title: Mouse alveolar rhabdomyosarcoma 1

description: Affymetrix


title: renal-cortex_wild-type recipent_wildtype graft_repl.1

status: Public on Aug 27 2009

type: RNA

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Rat Genome RAE 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol EukGe-Ws2v5.

scan_protocol: GeneChips were scanned using the GeneChip System Confocal Scanner 3000.

data_processing: After probe set summarization using MAS5.0 algorithm in GCOS, expression raw data were transferred to GeneSpring GX software (7.3.1) to perform per Chip median normalization for signals which were flagged present or marginal.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: renal cortex, wildtype graft

label_protocol: Probes for Affymetrix microarray analysis were prepared using 4µg total RNA with GeneChip Expression 3´Amplification One Cycle Target labeling and Control Reagents Kits according to the manufacturers instructions (Affymetrix).

extract_protocol: Renal cortical tissue was snap frozen in liquid nitrogen and homogenized in Trizol reagent using a MIKRO Dismembrator S. For gene expression profiling RNA was prepared according to manufacturer´s TRIZOL protocol. RNA integrity was checked using RNA 6000 N

tag: LEWIS rat

tag: gender

value: male

tag: renal graft of wildtype LEWIS rats (controls)


title: colon_INT_T130_exon

city: Milano

first: James

middle: F

last: Reid

address: Via Adamello, 16

department: Molecular Genetics of Cancer

country: Italy

institute: Fondazione Istituto FIRC di Oncologia Molecolare

description: Gene expression data of sporadic colon cancer patient (INTcartella:9918729, INTistologico:289331I)

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures using Gene ChIP Scanner 3000.

data_processing: RMA implementation of Affymetrix Power Tools version 1.8.6 was used to analyze the 'core' subset of probes (HuEx-1_0-st-v2.r2.dt1.hg18.core.mps). All additional analysis was performed in R/Bioconductor and is available as a reproducible Sweave document from <http://pierotti.group.ifom-ieo-campus.it/suppl/crc.html>.

organism: Homo sapiens

source_name: Colon, RNA

label_protocol: Standard Affymetrix procedures.

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

value: F

tag: age

tag: dimension

tag: stage

value: IV

tag: status

tag: survival

tag: apc

tag: kras


title: renal-cortex_wild-type recipent_wildtype graft_repl.6


title: Methanol_Rep1, TA

city: Sherbrooke

first: Nathalie

last: Beaudoin

state: Quebec

address: 2500, Blvd Universite

department: Faculte des Sciences

country: Canada

institute: Universite de Sherbrooke

description: Control CEL files are the same as for the IXB treatment.

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Fluidics protocol EukGE_WS2v5_450

scan_protocol: GeneChip scanner

data_processing: Robust Multichip Average (RMA) via FlexArray software package (http://genomequebec.mcgill.ca/FlexArray). Data for TA treatment were processed separately from IXB treatment.

organism: Arabidopsis thaliana

source_name: 100mL suspension cells, 20µL methanol, 6h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana ecotype Landsberg erecta suspension cultured cells were grown in Murashige and Skoog (MS) medium (pH 5.7, 0.6 g L-1 MES) supplemented with B5 vitamins and 1 mg L-1 2,4-D. Cells were maintained in the dark under continuous shaking (gyratory shaker) at 120 rpm at 21ºC. Suspensions of 100 mL were sub-cultured weekly in 250mL flasks using 3:7 dilution.

extract_protocol: Cells were vacuum-filtered. Then 500 mg were ground in liquid N2 and mixed vigorously with hot extraction buffer consisting in one part of RNA buffer (100 mM Tris pH 8, 10 mM EDTA, 100 mM LiCl, 1% SDS) and one part of equilibrated phenol heated at 80°C. Samples were extracted with chloroform/isoamyl alcohol (24:1) and RNA was precipitated from the supernatant with 4 M LiCl. Pellets were resuspended in DEPC-treated water and extracted with phenol/chloroform/isoamyl alcohol (25:24:1). RNA was precipitated from the aqueous phase with 3 M sodium acetate and ethanol. RNA pellets were dissolved in DEPC-treated water.

treatment_protocol: TA diluted in methanol (10 mM) was added to Arabidopsis cell suspensions at a final concentration of 2 µM. The same volume of methanol (20 µL) was added to all cells. Treatments were carried out the third day after sub-culture, at the beginning of the exponential phase. Samples consisted of four replicates for each condition, and each replicate was the combination of two 250 mL flasks containing 100 mL of cells pooled together before freezing in liquid N2 after 6 h of contact with the inhibitor.

tag: agent

value: 20µL methanol

tag: genotype

value: Ecotype Landsberg erecta

tag: tissue

value: Suspension cells

value: Third day after subculture


title: Human.AT.CP.FCU

status: Public on Aug 26 2009

city: San Diego

first: Lucas

middle: Robert

last: Smith

state: CA

address: 3350 La Jolla Village Drive Mail Code 151

department: Bioengineering

country: USA

institute: University of California San Diego

description: gene expression data from cerebral palsy muscle

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS5) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The data were also analyzed with Robust Multiarray Analysis (RMA) and GC Robust Multiarray Analysis (GCRMA) using GeneSpring GX 7.3 (Agilent Technologies). The RMA and GCRMA data are available as supplementary files to the Series record.

label: Biotin

source_name: Flexor carpi ulnaris from cerebral palsy patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA

extract_protocol: Rneasy Kit (Qaigen) extraction of total RNA was performed

tag: Sex

tag: Age

tag: SL

tag: House

tag: Severity

value: SS

tag: Ashworth

tag: Zancolli

tag: PEFF

tag: PESF

tag: AEFF:


title: Human.BP.CTRL.FCU

value: C

tag: AEFF


title: Human.BF.CP.FCU

value: female

value: SM


title: Human.AZ.CTRL.FCU


title: Human.AT.CP.ECRB

source_name: Extensor carpi radialis brevis muscle from cerebral palsy patient


title: Human.AZ.CTRL.ECRB


title: memory P14 T cells #1

city: seattle

first: Ruka

last: Setoguchi

state: WA

address: 1959 NE Pacific Street

institute: University of Washington

description:
FACS sorted CD8 P14 memory cells.
This sample is called memory P14 T cells #1.

hyb_protocol: by the Center for Array Technologies (University of Washington, Seattle, WA)

data_processing:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are 2 groups, memory P14 and memory HD-/-P14 T cells. Each group has 2 biological replicates. The biological replicates are numbered #1 to #2.
MAS5.0.

organism: Mus musculus

source_name: Mouse Spleen CD8 T cells

extract_protocol: RNA was isolated with Trizol (Invitrogen) from FACS-sorted memory P14 T cells after enrichment of CD8 T cells using negative selection. RNA was prepared using RNeasy Mini Kit (Qiagen) before amplification.

tag: genotype/variation

value: wildtype ThPOK (control)


title: Human.AQ.CP.FCU

value: M


title: Human.AQ.CP.ECRB


title: Human.AO.CP.ECRB


title: Human.AO.CP.FCU


title: Human.AN.CP.ECRB


title: Human.AI.CP.ECRB


title: Human.AN.CP.FCU


title: synovium_CIA_ModerateJointInflammation_rep3

city: Basel

first: Anton

last: Glück

country: Switzerland

institute: Novartis Institutes for BioMedical Research

description: no additional information

hyb_protocol: see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001

data_processing: Affymetrix MAS 5.0, trimmed mean (trimming off the top and bottom 2%) set to 150

source_name: knee joint synovium, CIA, moderate swelling

label_protocol: Affymetrix protocol following the manufacturer's recommendations

extract_protocol: Qiagen RNeasy protocol following the manufacturer's recommendations

treatment_protocol: Mice were immunized with 100 ug type II collagen with FCA on day 0 and subsequently boosted on day 21 with 100 ug type II collagen i. p.

tag: 102 days old male DBA-1 mice


title: synovium_CIA_SevereJointInflammation_rep3

description: no additional information

scan_protocol: see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001

source_name: knee joint synovium, CIA, severe swelling


title: Human.BP.CTRL.ECRB


title: synovium_CIA_ModerateJointInflammation_rep2

description: no additional information


title: Human.AI.CP.FCU


title: synovium_CIA_SevereJointInflammation_rep1

description: no additional information


title: synovium_CIA_NoJointInflammation_rep2

description: no additional information

source_name: knee joint synovium, CIA, no swelling


title: synovium_CIA_ModerateJointInflammation_rep1

description: no additional information


title: synovium_CIA_NoJointInflammation_rep1

description: no additional information


title: synovium_CIA_MildJointInflammation_rep1

description: no additional information

source_name: knee joint synovium, CIA, mild swelling


title: synovium_naive_rep3

description: no additional information

source_name: knee joint synovium, healthy


title: synovium_naive_rep1

description: no additional information


title: synovium_CIA_NoJointInflammation_rep3

description: no additional information


title: synovium_naive_rep2

description: no additional information


title: Lung 1.0 mg C60 fullerene (HD) 180 days

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Lung, at 180days following intratracheal instillation, 1.0mgC60fullerene for HD (n=4)

hyb_protocol: The hybridization was performed according to the Agilent manufacturer’s instructions.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions, and were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution. The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1.

data_processing:
Normalized data is the average of n=4
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold raw signals to 1.0
Normalization algorithm: Percentile Shift
Normalization: Shift to 50 percentile

label_protocol: cRNA labeled with fluorescent Cyanine 3-CTP was used for hybridization onto the 4 X 44K Whole Rat Genome Oligo Multiplex Microarray slides (#G4131F, Agilent Technologies, Santa Clara, CA) containing approximately 41,000 oligonucleotide probes.

extract_protocol: The right lungs were homogenized with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen, Tokyo, Japan) following the manufacturer’s instructions. RNA quality and concentration were determined using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) and a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: gender

value: Male

tag: strain

value: Wistar

tag: age

value: 9 wk

value: right lung


title: liver_PQQ(-/+)_3

city: davis

first: eskouhi

last: Tchaparian

address: one shields avenue

institute: UC-Davis

description:
The repletion was accomplished by administering PQQ to PQQ deficient rats by i.p. injection at 1.5 mg PQQ/Kg body weight every 12 hours for a period of 36 hours.
1021_73569

hyb_protocol: Hybridization was performed using the CodeLink Expression Assay Reagent Kit and following the standard procedure for the Codelink Array Bioassays.

scan_protocol: Scanning and image analyses were performed with Axon’s 4000B using CodeLink’s Expression Analysis software.

data_processing: Data exported from the CodeLink analysis software was normalized using global Loess normalization where signal intensities from each array are Loess normalized to the average intensity of all arrays after removing high variance data points.  Data from the individual single-dye experimental and reference arrays were combined and intensity values averaged and compared within and between groups to generate gene expression ratios along with t-test p-values and intensity-based ratio Z-scores.  Clustering of the data was performed with a partitioning algorithm substantially similar to the CAST algorithm (34), but with a dynamically chosen threshold set to the 15th percentile value of 500 randomly chosen gene expression distances.  These gene expression distances were calculated as cosine angle distances between the gene expression fold change vectors.

source_name: liver, PQQ repletion

label_protocol: Labeling was performed using standard procedures and instructions for the Codelink® Array Bioassays. The biotin-labelled cRNA target was prepared by a linear amplification method. The poly(A)+ RNA subpopulation (within the total RNA population) was primed for reverse transcription by a DNA oligonucleotide containing the T7 RNA polymerase promoter 5′ to a d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT was performed in the presence of biotinylated nucleotides to label the target cRNA.

extract_protocol: Total RNA was isolated from the liver of each rat using Trizol reagent (Invitrogen, Carlsbad, CA) and further purified using Qiagen RNA mini-kits (Qiagen, Valencia, CA). On-column DNA digestion using RNAse Free DNAase kit (Qiagen, Valencia, CA) was performed to remove DNA residues.

treatment_protocol: The effects of PQQ depletion and repletion were assessed using male rat pups derived from Sprague-Dawley dams fed the basal ASD (deficient or supplemented with PQQ).  To produce PQQ deficiency, 10-week-old virgin Sprague-Dawley rats were mated and during the last 10 days of gestation, two-thirds of the rats were fed the basal ASD, while the remaining one-third were fed a PQQ supplemented diet (2 mg PQQ [6.67 nmol]/g diet).  Offspring were then assigned to and fed the same diets as their corresponding dams.  At 6 ½ weeks, half of the PQQ deficient (PQQ-) and supplemented rats (PQQ+) were next divided to generate short-term repleted (PQQ-/+) and depleted (PQQ+/-) groups.  The repletion was accomplished by administering PQQ by i.p. injection at 1.5 mg PQQ/Kg body weight every 12 hours for a period of 36 hours.  Short-term depletion was achieved by switching PQQ+ rats to the PQQ deficient diet for 48 hours.  The depletion study was conducted for 48 hours to allow a washout period for cellular PQQ reserves.  An additional group of rats (n=6) fed a standard laboratory chow diet were used as a reference.

value: Sprague-Dawley

value: male

tag: tissue

value: liver

tag: diet

value: PQQ repletion


title: liver_PQQ(-/+)_1

description:
The repletion was accomplished by administering PQQ to PQQ deficient rats by i.p. injection at 1.5 mg PQQ/Kg body weight every 12 hours for a period of 36 hours.
1019_73567


title: liver_chow_4

description:
Rats on standard laboratory chow diet as reference.
1016_73564

source_name: liver, standard laboratory chow

value: standard laboratory chow


title: liver_PQQ(-/+)_2

description:
The repletion was accomplished by administering PQQ to PQQ deficient rats by i.p. injection at 1.5 mg PQQ/Kg body weight every 12 hours for a period of 36 hours.
1020_73568


title: liver_chow_5

description:
Rats on standard laboratory chow diet as reference.
1017_73565


title: Human.BF.CP.ECRB

tag: Sex

tag: Age


title: Lung Control (HD) 90 days

description: Lung, at 90days following intratracheal instillation, Control group for HD (n=4)


title: synovium_CIA_MildJointInflammation_rep3

description: no additional information


title: Lung 1.0 mg C60 fullerene (HD) 90 days

description: Lung, at 90days following intratracheal instillation, 1.0mgC60fullerene for HD (n=4)


title: liver_chow_6

description:
Rats on standard laboratory chow diet as reference.
1018_73566


title: liver_PQQ(+/-)_3

description:
Depletion was achieved by switching PQQ+ rats to the PQQ deficient diet for 48 hours. The depletion study was conducted for 48 hours to allow a washout period for cellular PQQ reserves.
1015_73563

source_name: liver, PQQ depletion

value: PQQ depletion


title: liver_PQQ(+/-)_2

description:
Depletion was achieved by switching PQQ+ rats to the PQQ deficient diet for 48 hours. The depletion study was conducted for 48 hours to allow a washout period for cellular PQQ reserves.
1014_73562


title: Lung Control (HD) 7 days

description: Lung, at 7days following intratracheal instillation, Control group for HD (n=4)


title: Lung Control (HD) 180 days

description: Lung, at 180days following intratracheal instillation, Control group for HD (n=4)


title: synovium_CIA_MildJointInflammation_rep2

description: no additional information


title: Lung Control (HD) 30 days

description: Lung, at 30days following intratracheal instillation, Control group for HD (n=4)


title: liver_PQQ(+/-)_1

description:
Depletion was achieved by switching PQQ+ rats to the PQQ deficient diet for 48 hours. The depletion study was conducted for 48 hours to allow a washout period for cellular PQQ reserves.
1013_73561


title: liver_PQQ(-)_4

description:
PQQ deficient rats.
1005_73558

source_name: liver, PQQ deficient

value: PQQ deficient


title: Lung 1.0 mg C60 fullerene (HD) 30 days

description: Lung, at 30days following intratracheal instillation, 1.0mgC60fullerene for HD (n=4)


title: Lung 1.0 mg C60 fullerene (HD) 7 days

description: Lung, at 7days following intratracheal instillation, 1.0mgC60fullerene for HD (n=4)


title: liver_PQQ(-)_6

description:
PQQ deficient rats.
1010_73560


title: synovium_CIA_SevereJointInflammation_rep2

description: no additional information


title: liver_PQQ_3

description:
PQQ supplemented rats.
998_73551

source_name: liver, PQQ supplemented

value: PQQ supplemented


title: Lung 0.1 mg C60 fullerene (LD) 6 month

description: Lung, at 6month following intratracheal instillation, 0.1mgC60fullerene for LD (n=4)


title: Lung 0.1 mg C60 fullerene (LD) 3 month

description: Lung, at 3month following intratracheal instillation, 0.1mgC60fullerene for LD (n=3)

data_processing:
Normalized data is the average of n=3
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold raw signals to 1.0
Normalization algorithm: Percentile Shift
Normalization: Shift to 50 percentile


title: Lung 0.2 mg C60 fullerene (LD) 6 month

description: Lung, at 6month following intratracheal instillation, 0.2mgC60fullerene for LD (n=4)


title: Lung 1.0 mg C60 fullerene (HD) 3 days

description: Lung, at 3days following intratracheal instillation, 1.0mgC60fullerene for HD (n=4)


title: liver_PQQ(-/+)_4

description:
The repletion was accomplished by administering PQQ to PQQ deficient rats by i.p. injection at 1.5 mg PQQ/Kg body weight every 12 hours for a period of 36 hours.
1022_73570


title: Lung Control (LD) 6 month

description: Lung, at 6month following intratracheal instillation, Control group for LD (n=4)


title: liver_PQQ(-)_1

description:
PQQ deficient rats.
1002_73555


title: liver_PQQ_1

description:
PQQ supplemented rats.
996_73549


title: liver_PQQ_6

description:
PQQ supplemented rats.
1001_73554


title: Lung 0.2 mg C60 fullerene (LD) 1 month

description: Lung, at 1month following intratracheal instillation, 0.2mgC60fullerene for LD (n=4)


title: Lung Control (HD) 3 days

description: Lung, at 3days following intratracheal instillation, Control group for HD (n=4)


title: Lung 0.1 mg C60 fullerene (LD) 1 month

description: Lung, at 1month following intratracheal instillation, 0.1mgC60fullerene for LD (n=4)


title: liver_chow_3

description:
Rats on standard laboratory chow diet as reference.
995_73548


title: liver_PQQ_5

description:
PQQ supplemented rats.
1000_73553


title: Lung 0.2 mg C60 fullerene (LD) 3 month

description: Lung, at 3month following intratracheal instillation, 0.2mgC60fullerene for LD (n=2)

data_processing:
Normalized data is the average of n=2
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold raw signals to 1.0
Normalization algorithm: Percentile Shift
Normalization: Shift to 50 percentile


title: liver_PQQ_4

description:
PQQ supplemented rats.
999_73552


title: Lung 0.2 mg C60 fullerene (LD) 1 week

description: Lung, at 1week following intratracheal instillation, 0.2mgC60fullerene for LD (n=5)

data_processing:
Normalized data is the average of n=5
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold raw signals to 1.0
Normalization algorithm: Percentile Shift
Normalization: Shift to 50 percentile


title: Lung 0.1 mg C60 fullerene (LD) 1 week

description: Lung, at 1week following intratracheal instillation, 0.1mgC60fullerene for LD (n=4)


title: 2221sRNA3

status: Public on Aug 25 2009

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

description: MGAS2221 chip 3

hyb_protocol: Labeled cDNA was hybridized to a custom array for 16h at 40 degrees C.  GeneChips were washed and stained using  the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneArray Scanner G2500A.

data_processing:
Data was quantile normalized and analyzed with Tiling Analysis Software (TAS).  Data from the three arrays were combined to  generate signal intensities. Signal and p-values are reported in BAR files, which are linked to the Series GSE17789 record as supplementary files.
The BAR files are generated by TAS software using PM/MM signal intensities.  Signal intensity data is reported in a linear scale while the p-value is reported in -10log10 scale.  Probe analysis used a bandwidth of 40.  Interval analysis used a threshold of 0, a maximum gap of 20, and a minimum run of 60.

organism: Streptococcus pyogenes

source_name: MGAS2221 culture 3 grown to an O.D.600 of 0.5

label_protocol: RNA was converted to cDNA, the cDNA was fragmented, and the cDNA labeled with biotin.

growth_protocol: MGAS2221 cultures were grown in THY broth to O.D. 600 of 0.5 (exponential phase).

extract_protocol: Total RNA was extracted via mechanical disruption and purified using the Qiagen Rneasy kit.

treatment_protocol: Two volumes of RNAprotect was added to each culture, incubated at RT for 5 mins, centrifuged, a bacterial cell pellet quick frozen in liquid nitrogen.

tag: serotype

value: M1 GAS

tag: growth phase

value: exponential phase


title: liver_PQQ(-)_5

description:
PQQ deficient rats.
1006_73559


title: Control 2R

city: Charlestown

first: Okay

last: Saydam

address: Building 149, 13th st. 6th Floor, Room:6101

department: Neurology

institute: MGH

description:
LMW RNA
Control 2

hyb_protocol: For hybridization, membranes were first prehybridized in MicroHyb Hybridization Buffer (Invitrogen) at 37ºC for 30 min followed by an overnight hybridization in the same solution containing RNA probes.

scan_protocol: Following hybridization, membranes were washed and exposed to a phosphor storage screen, scanned using a Phosphor Imager (Massachusetts General Hospital, core facility), and hybridization signals were quantified using ImageQuant software (Molecular Dynamics).

data_processing:
RNA samples were considered independent measurements for the purposes of the two-tailed, two-sample t test. Probe signals that showed high variance in technical replicates (more than 2-fold with p values >0.05) were excluded from further analysis. miRNA array data was first normalized using median-centric method within BRBArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html) and was further subjected to quantile normalization in Partek Genomics Suite (http://www.partek.com/). Differentiated miRNA lists comparing expression in control to all meningioma samples for miRNA arrays were generated using the significance analysis of microarrays (SAM) method (43) with cutoffs for FDR <30% and p value <0.05. The normalized array data for the derived differentiated miRNAs list was then transformed to z-scores for data of each miRNA across samples using WPS utility program (46), which was subjected to heatmap clustering analysis and visualization using TM4 program from TIGR (http://www.tm4.org/).

The quantile-normalized data is in the table on GSE17792.

source_name: Arachnoid Tissue

label_protocol: The LMW RNA was end-labeled with 30 µCi у33-P dATP (3000 Ci/mmole) by T4 polynucleotide kinase (New England Biolabs, Ipswich, MA) and purified using the Qiagen Nucleotide Removal Kit (Valencia, CA).

growth_protocol: Not applicable.

extract_protocol: Total RNA was isolated from tissues with Trizol (Invitrogen). RNA labeling and hybridization on a microarray was performed as previously described (21,27).  Briefly, 10 mg total RNA from each sample were filtered through Microcon YM-100 concentrators to obtain a low molecular weight (LMW) fraction of RNA enriched in molecules under 60 bp.

treatment_protocol: Not applicable.

value: arachnoid


title: Control 3R

description:
LMW RNA
Control 3


title: Control 3L

description:
LMW RNA
Control 3


title: 3002 R

description:
LMW RNA
Patient 13

source_name: Human Meningioma Tumor

value: meningioma

tag: nf2 association

value: NF2 positive


title: Control 1R

description:
LMW RNA
Control 1


title: Lung Control (LD) 3 month

description: Lung, at 3month following intratracheal instillation, Control group for LD (n=6)

data_processing:
Normalized data is the average of n=6
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold raw signals to 1.0
Normalization algorithm: Percentile Shift
Normalization: Shift to 50 percentile

value: Male


title: Control 1L

description:
LMW RNA
Control 1


title: 3016 R

description:
LMW RNA
Patient 14


title: liver_chow_2

description:
Rats on standard laboratory chow diet as reference.
994_73547


title: liver_PQQ(-)_3

description:
PQQ deficient rats.
1004_73557


title: Lung Control (LD) 1 week

description: Lung, at 1week following intratracheal instillation, Control group for LD (n=3)

value: Wistar


title: Lung Control (LD) 1 month

description: Lung, at 1month following intratracheal instillation, Control group for LD (n=5)

value: 9 wk


title: liver_chow_1

description:
Rats on standard laboratory chow diet as reference.
993_73546


title: 2221sRNA1

description: MGAS2221 chip 1

source_name: MGAS2221 culture 1 grown to an O.D.600 of 0.5


title: 2221sRNA2

description: MGAS2221 chip 2

source_name: MGAS2221 culture 2 grown to an O.D.600 of 0.5


title: liver_PQQ_2

description:
PQQ supplemented rats.
997_73550


title: Control 2L

description:
LMW RNA
Control 2


title: ada mutant MMS at 3.9 h

city: Bethesda

first: Jonghwan

last: Baek

state: MD

address: 37 Convent Dr

department: NCI

institute: NIH

hyb_protocol: 1.	Dissolve the dried labeled sample in a reasonable volume of hybridization buffer depending on the area to be covered. (Typically, 22X22mm cover-slip requires 25 ㎕ of hybridization buffer. 22X60mm cover-slip requires 60 ㎕). 2.	Heat the labeled sample preparation for 5min at 95℃. 3.	Spin down for 30 sec. Do not put on ice!!! 4.	Place slide in the hybridization chamber. Put 20㎕ of 3XSSC to the chamber at both ends of the slide. 5.	Pipette the labeled target onto the slide surface. 6.	Carefully place the cover-slip on top of the slide. Try to reduce the formation of air bubbles. 7.	Seal the hybridization chamber and incubate in 42℃. Water-bath or hybridization oven for more than 16 hr.

scan_protocol: DNA chips were scanned using an Axon GenePix 4000B Scanner(Axon Instruments, Union City, CA, USA) with the laser set to 532 and 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 µm.

data_processing: Scanned images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA) to obtain gene expression ratios. The signal intensities higher than the mean background intensities by 3-fold greater than the overall standard deviation were chosen. Global normalization was carried out by dividing each of fluorescence intensities by their sums. The expression level of each gene was normalized to the variance of 1.

organism: Escherichia coli K-12

source_name: Cy5 ada mutant with MMS at 3.9 h

label_protocol:
Indirectly labelled using the recommended protocol provided by Digital genomics (Korea)
1.	To 45 ug of total RNA, add necessary control RNA mixture and 2ul of oligo(dT) primer (0.5ug/ul ). Make the final volume up to 31uL with RNase-free water. For human and mouse RNA samples, 20ug of total RNA is sufficient for hybridization in ASP. For Drosophila RNA sample, 50 ug of total RNA is needed for ASP. For less amount of RNA, hybridization should be performed mannually in a smaller volume of hybridization buffer.
2.	Mix well and incubate at 70 degrees C for 10 minutes. Chill on ice for 1 min. Spin briefly.
3.	Add followings to the RNA solution:
5X First Strand buffer	 10uL
0.1 M DTT	 5uL
Rnasin	 1uL
50X aminoallyl-dNTP mix	1uL
SuperScript II (200U/uL)	 2uL
4.	Mix and incubate at 42 °C for 1 hr. Add additional 1ul of superscript II and incubate for another 1 hr.
5.	To hydrolyze RNA, add 16.5ul of 1 M NaOH and 16.5ul of 0.5 M EDTA. Mix and incubate at 65 °C for 15 minutes. Add 16.5uL of 1 M HCl to neutralize pH.
6.	Clean-up the cDNA reaction with Microcon YM-30 (Cat No. 42409)
7.	Dry sample in a speed vac. Add D.W. and 1M sodium carbonate buffer to resuspend cDNA pellet in 9.0ul of 0.1M sodium carbonate buffer
8.	Add 2.0uL of the appropriate NHS-ester Cy dye
9.	Incubate the reaction for 1 hour in the dark at room temperature.
10.	Clean up the coupling reaction with QIAquick PCR purification kit. Repeat the elution step twice with 30uL elution buffer to get 60uL of elution volumn.

growth_protocol: 100 ml LB medium, 37 degree C, 250 rpm shaking

extract_protocol: RNA extraction kit (RNeasy mini kit, Qiagen, USA) was used according to the manufacturer's protocol

tag: genotype

value: ada deletion mutant

tag: sampling point

tag: treatment

value: MMS

source_name: Cy3 ada mutant without MMS at 3.9 h

value: untreated


title: 2455 R

description:
LMW RNA
Patient 10


title: 4173 R

description:
LMW RNA
Patient 9


title: 2977 R

description:
LMW RNA
Patient 11


title: 2994 R

description:
LMW RNA
Patient 12


title: 3858 R

description:
LMW RNA
Patient 8


title: 3771 R

description:
LMW RNA
Patient 7

value: NF2 negative


title: 3009 R

description:
LMW RNA
Patient 5


title: 1670 R

description:
LMW RNA
Patient 6


title: 3633 R

description:
LMW RNA
Patient 4


title: ada mutant MMS 1.5 h

source_name: Cy5 ada mutant with MMS at 1.5 h

source_name: Cy3 ada mutant without MMS at 1.5 h


title: wildtype MMS 3.9 h

source_name: Cy5 wildtype with MMS at 3.9 h

value: wildtype

source_name: wildtype without MMS at 3.9 h


title: wildtype MMS at 1.5 h

source_name: Cy5 wildtype with MMS

source_name: Cy3 wildtype without MMS


title: ada mutant MMS at 0.5 h

source_name: Cy5 ada mutant with MMS at 0.5 h

source_name: Cy3 ada mutant without MMS at 0.5 h


title: ada mutant vs. wildtype

source_name: Cy5 mutant

source_name: Cy3 wildtype


title: 4263 R

description:
LMW RNA
Patient 3


title: wildtype MMS at 0.5

source_name: Cy5 wildtype with MMS at 0.5 h

source_name: Cy3 wildtype without MMS at 0.5


title: 3002 L

description:
LMW RNA
Patient 13

source_name: Human Meningioma Tumor


title: 3731 R

description:
LMW RNA
Patient 1


title: 3016 L

description:
LMW RNA
Patient 14


title: 3871 R

description:
LMW RNA
Patient 2


title: 2994 L

description:
LMW RNA
Patient 12


title: 2455 L

description:
LMW RNA
Patient 10


title: 3858 L

description:
LMW RNA
Patient 8


title: 4173 L

description:
LMW RNA
Patient 9


title: 2977 L

description:
LMW RNA
Patient 11


title: 3771 L

description:
LMW RNA
Patient 7


title: 3009 L

description:
LMW RNA
Patient 5


title: 3633 L

description:
LMW RNA
Patient 4


title: 3871 L

description:
LMW RNA
Patient 2


title: 4263 L

description:
LMW RNA
Patient 3


title: 3731 L

description:
LMW RNA
Patient 1


title: E coli LY180_w 0.5g/L Furfural_rep2

city: Gainesville

first: Peter

middle: Christopher

last: Turner

state: FL

address: Bldg 981, Museum Road

department: Micro and Cell Science

institute: University of Florida

description: This data is the second of 2 replicates (OID 14117)

hyb_protocol: Hybridization was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen 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 (Roche NimbleGen, Inc.).

organism: Escherichia coli

source_name: LY180 + furfural

label_protocol: Conversion of RNA to cDNA and labeling with Cy3 was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown in AM1 medium with 10% xylose to OD 550 = 1.5 (0.66 g dcw/liter). 4 replicate 350 ml fermentors per strain.

extract_protocol: Cells were chilled in dry ice/ethanol, centrifuged, and the pellet resuspended in RNA Later (Qiagen) before storing at –80 C. Total RNA was extracted using the RNeasy Mini kit (Qiagen), and DNA was removed by digestion with RNase-Free DNase I. RNA quality and concentration was checked with an Agilent bioanalyzer at the University of Florida Gene Expression core before submitting the RNA to Roche Nimblegen in Iceland for analysis.

treatment_protocol: Samples were taken at OD = 1.5, then furfural added to 0.5 g/L. Samples were taken at 15 min after furfural addition.

value: wild-type (ethanologenic)


title: E coli EMFR9_w 0.5g/L Furfural_rep2

source_name: EMFR9 + furfural

value: furfural resistant mutant


title: E coli EMFR9_rep2


title: E coli LY180_rep2


title: H2A.Z ChIP in  ∆msc1 cells

type: genomic

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: H2A.Z ChIP in  ∆msc1 cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated by anti-FLAG (M2; Sigma) antibody. Immunoprecipitated DNA was recovered by incubation with protein A or G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 18˚C.

tag: cells for ip

value: pht1-3xflag  ∆msc1 cells

source_name: input DNA


title: H2A.Z ChIP in wild-type cells

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

source_name: H2A.Z ChIP in wild-type cells

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated by appropriate antibody: H2A.Z-FLAG (M2; Sigma), Pol II (8WG16; Covance), and Rik1-Myc (A14: Santa Cruz). Immunoprecipitated DNA was recovered by incubation with protein A or G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 18˚C and chromatin proteins crosslinked by treatment with 10mM dimethyl adipimidate (crosslinking step was carried out only for Rik1 ChIP).

value: pht1-3xflag cells

value: wild type


title: 1670 L

description:
LMW RNA
Patient 6


title: Rik1 ChIP in  wild-type cells

source_name: Rik1 ChIP in  wild-type cells

value: rik1-13xmyc cells


title: H2A.Z ChIP in  wild-type

source_name: H2A.Z ChIP in  wild-type


title: Pol II ChIP in wild-type cells

source_name: Pol II ChIP in wild-type cells

value: wild-type cells


title: clr6-1 cells

hyb_protocol: Equal amounts of Cy5-labeled mutant cDNA and Cy3-labeled wild-type cDNA were mixed and combined with human Cot1DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

data_processing: Data were extracted using Agilent Feature Extraction Software (GE2-v5_95_Feb07 protocol) and subjected to combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

source_name: log. growing cells

label_protocol: Ribosomal RNA was depleted with RiboMinus kit (Invitrogen) and total RNA reverse-transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen).

extract_protocol: Total RNA was extracted using Master Pure Yeast RNA purification kit (Epicenter) according manufacturer's instructions.

value: clr6-1 cells


title: ∆set2 cells

value: ∆set2 cells


title: liver_PQQ(-)_2

description:
PQQ deficient rats.
1003_73556

source_name: liver, PQQ deficient

value: Sprague-Dawley

value: male

value: liver

value: PQQ deficient


title: The pqqE disruption mutant vs wild type under normal growth conditions_Rep1

city: Mumbai

first: Hari

middle: S

last: Misra

state: MS

address: 2-46 S, Moldular Laboratories, Central Avenue, Bhabha Atomic Research Centre

department: Molecular Biology Division

country: India

institute: Bhabha Atomic Research Centre

description:
pqqE mutant: Sensitive to gamma radiation and oxidative stress and defective in DSB repair
Wild type: Extreme resistance to gamma /UV/ desiccation/ oxidative stresses.
pqqE mutant unirradiated

hyb_protocol: The Cy3 and Cy5 labeled cDNA targets applied to microarrays kept in hybridization chambers. After hybridization, the slides were washed sequentially and Dye-swap is carried out.

scan_protocol: Scanned on a GenePix 4000B scanner. Immages were quantified using GenePix (version 5.0)

data_processing: Prior to channel normalization, microarray outputs were filtered to remove spot of poor signal quality by excluding those data points with a signal mean intensity less than two standard deviations above background. LOWESS normalized, background subtracted data obtained from log 2 of processed Red signal/ processed Green Signal by using Limma Software. Furthermore, the replicate spota on each array were merged to one value using lmFit function within Limma.

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

source_name: pqqE mutant

label_protocol: Approximately 10 mg of total RNA was annealed with 9 mg of hexadeoxyribonucleotide mixture at 70oC for 10 min. The RNA-DNA duplex was incubated with 100 mM of dGTP, dATP, dTTP with 25mM dCTP and 25mM Cy3 label, and 400 Units SuperScript II reverse transcriptase (Invitrogen) at 42oC for 3h.

growth_protocol: Cells were grown in under normal conditions in TGY medium

extract_protocol: Total RNA was extracted using Trizol following manufacturers protocols

treatment_protocol: Normal growth in TGY medium

value: pqqE mutant

tag: stress

value: unirradiated

label: Cyanine 3

source_name: Wild type


title: wild-type cells


title: The dr2518 knockout strain vs wild type under gamma irradiated conditions_Reps 3&4

description:
dr2518 mutant: A quinoprotein mem brane kinase stimulated by an antioxidant metabolites being made in this bacterium was found to be involved in radioresistance and DSB repair in Deinococus radiodurans. A possilbity of pyrroloquinoline -quinone acting as sensor of oxidative stress of gamma iradiation could be suggested.
wild type: Extreme tolerance to gamma/ MMC/ UVC/ Desiccation/hydrogen peroxide and effiicent DSB repair.
dr2518 mutant irradiated

scan_protocol: Scanned on a GenePix 4000B scanner. Immages were quantified using GenePic (version 5.0)

label: Cyanine 5

source_name: dr2518 mutant

label_protocol: Approximately 10 mg of total RNA was annealed with 9 mg of hexadeoxyribonucleotide mixture at 70oC for 10 min. The RNA-DNA duplex was incubated with 100 mM of dGTP, dATP, dTTP with 25mM dCTP and 25mM Cy5 label, and 400 Units SuperScript II reverse transcriptase (Invitrogen) at 42oC for 3h.

growth_protocol: Cells were grown at 30oC till late logarithmic phase in TGY medium under standard condition of this organism

treatment_protocol: gamma treated cells

tag: genotype/variation

value: dr2518 mutant

value: gamma irradiation

source_name: wild type


title: The pqqE disruption mutant vs wild type under gamma irradiated conditions_Rep 2

description:
pqqE mutant: Sensitive to gamma radiation and oxidative stress and defective in DSB repair
Wild type: Extreme resistance to gamma /UV/ desiccation/ oxidative stresses.
pqqE mutant irradiated

treatment_protocol: Cell were irradiated with 6.5 kGy gamma radiation


title: ∆alp13 cells

value: ∆alp13 cells


title: ∆pht1∆swi6 cells rep2


title: The dr2518 mutant vs wild type under normal growth conditions_Reps 1&2

description:
dr2518 mutant: A quinoprotein mem brane kinase stimulated by an antioxidant metabolites being made in this bacterium was found to be involved in radioresistance and DSB repair in Deinococus radiodurans. A possilbity of pyrroloquinoline -quinone acting as sensor of oxidative stress of gamma iradiation could be suggested.
wild type: Extreme tolerance to gamma/ MMC/ UVC/ Desiccation/hydrogen peroxide and effiicent DSB repair.
dr2518 mutant unirradiated

treatment_protocol: Unirradiated control


title: ∆set1 cells


title: ∆pht1∆set1 cells


title: ∆cph1∆pht1 cells

value: ∆cph1∆pht1 cells


title: drb0090 knockout strain vs wild type under gamma irradiated conditions_Reps 3&4

description:
drb0090 mutant: Two component system role in radioresistance and DSB repair. The drb0090 mutant is sensitive to gamma, MMC and higher doses of UVC radiation and recombinant DRB0090 protein phosphorylate its cognate response regulator.
wild-type: Extreme tolerance to gamma/ MMC/ UVC/ Desiccation/hydrogen peroxide and effiicent DSB repair
drb0090 mutant gamma treated

source_name: drb0090 mutant

value: drb0090 mutant


title: ∆cph1 cells

value: ∆cph1 cells


title: ∆swi6 cells


title: ∆swr1 cells


title: Soleus_HS-7days_rep2

city: Lexington

first: Esther

middle: E.

last: Dupont-Versteegden

state: KY

address: 900 S. Limestone

department: Rehabilitation Sciences

institute: University of Kentucky

description: Each chip contained 234 rat microRNA probes (Sanger miRBase 9.0) plus an additional 96 probes derived from predicted rat miRNAs. Supplementary RAW data files were provided by LC Sciences.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

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

data_processing: Expression values were normalized by removing system related variation (sample amount variations, different labeling dyes and signal gain differences of scanners) using a locally weighted regression (cyclic LOWESS). Data adjustment included data filtering, log2 transformation, gene centering and normalization. The data filtering removed miRs with normalized intensity values below a threshold value (twice the maximum background signal) across all samples. The log2 transformation converted intensity values into log2 scale. Gene centering and normalization transformed the log2 values using the mean and the standard deviation of individual genes across all samples using the following formula: Value = [(Value) - Mean (Gene)] / [Standard deviation (Gene)]. The "A" associated with the Density measurement represents arbitrary units, and Density is a measure of the average signal intensity for each specific spot on the array.

source_name: rat soleus muscle, hindlimb suspension 7 days

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  The assay started from 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.

growth_protocol: Rats were allowed free access to food and water, and were housed in a 12:12-h light-dark cycle.

extract_protocol: Total RNA was isolated from rat soleus muscle using ToTALLY RNA (Ambion, Austin, TX) according to manufacturer’s directions. RNA samples were treated with TURBO DNase to remove genomic DNA contamination and RNA integrity was assessed using the Agilent 2100 bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA); the average RIN (RNA integrity number) value for all samples was 8.4 ± 0.5 (scale 1-10) indicating high quality RNA with minimal degradation.

treatment_protocol: To induce muscle atrophy, rats were hindlimb suspended for 2 or 7 days. A tail device containing a hook was attached with gauze and cynoacrylate glue while the animals were anesthetized with pentobarbital sodium (50 mg/kg body wt). After the animal regained consciousness, the tail device was connected via a thin cable to a pulley sliding on a vertically adjustable stainless steel bar running longitudinally above a high-sided cage with standard floor dimensions. The system was designed in such a way that the rats could not rest their hindlimbs against any side of the cage but could reach their food and water without difficulty.

value: 6 months

value: soleus muscle


title: ∆pht1∆swi6 cells rep1

value: wild-type cells


title: Soleus_HS-7days_rep1


title: Soleus_HS-7days_rep3


title: ∆cid14 cells


title: drb0090 knockout strain vs wild type under normal growth conditions_Reps 1&2

description:
drb0090 mutant: Two component system role in radioresistance and DSB repair. The drb0090 mutant is sensitive to gamma, MMC and higher doses of UVC radiation and recombinant DRB0090 protein phosphorylate its cognate response regulator.
wild-type: Extreme tolerance to gamma/ MMC/ UVC/ Desiccation/hydrogen peroxide and effiicent DSB repair
drb0090 mutant normal growth

value: wild type


title: ∆rrp6 cells rep2

value: ∆rrp6 cells


title: ∆rrp6 cells rep1


title: Soleus_HS-2days_rep3

source_name: rat soleus muscle, hindlimb suspension 2 days

value: Sprague-Dawley


title: Soleus_HS-2days_rep2

value: male


title: Soleus_HS-2days_rep1


title: Soleus_control_rep1

source_name: rat soleus muscle, control


title: Soleus_control_rep3


title: Soleus_control_rep2


title: rik1 cells

value: rik1 cells


title: Strain 2221ΔPEL in THY, stationary, sample B

description: 2221ΔPEL T2 B

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

source_name: PEL mutant, stationary phase

growth_protocol: GAS strains were grown in THY broth to O.D. 600 of 0.5 (exponential phase) or 1.7 (stationary phase).

treatment_protocol: Two volumes of RNAprotect was added to each strain, incubated at RT for 5 mins, centrifuged, a bacterial cell pellet quick frozen in liquid nitrogen.

value: PEL mutant

value: stationary phase


title: Strain 2221ΔPEL in THY, stationary, sample A

description: 2221ΔPEL T2 A


title: ∆pht1∆clr4 cells rep1

value: ∆pht1∆clr4 cells


title: ∆clr4 cells

value: ∆clr4 cells


title: ∆pht1rik1 cells


title: Strain MGAS2221 in THY, stationary, sample C

description: MGAS2221 T2 C

source_name: WT, stationary phase

value: WT


title: Disc Cells 30

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

description: Grown in 3-D construct.

hyb_protocol: Fragmented cRNA was hybridized to the  X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned once via the Affymetrix 3000G scanner.

data_processing: The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).

source_name: Disc Cells

label_protocol: Biotin-labeled cRNA were prepared according to the Affymetrix protocol for IVT labeling.

growth_protocol: Cells were grown in a 3-D construct (Gelfoam, Pharmacia & Upjohn Co. Kalamazoo, MI) for 2-3 weeks.

extract_protocol: Total RNA was  harvested according to instructions with the Trizol isolation method.

treatment_protocol: Stem cells were treated with or without 10ng/nl TGF-B3.

value: disc tissue

tag: cell type

value: disc cells

value: Without TGF-B


title: Disc Cells 27

description: Grown in 3-D construct.


title: ∆pht1 cells rep2

value: ∆pht1 cells


title: ∆pht1∆ago1 cells rep2

value: ∆pht1∆ago1 cells


title: Disc Cells 23

description: Grown in 3-D construct.


title: ∆pht1 cells rep1


title: Disc Cells 24

description: Grown in 3-D construct.


title: ∆ago1 cells

value: ∆ago1 cells


title: ∆pht1∆ago1 cells rep1

value: wild-type cells


title: ∆clr4 cells rep2


title: Strain 2221ΔPEL in THY, exponential, sample C

description: 2221ΔPEL T1 C

source_name: PEL mutant, exponential phase

value: exponential phase


title: Strain MGAS2221 in THY, stationary, sample B

description: MGAS2221 T2 B


title: Strain 2221ΔPEL in THY, exponential, sample B

description: 2221ΔPEL T1 B


title: Strain MGAS2221 in THY, stationary, sample A

description: MGAS2221 T2 A


title: CSHL_9_Cyto_Aminus

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

source_name: Poly-A- cytoplasmic RNA

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 STarrays

extract_protocol: RNA was prepared by the ENCODE Transcriptiome group

tag: cell line

tag: fraction

value: Cytoplasmic RNA


title: CSHL_4_Nuclear_Total

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays

source_name: total nuclear RNA

value: Nuclear RNA


title: CSHL_8_Cyto_Aplus

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays

source_name: Poly-A+ cytoplasmic RNA


title: CSHL_7_Cyto_Total

source_name: total cytoplasmic RNA


title: Strain 2221ΔPEL in THY, exponential, sample A

description: 2221ΔPEL T1 A

tag: strain


title: Strain MGAS2221 in THY, exponential, sample B

description: MGAS2221 T1 B

source_name: WT, exponential phase


title: Disc Cells 22

description: Grown in 3-D construct.

tag: tissue


title: CSHL_6_Nuclear_Aminus

source_name: Poly-A- nuclear RNA


title: Disc Cells 18

description: Grown in 3-D construct.


title: Disc Cells 19

description: Grown in 3-D construct.


title: Stem Cells TGF-B 207

description: Grown in 3-D construct.

source_name: Stem Cells with TGF-B

value: adipose tissue

value: mesenchymal stem cells

value: With TGF-B


title: CSHL_3_K562_Aminus

source_name: Poly-A- whole cell RNA

value: Whole Cell RNA


title: Strain MGAS2221 in THY, exponential, sample C

description: MGAS2221 T1 C


title: Strain MGAS2221 in THY, exponential, sample A

description: MGAS2221 T1 A


title: CSHL_2_K562_Aplus

source_name: Poly-A+ whole cell RNA


title: Stem Cells Control 207

description: Grown in 3-D construct.

source_name: Stem Cells


title: CSHL_5_Nuclear_Aplus

source_name: Poly-A+ nuclear RNA


title: Stem Cells Control 79

description: Grown in 3-D construct.


title: Stem Cells TGF-B 168

description: Grown in 3-D construct.


title: Stem Cells Control 168

description: Grown in 3-D construct.


title: CSHL_1_K562_Total

source_name: total whole cell RNA


title: Stem CellsTGF-B 79

description: Grown in 3-D construct.


title: smoke-butenolide 24h, rep 2

status: Public on Aug 24 2009

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

hyb_protocol: The dye-labelled probes were cleaned up (Qiagen), mixed with the corresponding samples, concentrated, resuspended in the hybridization solution containing formamide and incubated at 42 °C overnight in a hybridization oven. Finally, slides were washed with different concentrations of  SSC at room temperature.

scan_protocol: Scanning was performed using an Amersham Typhoon Trio+ scanner with default settings. The detection of signal intensities and the grid adjustment were accomplished with ArrayVision software version 8.0 (Amersham). The intensity value of each spot and background region, multiplied by its area was used as signal intensity for further analysis.

data_processing: Raw intensity data were imported into the R 2.9.0 software after preprocessing it with custom made Perl scripts. Further analysis was carried out using the LIMMA package of BIOCONDUCTOR. Background correction was done using the normexp method. Normalization of data within arrays was done using the ‘loess’ method. To normalize the data between arrays the ‘quantile’ method was used. The microarray data for each gene were fitted to a linear model, and statistics were generated using the lmFit and eBayes functions of the LIMMA package. The P values were adjusted for multiple testing using the Benjamini and Hochberg method. Genes with fold change ≥ 2 were considered as differentially expressed.

organism: Zea mays

source_name: smoke-water treated maize kernel, 24h after germination

label_protocol: 400 ng total RNA was amplified and aminoallyl-UTP was incorporated using 101 TargetAmp Kit (Epicentre) and the resulting aaRNA was labelled with Cy3 and Cy5 (Amersham).

growth_protocol: The kernels were decontaminated in 3% sodium hypochlorite containing Tween 20 and 70% EtOH (10 min each). For germination, each treatments consisted of six biological replicates (15 kernels in each), and seeds were germinated in a controlled environmental chamber (25 °C, 100 µmol m–2 s–1 light intensity).

extract_protocol: For RNA isolation from control and smoke (1:1000) and butenolide-treated kernels, identical conditions were applied as for the germination tests and embryos were harvested 1,5, 3, 6,9,12, and 24 h after treatment. At 24h, only the kernels with ruptured testa were selected for further experiments. Total RNA was isolated from the maize kernel embryo axes (without scutellum) using TRIzol reagent (Invitrogen) and cleaned up with Qiagen RNeasy Plant Mini Kit (Qiagen) applying a few modifications. RNA was then treated with RNase-free DNase I (Qiagen) according to the manufacturer’s instructions. The RNA Integrity Number (RIN) of the samples was determined using the Agilent BioAnalyzer. Only samples with a RIN ≥ 8 were considered for further analysis.

treatment_protocol: The batches of kernels were submerged into 20 ml water (control), 1:1000 (v/v) dilution of smoke-water and 0,1 µM butenolide.

value: Embryo

tag: age

source_name: butenolide-water treated maize kernel, 24h after germination


title: control-butenolide 24h, rep 3

source_name: control maize kernel, 24h after germination


title: smoke-butenolide 24h, rep 3


title: control-butenolide 24h, rep 2


title: control-butenolide 12h, rep 1

source_name: control maize kernel, 12h after germination

source_name: butenolide-water treated maize kernel, 12h after germination


title: control-butenolide 12h, rep 3


title: smoke-butenolide 9h, rep 3

source_name: smoke-water treated maize kernel, 9h after germination

source_name: butenolide-water treated maize kernel, 9h after germination


title: smoke-butenolide 6h, rep 3

source_name: smoke-water treated maize kernel, 6h after germination

source_name: butenolide-water treated maize kernel, 6h after germination


title: smoke-butenolide 24h, rep 1


title: smoke-butenolide 12h, rep 3

source_name: smoke-water treated maize kernel, 12h after germination


title: control-butenolide 24h, rep 1


title: smoke-butenolide 12h, rep 1


title: control-butenolide 12h, rep 2


title: smoke-butenolide 9h, rep 1


title: smoke-butenolide 12h, rep 2


title: control-butenolide 9h, rep 3

source_name: control maize kernel, 9h after germination


title: control-butenolide 9h, rep 2


title: smoke-butenolide 3h, rep 3

source_name: smoke-water treated maize kernel, 3h after germination

source_name: butenolide-water treated maize kernel, 3h after germination


title: control-butenolide 9h, rep 1


title: smoke-butenolide 9h, rep 2


title: smoke-butenolide 3h, rep 2


title: control-smoke 27h, rep 2

source_name: control maize kernel, 27h after germination

source_name: smoke-water treated maize kernel, 27h after germination


title: smoke-butenolide 6h, rep 1


title: control-butenolide 6h, rep 3

source_name: control maize kernel, 6h after germination


title: control-butenolide 3h, rep 3

source_name: control maize kernel, 3h after germination


title: control-butenolide 3h, rep 1


title: smoke-butenolide 3h, rep 1


title: smoke-butenolide 6h, rep 2


title: control-smoke 27h, rep 3


title: control-smoke 24h, rep 1

source_name: smoke-water treated maize kernel, 24h after germination


title: control-smoke 24h, rep 3


title: control-butenolide 6h, rep 2


title: control-smoke 90m, rep 2

source_name: control maize kernel, 90m after germination

source_name: smoke-water treated maize kernel, 90m after germination


title: control-smoke 90m, rep 1


title: control-smoke 27h, rep 1


title: smoke-butenolide 90m, rep 2

source_name: butenolide-water treated maize kernel, 90m after germination


title: Treated(Adc3Q1 ) vs. Control

city: Pune

first: samit

last: chattopadhyay

state: Maharashtra

address: University of Pune Campus

institute: National Centre for Cell Science

description: Cells Vs SMAR1 overexpressing cells

hyb_protocol: 750ng of each Cyanine-3 and Cyanine-5 labeled cRNA were combined with 50μl of 10x Blocking agent. The volume is made upto 240 ul using Nuclease free water. 10μl of 25x Fragmentation buffer (Agilent) were added and incubated at 60°C for 30 minutes in dark. The fragmented cRNA were mixed with 250μl of 2x Hybridization Buffer (Agilent). About 490μl of the resulting mixture was applied to the 22k Gene Expression Microarray (Agilent Technologies), and hybridized at 65°C for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer-I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer-II at 37ºC. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Scanned on an Agilent G2505B scanner and Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1)

data_processing: Normalization of the data was done using Per spot per chip intensity dependant lowess normalization. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. One fold and above differentially regulated genes were filtered from the data. Ontology based biological analysis was done using Gene Ontology browser in GeneSpring Gx. Further, pathways that were significantly regulated was done using bio script library in GeneSpring Gx

source_name: SMAR1-stable B16F10 cells

label_protocol: Low RNA Input Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2μl of oligo dT-T7 Promoter Primer in nuclease-free water at 65ºC for 10 min followed by incubation with 4.0μl of 5× First strand buffer, 2μl of 0.1M DTT, 1 μl of 10mM dNTP mix, 1μl of 200 U/μl MMLV RT, and 0.5μl of 40U/μl RNaseOUT, at 40ºC for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 μl of 10 mM Cyanine-3 CTP or 2.4 μl of 10 mM Cyanine-5 CTP (Perkin-Elmer, Boston, MA), 20μl of 4X Transcription buffer, 8 μl of NTP mixture, 6 μl of 0.1M DTT, 0.5 μl of RNaseOUT, 0.6μl of Inorganic pyrophosphatase, 0.8 μl of T7 RNA polymerase, and 15.3μl of nuclease-free water at 40 ºC for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization.

growth_protocol: Cells were cultured in DMEM and 10% FBS medium at 37oC with 5% CO2 and Penstrip antibiotic.

extract_protocol: Total RNA extracted  using Qiagen’s RNeasy minikit following manufacturer's instructions

treatment_protocol: The Cells were transfected with SMAR1 using Liptofectamine according to the user guide. Stable line was made by selecting single positively transfected clone using medium containing G418.

value: B16F10 melanoma cells

tag: protocol

value: SMAR1 overexpression

source_name: B16F10 cells

value: control


title: control-butenolide 6h, rep 1


title: smoke-butenolide 90m, rep 1


title: control-smoke 24h, rep 2

source_name: control maize kernel, 24h after germination


title: control-butenolide 90m, rep 3


title: control-butenolide 90m, rep 2


title: smoke-delayed 6h, rep 2

source_name: smoke-water treated maize kernel, 6h after germination

source_name: control maize kernel, 3h after germination +  6h smoke-water


title: smoke-delayed 3h, rep 3

source_name: control maize kernel, 3h after germination +  3h smoke-water


title: smoke-delayed 3h, rep 1


title: smoke-delayed 6h, rep 3


title: smoke-delayed 3h, rep 2


title: smoke-delayed 6h, rep 1


title: control-delayed 6h, rep 1

source_name: control maize kernel, 9h after germination


title: control-delayed 3h, rep 3


title: control-delayed 6h, rep 2


title: control-butenolide 90m, rep 1


title: control-delayed 3h, rep 2


title: Waldenstrom's Macroglobulinemia sample MC4804_aCGH

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

description: no additional information

hyb_protocol: Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

scan_protocol: Scanned on DNA Microarray Scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: DNA tumor sample

label_protocol: 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns

extract_protocol: Genomic DNA obtained using standard phenol chloroform extraction method

tag: Tissue

value: bone marrow

tag: Age

value: information unavailable

tag: Gender

value: Male

tag: Bone marrow involvement

tag: Hemoglobin

tag: Newly diagnosed

value: No

source_name: Female reference DNA sample

tag: reference


title: control-delayed 6h, rep 3


title: Waldenstrom's Macroglobulinemia sample MC4765_aCGH

description: no additional information

value: Yes


title: Waldenstrom's Macroglobulinemia sample MC1336_aCGH

description: no additional information


title: control-butenolide 3h, rep 2

source_name: butenolide-water treated maize kernel, 3h after germination


title: Waldenstrom's Macroglobulinemia sample MC4777_aCGH

description: no additional information

value: Female


title: Waldenstrom's Macroglobulinemia sample MC4785_aCGH

description: no additional information


title: control-smoke 90m, rep 3


title: control-smoke 12h, rep 2

source_name: control maize kernel, 12h after germination

source_name: smoke-water treated maize kernel, 12h after germination


title: Waldenstrom's Macroglobulinemia sample MC1376_aCGH

description: no additional information


title: control-smoke 12h, rep 1


title: control-delayed 3h, rep 1

source_name: control maize kernel, 3h after germination

source_name: control maize kernel, 6h after germination


title: control-smoke 12h, rep 3


title: control-smoke 9h, rep 3

source_name: smoke-water treated maize kernel, 9h after germination


title: Waldenstrom's Macroglobulinemia sample MC4803_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC21_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC93_aCGH

description: no additional information


title: control-smoke 9h, rep 1


title: control-smoke 9h, rep 2


title: Waldenstrom's Macroglobulinemia sample MC97_aCGH

description: no additional information


title: control-smoke 6h, rep 2


title: Waldenstrom's Macroglobulinemia sample MC81_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC57_aCGH

description: no additional information


title: control-smoke 6h, rep 3


title: Waldenstrom's Macroglobulinemia sample MC4805_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4806_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4799_aCGH

description: no additional information


title: control-smoke 6h, rep 1


title: Waldenstrom's Macroglobulinemia sample MC4801_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4795_aCGH

description: no additional information


title: control-smoke 3h, rep 3

source_name: smoke-water treated maize kernel, 3h after germination


title: control-smoke 3h, rep 2


title: control-smoke 3h, rep 1


title: Waldenstrom's Macroglobulinemia sample MC4792_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4788_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4779_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4787_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4776_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4778_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4775_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4774_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4780_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4769_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC1372_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4761_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC1371_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC1374_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC4764_aCGH

description: no additional information


title: Mouse (GRS) Normal Mammary gland 02

first: Koji

last: Numata

address: 3-1-1 Koyadai

institute: RIKEN

description: Custom oligo (60mer) microarray was manufactured by Agilent Technologies.

hyb_protocol: The protocols supplied by Agilent Technologies were used.

data_processing:
Numerical processed signal values (gProcessedSignal) of the Agilent Feature Extraction File were obtained as representative expression levels for each probe within the array. If a spot had an intensity value lower than five, or if there was no prominent difference between foreground and background signals, then the intensity value was adjusted to five and the corresponding probe was treated as an “absent probe”. To perform normalization of signal intensity distribution between multiple arrays, the whole mean signal of every hybridization experiment was adjusted to that of the data from SL10 cells by oligo-dT priming. Probes with intensity values lower than five as well as being flagged as “saturated” were discarded for the inter-array-normalization step.

Unpublished data has been masked in the supplementary feature extraction files.

source_name: Mouse (GRS) Normal Mammary gland 02

label_protocol: RNA was labeled with random nanomers, CyScribe First-Strand cDNA Labeling Kit(Amersham), according to the manufacturer’s protocols.

extract_protocol: Total RNA was prepared from mouse brain using Trizol reagent according to manufacturer’s instruction (Invitrogen).

tag: Mouse (GRS) Normal Mammary gland 02


title: Mouse (GRS) Normal Mammary gland 01

scan_protocol: The protocols supplied by Agilent Technologies were used.

source_name: Mouse (GRS) Normal Mammary gland 01

tag: Mouse (GRS) Normal Mammary gland 01


title: fenofibrate_treated_HUVEC_18hr-1

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Biotin-labelled complex cRNAs were hybridized to CodeLink UniSet I Human 20K according to the manufacturer's protocols (Applied Microarrays, formally supplied by GE Healthcare).

scan_protocol: The arrays were scanned with Agilnet DNA Microarray Scanner model G2565BA.

data_processing: The scanned images were quantified with CodeLink Expression Array Software (Applied Microarrays, formally supplied by GE Healthcare), where the intensity of each spot was divided by the spot’s signal median.

source_name: HUVEC

label_protocol: Biotin-labelled complex cRNAs were prepared to according to the manufacturer's protocols (Applied Microarrays, formally supplied by GE Healthcare)

growth_protocol: HUVECs were isolated from umbilical cords by collagenase digestion and cultured at 37ºC/5%CO2 in basal culture medium supplemented with a proprietary mixture of heparin, hydrocortisone, epidermal growth factor, FGF and 2% foetal calf serum (FCS; EGM-2, Cambrex, Workingham, UK).

extract_protocol: Total RNA was prepared from fenofibrate-treated or -untreated HUVECs using Trizol reagent (Invitrogen)

treatment_protocol: HUVEC pools consisting of 10 biological isolates were treated with 25umol fenofibrate (Sigma-Aldrich, UK) dissolved in DMSO (Sigma-Aldrich, UK). Cells were incubated at 37ºC/5%CO2 for the time points in transcriptional profiling.

value: HUVEC

tag: drug treatment time point


title: fenofibrate_treated_HUVEC_8hr-3


title: Waldenstrom's Macroglobulinemia sample MC1362_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC1364_aCGH

description: no additional information


title: fenofibrate_treated_HUVEC_18hr-2


title: fenofibrate_treated_HUVEC_18hr-3


title: Mouse (GRS) Mammary Tumor 04

source_name: Mouse (GRS) Mammary Tumor 04

tag: Mouse (GRS) Mammary Tumor 04


title: Waldenstrom's Macroglobulinemia sample MC1353_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC1367_aCGH

description: no additional information


title: fenofibrate_treated_HUVEC_8hr-2


title: Waldenstrom's Macroglobulinemia sample MC1360_aCGH

description: no additional information


title: fenofibrate_treated_HUVEC_8hr-1


title: Waldenstrom's Macroglobulinemia sample MC4766_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC1354_aCGH

description: no additional information


title: Mouse (GRS) Mammary Tumor 03

source_name: Mouse (GRS) Mammary Tumor 03

tag: Mouse (GRS) Mammary Tumor 03


title: Waldenstrom's Macroglobulinemia sample MC1352_aCGH

description: no additional information


title: Waldenstrom's Macroglobulinemia sample MC1341_aCGH

description: no additional information


title: fenofibrate_treated_HUVEC_6hr-3


title: Mouse (GRS) Mammary Tumor 01

source_name: Mouse (GRS) Mammary Tumor 01

tag: Mouse (GRS) Mammary Tumor 01


title: Mouse (GRS) Mammary Tumor 02

source_name: Mouse (GRS) Mammary Tumor 02

tag: Mouse (GRS) Mammary Tumor 02


title: Waldenstrom's Macroglobulinemia sample MC1344_aCGH

description: no additional information


title: Mouse Thymus, random priming

source_name: Mouse Thymus, random priming

tag: Mouse Thymus, random priming


title: Mouse Spleen, random priming

source_name: Mouse Spleen, random priming

tag: Mouse Spleen, random priming


title: Mouse Placenta (10.5 d.p.c), random priming


title: Mouse Testis, random priming

source_name: Mouse Testis, random priming

tag: Mouse Testis, random priming


title: fenofibrate_treated_HUVEC_2hr-3

tag: tissue


title: fenofibrate_treated_HUVEC_4hr-2


title: fenofibrate_treated_HUVEC_6hr-2


title: fenofibrate_treated_HUVEC_4hr-3


title: Mouse Stomach, random priming

source_name: Mouse Stomach, random priming

tag: Mouse Stomach, random priming


title: fenofibrate_treated_HUVEC_6hr-1


title: fenofibrate_treated_HUVEC_4hr-1


title: Mouse Placenta (13.5 d.p.c), random priming


title: Mouse Lung, random priming

source_name: Mouse Lung, random priming

tag: Mouse Lung, random priming


title: Mouse Liver, random priming

source_name: Mouse Liver, random priming

tag: Mouse Liver, random priming


title: fenofibrate_treated_HUVEC_2hr-1


title: Mouse Kidney, random priming

source_name: Mouse Kidney, random priming

tag: Mouse Kidney, random priming


title: fenofibrate_treated_HUVEC_2hr-2


title: Mouse Intestine, random priming

source_name: Mouse Intestine, random priming

tag: Mouse Intestine, random priming


title: fenofibrate_untreated_HUVEC_4

value: untreated


title: fenofibrate_untreated_HUVEC_3


title: Mouse Heart, random priming

source_name: Mouse Heart, random priming

tag: Mouse Heart, random priming


title: Waldenstrom's Macroglobulinemia sample MC1375_GEP

description: Gene expression data from Waldenstrom's Macroglobulinemia samples

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on HG-U133A GeneChip.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings  as normalization method.

source_name: Bone marrow sample after CD19+ or concomitant CD19+/CD138+ sorting

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

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

tag: Tissue

tag: Gender

tag: Age

tag: Newly diagnosis

value: no


title: Mouse Thymus, oligo-dT priming

source_name: Mouse Thymus, oligo-dT priming

label_protocol: RNA was labeled using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer’s protocols.

tag: Mouse Thymus, oligo-dT priming


title: Mouse Stomach, oligo-dT priming

source_name: Mouse Stomach, oligo-dT priming

tag: Mouse Stomach, oligo-dT priming


title: Mouse Spleen, oligo-dT priming

source_name: Mouse Spleen, oligo-dT priming

tag: Mouse Spleen, oligo-dT priming


title: Mouse Placenta (13.5 d.p.c), oligo-dT priming


title: Mouse Brain, random priming

source_name: Mouse Brain, random priming

tag: Mouse Brain, random priming


title: Mouse Testis, oligo-dT priming

source_name: Mouse Testis, oligo-dT priming

tag: Mouse Testis, oligo-dT priming


title: Mouse Placenta (10.5 d.p.c), oligo-dT priming


title: Mouse Lung, oligo-dT priming

source_name: Mouse Lung, oligo-dT priming

tag: Mouse Lung, oligo-dT priming


title: Mouse Liver, oligo-dT priming

source_name: Mouse Liver, oligo-dT priming

tag: Mouse Liver, oligo-dT priming


title: fenofibrate_untreated_HUVEC_2

source_name: HUVEC

tag: tissue

tag: drug treatment time point


title: fenofibrate_treated_HUVEC_pretreatment_withPPARasiRNA_18hr

treatment_protocol: siRNA treatment was performed through lipid-based transfection method with either PPARa siRNA (Cat. No. M-00343400) or control siRNA (Cat. No. D-001206-13), using SmartPool reagents (Dharmacon, Lafayette CO, USA) according to the manufacturers' instructions. HUVECs from 10 individuals were pooled, plated at 2.2×105 cells in six-well plates and allowed to recover for 24 hours at 37ºC/5%CO2, at which time they were approximately 80% confluent. For transfection, 5ul/well of 20uM RNAi (PPARa or control), 42ul/ well of siFECTAMINE (ICVEC, UK no longer available) and 500ul/well of serum-free medium were incubated at room temperature for 5 minutes. The relevant transfection mix was then added to each well containing 500 μl of fully supplemented media and incubated at 37ºC/5%CO2 for 3 hours after which the transfection medium was replaced with 3ml of fresh fully supplemented medium. 24 hours post transfection relevant wells were treated with 25umol fenofibrate (Sigma-Aldrich, UK) dissolved in DMSO (Sigma-Aldrich, UK). Cells were incubated at 37ºC/5%CO2 for the time points in transcriptional profiling.

tag: sirna

value: PPARa siRNA

tag: sirna treatment time point


title: Waldenstrom's Macroglobulinemia sample MC1372_GEP

source_name: DNA tumor sample

tag: Bone marrow involvement

tag: Hemoglobin

tag: Newly diagnosed


title: Waldenstrom's Macroglobulinemia sample MC1373_GEP

tag: Tissue

tag: Gender

value: yes


title: fenofibrate_untreated_HUVEC_1


title: Mouse Kidney, oligo-dT priming

source_name: Mouse Kidney, oligo-dT priming

tag: Mouse Kidney, oligo-dT priming


title: fenofibrate_treated_HUVEC_pretreatment_withControlsiRNA_18hr

value: control siRNA


title: Waldenstrom's Macroglobulinemia sample MC1370_GEP

tag: Age

tag: Newly diagnosis


title: Waldenstrom's Macroglobulinemia sample MC1371_GEP


title: Mouse Intestine, oligo-dT priming

source_name: Mouse Intestine, oligo-dT priming

tag: Mouse Intestine, oligo-dT priming


title: Mouse Heart, oligo-dT priming

source_name: Mouse Heart, oligo-dT priming

tag: Mouse Heart, oligo-dT priming


title: Mouse Brain, oligo-dT priming

source_name: Mouse Brain, oligo-dT priming

tag: Mouse Brain, oligo-dT priming


title: fenofibrate_treated_HUVEC_pretreatment_withPPARasiRNA_12hr


title: fenofibrate_treated_HUVEC_pretreatment_withControlsiRNA_12hr


title: fenofibrate_treated_HUVEC_pretreatment_withControlsiRNA_8hr


title: Waldenstrom's Macroglobulinemia sample MC1366_GEP


title: V6-L1-6 GRO tpk2

city: Burjassot

first: Jose

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: In vivo labeled total RNA of tpk2 mutant strain. Replicate 1. Filter V6-L1-6.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2X SSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

data_processing: Raw image quantization background subtracted.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae Y01089 (Euroscarf) tpk2 mutant. Exponential growth in YPD.

label_protocol: In vivo labeling by run-on (GRO) using 33P-UTP.Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 Ci/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Exponential growth in YPD.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

tag: biomaterial


title: Waldenstrom's Macroglobulinemia sample MC1374_GEP


title: Mouse SL10 (fibroblast), oligo-dT priming


title: fenofibrate_treated_HUVEC_pretreatment_withPPARasiRNA_8hr


title: fenofibrate_treated_HUVEC_pretreatment_withPPARasiRNA_4hr


title: V6-L1-8 GRO tpk2

description: In vivo labeled total RNA of tpk2 mutant strain. Replicate 2. Filter V6-L1-8.

value: Saccharomyces cerevisiae Y01089 (Euroscarf) tpk2 mutant. Exponential growth in YPD.


title: Waldenstrom's Macroglobulinemia sample MC1367_GEP


title: fenofibrate_treated_HUVEC_pretreatment_withControlsiRNA_4hr


title: V6-L1-7 GRO rap1sil

description: In vivo labeled total RNA of SCR101 prap1sil strain. Replicate 2. Filter V6-L1-7.

source_name: Saccharomyces cerevisiae SCR101 prap1sil. Exponential growth in YPD.


title: V6-L1-8 GRO rap1sil

description: In vivo labeled total RNA of SCR101 prap1sil strain. Replicate 1. Filter V6-L1-8.

value: Saccharomyces cerevisiae SCR101 prap1sil. Exponential growth in YPD.


title: Waldenstrom's Macroglobulinemia sample MC1365_GEP


title: Waldenstrom's Macroglobulinemia sample MC1364_GEP


title: Waldenstrom's Macroglobulinemia sample MC1360_GEP


title: V6-L1-9 GRO RAP1

description: In vivo labeled total RNA of SCR101 pRAP1 strain. Replicate 3. Filter V6-L1-9.

source_name: Saccharomyces cerevisiae SCR101 pRAP1. Exponential growth in YPD.


title: Untreated_HUVEC

value: untreatment


title: V6-L1-6 GRO RAP1

description: In vivo labeled total RNA of SCR101 pRAP1 strain. Replicate 2. Filter V6-L1-6.

value: Saccharomyces cerevisiae SCR101 pRAP1. Exponential growth in YPD.


title: Waldenstrom's Macroglobulinemia sample MC1357_GEP

source_name: Bone marrow sample after CD19+ or concomitant CD19+/CD138+ sorting


title: V6-L1-10 GRO rap1sil

description: In vivo labeled total RNA of SCR101 prap1sil strain. Replicate 3. Filter V6-L1-10.


title: V6-L1-7 GRO RAP1

description: In vivo labeled total RNA of SCR101 pRAP1 strain. Replicate 1. Filter V6-L1-7.


title: V6-L1-8 WCE tpk2

description: Whole Cell Extract of tpk2 mutant strain. Replicate 2. Filter V6-L1-8.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

label_protocol: Ligation Mediated PCR (Ren B. et al. 2000) was used for DNA amplification. Briefly,the DNA was blunted by T4 phage DNA polymerase. The reaction was allowed to proceed for 20 minutes at 12°C. After phenol/chloroform/isoamylic alcohol extraction, DNA was ethanol-precipitated and ligated in a final volume of 50 μl with annealed linkers oJW102 and oJW103 (1.5 μM of each primer). The reaction was carried out overnight at 16°C and ligated DNA was precipitated and resuspended in 25 μl milliQ water. The ligated DNA was amplified by PCR. The PCR  program was 2 minutes at 95°C and 33 cycles of 30 s at 95°C, 30 s at 55°C and 2 minutes at 72°C. The DNA was precipitated overnight and resuspended in 50 μl of milliQ water. The LMPCR product was used as a template for the radioactive labeling reaction. The reaction mixture contained 5-15 μL of amplified DNA in 50 μl (1× DNApol buffer, 2 mM MgCl2, 0.2 mM dATP, dTTP and dGTP, 25 μM dCTP, 1 μM oJW102, 0.8 μCi α-33P-dCTP and 5 U DNApol). The mix was denatured for 5 minutes at 95°C, annealed 5 minutes at 50°C and was amplified during 30 minutes at 72°C. The reaction product was purified through a ProbeQuant G-50 column to remove unincorporated 33P-dCTP and oligonucleotides.

extract_protocol: 50 mL of cells were cross-linked by adding formaldehyde to a final concentration of 1% for 15 minutes at room temperature, and the cross-link was quenched by adding glycine to a final concentration of 125 mM. Cell were washed 4 times with 30 mL ice-cold TBS buffer (20mM Tris-HCl, 140 mM NaCl, pH 7.5) and frozen. Cells were thawed on ice and resuspended in 300 μl lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF (Phenylmethylsulfonyl fluoride), 1 mM benzamidine and 1 pill of protease inhibitor cocktail (Roche Diagnostics, Mannheim, Germany) dissolved in every 50 ml of buffer). The equivalent of 0.3 ml of frozen glass beads (425-600 mm; Sigma-Aldrich, St Louis, MO, USA) was added to the cellular suspension and cells were lysed at 4°C for 12 minutes of vortexing at maximum power. Lysis buffer (300 μl) was added and the extract was transferred to a new tube. Sonication of DNA was performed to obtain DNA fragments between 200 and 500 bp, with an average size of 350 bp. Chromatin was sonicated on ice-cold water, with 5 pulses of 30 s at High output (200W) in a Bioruptor (Diagenode SA, Liège, Belgium). Cell debris was removed by centrifugation at 12,000 rpm at 4°C for 5 minutes. An aliquot of 10 μl of this whole cell extract (WCE) was kept as positive control.


title: V6-L1-6 WCE rap1sil

description: Whole Cell Extract of SCR101 prap1-sil strain. Replicate 3. Filter V6-L1-6.

source_name: Saccharomyces cerevisiae SCR101 prap1-sil. Exponential growth in YPD.


title: V6-L1-6 WCE tpk2

description: Whole Cell Extract of tpk2 mutant strain. Replicate 1. Filter V6-L1-6.


title: V6-L1-10 WCE rap1sil

description: Whole Cell Extract of SCR101 prap1-sil strain. Replicate 2. Filter V6-L1-10.

value: Saccharomyces cerevisiae SCR101 prap1-sil. Exponential growth in YPD.


title: V6-L1-6 IP tpk2

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a tpk2 mutant  strain. Replicate 1. Filter V6-L1-6.


title: V6-L1-7 WCE rap1sil

description: Whole Cell Extract of SCR101 prap1-sil strain. Replicate 1. Filter V6-L1-7.


title: V6-L1-8 IP tpk2

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a tpk2 mutant strain. Replicate 2. Filter V6-L1-6.


title: Waldenstrom's Macroglobulinemia sample MC1353_GEP

value: bone marrow


title: V6-L1-6 IP rap1sil

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a SCR101 prap1-sil strain. Replicate 3. Filter V6-L1-6.


title: Waldenstrom's Macroglobulinemia sample MC1352_GEP

description: Gene expression data from Waldenstrom's Macroglobulinemia samples


title: Waldenstrom's Macroglobulinemia sample MC1351_GEP


title: V6-L1-7 IP rap1sil

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a SCR101 prap1-sil strain. Replicate 1. Filter V6-L1-7.


title: V6-L1-10 IP rap1sil

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a SCR101 prap1-sil strain. Replicate 2. Filter V6-L1-10.


title: V6-L1-7WCE RAP1

description: Whole Cell Extract of SCR101 pRAP1 strain. Replicate 3. Filter V6-L1-7.


title: Waldenstrom's Macroglobulinemia sample MC1350_GEP


title: Waldenstrom's Macroglobulinemia sample MC1344_GEP


title: Waldenstrom's Macroglobulinemia sample MC1341_GEP


title: V6-L1-9 WCE RAP1

description: Whole Cell Extract of SCR101 pRAP1 strain. Replicate 2. Filter V6-L1-9.


title: V6-L1-9 IP RAP1

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a SCR101 pRAP1 strain. Replicate 2. Filter V6-L1-9.


title: Waldenstrom's Macroglobulinemia sample MC1348_GEP


title: V6-L1-8 WCE RAP1

description: Whole Cell Extract of SCR101 pRAP1 strain. Replicate 1. Filter V6-L1-8.


title: Waldenstrom's Macroglobulinemia sample MC1340_GEP


title: V6-L1-8 IP RAP1

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a SCR101 pRAP1 strain. Replicate 1. Filter V6-L1-8.

growth_protocol: Exponential growth in YPD


title: V6-L1-7 IP RAP1

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a SCR101 pRAP1 strain. Replicate 3. Filter V6-L1-7.


title: V6-L1-10 IP Ser5P

description: IP of the RNApol II CTD Phosphorilated on Ser5. Replicate 3. Filter V6-L1-10.

source_name: Saccharomyces cerevisiae BQS252. Exponential growth in YPD.


title: V6-L1-10 WCE Ser5P

description: Whole Cell Extract. Replicate 3. Filter V6-L1-10.

value: Saccharomyces cerevisiae BQS252. Exponential growth in YPD.


title: V6-L1-9 WCE Ser5P 2

description: Whole Cell Extract. Replicate 2. Filter V6-L1-9.


title: V6-L1-9 WCE Ser5P 1

description: Whole Cell Extract. Replicate 1. Filter V6-L1-9.


title: V6-L1-9 IP Ser5P 2

description: IP of the RNApol II CTD Phosphorilated on Ser5. Replicate 2. Filter V6-L1-9.


title: Waldenstrom's Macroglobulinemia sample MC1339_GEP


title: V6-L1-9 IP Ser5P 1

description: IP of the RNApol II CTD Phosphorilated on Ser5. Replicate 1. Filter V6-L1-9.


title: GEK_gDNA_Filter 10

description: Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with a Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. New macroarrays were pre-treated for 30 min at 80ºC with 0.5% SDS to remove particles deposited during array printing. This step was not necessary in subsequent hybridizations. Filters were  inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X106dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1at 65ºC for 20 min in 2SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2SSC, 0.1% SDS. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.

data_processing: Raw image quantitation background subtracted. The data were normalized using a gDNA hybridization for each filter.

source_name: Yeast genomic DNA

label_protocol:
Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 ul distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 uCi [α-33P] dCTP (2500 Ci/mmol).
The mixture was incubated at 37C for 1–2 h. In order to eliminate non-incorporated components, Probe Quant G–50 columns (Amersham Biosciences) were used.

growth_protocol: Exponential growth in YPD medium

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267–272

value: Total genomic DNA from FY1679 yeast strain


title: GEK_gDNA_Filter 8


title: V5R2-L1-22 WCE

description: Whole Cell Extract. Replicate 3. Filter V5R2-L1-22.

source_name: Whole Cell Extract

value: Saccharomyces cerevisiae BQS252. Exponential growth in YPD


title: V5R2-L1-21 WCE

description: Whole Cell Extract. Replicate 2. Filter V5R2-L1-21.


title: GEK_gDNA_Filter 6


title: GEK_gDNA_Filter 9


title: Waldenstrom's Macroglobulinemia sample MC1336_GEP

description: Gene expression data from Waldenstrom's Macroglobulinemia samples

value: Male

value: No


title: V5R2-L1-20 WCE

description: Whole Cell Extract. Replicate 1. Filter V5R2-L1-20.


title: GEK_gDNA_Filter 7


title: V5R2-L1-22 IP Spt16

description: IP of Spt16-Myc. Replicate 3. Filter V5R2-L1-22.

source_name: Saccharomyces cerevisiae SJY25 (Spt16-Myc). Exponential growth in YPD


title: V5R2-L1-21 IP Spt16

description: IP of Spt16-Myc. Replicate 2. Filter V5R2-L1-21.

growth_protocol: Saccharomyces cerevisiae SJY25 (Spt16-Myc). Exponential growth in YPD


title: GRO2-7h-F14

description: In vivo labeled total RNA of SJY6 yeast strain. 7h after adding doxycycline. Hybridization on filter 14. Replicate 2.

source_name: SJY6 yeast strain,7 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: GRO3-5h-F14

description: In vivo labeled total RNA of SJY6 yeast strain. 5h after adding doxycycline. Hybridization on filter 14. Replicate 3.

source_name: SJY6 yeast strain,5 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: V5R2-L1-7 NA YPD

description: Mock IP, negative control. Replicate 3. Filter V5R2-L1-7.


title: GRO1-7h-F16

description: In vivo labeled total RNA of SJY6 yeast strain. 7h after adding doxycycline. Hybridization on filter 16. Replicate 1.

growth_protocol: SJY6 yeast strain,7 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: GRO3-7h-F15

description: In vivo labeled total RNA of SJY6 yeast strain. 7h after adding doxycycline. Hybridization on filter 15. Replicate 3.

value: SJY6 yeast strain,7 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.