title: rice root MT_two-leaf_2

city: Beijing,

first: Xiaoqiang

last: Liu

address: No.1 West Beichen Road,Chaoyang District

department: Chinese academy of sciences

institute: the institute of genetics and developmental biology

description:
Sample name: 209-2
gene expression of two_leaf stage root of mutant

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression  Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization  Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the  manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining  dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer  Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s  instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies,  Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT  100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA,  US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent  technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: root

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color  (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s  instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH,  Germany).

growth_protocol: were grown in a green house

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was  further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and  RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: no treatment

tag: genotype/variation

value: alt1 mutant

value: root

tag: developmental stage

value: two-leaf stage


title: rice root MT_two-leaf_3

status: Public on Sep 27 2014

type: RNA

country: China

description:
Sample name: 209-3
gene expression of two_leaf stage root of mutant

molecule: total RNA

tag: tissue


title: 0.5mM_11d_Root

city: Urrbrae

first: Darren

last: Plett

state: South Australia

address: Hartley Grove Road

department: ACPFG

country: Australia

institute: University of Adelaide

description: Double stranded DNA was amplified by an in-vitro transcription reaction and labeled with Cy3 fluorescent dye. cRNA was hybridized to a custom 4x44K Maize Oligo Microarray.

hyb_protocol: Overnight hybridizations were performed with equal amounts of labelled cRNA to a custom 4x44K Maize Oligo Microarray from Agilent Technologies (Palo Alto, CA) according to Agilent’s One-Color Microarray-Based Gene Expression Analysis protocol. After hybridization, the microarray slides were washed.

scan_protocol: The microarray slides were immediately scanned with Agilent’s G2505C DNA Microarray Scanner. The images were visually inspected for image artefacts and feature intensities were extracted, filtered, and normalized with Agilent’s Feature Extraction Software (v10.5.1.1). Further quality control and downstream analysis was performed using data analysis tools in GeneData Analyst (v2.2.2).

data_processing: Cy3 median signal intensities were imported into R for further processing, omitting 4825 probes with no and very low fluorescent signals. The intensity values were log2 transformed and quantile normalized. Differently expressed genes were identified by the moderated t-statistic implemented in the LIMMA package (Smyth 2004). P-values were adjusted employing the method by Benjamini & Hochberg (1995) to control the false discovery rate (FDR). Genes were considered differentially expressed between the two conditions when their adjusted p-values were less or equal to 0.01.

organism: Zea mays

source_name: Nitrate treatment

label_protocol: Total RNA was treated with DNase-I followed by polyA RNA isolation (Illustra mRNA Purification Kit, GE Biosciences) for all samples. The total RNA and polyA RNA samples were visualized and quantified on Agilent’s Bioanalyzer 2100 to check for degradation and to determine final concentration. Each mRNA sample was made into double stranded DNA, amplified by an in-vitro transcription reaction and labelled with Cy3 fluorescent dye using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. The cRNA product was purified with Agencourt’s RNAClean Kit that utilizes SPRI (Solid Phase Reversible Immobilization) paramagnetic bead-based technology.

extract_protocol: Dwarf maize (Zea mays L. var Gaspe Flint) were grown in hydroponic systems as described previously (Garnett et al., 2013). Plants were sampled between 5 and 7 h after the start of the light period (06:00). The whole root and the youngest fully emerged leaf blade were excised, snap frozen in liquid N and stored at -80°C. Total RNA was extracted  from frozen tissue (Chomczynski, 1993), and 10 µg aliquots were prepared for microarray analysis. RNA integrity was checked on a 1.2% (w/v) agarose gel. Three biological replicates were analysed in all experiments.

tag: cultivar

value: Gaspe Flint

tag: treatment

value: Nitrate

tag: mm no3-

value: Root

tag: harvest day

tag: replicate

value: consists of 3


title: 2.5mM_15d_Root


title: Control Group - MNCs from healthy subject - Replicate 1

city: Rome

first: fiorella

last: ciaffoni

state: Italy

address: Viale Regina Elena 299

department: Cellular Biology and Neurosciences

country: Italy

institute: Istituto Superiore di Sanità

description: Control

data_processing:
Three different subjects were analyzed per experimenalt point (replicate 1, 2 and 3). Differences in gene expression among groups were identified using the RT 2 Profiler PCR Array Data Analyses Web portal (QIAGEN) and considered statistically significant with a p<0.05 by two-tailed, Student’s t-test.
For the normalization it was used the average of GAPDH as housekeeping gene.
Target gene signals (Ct value cut-off 35) normalized to housekeeping gene; 2^-(Ave deltaCt), where deltaCt = (Ct_Target − Ave(Ct_HKG).
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Biological consequences of gene expression alterations were predicted with the David Bioinformatic Database (David Bioinformatics Resources 6.7 NIAID/NIH)
Normalized data file reports normalized signal (against housekeeping genes) (2^(-Avg.(Delta(Ct)))
Fold Change file reports test/control (i.e., Group1/Control Group) ratios.

label: SYBR Green

organism: Homo sapiens

source_name: bone marrow

label_protocol:
PCR assays were performed using the Human TGFβ/BMP Signaling Pathway PCR array (PAHS-035ZA - SABiosciences, Frederick, MD). Reverse transcription was performed from 500 ng total RNA using RT2 First Strand kit  (SABiosciences, Frederick, MD) following manufacturer's instructions.
RT-PCR was performed with RT2 SYBR ROX qPCR Mastermix (SABiosciences, Frederick,MD) following manufacturer's instructions
Absolute quantification was detected by 7300 Real-TimePCR System (Applied Biosystem).Termal cycling conditions were setted following manufacturer's instructions

extract_protocol: MNCs of patients with PMF were obtained by bone marrow aspirate followed by centrifugation on Ficoll Hypaque density gradient.

value: bone marrow

tag: cell type

value: mononuclear cells

tag: sample

value: BM3366 ALLCELLS, Emeryville, CA

tag: age

tag: Sex

tag: diagnosis (who)

value: healty subject

tag: genotype

value: WT

tag: dipss score at sampling

tag: date of sampling


title: rice root MT_two-leaf_1

description:
Sample name: 209-1
gene expression of two_leaf stage root of mutant


title: rice root WT_two-leaf_3

description:
Sample name: 133-3
gene expression of two_leaf stage root of wild type

value: wildtype


title: 557380A10 - NoDormancy_24h_Polysomal_BR2 vs Dormancy_24h_Polysomal_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Identification of transcripts that are differentially abundant (transcriptome) and transcripts that are addressed to translation (translatome) in imbibed Arabidopsis seeds in relation with dormancy. During imbibition of seeds (16h and 24h in darkness at 25°C, dormant and non-dormant seeds), transcriptome analysis is done on total RNA and translatome analysis on polysomal RNA.

hyb_protocol: Dormancy_24h_Polysomal_BR2 Cy5 / NoDormancy_24h_Polysomal_BR2 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

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

growth_protocol: seed - Media=soil Temperature=20°C/22°C Light=16h

treatment_protocol: Name:Dormancy+Imbibition_24h - time course study - temperature and imbibition,imbibition:time 24hour . At harvest dormant seeds are stored at -20°C. Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 24h at 25°C in darkness.

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)

treatment_protocol: Name:NoDormancy+Imbibition24h - time course study - temperature and imbibition,imbibition:time 24hour . Non-dormant seeds are obtained by after-ripening of dormant seeds: they are stored 3 weeks at 20°C at 56% relative humidity, and sored after at -20°C. Both type of seeds were imbibed 16h or 24h on water at 25°C.Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 24h at 25°C in darkness.


title: 557380A08 - NoDormancy_24h_Polysomal_BR1 vs Dormancy_24h_Polysomal_BR1

hyb_protocol: Dormancy_24h_Polysomal_BR1 Cy5 / NoDormancy_24h_Polysomal_BR1 Cy3 : 30pmol.


title: Group1 - MNCs from patient  Replicate 6

description: Test

data_processing:
Three different subjects (Cntrls) and six different patients (G1) were analyzed. Differences in gene expression among groups were identified using the RT 2 Profiler PCR Array Data Analyses Web portal (QIAGEN) and considered statistically significant with a p<0.05 by two-tailed, Student’s t-test.
For the normalization it was used the average of ACTB as housekeeping gene.
Target gene signals (Ct value cut-off 35) normalized to housekeeping gene; 2^-(Ave deltaCt), where deltaCt = (Ct_Target − Ave(Ct_HKG).
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Biological consequences of gene expression alterations were predicted with the David Bioinformatic Database (David Bioinformatics Resources 6.7 NIAID/NIH)
Normalized data file reports normalized signal (against housekeeping genes) (2^(-Avg.(Delta(Ct)))
Fold Change file reports test/control (i.e., Group1/Control Group) ratios.

source_name: spleen

extract_protocol: Spleen single cell suspension of patients or healthy subjects was obtained by  means of the Gentle MACS Dissociator (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) and mononuclear cells were obtained by centrifugation on ficoll hypaque density gradient.

value: spleen

value: M

value: PMF

value: High risk


title: Group1 - MNCs from patient  Replicate 4

description: Test

value: MF post PV or ET

value: JAK2V617F (homo)


title: 557380A09 - Dormancy_24h_Polysomal_BR2 vs NoDormancy_24h_Polysomal_BR2

hyb_protocol: NoDormancy_24h_Polysomal_BR2 Cy5 / Dormancy_24h_Polysomal_BR2 Cy3 : 30pmol.


title: 557380A07 - Dormancy_24h_Polysomal_BR1 vs NoDormancy_24h_Polysomal_BR1

hyb_protocol: NoDormancy_24h_Polysomal_BR1 Cy5 / Dormancy_24h_Polysomal_BR1 Cy3 : 30pmol.


title: 557380A06 - NoDormancy_24h_Total_BR3 vs Dormancy_24h_Total_BR3

hyb_protocol: Dormancy_24h_Total_BR3 Cy5 / NoDormancy_24h_Total_BR3 Cy3 : 30pmol.


title: Group1 - MNCs from patient  Replicate 3

description: Test

value: F

value: prefibrotic-PMF


title: 557380A02 - NoDormancy_24h_Total_BR1 vs Dormancy_24h_Total_BR1

hyb_protocol: Dormancy_24h_Total_BR1 Cy5 / NoDormancy_24h_Total_BR1 Cy3 : 30pmol.


title: Group1 - MNCs from patient  Replicate 2

description: Test

value: JAK2V617F (hetero)

value: Int-1 risk


title: Group1 - MNCs from patient  Replicate 5

description: Test

value: triple negative (JAK2-, MPL-, CARL-)

value: Int-2 risk


title: 557095A12 - NoDormancy_16h_Polysomal_BR3 vs Dormancy_16h_Polysomal_BR3

hyb_protocol: Dormancy_16h_Polysomal_BR3 Cy5 / NoDormancy_16h_Polysomal_BR3 Cy3 : 30pmol.

treatment_protocol: Name:Dormancy+Imbibition_16h - time course study - temperature and imbibition,imbibition:time 16hour . At harvest dormant seeds are stored at -20°C. Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 16h at 25°C in darkness.

treatment_protocol: Name:NoDormancy_Imbibition_16h - time course study - temperature and imbibition,imbibition:time 16hour . Non-dormant seeds are obtained by after-ripening of dormant seeds: they are stored 3 weeks at 20°C at 56% relative humidity, and sored after at -20°C. Both type of seeds were imbibed 16h or 24h on water at 25°C.Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 16h at 25°C in darkness.


title: 557380A04 - NoDormancy_24h_Total_BR2 vs Dormancy_24h_Total_BR2

hyb_protocol: Dormancy_24h_Total_BR2 Cy5 / NoDormancy_24h_Total_BR2 Cy3 : 30pmol.


title: 557380A05 - Dormancy_24h_Total_BR3 vs NoDormancy_24h_Total_BR3

hyb_protocol: NoDormancy_24h_Total_BR3 Cy5 / Dormancy_24h_Total_BR3 Cy3 : 30pmol.


title: 557095A11 - Dormancy_16h_Polysomal_BR3 vs NoDormancy_16h_Polysomal_BR3

hyb_protocol: NoDormancy_16h_Polysomal_BR3 Cy5 / Dormancy_16h_Polysomal_BR3 Cy3 : 30pmol.


title: rice root WT_two-leaf_2

description:
Sample name: 133-2
gene expression of two_leaf stage root of wild type

tag: genotype/variation

value: root

value: two-leaf stage


title: 557095A08 - NoDormancy_16h_Polysomal_BR1 vs Dormancy_16h_Polysomal_BR1

hyb_protocol: Dormancy_16h_Polysomal_BR1 Cy5 / NoDormancy_16h_Polysomal_BR1 Cy3 : 30pmol.


title: 557095A09 - Dormancy_16h_Polysomal_BR2 vs NoDormancy_16h_Polysomal_BR2

hyb_protocol: NoDormancy_16h_Polysomal_BR2 Cy5 / Dormancy_16h_Polysomal_BR2 Cy3 : 30pmol.


title: LNCAP_control_rep3

city: Woolloongabba

first: Inga

last: Mertens-Walker

address: 37 Kent St

institute: Queensland University of Technology, TRI

hyb_protocol: 1650 ng of the labeled cRNA were loaded into the array chambers and allowed to hybridize at 65⁰C for 17 hours.

scan_protocol: The arrays were scanned using an Agilent scanner (G2565CA) and feature extraction was performed using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: In Genespring GX11: quantile normalization, no baseline transformation, average intensity replicates group 1 / average intensity replicates group 2, t-test unpaired, asymptotic, 2-fold cut-off, p<= 0.05

source_name: LNCaP prostate cancer cell line

label_protocol: 100 ng of total RNA was amplified and labelled using Agilent Low Input Quick Amp Labeling Kit.     200 ng of total RNA was amplified and labelled using Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: In 24 well plates, 120,000 LNCaP cells were grown in RPMI supplemented with 10% FCS for 48 hrs before transfection with siRNAs.

extract_protocol: After 48hrs, RNA was extracted using TRIZOL

treatment_protocol: Lipofectamine 2000 (Life Technologies) was used to transiently transfect LNCaP cells with 20 nM of EphB4 siRNAs (SI00288589, SI04435053; Qiagen, Chadstone, VIC, Australia). The AllStars non-silencing negative control siRNA (Qiagen) was used at the same concentration as gene-specific siRNAs for all experiments.

value: control

tag: cell line

value: LNCaP


title: Group1 - MNCs from patient  Replicate 1

description: Test

tag: tissue

value: mononuclear cells


title: Control Group - MNCs from healthy subject  Replicate 3

description: Control

value: spleen

value: healthy subject

value: WT


title: LNCAP_control_rep1


title: rice root WT_two-leaf_1

description:
Sample name: 133-1
gene expression of two_leaf stage root of wild type

value: wildtype

tag: developmental stage


title: 557095A10 - NoDormancy_16h_Polysomal_BR2 vs Dormancy_16h_Polysomal_BR2

hyb_protocol: Dormancy_16h_Polysomal_BR2 Cy5 / NoDormancy_16h_Polysomal_BR2 Cy3 : 30pmol.


title: 557380A03 - Dormancy_24h_Total_BR2 vs NoDormancy_24h_Total_BR2

hyb_protocol: NoDormancy_24h_Total_BR2 Cy5 / Dormancy_24h_Total_BR2 Cy3 : 30pmol.


title: 557095A06 - NoDormancy_16h_Total_BR3 vs Dormancy_16h_Total_BR3

hyb_protocol: Dormancy_16h_Total_BR3 Cy5 / NoDormancy_16h_Total_BR3 Cy3 : 30pmol.


title: 557380A01 - Dormancy_24h_Total_BR1 vs NoDormancy_24h_Total_BR1

hyb_protocol: NoDormancy_24h_Total_BR1 Cy5 / Dormancy_24h_Total_BR1 Cy3 : 30pmol.


title: LNCAP_siRNA1_rep2

tag: treatment

value: EphB4 knock-down


title: Control Group - MNCs from healthy subject  Replicate 1

description: Control


title: LNCAP_siRNA2_rep1


title: LNCAP_control_rep2


title: LNCAP_siRNA1_rep1


title: 557095A05 - Dormancy_16h_Total_BR3 vs NoDormancy_16h_Total_BR3

hyb_protocol: NoDormancy_16h_Total_BR3 Cy5 / Dormancy_16h_Total_BR3 Cy3 : 30pmol.


title: Control Group - MNCs from healthy subject  Replicate 2

description: Control

value: M


title: 557095A04 - NoDormancy_16h_Total_BR2 vs Dormancy_16h_Total_BR2

hyb_protocol: Dormancy_16h_Total_BR2 Cy5 / NoDormancy_16h_Total_BR2 Cy3 : 30pmol.


title: LNCAP_siRNA1_rep3


title: B strain, wild type

status: Public on Sep 26 2014

city: Daejeon

first: Seungwoo

last: Hwang

address: 52 Eoeun-dong Yuseong-gu

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
BL21(DE3)
Gene expression in B wild type after 6hrs of growth under anaerobic condition

hyb_protocol: After checking labeling efficiency, each 600ng of cyanine 3-labeled cRNA target were fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60°C for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent E.coli Oligo microarray. The arrays hybridized at 65°C for 17 h using Agilent Hybridization oven(Agilent Technology, USA). The hybridized miroarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technology, USA).

data_processing: Data quantification was performed using Agilent Feature Extraction software 9.3.2.1 (Agilent Technology, USA). The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3.1 (Agilent Technology, USA). Normalization for Agilent one-color method was performed, which is Data transformation. Set measurements less than 5.0 to 5.0 and Per Chip : Normalize to 50th percentage. Reliable genes were filtered by flag as following the Agilent manual.

organism: Escherichia coli BL21(DE3)

source_name: B strain_wild type

label_protocol: The transcription master mix was prepared as the manufacturer’s protocol (5X Transcription buffer, 0.1M DTT, NTP mix, RNase-Out, T7-RNA polymerase, and Cyanine 3-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40ºC for 2 hours. Amplified and labeled cRNA was purified on RNase mini column (Qiagen) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: The E. coli strains were grown for six hours under anaerobic growth condition in glucose-containing complex medium.

extract_protocol: For control and test RNAs, the synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling Kit, one color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2ug total RNA was mixed with WT primer mix and incubated at 65ºC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40ºC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70ºC for 15min.

treatment_protocol: The microarray experiment was performed with two serotypes of wild type E. coli and their adhE mutants: (1) K-12 strain, wild type; (2) B strain, wild type; (3) BW25113, adhE mutants; (4) BL21(DE3), adhE mutants.

tag: strain background

value: B

value: wild type


title: BW25113, adhE mutant

description:
K4
Gene expression in K-12 mutant type after 6hrs of growth under anaerobic condition

organism: Escherichia coli BW25113

source_name: BW25113_adhE mutant

value: adhE mutant


title: Heart_12wks_knockout_rep1

city: Wakayama

first: Akira

last: Kohsaka

address: 811-1, Kimiidera

department: Physiology

country: Japan

institute: Wakayama Medical University

description: Gene expression in the heart tissues of 12-week-old heart-specific Bmal1 knockout mice

hyb_protocol: Cy3-labeled cRNA (1.65 μg) was fragmented and hybridized to the SurePrint G3 Mouse (8x60K) Microarray (Agilent Technologies, Santa Clara, CA) using standard procedures.

scan_protocol: After hybridization, the microarrays were washed with GE Wash Buffer 1 (Agilent) for 1 min at room temperature and for another 1 min with GE Wash Buffer 2 (Agilent).  The microarrays were then dried by centrifugation and scanned by an Agilent DNA Microarray Scanner (G2565CA).

data_processing: The scanned images were analyzed using Feature Extraction Software 10.5.1.1 (Agilent) to obtain (background-corrected and normalized) signal intensities.

organism: Mus musculus

source_name: Heart tissue, 12wks old, knockout, replicate 1

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 μg total RNA.

extract_protocol: Total RNA was extracted from frozen tissue with TRIzol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: The left ventricles of hearts were used to extract total RNA.  Tissues from heart-specific Bmal1 knockout (n = 6) and their controls (n = 6) were collected at ZT2 of the LD cycle (ZT0 defined as lights on).

value: Bmal1 knockout

value: heart

tag: gender

value: male


title: BL21(DE3), adhE mutant

description:
HK110
Gene expression in B mutant type after 6hrs of growth under anaerobic condition

source_name: BL21(DE3)_adhE mutant


title: 0.5mM_32d_Root

hyb_protocol: Overnight hybridizations were performed with equal amounts of labelled cRNA to a custom 4x44K Maize Oligo Microarray from Agilent Technologies (Palo Alto, CA) according to Agilent’s One-Color Microarray-Based Gene Expression Analysis protocol. After hybridization, the microarray slides were washed.

tag: cultivar

value: Gaspe Flint

value: Nitrate

tag: mm no3-

value: Root

tag: harvest day

tag: replicate

value: consists of 3


title: K-12 strain, wild type

description:
BW25113
Gene expression in K-12 wild type after 6hrs of growth under anaerobic condition

source_name: K-12 strain_wild type


title: 557095A03 - Dormancy_16h_Total_BR2 vs NoDormancy_16h_Total_BR2

hyb_protocol: NoDormancy_16h_Total_BR2 Cy5 / Dormancy_16h_Total_BR2 Cy3 : 30pmol.


title: WT#3

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Agilent Low Input QuickAmp, one-color, v6.5

scan_protocol: Innoscan 900 (Innopsys), 2µm resolution @ 635nm

data_processing: quantile normalization of mean spot intensities using R (v.2.15.1) and the package limma (v.3.14.4)

source_name: WT_8 wks_lung

growth_protocol: standard

extract_protocol: peqGOLD Total RNA isolation kit (PeqLab)

tag: background strain

tag: age

value: 8 weeks

tag: organ

value: lung


title: 2.5mM_29d_Root


title: TG#4

source_name: Fra-2 TG_8 wks_lung

label_protocol: Agilent Low Input QuickAmp, one-color, v6.5

value: Fra-2 over-expressing (Fra-2 TG)


title: TG#3


title: TG#2


title: WT#4


title: TG#1


title: Heart_12wks_control_rep1

description: Gene expression in the heart tissues of 12-week-old control mice

source_name: Heart tissue, 12wks old, control, replicate 1


title: 557095A01 - Dormancy_16h_Total_BR1 vs NoDormancy_16h_Total_BR1

hyb_protocol: NoDormancy_16h_Total_BR1 Cy5 / Dormancy_16h_Total_BR1 Cy3 : 30pmol.


title: 557095A07 - Dormancy_16h_Polysomal_BR1 vs NoDormancy_16h_Polysomal_BR1

hyb_protocol: NoDormancy_16h_Polysomal_BR1 Cy5 / Dormancy_16h_Polysomal_BR1 Cy3 : 30pmol.


title: 557095A02 - NoDormancy_16h_Total_BR1 vs Dormancy_16h_Total_BR1

hyb_protocol: Dormancy_16h_Total_BR1 Cy5 / NoDormancy_16h_Total_BR1 Cy3 : 30pmol.


title: Cdkn2a/Braf/Lkb1 melanoma, biol rep 2

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St, LCI 501

department: Dermatology

country: USA

institute: Yale School of Meicine

description: Gene expression data from uncultured Cdkn2a/Braf/Lkb1 melanoma

hyb_protocol: Following fragmentation, 10 ug of cRNA hybridized to the Mo Gene  Affy MoGene-1_0-st array as per manufacturer’s recommendations (3) for 16 hr at 45C at 60 rpm, double stained with streptavidin-PE using the Affymetrix 450 fluidics station

scan_protocol: GeneChips were scanned with the Affymetrix  3000-G7 scanner.

data_processing: RMA quantile normalization with background correction and median scaling performed by GenePattern software, no log transformation was performed.

label: biotin

source_name: Cdkn2a/Braf/Lkb1 melanoma, biol rep 2

label_protocol: RNA amplification, fragmentation, and labelin was performed using the Ovation V2 and Encore reagents by NuGEN technologies

growth_protocol: n/a in vivo specimens

extract_protocol: Qiagen Rneasy

tag: cell type

value: melanoma

tag: genotype

tag: source

value: unculture tissue


title: Cdkn2a/Braf melanoma, biol rep 2

description: Gene expresisond data from uncultured Cdkn2a/Braf melanoma

source_name: Cdkn2a/Braf melanoma, biol rep 2


title: Lkb1/Braf melanocytic proliferation, biol rep 2

description: Gene expression data from uncultured Lkb1/Braf melanocytic proliferations (pooled)

value: melanocytic proliferation


title: Cdkn2a only melanocytes (day 19), biol rep 2

description: Gene expression data from Cdkn2a only melanocytes (WT Braf) at day 19 control

value: melanocytes

value: FACS purified cells


title: WT#1

tag: genotype/variation

value: wild type


title: Cdkn2a/Braf melanocytes (day 50), biol rep 2

description: Gene expression data from Cdkn2a/Braf melanocytes after growth arrest


title: Cdkn2a/Braf/Lkb1 melanoma, biol rep 1

source_name: Cdkn2a/Braf/Lkb1 melanoma, biol rep 1


title: Cdkn2a only melanocytes (day 19), biol rep 1


title: Lkb1/Braf melanocytic proliferation, biol rep 1


title: Lkb1/Braf melanocytic proliferation, biol rep 3


title: Cdkn2a/Braf melanocytes (day 19), biol rep 2

description: Gene expression data from Cdkn2a/Braf melanocytes prior to growth arrest


title: Cdkn2a/Braf melanocytes (day 19), biol rep 1


title: Cdkn2a/Braf melanocytes (day 50), biol rep 1


title: C57BL/6J Quadriceps, High Fat Diet_Batch1_Nov11

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: All arrays were scanned on the same Affymetrix GSC3000 7G Scanner

data_processing: Samples were analyzed using Affymetrix Expression Console.

source_name: Mouse quadriceps

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice are housed 5 per cage in IVC GM500 cages (Tecniplast, 500 cm2) according to the Swiss cantonal rules.

extract_protocol: Samples were extracted for RNA at two distinct times: one set of 35 cohorts in September 2011, the other set of 44 cohorts in July 2012. All of the approximately 5 individuals per cohort were prepared at the same time with trizol extraction of total RNA. Sample concentrations were then measured by Nanodrop, and then all individuals from a cohort were evenly pooled together. These cohort pools were then cleaned up with a Qiagen RNEasy kit prior to preparation for microarray, which was performed on the same system and same batch of arrays in November 2011 or August 2012.

treatment_protocol: Mice were fed ad libitum Quadriceps, Chow diet (Harlan 2018) or Quadriceps, High fat diet (Harlan 06414) throughout their lifetime. For Quadriceps, High fat cohorts, the diet started at 8 weeks of age until sacrifice at 29 weeks. All animals were fasted overnight (6pm to 9am) before sacrifice.

value: quadriceps


title: Cdkn2a/Braf melanoma, biol rep 1

source_name: Cdkn2a/Braf melanoma, biol rep 1


title: DBA/2J Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD103 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD100 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: C57BL/6J Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD99 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: DBA/2J Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD103 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD98 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD99 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD100 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD90 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD96 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD96 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD89 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD97 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD87 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD90 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD87 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD92a Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD97 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD95 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD98 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD85 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD84 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD83 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD89 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD83 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD80 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD79 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD85 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD75 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD80 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD81 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD79 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD81 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD69 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD71 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD73 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD71 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD73 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: 0.1 chronic-1

first: Lee

last: Sunwoo

address: #211, Next2Vill, 278-2, Jangdae-dong, Yuseong-gu

institute: GenomicWorks

description: Gene expression after 0.1Gy-irradiated Drosophila larval whole body

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Drosophila melanogaster

source_name: whole body, 0.1Gy, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The wild-type Drosophila melanogaster Oregon-R strain was used for these studies. Flies were maintained at 25degC on medium containing dextrose anhydrous, dry yeast, cornmeal, agar, propionic acid, and tegosept in fly-food bottles with 60% relative humidity. Flies were maintained under a strict 12-h light/12-h dark photoperiod.

extract_protocol: RNA was prepared using TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Eggs were collected from 5-day-old female flies and cultivated for 24 h on standard medium. Then, twenty larvae were manually selected and seeded on fresh standard medium in a new vial. After transfer, the experimental group of first-instar larvae was immediately irradiated with chronic γ-radiation at a dose rate of 16.7 mGy/h. After treatment, gamma-irradiated flies and non-irradiated control flies were maintained in the same incubator at 25°C.

value: larval whole body

tag: strain

value: Oregon-R


title: BXD69 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data

tag: tissue


title: BXD70 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD75 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD68 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD66 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: 0.1 chronic-2

source_name: whole body, 0.1Gy, replicate 2


title: BXD68 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD64 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD66 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: control 3

description: Gene expression after 0Gy-irradiated Drosophila larval whole body

source_name: whole body, 0Gy, replicate 3


title: 0.1 chronic-3

source_name: whole body, 0.1Gy, replicate 3


title: BXD65 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: WT#2


title: control 2

source_name: whole body, 0Gy, replicate 2


title: PBMC_4h_non-rad rep4

city: Vienna

first: Lucian

last: Beer

address: Währginer Gürtel 18-20

department: Department of Surgery

country: Austria

institute: Medical University of Vienna

description: microRNA expression after 20hr in irradiated PBMC

hyb_protocol: Sample labeling and hybridization was performed according to the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies) following the manufacturer’s protocol. Briefly, 100 ng total RNA was labeled and subsequently hybridized overnight (20 hours, 55 °C) to Agilent Human microRNA Microarrays 8x60K v16 using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 5 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 5 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including ackground subtraction), rejects outliers and calculates statistical confidences. Background-corrected fluorescence intensity values were imported into GeneSpring v.11 log2-transformed and then normalized by quantile-normalization. GeneSpring calculates the mean values of identical replicate probes on each chip.
MiRNA data were processed as describe above for mRNA data. However, “Filter on Flags” was used as a filtering step in miRNA samples. Flags are attributes that denote the quality of the entities. These values are generated based on the feature quality on the chip. Genes which are given low significant attribute in the data file would be marked as “Absent” and high significant values would be marked as “Present”.

source_name: PBMC 20h rad

extract_protocol: At the end of incubation time (2h, 4h, and 20 h) as well as immediately after PBMC separation (0h – only 1 sample per donor) total RNA was isolated of irradiated and non-irradiated PBMCs, by using Trizol® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer´s instructions. Total RNA quantification was performed using a NanoDrop-1000 spectrophotometer (Peglab, Erlangen, Germany) and RNA quality was monitored with Agilent 2100 Bioanalyzer (Agilent, Böblingen, Germany).

treatment_protocol: PBMC were obtained from 4 healty volunteers by venous blood draw. Cells were separated by Ficoll-Paque density gradient centrifugation. In short, heparinized anticoagulated blood specimens were processed immediately after venipuncture, diluted 1:2 in Hanks balanced salt solution  and shifted carefully into 50 milliliter (ml) tubes containing Ficoll‐Paque solution. Tubes were centrifuged for 15 minutes at 800g at room temperaturewithout brake and buffy coats with mononuclear cells were obtained. Cells werewashed in HBSS and resuspended CellGro serum-free medium. Cells were irradiated with Caesium-13760 Gray.

tag: time

value: peripheral blood mononuclear cells

tag: donor


title: PBMC_4h_non-rad rep3

label_protocol: Sample labeling and hybridization was performed according to the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies) following the manufacturer’s protocol.

tag: treatment


title: BXD64 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD70 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD65 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD63 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: control 1

source_name: whole body, 0Gy, replicate 1


title: PBMC_4h_non-rad rep2


title: BXD63 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: PBMC_4h_rad rep4

description: microRNA expression after 20hr in non-radiated PBMC

source_name: PBMC 20h non-rad

value: ionizing radiation


title: PBMC_4h_rad rep3


title: PBMC_4h_non-rad rep1


title: PBMC_4h_rad rep2


title: BXD60 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD62 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD51 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD61 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD56 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD101 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD61 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD51 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD55 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD62 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: PBMC_2h_non-rad rep4

description: microRNA expression after 4hr in irradiated PBMC

source_name: PBMC 4h rad


title: BXD55 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: BXD56 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: PBMC_4h_rad rep1


title: 7ori∆ BrdU ChIP 60 min HU Replicate 2

type: genomic

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N.

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: According to Nimblegen suggested protocol

data_processing: Raw data was processed using NimbleScan software from Nimblegen

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: BrdU ChIP from 7ori∆ cells after 60 min in HU

label_protocol: 3 µg of DNA were used for a dUTP incorporation reaction with klenow Exo-, random hexamers and a dNTP mix containing 5% dUTP. Unincorporated hexamers and dNTPS were eliminated running the samples through Biospin 30 columns. Samples were cleaned up by phenol/chloroform extraction and ethanol precipitation. The recovered DNA was then subject to fragmentation by UDG and APE1. 4 µg of the fragmented DNA were labeled with either Cy5 (test sample) or Cy3 (Input) with Terminal transferase. Unincorporated Cy dye was eliminated by running the samples through Biospin 30 columns. Equal amounts of Cy5 and Cy3 labeled DNA were hybridized.

growth_protocol: Cells were grown in rich media to O.D.660 0.2, then arrested in G1 with α-factor. Cells were synchronously released from α-factor induced G1 arrest into S phase by filtration, into rich media containing 200 mM Hydroxyurea (HU). Cells were harvested after 1 hour in 200mM HU.

extract_protocol: Genomic DNA from ChIP samples was purified using PCR purification columns (Qiagen) according to manufacturer's protocol. Samples were then amplified using whole-genome amplification (Genome-Plex, Sigma-Aldrich).

treatment_protocol: Cells were released into rich media containing 200 mM Hydroxyurea (HU)

value: 7ori∆ (ars600::LEU2, ars601,602::loxP, ars603::loxP, ars603.5::KanMX, ars604::loxP, ars605::loxP, ars606::ADE2)  BrdU incorporation competent strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

tag: antibody

value: BrdU (GE Healthcare)

source_name: Input DNA from 7ori∆ cells arrested in G1

growth_protocol: Cells were grown in rich media to O.D.660 0.2, then arrested in G1 with α-factor and harvested.

extract_protocol: Genomic DNA was purified using PCR purification columns (Qiagen) according to manufacturer's protocol. Samples were then amplified using whole-genome amplification (Genome-Plex, Sigma-Aldrich).

value: None, input DNA


title: BXD50 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: 7ori∆ BrdU ChIP 60 min HU Replicate 1

scan_protocol: According to Nimblegen suggested protocol


title: PBMC_2h_non-rad rep2


title: PBMC_2h_non-rad rep3


title: PBMC_2h_rad rep4

description: microRNA expression after 4hr in non-radiated PBMC

source_name: PBMC 4h non-rad


title: BXD84 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD49 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data


title: WT BrdU ChIP 60 min HU Replicate 1

source_name: BrdU ChIP from WT cells after 60 min in HU

value: WT BrdU incorporation competent strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

source_name: Input DNA from WT cells arrested in G1


title: WT BrdU ChIP 60 min HU Replicate 2


title: 7ori∆ Orc2 ChIP 60 min nocodazole

source_name: Orc2 ChIP from 7ori∆ cells after 60 min in nocodazole

growth_protocol: Cells were grown in rich media to O.D.660 0.2, then arrested in G2/M with nocodazole (15µg/ml) for 2 hours and harvested.

value: 7ori∆ (ars600::LEU2, ars601,602::loxP, ars603::loxP, ars603.5::KanMX, ars604::loxP, ars605::loxP, ars606::ADE2) Orc2-2Xlinker-3XFlag epitope-tagged strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

value: Flag (Sigma)

source_name: Input DNA from 7ori∆ cells after 60 min in nocodazole


title: 7ori∆ Orc2 ChIP 90 min alpha factor

source_name: Orc2 ChIP from 7ori∆ cells after 90 min in alpha factor

growth_protocol: Cells were grown in rich media to O.D.660 0.2, then arrested in G1 with α-factor for 90 minutes and harvested.

source_name: Input DNA from 7ori∆ cells after 90 min in alpha factor


title: PBMC_2h_non-rad rep1


title: BXD48 Quadriceps, High Fat Diet_Batch2_Aug12

description: Gene expression data

source_name: Mouse quadriceps


title: BXD48 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: WT Orc2 ChIP 90 min alpha factor

source_name: Orc2 ChIP from WT cells after 90 min in alpha factor

value: WT Orc2-2Xlinker-3XFlag epitope-tagged strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

source_name: Input DNA from WT cells after 90 min in alpha factor


title: BXD44 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: BXD49 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: BXD45 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: BXD44 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data


title: PBMC_2h_rad rep2


title: PBMC_2h_rad rep3


title: WT Orc2 ChIP 60 min nocodazole

source_name: Orc2 ChIP from WT cells after 60 min in nocodazole

source_name: Input DNA from WT cells after 60 min in nocodazole


title: BXD45 Quadriceps, Chow Diet_Batch2_Aug12

description: Gene expression data


title: CD8+ T cells: SIVmac251 infected macaque, 3 weeks post-infection biological rep 6

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from SIVmac251 infected macaque blood CD8+ T cells, 3 weeks post-infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus macaque 3' IVT arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with BRB Array Tools, version 4.3

organism: Macaca mulatta

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

value: Blood

value: CD8+ T cells


title: CD8+ T cells: SIVmac251 infected macaque, 3 weeks post-infection biological rep 3

source_name: SIVmac251 infected macaque blood CD8+ T cells


title: PBMC_2h_rad rep1


title: PBMC_20h_non-rad rep4

description: microRNA expression after 2hr in irradiated PBMC

source_name: PBMC 2h rad


title: PBMC_20h_non-rad rep3


title: BXD43 Quadriceps, Chow Diet_Batch1_Nov11

description: Gene expression data


title: CD8+ T cells: SIVmac251 infected macaque, 3 weeks post-infection biological rep 1


title: Pcgf6_4_shRNA2-dox

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

hyb_protocol: standard Affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

label_protocol: biotin

growth_protocol: ESCs (OG2 ESCs carrying an Oct4-EGFP reporter construct and V6.5 ESC line) were cultured on mitomycinC-inactivated DR4 mouse embryo fibroblasts (MEFs) expressing multiple antibiotic-resistances in high-glucose Dulbecco's modified Eagle's medium (DMEM) (all reagents obtained from PAA Laboratories) supplemented with 15% fetal calf serum (FCS), leukemia inhibitory factor (LIF)-conditioned medium, 1% nonessential amino acids (NEAA), penicillin (100 U/ml)/streptomycin (100 U/ml), L-glutamine (2 mM), sodium pyruvate (1 mM), and 2ME (0.1 mM; Sigma-Aldrich) at 37°C in a 5%CO2 incubator. Medium was changed daily and cultures were passaged every 1-2 days before reaching confluence. For differentiation of Pcgf6 KD ESCs, cells were dissociated by trypsin treatment, and cultured in high-glucose Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% FCS (Gibco, Life Technologies), 1% nonessential amino acids (NEAA), penicillin (100 U/ml)/streptomycin (100 U/ml), L-glutamine (2 mM), sodium pyruvate (1 mM) and 2ME (0.1 mM; Sigma-Aldrich)) as hanging drops. EBs were harvested after 48h and transferred into suspension culture with fresh medium. The medium was changed every 2-3 days. For doxycycline treatment, cells were cultured in medium containing 1µg/ml dox (PAA). Representative pictures were taken by phase-contrast microscopy (EVOS) and ESC colony size was analyzed using ImageJ Software.

extract_protocol: RNeasy kit (Quiagen)

tag: cell line

value: embryonic stem cells


title: Pcgf6_6_Scrambled-dox

value: Scrambled-dox


title: neurons overexpressing ICD rep3

city: milano

first: Amelia

last: Trimarco

address: via olgettina 60

department: Divisione di Neuroscienze-INSPE

institute: Ospedale San Raffaele

description: dissociated DRG neurons

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data from the SampleProbeProfile txt file were exported from GenomeStudio software. Using the R beadarray package the data were log2 transformed, quantile normalized and filtered for detection p-value<0.01, therefore all probes with a detection p-value≥0.01 in all categories were excluded from the analysis.

organism: Rattus norvegicus

source_name: DRG neurons_overexpressing ICD

label_protocol: cRNA was biotin-UTP labelled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

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 by agarose gel electrophoresis.

tag: strain background

value: Sprague Dawley

tag: development stage

value: embryo E16.5

value: overexpressing ICD

value: dorsal root ganglis neuron


title: CD8+ T cells: SIVmac251 infected macaque, 3 weeks post-infection biological rep 4


title: neurons overexpressing ICD rep4

description: dissociated DRG neurons


title: Pcgf6_5_Scrambled+dox

value: Scrambled+dox


title: Pcgf6_2_shRNA1-dox


title: CD8+ T cells: SIVmac251 infected macaque, 3 weeks post-infection biological rep 2


title: neurons overexpressing ICD rep2

description: dissociated DRG neurons


title: Pcgf6_1_shRNA1+dox


title: Pcgf6_3_shRNA2+dox


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-challenge with SIVmac251 biological rep 4

description: Gene expression data from SIV∆nef vaccinated macaque blood CD8+ T cells, 3 weeks post-challenge with SIVmac251

source_name: SIV∆nef vaccinated, SIVmac251 challenged macaque blood CD8+ T cells


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-challenge with SIVmac251 biological rep 5


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-challenge with SIVmac251 biological rep 3


title: BXD43 Quadriceps, High Fat Diet_Batch1_Nov11

description: Gene expression data

value: quadriceps


title: CD8+ T cells: SIVmac251 infected macaque, 3 weeks post-infection biological rep 5


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-challenge with SIVmac251 biological rep 6


title: neurons overexpressing ICD rep1

description: dissociated DRG neurons


title: PBMC_20h_non-rad rep2

value: peripheral blood mononuclear cells


title: PBMC_20h_non-rad rep1


title: PBMC_20h_rad rep3

description: microRNA expression after 2hr in non-radiated PBMC

source_name: PBMC 2h non-rad

value: ionizing radiation


title: PBMC_20h_rad rep2


title: neurons overexpressing EGFP rep1

description: dissociated DRG neurons

source_name: DRG neurons_overexpressing ECD

value: overexpressing ECD


title: neurons wild-type rep4

description: dissociated DRG neurons

source_name: DRG neurons_wild-type

value: wild type


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-challenge with SIVmac251 biological rep 2


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-challenge with SIVmac251 biological rep 1


title: neurons overexpressing EGFP rep2

description: dissociated DRG neurons


title: neurons overexpressing EGFP rep4

description: dissociated DRG neurons


title: PBMC_20h_rad rep1


title: PBMC_0h rep4

description: miroRNA expression immediately after blood draw (0h) in PBMC

source_name: PBMC 0h

value: control


title: neurons wild-type rep1

description: dissociated DRG neurons


title: neurons overexpressing EGFP rep3

description: dissociated DRG neurons


title: PBMC_0h rep3


title: neurons wild-type rep2

description: dissociated DRG neurons


title: PBMC_4h_rad rep4

description: Gene expression after 4hr in irradiated PBMC

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent W hole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The las t washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). All Cy3 images can be found on the provided CD-ROM.

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including ackground subtraction), rejects outliers and calculates statistical confidences. Background-corrected fluorescence intensity values were imported into GeneSpring v.11 log2-transformed and then normalized by quantile-normalization. GeneSpring calculates the mean values of identical replicate probes on each chip.

source_name: PBMC 4h rad

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the  manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).


title: PBMC_0h rep2


title: PBMC_4h_non-rad rep2

description: Gene expression after 4hr in non-radiated PBMC

source_name: PBMC 4h non-rad


title: CD8+ T cells: SIV∆nef vaccinated macaque, 40 weeks post-vaccination biological rep 4

description: Gene expression data from SIV∆nef vaccinated macaque blood CD8+ T cells, 40 weeks post-vaccination


title: PBMC_4h_non-rad rep1


title: PBMC_4h_rad rep3


title: CD8+ T cells: SIV∆nef vaccinated macaque, 40 weeks post-vaccination biological rep 3

source_name: SIV∆nef vaccinated macaque blood CD8+ T cells


title: CD8+ T cells: SIV∆nef vaccinated macaque, 40 weeks post-vaccination biological rep 2


title: CD8+ T cells: SIV∆nef vaccinated macaque, 40 weeks post-vaccination biological rep 1


title: PBMC_0h rep1


title: PBMC_4h_non-rad rep3


title: PBMC_4h_non-rad rep4


title: PBMC_4h_rad rep1


title: PBMC_4h_rad rep2


title: CD8+ T cells: SIV∆nef vaccinated macaque, 20 weeks post-vaccination biological rep 6

description: Gene expression data from SIV∆nef vaccinated macaque blood CD8+ T cells, 20 weeks post-vaccination


title: CD8+ T cells: SIV∆nef vaccinated macaque, 20 weeks post-vaccination biological rep 5


title: PBMC_2h_non-rad rep4

description: Gene expression after 2hr in non-radiated PBMC


title: CD8+ T cells: SIV∆nef vaccinated macaque, 20 weeks post-vaccination biological rep 3


title: CD8+ T cells: SIV∆nef vaccinated macaque, 20 weeks post-vaccination biological rep 4


title: PBMC_2h_non-rad rep2


title: PBMC_2h_non-rad rep3


title: PBMC_2h_non-rad rep1


title: C57BL/6J brown adipose tissue

description: Gene expression data

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

source_name: Mouse brown adipose

extract_protocol: Trizol extraction of total RNA was performed on all individuals -- approximately 5 per cohort, for roughly 185 animals in all. Sample concentrations were then measured by Nanodrop, and then all individuals from a cohort were evenly pooled together. These cohort pools were then cleaned up with a Qiagen RNEasy kit prior to preparation for microarray.

treatment_protocol: Mice were fed ad libitum chow diet (Harlan 2018) throughout their lifetime until sacrifice at 29 weeks. All animals were fasted overnight (6pm to 9am) before sacrifice.

value: brown adipose tissue


title: PBMC_2h_rad rep3

description: Gene expression after 2hr in irradiated PBMC


title: PBMC_2h_rad rep4


title: PBMC_2h_rad rep2


title: BXD103 brown adipose tissue

description: Gene expression data


title: PBMC_20h_non-rad rep2

description: Gene expression after 20hr in non-radiated PBMC

source_name: PBMC 20h non-rad


title: PBMC_20h_non-rad rep1


title: CD8+ T cells: SIV∆nef vaccinated macaque, 20 weeks post-vaccination biological rep 1


title: PBMC_20h_non-rad rep4


title: BXD101 brown adipose tissue

description: Gene expression data


title: CD8+ T cells: SIV∆nef vaccinated macaque, 20 weeks post-vaccination biological rep 2


title: PBMC_2h_rad rep1


title: DBA/2J brown adipose tissue

description: Gene expression data


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-vaccination biological rep 4

description: Gene expression data from SIV∆nef vaccinated macaque blood CD8+ T cells, 3 weeks post-vaccination


title: PBMC_20h_rad rep4

description: Gene expression after 20hr in irradiated PBMC

source_name: PBMC 20h rad


title: PBMC_20h_non-rad rep3


title: BXD99 brown adipose tissue

description: Gene expression data


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-vaccination biological rep 5


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-vaccination biological rep 3


title: PBMC_20h_rad rep3


title: PBMC_20h_rad rep2


title: BXD98 brown adipose tissue

description: Gene expression data


title: BXD97 brown adipose tissue

description: Gene expression data


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-vaccination biological rep 2


title: PBMC_0h rep3

description: Gene expression immediately after blood draw (0h) in PBMC


title: PBMC_0h rep4


title: BXD96 brown adipose tissue

description: Gene expression data


title: PBMC_0h rep1


title: BXD95 brown adipose tissue

description: Gene expression data


title: PBMC_0h rep2


title: CD8+ T cells: healthy uninfected macaque biological rep 6

description: Gene expression data from healthy macaque blood CD8+ T cell

source_name: Healthy uninfected macaque blood CD8+ T cells


title: CD8+ T cells: healthy uninfected macaque biological rep 3


title: CD8+ T cells: healthy uninfected macaque biological rep 4


title: BXD90 brown adipose tissue

description: Gene expression data


title: PBMC_20h_rad rep1


title: CD8+ T cells: healthy uninfected macaque biological rep 5


title: CD8+ T cells: SIV∆nef vaccinated macaque, 3 weeks post-vaccination biological rep 1


title: BXD89 brown adipose tissue

description: Gene expression data


title: BXD92 brown adipose tissue

description: Gene expression data


title: CD8+ T cells: healthy uninfected macaque biological rep 2


title: CD8+ T cells: healthy uninfected macaque biological rep 1


title: BXD87 brown adipose tissue

description: Gene expression data


title: T1

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

source_name: Malignant glioma tissue

extract_protocol: Total RNA from frozen glioma and peritumoral brain tissues was extracted using standard Trizol (Invitrogen) method, according to manufacturer’s protocol. RNA samples were treated with DNase I using DNA-free DNase Treatement and Removal Reagent (Ambion). RNA was quantified and assessed using Agilent 2100 Bioanalyzer and RNA 6000 Nano Kit (Agilent Technologies). Only samples with RNA integrity >8 were used for further studies.

treatment_protocol: Malignant glioma tissues and peritumoral brain tissues  were obtained at the time of surgery. Tissues were flash frozen on the dry ice and preserved in -80ºC  prior to RNA isolation. Total RNA from normal human brain was obtained commercially (FirstChoice® Human Brain Reference RNA, Ambion).

value: Malignant glioma tissue

tag: tumor stage

value: WHO grade IV

tag: histology

value: glioblastoma

tag: gender

value: M

tag: tumor location

value: Right fronto-parietal with corpus callosum infiltration


title: T11

label_protocol: according to the manufacturer's protocol

value: glioblastoma recidivans

tag: age

value: Right fronto-parietal


title: B1

source_name: Glioma peritumoral tissue

value: Glioma peritumoral tissue

value: Peritumoral area of WHO grade III

value: peritumoral area of anaplastic astrocytoma

value: Left temporal


title: T6

value: Right temporal


title: PBMC_20h_rad rep4

value: ionizing radiation

tag: cell type

value: peripheral blood mononuclear cells


title: U937-Rep1

city: Lund

first: Carl

last: Sanden

address: BMC B13, Klinikgatan 26

department: Department of Hematology

country: Sweden

institute: Lund University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Genome Studio module 1.8

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: U937 cells were gowns in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol: DNA was extracted using the QIAamp DNA mini kit (Qiagen).


title: BXD85 brown adipose tissue

description: Gene expression data

tag: genotype


title: BXD83 brown adipose tissue

description: Gene expression data


title: neurons wild-type rep3

description: dissociated DRG neurons

value: Sprague Dawley

value: embryo E16.5

tag: genotype/variation

value: wild type

value: dorsal root ganglis neuron


title: U937-Rep2


title: BXD84 brown adipose tissue

description: Gene expression data

value: brown adipose tissue


title: T5

value: Malignant glioma tissue

value: WHO grade IV

value: glioblastoma

value: Right fronto-temporo-parietal


title: T7

value: glioblastoma recidivans

value: M

value: Right parietal


title: B4

value: Glioma peritumoral tissue

value: Peritumoral area of WHO grade IV

value: peritumoral area of glioblastoma

value: Left fronto-parietal parasagittal


title: T4

value: gliosarcoma


title: T12

value: WHO grade III

value: anaplastic astrocytoma recidivans

value: Left parietal


title: BXD81 brown adipose tissue

description: Gene expression data


title: T3

value: F


title: T8

value: Right fronto-temporal


title: T9

value: Malignant glioma tissue

value: Left parieto-occipital


title: B3

value: Peritumoral area of WHO grade III

value: peritumoral area of anaplastic oligoastrocytoma


title: BXD80 brown adipose tissue

description: Gene expression data

value: brown adipose tissue


title: BXD79 brown adipose tissue

description: Gene expression data


title: 387-PDAC T277(F) 20-07-10 CD31/45- MP1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
Pancreatic cancer, after cell dispersion with collagenase and staining with Hoechst 33342 during 90 minutes.
Main population (MP) cells.

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® Scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.26.1) of Bioconductor. Expression values are represented on a log2-scale.

source_name: PDAC, MP

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the NuGEN Ovation Pico WTA System, an amount of 2 ng of total RNA was amplified and converted to cDNA. An amount of 5 μg of cDNA was fragmented and labeled with biotin using the NuGEN Encore Biotin Module.

extract_protocol: RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the instructions of the manufacturer.

treatment_protocol: Tumor blocks were minced into small pieces and incubated with collagenase type IV for 2-3 hours while mechanically dispersed at regular 20-min time-points. The final cell suspension was filtered through a 40μm nylon. Cells were incubated with Hoechst 33342 during 90 minutes at a final concentration of 5µg/ml, and propidium iodide (2μg/ml) was added to mark non-viable cells. Using dual-wavelength FACS analysis, a side branch of “Hoechst-low” cells was identified as the SP, further verified by adding verapamil, which results in the reduction of the side branch by blocking the effluxing multidrug transporter(s). The main population (MP) was gated as the bulk of “Hoechst-bright” tumor cells. For further characterization, fluorescein (FITC)-labeled anti-human CD31 and phycoerythrin (PE)-antibodies were added.

value: male

value: 54 years

value: pancreatic ductal adenocarcinoma (PDAC)

tag: tumor grade

tag: cell subset

value: main population

tag: pdac sample identifier

value: PDAC T277(F)


title: T10

source_name: Human malignant glioma

tag: tissue

value: Human malignant glioma

value: WHO grade IV

value: glioblastoma

value: M

value: Left temporo-parieto-occipital


title: N1

source_name: Human normal brain, Commercial mRNA for normal human tissue

value: pooled from multiple, healthy donors and several brain regions

value: multiple, healthy donors 23-86y

value: mixed M and F

value: Several brain regions


title: T2

value: Malignant glioma tissue

value: F

value: Left temporal


title: B2

value: Glioma peritumoral tissue

value: Peritumoral area of WHO grade III

value: peritumoral area of anaplastic astrocytoma


title: 389-PDAC T277(F) 20-07-10 CD31/45- SP

description:
Pancreatic cancer, after cell dispersion with collagenase and staining with Hoechst 33342 during 90 minutes.
Side population (SP) cells.

source_name: PDAC, SP

value: male

value: 54 years

value: pancreatic ductal adenocarcinoma (PDAC)

value: side population


title: 371-PDAC T278(O) 09-06-10 CD31/45- SP

value: 62 years

value: PDAC T278(O)


title: 379-PDAC T257(F)-07-07-10 CD31/45- SP

value: 72 years

value: PDAC T257(F)


title: BXD71 brown adipose tissue

description: Gene expression data

value: brown adipose tissue


title: 373-PDAC T278(O) 09-06-10 CD31/45- MP2

value: main population


title: BXD69 brown adipose tissue

description: Gene expression data


title: BXD68 brown adipose tissue

description: Gene expression data


title: BXD75 brown adipose tissue

description: Gene expression data


title: 378-PDAC T257(F)-07-07-10 CD31/45- MP2


title: 325-PDAC 264 CD45- 30/03/2010 MP2

value: 74 years

value: PDAC 264


title: BXD66 brown adipose tissue

description: Gene expression data


title: 328-PDAC 271 CD45- 30/04/2010 SP

value: 57 years

value: PDAC 271


title: 327-PDAC 271 CD45- 30/04/2010 MP


title: 326-PDAC 264 CD45- 30/03/2010 SP


title: 375-PDAC T229(F)-30-06-10 CD31/45- SP

value: female

value: PDAC T229(F)


title: BXD70 brown adipose tissue

description: Gene expression data


title: BXD62 brown adipose tissue

description: Gene expression data


title: sexually mature eel males  [BM4]

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

institute: University of Padova

description: olfactory bulb, telencephalon and diencephalon  RNA of mature males of Anguilla anguilla

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization of gProcessed signal using R2.6.1 statistical software

label: Cyanine 3

organism: Anguilla anguilla

source_name: Pool of RNA extracted separately from olfactory bulb, telencephalon and diencephalon of 3 mature males

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: protocol

value: Eel males injected intramuscularly every week over a 140 day period with 2000 IU hCG/kg dissolved in 0.9% saline to induce sexual maturation.


title: BXD65 brown adipose tissue

description: Gene expression data


title: BXD64 brown adipose tissue

description: Gene expression data


title: BXD55 brown adipose tissue

description: Gene expression data


title: 315-PDAC 260 CD45- 3/03/2010 MP2

value: male

value: 63 years

value: PDAC 260


title: 374-PDAC T229(F)-30-06-10 CD31/45- MP1

value: pancreatic ductal adenocarcinoma (PDAC)


title: 317-PDAC 262 CD45- 17/03/2010 MP1

value: 79 years

value: PDAC 262


title: sexually mature eel males  [BM2]


title: sexually mature eel males  [BM3]


title: sexually mature eel males  [BM1]


title: BXD51 brown adipose tissue

description: Gene expression data


title: sexually immature eel males  [BI2]

description: olfactory bulb, telencephalon and diencephalon  RNA of immature males of Anguilla anguilla

source_name: Pool of RNA extracted separately from olfactory bulb, telencephalon and diencephalon of 3 immature males

value: Eel males injected intramuscularly every week over a 140 day period with with 0.9% NaCl


title: sexually immature eel males  [BI3]


title: U937-shDEK17-Rep3

hyb_protocol: Illumina hybridization protocol (Manuel 11322187 Revision A)

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE

source_name: U937 cell line

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevB

growth_protocol: U937 cells were grown in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen).

treatment_protocol: Two shRNAs in H1 lentiviral vectors targeting the DEK transcript (a kind gift from Dr David Markovitz) and the corresponding empty vector were used to transduce U937 cells. After 48h, successfully transduced cells were sorted based on GFP expression and expanded for 4 days before RNA extraction.

tag: shRNA


title: U937-shDEK17-Rep2

tag: cell line


title: BXD61 brown adipose tissue

description: Gene expression data


title: U937-shDEK17-Rep1


title: sexually immature eel males  [BI4]


title: U937-shDEK14-Rep3


title: 319-PDAC 262 CD45- 17/03/2010 SP

value: side population


title: BXD56 brown adipose tissue

description: Gene expression data

value: brown adipose tissue


title: 316-PDAC 260 CD45- 3/03/2010 SP


title: BXD50 brown adipose tissue

description: Gene expression data


title: 362-PDAC T174(F) 29-06-10 CD31/45- SP1

value: 69 years

value: PDAC T174(F)


title: 361-PDAC T174(F) 29-06-10 CD31/45- MP2

value: main population


title: BXD45 brown adipose tissue

description: Gene expression data


title: 295-PaCa252 CD45-MP2


title: BXD49 brown adipose tissue

description: Gene expression data


title: sexually immature eel males  [BI1]


title: U937-shDEK14-Rep2


title: 292-PaCa247 CD45-MP2

value: 62 years


title: BXD43 brown adipose tissue

description: Gene expression data


title: U937-shEMPTY-Rep1

value: empty vector


title: 293-PaCa252 CD45-SP


title: BXD48 brown adipose tissue

description: Gene expression data


title: U937-shDEK14-Rep1


title: U937-shEMPTY-Rep2


title: 290-PaCa247 CD45-SP


title: MG1655_under_Osmotic_Stress_rep1

status: Public on Sep 25 2014

city: Ames

first: Hui-Hsien

last: Chou

state: IA

address: 503 Science II

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: This sample is the first one which is exposed to Osmotic stress

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization kit and 4-Chip Workstation following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by GenePix 4100A, following their standard operating protocol. See http://www.moleculardevices.com/systems/microarray-scanners/genepix-4100a-microarray-scanner.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleGen Deva software, version 1.2 (Roche NimbleGen, Inc.).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655 Osmotic stress

label_protocol: Labeling was performed by NimbleGen Labelling kit following their standard operating protocol. See www.nimblegen.com.

growth_protocol: E. coli MG1655 Osmotic Stress was grown untill reach to half of O.D.600nm of Standard sample at 37°C in 45ml MOPS media with 6ml 4M Sodium Chloride.

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA  concentration was measured by SpectorPhotometer(NonoDrop).
cDNA were synthesized from the reverse transcription of Total RNA using the Life Technologies SuperScript II Double-Strand Synthesis Kit

tag: strain

tag: treatment

value: Osmotic stress


title: MG1655_under_minimal_C&N_source_rep1

description: This sample is the first one which is grown in minimal C & N source medium

source_name: E. coli MG1655 minimal C&N

growth_protocol: E. coli MG1655 minimal C&N Source was grown untill reach to quater of O.D.600nm of Standard sample at 37°C in minimal C and N source MOPS media(C-N- MOPS).

value: minimal C&N source


title: MG1655_under_Oxidative_Stress_rep1

description: This sample is the first one which is exposed to Oxidative stress

source_name: E. coli MG1655 Oxidative stress

growth_protocol: E. coli MG1655 Oxidative Stress was grown untill reach to half of O.D.600nm of Standard sample at 37°C in 49ml MOPS media with 400μl 7% Hydrogen peroxide.

value: Oxidative stress


title: MG1655_under_Osmotic_Stress_rep2

description: This sample is the second one which is exposed to Osmotic stress


title: MG1655_under_minimal_N_source_rep2

description: This sample is the second one which is grown in minimal N source medium

source_name: E. coli MG1655 minimal N

growth_protocol: E. coli MG1655 minimal N Source was grown untill reach to half of O.D.600nm of Standard sample at 37°C in minimal N source MOPS media(N- MOPS).

value: minimal N source


title: MG1655_under_Oxidative_Stress_rep2

description: This sample is the second one which is exposed to Oxidative stress


title: MG1655_under_minimal_C_source_rep1

description: This sample is the firest one which is grown in minimal C source medium

source_name: E. coli MG1655 minimal C

growth_protocol: E. coli MG1655 minimal C Source was grown untill reach to half of O.D.600nm of Standard sample at 37°C in minimal C source MOPS media(C- MOPS).

value: minimal C source


title: MG1655_under_HeatShock_rep2

description: This sample is the second one which is exposed to heat shock

source_name: E. coli MG1655 Heat Shock

growth_protocol: E. coli MG1655 Heat Shock was grown at 50°C for 4 hour then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media.

value: Heat Shock


title: MG1655_under_minimal_C&N_source_rep2

description: This sample is the second one which is grown in minimal C & N source medium


title: MG1655_UV_Treatment_rep2

description: This sample is the second one which is exposed to UV

source_name: E. coli MG1655 UV

growth_protocol: E. coli MG1655 UV was exposed to UV light for 15 minutes then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media.

value: UV


title: MG1655_under_minimal_N_source_rep1

description: This sample is the first one which is grown in minimal N source medium


title: MG1655_under_ColdShock_rep1

description: This sample is the first one which is exposed to cold shock

source_name: E. coli MG1655 Cold Shock

growth_protocol: E. coli MG1655 Cold Shock was grown at 15°C for 4 hour then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media.

value: Cold Shock


title: MG1655_under_Low_pH_rep1

description: This sample is the first one which is grown under low pH condition

source_name: E. coli MG1655 Low pH

growth_protocol: E. coli MG1655 Low pH was grown at 37°C for 1 hour in LB media with pH4.5 then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media.

value: Low pH


title: MG1655_UV_Treatment_rep1

description: This sample is the first one which is exposed to UV


title: MG1655_under_ColdShock_rep2

description: This sample is the second one which is exposed to cold shock


title: MG1655_standard_condition_rep2

description: This sample is the second one which is grown under standard condition

source_name: E. coli MG1655 Standard

growth_protocol: E. coli MG1655 Standard was grown to mid-log phase (O.D.600nm 0.6~0.8) at 37°C in LB media.

value: Standard


title: MG1655_standard_condition_rep1

description: This sample is the first one which is grown under standard condition


title: Cord_blood_Tartu_25

city: Turku

first: Essi

last: Laajala

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate (Affymetrix) with manufacturer´s protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (Affymetrix). GeneTitan MC Instrument (Affymetrix) was used to hybridize, wash, stain, and scan the arrays.

scan_protocol: GeneTitan MC Instrument was used to scan the arrays. The probe cell intensity data was summarized with Affymetrix GeneChip Command Consol 3.1.

data_processing: The intensity data was pre-processed using robust multi-array averaging (RMA). The absent call filtering was done by determining a threshold value empirically for each sample by fitting a two-component GMM for all non-control probesets. A probeset was filtered out if it was absent in at least 50 % of the samples from Espoo, Tartu and Petrozavodsk. Batch correction was done by applying the ComBat analysis method. Additional 15 rehybridized samples (in a separate data set) were utilized in this correction but excluded from further analysis steps. These intensities were then used to detect differential expression by fitting a linear model and computing a moderated t-statistic for each present probeset for all three contrasts: Espoo vs. Petrozavodsk, Tartu vs. Petrozavodsk and Espoo vs. Tartu. Gender, pregnancy week, month of birth and HLA risk class were included as confounding factors in the model.

source_name: Cord blood

label_protocol: 50 ng of total RNA was processed to cDNA with Ovation RNA amplification system v2, including the Ovation whole blood reagent (NuGEN Technologies). The amplified cDNA was subsequently biotin-labelled and fragmented with Encore biotin module (NuGEN Technologies).

growth_protocol: Umbilical cord blood was drawn into Tempus Blood RNA tubes according to the manufacturer´s protocol and then stored in −70 °C until analyzed.

extract_protocol: Total whole-blood RNA was extracted from the samples using Tempus Spin RNA isolation kit (Applied Biosystems) according to manufacturer's instructions. RNA quality and quantity was determined using NanoDrop ND-2000 (Thermo Scientific) and Experion Automated Electrophoresis System (Bio-Rad Laboratories).

tag: country

value: Estonia

tag: sample month

value: May

value: Male

tag: hla risk category (np=neutral/protective, m=medium, h=high, vh=very high)

value: NP

tag: gestational week

tag: hybridization batch


title: Cord_blood_Tartu_21

value: April

tag: gender


title: Cord_blood_Tartu_23

value: Female


title: Cord_blood_Tartu_22


title: Cord_blood_Tartu_24

value: M


title: Cord_blood_Tartu_16

value: February


title: Cord_blood_Tartu_15


title: Cord_blood_Tartu_17


title: Cord_blood_Tartu_6


title: Cord_blood_Tartu_2

value: January


title: Cord_blood_Tartu_13


title: Cord_blood_Tartu_19


title: Cord_blood_Tartu_4


title: Cord_blood_Tartu_7


title: Cord_blood_Tartu_10


title: Cord_blood_Tartu_14


title: Cord_blood_Tartu_8

value: H


title: U937-shEMPTY-Rep3

value: empty vector


title: Cord_blood_Tartu_9


title: Cord_blood_Tartu_20


title: Cord_blood_Petrozavodsk_40

value: Russia


title: Cord_blood_Tartu_18


title: Cord_blood_Tartu_5


title: Cord_blood_Tartu_12


title: Cord_blood_Tartu_3


title: Cord_blood_Tartu_11


title: Cord_blood_Tartu_1

value: VH


title: Cord_blood_Petrozavodsk_38


title: Cord_blood_Petrozavodsk_27

value: March


title: human iPSC Axol-C12502

city: Cambridgeshire

first: Yichen

last: Shi

address: Suite 3, The Science Village Building, Chesterford Research Park, Little Chesterford

country: United Kingdom

institute: Axol Bioscience Limited

description: genotyping data from human iPSC Axol-C12502

hyb_protocol: Atlasbiolabs provided the standard services for hybridization

scan_protocol: Atlasbiolabs provided the standard services for scanning

data_processing: Data was analyzed using the  Affymetrix Genotyping Console and Affymetrix default analysis settings

source_name: human iPSC Axol-C12502

label_protocol: Atlasbiolabs provided the standard services for labeling

growth_protocol: human iPSC cells were cultured on E8 medium; human fibroblast were induced with human fibroblast medium

extract_protocol: QIAGEN All prep DNA/RNA/protein mini kit extracted gDNA according to the manufacturer's instructions

treatment_protocol: No specific treatment

value: iPSC


title: Cord_blood_Petrozavodsk_36


title: Cord_blood_Petrozavodsk_28


title: human iPSC Axol-016

description: genotyping data from human iPSC Axol-016

source_name: human iPSC Axol-016


title: Cord_blood_Petrozavodsk_35


title: Cord_blood_Petrozavodsk_29


title: Cord_blood_Petrozavodsk_26


title: Cord_blood_Petrozavodsk_24


title: MG1655_under_minimal_C_source_rep2

description: This sample is the second one which is grown in minimal C source medium

value: minimal C source


title: Cord_blood_Petrozavodsk_33


title: Cord_blood_Petrozavodsk_22


title: Cord_blood_Petrozavodsk_32


title: Cord_blood_Petrozavodsk_31


title: Cord_blood_Petrozavodsk_23


title: Cord_blood_Petrozavodsk_20


title: Cord_blood_Petrozavodsk_25


title: Cord_blood_Petrozavodsk_34


title: Cord_blood_Petrozavodsk_19


title: Cord_blood_Petrozavodsk_17


title: Cord_blood_Petrozavodsk_18


title: Cord_blood_Petrozavodsk_15


title: Cord_blood_Petrozavodsk_37


title: Cord_blood_Petrozavodsk_30


title: Cord_blood_Petrozavodsk_21


title: Cord_blood_Petrozavodsk_16


title: human fibroblast Axol-AI01

description: genotyping data from human fibroblast Axol-AI01

source_name: human fibroblast Axol-AI01

value: fibroblast


title: human iPSC Axol-015

description: genotyping data from human iPSC Axol-015

source_name: human iPSC Axol-015


title: Cord_blood_Petrozavodsk_10


title: Cord_blood_Petrozavodsk_8


title: Cord_blood_Petrozavodsk_14


title: Cord_blood_Petrozavodsk_9


title: Cord_blood_Petrozavodsk_6


title: Cord_blood_Petrozavodsk_12


title: Cord_blood_Petrozavodsk_5


title: Cord_blood_Petrozavodsk_2


title: Cord_blood_Petrozavodsk_13


title: Cord_blood_Espoo_43

value: Finland


title: Cord_blood_Espoo_39


title: Cord_blood_Espoo_46


title: Cord_blood_Espoo_47


title: Cord_blood_Petrozavodsk_3


title: Cord_blood_Espoo_36


title: Cord_blood_Petrozavodsk_7


title: Cord_blood_Espoo_40


title: Cord_blood_Espoo_44


title: Cord_blood_Espoo_45


title: Cord_blood_Petrozavodsk_1


title: Cord_blood_Espoo_42


title: Cord_blood_Petrozavodsk_11


title: Cord_blood_Espoo_38


title: Cord_blood_Espoo_48


title: Cord_blood_Petrozavodsk_4


title: Cord_blood_Espoo_37


title: Cord_blood_Petrozavodsk_39

value: May


title: Cord_blood_Espoo_35


title: Cord_blood_Espoo_33


title: Cord_blood_Espoo_31

value: Male


title: Cord_blood_Espoo_32

value: NP


title: Cord_blood_Espoo_41


title: Cord_blood_Espoo_30


title: Cord_blood_Espoo_25


title: Cord_blood_Espoo_26


title: Cord_blood_Espoo_29


title: Cord_blood_Espoo_27


title: Cord_blood_Espoo_34


title: Cord_blood_Espoo_24


title: Cord_blood_Espoo_28


title: Cord_blood_Espoo_20


title: Cord_blood_Espoo_17


title: Cord_blood_Espoo_19


title: Cord_blood_Espoo_21


title: Cord_blood_Espoo_14


title: Cord_blood_Espoo_18


title: Cord_blood_Espoo_16


title: Cord_blood_Espoo_23


title: Cord_blood_Espoo_10


title: Cord_blood_Espoo_12


title: Cord_blood_Espoo_9


title: Cord_blood_Espoo_6

value: April


title: Cord_blood_Espoo_8


title: Cord_blood_Espoo_13

value: Female


title: Cord_blood_Espoo_11


title: Cord_blood_Espoo_5


title: Cord_blood_Espoo_7


title: Cord_blood_Espoo_22


title: Cord_blood_Espoo_15


title: Cord_blood_Espoo_4


title: Cord_blood_Espoo_3

value: M


title: Cord_blood_Espoo_1


title: Cord_blood_Espoo_2


title: OCI-LY3, Monastrol, 50 uM, 24hrs, Replicate1

city: New York

first: Mukesh

last: Bansal

state: NY

address: 1130 St. Nicholas Ave. Room 908

institute: Columbia University

description: OCI-LY3 cell line profiled at 24hrs following Monastrol treatment with 50 uM concentration

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized on HG-U219 arrays in 120ul volume/well. The GeneTitan Hybridization, Wash and Stain kit (Affymetrix) was used for preparing hybridization mixes and automated processing of 96-array plates on the GeneTitan Instrument (Affymetrix).

scan_protocol: HG-U219 Array Plates were scanned on the GeneTitan instrument (Affymetrix) imaging device according to manufacturer's instructions.

data_processing: Determination of the signal values were obtained with GeneChip Command Console Software (AGCC) (Affymetrix). Raw data were normalized with the Robust Multichip Analysis (RMA) algorithm using BioConductor Affy Package.  Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm of the BioConductor Affy Package.

label_protocol: cRNA synthesis and biotin-labelling was performed starting with 300 ng of total RNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) following manufacterer's protocol.

growth_protocol: OCI-LY3 cells were cultured under standard conditions in IMDM supplemented with 10% FCS.

extract_protocol: Total RNA was isolated from each well on an automated liquid handling system using the RNAqueous-96 Automated Kit (Ambion) following the manufacturer’s instructions. RNA quantification was performed by NanoDrop 8000 spectrophotometer and itd integrity evaluated by Agilent Bioanalyser.

treatment_protocol: Cells were seeded at 5x10^4 cells/well in 96-well culture plates and 12 hrs post-plating were treated with the specified drug. Samples were harvested in triplicate at 6, 12 and 24 hours post compound addition. In each experiment, vehicle (DMSO)-treated samples were used as controls.

tag: drug

value: Monastrol

tag: concentration

value: 50 uM

tag: time point

tag: replicate


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate8

description: OCI-LY3 cell line profiled at 24hrs following DMSO treatment with 0.01 concentration

value: DMSO


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following H-7, Dihydrochloride treatment with 12.4 uM concentration

value: H-7, Dihydrochloride


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following H-7, Dihydrochloride treatment with 12.4 uM concentration


title: OCI-LY3, Vincristine, 0.005 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Vincristine treatment with 0.005 uM concentration

value: Vincristine


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following H-7, Dihydrochloride treatment with 20.2 uM concentration


title: OCI-LY3, Vincristine, 0.005 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Vincristine treatment with 0.005 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 24hrs, Replicate3


title: OCI-LY3, Vincristine, 0.005 uM, 24hrs, Replicate2


title: OCI-LY3, Monastrol, 50 uM, 24hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 24hrs following Monastrol treatment with 50 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following H-7, Dihydrochloride treatment with 20.2 uM concentration


title: OCI-LY3, Monastrol, 100 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Monastrol treatment with 100 uM concentration


title: OCI-LY3, Monastrol, 50 uM, 24hrs, Replicate3


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate6

source_name: OCI-LY3 cell line profiled at 24hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate7


title: OCI-LY3, Trichostatin A, 0.143 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Trichostatin A treatment with 0.143 uM concentration

value: Trichostatin A


title: OCI-LY3, Trichostatin A, 0.114 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Trichostatin A treatment with 0.114 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 24hrs, Replicate3


title: OCI-LY3, Rapamycin, 13.8 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Rapamycin treatment with 13.8 uM concentration

value: Rapamycin


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate5


title: OCI-LY3, Monastrol, 100 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Monastrol treatment with 100 uM concentration


title: OCI-LY3, Monastrol, 100 uM, 24hrs, Replicate1


title: OCI-LY3, Trichostatin A, 0.114 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Trichostatin A treatment with 0.114 uM concentration


title: OCI-LY3, Rapamycin, 13.8 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Rapamycin treatment with 13.8 uM concentration


title: OCI-LY3, Trichostatin A, 0.114 uM, 24hrs, Replicate1


title: OCI-LY3, Rapamycin, 22 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Rapamycin treatment with 22 uM concentration

value: 22 uM


title: OCI-LY3, Vincristine, 0.01 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Vincristine treatment with 0.01 uM concentration


title: OCI-LY3, Vincristine, 0.01 uM, 24hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 24hrs following Vincristine treatment with 0.01 uM concentration


title: OCI-LY3, Rapamycin, 13.8 uM, 24hrs, Replicate1


title: OCI-LY3, Vincristine, 0.01 uM, 24hrs, Replicate1


title: OCI-LY3, Mitomycin C, 0.553 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Mitomycin C treatment with 0.553 uM concentration

value: Mitomycin C


title: OCI-LY3, Trichostatin A, 0.143 uM, 24hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 24hrs following Trichostatin A treatment with 0.143 uM concentration


title: OCI-LY3, Mitomycin C, 0.553 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Mitomycin C treatment with 0.553 uM concentration


title: OCI-LY3, Mitomycin C, 0.553 uM, 24hrs, Replicate2


title: OCI-LY3, Media, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs after growing them in Media

value: Media


title: OCI-LY3, Mitomycin C, 2.56 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Mitomycin C treatment with 2.56 uM concentration


title: OCI-LY3, Rapamycin, 22 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Rapamycin treatment with 22 uM concentration


title: OCI-LY3, Geldanamycin, 0.001 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Geldanamycin treatment with 0.001 uM concentration

value: Geldanamycin


title: OCI-LY3, Geldanamycin, 0.032 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Geldanamycin treatment with 0.032 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Aclacinomycin A treatment with 0.036 uM concentration

value: Aclacinomycin A


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate4


title: OCI-LY3, Mitomycin C, 2.56 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Mitomycin C treatment with 2.56 uM concentration


title: OCI-LY3, Geldanamycin, 0.001 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Geldanamycin treatment with 0.001 uM concentration


title: OCI-LY3, Geldanamycin, 0.001 uM, 24hrs, Replicate3


title: OCI-LY3, Trichostatin A, 0.143 uM, 24hrs, Replicate1


title: OCI-LY3, Etoposide, 0.812 uM, 24hrs, Replicate1

description: OCI-LY3 cell line profiled at 24hrs following Etoposide treatment with 0.812 uM concentration

value: Etoposide