river Fisheries

value: Lower river Fisheries


title: Lower Shuswap salmon W_F_FN_LAF_353_HH008_164, Lower river Fisheries

value: Lower Shuswap


title: Lower Adams salmon W_F_FN_LAF_67_HH008_129, Fisheries


title: Lower Adams salmon W_F_FN_LAF_117_HH008_055, Fisheries


title: Scotch salmon W_F_SF_146_HH008_259, Fisheries


title: Lower Adams salmon W_U_LAM_193_HH008_058, Upper river mort

value: Upper river mort


title: Chilko salmon W_F_CM_254_HH008_155, Lower river Fisheries


title: Scotch salmon W_U_SM_177_HH008_163, Upper river mort


title: Scotch salmon W_F_SF_91_HH008_018, Fisheries


title: Chilko salmon W_F_CM_340_HH008_153, Fisheries


title: Scotch salmon W_F_SF_103_HH008_162, Fisheries


title: Lower Adams salmon W_U_LAM_371_HH008_054, Upper river mort


title: Lower Adams salmon W_F_FN_LAM_150_HH008_080, Fisheries


title: Stellako salmon W_F_CM_98_HH008_158, Fisheries

value: Stellako


title: Chilko south salmon W_F_CF_56_HH008_082, Fisheries

value: gill

value: Chilko south


title: Chilko south salmon W_F_CM_190_HH008_081, Fisheries


title: Lower Adams salmon W_F_FN_LAF_224_HH008_105, Fisheries

value: F


title: Lower Adams salmon W_F_FN_LAF_122_HH008_146, Fisheries


title: Scotch salmon W_F_SF_183_HH008_069, Fisheries

value: Early summer


title: Lower Adams salmon W_F_FN_LAM_138_HH008_067, Fisheries


title: Chilko salmon W_F_CF_367_HH008_148, Fisheries


title: Chilko south salmon W_F_CF_47_HH008_011, Fisheries


title: Chilko salmon W_F_CF_284_HH008_108, Fisheries


title: Lower Adams salmon W_F-Sp_LAM_345_HH008_075, Fisheries


title: Chilko salmon W_F_CF_235_HH008_060, Fisheries


title: Lower Adams salmon W_U_LAM_96_HH008_008, Upper river mort


title: Scotch salmon W_U_SF_320_HH008_142, Upper river mort

value: Scotch


title: MiddleShuswap salmon W_F-Sp_LAF_227_HH008_157, Fisheries

value: MiddleShuswap

value: Pooled RNA reference


title: Lower Adams salmon W_F-Sp_LAM_206_HH008_135, Fisheries

value: M

value: Fisheries


title: Scotch salmon W_U_SF_63_HH008_009, Upper river mort


title: Scotch salmon W_U_SF_327_HH008_137, Upper river mort


title: Scotch salmon W_U_SF_129_HH008_014, Upper river mort


title: Lower Shuswap salmon W_F-Sp_LAF_300_HH008_128, Fisheries


title: Lower Adams salmon W_U_LAM_95_HH008_016, Upper river mort


title: Lower Adams salmon W_U_LAM_173_HH008_147, Upper river mort


title: Scotch salmon W_U_SM_123_HH008_249, Upper river mort


title: Lower Adams salmon W_U_LAF_62_HH008_106, Upper river mort


title: Scotch salmon W_U_SM_269_HH008_264, Upper river mort


title: Lower Adams salmon W_U_LAM_204_HH008_134, Upper river mort


title: Lower Adams salmon W_U_LAF_329_HH008_059, Upper river mort


title: Lower Adams salmon W_U_LAF_158_HH008_050, Upper river mort


title: Scotch salmon W_U_SF_303_HH008_061, Upper river mort


title: Lower Adams salmon W_U_LAM_255_HH008_065, Upper river mort


title: Lower Adams salmon W_U_LAF_162_HH008_250, Upper river mort


title: MiddleShuswap salmon W_F-Sp_LAM_250_HH008_254, Fisheries


title: Lower Adams salmon W_U_LAM_167_HH008_053, Upper river mort


title: Lower Adams salmon W_U_LAF_217_HH008_049, Upper river mort


title: Chilko south salmon W_U_CM_315_HH008_140, Upper river mort

value: Summer run


title: Pancreas_normal_rep2

value: Pancreas

value: normal


title: Lower Adams salmon W_U_LAF_330_HH008_248, Upper river mort

value: Late run

value: Lower Adams


title: Lower Adams salmon W_U_LAM_317_HH008_057, Upper river mort


title: Chilko south salmon W_U_CM_274_HH008_136, Upper river mort


title: Chilko salmon W_U_CM_210_HH008_056, Upper river mort

value: Chilko


title: Chilko salmon W_U_CF_237_HH008_045, Upper river mort

value: Upper river mort


title: Chilko south salmon W_U_CM_144_HH008_150, Upper river mort


title: LymphNode_normal_rep1

value: Lymph Node


title: Scotch salmon W_S_SF_106_HH008_247, Survivor

value: gill

value: Survivor


title: Scotch salmon W_S_SM_24_HH008_149, Survivor


title: Scotch salmon W_S_SF_362_HH008_265, Survivor

value: F


title: MiddleShuswap salmon W_S_LAM_339_HH008_127, Survivor


title: Chilko salmon W_U_CF_228_HH008_071, Upper river mort


title: Chilko salmon W_U_CM_249_HH008_078, Upper river mort


title: Chilko south salmon W_U_CM_208_HH008_152, Upper river mort

value: Chilko south


title: Scotch salmon W_S_SF_83_HH008_145, Survivor

value: Early summer

value: Scotch


title: MiddleShuswap salmon W_S_LAM_308_HH008_074, Survivor

value: MiddleShuswap

value: Pooled RNA reference


title: Lower Adams salmon W_S_LAM_377_HH008_077, Survivor

value: M


title: Lower Adams salmon W_S_LAF_312_HH008_159, Survivor


title: Lower Adams salmon W_S_LAM_304_HH008_252, Survivor


title: Chilko salmon W_U_CF_275_HH008_258, Upper river mort

value: Summer run


title: Chilko salmon W_U_CM_174_HH008_253, Upper river mort


title: Lower Shuswap salmon W_S_LAM_365_HH008_083, Survivor

value: Lower Shuswap


title: Lower Shuswap salmon W_S_LAM_344_HH008_020, Survivor


title: Lower Adams salmon W_S_LAF_373_HH008_124, Survivor


title: Seymour salmon W_S_SF_74_HH008_257, Survivor

value: Seymour


title: Scotch salmon W_S_SM_279_HH008_047, Survivor


title: Lower Shuswap salmon W_S_LAM_278_HH008_132, Survivor

value: Late run


title: Chilko salmon W_S_CM_350_HH008_052, Survivor


title: Seymour salmon W_S_SF_110_HH008_070, Survivor


title: Chilko salmon W_S_CM_309_HH008_126, Survivor


title: Chilko salmon W_S_CM_111_HH008_048, Survivor


title: Chilko salmon W_S_CF_325_HH008_131, Survivor


title: Chilko salmon W_S_CF_252_HH008_255, Survivor


title: Chilko south salmon W_S_CM_240_HH008_046, Survivor


title: Scotch salmon W_L_SF_296_HH008_062, Lower river mort

value: Lower river mort


title: Lower Adams salmon W_L_LAF_143_HH008_006, Lower river mort

value: Lower Adams


title: Chilko salmon W_L_CF_348_HH008_143, Lower river mort

value: Chilko


title: Lower Adams salmon W_L_LAM_213_HH008_012, Lower river mort


title: Lower Adams salmon W_L_LAM_179_HH008_156, Lower river mort


title: Stellako salmon W_S_CF_359_HH008_019, Survivor

value: Stellako


title: Lower Adams salmon W_L_LAF_302_HH008_138, Lower river mort

value: gill


title: Chilko salmon W_L_CF_156_HH008_260, Lower river mort


title: Scotch salmon W_L_SF_326_HH008_044, Lower river mort


title: Scotch salmon W_L_CF_163_HH008_043, Lower river mort


title: Chilko salmon W_L_CM_368_HH008_154, Lower river mort


title: Lower Adams salmon W_L_LAM_248_HH008_079, Lower river mort


title: Lower Adams salmon W_L_LAM_84_HH008_107, Lower river mort


title: Chilko salmon W_L_CF_51_HH008_266, Lower river mort


title: Lower Adams salmon JS_n1_LA_1626_GI002_051, Survivor

value: Survivor


title: Chilko salmon W_L_CF_270_HH008_072, Lower river mort

value: F


title: Lower Adams salmon JS_n1_LA_1745_GI002_068, Survivor


title: LittleRiver - Little Shuswap salmon JS_n1_LR_1567_GI002_174, Survivor

value: LittleRiver - Little Shuswap


title: LittleRiver - Little Shuswap salmon JS_n1_LR_1740_GI002_088, Upper river mort

value: Upper river mort


title: LittleRiver - Little Shuswap salmon JS_LSh_urm_1501_GI002_029, Upper river mort


title: Lower Adams salmon JS_n1_LA_1363_GI002_153, Survivor


title: LittleRiver - Little Shuswap salmon JS_LSh_suv_1520_GI002_065, Survivor


title: Lower Adams salmon JS_n1_LA_1587_GI002_017, Survivor


title: LittleRiver - Little Shuswap salmon JS_LSh_suv_1453_GI002_064, Survivor


title: Lower Adams salmon JS_n1_LA_1563_GI002_132, Survivor


title: LittleRiver - Little Shuswap salmon JS_LSh_urm_1298_GI002_004, Upper river mort


title: LittleRiver - Little Shuswap salmon JS_LSh_urm_1421_GI002_164, Upper river mort


title: Lower Adams salmon JS_LA_suv_1467_GI002_148, Survivor


title: LittleRiver - Little Shuswap salmon JS_LSh_suv_1452_GI002_167, Survivor


title: LittleRiver - Little Shuswap salmon JS_e1_LR_1376_GI002_016, Upper river mort


title: Lower Adams salmon JS_LA_suv_1556_GI002_166, Survivor


title: Chilko salmon W_L_CF_184_HH008_010, Lower river mort


title: Lower Adams salmon JS_LA_suv_1651_GI002_007, Survivor


title: Lower Adams salmon JS_LA_suv_1677_GI002_008, Survivor


title: Lower Adams salmon JS_LA_suv_1439_GI002_063, Survivor


title: Lower Adams salmon JDFS_e1_LA_1203_GI002_176, Upper river mort


title: Lower Adams salmon JS_e1_LA_1637_GI002_087, Upper river mort


title: Lower Adams salmon JDFS_n1_LA_1273_GI002_111, Survivor


title: Lower Adams salmon JDFS_e1_LA_1213_GI002_018, Upper river mort


title: Lower Adams salmon JS_e1_LA_1493_GI002_050, Survivor


title: LittleRiver - Little Shuswap salmon JDFS_n1_LR_1237_GI002_053, Survivor


title: Lower Adams salmon JS_LA_suv_1769_GI002_006, Survivor


title: LittleRiver - Little Shuswap salmon JDFS_n1_LR_1259_GI002_134, Survivor


title: LittleRiver - Little Shuswap salmon JDFS_n1_LR_1284_GI002_090, Survivor


title: Lower Adams salmon JDFS_n1_LA_1191_GI002_155, Survivor


title: Lower Adams salmon JDFS_n1_LA_1248_GI002_019, Survivor


title: EDL 933 at 37oC at OD 1.0

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

description: RNA extracted from EHEC cells (OD = 1.0) grown in LB at 37oC

hyb_protocol: Fragmented end-labeled cDNA was hybridized to the GeneChip® E.coli  Genome arrays for 16 hours at 45 ℃ and 60 rpm as described in the Gene Chip Expression Analysis Technical Manual (Affymetrix)

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing:
After the final wash & staining step, Affymetrix GeneChip® E.coli Genome array was scanned using Affymetrix Model 3000 G7 scanner and the image data was extracted through Affymetrix Commnad Console software. The raw .cel file generated through above procedure meant expression intensity data and was used for the next step.
Expression data were normalized using the Affymetrix microarray suite 5(MAS5) algorithm implemented in Affymetrix expression console software .  To reduce noise for the significance analysis, probe sets that did not show detection call rate at least 50% of the samples in the comparison were filtered out. Highly expressed genes that showed a 2-fold change in expression were selected.
The web-based tool, DAVID (the Database for Annotation, Visualization, and Integrated Discovery) was used to perform the biological interpretation of differentially expressed genes. Then, these genes were classified based on the information of gene function in Gene ontology database.
(http://david.abcc.ncifcrf.gov/home.jsp)

organism: Escherichia coli

source_name: EDL 933 at 37oC at OD 1.0

label_protocol: The purified double-stranded cDNA was fragmented using 0.6U/ ㎍ of DNAse I  and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

extract_protocol: Total RNA was isolated using Ribopure Bacteria Kit as described by the manufacturer (Ambion, Huntingdon, UK). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

value: EDL 933


title: Lower Adams salmon JS_e1_LA_1759_GI002_066, Survivor


title: Lower Adams salmon JDFS_e1_LA_1200_GI002_069, Survivor


title: LittleRiver - Little Shuswap salmon JS_e1_LR_1433_GI002_131, Survivor


title: EDL 933 with 0.1 mg/ml IAN at 37oC at OD 1.0

description: RNA extracted from EHEC cells (OD = 1.0) with 0.1 mg/ml IAN grown in LB at 37oC


title: Lethal Replicate 5

city: Serdang

first: Phelim

last: Yong

state: Selangor

address: Faculty of Medicine and Health Sciences

department: Biomedical Sciences

country: Malaysia

institute: Universiti Putra Malaysia

description: Six-week-old female BALB/c mice (weighing 20-25g) were used for all animal experiments. The animals were randomized, assigned to groups of eight to ten individuals and given food and water ad libitum.

hyb_protocol: The cRNA hybridization mix was heated to 65 °C for 5 min and equilibrated to room temperature. Aliquots of each sample (750 ng of cRNA in 15 µl of the hybridization mix) were hybridized to the corresponding bead arrays, inserted in BeadChip Hyb Chamber (Illumina, USA) and incubated at 58 °C for 16 h in a rocker speed Hyb Oven (Illumina, USA) set a speed of 5. Then, the arrays were washed with 1 X High Temperature Wash Buffer (Illumina, USA), E1BC Buffer (Illumina, USA), blocked with E1 Buffer (Illumina, USA), stained with streptavidin-Cy3 (GE Healthcare, USA) and washed again. The washing procedures were carried out in Hybex Water Bath (Illumina, USA) and orbital shaker. Lastly, the arrays were dried by low-speed centrifugation and scanned with Illumina BeadStation (Illumina, USA).

scan_protocol: Arrays were dried by low-speed centrifugation and scanned with Illumina BeadStation (Illumina, USA). Scanning were performed according to manufacturer's suggestion.

data_processing: Raw data from BeadStudio Version 3.0 (Illumina, USA) was imported to Genespring 7.0 (Agilent, USA) for preprocessing and data analysis. The data for each array were normalized accordingly to per-chip normalization to the distribution of all genes on that array as well as the median expression for that gene across all chips in the study and data transformation. The different sets of data in the mice groups were compared with each other by one-way analysis of variance (ANOVA) test with a P-value cut-off of 0.05.

organism: Mus musculus

source_name: BALB/c

label_protocol: Illumina TotalPrep RNA amplification (Ambion Inc, USA) was used in cDNA synthesis and in vitro transcription. Briefly, the first-strand cDNA was synthesized from 100 ng of total RNA with T7 Oligo (dT) primer which contained T7 promoter sequence. The second strand cDNA synthesis was then synthesized in second-strand Master Mix for 2 h at 16 °C. Then, cDNA was purified with filter cartridge and eluted with nuclease free water. All enzymes were from Ambion (Ambion Inc, USA). Following purification, in vitro transcription from the cDNA sample was carried out using T7 enzyme mix (Ambion Inc, USA) to generate biotin-labeled cRNA. Subsequently, the labeled cRNA was separated from unincorporated ribonucleotides by passing through filter cartridge.

growth_protocol: The end-point of infection evaluation was day 7 in this model. At the time of killing, mice were anesthetized and exsanguinated by cardiac puncture. Whole blood and serum was collected and stored in -80 °C for future usage.

extract_protocol: RNA isolation was performed by using Mouse RiboPure™-Blood RNA Isolation Kit (Ambion Inc, USA) according to manufacturer’s instructions. Briefly, the frozen whole blood was thawed at room temperature and centrifuged at high speed to separate the blood cells from RNAlater. Lysis solution was added to the blood pellet and the cells were vortexed vigorously. Subsequently, samples were extracted with sodium acetate and acid-phenol chloroform, centrifuged and precipitated with 0.5 volume of 100 % ethanol (Merck KGaA, USA). Then, samples were further purified by using filter cartridge and eluted with nuclease free water. DNase digestion was carried out by utilizing TURBO DNAfree™ (Ambion Inc, USA). In addition, GLOBINclear™ (Ambion Inc, USA) was used to deplete alpha and beta globin mRNA from total RNA preparations by employing the biotin/ streptavidin binding, nucleic acid hybridization and magnetic bead separation. Briefly, the globin mRNA was captured by using biotinylated oligonucleotide mix and hybridized to streptavidin magnetic beads. Then, the bound globin mRNA with streptavidin magnetic beads were removed by magnetic field, producing RNA with depleted globin mRNA. Finally, the RNA was purified using rapid magnetic bead-based purification method and eluted with nuclease free water.

treatment_protocol: For acute systemic candidiasis, mice in groups of eight to ten were challenged by intravenous tail-vein injection of an inoculum of 1 x 10E7 (lethal infection group) and 1 x 10E5 c.f.u. (sublethal infection group), respectively, in a 200 µl of a Candida tropicalis suspension via a 25-gauge syringe. In control group, 100 µl of PBS was used instead of the yeast suspension.

value: 6 weeks

tag: gender

value: female

value: BALB/c

value: whole blood


title: Lethal Replicate 4

tag: age


title: Lethal Replicate 3


title: Sublethal Replicate 4


title: Control Replicate 4


title: Lower Adams salmon JDFS_n1_LA_1250_GI002_070, Upper river mort

value: Pooled RNA reference


title: Sublethal Replicate 5


title: Lethal Replicate 2


title: SKBR3_miRNA_rep2

type: other

city: Bethesda

first: Mark

last: Mackiewicz

department: National Cancer Institute

institute: National Institutes of Health

description: Each miRVana miRNA Bioarray is comprised of 328 human miRNAs in addition to 114 mouse and 46 rat miRNAs.

hyb_protocol: Labeled products were hybridized to miRVana miRNA Bioarrays V2 and washed according to the manufacturer's protocols.

scan_protocol: Processed arrays were scanned for dual channel hybridization using a GenePix 4000B scanner and its corresponding software.

data_processing: Replicate spots for each miRNA or control were averaged within the array, background adjusted, and log2 normalized using a per chip median normalization method.  The reported value represents the Cy5/Cy3 median signal ratio.

molecule: other

source_name: SKBR3_replicate 2

label_protocol: Five micrograms of RNA was labeled with Cy5 fluorescent label (GE Healthcare) using the mirVana miRNA labeling kit (Ambion), following the manufacturer's instructions.

growth_protocol: Cells were grown in RPMI 1640 basal medium + 10% FBS in a T75 flask at 37C with 5% carbon dioxide.  Cells were harvested at 80-90% confluency for total RNA extraction.

extract_protocol: The small RNA fraction was extracted from these cells using Qiagen's miRNeasy kit by following the manufacturer's protocol.

treatment_protocol: Cells were untreated.

tag: estrogen receptor

value: negative

tag: progesterone receptor

value: positive

tag: cell line

source_name: MCF10A, Immortalized, non-tumorigenic breast cell line used as the reference

growth_protocol: Cells were grown in DMEM/F12 basal medium supplemented with 5% horse serum, 20 ng/ml final epidermal growth factor, 0.5 ug/ml final hydrocortisone, 100 ng/ml final cholera toxin, and 10 ug/ml final insulin in a T75 flask at 37C with 5% carbon dioxide.  Cells were harvested at 80-90% confluency for total RNA extraction.


title: MCF7_miRNA_rep4

source_name: MCF7_replicate 4


title: MCF7_miRNA_rep1

source_name: MCF7_replicate 1


title: MCF7_miRNA_rep3

source_name: MCF7_replicate 3


title: MB231_miRNA_rep4

source_name: MB231_replicate 4


title: SKBR3_miRNA_rep1

source_name: SKBR3_replicate 1


title: SKBR3_miRNA_rep4

source_name: SKBR3_replicate 4


title: Control Replicate 3

tag: strain


title: MB231_miRNA_rep2

source_name: MB231_replicate 2


title: MCF7_miRNA_rep2

source_name: MCF7_replicate 2


title: MB231_miRNA_rep1

source_name: MB231_replicate 1


title: SKBR3_miRNA_rep3

source_name: SKBR3_replicate 3


title: Sublethal Replicate 1


title: MiddleShuswap salmon W_S_LAF_198_HH008_151, Survivor

value: Late run

value: MiddleShuswap


title: MB231_miRNA_rep3

source_name: MB231_replicate 3


title: Chilko salmon W_S_CM_380_HH008_017, Survivor

source_name: gill

value: M

value: Summer run

value: Chilko


title: Lethal Replicate 1


title: Lower Adams salmon JS_e1_LA_1448_GI002_173, Upper river mort

value: gill

value: Lower Adams

source_name: gill from all samples in the series


title: Sublethal Replicate 2


title: Control Replicate 2

source_name: BALB/c Mice


title: nMncN4

city: Seattle

first: David

middle: K

last: Pritchard

state: WA

address: 815 Mercer Street Rm.  418

department: Pathology

institute: University of Washington

description: no loading replicate 4

hyb_protocol: Labeled probe was hybridized using standard Affymetrix protocols at the University of Washington Center for Array Technology

scan_protocol: Arrays were scanned using standard Affymetrix protocols at the University of Washington Center for Array Technology

data_processing: Data was processed using the RMA algorithm

source_name: thioglycollate elicited peritoneal macrophage

label_protocol: Total RNA was labeled using standard Affymetrix protocols at the University of Washington Center for Array Technology

growth_protocol: Macrophages harvested from the peritoneum of C57Bl/6J mice 5 days after injection of thioglycolate.

extract_protocol: Total RNA was isolated from cultured cells by using RNeasy Mini Kit (Qiagen) using manufacturers protocols.

treatment_protocol: Thioglycollate elicited macrophage were cultured for 3 days in DMEM + 10%FBS either in the presence or absence of 20 microgram/mL acLDL.

tag: agent


title: IMncN1

description: acLDL loaded replicate 1

value: acLDL


title: OB-TUDCA, biological rep2

city: Pohang

first: Jae-Seong

last: Yang

address: San 31 Hyoja-dong

department: School of Interdisciplinary Bioscience and Bioengineering

institute: Pohang University of Science and Technology

description: Gene expression data from liver of ob/ob control with oral TUDCA treatment

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4,  Affymetrix).

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

data_processing: Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara), using RMA algorithms.

source_name: liver of TUDCA-treated ob/ob mice

label_protocol: The extraction of total RNA was performed according to the manufacturer's instructions.

growth_protocol: Mice ob/ob mice and control littermate (C57BL/6J) were fed a normal chow diet (Purina LabDiet, St Louis, MO, USA) ad libitum.

extract_protocol: The mice were killed after an 8 hour fasting.  The livers were immediately retrieved and kept freshly frozen.

treatment_protocol: The ob/ob mice were given TUDCA (Tokyo Tanabe, Tokyo, Japan) at a dose of 500 mg/kg twice a day (8:00 AM and 8:00 PM) by gastric gavage for 3 weeks (OB-TUDCA group, n = 3). We administered tap water to control ob/ob mice (OB-control group, n = 3) and normal control C57BL/6J mice (N-control group, n = 3) twice a day by gastric gavage for 3 weeks.

tag: genotype

value: ob/ob

value: liver

value: TUDCA


title: N-control, biological rep2

description: Gene expression data from liver of normal control

source_name: liver of C57BL/6J mice

value: wildtype

value: control


title: IMncN4

description: acLDL loaded replicate 4


title: OB-control, biological rep3

description: Gene expression data from liver of ob/ob control

source_name: liver of ob/ob mice


title: IMncN3

description: acLDL loaded replicate 3


title: OB-control, biological rep1


title: N-control, biological rep1


title: nMncN3

description: no loading replicate 3


title: OB-TUDCA, biological rep3


title: nMncN2

description: no loading replicate 2


title: nMncN1

description: no loading replicate 1


title: Control Replicate 1

source_name: BALB/C mice

value: 6 weeks

value: female

value: BALB/c

value: whole blood


title: OB-control, biological rep2


title: Sublethal Replicate 3

source_name: BALB/c


title: IMncN2

description: acLDL loaded replicate 2


title: OB-TUDCA, biological rep1


title: STA-NB-10_polyRNA

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

institute: "San Martino" Hospital

description: Gene expression from untreated cell line

hyb_protocol: Labelled cRNAs were hybridized to whole-genome oligonucleotide microarrays containing 41,000 human transcripts (Agilent Technologies) following the manufacture's instructions (One-color microarray-based gene expression analysis protocol, v5.5). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4x44K Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%). Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (Agilent protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities. The output of Feature Extraction was analyzed with the Agi4x44PreProcess package. After within-array median-summarization of probe intensities within replicates, probe intensities were log base 2 transformed and normalized across arrays with the quantile normalization method implemented in Bioconductor.

molecule: polyA RNA

source_name: human neuroblastoma cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng polysomal RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com).  Dye incorporation and cRNA yield were checked with the Biophotometer (Eppendorf).

growth_protocol: See specific description in additional description column Characteristics. Growth conditions in the SAMPLE section.

extract_protocol: Cells were washed once with phosphate buffer saline (PBS + cycloheximide 10 µg ml-1) and treated directly on the plate with 300 µl lysis buffer [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U µl-1 RNase inhibitor (Fermentas), cycloheximide 10 µg ml-1 and 1 mM dithiothreitol] and transferred to an Eppendorf tube. After a few minute incubation on ice with occasional vortexing, the extracts were centrifuged for 5 min at 12,000 g at 4°C. The supernatant was stored at –80°C or loaded directly onto a 15–50% linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged in an Sorvall rotor for 100 min at 180,000 g. Fractions (polysomal and subpolysomal) were collected monitoring the absorbance at 254 nm and treated directly with proteinase K. After phenol–chloroform extraction and isopropanol precipitation, polysomal RNA was resuspended in 30 µl of water and repurified, when necessary, with the RNeasy kit (Qiagen, Hilden, Germany). Polysomal RNA was quantified and quality control assessed by Nano LabChip® assay on the 2100 Bioanalyzer (Agilent Technologies). Only samples with a RNA Integrity Number >7 were included in the study.

treatment_protocol: All samples were untreated cell lines

tag: sample type

value: Neuroblastoma cell line established at the Children’s Cancer Research Institute (CCRI) in Vienna. The doubling time is unknown, split ratio is about 1:2 one-two times per month.

tag: growth conditions

value: STA-NB-10 adherent cells were grown in RPMI 160 with Ultraglutamine medium (Lonza) supplemented with 10% FBS (Lonza), 2.5% Hepes Buffer Solution 1M (Sigma) and 1% sodium pyruvate (Lonza).


title: N-control, biological rep3


title: SIMA_polyRNA

value: Established from the adrenal tumor tissue resected after treatment from a 20-month-old boy of European origin wit Neuroblastoma (stage 3). The doubling time is highly variable about 34-100 hours.

value: SIMA cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).

value: SIMA


title: IMR-32_polyRNA

value: Established from an abdominal mass occurring in a 13-month-old Caucasian male in 1967. The tumor was diagnosed as a neuroblastoma with two rare areas of origin of differentiation. The culture is a mixture of two morphologically distinct cell types, a small neuroblast-like cell and the other a large hyaline fibroblast. IMR 32 is partially resistant to polioviruses type 3 and highly resistant to ECHO-II. It is susceptible to Coxsackie B3.

value: IMR-32 adherent cells were grown in EMEM ( Sigma), 1% Non Essential Amino Acid (NEAA) (Lonza) 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: STA-NB-7_polyRNA

value: STA-NB-7 adherent cells were grown in RPMI 160 with Ultraglutamine medium (Lonza) supplemented with 10% FBS (Lonza), 2.5% Hepes Buffer Solution 1M (Sigma) and 1% sodium pyruvate (Lonza).


title: CHP-126_polyRNA

value: Cell line were established from a large retroperitoneal mass excised from a 14-month-old girl with neuroblastoma (stage 3) in 1973; NMYC and DDX1 have been reported to be amplified. The doubling time is 150-200 hrs and split ratio is about 1:2-1:3 every 3-5 days. This type of cell line grows in suspension.

value: CHP-126 cells were maintained in suspension in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: SK-N-BE(2)_polyRNA

value: The morphology varies with sub-population from cells with long processes though small flattened  ephitelioid cells. The doubling time is 20 hrs, split ratio is about 1:4 - 1:10 one two times per week.

value: SK-N-BE(2) adherent cells were grown in 1:1 EMEM (Sigma) and Ham’s F12  (Sigma) supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: SK-N-SH_polyRNA

value: Cell line established from a bone marrow metastasis from a 4-years-old Caucasian female suffering with Neuroblastoma. The cells have been used as a target cell in cell-mediated cytotoxicity tests. The doubling time is 44 hrs, split ratio time 1:3 – 1:4 two times per week.

value: SK-N-SH adherent cells were grown in DMEM (Lonza), 10% FBS (Lonza) and 2mM L-Glutamine  (Lonza).

value: SK-N-SH


title: SK-N-AS_polyRNA

value: Neuroblastoma cell line derived from a female patient with neuroblastoma from the metastasis of the bone marrow. Tumorigenic in nude mice. The doubling time is 39 hrs, split ratio is about 1:3-1:4 two times per week.

value: SK-N-AS adherent cells were grown in DMEM (Lonza), 10% FBS (Lonza) and 2mM L-Glutamine  (Lonza).

value: SK-N-AS


title: NB-69_polyRNA

value: Neuroblastoma cell line derived from a tumor isolated from a 16-month old male. The tissue of origin is the Brain. The doubling time is 18 - 20 hrs and split ratio is about 1:4

value: NB-69 cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: KELLY_polyRNA

value: Neuroblastoma cell line established from a patient with neuroblastoma; ca. 100-fold genomic amplification of N-myc in der(17)hsr confirmed as human with IEF of AST, LDH, MDHA. The cells grow as adherent, round to fusiform with polar neuritic processes, growing in mono- and multilayers. The doubling time is 30 - 40 hrs and split ratio is about 1:3 to 1:10 every 3-6 days using trypsin/EDTA.

value: KELLY cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).

value: KELLY


title: IMR-32_totRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com).  Dye incorporation and cRNA yield were checked with the Biophotometer (Eppendorf).

extract_protocol: Total RNA was isolated by using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s protocol. Total RNA was quantified and quality control assessed by Nano LabChip® assay on the 2100 Bioanalyzer (Agilent Technologies). Only samples with a RNA Integrity Number >7 were included in the study.

value: Established from an abdominal mass occurring in a 13-month-old Caucasian male in 1967. The tumor was diagnosed as a neuroblastoma with two rare areas of origin of differentiation. The culture is a mixture of two morphologically distinct cell types, a small neuroblast-like cell and the other a large hyaline fibroblast. IMR 32 is partially resistant to polioviruses type 3 and highly resistant to ECHO-II. It is susceptible to Coxsackie B3.

value: IMR-32 adherent cells were grown in EMEM ( Sigma), 1% Non Essential Amino Acid (NEAA) (Lonza) 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: STA-NB-10_totRNA

value: Neuroblastoma cell line established at the Children’s Cancer Research Institute (CCRI) in Vienna. The doubling time is unknown, split ratio is about 1:2 one-two times per month.

value: STA-NB-10 adherent cells were grown in RPMI 160 with Ultraglutamine medium (Lonza) supplemented with 10% FBS (Lonza), 2.5% Hepes Buffer Solution 1M (Sigma) and 1% sodium pyruvate (Lonza).


title: SIMA_totRNA

value: Established from the adrenal tumor tissue resected after treatment from a 20-month-old boy of European origin wit Neuroblastoma (stage 3). The doubling time is highly variable about 34-100 hours.

value: SIMA cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).

value: SIMA


title: SK-N-SH_totRNA

value: Cell line established from a bone marrow metastasis from a 4-years-old Caucasian female suffering with Neuroblastoma. The cells have been used as a target cell in cell-mediated cytotoxicity tests. The doubling time is 44 hrs, split ratio time 1:3 – 1:4 two times per week.

value: SK-N-SH adherent cells were grown in DMEM (Lonza), 10% FBS (Lonza) and 2mM L-Glutamine  (Lonza).


title: CHP-212_totRNA

value: Neuroblastoma cells grow as adherent colonies consisting of epithelial-like cells. Doubling time 20 hrs, split ratio is about 1:4-1:10 one-two times per week

value: CHP-212 adherent cells were grown in 1:1 EMEM (Sigma) and Ham’s F12  (Sigma) supplemented with 10% FBS (Lonza) and 2mM L-Glutamine  (Lonza).


title: STA-NB-1_polyRNA

value: STA-NB-1 adherent cells were grown in RPMI 160 with Ultraglutamine medium (Lonza) supplemented with 10% FBS (Lonza), 2.5% Hepes Buffer Solution 1M (Sigma) and 1% sodium pyruvate (Lonza).


title: LAN-1_polyRNA

value: Neuroblastoma cells isolated from the bone marrow of a 2-years-old male clinical stage 4 of Neuroblastoma. The Doubling time is 32 hrs, split ratio is about 1:2 once times per week.

value: LAN-1 cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: CHP-126_totRNA

value: Cell line were established from a large retroperitoneal mass excised from a 14-month-old girl with neuroblastoma (stage 3) in 1973; NMYC and DDX1 have been reported to be amplified. The doubling time is 150-200 hrs and split ratio is about 1:2-1:3 every 3-5 days. This type of cell line grows in suspension.

value: CHP-126 cells were maintained in suspension in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: SK-N-BE(2)_totRNA

value: The morphology varies with sub-population from cells with long processes though small flattened  ephitelioid cells. The doubling time is 20 hrs, split ratio is about 1:4 - 1:10 one two times per week.

value: SK-N-BE(2) adherent cells were grown in 1:1 EMEM (Sigma) and Ham’s F12  (Sigma) supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: STA-NB-7_totRNA

value: STA-NB-7 adherent cells were grown in RPMI 160 with Ultraglutamine medium (Lonza) supplemented with 10% FBS (Lonza), 2.5% Hepes Buffer Solution 1M (Sigma) and 1% sodium pyruvate (Lonza).


title: LAN-1_totRNA


title: CHP-134_totRNA

value: Neuroblastoma cell line established from a tumor of the left adrenal area of an 18-month-old male patient. The patient was previously treated with vincristine, cyclophosphamide, dimethyltriazenoimidazole carboxamide, adriamycin, and irradiation. The cells grow as adherent colonies consisting of Neuroblasts-like cells forming dense mounds. Individual cells radiate from the mounds which reach confluence after routine passaging for several months. The doubling time is 57.6 hrs and split ratio is about 1:3-1:4.

value: CHP-134 cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: KELLY_totRNA

value: Neuroblastoma cell line established from a patient with neuroblastoma; ca. 100-fold genomic amplification of N-myc in der(17)hsr confirmed as human with IEF of AST, LDH, MDHA. The cells grow as adherent, round to fusiform with polar neuritic processes, growing in mono- and multilayers. The doubling time is 30 - 40 hrs and split ratio is about 1:3 to 1:10 every 3-6 days using trypsin/EDTA.

value: KELLY cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).

value: KELLY


title: SK-N-AS_totRNA

value: Neuroblastoma cell line derived from a female patient with neuroblastoma from the metastasis of the bone marrow. Tumorigenic in nude mice. The doubling time is 39 hrs, split ratio is about 1:3-1:4 two times per week.

value: SK-N-AS adherent cells were grown in DMEM (Lonza), 10% FBS (Lonza) and 2mM L-Glutamine  (Lonza).

value: SK-N-AS


title: polysomal RNA, untreated, biological replicate #3

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

description: Polysomal RNA sample extracted from serum starved MCF7 cells.

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: MCF7 cells, untreated, 0 min, polysomal RNA, biological replicate #3

growth_protocol: MCF7 cells were cultured in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: Cells were washed once with phosphate buffer saline (PBS) and treated directly on the plate with 300 µl lysis buffer [10 mM NaCl, 10 mM MgCl2, 10 mM Tris–HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/µl RNase inhibitor (Fermentas) and 1 mM dithiothreitol] and transferred to an Eppendorf tube. After a few minute incubation on ice with occasional vortexing, the extracts were centrifuged for 10 min at 12000 g at 4°C. The supernatant was stored at –80°C or loaded directly onto a 15–50% linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and centrifuged in an Sorvall rotor for 120 min at 40000 rpm. Polysomal fractions were collected monitoring the absorbance at 254 nm and treated directly with proteinase K. After phenol–chloroform extraction and isopropanol precipitation, polysomal RNA was resuspended in 30 µl of water and then repurified with RNeasy kit (Qiagen, Hilden, Germany). RNA quality was assessed by agarose gel electrophoresis and the Agilent 2100 Bioanalyzer platform.

treatment_protocol: MCF7 cells were seeded on adherent plates and starved with 0.5% charcoal treated serum for 48h in white DMEM, 2mM glutamine.

value: MCF7 cells

tag: time point

value: 0 min

tag: population

value: polysomal RNA

tag: biological replicate


title: total RNA, untreated, biological replicate #4

description: Total RNA sample extracted from serum starved MCF7 cells.

source_name: MCF7 cells, untreated, 0 min, total RNA, biological replicate #4

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to the manufacturer's protocol (Qiagen, Hilden, Germany). RNA was quantified using a spectrophotometer and its quality was checked by agarose gel electrophoresis and by Agilent 2100 Bioanalyzer platform, following the manifacturer’s guidelines for sample preparation and analysis of data (Agilent 2100 Bioanalyzer 2100 Expert User's Guide, http://www.agilent.com).

value: total RNA


title: CHP-212_polyRNA

value: Neuroblastoma cells grow as adherent colonies consisting of epithelial-like cells. Doubling time 20 hrs, split ratio is about 1:4-1:10 one-two times per week

value: CHP-212 adherent cells were grown in 1:1 EMEM (Sigma) and Ham’s F12  (Sigma) supplemented with 10% FBS (Lonza) and 2mM L-Glutamine  (Lonza).


title: total RNA, untreated, biological replicate #2

source_name: MCF7 cells, untreated, 0 min, total RNA, biological replicate #2


title: polysomal RNA, untreated, biological replicate #2

source_name: MCF7 cells, untreated, 0 min, polysomal RNA, biological replicate #2


title: NB-69_totRNA

value: Neuroblastoma cell line derived from a tumor isolated from a 16-month old male. The tissue of origin is the Brain. The doubling time is 18 - 20 hrs and split ratio is about 1:4

value: NB-69 cells were maintained as a monolayer culture in RPMI 160 medium (Lonza) and supplemented with 10% FBS (Lonza) and 2mM L-Glutamine (Lonza).


title: polysomal RNA, untreated, biological replicate #1

source_name: MCF7 cells, untreated, 0 min, polysomal RNA, biological replicate #1


title: total RNA, untreated, biological replicate #3

source_name: MCF7 cells, untreated, 0 min, total RNA, biological replicate #3


title: polysomal RNA, untreated, biological replicate #4

source_name: MCF7 cells, untreated, 0 min, polysomal RNA, biological replicate #4


title: CHP-134_polyRNA


title: STA-NB-1_totRNA

value: Neuroblastoma cell line established at the Children’s Cancer Research Institute (CCRI) in Vienna. The doubling time is unknown, split ratio is about 1:2 one-two times per month.

value: STA-NB-1 adherent cells were grown in RPMI 160 with Ultraglutamine medium (Lonza) supplemented with 10% FBS (Lonza), 2.5% Hepes Buffer Solution 1M (Sigma) and 1% sodium pyruvate (Lonza).


title: total RNA, untreated, biological replicate #1

source_name: MCF7 cells, untreated, 0 min, total RNA, biological replicate #1


title: polysomal RNA, E2 treated, 60 min, biological replicate #4

description: Polysomal RNA sample extracted from serum starved MCF7 cells treated with E2 (10nM final concentration) for 60 minutes.

source_name: MCF7 cells, E2 treated, 60 min, polysomal RNA, biological replicate #4

treatment_protocol: MCF7 cells were seeded on adherent plates and starved with 0.5% charcoal treated serum for 48h in white DMEM, 2mM glutamine. Cells were treated for 60 minutes with estradiol (E2) at final concentration of 10 nM.

value: 60 min


title: total RNA, E2 treated, 60 min, biological replicate #4

description: Total RNA sample extracted from serum starved MCF7 cells treated with E2 (10nM final concentration) for 60 minutes.

source_name: MCF7 cells, E2 treated, 60 min, total RNA, biological replicate #4


title: polysomal RNA, E2 treated, 60 min, biological replicate #3

source_name: MCF7 cells, E2 treated, 60 min, polysomal RNA, biological replicate #3


title: polysomal RNA, E2 treated, 60 min, biological replicate #1

source_name: MCF7 cells, E2 treated, 60 min, polysomal RNA, biological replicate #1


title: polysomal RNA, E2 treated, 60 min, biological replicate #2

source_name: MCF7 cells, E2 treated, 60 min, polysomal RNA, biological replicate #2


title: Normal adrenal tissue MEDULA

city: Madrid

first: Elena

middle: López

last: Jiménez

address: Melchor Fernandez Almagro nº3

department: Human Cancer Genetics

country: Spain

institute: Spanish National Cancer Centre

description: MEDULA

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

scan_protocol: Images were scanned using Agilent scanner, G2565BA

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

source_name: RNA extracted from normal adrenal gland

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

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

tag: tissue type

value: Normal adrenal tissue

source_name: Universal Human Reference RNA (Stratagene)

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


title: total RNA, E2 treated, 60 min, biological replicate #2

source_name: MCF7 cells, E2 treated, 60 min, total RNA, biological replicate #2


title: total RNA, E2 treated, 60 min, biological replicate #3

source_name: MCF7 cells, E2 treated, 60 min, total RNA, biological replicate #3


title: total RNA, E2 treated, 60 min, biological replicate #1

source_name: MCF7 cells, E2 treated, 60 min, total RNA, biological replicate #1


title: WL_control_rep2

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

description: ChIP-chip

hyb_protocol: DNA was hybridized according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3.

scan_protocol: Whole Genome Tiling arrays were scanned on an Affymetrix scanner G7.

data_processing:
Raw microarray data were log2 transformed and quantile normalized using Cisgenome (http://www.biostat.jhsph.edu/~hji/cisgenome). A two sample comparison test was performed on the processed data using TileMap Version2 with the HMM method to detect the peaks in the light and dark.

The GSE24973 supplementary file 'GSE24973_processed_data.txt' contains the log2 normalized intensities of the probes.

organism: Arabidopsis thaliana

source_name: 4-day-old whole seedlings grown under WL, input

label_protocol: DNA was labeled according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3.

growth_protocol: 4-day-old whole seedlings were grown under WL.

extract_protocol: Chromatin isolation was performed with 4-day-old whole seedlings grown under WL or 8hr darkness treatment according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). An aliquot of untreated sonicated chromatin was reverse cross-linked and used as a total input DNA control for ChIP-PCR experiments.

tag: ecotype

value: Columbia (Col-0)

value: wild type

value: 4 days

value: whole seedling

tag: growth condition

value: wild type light (WL)


title: WL_Hy5_rep4

description: ChIP-chip

source_name: 4-day-old whole seedlings grown under WL, HY5 ChIP

extract_protocol: Chromatin isolation was performed with 4-day-old whole seedlings grown under WL or 8hr darkness treatment according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). The DNA was sheared to an average size of approximately 500 bp. Chromatin was immunoprecipitated, washed, reverse cross-linked, amplified, and hybridized according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3. A polyclonal HY5 antibody purified from anti-HY5 rabbit IgG using Sepharose 4B beads coupled with purified recombinant HY5 protein was used.

tag: tissue

tag: chip antibody

value: rabbit polyclonal anti-HY5 IgG


title: WL_control_rep1

description: ChIP-chip

tag: age


title: Normal adrenal tissue 07N220


title: Normal adrenal tissue 03N276


title: Dark_control_rep2

description: ChIP-chip

source_name: 4-day-old whole seedlings grown under 8hr darkness, input

growth_protocol: 4-day-old whole seedlings were grown under 8hr darkness treatment.

value: dark

tag: treatment time

value: 8 hours


title: Dark_control_rep1

description: ChIP-chip


title: Dark_Hy5_rep2

description: ChIP-chip

source_name: 4-day-old whole seedlings grown under 8hr darkness, HY5 ChIP


title: WL_Hy5_rep3

description: ChIP-chip


title: Dark_Hy5_rep4

description: ChIP-chip


title: Dark_Hy5_rep1

description: ChIP-chip


title: Normal adrenal tissue 03N275


title: WL_Hy5_rep1

description: ChIP-chip


title: Normal adrenal tissue 07N217


title: Normal adrenal tissue 0364N


title: PCC primary tumor 227

source_name: RNA extracted from primary tumors

value: PCC primary tumor


title: PGL primary tumor 06T66

value: PGL primary tumor


title: PCC primary tumor 291


title: Dark_Hy5_rep3

description: ChIP-chip


title: PGL primary tumor 03T8


title: PCC primary tumor 05T04


title: WL_Hy5_rep2

description: ChIP-chip


title: W2C ChIP

city: Stanford

first: Yu

last: Sun

address: 260 panama street

department: plant biology

institute: Carnegie Institution of Washington

description:
BZR1-CFP ChIP biologic repeat with control 1-3 assayed on Affymetrix GeneChip Arabidopsis Tiling array.
W2C is the name of BZR1-CFP transgenic line used for this experiment.

hyb_protocol: The labeled DNA was  hybridized to the Affymetrix GeneChip Arabidopsis Tiling 1.0R array according to affymetrix's Eukaryotic Target Protocol.

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G Scanner

data_processing:
Data was analyzed by two Tiling Analysis Software: TAS (version 1.1, Affymetrix) and Tilemap (Ji and Wong, 2005).  Arabidopsis genome version/build: TAIR7.
With TAS software, the analysis was performed using the “two sample comparison analysis” option.  Probes were analyzed using signal from both PerfectMatch and MisMatch with a bandwidth 250 bps, and the enriched intervals were defined by p<0.001 and signal ratio > 2, maximum gap 100 bps and minimum run 100 bps.
The analysis using Tilemap was performed using HMM option with posterior probability 0.5 and maximum gap 100 bps.
Results files descriptions:
The pvalue.bar file contains the p value of each probe generated by TAS, signal.bar file contains the signal value of each probe generated by TAS.  W2C_tile.txt file contains the p value of each probe generated by tilemap.
TileGroup full set_p30.bed:  The binding region identified by TAS software at P<0.001.  TileGroup PM-MM_signal_1.bed:  The binding region identified by TAS at signal> 2 fold. Both files are generated using signal from perfectMatch-MisMatch with a bandwidth of 250bps, maximum gap 100bps and minimum run 100bps.  W2C_tile_hmm0.5.bed:  The binding region identified by Tilemap at posterior probability >0.5 using HMM option and maximum gap 100bps.

source_name: [test]: ChIP DNA from pBZR1::BZR1-CFP tissue (W2C is the name of BZR1-CFP transgenic line)

label_protocol: The fragmented DNA was labeled by TdT according to Affymetrix Chromatin Immunoprecipitation Protocol.

growth_protocol: Light-grown rosettes. 16 hour light 8 hour dark cycle, 4 weeks.

extract_protocol: Rosette tissue was cross-linked by 1% formaldehyde. Chromatin immunoprecipitation using anti-YFP antibodies and qPCR was performed according to our protocol (He et al., 2005).The precipitated DNA was amplified by Whole Genome Amplification Kit following the manufacturer’s instruction (Sigma), and fragmented to an average of 50-100 bps with DNase I (Cat. No. 18068-015 Invitrogen) at 30°C for 10 minutes.

treatment_protocol: 100nM Brassinolide, 2 hours

value: test

value: Columbia

value: rosette

value: Polyclonal anti-YFP

tag: chip antibody source

value: home-made

source_name: [ctrl]: ChIP DNA from wild type tissue

value: control

value: Polyclonal anti-GFP


title: Bipolar and Epilepsy-78

city: Houston

first: April

middle: Burant

last: Hall

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: The nanodrop fluorospectrometer was used to measure DNA concentrantion and Dye incorporation inorder to pair subjects with controls according to the following criteria: pmoles of dye were required to be within 3 units and DNA concentration within 100ng/uL. For each hybridization, the labeled experimental and reference DNAs were boiled for 3 minuted and incubated at 37°C for 30-90 minutes with human Cot-1 DNA (Invitrogen, Carlsbad, CA), blocking agent and hybridization buffer (Agilent Technologies, Santa Clara, CA).  The samples were then added to an array, which was placed inside a microarray hybridization chamber (Agilent Technologies, Santa Clara, CA), and allowed to hybridize at 65°C for 35-68 hours in a rotating hybridization oven (Agilent Technologies, Santa Clara, CA).  Following hybridization, slides were washed following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent G2565 DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA) with 3 um resolution.

data_processing: scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies)

source_name: lymphobast cell lines

label_protocol: The digested DNA was labeled with Bioprime Array CGH Genomic Labeling System following the manufacturer’s recommended protocol with minor additions (Invitrogen, Carlsbad, CA). Following the addition of random primers to the digested DNA, the mixture was boiled for 5 minutes then cooled on ice for 5 minutes. Cyanine 5-dCTP (for the experimental sample), cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA), dCTP nucleotide mix, and exo-Klenow fragment (40 units/µL) were added and the reaction was incubated at 37°C for 2 hours then incubated at 65°C for10 minutes to inactivate the enzyme.  The labeled product was purified from unincorporated nucleotides using Millipore columns or plate (Millipore, Billerica, MA, USA)

growth_protocol: Lymphoblastoid cell lines were establihsed and maintained by Rutgers University for the NIMH

extract_protocol: DNA was isolated from lymphoblastoid cell lines by Rutgers University by desalting using the Autopure LS robotic workstation with Autopure reagents (Qiagen, Inc., Valencia, CA)

tag: cell type

value: lymphoblast cell line

tag: disease state

value: Bipolar and Epilepsy

tag: id (rutgers)

tag: nimh identifier

tag: sex

value: F

source_name: blood

value: M

value: blood


title: Bipolar and Epilepsy-76

tag: sample type


title: Bipolar and Epilepsy-75


title: Bipolar and Epilepsy-73


title: Bipolar and Epilepsy-70


title: Bipolar and Epilepsy-77


title: Bipolar and Epilepsy-80


title: Bipolar and Epilepsy-68


title: Bipolar and Epilepsy-72


title: Bipolar and Epilepsy-71


title: Bipolar and Epilepsy-79


title: Bipolar and Epilepsy-69


title: Bipolar and Epilepsy-74


title: Bipolar and Epilepsy-67


title: Bipolar and Epilepsy-63


title: Bipolar and Epilepsy-62


title: Bipolar and Epilepsy-64


title: Bipolar and Epilepsy-61


title: Bipolar and Epilepsy-60


title: Bipolar and Epilepsy-54


title: Cast/Ei_3

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

hyb_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.

data_processing: qspline normalised log ratios

source_name: Cast/Ei, Male, liver

extract_protocol: Genomic DNA was prepared from liver using a chloroform-based extraction protocol.

tag: strain

value: Cast/Ei

tag: gender

value: Male

value: liver

source_name: C57BL/6J, Male, liver


title: Bipolar and Epilepsy-56


title: Bipolar and Epilepsy-59


title: Bipolar and Epilepsy-55


title: Bipolar and Epilepsy-66


title: A/J_3

scan_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.

source_name: A/J, Male, liver

value: A/J


title: DBA/2J_3

source_name: DBA/2J, Male, liver

label_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.


title: wild_11

source_name: Wild mouse, Switzerland, Female, liver

value: Wild mouse

tag: country

value: Switzerland

value: Female


title: Bipolar and Epilepsy-53


title: Bipolar and Epilepsy-65


title: wild_5

source_name: Wild mouse, Tahiti (French Polynesia), Male, liver

value: Tahiti (French Polynesia)


title: Bipolar and Epilepsy-52


title: Bipolar and Epilepsy-50


title: Spret/Ei_2

organism: Mus spretus

source_name: Spret/Ei, Male, liver

value: Spret/Ei


title: SJL/J_2

source_name: SJL/J, Male, liver

value: SJL/J


title: LP/J_3

source_name: LP/J, Male, liver

value: LP/J


title: Bipolar and Epilepsy-57

value: control


title: 129S2_1

source_name: 129S2, Male, liver


title: C3HeB/FeJ_2

source_name: C3HeB/FeJ, Male, liver


title: wild_20

source_name: Wild mouse, Corsica (France), Male, liver

value: Corsica (France)


title: Bipolar and Epilepsy-48

value: lymphoblast cell line

value: Bipolar and Epilepsy


title: wild_7

source_name: Wild mouse, France, Male, liver

value: France


title: Bipolar and Epilepsy-58

value: F

value: M

value: blood


title: Bipolar and Epilepsy-44


title: AKR/J_1

source_name: AKR/J, Male, liver

value: AKR/J

value: Male

value: liver


title: Bipolar and Epilepsy-51


title: C57BL/6J_1


title: wild_17

source_name: Wild mouse, Italy, Male, liver

value: Wild mouse

value: Italy


title: Bipolar and Epilepsy-43

source_name: lymphobast cell lines


title: Bipolar and Epilepsy-41

source_name: blood


title: BALB/cByJ_3

source_name: BALB/cByJ, Male, liver

value: BALB/cByJ


title: PL/J_3

source_name: PL/J, Male, liver

value: PL/J

source_name: C57BL/6J, Male, liver


title: Bipolar and Epilepsy-47


title: Bipolar and Epilepsy-38


title: Bipolar and Epilepsy-49


title: Bipolar and Epilepsy-46


title: Bipolar and Epilepsy-36


title: Bipolar and Epilepsy-33


title: Bipolar and Epilepsy-45


title: Bipolar and Epilepsy-40


title: Bipolar and Epilepsy-21


title: Bipolar and Epilepsy-37


title: Bipolar and Epilepsy-24


title: Bipolar and Epilepsy-35


title: Bipolar and Epilepsy-31


title: Bipolar and Epilepsy-39


title: Bipolar and Epilepsy-22


title: Bipolar and Epilepsy-26


title: Bipolar and Epilepsy-30


title: Bipolar and Epilepsy-23


title: Bipolar and Epilepsy-20


title: Bipolar and Epilepsy-42


title: Bipolar and Epilepsy-29


title: Bipolar and Epilepsy-19


title: Bipolar and Epilepsy-18


title: Bipolar and Epilepsy-32


title: Bipolar and Epilepsy-34


title: Bipolar and Epilepsy-27


title: Bipolar and Epilepsy-15


title: Bipolar and Epilepsy-10


title: Bipolar and Epilepsy-17


title: Bipolar and Epilepsy-6


title: Bipolar and Epilepsy-16


title: Bipolar and Epilepsy-9


title: Bipolar and Epilepsy-5


title: Bipolar and Epilepsy-4


title: Bipolar and Epilepsy-8


title: Bipolar and Epilepsy-1


title: Bipolar and Epilepsy-3


title: Schizophrenia and Epilepsy-232

value: Schizophrenia and epilepsy


title: Bipolar and Epilepsy-2


title: Schizophrenia and Epilepsy-228


title: Bipolar and Epilepsy-11


title: Bipolar and Epilepsy-7


title: Bipolar and Epilepsy-25


title: Schizophrenia and Epilepsy-235


title: Schizophrenia and Epilepsy-229


title: Schizophrenia and Epilepsy-230


title: Bipolar and Epilepsy-12


title: OPN4

city: Stockholm

first: Erik

last: Karlström

address: Division of Pathology

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from OPN adherent bone cells

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, USA).

scan_protocol: Arrays were scanned on a GeneChip scanner 3000 7G using default scanner settings. Affymetrix GeneChip® Command Console® (AGCC) was used to process all Affymetrix arrays through fluidics and scanning, and the generation of CEL-files.

data_processing: Probe set signal values were calculated using GeneChip® Expression Console software using the following methods; Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: OPN adherent bone cell

label_protocol: GeneChip Whole Transcript (WT) sense target labeling assay manual (Affymetrix, USA), version 4 - starting with 300 ng RNA and following the Total RNA labeling protocol to prepare targets for GeneChip gene 1.0 ST Arrays (omitting RiboMinus procedure).

growth_protocol: Prothrombin (PT) and osteopontin (OPN) promotes adhesion of different TRAP-positive multinucleated cells isolated from rat long bone (Hu et al. Exp Cell Res. 2008; 314: 638-50).

extract_protocol: RNA was extracted with the RNeasy plus mini kit (Qiagen, USA)

treatment_protocol: Rat bone cells from 2-5 day old Sprague Dawley rats were extracted, as described by Hu et al. Exp Cell Res. 2008; 314: 638-50, in α-Minimum Essential Medium Eagle (α-MEM, Sigma-Aldrich, USA) supplemented with 1 mg/ml BSA and 100 mM HEPES, pH 7.4 (Invitrogen, USA). After the extraction were bone cells adhered to 96-well Nunc MaxiSorp plates (Nunc, Germany), coated with bovine milk OPN or mouse PT.

value: osteopontin adherent cells from long bone

value: Sprague Dawley


title: Bipolar and Epilepsy-13

value: control


title: Schizophrenia and Epilepsy-233

value: lymphoblast cell line


title: Schizophrenia and Epilepsy-227


title: Schizophrenia and Epilepsy-231


title: Schizophrenia and Epilepsy-225


title: Schizophrenia and Epilepsy-234


title: OPN3


title: Schizophrenia and Epilepsy-226


title: Schizophrenia and Epilepsy-224


title: Schizophrenia and Epilepsy-223


title: Bipolar and Epilepsy-14

value: Bipolar and Epilepsy


title: PT1

description: Gene expression data from PT adherent bone cells

source_name: PT adherent bone cell

value: prothrombin adherent cells from long bone


title: Schizophrenia and Epilepsy-222


title: OPN2


title: Schizophrenia and Epilepsy-221

value: F


title: Non-transfected RA-FLS biological replicate 3

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: The fibroblast-like synoviocytes (FLS) were isolated from the synovial tissues of rheumatoid arthritis

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were treated using R (version 2.9.1) with beadarray (version 1.12.1)

source_name: RA-FLS

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: FLS: refer to [PMID:16888030], HUVEC: maintained in M 199 medium containing 20% FCS

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Primary fibroblast-like synoviocytes drived from patients with rheumatoid arthritis

tag: transfection


title: NFAT5 siRNA transfected RA-FLS biological replicate 3

value: NFAT5 siRNA


title: PT2


title: Non-transfected RA-FLS biological replicate 2


title: NFAT5 siRNA transfected RA-FLS biological replicate 2


title: Control siRNA transfected RA-FLS biological replicate 1

value: control siRNA


title: Bipolar and Epilepsy-28

value: M

value: blood


title: Control siRNA transfected RA-FLS biological replicate 2


title: Schizophrenia and Epilepsy-220


title: Schizophrenia and Epilepsy-216


title: Control siRNA transfected RA-FLS biological replicate 3


title: Schizophrenia and Epilepsy-219


title: Schizophrenia and Epilepsy-217


title: Non-transfected RA-FLS biological replicate 1


title: Schizophrenia and Epilepsy-215


title: Schizophrenia and Epilepsy-213


title: Schizophrenia and Epilepsy-218


title: Schizophrenia and Epilepsy-209


title: NFAT5 siRNA transfected RA-FLS biological replicate 1


title: Schizophrenia and Epilepsy-214


title: Schizophrenia and Epilepsy-212


title: Schizophrenia and Epilepsy-211


title: Schizophrenia and Epilepsy-210


title: Schizophrenia and Epilepsy-208


title: Schizophrenia and Epilepsy-207


title: PT4


title: Schizophrenia and Epilepsy-203


title: Schizophrenia and Epilepsy-200


title: Schizophrenia and Epilepsy-201


title: Schizophrenia and Epilepsy-204


title: Schizophrenia and Epilepsy-199


title: Schizophrenia and Epilepsy-205


title: Schizophrenia and Epilepsy-206


title: Daphnia_LC25_SiO_exp4,rep1

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

description: 5.1 mg/L SiO NP

hyb_protocol: The labeled cDNA for the unexposed and exposed D. magna was mixed and hybridized to the D. magna cDNA microarray (protocols available at http://cmgm.stanford.edu/pbrown/mguide).

scan_protocol: Axon GenePix 4000B scanner

data_processing: Microarray images acquired from the scanner were analyzed using GenePix Pro 6.1 (Molecular Devices/MDS Analytical Technologies, Sunnyvale, CA).  Resulting GenePix result files were converted into a format compatible with The Institute for Genomic Research (TIGR) microarray software suite (TM4) using Express Converter (available through TIGR, www.tm4.org).  All downstream data analysis was performed using TIGR TM4 (available at www.tm4.org) (21).  Background subtracted signal intensities were normalized by total intensity and also underwent lowess normalization, standard deviation normalization using Microarray Data Analysis System ver. 2.19 (MIDAS).   In addition, MIDAS was used to check the consistency of dye flipped pairs and to detect outlier genes using slice analysis (22).  Normalized signal intensities were then analyzed using MultiExperiment Viewer ver. 4.3 (MeV) to detect differentially expressed genes using both a one-class T-test (23) and Statistical Analysis for Microarrays (SAM) (24) (user guide available at www-stat.stanford.edu/~tibs/SAM/).  The three resulting gene lists from MIDAS slice analysis, T-test, and SAM were compared and any genes not reproduced in at least two gene lists were eliminated.  The remaining genes were selected as candidate differentially expressed genes and were sequenced.

organism: Daphnia magna

source_name: unexposed 24h

label_protocol: RNA was reverse transcribed with M-MuLV Reverse Transcriptase (New England Biolabs, Ipswich, MA) in the presence of  aminoallyl-labeled dUTP (Applied Biosystems/Ambion, Austin, TX).  Flourescence labeling proceeded by incubating the aminoallyl-labeled cDNA with Cy5 or Cy3 fluorescent dyes (GE Healthcare, Piscataway, NJ).

growth_protocol: Daphnia magna were cultured at the US EPA culture facility in Cincinnati OH in Moderately Hard Reconstituted water at 25 degrees C.  They were fed 3 times weekly a combination of Pseudokirchneriella subcapitata and alfalfa extract.

extract_protocol: D. magna were removed from the exposure vessels with a pipet and immersed immediately in Tri Reagent (Molecular Research Center, Cincinnati, OH).  Whole organism daphnid tissue was homogenized for 5 min. at 30 vibrations/s using a Retsch MM 300 mixer mill (Retsch, Newtown, PA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK).  Following homogenization, RNA was isolated using Tri Reagent according to the manufacturer’s methods (Molecular Research Center, Cincinnati, OH) and treated with DNAse I using Ambion's DNAfree kit (Ambion, Austin, TX).

treatment_protocol: All exposures to the nanoparticles or Zn salt were conducted on adult female daphnids 10 days old and occurred at 25.0 C for 24 hours

value: 16 pooled daphnids

value: 10d old

value: female

source_name: LC25 SiO NP exposed 24 h


title: Daphnia_LC25_SiO_exp3,rep2

description: 5.1 mg/L SiO NP


title: Schizophrenia and Epilepsy-193


title: Schizophrenia and Epilepsy-192


title: Schizophrenia and Epilepsy-184


title: Schizophrenia and Epilepsy-198


title: Schizophrenia and Epilepsy-188


title: Daphnia_LC25_SiO_exp3,rep1

description: 5.1 mg/L SiO NP


title: Schizophrenia and Epilepsy-196


title: Schizophrenia and Epilepsy-195


title: Schizophrenia and Epilepsy-190


title: Schizophrenia and Epilepsy-191


title: Daphnia_LC25_SiO_exp2,rep1

description: 5.1 mg/L SiO NP


title: Schizophrenia and Epilepsy-197


title: Schizophrenia and Epilepsy-189


title: Schizophrenia and Epilepsy-187


title: Schizophrenia and Epilepsy-186


title: Schizophrenia and Epilepsy-183


title: Schizophrenia and Epilepsy-194


title: Schizophrenia and Epilepsy-182


title: Schizophrenia and Epilepsy-181


title: Schizophrenia and Epilepsy-185


title: Daphnia_1/10LC50_SiO2_exp3,rep2

description: 1.4 mg/L SiO NP

source_name: 1/10 LC50 SiO NP exposed 24 h


title: Daphnia_LC25_SiO_exp1,rep1

description: 5.1 mg/L SiO NP


title: Schizophrenia and Epilepsy-202


title: Daphnia_1/10LC50_SiO2_exp2,rep1

description: 1.4 mg/L SiO NP


title: Daphnia_1/10LC50_SiO2_exp2,rep2

description: 1.4 mg/L SiO NP


title: Daphnia_1/10LC50_SiO2_exp3,rep1

description: 1.4 mg/L SiO NP


title: Daphnia_LC25_ZnSO4_exp5,rep1

description: 0.91 mg/L ZnSO4

source_name: LC25 ZnSO4 exposed 24 h


title: Daphnia_1/10LC50_SiO2_exp1,rep1

description: 1.4 mg/L SiO NP


title: Daphnia_LC25_ZnSO4_exp4,rep2

description: 0.91 mg/L ZnSO4


title: Daphnia_1/10LC50_SiO2_exp1,rep2

description: 1.4 mg/L SiO NP


title: Daphnia_LC25_ZnSO4_exp2,rep1

description: 0.91 mg/L ZnSO4


title: Daphnia_1/10LC50_ZnSO4_exp3,rep1

description: 0.13 mg/L ZnSO4

source_name: 1/10 LC50 ZnSO4 exposed 24 h


title: Daphnia_LC25_ZnSO4_exp4,rep1

description: 0.91 mg/L ZnSO4


title: Daphnia_LC25_ZnSO4_exp3,rep1

description: 0.91 mg/L ZnSO4


title: Schizophrenia and Epilepsy-172


title: Schizophrenia and Epilepsy-176


title: Schizophrenia and Epilepsy-179


title: Schizophrenia and Epilepsy-171


title: Schizophrenia and Epilepsy-177


title: Daphnia_LC25_ZnSO4_exp1,rep1

description: 0.91 mg/L ZnSO4


title: Schizophrenia and Epilepsy-175


title: Daphnia_1/10LC50_ZnSO4_exp3,rep2

description: 0.13 mg/L ZnSO4


title: Schizophrenia and Epilepsy-174


title: Schizophrenia and Epilepsy-173


title: Daphnia_1/10LC50_ZnSO4_exp2,rep2

description: 0.13 mg/L ZnSO4


title: Daphnia_1/10LC50_ZnSO4_exp2,rep1

description: 0.13 mg/L ZnSO4


title: Schizophrenia and Epilepsy-178


title: Daphnia_1/10LC50_ZnSO4_exp1,rep1

description: 0.13 mg/L ZnSO4


title: Daphnia_1/10LC50_ZnSO4_exp1,rep2

description: 0.13 mg/L ZnSO4


title: Schizophrenia and Epilepsy-170


title: Daphnia_LC25_SiO_exp1,rep2

description: 5.1 mg/L SiO NP


title: Daphnia_LC25_ZnO_exp3,rep2

description: 9.0 mg/L ZnO NP

source_name: LC25 ZnO NP exposed 24 h


title: Schizophrenia and Epilepsy-165


title: Schizophrenia and Epilepsy-168


title: Schizophrenia and Epilepsy-167


title: Daphnia_LC25_ZnO_exp3,rep1

description: 9.0 mg/L ZnO NP


title: Daphnia_LC25_ZnO_exp2,rep2

description: 9.0 mg/L ZnO NP


title: Daphnia_LC25_ZnO_exp2,rep1

description: 9.0 mg/L ZnO NP


title: Schizophrenia and Epilepsy-160


title: Schizophrenia and Epilepsy-169


title: Daphnia_LC25_ZnO_exp1,rep1

description: 9.0 mg/L ZnO NP


title: Schizophrenia and Epilepsy-166


title: Schizophrenia and Epilepsy-163


title: Schizophrenia and Epilepsy-180


title: Schizophrenia and Epilepsy-159


title: Daphnia_1/10LC50_ZnO_exp2,rep2

description: 2.2 mg/L ZnO NP

source_name: 1/10 LC50 ZnO NP exposed 24h


title: Schizophrenia and Epilepsy-164


title: Daphnia_1/10LC50_ZnO_exp4,rep1

description: 2.2 mg/L ZnO NP


title: Schizophrenia and Epilepsy-158


title: Schizophrenia and Epilepsy-162


title: Schizophrenia and Epilepsy-156


title: Schizophrenia and Epilepsy-161


title: Schizophrenia and Epilepsy-157


title: Daphnia_1/10LC50_ZnO_exp3,rep1

description: 2.2 mg/L ZnO NP


title: Daphnia_1/10LC50_ZnO_exp2,rep1

description: 2.2 mg/L ZnO NP


title: Daphnia_1/10LC50_ZnO_exp1,rep1

description: 2.2 mg/L ZnO NP


title: Schizophrenia and Epilepsy-154


title: Daphnia_1/10LC50_ZnO_exp1,rep2

description: 2.2 mg/L ZnO NP


title: Schizophrenia and Epilepsy-152


title: Schizophrenia and Epilepsy-153


title: Schizophrenia and Epilepsy-151


title: Schizophrenia and Epilepsy-149


title: Schizophrenia and Epilepsy-155


title: Schizophrenia and Epilepsy-150


title: Schizophrenia and Epilepsy-147


title: Schizophrenia and Epilepsy-148