title: WT antimiR-miR-29 3

city: San FRANCISCO

first: David

last: Steiner

state: CA

address: 513 Parnassus Ave UCSF Box 0414 HSE 201

department: Microbiology and Immunology

institute: UCSF

description: gene expression 24hr post-transfection

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturers protocol. (http://www.arrays.ucsf.edu and http://www.agilent.com)

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.1 software.

data_processing: This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.   A one-way ANOVA linear model was fit to the comparison to estimate the mean M values and calculated moderated t-statistic, B statistic, false discovery rate and p-value for each gene for the comparison of interest. Adjusted p-values were produced by the method proposed by Holm (1979). All procedures were carried out using functions in the R package limma in Bioconductor [Smyth (2004), Gentleman (2004)].

organism: Mus musculus

source_name: Helper T cells, d5 in vitro, 24hr post-transfection

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays.

growth_protocol: Cells stimulated on anti-CD3 and anti-CD28 for 65 hours in media (DMEM with 10% FBS) with IL-2 for an additional 48 hours.

extract_protocol: Total RNA was extrated with Trizol according to manufacturers reccommended procedure.

treatment_protocol: Cells were transfected with miRNA mimics, inhibitors, or controls by electroporation (Neon, Invitrogen) on d1 and d4 and were harvested for RNA extraction on d5.

tag: age

value: 7 weeks

tag: genotype

value: wild type

tag: transfector

value: miR-29 inhibitors


title: SM_BASE

status: Public on Aug 01 2011

type: RNA

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

country: USA

institute: Duke University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Expression Console (Affymetrix) was used to generate the RMA file

label: biotin

molecule: total RNA

organism: Canis lupus familiaris

source_name: Canine Spontaneous Sarcoma

label_protocol: Affymetrix standard protocol

growth_protocol: Spontaneous Tumors from Dogs

extract_protocol: RNAs were extracted with Qiagen RNA easy mini

treatment_protocol: Tissue used for gene expression analysis was placed immediately into RNAlater before RNA isolation

tag: cell type

value: Sarcoma tumor

tag: treatment


title: 253142210061_TIGR4_CY5_SK635_CY3.mev.refIsIB.out

type: genomic

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Query/Reference) from the normalized .mev file:
3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

molecule: genomic DNA

organism: Streptococcus mitis

source_name: Genomic DNA purified from wild type bacteria

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: cells were grown in blood agar plates in an anaerobic chamber, overnight at 37 degrees celcius.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.

tag: strain

organism: Streptococcus pneumoniae TIGR4


title: 253142210061_TIGR4_CY5_SK640_CY3.mev.refIsIB.out


title: 253142210062_TIGR4_CY5_1123_97_CY3.mev.refIsIB.out

organism: Streptococcus pneumoniae


title: 253142210014_TIGR4_CY5_889_96_CY3.mev.refIsIB.out

growth_protocol: Cells were grown in blood agar plates in an anaerobic chamber, overnight at 37 degrees celcius.


title: 253142210039_TIGR4_CY5_6831_06_CY3.mev.refIsIB.out


title: WT antimiR-miR-29 4

description: gene expression 24hr post-transfection


title: 253142210014_TIGR4_CY5_327_95_CY3.mev.refIsIB.out


title: WT control 4

description: gene expression 24hr post-transfection

value: control inhibitors


title: 253142210060_TIGR4_CY5_1178_96_CY3.mev.refIsIB.out


title: BA_TREATMENT

value: hyperthermia


title: WT antimiR-miR-29 2

description: gene expression 24hr post-transfection


title: BA_BASE


title: 253142210060_TIGR4_CY5_327_98_CY3.mev.refIsIB.out


title: Control vs. CPF (0.5mg/l) + DZN (1mg/l). Replicate 3

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

country: United Kingdom

institute: King's College London

hyb_protocol: The cDNA samples were hybridized to the arrays using a modified version of the Genisphere Array 900 HS protocol.

scan_protocol: ScanArray Express HT (PerkinElmer Inc) Software: Easy Quant with Adaptive circle.

data_processing: Preprocessing and normalization was done in the R software (http://www.r-project.org/), version 2.10.1, using Limma package, version 3.2.3 (Smyth, 2005). Loess method (Smyth & Speed, 2003) was used for normalization within arrays and normalization between arrays was done using aquantile method (Yang,et al., 2003), both of them included in limma package. The expression data from all the treatments were normalized together with the expression data from identical treatments at 16C (GEO accession number GSE16719), to allow comparison between both dataset. Outliers from each experiment were identified and removed using a linear model. Expression values from each treatment were treated in separately linear models. The models fit expression values according to the treatment (CPF, DZN or Mixture) and remove values outside the 0.995 confidence interval, one spot at the time, recursively. No more than 6 values were allowed to be removed.

organism: Caenorhabditis elegans

source_name: Control nematodes

label_protocol: cDNA was obtained form a minimum of 400 ng/µl of total RNA, using Array 900 HS kit (Genisphere, http://www.genisphere.com) and Superscript II (Invitrogen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and cleaned up with the RNeasy Micro kit (Qiagen, http://www1.qiagen.com/)

treatment_protocol: All nematodes were grow on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Experiments were carried out with nematodes belonging to the L3 life stage. Populations of C. elegans strain N2 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each treatment were kept in 24° C until L3 was reached. At 72 hours of age, nematodes kept at 24° C were at the L3 stage. Chlorpyrifos (Cyren®/Nufos®, Cheminova A/S, Lemvig, Denmark) and Diazinon (Supelco, Bellefonte, Pennsylvania, USA) dissolved in acetone were added to NGM agar in a final concentration of 0.5mg/l of Chlorpyrifos and 1mg/l of Diazinon. Control population were grown in NGM agar dishes with acetone in an equivalent concentration. The nematodes were then collected and frozen in liquid nitrogen.

tag: Stage

value: L3/L4 nematodes (72h at 24°C)

source_name: Nematodes treated with 0.5mg/l of Chlorpyrifos and 1mg/l of Diazinon


title: 253142210062_TIGR4_CY5_283_95_CY3.mev.refIsIB.out


title: Control vs. CPF (0.5mg/l) + DZN (1mg/l). Replicate 2


title: 253142210060_TIGR4_CY5_236_95_CY3.mev.refIsIB.out


title: WT control 2

description: gene expression 24hr post-transfection


title: 253142210059_TIGR4_CY5_Holland1752_CY3.mev.refIsIB.out


title: 253142210059_TIGR4_CY5_Verbist149_CY3.mev.refIsIB.out


title: DZN (0.5mg/l) vs. Control. Replicate 2

source_name: Nematodes treated with 0.5mg/l of Diazinon

treatment_protocol: All nematodes were grow on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Experiments were carried out with nematodes belonging to the L3 life stage. Populations of C. elegans strain N2 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each treatment were kept in 24° C until L3 was reached. At 72 hours of age, nematodes kept at 24° C were at the L3 stage. Diazinon (Supelco, Bellefonte, Pennsylvania, USA) dissolved in acetone were added to NGM agar in a final concentration of 0.5mg/l. Control population were grown in NGM agar dishes with acetone in an equivalent concentration. The nematodes were then collected and frozen in liquid nitrogen.


title: DZN (0.5mg/l) vs. Control. Replicate 3


title: WT control 3

description: gene expression 24hr post-transfection


title: 253142210059_TIGR4_CY5_48241_CY3.mev.refIsIB.out


title: 253142210058_TIGR4_CY5_SK328_CY3.mev.refIsIB.out

organism: Streptococcus oralis


title: 253142210039_TIGR4_CY5_3988_07_CY3.mev.refIsIB.out


title: Dgcr8 KO miR-29b 2

description: gene expression 24hr post-transfection


title: Dgcr8 KO miR-29b 3

description: gene expression 24hr post-transfection


title: DZN (0.5mg/l) vs. Control. Replicate 1


title: Control vs. DZN (0.5mg/l). Replicate 2


title: Control vs. CPF (0.5mg/l) + DZN (1mg/l). Replicate 1


title: Dgcr8 KO control 3

description: gene expression 24hr post-transfection

value: control miRNA


title: 253142210058_TIGR4_CY5_SK313_CY3.mev.refIsIB.out


title: Control vs. DZN (0.5mg/l). Replicate 3


title: 253142210059_TIGR4_CY5_1298_96_CY3.mev.refIsIB.out


title: Dgcr8 KO control 2

description: gene expression 24hr post-transfection


title: Dgcr8 KO miR-29b 4

description: gene expression 24hr post-transfection


title: 253142210057_TIGR4_CY5_SK271_CY3.mev.refIsIB.out


title: 253142210057_TIGR4_CY5_SK142_CY3.mev.refIsIB.out


title: 253142210058_TIGR4_CY5_SK304_CY3.mev.refIsIB.out


title: 253142210057_TIGR4_CY5_SK569_CY3.mev.refIsIB.out


title: 253142210058_TIGR4_CY5_SK1074_CY3.mev.refIsIB.out


title: Dgcr8 KO control 4

description: gene expression 24hr post-transfection


title: 253142210057_TIGR4_CY5_SK659_CY3.mev.refIsIB.out


title: H3 ChIP vs. Input DNA

city: Los Angeles

first: Adam

middle: S

last: Sperling

address: 611 Charles E. Young Dr. East

department: Biological Chemistry

institute: University of California Los Angeles

description:
Two biological replicates.
Tiling Array.

hyb_protocol: The hybridization was done at the UCLA microarray core facility according to the Affymetrix 500K manual.

scan_protocol: The scanning was done at the UCLA microarray core facility according to the Affymetrix 500K manual.

data_processing:
Affymetrix Tiling Array Software (v 1.1.02) was used to generate the BAR files.  The following parameters were used: PM only; Bandwidth=50. Data were quantile normalized to 13 input samples. Log2 (IP/input) is reported in the bar files.

For input DNA, we accumulated 13 total arrays in a RMY200 strain and found the reduced noise in a control channel. Although we arrived at the same conclusion using one or two control arrays, we normalized Top2 or H3 ChIP data with 13 arrays for the best results. The CEL files for the input arrays are linked to the Series GSE22626 record.

H3_vs13i_signal: H3 ChIP from RMY200 was compared with input DNA.

GSM561020_H3_87295-87293.CEL and
GSM561020_H3_97612-97609.CEL represent biological replicates.

organism: Saccharomyces cerevisiae

source_name: H3 ChIP

label_protocol: 4 µg of amplified DNA were fragmented with 5 µl of 10x fragmentation buffer and reagent (Invitrogen) at 37°C for 35 min, followed by incubation at 95°C for 15 min. The labeling was done at the UCLA microarray core facility according to the Affymetrix 500K manual.

growth_protocol: Grown to log phase in YPD.

extract_protocol: The ChIP assays were performed as previously described (Hecht et al. Nature 1996 [PMID 8779721]). Briefly, crosslinked whole-cell extract was incubated overnight with antibodies directed against histone H3 C-terminus (Abcam, 1791) or Top2 (TopoGEN Inc., 2014), together with Protein A-agarose beads. The beads were washed and the crosslinked DNA was eluted. After reverse crosslinking, eluate samples were purified with phenol-chloroform extraction.

treatment_protocol: Top2 and H3 ChIPs were done under non-challenged conditions in YPD media.

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog #

source_name: Input DNA


title: Top2 ChIP vs. Input DNA

description: Tiling Array

data_processing:
Affymetrix Tiling Array Software (v 1.1.02) was used to generate the BAR files.  The following parameters were used: PM only; Bandwidth=50. Data were quantile normalized to 13 input samples. Log2 (IP/input) is reported in the bar files.

For input DNA, we accumulated 13 total arrays in a RMY200 strain and found the reduced noise in a control channel. Although we arrived at the same conclusion using one or two control arrays, we normalized Top2 or H3 ChIP data with 13 arrays for the best results. The CEL files for the input arrays are linked to the Series GSE22626 record.

Top2vs13input_signal.bar: Top2 ChIP from RMY200 was compared with input DNA.

source_name: Top2 ChIP

value: TopoGen Inc.


title: 253142210056_TIGR4_CY5_SK677_CY3.mev.refIsIB.out


title: Control vs. DZN (0.5mg/l). Replicate 1


title: CPF (0.5mg/l) vs. Control. Replicate 1

source_name: Nematodes treated with 0.5mg/l of Chlorpyrifos

treatment_protocol: All nematodes were grow on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Experiments were carried out with nematodes belonging to the L3 life stage. Populations of C. elegans strain N2 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each treatment were kept in 24° C until L3 was reached. At 72 hours of age, nematodes kept at 24° C were at the L3 stage. Chlorpyrifos (Cyren®/Nufos®, Cheminova A/S, Lemvig, Denmark) dissolved in acetone were added to NGM agar in a final concentration of 0.5mg/l. Control population were grown in NGM agar dishes with acetone in an equivalent concentration. The nematodes were then collected and frozen in liquid nitrogen.


title: ASK_TTA-ctr [SIQ2]

city: aas

first: Fabian

last: Grammes

address: Arboretvn. 2

department: CIGENE

country: Norway

institute: Norwegian University of Life Sciences

hyb_protocol: Custom printed Agilent oligonucleotide microarrays in the 4x44 format were hybridized with Cy3 labled cRNA according to the manufacturerÕs protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

scan_protocol: Agilent scanner (G2565BA) with Agilent Feature Extraction Software (v.10.7.1.1) according to Agilents GE1_107_Sep09 protocol)

data_processing: txt files produced by Feature Extraction were analyzed using the statistical software R with Bioconductor package limma. Signal intensities  (background corrected: gProcessed Signal) of duplicated spots were averaged and Control spots removed. Signal Intensities were quantile-normalized and log2 transformed.

organism: Salmo salar

source_name: ASK (Atlantic salmon kideney) cell culture (ATCC: CRL-2747)

label_protocol: The synthesis of cRNA was performed using the Quick Amp Labeling Kit, One color (Agilent p/n 5190-0442), according to manufacturerÕs protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

extract_protocol: RNA was extracted using QUIAzol followed by RNeasy column cleanup (Qiagen) according to the manufacturers protocols.

tag: cell line

value: ASK (Atlantic salmon kideney) cell culture (ATCC:CRL-2747)

tag: pretreatment

value: TTA

value: Control


title: 253142210056_TIGR4_CY5_SK615_CY3.mev.refIsIB.out


title: AP2d-- midbrain RNA

city: Martinsried

first: Markus

last: Moser

address: Am Klopferspitz 18

country: Germany

institute: Max-Planck-Institute of Biochemistry

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: ExpressionStat 5.0

source_name: E15 midbrain

label_protocol: labeling, hybridization, scanning and data processing were performed according to the standard protocol of the Affimetrix genechip platform

growth_protocol: For microarray analyses, we used the Affymetrix GeneChip platform employing a standard protocol for sample preparation and microarray hybridization. Total RNA (2.5 μg) was converted into biotinylated cRNA according to the Affymetrix standard protocol version 2, purified, fragmented and hybridized to Affimetrix GeneChip Mouse Genome xY 2.= ArraysHG-U133Plus_2.0 microarrays (Affymetrix Inc.).

extract_protocol: Total brain RNA was purified from E15 Ap-2δ-/- and wild-type mice using the RNeasyMini-kit from Qiagen as specified by the manufacturer.

treatment_protocol: freshly isolated embryonic mouse brain

tag: genotype/variation

value: AP-2d knockout

tag: tissue

value: midbrain

tag: developmental stage


title: AP2d++ midbrain RNA


title: CPF (0.5mg/l) vs. Control. Replicate 3


title: Control vs. CPF (0.5mg/l). Replicate 2


title: 253142210002_TIGR4_CY5_4029_99_CY3.mev.refIsIB.out


title: ASK_TTA-TTA [SIQ2]


title: 253142210055_TIGR4_CY5_SK673_CY3.mev.refIsIB.out


title: 253142210056_TIGR4_CY5_SK568_CY3.mev.refIsIB.out


title: 253142210055_TIGR4_CY5_L32F_CY3.mev.refIsIB.out


title: 253142210002_TIGR4_CY5_3223_99_CY3.mev.refIsIB.out


title: Control vs. CPF (0.5mg/l). Replicate 1


title: ASK_TTA-TTAIC [SIQ2]

value: TTA+polyIC


title: 253142210056_TIGR4_CY5_SK667_CY3.mev.refIsIB.out


title: Spp1-/- smoke-2

city: Houston

first: Farrah

last: Kheradmand

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were processed by variance stabilizing transform and quantile normalization using R2.12/Bioconductor 2.6 including lumi and limma.

source_name: Lung antigen presenting cells

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

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: Mouse were exposed to cigarette smoke for 4 months.

tag: gender

value: Female

value: Cigarette smoke


title: 253142210054_TIGR4_CY5_SK23_CY3.mev.refIsIB.out


title: 253142210055_TIGR4_CY5_48243_CY3.mev.refIsIB.out


title: 253142210055_TIGR4_CY5_14860_CY3.mev.refIsIB.out


title: 253142210054_TIGR4_CY5_SK105_CY3.mev.refIsIB.out


title: Control vs. CPF (0.5mg/l). Replicate 3


title: CPF (0.5mg/l) vs. Control. Replicate 2


title: 253142210002_TIGR4_CY5_6377_99_CY3.mev.refIsIB.out


title: 253142210054_TIGR4_CY5_SK39_CY3.mev.refIsIB.out


title: ASK_ctr-ctr [SIQ2]


title: 253142210053_TIGR4_CY5_A9812_CY3.mev.refIsIB.out


title: 253142210054_TIGR4_CY5_SK309_CY3.mev.refIsIB.out


title: ASK_ctr-IC [SIQ2]

value: polyIC


title: ASK_ctr-TTA [SIQ2]


title: 253142210001_TIGR4_CY5_1087_00_CY3.mev.refIsIB.out


title: WT smoke-2

value: Wild type


title: ASK_ctr-TTAIC [SIQ2]


title: Spp1-/- smoke-1


title: 253142210001_TIGR4_CY5_1748_96_CY3.mev.refIsIB.out


title: E2CTR4

description: TODO

hyb_protocol: Custom printed Agilent oligonucleotide microarrays in the 4x44 format were hybridized with Cy3 labled cRNA according to the manufacturer's protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

scan_protocol: Agilent scanner (G2565BA) with Agilent Feature Extraction Software (v.10.5.1.1) according to Agilents GE1_105_Dec08 protocoll)

data_processing: txt files produced by Feature Extraction were analyzed using the statistical software R with Bioconductor package limma. Signal intensities  (background corrected: gProcessed Signal) of duplicated spots were averaged and Control spots removed. Signal Intensities were quantilenormalized and log2 transformed.

source_name: Heart ventricle

label_protocol: The synthesis of cRNA was performed using the Quick Amp Labeling Kit, One color (Agilent p/n 5190-0442), according to manufacturer's protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

extract_protocol: Tissue samples were stored at -80. Total RNA was extracted by sample homogenization in QUIAzol followed by RNeasy column cleanup (Qiagen) according to the manufacturers protocols.

value: Heart ventricle

tag: diet

tag: sampling time point


title: E2CTR5

description: TODO


title: hybrid at rich media (YPD), before Phenanthroline, Red dye, repeat #2

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Agilent Gene Expression Hybridization Kit.

scan_protocol: Arrays were scanned using Agilent Microarray Scanner (p/n G2565BA) with a 5 micron resolution and photomultiplier tube (PMT) set to 100. The raw images were analyzed and quantified using Agilent Feature Extraction software.

data_processing: Raw hybridization intensities were processed by Agilent Feature Extraction software (default settings), log2-transformed, averaged over two replicate probes and corrected for %GC (the correction factor was defined by subtracting the avarage deviation of all probes with similar %GC from the avaerge of all probes).

molecule: polyA RNA

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: S. cerevisiae BY4741 X  S. paradoxus CBS432 (ho::kanMX4/ho::nat1 MATa/MATα)

label_protocol: Agilent Low RNA Input Amplificarion Kit (LRIAK) plus, two color.

growth_protocol: S. cerevisiae, S. paradoxus and their hybrid were subjected to 150 ug/ml of 1,10-phenanthroline at log-phase and sampled after 0, 20, 40 and 60 minutes.

extract_protocol: Total RNA was extracted using MasterPure™ Yeast RNA purification Kit (EPICENTRE).

tag: organism(s)

value: hybrid

tag: growth protocol

value: YPD rich medium at 30°C


title: WT smoke-1

tag: genotype


title: hybrid at rich media (YPD), 60min with Phenanthroline, Red dye, repeat #2

value: YPD rich medium at 30°C, 60min with Phenanthroline


title: hybrid at rich media (YPD), 20min with Phenanthroline, Red dye, repeat #2

value: YPD rich medium at 30°C, 20min with Phenanthroline


title: hybrid at rich media (YPD), 40min with Phenanthroline, Red dye, repeat #1

value: YPD rich medium at 30°C, 40min with Phenanthroline


title: WT Air-1

tag: treatment

value: Room air


title: 253142210001_TIGR4_CY5_9371_03_CY3.mev.refIsIB.out

tag: strain


title: hybrid at rich media (YPD), 20min with Phenanthroline, Red dye, repeat #1


title: WT Air-2


title: 253142210053_TIGR4_CY5_48242_CY3.mev.refIsIB.out


title: hybrid at rich media (YPD), 60min with Phenanthroline, Red dye, repeat #1


title: hybrid at rich media (YPD), before Phenanthroline, Red dye, repeat #1


title: E2CTR2

description: TODO


title: E2CTR1

description: TODO


title: S.cerevisiae and S.paradoxus at rich media (YPD), 20min with Phenanthroline, Green dye, repeat #2

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

source_name: S. cerevisiae (diploid BY4741 ho::kanMX4), S. paradoxus (diploid CBS432 ho::nat1)

value: pooled sample of both species


title: Rn SD NAc Saline 24h #1

city: Baltimore

first: Jean Lud

last: Cadet

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

hyb_protocol: Microarray hybridization was carried out using RatRef-12 Expression BeadChips arrays (22, 523 probes) (Illumina Inc., San Diego, CA) as previously described (Cadet et al., 2010a). In brief, a 600 ng aliquot of total RNA from each NAc sample was amplified using Illumina RNA Amplification kit (Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics, Indianapolis, IN). 750 ng of each cRNA sample were hybridized to Illumina arrays at 55°C overnight according to the Whole-Genome Gene Expression Protocol for BeadStation (Illumina Inc.). Hybridized biotinylated cRNA was detected with Cyanine3-streptavidin (GE Healthcare, Piscataway, NJ) and quantified using Illumina's BeadStation 500GX Genetic Analysis Systems scanner.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina. Quantitative polymerase chain reaction (qPCR):  Total RNA was reverse-transcribed to cDNA with oligo dT primer using Advantage RT for PCR kits (BD Biosciences Clontech Laboratories, Palo Alto, CA, USA). Gene-specific primers were generated using Light Cycler Probe Design software and synthesized by the Synthesis and Sequencing Facility of Johns Hopkins University (Baltimore, MD, USA). Real-time PCR experiments were performed using iQ SYBR Green supermix (Bio-Rad Laboratories, Hercules, CA) and Chromo 4 Detector (MJ Research, Inc. Waltham, MA. Fluorescence data collection was performed at the end of each extension phase.  For all qPCR experiments, individual data were normalized using the corresponding OAZ1 signal as described (McCoy et al., 2011).  Western Blot Analysis:  NAc tissues were first washed with chilled 0.01 M PBS. Cytoplasmic and nuclear protein fractions were separated using NE-PER nuclear and cytoplasmic extraction reagents based on the manufacturer's instruction (Pierce, Rockford, IL). Protein concentrations were determined with the BioRad Dc Protein assay reagent (BioRad, Temecula, CA). The lysates were then denatured with sample buffer (62.5 mM Tris-HCl, 10% glycerol, 2% SDS, 0.1% bromophenol blue, and 50 mM DTT) at 100°C for 5 min, and subjected to SDS-PAGE. Proteins were electrophoretically transferred to Hybond-PTM membrane (Amersham Pharmacia Biotech, Piscataway, NJ) and then incubated with specific antibodies: anti-acetyl-histone H3 (Lys 9) and H3 (Lys 18), anti-acetyl-histone H4 (Lys 8),  H4 (Lys 12), and H4 (Lys 16) (Millipore, Billirica, MA 01821, USA); anti-HDAC1 and anti-HDAC2 (Santa Cruz Biotechnology, Inc., Santa Cruz, CA 95060, USA); anti-phospho-CREB and anti-ATF2 (Cell Signaling Technology, Danvers, MA 01923, USA). After washing in Tris-buffered saline with 0.1% Tween-20, membranes were pre-incubated in the detergent/blocking buffer containing 1:2000 horseradish peroxidase (HRP)-conjugated anti-rabbit secondary antibody (Cell Signaling Technology Inc., Danvers, MA, USA) for 1 hr at room temperature. To confirm equal protein loading, blots were re-probed with α-tubulin antibody (1:4000; Sigma, 2 h at RT). LumiGLO chemiluminescent reagents (Cell Signaling Technology Inc., Danvers, MA, USA) were used to detect protein expression. Signal intensity was measured densitometrically with LabWorks version 4.5 (BioImaging Systems analysis software, BioImaging System, UVP Inc., Upland, CA). For quantification, the signal intensity was normalized using the signal intensity of tubulin.

data_processing: The Illumina BeadStudio software was used to measure fluorescent hybridization signals. Data were extracted by BeadStudio (Illumina) and analyzed using GeneSpring software v. 7.3.1 (Silicon Genetics, Redwood City, CA). Raw data were imported into GeneSpring and normalized using global normalization. The normalized data were used to identify changes in gene expression at the different time points after the injection of METH. A gene was identified as significantly affected if it showed increased or decreased expression according to an arbitrary cut-off of 1.7-fold changes at p<0.05, according to the GeneSpring statistical package (unpaired t-test). Similar criteria have been successfully used in our previous microarray studies (Cadet et al., 2009: Jayanthi et al., 2009; Cadet et al., 2011). Network analyses were performed using the Ingenuity Pathway Analysis (IPA) software (Ingenuity Systems, Redwood City, CA). The IPA software allows for the identification of networks, canonical pathways, and biological pathways that are affected by the drug. We also used the IPA software to graphically show the cellular location of genes significantly affected by METH and to overlay differentially affected networks of interest.   Data for quantitative PCR and Western blot analyses are presented as means ± SEM. Statistical analyses were performed using one-way ANOVA analysis followed by Fisher’s protected least significant difference (StatView 4.02, SAS Institute, Cary, NC). Criteria for significance were set at p < 0.05.

organism: Rattus norvegicus

source_name: Nacc tissue

extract_protocol: At the indicated time after the METH or saline injections, rats (n = 5 per group) were euthanized and the NAc was dissected and immediately put on dry ice. The tissues were kept at -70 oC until RNA extraction. Total RNA was isolated from the nucleus accumbens according to the manufacturer’s manual using Qiagen RNeasy mini kit (Qiagen, Valencia, CA, USA). RNA integrity was detected using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: Male Sprague-Dawley rats (Charles River Labs, Raleigh, NC, USA), weighing 375 ±25 g, were used in the experiments. Rats were housed in a temperature-controlled (22.2 + 0.2ºC) room with free access to food and water. The animals received a single injection of METH (20 mg/kg) and were euthanized at various time points afterwards. All animal use procedures were according to the NIH Guide for the Care and Use of Laboratory Animals and were approved by the local Animal Care Committee.

value: Sprague Dawley

tag: weight

tag: agent

value: control

tag: time


title: Rn SD NAc Saline 24h #2


title: S.cerevisiae and S.paradoxus at rich media (YPD), 40min with Phenanthroline, Green dye, repeat #2


title: E2CTR3

description: TODO

value: Control


title: Rn SD NAc Saline 04h #2


title: S.cerevisiae and S.paradoxus at rich media (YPD), 60min with Phenanthroline, Green dye, repeat #2


title: S.cerevisiae and S.paradoxus at rich media (YPD), before Phenanthroline, Green dye, repeat #1


title: S.cerevisiae and S.paradoxus at rich media (YPD), 40min with Phenanthroline, Green dye, repeat #1


title: E2TTA6

description: TODO

value: TTA


title: E2TTA4

description: TODO


title: Rn SD NAc Saline 04h #1


title: E2TTA5

description: TODO


title: hybrid at rich media (YPD), 40min with Phenanthroline, Red dye, repeat #2


title: E2TTA3

description: TODO


title: S.cerevisiae and S.paradoxus at rich media (YPD), 60min with Phenanthroline, Green dye, repeat #1


title: Rn SD NAc 20mg/kg METH 24h #6

value: METH


title: BB_3

city: Toronto

first: Sergei

last: Doulatov

state: Ontario

address: 101 College Street, TMDT 8-301

department: Division of Stem Cell and Developmental Biology

country: Canada

institute: Campbell Family Institute for Cancer  Research/Ontario Cancer Institute

description: cord blood #3

data_processing: The data were normalised using quantile normalisation in R

organism: Homo sapiens

source_name: LIN- CD34+ CD38- CD45RA- THY1- CD49F-

extract_protocol: Lineage-depleted cord blood cells were thawed and flow-sorted. RNA was extracted from 5,000-10,000 sorted cells with Trizol reagent, followed by re-precipitation with EtOH. Quality control was performed with Agilent Bioanalyser.

tag: age

value: newborn

value: umbilical cord blood

tag: cell surface expression

value: LIN- CD34+ CD38- CD45RA- THY1- CD49F-


title: BB_2

description: cord blood #2


title: BB_1

description: cord blood #1


title: BA_3

description: cord blood #3

source_name: LIN- CD34+ CD38- CD45RA- THY1- CD49F+

value: LIN- CD34+ CD38- CD45RA- THY1- CD49F+


title: Rn SD NAc 20mg/kg METH 16h #6


title: Rn SD NAc 20mg/kg METH 16h #5


title: S.cerevisiae and S.paradoxus at rich media (YPD), before Phenanthroline, Green dye, repeat #2


title: Rn SD NAc 20mg/kg METH 24h #4


title: S.cerevisiae and S.paradoxus at rich media (YPD), 20min with Phenanthroline, Green dye, repeat #1


title: BA_1

description: cord blood #1


title: Rn SD NAc 20mg/kg METH 08h #6


title: Rn SD NAc 20mg/kg METH 08h #5


title: 6h post-LH vs. 22h post-LH Non-superovulated Post-LH replicate 1

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description:
the cows were pre-synchronized using an ear implant (3mg norgestomet, Crestar) for 5 days. From day 10 of the estrus cycle onwards, the cow received o-FSH i.m. (Ovagen ICP) twice a day in decreasing doses over 4 days (3.5ml, 2.5ml, 1.5ml and 1ml in total 17ml, equivalent to 299 iu NIH-FSH-S1). Two days before implant removal, prostaglandin (22.5 mg) was administered with the fifth dose of FSH to induce a new estrus cycle and 55h later the ear implants were removed. The day after the last FSH dose, transrectal ultrasound technology was used to collect oocytes from cows with more than eight follicles >8mm. For the pre-LH group cows were ovariectomized 2h after removal of the implant. In the post-LH group, cows received GnRH (1.0 mg Fertagyl in 10ml saline im, Intervet International) at the time of removal of the implant and were ovariectomized 6h and 22h after receiving GnRH. Ovariectomy was performed by laparotomy through a flank incision under local anaesthetic, using lidocaine. The oocyte of the cow non super ovulation and collected 2 hours before, 6 hours after and 22 hours after the GnRH-induced LH surge. Ovaries were collected in 0.9% (w/v) NaCl aqueous solution containing antimycotic agent at 370C and were immediately transported to the laboratory.
cumulus-oocyte complexes (COCs) were collected individually (groups 2hPre-LH, 6hPost-LH, 22hPost-LH, Stimulated preLH, Stimulated postLH, Non-Stimulated preLH, Non-Stimulated postLH) by ovariectomy. For the pre-LH group. Immediately after ovariectomy, COCs were aspirated from putative preovulatory follicles > 8 mm. For the post-LH group immediately after ovariectomy at 6h and 24 h after the LH surge, COCs matured in vivo were aspirated from preovulatory follicles > 8 mm. The oocytes were mechanically denuded by vortexing and washed several times in PBS solution to prevent cumulus cell contamination, pooled in 5, snap-frozen in liquid nitrogen and kept at -80°C until RNA extraction.
Total RNA was amplified by three rounds of linear amplification using the RiboAmp HS RNA Amplification kit (Molecular Devices Corporation). During the third round of amplification, UTP amino-allyl (Ambion, Austin, TX) was incorporated.

hyb_protocol: Hybridizations were performed using Slidehyb buffer #1 (Ambion) at 50ºC for 18 h in the SlideBooster (Advalytix). Slides were then washed twice with 2X SSC-0.5% SDS at 50ºC for 15 minutes and twice with 0.5X SSC-0.5% SDS at 50ºC for 15 minutes. Next, the slides were dipped 3 times in 1X SSC and 3 times in H2O. Finally, the slides were dried by centrifugation at room temperature at 1,200g for 5 minutes.

scan_protocol: Scanned on an VersArray Chipreader system (Bio-Rad laboratories) Images were quantified using Array Pro (version 4.5) (Media Cybernetics).

data_processing: LOESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

label: Alexa 555

organism: Bos taurus

source_name: Oocytes

label_protocol: Three micrograms of amplified amino-allyl modified RNA from each sample was used for labeling with Alexa fluor 555 or 647 (Molecular Probes, Burlington, ON, Canada) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from oocytes using the Picopure RNA extraction kit (Molecular Devices Corporation, Sunnyvale, CA) according to the manufacturer’s instructions, and included DNAse I treatment to remove genomic DNA. Extracted RNA was dissolved in elution buffer and stored at    -80C.

tag: subject

value: non-lactating Holstein Friesian cows

tag: breeed

value: Holstein Friesian

tag: time of collection

value: 6h post-LH

value: non-superovulated cows

tag: sample size

value: total RNA from 5 oocytes

label: Alexa 647

value: 22h post-LH


title: E2TTA1

description: TODO

scan_protocol: Agilent scanner (G2565BA) with Agilent Feature Extraction Software (v.10.5.1.1) according to Agilents GE1_105_Dec08 protocol)

tag: tissue

value: Heart ventricle


title: AA_3

description: cord blood #3

source_name: LIN- CD34+ CD38- CD45RA- THY1+ CD49F+

value: LIN- CD34+ CD38- CD45RA- THY1+ CD49F+


title: E2TTA2

description: TODO

tag: diet


title: 6h post-LH vs. 2h pre-LH Non-superovulated Pre-LH replicate 2

value: 2h pre-LH


title: AA_2

description: cord blood #2


title: Rn SD NAc 20mg/kg METH 16h #4

value: Sprague Dawley


title: AA_1

description: cord blood #1


title: 22h post-LH vs. 6h post-LH Non-superovulated Post-LH replicate 2


title: 2h pre-LH vs. 6h post-LH Non-superovulated Pre-LH replicate 1


title: Adipose_Hispanics_4648891030_K

first: Swapna

last: Mahurkar

address: 2250 Alcazar St

department: Preventive Medicine, Keck School of Medicine

institute: University of Southern California

data_processing: The data were normalised using quantile normalisation with  Genome studio software from Illumina

source_name: Subcutaneous Adipose tissue

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

tag: disease

value: obese

tag: age range

value: 18-25 yr old

tag: ethnicity

value: Hispanics


title: Rn SD NAc Saline 02h #2

value: control


title: Adipose_Hispanics_4648891030_G


title: Adipose_Hispanics_4648891030_J


title: Rn SD NAc 20mg/kg METH 08h #4

value: METH


title: Adipose_Hispanics_4648891030_H


title: Adipose_Hispanics_4648891029_K


title: Rn SD NAc Saline 02h #1


title: Rn SD NAc 20mg/kg METH 24h #3


title: Adipose_Hispanics_4648891029_H


title: Adipose_Hispanics_4648891029_G


title: Adipose_Hispanics_4648891029_I


title: Adipose_Hispanics_4648891029_D


title: 22h post-LH vs. 6h post-LH Superovulated Post-LH replicate 2

value: superovulated cows


title: Adipose_Hispanics_4648891029_F


title: Adipose_Hispanics_4648891028_L


title: 6h post-LH vs. 22h post-LH Superovulated Post-LH replicate 1


title: Adipose_Hispanics_4648891028_K


title: 2h pre-LH vs. 6h post-LH Superovulated Pre-LH replicate 1


title: 6h post-LH vs. 2h pre-LH Superovulated Pre-LH replicate 2


title: Rn SD NAc 20mg/kg METH 24h #2


title: Adipose_Hispanics_4648891028_F


title: non-superovulated vs. superovulated 22h Post-LH replicate 1


title: superovulated vs. non-superovulated 22h Post-LH replicate 2


title: Rn SD NAc 20mg/kg METH 16h #3


title: non-superovulated vs. superovulated 6h Post-LH replicate 1


title: superovulated vs. non-superovulated 6h Post-LH replicate 2


title: Adipose_Hispanics_4648891028_D


title: superovulated vs. non-superovulated 2h Pre-LH replicate 2


title: Rn SD NAc 20mg/kg METH 24h #1


title: Rn SD NAc 20mg/kg METH 16h #1


title: Adipose_Hispanics_4648891028_J


title: Adipose_Hispanics_4648891028_B


title: Adipose_Hispanics_4648891028_H


title: Rn SD NAc 20mg/kg METH 08h #3


title: Adipose_AfricanAmerican_4648891030_I

value: African American


title: Adipose_AfricanAmerican_4648891030_E


title: Rn SD NAc 20mg/kg METH 08h #2


title: non-superovulated vs. superovulated 2h Pre-LH replicate 1

value: non-lactating Holstein Friesian cows


title: Rn SD NAc 20mg/kg METH 08h #1


title: Rn SD NAc 20mg/kg METH 16h #2


title: Adipose_Hispanics_4648891028_E


title: Adipose_AfricanAmerican_4648891030_B


title: METH 20x1 1H4


title: Adipose_AfricanAmerican_4648891030_F


title: Adipose_AfricanAmerican_4648891030_L


title: Adipose_AfricanAmerican_4648891030_C


title: METH 20x1 1H5


title: Adipose_Hispanics_4648891028_C


title: Adipose_AfricanAmerican_4648891030_D


title: Adipose_AfricanAmerican_4648891029_C


title: Adipose_AfricanAmerican_4648891029_J


title: 1 Gy 5

city: Kuopio

first: Katriina

last: Huumonen

address: PO. Box 1627

department: Department of Environmental Sciences

country: Finland

institute: University of Eastern Finland

hyb_protocol: Samples were incubated at 95˚C for 2 minutes and hybridized to whole genome oligoarrays (Washington University, St. Louis, MO, USA) containing 22,490 oligo features.

scan_protocol: ScanArray 5000 chip reader (GSI Lumonics, Bedford, MA, USA) was used at 532 nm to obtain quantitative gene expression levels.

data_processing: The scanned images were quantified in ScanArray Express 3.0 (Perkin-Elmer, Waltham, MA, USA). Data of each slide was imported to Matlab computing environment (The Mathworks, Natick, MA, USA). Mean of spot fore- and background intensities were used in the analysis. Slide intensities were visually inspected with boxplots and spatial plots to find deficiencies and anomalies.

source_name: 1 Gy exposed nematodes

label_protocol: 25 µg of total RNA was reverse-transcribed using anchored oligo-dT primer (Sigma-Aldrich, St. Louis, MO, USA) and SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA) in the presence of Cy3-dUTP (Amersham Biosciences, Little Chalfont, Bucks, UK).

growth_protocol: Nematodes were thawed and grown at +20˚C according to standard procedures. After 2 days 5-10 L4 stage larvae (per dish) were transferred to 20 of 60-mm Petri dishes. After a week nematodes were collected with M9 buffer and redistributed to ten 90-mm Petri dishes to fasten the growth. To synchronize nematodes for RNA isolation they were collected again a week after the redistribution and embryos were isolated from adults with 1% hypochlorite solution with 250 mM KOH. After 2-3 days L4 stage nematodes were collected.

extract_protocol: Total RNA was isolated using Ribopure Total RNA isolation-kit (Ambion, Foster City, CA, USA) with one exception to manufacturer’s instructions: bromochloropropane (BCP) was replaced by chloroform.

treatment_protocol: Nematodes were exposed to X-radiation in the radiation therapy unit of the Kuopio University Hospital with Varian 600C linear accelerator (Varian Medical Systems, Palo Alto, CA, USA).

value: 1 Gy exposed

tag: Stage


title: 1 Gy 2


title: METH Control Saline 1H4


title: Adipose_AfricanAmerican_4648891030_A


title: Adipose_AfricanAmerican_4648891029_A


title: METH 20x1 1H3


title: Adipose_AfricanAmerican_4648891028_G


title: Adipose_AfricanAmerican_4648891029_B


title: Adipose_AfricanAmerican_4648891028_I


title: Control 10

source_name: Sham-irradiated nematodes

value: Sham-irradiated


title: 1 Gy 15


title: Adipose_AfricanAmerican_4648891029_L


title: Adipose_AfricanAmerican_4648891029_E


title: Adipose_AfricanAmerican_4648891028_A


title: 1 Gy 3


title: METH Control Saline 1H3


title: METH 20x1 1H2


title: Control 1


title: Control 7


title: Control 9


title: METH Control Saline 1H1


title: METH Control Saline 1H2


title: Pol2 ChIP vs input in top1 at 37C

description: ChIP of Pol2 vs input DNA in top1 cells after growth to log phase at room temperature and then shift to 37C for 1 hour.  Two replicates.

hyb_protocol: Done according to Agilent Yeast Tiling Array (G4491A) manufacturer's instructions.

scan_protocol: According to manufacturer's instructions.

data_processing:
Following scanning, features were extracted using Agilent Feature Extraction and normalized using Agilent ChIP Analytics using default settings except that dye swaps were done when appropriate.
Full processed data is available in the ChIP_Analytics tsv supplementary files.  VALUE in the data table represents the normalized log ratio test/ref.

source_name: AMR51, input

label_protocol: Done as in Robyr and Grunstein, Methods 2003.

growth_protocol: Cells were grown to log phase in YPD at room temperature.

extract_protocol: Done as in Hecht et al., Nature 1996.

treatment_protocol: Cells were shifted to Galactose or 37C for 30 minutes or 1 hour depending upon experiment.

tag: antibody

source_name: AMR51, Pol2 ChIP

value: anti-Pol2 (Covance #8WG16)


title: METH 20x1 1H1

tag: strain


title: BA_2

description: cord blood #2

value: newborn

value: umbilical cord blood

value: LIN- CD34+ CD38- CD45RA- THY1- CD49F+


title: CD70TG*IFNg-/- biological rep 2

city: Amsterdam

first: Laura

last: Gutierrez

address: Plesmanlaan 125

department: Blood Cell Research

country: Netherlands

institute: Sanquin Research

description: Gene expression in CD71+ bone marrow cells from CD70TG*Ifng-/- mice

hyb_protocol: FS450_0001 100-300ng of total RNA was hybridized to Mouse Gene 1.0 ST Array GeneChips, according to the manufacturer’s protocols (Affymetrix).

scan_protocol: According to affymetrix scan protocol, available at www.affymetrix.com using a Scanner 3000 7G. P/N 702569 Rev. 5

data_processing: RMA pre-processing and baseline transformation to median of all samples using Genespring GX Software (Agilent Technologies).

source_name: CD71+ bone marrow cells from CD70TG*Ifng-/- mouse 2

label_protocol: A comprehensive description of step-by-step instructions and lists of reagents required for the optimized Whole Transcript (WT) Sense Target Labeling Assay are described in the GeneChip Whole Transcript Sense Target Labeling Assay Manual (P/N 701880), available at www.affymetrix.com.

growth_protocol: Mice were bred and maintained on a C57BL/6 background in the animal facilities of the Academic Medical Center (University of Amsterdam, Amsterdam, The Netherlands) in specific pathogen-free conditions. Mice were given standard chow and acidified drinking water ad libitum.

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

treatment_protocol: Single cell suspensions from bone marrow were obtained by crushing the bones of the hindlegs, and filtering the suspension through a 40µm cell strainer. CD71+ cells were MACS-enriched from the bone marrow of WT, CD70TG, IFNg-/- and CD70TG*IFNg-/- mice by labelling with biotin-conjugated CD71 antibodies (eBioscience) and using streptavidin-conjugated microbeads (Miltenyi Biotech).

tag: genotype/variation

value: Bone marrow

tag: cell type

value: CD71+ cells (MACS-enriched)


title: Top2 ChIP in top1,top2-ts mutant

description: Top2 ChIP in top1,top2-ts cells vs wild type cells following shift to 37C.

source_name: RS192, Top2 ChIP

value: anti-Top2 (Topogent #2014)

source_name: W303-1a, Top2 ChIP


title: Top2 ChIP vs input in top1 at 37C

description: ChIP of Top2 vs input DNA in top1 cells after growth to log phase at room temperature and then shift to 37C for 1 hour.  Two replicates.

source_name: AMR51, Top2 ChIP


title: Pol2 ChIP vs input in top1,top2-ts at 37C

description: ChIP of Pol2 vs input DNA in top1,top2-ts cells after growth to log phase at room temperature and then shift to 37C for 1 hour.  Two replicates.

source_name: RS192, input

source_name: RS192, Pol2 ChIP


title: Top2 ChIP vs input in top1,top2-ts at 37C

description: ChIP of Top2 vs input DNA in top1,top2-ts cells after growth to log phase at room temperature and then shift to 37C for 1 hour.  Two replicates.


title: Top2 ChIP vs input in wild type at 37C

description: ChIP of Top2 vs input DNA in wild type cells after growth to log phase at room temperature and then shift to 37C for 1 hour.  Two replicates.

source_name: W303-1a, input


title: CD70TG*IFNg-/- biological rep 3

source_name: CD71+ bone marrow cells from CD70TG*Ifng-/- mouse 3


title: Ifng-/- biological rep 3

description: Gene expression in CD71+ bone marrow cells from Ifng-/- mice

source_name: CD71+ bone marrow cells from Ifng-/- mouse 3

value: Ifng-/-


title: WT CFTR exposed to PA01 replicate 3

city: Hanover

first: Thomas

middle: H

last: Hampton

state: NH

address: North College Street

department: Pharm/Tox

institute: Dartmouth Medical School

description: GT051310_Sample Wt Bact-3.CEL

hyb_protocol: Biotinylated cRNA products were hybridized to Affymetrix genechip HGU 133Plus2 arrays for 16 h at 40°C in a Gene Chip Hybridization oven 640 using the manufacturer's hybridization buffer (Affymetrix, Santa Clara, CA) in the Dartmouth Genomics and Microarray Laboratory (http://dms.dartmouth.edu/dgml/background/).

scan_protocol: Arrays were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). The chips were scanned with the 7G Affymetrix Gene Scanner (Affymetrix) according to manufacturer's procedures.

data_processing: Raw fluorescence values were normalized and summarized raw gene array data using RMA as implemented in Bioconductor.

source_name: WT CFTR exposed to PA01

label_protocol: First-strand cDNA synthesis was conducted by priming the mRNA with a T7-(dT24) primer. Double-stranded cDNA was prepared using Life Technology Superscript cDNA Synthesis System (Invitrogen, Carlsbad, CA). From cDNA, cRNA was synthesized using the T7 MegaScript In Vitro Transcription kit (Ambion, Austin, TX). Synthesized cRNA was labeled during transcription (Megascript system; Ambion) with biotin-11–cytidine triphosphate and biotin-16–uridine triphosphate (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: CFBE41o- cells, a human bronchial epithelial cell line homozygous for the ∆F508-CFTR mutation, and CFBE41o- cells complemented with either ∆F508-CFTR (CFBE-∆F508-CFTR) or wt-CFTR (CFBE-wt-CFTR) were generously provided by Dr. J.P. Clancy (University of Alabama).  In all studies, we examined the effect of P. aeruginosa strain PAO1 on CFBE-∆F508-CFTR cells compared to CFBE-wt-CFTR cells, since both lines contain three copies of CFTR (either ∆F508/∆F508/∆F508 or ∆F508/∆F508/wt-CFTR).  Cells were grown as polarized monolayers in air-liquid interface culture on Transwell filters as described previously. Briefly, cells were seeded at 1 x 106 on 24 mm Transwell filters and grown for 8 days (to develop polarized monolayers) in minimal essential medium (MEM) (Mediatech, Herndon, VA) with 10% fetal bovine serum, 2 mM L-glutamine, 50 U/ml penicillin, and 50 g/ml streptomycin at 37°C and 5% CO2, balance air.

extract_protocol: Cells were then homogenized with 600 μl RLT lysis buffer from the Qiagen  RNeasy kit, and the homogenate was vortexed for several seconds and drawn  through a 20-gauge needle 10 times. We then added 600 μl of 100% ethanol, and  applied samples to an RNeasy column for separation following manufacturer’s instructions.

treatment_protocol: PAO1 was added to the apical side of monolayers at a multiplicity of infection (MOI) of 30:1 for 1 hour in the absence of antibiotics, and then planktonic PAO1 was removed by replacing the apical medium with MEM supplemented with 0.4% arginine. Control monolayers were treated identically except that vehicle only (medium used to grow PAO1, MEM supplemented with 0.4% arginine) was added to the apical side of cells.

value: CFBE41o-  wt-CFTR


title: CD70TG*IFNg-/- biological rep 1

source_name: CD71+ bone marrow cells from CD70TG*Ifng-/- mouse 1


title: WT CFTR exposed to PA01 replicate 2

description: GT051310_Sample Wt BAct-2.CEL


title: WT CFTR exposed to PA01 replicate 4

description: GT051310_Sample Wt Bact-4.CEL


title: Ifng-/- biological rep 2

source_name: CD71+ bone marrow cells from Ifng-/- mouse 2


title: Ifng-/- biological rep 1

source_name: CD71+ bone marrow cells from Ifng-/- mouse 1


title: Pol2 ChIP vs input in top2-ts at 37C

description: ChIP of Pol2 vs input DNA in top2-ts cells after growth to log phase at room temperature and then shift to 37C for 1 hour.  Two replicates.

source_name: RS191, input

source_name: RS191, Pol2 ChIP


title: Pol2 ChIP vs input in wild type at 37C

description: ChIP of Pol2 vs input DNA in wild type cells after growth to log phase at room temperature and then shift to 37C for 1 hour. Two replicates.

source_name: W303-1a, Pol2 ChIP


title: Pol II ChIP during Pol II inhibition

hyb_protocol: Blocking and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added and incubated 95°C for 3 min and 37°C for 15 min, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: The Agilent DNA microarray scanner (G2565CA) was used for scanning. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization. Agilent Analytics software (v. 1.3) was used to generate the TSV files.

source_name: Z460, Pol II ChIP

label_protocol: 500 ng of amplified DNA were primed with 20 µl of 2.5x random primer (BioPrime kit; Invitrogen) at 95°C for 5 min, then dNTP mix (each 1.2mM, dCTP 0.6 mM), Cy3-dCTP or Cy5-dCTP and Klenow (40U) were added and incubated at 37°C for 3 hours.

extract_protocol: The ChIP assays were performed as previously described (Hecht et al., 1996). Briefly, crosslinked whole cell extract was incubated overnight with the antibodies directed against histone H3 C-terminus (Abcam, 1791), Top2 (TopoGEN Inc., 2014), Pol II C-terminus (Covance, 8WG16) or TBP (Santa Cruz Biotechnology, sc26143) together with Protein A-agarose beads. The beads were washed and the crosslinked DNA was eluted. After reverse crosslinking, eluate samples were purified with phenol-chloroform extraction.

treatment_protocol: The rpb1-1 mutant and isogenic wild type strains were treated as previously described (Holstege et al., 1998).

tag: genotype

tag: treatment

value: temperature shift

value: anti-Pol II

tag: antibody vendor

value: Covance

tag: antibody catalog #

source_name: Z579, Pol II ChIP


title: WT CFTR exposed to PA01 replicate 1

description: GT051310_Sample Wt BAct-1.CEL


title: H3 ChIP in top1,top2-ts mutant

description: H3 ChIP in top1,top2-ts cells vs wild type cells following shift to 37C.

source_name: RS192, H3 ChIP

value: anti-H3 (Abcam #1791)

source_name: W303-1a, H3 ChIP


title: WT CFTR unexposed replicate 2

description: GT051310_Sample Wt -2.CEL

source_name: WT CFTR unexposed


title: WT CFTR unexposed replicate 3

description: GT051310_Sample Wt -3.CEL


title: Top2 ChIP during Pol II inhibition

source_name: Z460, Top2 ChIP

value: TopoGen Inc.

source_name: Z579, Top2 ChIP


title: CF CFTR exposed to PA01 replicate 3

description: GT051310_Sample delta F Bact-3.CEL

source_name: CF CFTR exposed to PA01

value: CFBE41o-  ∆F508-CFTR


title: WT CFTR unexposed replicate 4

description: GT051310_Sample Wt -4.CEL


title: WT CFTR unexposed replicate 1

description: GT051310_Sample Wt-1.CEL


title: CF CFTR exposed to PA01 replicate 4

description: GT051310_Sample Delta F Bact-4.CEL


title: H3 ChIP during H4 depletion

source_name: UKY403, H3 ChIP

treatment_protocol: For nucleosome depletion we repressed the unique GAL-H4 gene in UKY403 cells by growing in YEPD for 6 hours after the shift from YEPG culture. Control cells were obtained from identical cultures grown in YEPG.

value: glucose

value: anti-histone H3-C terminus

value: Abcam

value: galactose


title: HK2-4031 at 0nM biological replicate 1

city: Worcester

first: Daniel

middle: R

last: Caffrey

state: MA

address: 364 Plantation St

institute: UMASS Medical School

description:
HK2-4031_0nM-1
HK2-4031_0nMsiRNA-10nMas-15.CEL

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Human U133plus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were normalized in Bioconductor using the RMA method. Differentially regulated genes were identified using a moderated t-test.  False discovery rate adjusted P-values were calculated using the method of Benjamini and Hochberg.

source_name: Hep3B liver cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNA was purified 48 hours post-transfection using the RNeasy mini kit from Qiagen.

tag: cell line

value: Hep3B liver cancer cells

tag: sirna

tag: sirna concentration

tag: biological replicate


title: CD70Tg biological rep 3

description: Gene expression in CD71+ bone marrow cells from CD70TG mice

source_name: CD71+ bone marrow cells from CD70TG (clone F13) mouse 3

tag: tissue


title: HK2-4031 at 0nM biological replicate 2

description:
HK2-4031_0nM-2
HK2-4031_0nMsiRNA-10nMas-18.CEL


title: HK2-4031 at 1nM biological replicate 2

description:
HK2-4031_1nM-2
HK2-4031_1nMsiRNA-9nMas-22.CEL


title: CD70Tg biological rep 2

source_name: CD71+ bone marrow cells from CD70TG (clone F13) mouse 2


title: CF CFTR exposed to PA01 replicate 2

description: GT051310_Sample delta F Bact-2.CEL


title: HK2-4031 at 1nM biological replicate 1

description:
HK2-4031_1nM-1
HK2-4031_1nMsiRNA-9nMas-19.CEL


title: CF CFTR unexposed replicate 3

description: GT051310_Sample delta F -3.CEL

source_name: CF CFTR unexposed


title: CF CFTR unexposed replicate 4

description: GT051310_Sample Delta F -4.CEL


title: CF CFTR unexposed replicate 2

description: GT051310_Sample delta F -2.CEL


title: WT biological rep 3

description: Gene expression in CD71+ bone marrow cells from WT mice

source_name: CD71+ bone marrow cells from WT mouse 3

value: WT


title: CF CFTR exposed to PA01 replicate 1

description: GT051310_Sample delta F Bact-1.CEL


title: HK2-4031 at 10nM biological replicate 2

description:
HK2-4031_10nM-2
HK2-4031_10nMsiRNA-0nMas-16b.CEL


title: CF CFTR unexposed replicate 1

description: GT051310_Sample delta F-1.CEL


title: BJ cells, IR, 6h, rep2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

description: Expression data from irradiated BJ cells, 6h (5 Gy)

hyb_protocol: Five ug of fragmented cRNAs were hybridized  for 16 hr at 45°C  to Affymetrix Human Genome U133A 2.0 Arrays; Arrays were washed and stained in the Affymetrix Fluidics Station 450. Hybridization and downstream processing of the arrays were performed as recommended by the manufacturer.

scan_protocol: Arrays were scanned using GeneChip® Scanner 3000.

data_processing: CEL files were processed using Affy Eexpression Console Tool (rma method).

source_name: BJ cells, IR 6h

label_protocol: Biotinylated cRNAs were prepared according to Affymetrix standard GeneChip® Array Protocols, as instructed in the Affymetrix  GeneChip® Expression analysis technical manual.

growth_protocol: Cells were grown  in DMEM which was routinely supplemented with 10% FCS; Cells were maintained in a humidified, 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was extracted from cells using the RNeasyÒ Plus mini kit (Qiagen), in combination with QIAshredderTM columns (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Cells were irradiated at 63.25 R/min to a dose of either 5 Gy, using a Keithly model 96035 (15 cc) ion chamber accompanied with a Keithly model 35050A electrometer. Irradiated cells were incubated for selected time periods at 37°C. Mock-irradiated controls were treated identically, excluding the IR treatment.

value: BJ

tag: stress

value: 5 Gy IR

tag: time


title: HK2-4031 at 10nM biological replicate 1

description:
HK2-4031_10nM-1
HK2-4031_10nMsiRNA-0nMas-13.CEL


title: WT biological rep 1

source_name: CD71+ bone marrow cells from WT mouse 1

value: Bone marrow

value: CD71+ cells (MACS-enriched)


title: BJ cells, IR, 6h, rep1


title: HK2-3581M at 0nM biological replicate 1

description:
HK2-3581M_0nM-1
HK2-3581M_0nMsiRNA-25nMsg2-10.CEL


title: Pancreatic-iPS Cells clone 3

city: Boston

first: Ori

last: Bar-Nur

address: 185 Cambridge st.

department: Center of Regenerative medicine

institute: Harvard University

description:
PiPSCs #3
Gene expression data from Pancreatic-iPS #3.

hyb_protocol: 11ug cRNA, Affymetrix protocol.

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4.

data_processing: Data were RMA normalized using Affymetrix Expression Console.

source_name: iPS cells from pancreatic non-beta cells

label_protocol: 200ng total RNA, Affymetrix protocol.

growth_protocol: Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium.

extract_protocol: Total RNA from the BiPSCs and PiPSCs was isolated using the Qiagen RNeasy mini kit.

treatment_protocol: Total RNA was isolated from undifferentiated pluripotent stem cells grown in standard HESC growth conditions on a mouse embryonic fibroblast feeder layer.

tag: gender

value: male

value: undifferentiated induced pluripotent stem cells (iPSCs)

tag: cell type derived from

value: pancreatic non-beta cells


title: HK2-3581M at 0nM biological replicate 3

description:
HK2-3581M_0nM-3
HK2-3581M_0nMsiRNA-25nMsg2-12.CEL


title: BJ cells, IR, 6h, rep3


title: HK2-3581M at 0nM biological replicate 2

description:
HK2-3581M_0nM-2
HK2-3581M_0nMsiRNA-25nMsg2-11.CEL


title: Top2 ChIP during H4 depletion

source_name: UKY403, Top2 ChIP

tag: antibody


title: Beta-iPS Cells clone 4

description:
BiPSCs #4
Gene expression data from Beta-iPS #4.

source_name: iPS cells from pancreatic beta cells

value: pancreatic islet beta cells


title: BJ cells, IR, 3h, rep2

description: Expression data from irradiated BJ cells, 3h (5 Gy)

source_name: BJ cells, IR 3h


title: CD70Tg biological rep 1

source_name: CD71+ bone marrow cells from CD70TG (clone F13) mouse 1

tag: strain


title: BJ cells, IR, 3h, rep3


title: BJ cells, IR, 3h, rep1


title: Beta-iPS Cells clone 1

description:
BiPSCs #1
Gene expression data from Beta-iPS #1.


title: HK2-3581M at 1nM biological replicate 2

description:
HK2-3581M_1nM-2
HK2-3581M_1nMsiRNA-24nMsg2-8.CEL


title: Beta-iPS Cells clone 2

description:
BiPSCs #2
Gene expression data from Beta-iPS #2.

value: female


title: WT biological rep 2

source_name: CD71+ bone marrow cells from WT mouse 2

tag: genotype/variation


title: HK2-3581M at 1nM biological replicate 3

description:
HK2-3581M_1nM-3
HK2-3581M_1nMsiRNA-24nMsg2-9.CEL


title: BJ cells, untreated, 6h, rep2

description: Expression data from untreated BJ cells, 6h

source_name: BJ cells, untreated, 6h

value: untreated


title: HK2-3581M at 1nM biological replicate 1

description:
HK2-3581M_1nM-1
HK2-3581M_1nMsiRNA-24nMsg2-7.CEL


title: AT120

city: Cambridge

first: Bernardo

last: Lemos

address: 16 Divinity Avenue, Room 2105

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Drosophila melanogaster

source_name: Total RNA from XXYrDNA.1.0 female genotype.

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

tag: sex

value: female (XXY)

tag: age

value: 2 days old, unmated

source_name: Total RNA from XXYrDNA.0.46 female genotype.


title: BJ cells, untreated, 6h, rep3


title: HK2-3581M at 10nM biological replicate 3

description:
HK2-3581M_10nM-3
HK2-3581M_10nMsiRNA-15nMsg2-6.CEL


title: HK2-3581M at 10nM biological replicate 2

description:
HK2-3581M_10nM-2
HK2-3581M_10nMsiRNA-15nMsg2-5.CEL


title: Human Exocervix Female 8

city: Mexico City

first: Jaime

last: Berumen

address: Dr. Balmis #148 Col. Doctores

department: Departamento de Medicina Experimental

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: RMA default expression value derived from Affymetrix Expression Console software

hyb_protocol: Following fragmentation, ssDNA were hybridized for 16 hr at 45C and 60 rpm on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_0007

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing:
Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console. The analysis was done at Gene Level Default: RMA-Sketch
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label: Biotin

source_name: Healthy female exocervix

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cell lines were grown according to standard conditions.

value: Female


title: BJ cells, untreated, 6h, rep1


title: Human Exocervix Female 10


title: AT119

description: Biological replicate

tag: genotype


title: Human Exocervix Female 9


title: HK2-3581M at 10nM biological replicate 1

description:
HK2-3581M_10nM-1
HK2-3581M_10nMsiRNA-15nMsg2-4.CEL

source_name: Hep3B liver cancer cells


title: BJ cells, untreated, 3h, rep3

description: Expression data from untreated BJ cells, 3h

source_name: BJ cells, untreated, 3h


title: AT118

description: Biological replicate


title: BJ cells, untreated, 3h, rep2


title: HK2-3581M at 25nM biological replicate 3

description:
HK2-3581M_25nM-3
HK2-3581M_25nMsiRNA-0nMsg2-3.CEL


title: Human Exocervix Female 7


title: AT117

description: Biological replicate


title: BJ cells, untreated, 3h, rep1


title: Human Exocervix Female 6


title: AT116

description: Biological replicate


title: BJ cells, untreated, 0h, rep3

description: Expression data from untreated BJ cells, 0h

source_name: BJ cells, untreated, 0h


title: HK2-3581M at 25nM biological replicate 2

description:
HK2-3581M_25nM-2
HK2-3581M_25nMsiRNA-0nMsg2-2.CEL


title: HK2-3581M at 25nM biological replicate 1

description:
HK2-3581M_25nM-1
HK2-3581M_25nMsiRNA-0nMsg2-1.CEL


title: BJ cells, untreated, 0h, rep2


title: AT115

description: Biological replicate


title: Human Exocervix Female 4


title: AT114

description: Biological replicate


title: STAT3-1676M at 0nM biological replicate 2

description:
STAT3-1676M_0nM-2
STAT3-1676M_0nM-25nMsg2-14.CEL

source_name: MCF-7 breast cancer cells

value: MCF-7 breast cancer cells


title: STAT3-1676M at 0nM biological replicate 1

description:
STAT3-1676M_0nM-1
STAT3-1676M_0nM-25nMsg2-13.CEL


title: AT113

description: Biological replicate


title: Human Exocervix Female 5


title: BJ cells, untreated, 0h, rep1


title: A194

description: Biological replicate

source_name: Total RNA from XYrDNA.0.85 male genotype.

value: male (XY)

source_name: Total RNA from XYrDNA.1.0 male genotype.


title: U2OS cells, IR, 6h, rep1

description: Expression data from irradiated U2OS cells, 6h (5 Gy)

source_name: U2OS cells, IR 6h


title: Human Exocervix Female 1


title: STAT3-1676M at 1nM biological replicate 1

description:
STAT3-1676M_1nM-1
STAT3-1676M_1nM-24nMsg2-10.CEL


title: STAT3-1676M at 0nM biological replicate 3

description:
STAT3-1676M_0nM-3
STAT3-1676M_0nM-25nMsg2-15.CEL


title: Human Exocervix Female 2


title: U2OS cells, IR, 6h, rep2


title: STAT3-1676M at 1nM biological replicate 2

description:
STAT3-1676M_1nM-2
STAT3-1676M_1nM-24nMsg2-11.CEL


title: STAT3-1676M at 1nM biological replicate 3

description:
STAT3-1676M_1nM-3
STAT3-1676M_1nM-24nMsg2-12.CEL


title: A188

description: Biological replicate

source_name: Total RNA from XYrDNA.0.46 male genotype.


title: Human Exocervix Female 3


title: A187

description: Biological replicate


title: STAT3-1676M at 10nM biological replicate 3

description:
STAT3-1676M_10nM-3
STAT3-1676M_10nM-15nMsg2-6.CEL


title: A196

description: Biological replicate


title: A167

description: Biological replicate

source_name: Total RNA from XYrDNA.0.87 male genotype.


title: A185

description: Biological replicate


title: U2OS cells, IR, 3h, rep1

description: Expression data from irradiated U2OS cells, 3h (5 Gy)

source_name: U2OS cells, IR 3h


title: U2OS cells, IR, 6h, rep3


title: U2OS cells, IR, 3h, rep3


title: STAT3-1676M at 10nM biological replicate 2

description:
STAT3-1676M_10nM-2
STAT3-1676M_10nM-15nMsg2-5.CEL


title: A186

description: Biological replicate


title: U2OS cells, IR, 3h, rep2


title: U2OS cells, untreated, 6h, rep2

description: Expression data from untreated U2OS cells, 6h

source_name: U2OS cells, untreated, 6h


title: STAT3-1676M at 10nM biological replicate 1

description:
STAT3-1676M_10nM-1
STAT3-1676M_10nM-15nMsg2-4.CEL


title: STAT3-1676M at 25nM biological replicate 3

description:
STAT3-1676M_25nM-3
STAT3-1676M_25nM-0nMsg2-3.CEL


title: U2OS cells, untreated, 6h, rep3


title: STAT3-1676M at 25nM biological replicate 2

description:
STAT3-1676M_25nM-2
STAT3-1676M_25nM-0nMsg2-2.CEL


title: U2OS cells, untreated, 6h, rep1


title: STAT3-1676M at 25nM biological replicate 1

description:
STAT3-1676M_25nM-1
STAT3-1676M_25nM-0nMsg2-1.CEL


title: A179

description: Biological replicate


title: A180

description: Biological replicate


title: HK2-3581 at 0nM biological replciate 3

description:
HK2-3581_0nMs-3
HK2-3581_0nMsiRNA-25nMsg2-12.CEL

value: Hep3B liver cancer cells


title: A176

description: Biological replicate


title: A178

description: Biological replicate


title: HK2-3581 at 0nM biological replciate 2

description:
HK2-3581_0nMs-2
HK2-3581_0nMsiRNA-25nMsg2-11.CEL


title: U2OS cells, untreated, 3h, rep2

description: Expression data from untreated U2OS cells, 3h

source_name: U2OS cells, untreated, 3h


title: HK2-3581 at 0nM biological replciate 1

description:
HK2-3581_0nMs-1
HK2-3581_0nMsiRNA-25nMsg2-10.CEL


title: U2OS cells, untreated, 3h, rep1


title: U2OS cells, untreated, 3h, rep3


title: U2OS cells, untreated, 0h, rep2

description: Expression data from untreated U2OS cells, 0h

source_name: U2OS cells, untreated, 0h


title: A175

description: Biological replicate


title: A174

description: Biological replicate


title: HK2-3581 at 1nM biological replciate 3

description:
HK2-3581_1nMs-3
HK2-3581_1nMsiRNA-24nMsg2-9.CEL


title: HK2-3581 at 1nM biological replciate 2

description:
HK2-3581_1nMs-2
HK2-3581_1nMsiRNA-24nMsg2-8.CEL


title: A177

description: Biological replicate


title: A173

description: Biological replicate


title: TK6 cells, IR, 6h, rep3

description: Expression data from irradiated TK6 cells, 6h (5 Gy)

source_name: TK6 cells, IR 6h


title: U2OS cells, untreated, 0h, rep1


title: U2OS cells, untreated, 0h, rep3


title: TK6 cells, IR, 6h, rep2


title: Human derived leukemia sample isolated from mouse (corresponded to sample 4)

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

hyb_protocol: Standard Affymetrix hybridisation for Human GeneArrays

scan_protocol: Standard Affymetrix with Scanner System 3000 7G

data_processing: Genespring software version 11.5, RMA normalization

source_name: bone marrow

label_protocol: Standard Affymetrix labeling for Human GeneArrays

growth_protocol: 4 pre-pubertal female B-ALL patients at the time of diagnosis together with patient-specific NSG-derived bone marrow resident blasts obtained after the 2nd re-transplantation

extract_protocol: Isolation of total RNA with Qiagen RNAeasy

tag: cell type


title: A165

description: Biological replicate


title: TK6 cells, IR, 6h, rep1


title: Human derived leukemia sample isolated from mouse (corresponded to sample 3)


title: A161

description: Biological replicate


title: A155

description: Biological replicate


title: HK2-3581 at 10nM biological replicate 1

description:
HK2-3581_10nM-1
HK2-3581_10nMsiRNA-15nMsg2-4.CEL


title: HK2-3581 at 25nM biological replicate 3

description:
HK2-3581_25nM-3
HK2-3581_25nMsiRNA-0nMsg2-3.CEL


title: TK6 cells, IR, 3h, rep3

description: Expression data from irradiated TK6 cells, 3h (5 Gy)

source_name: TK6 cells, IR 3h


title: TK6 cells, IR, 3h, rep2


title: Human derived leukemia sample isolated from mouse (corresponded to sample 2)


title: Human derived leukemia sample isolated from mouse (corresponded to sample 1)


title: HK2-3581 at 10nM biological replicate 3

description:
HK2-3581_10nM-3
HK2-3581_10nMsiRNA-15nMsg2-6.CEL


title: HK2-3581 at 25nM biological replicate 2

description:
HK2-3581_25nM-2
HK2-3581_25nMsiRNA-0nMsg2-2.CEL


title: Human derived leukemia sample 4

description: Human derived leukemia sample 4

value: Human derived leukemia


title: TK6 cells, IR, 3h, rep1


title: HK2-3581 at 1nM biological replciate 1

description:
HK2-3581_1nMs-1
HK2-3581_1nMsiRNA-24nMsg2-7.CEL


title: Human derived leukemia sample 3

description: Human derived leukemia sample 3


title: A154

description: Biological replicate


title: A152

description: Biological replicate


title: HK2-3581 at 25nM biological replicate 1

description:
HK2-3581_25nM-1
HK2-3581_25nMsiRNA-0nMsg2-1.CEL


title: STAT3-1676 at 0nM biological replicate 3

description:
STAT3-1676_0nM-3
STAT3-1676_25nM-0nMsg2-3.CEL


title: A153

description: Biological replicate


title: HK2-3581 at 10nM biological replicate 2

description:
HK2-3581_10nM-2
HK2-3581_10nMsiRNA-15nMsg2-5.CEL


title: Human derived leukemia sample 2

description: Human derived leukemia sample 2


title: TK6 cells, untreated, 6h, rep3

description: Expression data from untreated TK6 cells, 6h

source_name: TK6 cells, untreated, 6h


title: AT28

description: Biological replicate


title: Human derived leukemia sample 1

description: Human derived leukemia sample 1


title: TK6 cells, untreated, 6h, rep1


title: AT26

description: Biological replicate


title: A163

description: Biological replicate


title: STAT3-1676 at 0nM biological replicate 2

description:
STAT3-1676_0nM-2
STAT3-1676_25nM-0nMsg2-2.CEL


title: TK6 cells, untreated, 6h, rep2


title: TK6 cells, untreated, 3h, rep3

description: Expression data from untreated TK6 cells, 3h

source_name: TK6 cells, untreated, 3h


title: MCF7 cell line_resveratrol_250mM_biological replicate 2

middle: I

last: Uribe

state: DF

address: Periferico Sur 4124 Col. Ex rancho de Anzaldo

department: Research

institute: INMEGEN

hyb_protocol: After fragmentation,  700 ng of terminal labeled cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using the Affymetrix Command Console software  and the Affymetrix Genechip Scanner 3000  7G.

data_processing: The data was analyzed using Partek Genomic Suite. Raw intensity probes wer imported by setting up RMA background correction and the differential gene expression intensities were calculated with the default  one way ANOVA parameters.

source_name: RNA from 3 MCF7 cell culture plates treated with 250 mM of resveratrol (SIGMA St. Louis MO)

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 300 ng total RNA  for each sample ( Gene Chip Whole transcript labeling manual ,2005-2007, Affymetrix).

growth_protocol: The MCF-7 human breast cancer cells (ATCC) were maintained in DMEM (Dulbecco´s Modified Eagle´s Medium) supplemented with 10% fetal bovine serum (FBS), in a 5% CO2 incubator at 37°C

extract_protocol: RNA was extracted using the TRIzol reagent as per  manufacturers instructions and a second round of purification was performed using the Rnaeasy Mini Kit columns (Qiagen).

treatment_protocol: Cells were plated at a density of 2 × 105 cells/dish in p60 cell culture dishes 24 hours before the assay. Then, cells were cultured for 48  hours under three conditions: control (0.03% ethanol), RES150 (150 μM of resveratrol in 0.03% ethanol)  and RES250 (250 μM  of resveratrol in 0.3 % ethanol). At the end of the 48 hours treatment period cells were harvested for further RNA extraction.

tag: agent

value: mammary epithelium adenocarcinoma


title: STAT3-1676 at 1nM biological replicate 1

description:
STAT3-1676_1nM-1
STAT3-1676_1nM-24nMsg2-10.CEL

tag: cell line


title: MCF7 cell line_resveratrol_250mM_biological replicate 1


title: TK6 cells, untreated, 3h, rep1


title: STAT3-1676 at 0nM biological replicate 1

description:
STAT3-1676_0nM-1
STAT3-1676_25nM-0nMsg2-1.CEL

tag: sirna


title: MCF7 cell line_resveratrol_150mM_biological replicate 3

source_name: RNA from 3 MCF7 cell culture plates treated with 150 mM of resveratrol (SIGMA St. Louis MO)


title: STAT3-1676 at 10nM biological replicate 3

description:
STAT3-1676_10nM-3
STAT3-1676_10nM-15nMsg2-6.CEL

source_name: MCF-7 breast cancer cells

tag: sirna concentration


title: STAT3-1676 at 1nM biological replicate 3

description:
STAT3-1676_1nM-3
STAT3-1676_1nM-24nMsg2-12.CEL

tag: biological replicate


title: TK6 cells, untreated, 3h, rep2


title: TK6 cells, untreated, 0h, rep2

description: Expression data from untreated TK6 cells, 0h

source_name: TK6 cells, untreated, 0h


title: STAT3-1676 at 10nM biological replicate 2

description:
STAT3-1676_10nM-2
STAT3-1676_10nM-15nMsg2-5.CEL


title: STAT3-1676 at 1nM biological replicate 2

description:
STAT3-1676_1nM-2
STAT3-1676_1nM-24nMsg2-11.CEL


title: MCF7 cell line_resveratrol_150mM_biological replicate 1

tag: tissue


title: Pho4-P1

city: singapore

first: Xiaowei

last: XUE

address: 60 Biopolis Street, #02-01, Genome

department: systems biology 1

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Afer fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. The protocol used for infividual module array stain is EuKGE_WS2v4_450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Phosphate concentratin in medium raised from 0 to 1 mM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug cDNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Yeast S. cerevisiae in log phase was grown in PNB medium with no phosphate for 3 hours and then shift to various phosphate concentration (from 0 to 10 mM) for 80 minutes.

extract_protocol: Extraction of total RNA was performed as manufacture's instractions


title: TK6 cells, untreated, 0h, rep1

tag: stress


title: Pho4-P01

source_name: Phosphate concentratin in medium raised from 0 to 0.1 mM


title: MCF7 cell line_resveratrol_150mM_biological replicate 2


title: Pho4-P0

source_name: Phosphate concentratin in medium raised from 0 to 0 mM


title: Pho4-P10

source_name: Phosphate concentratin in medium raised from 0 to 10 mM


title: STAT3-1676 at 10nM biological replicate 1

description:
STAT3-1676_10nM-1
STAT3-1676_10nM-15nMsg2-4.CEL


title: MCF7 cell line_resveratrol_250mM_biological replicate 3


title: TK6 cells, untreated, 0h, rep3

tag: time


title: MCF7 cell line _vehicle (control)_biological replicate 2

source_name: RNA from 3 MCF7 cell culture plates treated with vehicle (ethanol 0,3%).

value: 0.03% ethanol (control)


title: Pho4-P001

source_name: Phosphate concentratin in medium raised from 0 to .01 mM


title: MCF7 cell line _vehicle (control)_biological replicate 3


title: HepG2 cells, IR, 6h, rep1

description: Expression data from irradiated HepG2 cells, 6h (5 Gy)

source_name: HepG2 cells, IR 6h

value: 5 Gy IR


title: HepG2 cells, IR, 6h, rep3


title: HepG2 cells, IR, 6h, rep2


title: 0minSucChemostat_30minFlaskTransferNoMeOH_BioRep1_TechRep2

city: Seattle

first: Elizabeth

last: Skovran

state: WA

address: 616 NE Northlake Place, Benjamin Hall Rm 440

department: Chemical Engineering

institute: University of Washington

hyb_protocol: Hybridization was carried out by MOgene.

scan_protocol: Scanning was carried out by MOgene.

data_processing: Data processing was carried out as described in Okubo and Skovran et al, 2007. Essentially, data from duplicated probes within each array were averaged and the two technical replicates for each biological replicate were merged together by averaging the Log10 ratios of set "a" with the inverse Log10 ratios of set "b" since the replicates were dye-swaps (see GSE22031 supplementary file: Processed_Matrix.xls). Biological replicates were not averaged and are displayed as "Set 1" and Set 2" in published Supplementary Tables.

organism: Methylorubrum extorquens AM1

source_name: Succinate limited chemostat grown cells

label_protocol: cDNA production and labelling were carried out by MOgene (St. Louis, MO).

growth_protocol: For a starting point (time = 0 min), the carbon-shift experiment utilized cells from a steady-state chemostat culture of M. extorquens AM1 growing on limiting succinate. M. extorquens AM1 was cultivated in a minimal medium (Okubo and Skovran et al, 2007) containing 3.7 mM succinate as a growth-limiting nutrient and 50 mg/mL rifamycin in a 2.2-liter bench-top BioFlo 110 Modular Fermentor (New Brunswick Scientific) with a 1 liter working volume, resulting in an OD600 of ~0.63. Dilution rate was maintained at 0.163 h-1. Cells were maintained at 28 degrees and at pH 6.8 as described previously (Guo and Lidstrom, 2006). After the culture reached steady-state, cells were transferred to flasks before 50 mM methanol addition and incubated at 28 degrees C shaking in a floor incubator, harvesting cells/RNA at time= 0, 10, 30, 60, 120, 240 and 360 min post methanol addition.  For a carbon starvation control, cells were transferred to a flask and incubated in a separate incubator (to avoid methanol vapours) as described above but with no methanol added.

extract_protocol: Total RNA was isolated as described by Okubo and Skovran et al., OMICS. 2007, 11:325-340.

treatment_protocol: Cells were processed as previously described ( Okubo et al., OMICS. 2007, 11:325-340.).

source_name: T=30 min no MeOH added


title: STAT3-1676 at 25nM biological replicate 3

description:
STAT3-1676_25nM-3
STAT3-1676_0nM-25nMsg2-15.CEL


title: 0minSucChemostat_30minFlaskTransferNoMeOH_BioRep1_TechRep1


title: 0minSucChemostat_120minMeOH_BioRep2_TechRep1

source_name: T=120 min post MeOH addition


title: liver_200 mg/kg SP300_6h_biological rep5

city: Hangzhou

first: Xiaoyan

last: Lu

address: Yuhang Road 866

country: China

institute: Zhejiang University

description:
SP300-200-5
Gene expression data from the liver of 200 mg/kg SP300-treated mouse

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) in Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: GeneChips were scanned by GeneChip® Scanner 3000 (Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method in ArrayTrack. Raw microarray intensity data were normalized per chip to the same median intensity value of 1000.

source_name: left lateral liver of the 200 mg/kg SP300-treated mouse, 6 h after injection

label_protocol: Total RNA were amplified, labeled and purified using GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The mice were randomly assigned to one of the following seven treatment groups (5 mice per group): vehicle control (deionized water at 0.1 ml/10 g), SP30 at 10 mg/kg, SP70 at 10 mg/kg, SP70 at 20 mg/kg, SP70 at 40 mg/kg, SP300 at 10 mg/kg, and SP300 at 200 mg/kg. The mice were intravenously injected with the silica particles at 10–200 mg/kg body weight as described above, and sacrificed at 6 h after injection.

extract_protocol: Total RNA was collected using TRIZol Reagent (Invitrogen) for extraction and RNeasy Mini kits (QIAGEN) for purification, in accordance with the manufacturer’s protocols.

treatment_protocol: After 6 h post-injection, an aliquot of the sample for RNA analysis was obtained from the left lateral lobe of the liver in each animal immediately after sacrifice.The excised samples were immediately flash frozen in liquid nitrogen, and stored at -80 °C for microarray analysis.

value: BALB/c

value: left lateral liver


title: STAT3-1676 at 25nM biological replicate 2

description:
STAT3-1676_25nM-2
STAT3-1676_0nM-25nMsg2-14.CEL


title: n-22-9

city: Wuerzburg

first: Burkhard

middle: Gerhard

last: Kneitz

address: Oberdürrbacher Str. 6

department: Klinik und Poliklinik für Urologie und Kinderurologie

institute: University of Wuerzburg

description: mirRNA expression data from a benign prostatic hyperplasia isolated from patient n-22-9

hyb_protocol: hybridization for 16 hr at 42C using a Agilent hybridization oven, labeled targets from 15ug total RNA were used for hybridization

scan_protocol: Arrays were scanned using the ScanArray 4000 (PerkinElmer)

data_processing: The data were analyzed with Bioconductor packages (under R) 1st median value of 4 replicates (flaged spots excluded) was calculated,  2nd vsn normalization, 3rd gene finding using the Limma-package

source_name: benign prostatic hyperplasia

label_protocol: labeling according to the Applied Biosystems mirVana™ manual without deviation from the original protocol

extract_protocol: purification from formalin-fixed paraffin embedded (FFPE) material (RecoverAll™ Total Nucleic Acid Isolation Kit), subsequent miRNA purification (flashPAGE™ Fractionator) without deviation from the original protocol

tag: disease state

value: benign prostatic hyperplasia


title: n-22-6

description: mirRNA expression data from a benign prostatic hyperplasia isolated from patient n-22-6


title: STAT3-1676 at 25nM biological replicate 1

description:
STAT3-1676_25nM-1
STAT3-1676_0nM-25nMsg2-13.CEL


title: liver_200 mg/kg SP300_6h_biological rep4

description:
SP300-200-4
Gene expression data from the liver of 200 mg/kg SP300-treated mouse


title: HepG2 cells, IR, 3h, rep3

description: Expression data from irradiated HepG2 cells, 3h (5 Gy)

source_name: HepG2 cells, IR 3h


title: HepG2 cells, untreated, 6h, rep3

description: Expression data from untreated HepG2 cells, 6h

source_name: HepG2 cells, untreated, 6h


title: HepG2 cells, IR, 3h, rep2


title: HepG2 cells, IR, 3h, rep1


title: n-22-12

description: mirRNA expression data from a benign prostatic hyperplasia isolated from patient n-22-12


title: 0minSucChemostat_60minMeOH_BioRep2_TechRep2

source_name: T=60 min post MeOH addition


title: MCF7 cell line _vehicle (control)_biological replicate 1


title: 0minSucChemostat_120minMeOH_BioRep2_TechRep2


title: 0minSucChemostat_60minMeOH_BioRep2_TechRep1


title: liver_200 mg/kg SP300_6h_biological rep3

description:
SP300-200-3
Gene expression data from the liver of 200 mg/kg SP300-treated mouse


title: liver_10 mg/kg SP300_6h_biological rep5

description:
SP300-10-5
Gene expression data from the liver of 10 mg/kg SP300-treated mouse

source_name: left lateral liver of the 10 mg/kg SP300-treated mouse, 6 h after injection


title: liver_200 mg/kg SP300_6h_biological rep2

description:
SP300-200-2
Gene expression data from the liver of 200 mg/kg SP300-treated mouse


title: HepG2 cells, untreated, 6h, rep2


title: liver_200 mg/kg SP300_6h_biological rep1

description:
SP300-200-1
Gene expression data from the liver of 200 mg/kg SP300-treated mouse


title: n-22-13

description: mirRNA expression data from a benign prostatic hyperplasia isolated from patient n-22-13


title: 0minSucChemostat_30minMeOH_BioRep2_TechRep2

source_name: T=30 min post MeOH addition


title: n-21-6

description: mirRNA expression data from a benign prostatic hyperplasia isolated from patient n-21-6


title: liver_10 mg/kg SP300_6h_biological rep4

description:
SP300-10-4
Gene expression data from the liver of 10 mg/kg SP300-treated mouse


title: HepG2 cells, untreated, 6h, rep1


title: liver_10 mg/kg SP300_6h_biological rep3

description:
SP300-10-3
Gene expression data from the liver of 10 mg/kg SP300-treated mouse


title: n-21-1

description: mirRNA expression data from a benign prostatic hyperplasia isolated from patient n-21-1


title: HepG2 cells, untreated, 3h, rep3

description: Expression data from untreated HepG2 cells, 3h

source_name: HepG2 cells, untreated, 3h


title: liver_10 mg/kg SP300_6h_biological rep2

description:
SP300-10-2
Gene expression data from the liver of 10 mg/kg SP300-treated mouse


title: 0minSucChemostat_10minMeOH_BioRep2_TechRep2

source_name: T=10 min post MeOH addition


title: l7+22-21

description: Gene expression data from a low risk prostate carcinoma l7+22-21

source_name: prostate carcinoma

value: low risk prostate carcinoma


title: 0minSucChemostat_30minMeOH_BioRep2_TechRep1


title: l7+22-19

description: Gene expression data from a low risk prostate carcinomal7+22-19


title: l7+21-12

description: Gene expression data from a low risk prostate carcinoma  l7+21-12


title: l7-21-9

description: Gene expression data from a low risk prostate carcinoma l7-21-9


title: l6-22-20

description: Gene expression data from a low risk prostate carcinoma l6-22-20


title: 0minSucChemostat_10minMeOH_BioRep2_TechRep1


title: l6-22-17

description: Gene expression data from a low risk prostate carcinoma  l6-22-17


title: liver_10 mg/kg SP30_6h_biological rep5

description:
SP30-10-5
Gene expression data from the liver of 10 mg/kg SP30-treated mouse

source_name: left lateral liver of the 10 mg/kg SP30-treated mouse, 6 h after injection


title: 0minSucChemostat_360minMeOH_BioRep1_TechRep1

source_name: T=360 min post MeOH addition


title: liver_10 mg/kg SP300_6h_biological rep1

description:
SP300-10-1
Gene expression data from the liver of 10 mg/kg SP300-treated mouse


title: 0minSucChemostat_240minMeOH_BioRep1_TechRep1

source_name: T=240 min post MeOH addition


title: liver_10 mg/kg SP30_6h_biological rep4

description:
SP30-10-4
Gene expression data from the liver of 10 mg/kg SP30-treated mouse


title: HepG2 cells, untreated, 0h, rep3

description: Expression data from untreated HepG2 cells, 0h

source_name: HepG2 cells, untreated, 0h


title: HepG2 cells, untreated, 3h, rep2


title: 0minSucChemostat_360minMeOH_BioRep1_TechRep2

source_name: Succinate limited chemostat grown cells


title: liver_10 mg/kg SP30_6h_biological rep3

description:
SP30-10-3
Gene expression data from the liver of 10 mg/kg SP30-treated mouse


title: HepG2 cells, untreated, 3h, rep1


title: HepG2 cells, untreated, 0h, rep2


title: liver_10 mg/kg SP30_6h_biological rep1

description:
SP30-10-1
Gene expression data from the liver of 10 mg/kg SP30-treated mouse


title: 0minSucChemostat_120minMeOH_BioRep1_TechRep1


title: 0minSucChemostat_120minMeOH_BioRep1_TechRep2


title: HepG2 cells, untreated, 0h, rep1


title: G361 cells, IR, 6h, rep3

description: Expression data from irradiated G361 cells, 6h (5 Gy)

source_name: G361 cells, IR 6h


title: 0minSucChemostat_240minMeOH_BioRep1_TechRep2


title: liver_40 mg/kg SP70_6h_biological rep5

description:
SP70-40-5
Gene expression data from the liver of 40 mg/kg SP70-treated mouse

source_name: left lateral liver of the 40 mg/kg SP70-treated mouse, 6 h after injection


title: liver_40 mg/kg SP70_6h_biological rep4

description:
SP70-40-4
Gene expression data from the liver of 40 mg/kg SP70-treated mouse


title: l6-21-11

description: Gene expression data from a low risk prostate carcinoma l6-21-11


title: G361 cells, IR, 6h, rep1


title: liver_10 mg/kg SP30_6h_biological rep2

description:
SP30-10-2
Gene expression data from the liver of 10 mg/kg SP30-treated mouse


title: h-21-5

description: Gene expression data from a high risk prostate carcinoma h-21-5

value: high risk prostate carcinoma


title: 0minSucChemostat_60minMeOH_BioRep1_TechRep2


title: G361 cells, IR, 3h, rep3

description: Expression data from irradiated G361 cells, 3h (5 Gy)

source_name: G361 cells, IR 3h


title: G361 cells, IR, 6h, rep2


title: liver_40 mg/kg SP70_6h_biological rep3

description:
SP70-40-3
Gene expression data from the liver of 40 mg/kg SP70-treated mouse


title: h-22-4

description: Gene expression data from a high risk prostate carcinoma h-22-4


title: 0minSucChemostat_60minMeOH_BioRep1_TechRep1


title: l8+21-8

description: Gene expression data from a low risk prostate carcinoma


title: G361 cells, IR, 3h, rep2


title: 0minSucChemostat_30minMeOH_BioRep1_TechRep1


title: 0minSucChemostat_10minMeOH_BioRep1_TechRep2


title: liver_40 mg/kg SP70_6h_biological rep2

description:
SP70-40-2
Gene expression data from the liver of 40 mg/kg SP70-treated mouse


title: h+22-5

description: Gene expression data from a high risk prostate carcinoma h+22-5


title: 0minSucChemostat_30minMeOH_BioRep1_TechRep2


title: 0minSucChemostat_10minMeOH_BioRep1_TechRep1


title: G361 cells, IR, 3h, rep1


title: h+21-7

description: Gene expression data from a high risk prostate carcinoma


title: liver_20 mg/kg SP70_6h_biological rep5

description:
SP70-20-5
Gene expression data from the liver of 20 mg/kg SP70-treated mouse

source_name: left lateral liver of the 20 mg/kg SP70-treated mouse, 6 h after injection


title: liver_40 mg/kg SP70_6h_biological rep1

description:
SP70-40-1
Gene expression data from the liver of 40 mg/kg SP70-treated mouse


title: G361 cells, untreated, 6h, rep1

description: Expression data from untreated G361 cells, 6h

source_name: G361 cells, untreated, 6h


title: h+22-7

description: Gene expression data from a high risk prostate carcinoma h+22-7


title: G361 cells, untreated, 6h, rep2


title: liver_20 mg/kg SP70_6h_biological rep3

description:
SP70-20-3
Gene expression data from the liver of 20 mg/kg SP70-treated mouse


title: G361 cells, untreated, 6h, rep3


title: 0minSucChemostat_0minFlaskTransfer_BioRep1_TechRep2

source_name: T=0 min cells transferred to flask


title: 0minSucChemostat_0minFlaskTransfer_BioRep1_TechRep1


title: liver_20 mg/kg SP70_6h_biological rep4

description:
SP70-20-4
Gene expression data from the liver of 20 mg/kg SP70-treated mouse


title: liver_20 mg/kg SP70_6h_biological rep2

description:
SP70-20-2
Gene expression data from the liver of 20 mg/kg SP70-treated mouse


title: G361 cells, untreated, 3h, rep2

description: Expression data from untreated G361 cells, 3h

source_name: G361 cells, untreated, 3h


title: G361 cells, untreated, 3h, rep1


title: liver_10 mg/kg SP70_6h_biological rep5

description:
SP70-10-5
Gene expression data from the liver of 10 mg/kg SP70-treated mouse

source_name: left lateral liver of the 10 mg/kg SP70-treated mouse, 6 h after injection


title: liver_20 mg/kg SP70_6h_biological rep1

description:
SP70-20-1
Gene expression data from the liver of 20 mg/kg SP70-treated mouse


title: Ewing's Sarcoma Cell Line WE68

city: Salamanca

first: Carlos

last: Mackintosh

address: Campus Miguel de Unamuno S/N

country: Spain

institute: Centro de Investigación del Cáncer

hyb_protocol: Labeled DNA was purified through Illustra G-50 Microspin Columns (Amersham, GE), mixed and then precipitated along with Cot Human DNA (Roche). Hybridization was performed for 48 hours at 42°C and excess probe was removed.

scan_protocol: Data were acquired using an Axon 4000B scanner and GenePix software (Axon Laboratories).

data_processing: Normalization was carried out with GenePix software using the mean of the median of ratios of all the autosomal features in the array.

source_name: Ewing's Sarcoma Cell Line

label_protocol: Tumor and reference DNA was Cy5/Cy3-dCTP-labelled (Amersham, GE) using a non-commercial Random Priming kit composed of random octamers dissolved in Exo-Minus Klenow buffer (Eppicentre), a dNTPs mix depleted in dCTP (Eppendorf), and Exo-Minus Klenow enzyme (Eppicentre).

growth_protocol: In case of cell lines, they were cultured in their corresponding mediums, most of them in RPMI supplemented with 10% FBS. SKES1 in McCoy's 15% FBS and TC71 in IMDM 20% FBS

extract_protocol: Cell lines: DNA was extracted using QIAamp DNA Mini Kit (Qiagen) following manufacturer's instructions for extracting DNA from cell lines; Tumors: Genomic DNA was extracted from frozen tumor biopsies containing at least 70% of tumor cells. Tissue samples containing less than 80% of tumor cells, as quantified by histological examination, were microdissected from unstained glass slides prior to DNA extraction. DNA was isolated using the Qiagen DNA Extraction kit (Qiagen) or the High Pure PCR Template Preparation kit (Roche) following the manufacturer’s recommendations.

treatment_protocol: no treatment was applied to samples before DNA extraction

tag: sample type

value: DNA sample from cell line

tag: primary tumor/metas

tag: overall metastasis

source_name: DNA pooled from 100 healthy donors

tag: source

value: Spanish National Tumor Bank


title: Ewing's Sarcoma Cell Line TTC466

tag: sex


title: Ewing's Sarcoma Cell Line TC71

tag: age