title: SK-Mel28#8 MR105 Untreated

status: Public on Jun 30 2013

type: RNA

city: Westmead

first: Gulietta

last: Pupo

state: NSW

address: Darcy Road

country: Australia

institute: University of Sydney

description: SK-Mel28#8 MR105 Untreated

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using with cubic spline using the Illumina GenomeStudio v2011.1

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Melanoma Cell Line

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

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

tag: genotype

value: BRAF V600E

tag: tissue

value: Melanoma

tag: cell line

tag: clone

tag: treatment

value: untreated


title: SK-Mel28#8 MR201 Treated 10nM trametinib 24h

value: 10nM trametinib


title: SK-Mel28#8 MR105 Treated 10nM trametinib 24h


title: SK-Mel28#8 Parent Treated 10nM trametinib 24h

value: parental


title: SK-Mel28#8 Parent Untreated (Control for 10nM trametinib 24h)

value: untreated (Control for 10nM trametinib)


title: SK-Mel28#8 MR201 Untreated

description: SK-Mel28#8 MR201 Untreated


title: SK-Mel28#8 Parent Untreated (Control for 100nM dabrafenib and 5nM trametinib 24h)

value: untreated (Control for 100nM dabrafenib and 5nM trametinib)


title: SK-Mel28#8 Parent Treated 100nM dabrafenib and 5nM trametinib 24h

value: 100nM dabrafenib and 5nM trametinib


title: SK-Mel28#8 CR201 Untreated

description: SK-Mel28#8 CR201 Untreated


title: SK-Mel28 BR8 Treated 100nM dabrafenib 24h

value: 100nM dabrafenib


title: SK-Mel28#8 CR401 Untreated

description: SK-Mel28#8 CR401 Untreated


title: SK-Mel28 BR6 Untreated

description: SK-Mel28 BR6 Untreated


title: SK-Mel28 BR6 Treated 100nM dabrafenib 24h


title: SK-Mel28#8 CR401 Treated 100nM dabrafenib and 5nM trametinib 24h


title: SK-Mel28 Parent Treated 100nM dabrafenib 24h


title: SK-Mel28 BR8 Untreated

description: SK-Mel28 BR8 Untreated


title: lyr-expressing MDA cells starved Rep3

city: New York

first: Nicholas

last: Gauthier

state: NY

address: 1275 York Avenue, Box #460

country: USA

institute: MSKCC

description:
Starve_rep3
replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina Human HT-12 V4 Array. Slides were washed and stained in the Illumina instrument.

data_processing: The data were median centered using R

source_name: MDA-MB-231 Breast Carcinoma Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

value: MDA-MB-231 Breast Carcinoma Cells

tag: growth protocol

value: starved


title: lyr-expressing MDA cells starved Rep2

description:
Starve_rep2
replicate 2


title: SK-Mel28 Parent Untreated

description: SK-Mel28 Parent Untreated


title: lyr-expressing MDA cells in D-Lysine Rep3

description:
Dlys_rep3
replicate 3

value: D-Lysine


title: lyr-expressing MDA cells in D-Lysine Rep1

description:
Dlys_rep1
replicate 1


title: lyr-expressing MDA cells in L-Lysine Rep3

description:
LLys_rep3
replicate 3

value: L-Lysine


title: lyr-expressing MDA cells in L-Lysine Rep2

description:
LLys_rep2
replicate 2


title: lyr-expressing MDA cells in D-Lysine Rep2

description:
Dlys_rep2
replicate 2


title: Spinal cord_lewis female_MBP EAE_219

city: Brisbane

first: Hayley

middle: Ruth

last: Inglis

state: Queensland

address: Building 71/918, Royal Brisbane & Women’s Hospital Campus,Herston, QLD, 4029

department: Clinical Neurosciences

institute: University of Queensland , Centre for Clinical Research

description: Total snap frozen spinal cord ,Lewis rat # 219

hyb_protocol: 5ug of fragmented biotinylated ssDNA was hybridised for 16hrs at 45oC, 60rpm on a Rat Exon 1.0 ST Array. After 16hrs GeneChips were washed on a FS_450 Fluidics Station using the washing script FS450_0001 with buffers and stains supplied with the GeneChip Hybridization, Wash, and Stain Kit from Affymetrix.

scan_protocol: Data was acquired on a 7G GeneChip Scanner 3000 and .CEL file generation performed using AGCC

data_processing:
Expression Console with RMA was used initially to extract probe intensity data. This data was used to access Affymetrix supplied PolyA and Eukaryotic Hybridisation controls to confirm consistent processing of the RNA samples. Subsequent analysis was performed in Partek Genomics Suite - Version 6.11.0801.  RMA background correction was applied including pre-background adjustment for CG content and quantile normalization across all chips in the experiment.  Probe data was log2 transformed.
probe group file: RaEx-1_0-st-v1.r2.pgf

organism: Rattus norvegicus

source_name: Lewis female, virgin ,MBP EAE

label_protocol: Samples were enzymatically fragmented and biotinylated using the Encore Biotin Module labelling kit (NuGEN)

growth_protocol: Rat spinal cords extracted by insuflation at the peak of disease in EAE animals and at the same time from healthy control age matched (littermates)

extract_protocol: Spinal cords were excised from the spinal column by insufflation using a large bore blunt ended needle and 60 ml syringe. Tissue was snap frozen in liquid nitrogen prior to being stored at -80˚C. Total RNA was prepared using the Rneasy®Lipid Tissue Midi Kit (QIAGEN) and treated with DNase I to remove all traces of genomic DNA prior to storage at -80˚C . cDNA synthesis and amplification was performed using the Applause WT-Amp Plus ST kit (NuGEN).

treatment_protocol: EAE animals were treated by subcutanious injection with 50 ug of guinea-pig brain MBP (Sigma-Aldrich) in Freund's incomplete adjuvant containing 4.0 mg/ml M.Butiricium, at the base of the tail.  Healthy controls were age matched untreated littermates .

tag: strain

value: Lewis

tag: gender

value: Female

tag: age

value: 16 wks

value: 50 ug MBP

tag: days post injection

value: spinal cord


title: lyr-expressing MDA cells starved Rep1

description:
Starve_rep1
replicate 1


title: Spinal cord_lewis female_healthy control_195

description: Total snap frozen spinal cord ,Lewis rat # 195

source_name: Lewis female, virgin ,healthy control


title: Spinal cord_lewis female_healthy control_196

description: Total snap frozen spinal cord ,Lewis rat # 196


title: Spinal cord_lewis female_MBP EAE_218

description: Total snap frozen spinal cord ,Lewis rat # 218


title: lyr-expressing MDA cells in L-Lysine Rep1

description:
LLys_rep1
replicate 1


title: P. aeruginosa PAO1_anaerobic_AUM_rep 3

city: Braunschweig

first: Petra

last: Tielen

address: Spielmannstrasse 7

country: Germany

institute: Technische Universität Braunschweig

description:
This sample was excluded from data analysis
Probe_Aa3
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.

hyb_protocol: The GeneChip was hybridized at the Affymetrix core facility at the Helmholtz Centre for Infection Research in Braunschweig for 16 h at 50°C and 60 rpm using an GeneChip Hybridisation oven 640. Washing was done using an Affymetrix Fluidics Station 400.

scan_protocol: Scanning was done at the Affymetrix core facility at the Helmholtz Centre for Infection Research in Braunschweig using an HP GeneArray scanner for quantification with Affymetrix Microarray Suite Version 5.0.

data_processing: Raw data obtained from the Affymetrix GeneArray Scanner (CEL files) were preprocessed with the Bioconductor software framework. Expression values were computed with the Robust Multichip Average (rma) method (Irizarry et al. 2003, Biostatistics, 4, 249-264, Irizarry et al. 2003, Nucleic Acids Res. , 31, e15) from the perfect match intensities, using quantile normalization and median polish as summarization method.

organism: Pseudomonas aeruginosa PAO1

source_name: P. aeruginosa PAO1 colony biofilms, grown under anaerobic conditions on AUM + 50 mM KNO3

label_protocol: cDNA was synthesized from RNA pooled from three independent cultures and subsequently hybridyzed on one GeneChip. The cDNA synthesis, fragmentation and labeling were performed according to protocols for the Affymetrix Pseudomonas GeneChip (Santa Clara, California) with the following modification: 1.0 U DNase I were used per µg cDNA for fragmentation to yield the desired cDNA size range of 50 - 200 bases as confirmed by gel electrophoresis. This was verified by separating 200 ng of fragmented cDNA on a 15 % acrylamide gel and staining with SYBRgold (Molecular Probes, Eugene, United States).

growth_protocol: Pseudomonas aeruginosa was grown as colony biofilms on AUM and 10-fold diluted LB agar plates, respectively. Anaerobic cultivation for 2 days. The colony biofilms were replaced to a new agar plate, containing 50 mM KNO3 every 24 h. Cells were harvested in the late logarithmic to early stationary phase. AUM minimal medium described in: Brooks & Keevil (1997). A simple artificial urine for the growth of urinary pathogens. Letters in Applied Microbiology, 24: 203-206.

extract_protocol: An appropriate number of colony biofilms were harvested in ice cold killing buffer and subjected to total RNA isolation by a modified hot phenol method (Aiba et al., 1981, J Biol Chem 256: 11905-11910;  von Gabain et al., 1983, Proc Natl Acad Sci U S A 80: 653-657). The obtained RNA was treated with RNase-free DNase I and further purified by RNeasy columns (Qiagen, Hilden, Germany). The integrity of total RNA as well as the transcription of anaerobic marker genes in the harvested cells was confirmed by Northern Blot analysis.

tag: genotype/variation

value: wild type

tag: medium

value: artificial urine medium (AUM) +50 mM KNO3

tag: condition

value: anaerobic


title: P. aeruginosa PAO1_anaerobic_10-fold diluted LB_rep 3

description:
This sample was excluded from data analysis
Probe_La3
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.

source_name: P. aeruginosa PAO1 colony biofilms, grown under anaerobic conditions on 10-fold diluted LB + 50 mM KNO3

value: 10-fold diluted Luria Bertani (LB) + 50 mM KNO3


title: P. aeruginosa PAO1_anaerobic_10-fold diluted LB_rep 2

description:
Probe_La2
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.


title: Spinal cord_lewis female_MBP EAE_217

description: Total snap frozen spinal cord ,Lewis rat # 217


title: P. aeruginosa PAO1_anaerobic_AUM_rep 1

description:
Probe_Aa1
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.


title: female_BMM_DBA_loaded_3

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

description: Bone marrow derived macrophages were loaded with 50-100 ug/ml AcLDL and washed twice with PBS for collection of RNA.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was log2 transformed and quantile normalized.

organism: Mus musculus

source_name: bone marrow derived macrophage, 100mg acetylated low density lipoprotein loaded

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: female

tag: cell type

value: bone marrow derived macrophage

tag: agent

value: AcLDL

tag: dose


title: P. aeruginosa PAO1_anaerobic_10-fold diluted LB_rep 1

description:
Probe_La1
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.


title: female_BMM_DBA_loaded_1


title: P. aeruginosa PAO1_anaerobic_AUM_rep 2

description:
Probe_Aa2
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.


title: Spinal cord_lewis female_MBP EAE_241

description: Total snap frozen spinal cord ,Lewis rat # 241


title: female_BMM_DBA_loaded_4


title: female_BMM_DBA_loaded_2


title: female_BMM_AKR_unloaded_4

source_name: bone marrow derived macrophage, control

value: AKR

value: control


title: female_BMM_AKR_unloaded_3


title: SK-Mel28#8 CR201 Treated 100nM dabrafenib and 5nM trametinib 24h

value: BRAF V600E

value: Melanoma

value: 100nM dabrafenib and 5nM trametinib


title: female_BMM_DBA_unloaded_3


title: female_BMM_AKR_loaded_4


title: female_BMM_AKR_loaded_3


title: female_BMM_DBA_unloaded_4


title: Spinal cord_lewis female_healthy control_193

description: Total snap frozen spinal cord ,Lewis rat # 193

value: Lewis


title: female_BMM_AKR_loaded_1


title: P. aeruginosa PAO1_aerobic_10-fold diluted LB_rep 2

description:
Probe_L2
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.

source_name: P. aeruginosa PAO1 colony biofilms, grown under aerobic conditions on 10-fold diluted LB

growth_protocol: Pseudomonas aeruginosa was grown as colony biofilms on AUM and 10-fold diluted LB agar plates, respectively. Aerobic cultivation for 18 h. Cells were harvested in the late logarithmic to early stationary phase. AUM minimal medium described in: Brooks & Keevil (1997). A simple artificial urine for the growth of urinary pathogens. Letters in Applied Microbiology, 24: 203-206.

value: 10-fold diluted Luria Bertani (LB)

value: aerobic


title: P. aeruginosa PAO1_aerobic_AUM_rep 2

description:
Probe_A2
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.

source_name: P. aeruginosa PAO1 colony biofilms, grown under aerobic conditions on AUM

value: artificial urine medium (AUM)


title: female_BMM_DBA_unloaded_2


title: P. aeruginosa PAO1_aerobic_10-fold diluted LB_rep 1

description:
Probe_L1
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.


title: P. aeruginosa PAO1_aerobic_10-fold diluted LB_rep 3

description:
Probe_L3
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.


title: P. aeruginosa PAO1_aerobic_AUM_rep 3

description:
Probe_A3
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.


title: Spinal cord_lewis female_healthy control_194

description: Total snap frozen spinal cord ,Lewis rat # 194

value: Female

value: 16 wks

value: spinal cord


title: female_BMM_DBA_unloaded_1


title: G_200nM_rep3B

city: Padova

first: Laura

last: Varotto

address: via U. Bassi 58/3

department: Biology Department

country: Italy

institute: University of Padova

hyb_protocol: Equal amounts of Cy3- or Cy5-reference and Cy5- or Cy3-test samples were combined in the same tube and ethanol-precipitated. After re-suspension in 18 µl of hybridisation buffer (5x SSC, 50% formamide, 0.1% SDS) and denaturation for 3 min at 70°C, the Cy3/Cy5-coupled samples were competitively hybridised to the DNA microarray slides, covered with a 22×22 mm cover-slip and incubated overnight at 42°C in a humidified dual-slide chambers (HybChamber, GeneMachines).

scan_protocol: Slides were examined with a GSI Lumonics LITE dual confocal laser scanner at 5 µm resolution. Image processing and quantification of the fluorescence signals were performed by the ScanArray Express® software (PerkinElmer), at 570 and 670 nm for Cy3 and Cy5 detection, respectively.

data_processing: Normalisation of the fluorescence signals was performed by using the total and LOWESS (logfit) algorithm with MIDAS (http://www.tigr.org/software).

organism: Mytilus galloprovincialis

source_name: control pool (N=5)

label_protocol: Reference and test RNAs (10 µg) were separately incubated with a degenerated oligo-dT18 primer (10 min at 70°C) in a volume of 10 µl each, added to 20 µl of reaction mix (1x first-strand buffer, 400 U SuperScript II InvitrogenTM, 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.3 mM TTP, 0.2 mM 5-(3-aminoallyl)-dUTP, 0.5 mM DTT) and reverse transcribed for 2 h at 42°C. RNA was removed from single-stranded cDNA with 3 µl of 1 N NaOH, 0.6 µl of 500 mM Na2-EDTA and the reaction mixture was then neutralized with 3 µl of 1 N HCl and 8.5 µl of 2 M HEPES. We used Microcon YM-30 (Amicon separation, MILLIPORE®) to remove buffer, unincorporated dNTPs and free amines. Finally, the cDNA samples were vacuum dried. Mono-functional NHS-esters of Cy3 or -Cy5 dyes (CyDye Post-Labeling Reactive Dye Pack, Amersham GE Healthcare) were covalently coupled to the aminoallyl-cDNA probes in DMSO for 1 h at room temperature in the dark. Then, the samples were quenched with 4.5 µl 4 M hydroxylamine for 15 min and purified with the GeneEluteTM PCR Clean-Up Kit (Sigma).

growth_protocol: Adult mussels (Mytilus galloprovincialis, Lmk. 1819) of mixed sex were collected from a farming site offshore Alberoni (Venice area, North Italy), acclimatized in standard conditions (18±1 °C, 32‰ artificial sea water, ASW).

extract_protocol: Total RNA was purified from individual half-gill samples using the Trizol reagent (Invitrogen) in agreement to the manufacturer’s instructions and a further purification with LiCl was applied. Equal amounts of RNA obtained from the five control mussels were pooled and used as reference against individual RNAs from three treated mussels/tank in the competitive hybridisation to the DNA microarray slides.

treatment_protocol: Mussels of average size (shell length 4.93 ± 0.17 cm) were placed in plastic tanks (5 mussels/tank, 1 litre ASW/mussel) and exposed for 48 hours to equimolar mixtures of Cd, Cu and Hg, prepared at 50, 100 and 200 nM concentration from  chloride salts. We changed the water, food (Coralife® Sera, Heinsberg, Germany) and metal salts every 12 h and monitored regularly the mussel reactivity. Control mussels were maintained in a fourth tank in parallel.

value: gills

tag: developmental stage

value: adult

source_name: 200nM heavy metal treatment


title: P. aeruginosa PAO1_aerobic_AUM_rep 1

description:
Probe_A1
RNA was pooled from min. three independent colony biofilms prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.

value: wild type


title: female_BMM_AKR_unloaded_1

value: female

value: bone marrow derived macrophage


title: G_200nM_rep2A


title: female_BMM_AKR_unloaded_2

value: AKR


title: G_200nM_rep2B


title: G_200nM_rep1B


title: female_BMM_ARK_loaded_2

value: AcLDL


title: G_200nM_rep3A


title: G_100nM_rep2B

source_name: 100nM heavy metal treatment


title: G_100nM_rep3A


title: G_200nM_rep1A


title: G_100nM_rep3B


title: G_100nM_rep2A


title: G_100nM_rep1B


title: A549 Hypoxic + BB2-282, biological rep3

city: Los Angeles

first: Bogdan

last: Olenyuk

state: CA

address: 1985 Zonal Ave. PSC B15-C

department: Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

hyb_protocol: Hybridization reaction used following the Hybridization protocol from the Affymetrix Genechip WT terminal labeling and hybridization kit (page 16). Array format/size is 169 for Human Gene 1.0 ST Array. Reaction mix per sample: DMSO- 7µl, Water- 7.3 µl, 2x Hybridization Buffer- 50 µl, Control Oligonucleotide B2- 1.7 µl, Heated 20X Eukaryotic Hybridization Controls- 5 µl, Bovin Serum Albumin - 1.0 µl, Herring Sperm DNA- 1.0 µl, total volume of mix is 73 µl. 73 µl of mix added to 27 µl (25ng/µl) of fragmented & labeled DNA, now named hybridization cocktail. The hyb. cocktail is vortexed, spun down, & transferred to a heat block for 5 minutes @ 99°C, then transferred to 45°C heat block for 5 minutes, and then spun down for 1 min @ 13,000 xg (room temp.) in Eppendorf Microcentrifuge. Chips are removed from packaging, 80 µl of hyb. cocktail (as per the 169 array format, page 17) is inserted into each chip. Samples are hybridized in Genechip Hybridization oven for 17 hours at 45°C at 60 rpm rotation.

scan_protocol: After 17 hrs, The chips are removed from oven. Sample mix is removed from interior portion of chips. 85 µl of Wash Buffer A is inserted. Chips are run on Genechip Fluidics Station 450 using Fluidics Script: FS450_0007. Staining protocol used for this script is Position 1- Sape (S1) solution mix- 600 µl, Position 2- Antibody (S2) solution mix- 600 µl, and Position 3- 1x Array Holding Buffer- 800 µl. Total Run time is 1hour, 20 mins. Chips are inspected and any bubbles are removed from interior portion of chip by adding more 1x Array Holding Buffer. Chips are cleaned with a lint wipe and scanned in the Affymetrix Genechip 7G Scanner to generate CHP and CEL files.

data_processing: The data were analyzed with RMAExpress version 1.0.5  using Affymetrix default RMA expression settings with quantile normalization and summarizing using median polish.

source_name: A549_hypoxic_treated with BB2-282

label_protocol: Ambion Whole Transcript (WT) Expression Kit from Applied Biosystems used as per kit instructions. The Affymetrix Genechip WT Terminal Labeling and Hybridization kit used for Fragmentation and Labeling as per the kit instructions.

growth_protocol: A549 cells (~70% confluent) were plated in 6-well dishes (BD Falcon) at density of 150,000 cells/mL.

treatment_protocol: Compounds were examined under both normoxic and hypoxic conditions. Briefly,  after attachment cells were treated with 1.5 mL of fresh media containing OOPs BB2-125, BB2-162, or BB2-282 at final concentrations of 10 µM. All samples contained a final concentration of 0.1% DMSO; vehicle samples were treated with cell culture media containing 0.1% DMSO.  After 6 h, hypoxia was induced with GasPak EZ pouch and cells were incubated for another 42 hours.  Cells were washed twice with ice-cold PBS and lysed. Total RNA was isolated with an RNeasy kit (Qiagen) according to the manufacturer’s instructions and quantified by UV absorbance. The RNA was further treated with DNase I (Ambion, DNAfree kit) to remove any remaining genomic DNA. Reverse transcription was performed with Superscript III Reverse Transcriptase (Invitrogen) as recommended by the manufacturer.

tag: oxygen condition

value: hypoxic

tag: treated with


title: A549 Hypoxic + BB2-282, biological rep1

extract_protocol: Total RNA was isolated with an RNeasy kit (Qiagen) according to the manufacturer’s instructions and quantified by UV absorbance. The RNA was further treated with DNase I (Ambion, DNAfree kit) to remove any remaining genomic DNA. Reverse transcription was performed with Superscript III Reverse Transcriptase (Invitrogen) as recommended by the manufacturer.

tag: cell line


title: A549 Hypoxic, vehicle, biological rep3

value: 0.1% DMSO (vehicle)


title: A549 Hypoxic + BB2-162, biological rep3

source_name: A549_hypoxic_treated with BB2-162


title: A549 Hypoxic + BB2-125, biological rep3

source_name: A549_hypoxic_treated with BB2-125


title: G_50nM_rep3B

tag: tissue

source_name: 50nM heavy metal treatment


title: A549 Hypoxic + BB2-282, biological rep2


title: A549 Hypoxic, vehicle, biological rep1


title: A549 Hypoxic + BB2-162, biological rep1


title: G_100nM_rep1A


title: A549 Hypoxic + BB2-125, biological rep2


title: A549 Hypoxic, vehicle, biological rep2


title: A549 Hypoxic + BB2-162, biological rep2


title: A549 Normoxic, vehicle, biological rep3

value: normoxic


title: A549 Hypoxic + BB2-125, biological rep1


title: Uremic_10_ResFn_PostD_Prob

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description: Sample 80 121411

hyb_protocol: Biotin-labeled and fragmented cRNA hybridized to Affymetrix Genechip Human Gene 1.0 ST arrays using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the ExonRMA16 algorithm including quantile normalization using GeneSpring GX11 program. No further adjustments were made to the data in the table.

source_name: non-immortalized human renal cortical cells_post-dialysis uremic plasma from a donor w/ some residual renal function treated w/ probenecid for 24h

label_protocol: The Affymetrix GeneChip WT Terminal Labeling and Controls Kit, combined with the Ambion WT Expression Kit following the recommended protocol.

growth_protocol: Non-immortalized human renal cortical cells from a single donor were purchased from InnovativeBiotherapies.  Cells were grown on Type IV collagen plates.  The cells were plated, split twice, and divided into six experimental groups until cells were confluent.

extract_protocol: Total RNA was extracted using Buffer RLT (Qiagen), purified using RNeasy columns according to the manufacturers’ protocol (Rneasy Mini Kit). After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. Quality and quantity were determined using a  Bioanalyzeand Nanodrop (Agilent Technologies).

treatment_protocol: Cells were divided into six experimental groups and when cells were confluent, plasma was added as follows: normal control plasma (n=5),) control plasma spiked with 60 μg/ml indoxyl sulfate (n=5), pre-dialysis uremic plasma (n=10), post-dialysis uremic plasma (n=10), pre-dialysis uremic plasma with 1 mM probenecid (n=5), and post-dialysis uremic plasma with 1 mM probenecid (n=5).   Cells were with the plasma-growth medium mixture at 37° C for 24 hours. The concentration of plasma in growth medium was 20% in each condition.

value: probenecid


title: A549 Normoxic, vehicle, biological rep2


title: G_50nM_rep1B


title: G_50nM_rep3A


title: G_50nM_rep2A


title: G_50nM_rep2B


title: Uremic_10_ResFn_PreD_Prob

description: Sample 78 121411

source_name: non-immortalized human renal cortical cells_pre-dialysis uremic plasma from a donor w/ some residual renal function treated w/ probenecid for 24h

value: Non-immortalized human renal cortical cells from a single donor


title: A549 Normoxic, vehicle, biological rep1


title: G_50nM_rep1A


title: Uremic_10_ResFn_PreD

description: Sample 74 121411

source_name: non-immortalized human renal cortical cells_pre-dialysis uremic plasma from a donor w/ some residual renal function for 24h

value: pre-dialysis uremic plasma from a donor with some residual renal function


title: Ctrl_5_IS

description: Sample 68 121411

source_name: non-immortalized human renal cortical cells_normal control plasma spiked w/ indoxyl sulfate for 24h

value: normal control plasma spiked with indoxyl sulfate


title: Uremic_10_ResFn_PostD

description: Sample 76 121411

source_name: non-immortalized human renal cortical cells_post-dialysis uremic plasma from a donor w/ some residual renal function for 24h

value: post-dialysis uremic plasma from a donor with some residual renal function


title: DDC-expressing 3T3 cells starved Rep3

description:
Starve_rep3
replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX mouse-ref8 v2 R3 Array. Slides were washed and stained in the Illumina instrument.

source_name: 3T3 Fibroblasts

value: 3T3 Fibroblasts

value: starved


title: DDC-expressing 3T3 cells starved Rep1

description:
Starve_rep1
replicate 1


title: DDC-expressing 3T3 cells in D-Lysine Rep3

description:
DAP_rep3
replicate 3

value: D-Lysine


title: Uremic_6_ResFn_PreD_Prob

description: Sample 54 122811


title: Ctrl_5_Unt

description: Sample 66 121411

source_name: non-immortalized human renal cortical cells_normal control plasma for 24h

value: normal control plasma


title: Uremic_9_NoResFn_PostD

description: Sample 72 121411

source_name: non-immortalized human renal cortical cells_post-dialysis uremic plasma from a donor w/x any residual renal function for 24h

value: post-dialysis uremic plasma from a donor without any residual renal function


title: Uremic_8_NoResFn_PostD_Prob

description: Sample 64 121411

source_name: non-immortalized human renal cortical cells_post-dialysis uremic plasma from a donor w/x any residual renal function treated w/ probenecid for 24h


title: Uremic_5_NoResFn_PreD_Prob

description: Sample 50 122811

source_name: non-immortalized human renal cortical cells_pre-dialysis uremic plasma from a donor w/x any residual renal function treated w/ probenecid for 24h


title: Uremic_8_NoResFn_PreD_Prob

description: Sample 62 121411


title: DDC-expressing 3T3 cells starved Rep2

description:
Starve_rep2
replicate 2


title: Uremic_9_NoResFn_PreD

description: Sample 70 121411

source_name: non-immortalized human renal cortical cells_pre-dialysis uremic plasma from a donor w/x any residual renal function for 24h

value: pre-dialysis uremic plasma from a donor without any residual renal function


title: DDC-expressing 3T3 cells in D-Lysine Rep2

description:
DAP_rep2
replicate 2


title: DDC-expressing 3T3 cells in D-Lysine Rep1

description:
DAP_rep1
replicate 1


title: DDC-expressing 3T3 cells in L-Lysine Rep3

description:
LLys_rep3
replicate 3

value: L-Lysine


title: Uremic_7_NoResFn_PreD_Prob

description: Sample 58 121411


title: DDC-expressing 3T3 cells in L-Lysine Rep2

description:
LLys_rep2
replicate 2


title: Uremic_7_NoResFn_PostD_Prob

description: Sample 60 121411


title: Uremic_8_NoResFn_PostD

description: Sample 48 112311


title: Uremic_5_NoResFn_PostD_Prob

description: Sample 52 122811


title: Uremic_6_ResFn_PostD

description: Sample 40 112311


title: Uremic_6_ResFn_PreD

description: Sample 38 112311


title: Uremic_8_NoResFn_PreD

description: Sample 46 112311


title: Uremic_7_NoResFn_PreD

description: Sample 42 112311


title: DDC-expressing 3T3 cells in L-Lysine Rep1

description:
LLys_rep1
replicate 1


title: Uremic_5_NoResFn_PostD

description: Sample 36 112311


title: Uremic_5_NoResFn_PreD

description: Sample 34 112311


title: Ctrl_3_IS

description: Sample 28 101311


title: Uremic_4_NoResFn_PreD

description: Sample 22 101311


title: heart-DOC/salt-pooled WT

city: Clayton

first: Morag

middle: J

last: Young

state: Victoria

address: Level 4 Block E 246 Clayton Rd

institute: Prince Henry's Institute of Medical Research

description: pooled RNA

hyb_protocol: Preparation of labelled cDNA and microarray hybridization was performed at the Australian Genome Research Facility (AGRF; VIC, Australia).

scan_protocol: Direct Hybridization gene expression assays are run on the iScan system or BeadArray Reader.

data_processing: Raw signal intensity values were subjected to variance stabilization transformation including background correction, log2 transformation and variance stabilization using the lumiR package of R Bioconductor (www.Bioconductor.org) [Ref; PMID 18467348, 18178591]. ANOVA analysis of normalized probe intensities values was performed in Partek  Genomic SuiteTM software, version 6.6 build 6.12.0420; Copyright  2003-20012 Partek Inc., St. Louis, MO, USA.  ANOVA was used to calculate significance of variation in normalized expression values between sample groups, fold change of gene expressions was calculated as mean ratio. Probes with an unadjusted p-value of 0.05 or less (no False Discovery Rate correction was applied) and an absolute fold change of 1.5 or more were defined as differentially expressed. Gene ontology enrichment analysis was performed on the list of differentially expressed probes in Partek.

source_name: WT_DOC/salt treated

label_protocol: second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining

growth_protocol: 8-9 week old mice

extract_protocol: RNA isolated from 30mg tissue using Trizol

treatment_protocol: uninephrectomised and treated with vehicle for 8 days

tag: strain background

value: MR flox/flox

value: wild type

value: 8-9 wks

value: whole heart

value: DOC/salt for 8 days


title: Ctrl_4_Unt

description: Sample 30 101311


title: Ctrl_3_Unt

description: Sample 26 101311


title: male_BMM_AKR_unloaded_3

source_name: bone marrow derived macrophage, control

value: male

value: AKR

value: bone marrow derived macrophage

value: control


title: Uremic_1_ResFn_PostD

description: Sample 12 081911

value: Non-immortalized human renal cortical cells from a single donor

value: post-dialysis uremic plasma from a donor with some residual renal function


title: Uremic_4_NoResFn_PostD

description: Sample 24 101311


title: male_BMM_DBA_loaded_4

source_name: bone marrow derived macrophage, 50mg acetylated low density lipoprotein loaded

value: AcLDL


title: male_BMM_AKR_loaded_4


title: heart-DOC/salt-pooled CM MRKO

description: pooled RNA

source_name: Cardiomyocyte MR-null_DOC/salt treated

value: MR flox/flox MLC2v Cre

value: Cardiomyocyte MR-null mice (CM-MRKO)


title: Uremic_6_ResFn_PostD_Prob

description: Sample 56 122811

value: probenecid


title: heart-vehicle-pooled CM MRKO

description: pooled RNA

source_name: Cardiomyocyte MR-null_vehicle treated

value: vehicle for 8 days


title: Uremic_7_NoResFn_PostD

description: Sample 44 112311

value: post-dialysis uremic plasma from a donor without any residual renal function


title: Ctrl_4_IS

description: Sample 32 101311

value: normal control plasma spiked with indoxyl sulfate


title: Uremic_3_ResFn_PreD

description: Sample 18 101311

value: pre-dialysis uremic plasma from a donor with some residual renal function


title: Uremic_2_ResFn_PreD

description: Sample 14 081911


title: Uremic_2_ResFn_PostD

description: Sample 16 081911


title: Uremic_3_ResFn_PostD

description: Sample 20 101311


title: male_BMM_DBA_unloaded_4


title: male_BMM_DBA_loaded_3


title: male_BMM_DBA_unloaded_3


title: male_BMM_AKR_unloaded_4


title: male_BMM_DBA_loaded_2


title: heart-vehicle-pooled WT

description: pooled RNA

source_name: WT_vehicle treated

value: MR flox/flox

value: wild type

value: 8-9 wks


title: male_BMM_AKR_loaded_3

value: male


title: male_BMM_ARK_loaded_2

value: AKR


title: male_BMM_DBA_unloaded_2

value: bone marrow derived macrophage


title: male_BMM_DBA_loaded_1


title: Ctrl_1_IS

description: Sample 4 081911


title: Ctrl_1_Unt

description: Sample 2 081911

value: normal control plasma


title: male_BMM_AKR_unloaded_2

value: control


title: Uremic_1_ResFn_PreD

description: Sample 10 081911

value: Non-immortalized human renal cortical cells from a single donor


title: male_BMM_AKR_unloaded_1


title: male_BMM_DBA_unloaded_1


title: male_BMM_AKR_loaded_1

value: AcLDL


title: Paired non-neoplastic tissue ZPI58

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: Control

data_processing:
Raw data were processed by SPSS v16.0 software (SPSS Inc., Chicago, IL).
For the normalization it uses the average of three housekeeping genes: MRPL19, ELF1 and POLR2A
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_HKG)
Matrix normalized worksheet reports normalized signal (against housekeeping genes).

label: FAM

source_name: Paired non-neoplastic tissue

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in RotorGene 6000 produced by Corbett Research (Sydney, Australia) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. cDNA was preamplified using TaqMan PreAmp Master Mix (Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated from frozen tissues using Trizol reagent according to manufacturers protocol (Invitrogen, Carlsbad, CA, USA)

value: Paired non-neoplastic tissue

tag: sampleID

tag: grade

tag: tumor size

tag: nodes

tag: angioinvasion

tag: perineural invasion

tag: resection

tag: os in days

tag: status

tag: chemotherapy


title: Paired non-neoplastic tissue ZPI53

description: Control


title: Paired non-neoplastic tissue ZPI54

description: Control


title: Paired non-neoplastic tissue ZPI56

description: Control


title: Paired non-neoplastic tissue ZPI62

description: Control


title: Paired non-neoplastic tissue ZPI60

description: Control


title: Paired non-neoplastic tissue ZPI51

description: Control


title: Ctrl_2_Unt

description: Sample 6 081911

tag: cell type


title: Paired non-neoplastic tissue ZPI50

description: Control


title: Paired non-neoplastic tissue ZPI44

description: Control


title: Paired non-neoplastic tissue ZPI41

description: Control


title: Ctrl_2_IS

description: Sample 8 081911


title: Paired non-neoplastic tissue ZPI47

description: Control


title: Paired non-neoplastic tissue ZPI42

description: Control


title: MRC5CVI 24Hr UVB/24Hr Control

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: SV40 transformed human lung fibroblast MRC5CVI were kindly provided by Dr. Hong JH, Chang-Gung memorial hospital, Taiwan.

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer's instruction of 3DNA array 350 kit.

scan_protocol: Microarrays were scanned by using GenePix 4100A (Axon, Foster City, CA) and images were taken at a resolution of 5μm. GenePix Pro 5.1 software was used to analyze image data.

data_processing:
GenePix Pro 5.1 software
Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 1 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

source_name: Sample harvested at 24 hours after UVB irradiation

label_protocol: 3DNA Array 50 kit was used for fluorescence labeling on cDNA. Each total RNA (20μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA was then purified by microcon YM-30 column.

growth_protocol: MRC5CVI were grown in Dulbecco's modified Eagle medium (Gibco-BRL, Grand Island, NY) supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Logan, UT), 100 U/ml penicillin, 10 μg/ml streptomycin with 0.29 mg/ml glutamine (Gibco-BRL, Grand Island, NY) at 37℃ in humidified air with 5% CO2.

extract_protocol: MRC5CVI cells were harvested with TRIzol reagent (Invitrogen) to extract total RNA according to the manufacture's protocols at scheduled time points. Total RNA were further purified by RNeasy (Quiagen). The quality of total RNA was assessed using the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent Technologies).

treatment_protocol: Cells were seeded in 10 cm cell culture dish and incubated for at least 24 hr. Before UVB irradiation, culture medium for each dish was collected in centrifuge tube; cells were washed twice with PBS and then irradiated with 600 J/m2 UVB in uncovered dish with a thin layer of PBS. An accompanied control dish of cells was treated identically for each time point except for UVB radiation. After UVB irradiation, cells were replenished with previously collected medium and incubated for 4, 8, 16 or 24 hours before harvest.

tag: treatment

value: UVB

tag: time

tag: gender

tag: age

value: 14 weeks

value: lung fibroblast

tag: transformation

value: SV40 transformed

source_name: Control samples of 24Hr


title: MRC5CVI 16Hr Control/8Hr UVB

source_name: Control samples of 16Hr

tag: cell line

tag: tissue

source_name: Sample harvested at 8 hours after UVB irradiation


title: MRC5CVI 8Hr Control/4Hr UVB

source_name: Control samples of 8Hr

source_name: Sample harvested at 4 hours after UVB irradiation


title: MRC5CVI 8Hr UVB/8Hr Control


title: MRC5CVI 24Hr Control/16Hr UVB

source_name: Sample harvested at 16 hours after UVB irradiation


title: SS (4886312015_H)

city: Baltimore

first: Jean Lud

last: Cadet

state: MD

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

description: SAMPLE 20

hyb_protocol: Microarray hybridization was carried out using RatRef-12 Expression BeadChips arrays (22, 523 probes) (Illumina Inc., San Diego, CA) essentially as described (Cadet et al., 2009; Marting et al., 2012). Briefly, a 600 ng aliquot of total RNA from each striatal sample was amplified using Illumina RNA Amplification kit (Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics, Indianapolis, IN). 750 ng of each cRNA sample were hybridized to Illumina arrays at 55°C overnight according to the Whole-Genome Gene Expression Protocol for BeadStation (Illumina Inc.).

scan_protocol: Hybridized biotinylated cRNA was detected with Cyanine3-streptavidin (GE Healthcare, Piscataway, NJ) and quantified using Illumina's BeadStation 500GX Genetic Analysis Systems scanner.

data_processing:
The Illumina BeadStudio software was used to measure fluorescent hybridization signals. Data were extracted by BeadStudio (Illumina) and analyzed using GeneSpring software v. 7.3.1 (Silicon Genetics, Redwood City, CA). Raw data were imported into GeneSpring and normalized using global normalization. The normalized data were used to identify changes in gene expression at the different time points after the injection of METH.
A gene was identified as significantly changed if it showed increased or decreased expression according to an arbitrary cut-off of 1.8-fold changes at p<0.01, according to the GeneSpring statistical package. Similar criteria have been used successfully in our other studies (Cadet et al., 2009; Martin et al., 2012).

source_name: Striatal Brain Tissue_saline saline

label_protocol: Brains were quickly removed, tissues were dissected on ice, snap frozen on dry ice, and stored at -80°C until used in HPLC, microarray, and quantitative PCR experiments.   The experimental groups were labelled as: saline-saline controls (SS), saline-meth (SM),meth-saline (MS) and meth-meth (MM).

growth_protocol: Animals. Male Sprague-Dawley rats (Charles Rivers Laboratories, Raleigh, NC), weighing 375g+25g at the beginning of the experiments were used in the present study. Animals were housed in a humidity- and temperature-controlled room and were given free access to food and water. All animal procedures were performed according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the local Animal Care Committee.

extract_protocol: Rats were euthanized at 2 hours after the second injection of either METH or saline. All animal use procedures were according to the NIH Guide for the Care and Use of Laboratory Animals and were approved by the local Animal Care Committee.  Total RNA was isolated according to the manufacturer’s manual using Qiagen RNeasy mini kit (Qiagen, Valencia, CA, USA). RNA integrity was detected using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: Following habituation, the animals received a single injection of either saline or METH (10 mg/kg). This injection was followed after a month delay by a second injection of either saline or METH (2.5 mg/kg). The pattern of injections yielded four groups of rats: saline-pretreated and saline-challenged (SS); saline-pretreated and METH-challenged (SM); METH-pretreated and saline-challenged (MS); and METH-pretreated and METH-challenged (MM).

tag: strain

value: Sprague-Dawley

tag: agent

value: nucleus accumbens (NAc)


title: MM (4886312015_L)

description: SAMPLE 24

source_name: Striatal Brain Tissue_meth meth

value: METH-pretreated and METH-challenged (MM)


title: MS (4886312015_G)

description: SAMPLE 19

source_name: Striatal Brain Tissue_meth saline

value: METH-pretreated and saline-challenged (MS)


title: Paired non-neoplastic tissue ZPI28

description: Control

tag: sampleID

tag: grade

tag: tumor size

tag: nodes


title: Paired non-neoplastic tissue ZPI29

description: Control

tag: angioinvasion

tag: perineural invasion

tag: resection

tag: os in days


title: Paired non-neoplastic tissue ZPI30

description: Control

tag: status

tag: chemotherapy


title: MM (4886312015_I)

description: SAMPLE 21

tag: gender


title: MS (4886312015_D)

description: SAMPLE 16


title: MRC5CVI 24Hr UVB/8Hr UVB

tag: treatment

tag: time

tag: age


title: SM (4886312015_E)

description: SAMPLE 17

source_name: Striatal Brain Tissue_saline meth

value: saline-pretreated and METH-challenged (SM)

tag: tissue


title: MS (4886312014_L)

description: SAMPLE 12

value: male

tag: strain


title: SM (4886312014_K)

description: SAMPLE 11

tag: agent


title: SM (4886312015_J)

description: SAMPLE 22


title: SS (4886312015_C)

description: SAMPLE 15

value: saline-pretreated and saline-challenged (SS)


title: MM (4886312014_J)

description: SAMPLE 10


title: Paired non-neoplastic tissue ZPI25

description: Control

tag: sampleID


title: MRC5CVI 4Hr UVB/4Hr Control

tag: cell line

tag: transformation

source_name: Control samples of 4Hr


title: Paired non-neoplastic tissue ZPI20

description: Control

tag: grade

tag: tumor size

tag: nodes


title: Paired non-neoplastic tissue ZPI15

description: Control

tag: angioinvasion

tag: perineural invasion

tag: resection


title: Paired non-neoplastic tissue ZPI17

description: Control

tag: os in days

tag: status

tag: chemotherapy


title: Paired non-neoplastic tissue ZPI12

description: Control


title: Paired non-neoplastic tissue ZPI10

description: Control


title: Paired non-neoplastic tissue ZPI09

description: Control


title: Paired non-neoplastic tissue ZPI08

description: Control


title: Paired non-neoplastic tissue ZPI07

description: Control


title: Paired non-neoplastic tissue ZPI05

description: Control


title: Paired non-neoplastic tissue ZPI02

description: Control


title: Pancreatic ductal adenocarcinoma tumorPCI62

description: Tumor

source_name: pancreatic ductal adenocarcinoma

value: Tumor

value: dead

value: Gemcitabin


title: Pancreatic ductal adenocarcinoma tumorPCI60

description: Tumor


title: Paired non-neoplastic tissue ZPI04

description: Control


title: SS (4886312014_H)

description: SAMPLE 8

tag: gender


title: MM (4886312014_F)

description: SAMPLE 6


title: MS (4886312015_K)

description: SAMPLE 23


title: Pancreatic ductal adenocarcinoma tumorPCI58

description: Tumor

value: alive


title: MM (4886312015_A)

description: SAMPLE 13


title: MRC5CVI 4Hr UVB/16Hr UVB

tag: treatment

tag: time

tag: age


title: SM (4886312015_B)

description: SAMPLE 14

tag: strain

tag: agent

tag: tissue


title: Pancreatic ductal adenocarcinoma tumorPCI55

description: Tumor

tag: sampleID


title: Pancreatic ductal adenocarcinoma tumorPCI56

description: Tumor

tag: grade

value: FUFA


title: Pancreatic ductal adenocarcinoma tumorPCI54

description: Tumor

tag: tumor size

value: Gemcitabin + 5FU


title: Pancreatic ductal adenocarcinoma tumorPCI53

description: Tumor

tag: nodes


title: Pancreatic ductal adenocarcinoma tumorPCI50

description: Tumor

tag: angioinvasion

value: Unknown


title: SM (4886312014_E)

description: SAMPLE 5


title: Pancreatic ductal adenocarcinoma tumorPCI51

description: Tumor

tag: perineural invasion


title: MM (4886312015_F)

description: SAMPLE 18


title: MS (4886312014_G)

description: SAMPLE 7


title: Control_Clone1, biological rep1

city: Cincinnati

first: Susumu

last: Goyama

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from EtOH-treated (control) MLL-AF9 cells

hyb_protocol: Labeled probes were hybridized to GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

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

data_processing: Raw data files are created by Command Console, the Affymetrix operating software program. RMA was used to normalize all samples.

source_name: Runx1/Cbfb-intact MLL-AF9 cells

label_protocol: For each sample, the Ambion® WT Expression Kit (Life Technologies) synthesizes cDNA target from 300 nanograms of total RNA.Then the GeneChip® WT Terminal Labeling Kit (Affymetrix) is used to both chemically fragment and biotin-label the cDNA target.

growth_protocol: Cells were cultured in M3434 cytokine-enriched methylcellulose according to manufacturer’s instructions.

extract_protocol: Total RNA was prepared using Rneasy mini kit (QIAGEN).

treatment_protocol: Cells were treated with EtOH or 4OHT (1 uM) for 24 h in M3434 methylcellulose.

tag: genotype


title: SM (4886312014_B)

description: SAMPLE 2


title: Control_Clone2, biological rep2


title: MM (4886312014_D)


title: MS (4886312014_I)

description: SAMPLE 9


title: Runx1Cbfb-KO_Clone1, biological rep1

description: Gene expression data from 4OHT-treated (Runx1/Cbfb-deleted) MLL-AF9 cells

source_name: Runx1/Cbfb-deleted MLL-AF9 cells


title: Pancreatic ductal adenocarcinoma tumorPCI49

description: Tumor

tag: resection

tag: os in days

value: FUFA + Gemcitabin


title: Pancreatic ductal adenocarcinoma tumorPCI47

description: Tumor

tag: status

tag: chemotherapy


title: Pancreatic ductal adenocarcinoma tumorPCI44

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI29

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI42

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI37

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI30

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI41

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI39

description: Tumor


title: Runx1Cbfb-KO_Clone1, biological rep2


title: Control_Clone2, biological rep1


title: SS (4886312014_A)

description: SAMPLE 1

tag: gender


title: Pancreatic ductal adenocarcinoma tumorPCI25

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI26

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI28

description: Tumor


title: MS (4886312014_C)

description: SAMPLE 3


title: Pancreatic ductal adenocarcinoma tumorPCI20

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI17

description: Tumor


title: Runx1Cbfb-KO_Clone2, biological rep1


title: Untreated ES cells, Rep 1

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 675 West 10th Avenue

department: Epigenomics

country: Canada

institute: BCCA Genome Sciences Centre

hyb_protocol: Hybridization was performed by Gladstone Genomics Core facility according to GeneChip Expression Analysis Technical Manual 702232 Rev. 3

scan_protocol: Arrays were scanned with GCS3000 using the standard procedures recommended by Affymetrix.

data_processing: Intensities of the Affymetrix CEL files were background subtracted, quantile normalized, and summarized for each probe set into a logarithm base two intensity value using the robust multi-array average method (RMA) implemented in the Affymetrix package AGCC 3.2.2.

source_name: Embryonic stem cells, untreated

label_protocol: Samples were amplified with NuGEN Ovation Pico WTA V2 and labelled with the Encore Biotin Module by the Gladstone Genomics Core facility according to manufacturer's protocol.

growth_protocol: ES cells were cultured on 0.1% gelatin coated plates in N2B27 medium supplemented with the MEK inhibitor PD0325901 (1μM, Stemgent), and the GSK3β inhibitor CHIR99021 (3μM, Selleck Chemicals), and LIF (1000U/ml, Millipore).

extract_protocol: Total RNA was extracted with Qiagen RNeasy kit with on-column DNAse digestion

treatment_protocol: ES cells were cultured in the presence or absence of Vitamin C (L-ascorbic acid 2-phosphate, 200 μg/ml) for 72 hours.  Vitamin C was added to ES cells one day after seeding.  Medium with or without Vitamin C supplementation was replaced daily.

tag: cell type

value: Oct4-GiP ES cells


title: Vitamin C treated ES cells, Rep 3

source_name: Embryonic stem cells, Vitamin C treated


title: Pancreatic ductal adenocarcinoma tumorPCI15

description: Tumor


title: Untreated ES cells, Rep 2


title: Pancreatic ductal adenocarcinoma tumorPCI12

description: Tumor


title: Vitamin C treated ES cells, Rep 1


title: Vitamin C treated ES cells, Rep 2


title: Pancreatic ductal adenocarcinoma tumorPCI09

description: Tumor


title: Pancreatic ductal adenocarcinoma tumorPCI10

description: Tumor


title: Untreated ES cells, Rep 3


title: IMIM8

city: Barcelona

first: Olga

last: Castaner

address: Aiguader 88

department: Nutrition and cardiovascular risk department

country: Spain

institute: IMIM

description: Gene expression data from Human peripheral blood mononuclear cells

hyb_protocol: Sample was hybridized to Human Genome U133A 2.0 Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then SAM was applied to calculate significant differential expression between samples

label: Biotin

source_name: Total RNA from PBMCS, olive oil, 3 months

label_protocol: 300 ng of total RNA were amplified and labeled using the 3´ IVT Express Kit and control reagents (Affymetrix)

extract_protocol: Ultraspec RNA isolation system (Biotecx Laboratories)

tag: intervention

value: olive oil

tag: timepoint

value: 3 months


title: IMIM10

source_name: Total RNA from PBMCS, nuts, 3 months

value: nuts


title: IMIM4

source_name: Total RNA from PBMCS, low fat, 3 months

value: low fat


title: Control_Clone1, biological rep2


title: IMIM9

source_name: Total RNA from PBMCS, nuts, baseline

value: baseline


title: IMIM2


title: IMIM7

source_name: Total RNA from PBMCS, olive oil, baseline


title: Pancreatic ductal adenocarcinoma tumorPCI08

description: Tumor


title: OP52


title: Runx1Cbfb-KO_Clone2, biological rep2


title: OP57

source_name: Total RNA from PBMCS, low fat, baseline


title: IMIM3


title: OP56


title: OP58


title: IMIM6


title: QM 9414 on glycerol 2

city: Vienna

first: Christian

middle: P.

last: Kubicek

address: Getreidemarkt 9

country: Austria

institute: TU Vienna

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichoderma reesei

source_name: Trichoderma reesei growing on glycerol for 24 hrs

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Trichoderma reesei strain QM9414 (ATCC 26921) was grown in duplicate grown in 1 l Erlenmeyerflasks flasks on a rotary shaker (250 rpm) at 30 C in the medium described by Seiboth et al. (2004) [Mol Microbiol 51:1015-25] with lactose, glucose and glycerol (each two flasks) as a carbon source at a final concentration of 10 g l-1.

extract_protocol: Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.

treatment_protocol: Mycelia from both stages were freeze-dried and ground in liquid nitrogen using a mortar and pestle. For each of the two experimental conditions, five independent replicates of mycelium were mixed.

tag: strain

value: mycelia

tag: medium

value: growth on glycerol for 24 hrs


title: 3d old, 10mM sucrose only, rep2

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

institute: University of Toronto

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization.

scan_protocol: Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073.

data_processing: Analysis performed using the BioConductor suite in R. All 12 arrays were pre-processed together using GCRMA. Expression data were filtered to remove probe sets which reported low transcript abundance and low variance across all arrays (minimum intensity of 100 on at least two arrays, minimum inter-quartile range of 0.5 on the log2-scale). The pre-processed data were analysed as a 2 X 2 factorial complete randomized ANOVA using the linear model for microarray (limma) package in R (R Development Core Team, 2009). The linear model was parameterized by group means with a manually defined sum-to-zero contrast matrix to test directly for the contrasts of interest: the main and interaction effects overall, as well as the effect of the co-treatment with sucrose and SMX. A Benjamini-Hochberg false discovery rate of 0.1 was applied to the output of all tests (Benjamini and Hochberg, 1995).

organism: Arabidopsis thaliana

source_name: 3d old, 10mM sucrose only

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay.

growth_protocol: Wild-type Arabidopsis thaliana (Col) seeds were sown in sterile liquid MS growth media in 24-well plates and wrapped in light-blocking foil. Plates were cold-stratified at 4C for three days, then exposed to light for six hours to promote germination. Seedlings were grown for three days at 21C prior to RNA extraction.

extract_protocol: Total RNA extracted using RNeasy extraction kit (Qiagen).

tag: ecotype

value: Columbia

tag: tissue

value: Whole seedling

value: Wild type


title: OP59


title: Pancreatic ductal adenocarcinoma tumorPCI05

description: Tumor

value: Tumor

tag: sampleID

tag: grade

tag: tumor size

value: dead


title: IMIM11


title: IMIM5


title: Pancreatic ductal adenocarcinoma tumorPCI02

description: Tumor

tag: nodes

tag: angioinvasion

tag: perineural invasion


title: Pancreatic ductal adenocarcinoma tumorPCI04

description: Tumor

tag: resection

tag: os in days


title: Pancreatic ductal adenocarcinoma tumorPCI07

description: Tumor

tag: status

tag: chemotherapy


title: QM 9414 on glucose 2

source_name: Trichoderma reesei growing on glucose for 24 hrs

value: growth on glucose for 24 hrs


title: IMIM1


title: QM 9414 on glycerol 1


title: Adenoma_5

type: mixed

city: Grenoble Cedex 09

first: Nadia

last: Cherradi

address: 17 Rue des Martyrs

department: iRTSV/CEA

institute: INSERM U1036

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXploreTM Microarrays using the a-HybTM Hybridization Station

scan_protocol: Fluorescence signals of the hybridized miRXploreTM Microarrays were detected using a laser scanner from Agilent (Agilent Technologies).

data_processing:
Mean signal and mean local background intensities were obtained for each spot of the microarray images using the ImaGene software (Biodiscovery). Low-quality spots were flagged and excluded from data analysis. Unflagged spots were analysed with the PIQORTM Analyzer software. The PIQOR Analyzer allows automated data processing of the raw data text files derived from the ImaGene software. This includes background subtraction to obtain the net signal intensity, data normalization, and calculation of the Hy5/Hy3 ratios for the species of interest. As an additional quality filtering step, only spots/genes are taken into account for the calculation of the Hy5/Hy3 ratio that have a signal that is equal or higher than the 50% percentile of the background signal intensities.
For the identification of differentially regulated miRNA, the original dataset using the Universal Reference as hybridization control was used.  All ratio data were transformed to logarithms to the base 2 (log2 ratio). For the discriminatory gene analysis (DGA) of the two different carcinoma subtypes, only miRNA were used which have valid expression values in at least four of the six samples provided for each subtype. 501 miRNA were retained after this filtering step. Regarding the DGA of adenoma and the combined carcinoma samples, at least six carcinoma samples out of twelve had to show valid expression values, while there had to be four out of six adenoma samples with valid expression values. 511 miRNA were retained after this filtering step. Heat maps showing filtered miRNA and their expression in the different cell samples relative to the Universal Reference were clustered using Euclidean distance and average linkage clustering. The log2 ratios were translated into a color code: red depicts a stronger expression of the miRNA in the sample relative to the control, green indicates a weaker expression, black stands for no differential regulation between sample and control and grey marks missing values.

molecule: other

organism: synthetic construct

source_name: Pool of Synthetic microRNAs

label_protocol: Sample labeling was performed according to the undisclosed miRXploreTM User manual. Control samples (miRXplore Universal Reference provided by Miltenyi ) were labeled with Hy3 and experimental samples were labeled with Hy5. The miRXplore Universal Reference represents a defined pool of synthetic microRNAs for comparison of multiple samples.

extract_protocol: Total RNA was isolated using standard RNA extraction protocols (Trizol) and afterwards repurified by using the miRNeasy kit (Qiagen). RNA samples  were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies). RNA samples revealed RIN values between 6.6 and 9.4.

tag: reference

source_name: Adenoma

value: Adrenal cortex


title: Adenoma_6

value: miRXplore Universal Reference provided by Miltenyi


title: OP55

tag: intervention


title: OP53

tag: timepoint


title: QM 9414 on glucose 1

tag: strain


title: QM 9414 on lactose 1

source_name: Trichoderma reesei growing on lactose for 28 hrs

tag: medium

value: growth on lactose for 28 hrs


title: OP51


title: OP50


title: OP46


title: Adenoma_2


title: Adenoma_3


title: Adenoma_4


title: Carcinoma B6

source_name: Non-Agressive carcinoma


title: QM 9414 on lactose 2


title: Adenoma_1


title: late alcohol drinker-2

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

country: China

institute: Shanghai Biochip Co., Ltd.

description: Hypothalamic gene expression after chronic alcohol consumption from adolescence-to-adulthood in mice, which was a late high alcohol drinker

hyb_protocol: Hybridized onto Agilent Whole Mouse Genome 4 × 44K G4122F microarrays containing 43 604 probes as described in the manufacturer's protocol.

scan_protocol: Slides were scanned (Agilent G2505B) at 5 μm resolution using an extended dynamic range protocol, and images were processed with Agilent Feature Extraction software 9.5.

data_processing: Within-array normalization was performed using the “Background detrending” software (Agilent). The nonuniform outlier features (spots) were removed.

label_protocol: Total RNA was Cy3 labelled according to Agilent’s Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Before chronic alcohol drinking began, mice (3 weeks old) were allowed to adapt to drinking tubes with both tubes containing water from experimental day 1-5. After adaptation period, mice were randomly aside to 5% alcohol group, 10% alcohol group or water-only control group (n=16-18). For the water-only control group, two drinking tubes in each cage contained deionized water throughout the duration of the experiment. For the alcohol group, one drinking tube contained 5% or 10% alcohol solution while the other contained water.

extract_protocol: Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified with RNeasy column (Qiagen, Valencia, CA).The RNA concentration and purity were analyzed by a Nanodrop spectrophotometer (Nanodrop technologies, Wilmington, DE), with the spectral absorption at 260 and 280 nm. The assessment of the RNA integrity was conducted by the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples had RNA Integrity Numbers (RIN) of 8.0 or higher.

treatment_protocol: On day 51 of the experiment, each mouse is sacrificed by decapitation, and their hypothalami were quickly removed and frozen in N-hexane (−70 °C) for approximately 40 s. The samples were then stored at −80 ◦C until further use.

tag: group

value: late alcohol drinker

value: ICR

value: Hypothalamus

tag: gender

value: Male


title: early alcohol drinker-2

description: Hypothalamic gene expression after chronic alcohol consumption from adolescence-to-adulthood in mice, which was an early high alcohol drinker

value: early alcohol drinker

tag: tissue


title: OP42

value: low fat

value: 3 months


title: OP40

value: nuts


title: OP44


title: early alcohol drinker-1


title: low alcohol drinker-3

description: Hypothalamic gene expression after chronic alcohol consumption from adolescence-to-adulthood in mice, which was a low alcohol drinker

value: low alcohol drinker


title: OP41

value: baseline


title: OP49bis

value: olive oil


title: OP39


title: OP48


title: OP54


title: Carcinoma B5


title: Carcinoma B4


title: Carcinoma B3


title: Carcinoma B2


title: water group-3

description: Hypothalamic gene expression from no alcohol exposure mice

value: water group


title: low alcohol drinker-1


title: low alcohol drinker-2


title: OP37


title: OP36


title: OP38


title: water group-2


title: early alcohol drinker-3


title: late alcohol drinker-3


title: Carcinoma A6

source_name: Agressive carcinoma


title: Carcinoma B1


title: OP35


title: OP34


title: Carcinoma A2


title: Carcinoma A5


title: Carcinoma A4


title: KO TFH rep4

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

institute: University Hospital Bonn

hyb_protocol: Labeled Cy3-cDNA was assessed using the Nandrop ND-8000 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 8X60K in-jet arrays. Hybridizations were performed for 17 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner.

data_processing: Raw signal intensities were extracted with Feature Extraction v10.6 software.

source_name: KO SMARTA TFH, d5.5 after infection

label_protocol: Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI).

growth_protocol: Naïve SMARTA cells were purified by FACS sorting from T17~92+/+ control or T17~92∆/∆ donor mice and adoptively transferred into wildtype mice.

extract_protocol: Spleens were dissected 5.5 days after infection and spleen cells were pooled for each condition (n = 3-5 mice). CD4+ T cells were enriched with the CD4+ negative isolation kit (Invitrogen) and congenically marked SMARTA TFH cells (7AAD–CD4+CD8–CD19–CXCR5hiPD-1hi) were sorted directly into Trizol LS reagent and stored at -80°C until further processing. RNA from four independent experiments was purified using RNeasy columns (Qiagen). RNA was amplified using the Sigma whole transcriptome amplification kits following the manufacturer’s protocol (Sigma-Aldrich, St Louis, MO)

treatment_protocol: Recipient mice were infected i.p. with LCMV Armstrong.

value: female

tag: origin

value: FACS sorting from T17~92delta/delta


title: Carcinoma A3

value: Adrenal cortex


title: OP33


title: Carcinoma A1

value: miRXplore Universal Reference provided by Miltenyi


title: water group-1


title: KO TFH rep3


title: late alcohol drinker-1


title: OP29


title: MRC5CVI 4Hr Control/24Hr UVB

source_name: Control samples of 4Hr

tag: treatment

value: control

tag: time

tag: cell line

value: male

tag: age

value: 14 weeks

value: lung fibroblast

tag: transformation

value: SV40 transformed

source_name: Sample harvested at 24 hours after UVB irradiation

value: UVB


title: KO TFH rep2


title: OP30


title: KO TFH rep1


title: OP32


title: OP24


title: OP27


title: OP31


title: TP_null_2

city: Chapel HIll

first: Ryan

last: Miller

state: North Carolina

department: Pathology

institute: University of North Carolina

description:
Batch: MV
Sample name: MV52_TP_null_P6_246026

hyb_protocol: Labeled sample RNA and Stratagen Universal Mouse Reference RNA (Agilent, #740100)  as a reference were cohybridized at 65 C for 17 hours in a rotating hybridization oven.

scan_protocol: Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology (Part no. G2565CA)

data_processing: Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD).  Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels.  Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapse by averaging. Cell line samples from 2 different batches (see overall design) were combined using the nonparametric settings in combatR, a module in the R statistical programming language (R Development Core Team, 2006 http://www.R-project.org).  Normalized data provided is the filtered, batch combined,  non-median centered data used to draw conclusions in the study.

source_name: primary cortical astrocytes

label_protocol: Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent.  1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes.  Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes.  Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.

growth_protocol: cells were grown in DMEM 10% FBS, 1% pen-strep and passaged when confluent.

extract_protocol: Total RNA was extracted with Qiagen RNeasy kit according to manufacturer's instructions

tag: cell type

value: primary cortical astrocyte

tag: genotype/variation

tag: passage post cre infection

tag: isolate

source_name: Stratagene whole mouse reference RNA

tag: sample type

value: reference


title: OP25

tag: intervention

value: nuts

tag: timepoint


title: OP26

source_name: Total RNA from PBMCS, nuts, 3 months

value: 3 months


title: TP_het_2

description:
Batch: MV
Sample name: MV52_TP_het_P7_246028

tag: strain


title: Control TFH rep4

source_name: Control SMARTA TFH, d5.5 after infection

value: FACS sorting from T17~92+/+


title: Control TFH rep3


title: OP23

source_name: Total RNA from PBMCS, nuts, baseline

value: baseline


title: OP28


title: OP18

source_name: Total RNA from PBMCS, olive oil, 3 months

value: olive oil


title: MRC5CVI 16Hr UVB/16Hr Control

source_name: Sample harvested at 16 hours after UVB irradiation

source_name: Control samples of 16Hr


title: OP22


title: Control TFH rep1


title: TRP_null_1

description:
Batch: MV
Sample name: MV52_TRP_null_P8_250999

value: TRP-/-


title: TRP_het_4

description:
Batch: MV
Sample name: MV52_TRP_het_P7_244044

value: TRP+/-


title: TRP_het_5

description:
Batch: MV
Sample name: MV52_TRP_het_P7_250998


title: OP17

source_name: Total RNA from PBMCS, olive oil, baseline


title: Giardia lamblia WB: 5'5npac control vs pPTopoII

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

description: stable cell lines

hyb_protocol: Correspondingly fragmented labeled cRNA was then pooled and hybridized to a G. lamblia oligonucleotide microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images were analyzed by Feature Extraction version 9.1 software (Agilent Technologies, USA), and image analysis and normalization software was used to quantify signal and background intensity for each feature; data were substantially normalized by the rank consistency filtering LOWESS method.

organism: Giardia duodenalis

source_name: Giardia lamblia WB

label_protocol: 0.5 mg of total RNA was amplified by a Low RNA Input Fluor Linear Amp kit (Agilent Technologies) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer Life Sciences) during the in vitro transcription process. 0.825 mg of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes.

growth_protocol: PCR amplification and standard cloning techniques were used to insert TopoII gene from genomic DNA and then cloned into the pPop2NHA vector, resulting in plasmid pPTopoII.

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

treatment_protocol: Giardia  cells were transfected with the pPTopoII or 5'5npac plasmid containing the pac gene were selected and maintained with 54 ug/ml puromycin.

tag: vector

value: 5'pac5n control

value: pPTopoII


title: Control TFH rep2

tag: gender

value: female


title: TP_het_1

description:
Batch: MV
Sample name: MV52_TP_het_P8_243616


title: OP14


title: OP21


title: OP15


title: TR_4

description:
Batch: MV
Sample name: MV52_TR_P7_D

value: TR


title: TRP_het_3

description:
Batch: MV
Sample name: MV52_TRP_het_P9_243612


title: OP11


title: TP_null_1

description:
Batch: MV
Sample name: MV52_TP_null_P4_246030


title: OP12


title: OP13


title: T_4

description:
Batch: MV
Sample name: MV52_T_P2_239213

value: T


title: T_3

description:
Batch: AP
Sample name: AP3_T_p3_C


title: OP16


title: TRP_null_5

description:
Batch: AP
Sample name: AP_1_TRP_null_P5


title: TRP_null_2.1

description:
Batch: MV
Sample name: MV52_TRP_null_P10_B


title: TRP_het_2

description:
Batch: MV
Sample name: MV52_TRP_het_P6_243614


title: OP6


title: TRP_null_2

description:
Batch: AP
Sample name: AP2_TRPnull_p5_B


title: OP10


title: HiTCE gDNA_rep3

type: genomic

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

description:
gene presence/absence data
Dehalococcoides-containing mixed culture

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using Affymetrix GeneChip software and the MAS5 algorithm. Each microarray was normalized by scaling the signal intensities of the positive control spike-mix to a target signal intensity of 2500 to allow comparison between microarrays.

molecule: genomic DNA

organism: environmental samples

source_name: TCE-dechlorinating enrichment without methanogenesis without the addition of cobalamin grown after 13 days

label_protocol: One µg of DNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: MethB12 was enriched from groundwater and maintained using defined medium amended with 20mM lactate, 100ug/L vitamin B12 and 2uL TCE.  Meth was constructed using the same growth condition as MethB12 but without the addition of vitamin B12.  NoMethB12 was constructed from MethB12 by adding 7ul TCE initially instead of 2uL.  NoMeth was constructed from NoMethB12 without adding vitamin B12.  Lactate and TCE were re-amended in all four enrichments resulting in a total of 2.7mmol lactate and 20uL TCE added.  On day 15 for MethB12 and Meth, day 13 for NoMethB12 and NoMeth, when all TCE was dechlorinated, ~40mL cells were collected by centrifugation as one biological replicate. Three biological replicates were prepared.

extract_protocol: Genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen,Valencia, CA) according to the manufacturer’s instructions. cDNA was synthesized according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

tag: bacteria

value: enrichment


title: TR_3

description:
Batch: MV
Sample name: MV52_TR_P9_C


title: HiTCE gDNA_rep2

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: Longssimus dorsi muscle_bull_rep3

city: Gwangju

first: Myunggi

last: Baik

address: 77 yongbong-ro buk-gu

country: South Korea

institute: chonnam university

hyb_protocol: 1-5㎍ of aRNA were hybridized to the CombiMatrix microarray according to the protocols provided by the manufacturer (CombiMatrix Diagnostics; CustomArray™ 12K Microarray: Hybridization and Imaging Protocol (PTL006)).

scan_protocol: Arrays were scanned using the high-resolution scanners (Axon Instruments Genepix 4000B, 4200A microarray scanner).

data_processing: Array data export processing and analysis was performed using Microarray imager v5.9.3. (ArrayAssist® 5.5.1; Agilent Technologies, Inc., Santa Clara, CA, USA). Array Images were adjusted by background correction by deleting Median value for the lowest 1~5% of Median. Data were filtered by deleting factory-built controls, saturated data (signal≥60000), and negative value and value < 1. Data were transformed to logarithmic values, and systemic bias was corrected by Mean shift Normalization method.

organism: Bos taurus

source_name: Longissimus dorsi muscle of bull

label_protocol: Biotinylated amplified RNA (aRNA) were prepared from 0.5-1㎍ total RNA using the CombiMatrix TotalPrep RNA Amplification Kit (Ambion, MessageAmpTM ll-Biotin Enhanced Kit).

growth_protocol: Korean cattle bulls and steers were grown by conventional feeding, and slaugthered at 28 and 20 months of age, respectively. Some of bulls were castrated at 6 months of age.

extract_protocol: Total RNA of frozen muscle tissues was extracted using Trizol following manufacturer's instructions.

tag: group

value: Korean cattle bull


title: OP8


title: OP9


title: TRP_null_3

description:
Batch: AP
Sample name: AP2_TRPnull_p3_C


title: TRP_null_4

description:
Batch: AP
Sample name: AP2_TRPnull_p3_D


title: OP7


title: T_2

description:
Batch: AP
Sample name: AP2_T_p3_B


title: OP3


title: HiTCEB12 gDNA_rep3

source_name: TCE-dechlorinating enrichment without methanogenesis with the addition of cobalamin grown after 13 days


title: HiTCEB12 gDNA_rep2


title: HiTCE gDNA_rep1


title: TRP_het_1

description:
Batch: AP
Sample name: AP2_TRPhet_p7_A


title: OP4


title: HiTCEB12 gDNA_rep1


title: LoTCE gDNA_rep3

source_name: TCE-dechlorinating enrichment with methanogenesis without the addition of cobalamin grown after 15 days


title: LoTCE gDNA_rep1


title: Longssimus dorsi muscle_bull_rep1


title: TR_1

description:
Batch: AP
Sample name: AP2_TR_p7p_A


title: LoTCE gDNA_rep2


title: Longssimus dorsi muscle_low-marbled steer_rep3

source_name: Longissimus dorsi muscle of low-marbled steer

value: low-marbled steer


title: Longssimus dorsi muscle_bull_rep2


title: Longssimus dorsi muscle_low-marbled steer_rep2


title: OP1


title: Longssimus dorsi muscle_low-marbled steer_rep1


title: OP5


title: T_1

description:
Batch: AP
Sample name: AP2_T_p5p_A

value: primary cortical astrocyte


title: TR_2

description:
Batch: AP
Sample name: AP2_TR_p5_B

value: reference


title: LoTCEB12 gDNA_rep2

source_name: TCE-dechlorinating enrichment with methanogenesis and the addition of cobalamin grown after 15 days


title: VIC_study_hAVIC

city: Nanjing

first: xiangqing

last: kong

address: No.300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

description: AVIC

hyb_protocol: Hybridization was carried out according to the NimbleGen`s Expression user`s guide(see manufacture`s user guide)and performed at CapitalBio Corporation(Beijing,China). See www.nimblegen.com.

scan_protocol: Scanning was carried out according to the NimbleGen`s Expression user`s guide(see manufacture`s user guide)and performed at CapitalBio Corporation(Beijing,China). See www.nimblegen.com.

source_name: human aortic valve interstitial cells

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described[Guo,Y. et al. J. Virol. 2005,79:14392-14403.], and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol:
cell isolation protocol: Normal aortic and mitral valves were obtained from five healthy donor hearts following the donors’deaths in traffic accidents (three males and two females, 25 to 34 years old). Small portions of each valve were used for VIC isolation. Human aortic interstitial cells (hAVICs) and mitral valve interstitial cells (hMVICs) were isolated by collagenase digestion as previously described [Taylor et al.J Heart Valve Dis 2000;9:150-158.] and then cultured in DMEM (Hyclone) supplemented with 10% fetal bovine serum (FBS; Hyclone), 1% penicillin-streptomycin, and 2 mM L-glutamine.Primary Cells were used for microarray analysis.
Total RNA was extracted using Trizol reagent (Invitrogen) and further purified using NucleoSpin® RNA clean-up (MACHEREY-NAGEL, Germany) according to the manufacturer’s instructions. The RNA quality was assessed with formaldehyde agarose gel electrophoresis and quantitated spectrophotometrically. Equivalent RNA from primary VICs of five donors was pooled, and 1ug total RNA was converted to cDNA and labeled for advance microarray according to the manufacturer’s protocol (CapitalBio Corporation, Beijing, China).

tag: tissue source

value: five healthy donor

value: 3 males and 2 females

value: 25 to 34 years

tag: tissue

value: heart

value: human aortic interstitial cells (hAVICs)

tag: phenotype

value: normal


title: OP2

value: olive oil

value: 3 months


title: VIC_study_hDF

description: HDF

source_name: human dermal fibroblasts

value: human dermal firbroblasts (hDFs)


title: Longssimus dorsi muscle_high-marbled steer_rep3

source_name: Longissimus dorsi muscle of high-marbled steer

value: high-marbled steer


title: Longssimus dorsi muscle_high-marbled steer_rep2


title: VIC_study_hMVIC

description: MVIC

source_name: human mitral valve interstitial cells

tag: age

value: human mitral valve interstitial cells (hMVICs)


title: LoTCEB12 gDNA_rep1


title: 442111A03 - WT_2 vs. mtr4_2

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: Identification and comparison of the RNA substrates that accumulate in hen2 and mtr4 mutants.

hyb_protocol: mtr4_2 Cy5 / WT_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: InnoScan900_MAPIX, Cy3:pmt voltage 532nm,650V,laser power 5%, Cy5:635nm,pmt voltage 700V,laser power 5%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.

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

growth_protocol: whole plant - Media   MS agar + 0.5% glucose  hygrometry   n.d.  Temperature   20°C  Light   16 h light/8h darkness

treatment_protocol: No treatment

tag: ecotype

value: Columbia

value: mtr4 mutant

tag: harvest date

value: wild-type


title: 442230A02 - hen2_2 vs. WT_2

hyb_protocol: WT_2 Cy5 / hen2_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype/variation

tag: genotype/variation = hen2 mutant


title: Ad-3

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

description: lncRNAs and mRNAs expression

hyb_protocol: Each labeled cRNA was fragmented and heated at 60°C for 30min,50ul hybridization solution was assembled to the lncRNA expression microarray slide and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent  DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Median normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies)

source_name: whole testis from Adult

label_protocol: Each sample was amplified and transcribed into Cy3 fluorescent cRNA without 3' bias utilizing a random priming method

extract_protocol: RNA were extracted using Trizol reagent and DNAase I treatment were performed to eliminate genomic DNA contamination, then mRNA was purified from total RNA after removal of rRNA

treatment_protocol: testes were freshly dissected out from embryonic or postnatal mice, snap freezed in liquid nitrogen and stored at -80 freezer.

value: whole testis

tag: developmental stage

value: Adult


title: 442217A02 - WT_1 vs. hen2_1

hyb_protocol: hen2_1 Cy5 / WT_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: hen2 mutant


title: Ad-1

description: lncRNAs and mRNAs expression


title: 442217A01 - mtr4_2 vs. WT_2

hyb_protocol: WT_2 Cy5 / mtr4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype/variation = mtr4 mutant


title: LoTCEB12 gDNA_rep3

value: enrichment


title: 442111A02 - mtr4_1 vs. WT_1

hyb_protocol: WT_1 Cy5 / mtr4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Ad-2

description: lncRNAs and mRNAs expression


title: P21-2

description: lncRNAs and mRNAs expression

source_name: whole testis from postnatal day 21

value: postnatal day 21


title: P21-3

description: lncRNAs and mRNAs expression


title: 442217A03 - hen2_1 vs. WT_1

hyb_protocol: WT_1 Cy5 / hen2_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Longssimus dorsi muscle_high-marbled steer_rep1


title: P21-1

description: lncRNAs and mRNAs expression


title: 442230A01 - WT_2 vs. hen2_2

hyb_protocol: hen2_2 Cy5 / WT_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: P14-3

description: lncRNAs and mRNAs expression

source_name: whole testis from postnatal day 14

value: postnatal day 14


title: Cebpg-/- MEFs at passage 3_biological replicate 3

city: FREDERICK

first: Peter

middle: F

last: Johnson

address: 1050 Boyles St

department: Center for Cancer Research

institute: National Cancer Institute

hyb_protocol: Four replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse 430 2.0 GeneChip

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000

data_processing: Following QC checks, microarray probe level data were normalized, background adjusted, and summarized with the RMA algorithm (Robust Multichip Analysis)

source_name: Mouse embryonic fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.  RNA was reverse transcribed with T7-oligo(dT) primer and biotin-labeled

growth_protocol: MEFs cells were passaged in DMEM supplemented with 10% FBS and pen/strep.

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

treatment_protocol: MEFs were isolated from E13.5 embryos and passaged 3 times prior to experiment plating and collection.

tag: cell type

value: MEFs

value: Cebpg-/-


title: Cebpg-/- MEFs at passage 3_biological replicate 4


title: Cebpg-/- MEFs at passage 3_biological replicate 1


title: Cebpg-/- MEFs at passage 3_biological replicate 2


title: WT MEFs at passage 3_biological replicate 3

value: wild type


title: WT MEFs at passage 3_biological replicate 1


title: WT MEFs at passage 3_biological replicate 2


title: WT MEFs at passage 3_biological replicate 4


title: P7-3

description: lncRNAs and mRNAs expression

source_name: whole testis from postnatal day 7

value: postnatal day 7


title: P14-1

description: lncRNAs and mRNAs expression


title: P14-2

description: lncRNAs and mRNAs expression