title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_stress_Animal-17

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by the factors breed (Italian Duroc, Italian Large White or Pietrain), Halothane genotype (NN, Nn or nn), and pre-slaughter stress or no stress treatment.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press the button on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press the button and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.27, Molecular Devices) using FeatureType = Irregular Filled and MorphologicalClosingFollowedByOpening as background measurement.

data_processing: Statistical analysis was carried out using the median values of the intensities of the spots. The background signal was subtracted before normalising the values using the Lowess procedure of SAS (Li and Quin, 2005, SAS Conference Proceedings: PharmaSUG 2005, May 22-25, 2005, Phoenix, Arizona" poster PO34. http://www.lexjansen.com/pharmasug/). Furthermore, some filters were utilised to eliminate spots having in at least one channel: a) spots with signal-to-noise ratio less than 1, b) spots with median minus background less than one, c) saturated spots (with at least 50% of saturated pixel). The normalized data were analyzed in SAS using a mixed model (Cui and Churchill, 2003, Genome Biology 4:210). T tests were performed to identify genes differentially expressed. A cutoff at p<0.001 (PFDR=0.05) was used to obtain the toplists of differntially expressed genes. For some contrasts where the number of significant genes found in the toplists was very high a cutoff at p<0.00005 (PFDR=0.05) was used.

organism: Sus scrofa

growth_protocol: A total of 38 barrows were examined. The utilised animals were of three breeds: 10 Italian Large White and 10 Italian Duroc with genotype RYR1 c.1843CC and 18 Pietrain with different RYR1 genotype (8= c.1843CC, 7= c.1843CT and 3= c.1843TT). Pigs were collected at about 30 kg of live weight in the experimental farm of the Department. They were randomly distributed in 8 pens, two for each breed and with the same number of animals per pen. Throughout the experiment, pigs were fed ad libitum for 115 days using a commercial feed in pellet with 16% crude protein (0.8% lysine) and 14.1 MJ/kg digestible energy. All pigs had ad libitum access to water via a nipple drinker. At the end of the growing period of 115 days all pigs were slaughtered in a single day on the same abbattoir. The day of slaughtering one pen for each breed was random selected to be used as control and the other was used for the pre-slaughter stress treatment (see "Sample_treatment_protocol_ch1" section). Only the three Pietrain pigs with genotype RYR1 c.1843TT were assigned to the control group in order to avoid a highly likely chance of death before slaughtering as consequence of the treatment. Among the seven Pietrain pigs with genotype RYR1 c.1843CT three were assigned by chance to the control group and four to the treatment group. The animals were loaded in the same lorry to be transported to the abbattoir. All control animals were grouped on the low deck and the treatment group was loaded in the upper deck on the lorry.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen)

treatment_protocol: At the abattoir the control group of pigs (see "Sample_growth_protocol" section for details) was treated using minimal pre-slaughter stress, i.e.the pigs walked slowly 4 times along a raceway of 25 metres before stunning. Conversely, the pigs of the treatment group were exposed to high pre-slaughter physiscal stress by pushing to run four times along the raceway of 25 metres using an electric goad to press the animals. Semimembranosus muscles were sampled within one hour post mortem and immediately immersed in liquid nitrogen. The samples were then stored in a -80°C deep freezer until RNA extraction.

tag: Breed

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:17

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany). The labelled reference samples were mixed and divided into aliquots before combining it with a labelled sample.

treatment_protocol: At the abattoir the control group of pigs (see "Sample_growth_protocol" section for details) was treated using minimal pre-slaughter stress, i.e.the pigs walked slowly 4 times along a raceway of 25 metres before stunning. Conversely, the pigs of the treatment group were exposed to high pre-slaughter physiscal stress by pushing to run four times along the raceway of 25 metres using an electric goad to press the animals. The heart samples were collected within one hour post mortem and immediately immersed in liquid nitrogen. The samples were then stored in a -80°C deep freezer until RNA extraction.

tag: Pool of total-RNA extracted from Semimembranosus muscle samples of 12 pigs and from heart muscle samples obtained from 10 pigs. The 12 animals used for the extraction from Semimembranosus muscle were

value: 2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 5 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT. The 10 animals used for the extraction from heart muscle were:2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 3 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT.


title: FAIRE-array1

status: Public on Jan 01 2013

type: genomic

city: Chicago

first: Jie

last: Zhou

state: ILLINOIS

address: 900 East 57th Street, KCBD 10100

country: USA

institute: University of Chicago IGSB

description:
control CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
FAIRE ChIP - Array 1

hyb_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

data_processing:
Tiling array data were normalized and analyzed as described (Hua et al, 2009). Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of +/-250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions. Significantly enriched probes (p < 1e-3) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.
results file descriptions: Bed files for enriched ChIP sites of each of 6 chromatins marks.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: FAIRE ChIP

label_protocol: ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.

extract_protocol: According to the standard chromatin extraction protocol (see Sujun et al, 2009).

treatment_protocol: MCF7 Cells were grown in growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml),  until 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

tag: cell type

value: MCF7 cells

tag: chromatin mark

value: FAIRE

tag: antibody vendor

tag: antibody catalog #

source_name: Input DNA


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_no-stress_Animal-32

type: RNA

molecule: total RNA

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany).

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:32


title: AML [1299_27may08]

city: Rotterdam

first: Martin

middle: van

last: Vliet

address: Lichtenauerlaan 40

department: Bioinformatics

country: Netherlands

institute: SkylineDx

description: Not Applicable

hyb_protocol: As described in the AMLprofiler IFU (instructions for use), Hybridized for 17 hours, 45C at 60 rpm in Affymetrix Hybridization oven

scan_protocol: As described in the AMLprofiler IFU (instructions for use) on an Affymetrix GeneChip System 3000Dx v.2

data_processing: DM algorithm implemented in the Affymetrix Power Tools (APT 1.10.2).

label: Biotin

source_name: AML

label_protocol: We used 10 µg of total RNA to prepare antisense biotinylated RNA. Single-stranded complementary DNA (cDNA) and double-stranded cDNA were synthesized according to the manufacturer’s protocol (Invitrogen Life Technologies) with the use of the T7-(deoxythymidine)24-primer (Genset). In vitro transcription was performed with biotin-11-cytidine triphosphate and biotin-16-uridine triphosphate (Perkin–Elmer) and the MEGAScript T7 labeling kit (Ambion). Double-stranded cDNA and complementary RNA (cRNA) were purified and fragmented with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Not Applicable

extract_protocol: After thawing, cells were washed once with Hanks’balanced-salt solution. High-quality total RNA was extracted by lysis with guanidinium thiocyanate followed by cesium chloride–gradient purification. RNA levels, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent). None of the samples showed RNA degradation (ratio of 28S ribosomal RNA to 18S ribosomal RNA of at least 2) or contamination by DNA.

treatment_protocol: Not Applicable

tag: cohort

value: Training

tag: npm1 status

value: NPM1 A


title: NR2C2-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR2C2 ChIP - Array 1

scan_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

data_processing: Tiling array data were normalized and analyzed as described (Hua et al, 2009). Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of +/-250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions. Significantly enriched probes (p < 1e-3) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions. Peaks located in the BAC regions, overlaps with GFP peaks, and overlaps with repetitive regions in the genome are filtered.

source_name: NR2C2 ChIP

growth_protocol:
MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.
For each NR with known ligand, MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM NR ligand at 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine. For orphan NRs and NR-cofactors, no ligand was used and ChIP was performed with cells growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml).

extract_protocol: ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.

treatment_protocol: According to the standard chromatin extraction protocol (Shang et al., 2000).

value: transgenic MCF7

tag: transcription factor

tag: tag

value: modified LAP (localization and affinity purification) tag containing GFP

tag: chip antibody

value: Goat anti-GFP


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_no-stress_Animal-28

source_name: Muscle-Semimembranosus_Italian Large White_NN_no stress_Animal-28

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:28


title: FOSL2-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
FOSL2 ChIP - Array 2

source_name: FOSL2 ChIP


title: AML [1197_07may08]

description: Not Applicable

value: NPM1 wt


title: NR2C1-L-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR2C1-L ChIP - Array 1

source_name: NR2C1-L ChIP


title: Staphylococcus aureus_OBPCP_10min_replicate2

city: Ft. Meade

first: Prashanthi

last: Mulinti

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description:
SAMPLE 7
OBPCP treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Command Console (AGCC) version 3.0, MAS5 algorithm

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_OBPCP_10min

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated aRNA targets.500 ng of total RNA sample was first polyadenylated at the 3′ end with Poly(A) Polymerase. The A-tailed RNA was then reverse transcribed using oligo(dT) primers containing a T7 RNA polymerase promoter. The resulting cDNA with a T7 promoter was purified and further used to produce biotin labeled aRNA by incorporating Biotin 11-UTP (Ambion) in the vitro transcription (IVT) reaction. The quality of the aRNA synthesized was assessed on a RNA LabChip using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.). The biotin labeled aRNA was fragmented using 5X fragmentation buffer (200mM Tris-acetate (pH 8.1), 500mM KOAc, 150mM MgOAc) and 20 μg of the fragmented aRNA was hybridized to the S.aureus Affymetrix® GeneChip array for 16 hours at 45°C according to manufacturer’s instructions (Affymetrix, Inc.).

growth_protocol: S.aureus cultures were grown until an optical density at 600nm (OD600) reached the early logarithmic phase (~ 0.8). OD600  was measured using a Lambda 25 spectrophotometer (Perkin-Elmer). For microarray study. a concentration of 0.07 mM OBPCP dissolved in DMSO was added to 5 ml of the log phase culture and equivalent amount of DMSO only was added to the control culture. The cultures were incubated for 10 and 60 min at 37ºC.

extract_protocol: S. aureus cultures (five control, five 10 min and five 60 min treatments) were collected at the indicated times (10 and 60 min) and immediately mixed with 2 volumes of RNA protect (Qiagen) for 5 min at room temperature. Cells were harvested by centrifugation at 5000 rpm for 10 min at 25ºC. Cells were frozen at −80°C. Frozen cells were thawed and lysed using 100 μl of a 5 mg/ml lysostaphin (AMBI products, LLC) solution in 20 mM sodium acetate buffer (pH 4.6) for 30 min at 37ºC with gently shaking. Total RNA was extracted from the lysed cells using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. RNA was eluted in 25 μl of RNase free distilled H2O (Fisher Scientific) and quantified by NanoDrop spectrophotometer (NanoDrop Technologies), and the quality of the sample was assessed by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.). Approximately 5 μl (~ 500 ng) of total RNA from each sample was linearly amplified (two rounds) using MessageAmp™ II Bacteria Kit (Ambion) following manufacturer’s instruction.

tag: strain

value: NCTC 8325


title: THRA-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
THRA ChIP - Array 1

source_name: THRA ChIP

value: THRA


title: AML [1188_18apr08]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_A56_13aug2009]

description: Not Applicable

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols.

value: Validation


title: SPDEF-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
SPDEF ChIP - Array 1

source_name: SPDEF ChIP

value: SPDEF


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_stress_Animal-5

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:5


title: RXRB-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
RXRB ChIP - Array 1

source_name: RXRB ChIP

value: RXRB


title: Staphylococcus aureus_PTAP_60min_replicate2

description: PTAP treatment

data_processing: Affymetrix GeneChip Command Console (AGCC) version 3.0, MAS5.0 algorithm

source_name: Staphylococcus aureus_PTAP_60min

growth_protocol: S.aureus cultures were grown until an optical density at 600nm (OD600) reached the early logarithmic phase (~ 0.8). OD600  was measured using a Lambda 25 spectrophotometer (Perkin-Elmer). For microarray study. a concentration of 0.07 mM PTAP dissolved in DMSO was added to 5 ml of the log phase culture and equivalent amount of DMSO only was added to the control culture. The cultures were incubated for 10 and 60 min at 37ºC.

treatment_protocol: No treatment


title: AML [Ulm_CN_xx_xx_A120_13aug2009]

description: Not Applicable


title: Staphylococcus aureus_no treatment_0min_replicate4

description:
SAMPLE 4
No treatment

source_name: Staphylococcus aureus_no treatment_0min


title: Staphylococcus aureus_OBPCP_10min_replicate1

description:
SAMPLE 6
OBPCP treatment


title: Staphylococcus aureus_no treatment_0min_replicate5

description:
SAMPLE 5
No treatment


title: H3R17ME2-array6

description:
control CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
H3R17ME2 ChIP - Array 6

source_name: H3R17ME2 ChIP

value: abcam


title: AML [Ulm_CN_xx_xx_A115_13aug2009]

description: Not Applicable


title: RXRA-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
RXRA ChIP - Array 1

source_name: RXRA ChIP

value: RXRA


title: Staphylococcus aureus_no treatment_0min_replicate3

description:
SAMPLE 3
No treatment


title: Staphylococcus aureus_no treatment_0min_replicate2

description:
SAMPLE 2
No treatment


title: Staphylococcus aureus_no treatment_0min_replicate1

description:
SAMPLE 1
No treatment


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_no-stress_Animal-38

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:38

value: 2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 5 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT. The 10 animals used for the extraction from heart muscle were:2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 3 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT.


title: RORC-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
RORC ChIP - Array 1

source_name: RORC ChIP

value: RORC


title: Muscle-Semimembranosus_Pietrain_Hal-NN_stress_Animal-14

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:14


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_stress_Animal-15

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:15


title: AML [Ulm_CN_xx_xx_A05KM2770_13aug2009]

description: Not Applicable


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_no-stress_Animal-21

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:21


title: Muscle-Semimembranosus_Pietrain_Hal-Nn_stress_Animal-3

value: Pietrain, Gender:castrated males, Hal genotype:Nn, Treatment:stress, Animal:3


title: Muscle-Semimembranosus_Pietrain_Hal-Nn_stress_Animal-2

value: Pietrain, Gender:castrated males, Hal genotype:Nn, Treatment:stress, Animal:2


title: AML [Ulm_CN_xx_xx_98_14aug2009]

description: Not Applicable

value: NPM1 wt


title: H3K4triM_E-array6

description:
control CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
H3K4triM_E ChIP - Array 6

source_name: H3K4triM_E ChIP

value: MCF7 cells


title: RORA-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
RORA ChIP - Array 1

source_name: RORA ChIP

value: transgenic MCF7

value: RORA

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: H3K4mM-array6

description:
control CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
H3K4mM ChIP - Array 6

source_name: H3K4mM ChIP

source_name: Input DNA


title: AML [Ulm_CN_xx_xx_97_18aug2009]

description: Not Applicable

source_name: AML

value: Validation


title: PPARG-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
PPARG ChIP - Array 1

source_name: PPARG ChIP

value: PPARG


title: Muscle-Semimembranosus_Pietrain_Hal-nn_no-stress_Animal-34

value: Pietrain, Gender:castrated males, Hal genotype:nn, Treatment:no stress, Animal:34


title: PPARD-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
PPARD ChIP - Array 1

source_name: PPARD ChIP

value: PPARD


title: H2AZ_Ace-array6

description:
control CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
H2AZ_Ace ChIP - Array 6

source_name: H2AZ_Ace ChIP

value: Abcam


title: AML [Ulm_CN_xx_xx_86_20aug2009]

description: Not Applicable


title: FAIRE-array6

description:
control CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
FAIRE ChIP - Array 6

source_name: FAIRE ChIP

value: FAIRE


title: FOSB-array2

description:
Ch2 input ctrl CEL files: input1-2.CEL, input2-2.CEL, input3-2.CEL
FOSB ChIP - Array 2

source_name: FOSB ChIP

value: FOSB


title: AML [Ulm_CN_xx_xx_85_06aug2009]

description: Not Applicable


title: PPARA-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
PPARA ChIP - Array 1

source_name: PPARA ChIP

value: PPARA


title: AML [Ulm_CN_xx_xx_84_12aug2009]

description: Not Applicable

value: NPM1 A


title: XBP1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
XBP1 ChIP - Array 6

source_name: XBP1 ChIP


title: NR4A2-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NURR1 ChIP - Array 1

source_name: NR4A2 ChIP


title: PGR-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR3C1 ChIP - Array 1

source_name: PGR ChIP

value: PGR


title: VDR-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
VDR ChIP - Array 6

source_name: VDR ChIP

value: VDR


title: AML [Ulm_CN_xx_xx_83_12aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_87_07aug2009]

description: Not Applicable


title: H3K27triM-array6

description:
control CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
H3K27triM ChIP - Array 6

source_name: H3K27triM ChIP

value: Upstate


title: NR4A1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR4A1 ChIP - Array 1

source_name: NR4A1 ChIP


title: Muscle-Semimembranosus_Pietrain_Hal-NN_stress_Animal-8

description: Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by the factors breed (Italian Duroc, Italian Large White or Pietrain), Halothane genotype (NN, Nn or nn), and pre-slaughter stress or no stress treatment.

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:8

value: 2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 5 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT. The 10 animals used for the extraction from heart muscle were:2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 3 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT.


title: NR2C2-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR2C2 ChIP - Array 6

source_name: NR2C2 ChIP

value: transgenic MCF7


title: AML [Ulm_CN_xx_xx_82_12aug2009]

description: Not Applicable

value: NPM1 wt


title: AML [Ulm_CN_xx_xx_81_21aug2009]

description: Not Applicable


title: NR2F1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR2F1 ChIP - Array 1

source_name: NR2F1 ChIP

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: NR2C1-S-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR2C1-S ChIP - Array 1

source_name: NR2C1-S ChIP


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_stress_Animal-11

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:11


title: NR2C1-L-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR2C1-L ChIP - Array 6

source_name: NR2C1-L ChIP

source_name: Input DNA


title: Muscle-Semimembranosus_Pietrain_Hal-nn_no-stress_Animal-36

value: Pietrain, Gender:castrated males, Hal genotype:nn, Treatment:no stress, Animal:36


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_stress_Animal-9

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:9


title: Muscle-Semimembranosus_Pietrain_Hal-Nn_no-stress_Animal-19

value: Pietrain, Gender:castrated males, Hal genotype:Nn, Treatment:no stress, Animal:19


title: Muscle-Semimembranosus_Pietrain_Hal-NN_stress_Animal-18

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:18


title: AML [Ulm_CN_xx_xx_A77_13aug2009]

description: Not Applicable

source_name: AML

value: Validation

value: NPM1 non-ABD


title: AML [Ulm_CN_xx_xx_80_21aug2009]

description: Not Applicable


title: NR1D1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR1D1 ChIP - Array 1

source_name: NR1D1 ChIP


title: NR1D2-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR1D2 ChIP - Array 1

source_name: NR1D2 ChIP


title: THRA-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
THRA ChIP - Array 6

source_name: THRA ChIP

value: THRA


title: AML [Ulm_CN_xx_xx_79_12aug2009]

description: Not Applicable

value: NPM1 B


title: SPDEF-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
SPDEF ChIP - Array 6

source_name: SPDEF ChIP

value: SPDEF


title: Muscle-Semimembranosus_Pietrain_Hal-NN_stress_Animal-6

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:6


title: NR1H2-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR1H3 ChIP - Array 1

source_name: NR1H3 ChIP


title: AML [Ulm_CN_xx_xx_78_14aug2009]

description: Not Applicable

value: NPM1 A


title: NR2C1-S-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR2C1-S ChIP - Array 6


title: AML [Ulm_CN_xx_xx_75_14aug2009]

description: Not Applicable


title: RXRB-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
RXRB ChIP - Array 6

source_name: RXRB ChIP

value: RXRB


title: Muscle-Semimembranosus_Pietrain_Hal-NN_no-stress_Animal-30

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:30

value: 2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 5 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT. The 10 animals used for the extraction from heart muscle were:2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 3 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT.


title: Muscle-Semimembranosus_Pietrain_Hal-Nn_stress_Animal-16

value: Pietrain, Gender:castrated males, Hal genotype:Nn, Treatment:stress, Animal:16


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_no-stress_Animal-24

source_name: Muscle-Semimembranosus_Italian Large White_NN_no stress_Animal-24

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:24


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_no-stress_Animal-22

source_name: Muscle-Semimembranosus_Italian Large White_NN_no stress_Animal-22

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:22


title: Muscle-Semimembranosus_Pietrain_Hal-Nn_stress_Animal-4

value: Pietrain, Gender:castrated males, Hal genotype:Nn, Treatment:stress, Animal:4


title: JUND-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
JUND ChIP - Array 1

source_name: JUND ChIP

value: transgenic MCF7

value: JUND

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: AML [Ulm_CN_xx_xx_74_18aug2009]

description: Not Applicable

value: Validation

value: NPM1 wt


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_stress_Animal-7

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:7


title: RXRA-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
RXRA ChIP - Array 6

source_name: RXRA ChIP

value: RXRA


title: JUNB-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
JUNB ChIP - Array 1

source_name: JUNB ChIP

value: JUNB


title: RORC-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
RORC ChIP - Array 6

source_name: RORC ChIP

value: RORC


title: AML [Ulm_CN_xx_xx_73_21aug2009]

description: Not Applicable


title: RORA-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
RORA ChIP - Array 6

source_name: RORA ChIP

value: RORA


title: NR3C1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR3C1 ChIP - Array 1

source_name: NR3C1 ChIP


title: PPARG-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
PPARG ChIP - Array 6

source_name: PPARG ChIP

value: PPARG


title: JUN-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
JUN ChIP - Array 1

source_name: JUN ChIP

value: JUN

source_name: Input DNA


title: Muscle-Semimembranosus_Pietrain_Hal-NN_no-stress_Animal-29

description: Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by the factors breed (Italian Duroc, Italian Large White or Pietrain), Halothane genotype (NN, Nn or nn), and pre-slaughter stress or no stress treatment.

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:29

value: 2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 5 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT. The 10 animals used for the extraction from heart muscle were:2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 3 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT.


title: FOSL2-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
FOSL2 ChIP - Array 1

source_name: FOSL2 ChIP


title: H2AZ_Ace-array1

description:
control CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
H2AZ_Ace ChIP - Array 1

source_name: H2AZ_Ace ChIP

value: MCF7 cells

value: Abcam


title: AML [Ulm_CN_xx_xx_71_12aug2009]

description: Not Applicable

source_name: AML


title: AML [1766_19jun08]

description: Not Applicable

value: Training

value: NPM1 A


title: AML [Ulm_CN_xx_xx_72_21aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_70_18aug2009]

description: Not Applicable


title: PPARD-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
PPARD ChIP - Array 6

source_name: PPARD ChIP

value: transgenic MCF7

value: PPARD

value: modified LAP (localization and affinity purification) tag containing GFP


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_no-stress_Animal-26

source_name: Muscle-Semimembranosus_Italian Large White_NN_no stress_Animal-26

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:26


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_no-stress_Animal-20

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:20


title: PPARA-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
PPARA ChIP - Array 6

source_name: PPARA ChIP

value: PPARA

value: Goat anti-GFP


title: FOSL1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
FOSL1 ChIP - Array 1

source_name: FOSL1 ChIP


title: FOSB-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
FOSB ChIP - Array 1

source_name: FOSB ChIP

value: FOSB


title: AML [Ulm_CN_xx_xx_69_12aug2009]

description: Not Applicable

value: Validation


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_stress_Animal-12

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:12


title: PGR-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR3C1 ChIP - Array 6

source_name: PGR ChIP

value: PGR


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_stress_Animal-13

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:13


title: Muscle-Semimembranosus_Pietrain_Hal-Nn_no-stress_Animal-37

value: Pietrain, Gender:castrated males, Hal genotype:Nn, Treatment:no stress, Animal:37

value: 2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 5 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT. The 10 animals used for the extraction from heart muscle were:2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 3 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT.


title: AML [Ulm_CN_xx_xx_68_12aug2009]

description: Not Applicable


title: FOS-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
FOS ChIP - Array 1

source_name: FOS ChIP

value: FOS


title: AML [Ulm_CN_xx_xx_67_21aug2009]

description: Not Applicable

value: NPM1 B


title: NR4A2-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NURR1 ChIP - Array 6

source_name: NR4A2 ChIP


title: ELK-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
ELK ChIP - Array 1

source_name: ELK ChIP

value: ELK


title: Muscle-Semimembranosus_Pietrain_Hal-nn_no-stress_Animal-31

value: Pietrain, Gender:castrated males, Hal genotype:nn, Treatment:no stress, Animal:31


title: CREB1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
CREB1 ChIP - Array 1

source_name: CREB1 ChIP

value: transgenic MCF7


title: NR2F2-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
NR2F2 ChIP - Array 1

source_name: NR2F2 ChIP

value: modified LAP (localization and affinity purification) tag containing GFP


title: ATF1-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
ATF1 ChIP - Array 1

source_name: ATF1 ChIP


title: NR4A1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR4A1 ChIP - Array 6

source_name: NR4A1 ChIP


title: Muscle-Semimembranosus_Pietrain_Hal-NN_no-stress_Animal-27

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:27


title: AML [Ulm_CN_xx_xx_64_21aug2009]

description: Not Applicable

value: NPM1 wt


title: Muscle-Semimembranosus_Italian-Duroc_Hal-NN_stress_Animal-1

value: Italian Duroc, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:1


title: AML [Ulm_CN_xx_xx_62_07aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_63_14aug2009]

description: Not Applicable


title: NR1D2-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR1D2 ChIP - Array 6

source_name: NR1D2 ChIP

value: Goat anti-GFP

source_name: Input DNA


title: Muscle-Semimembranosus_Italian-Large-White_Hal-NN_stress_Animal-10

value: Italian Large White, Gender:castrated males, Hal genotype:NN, Treatment:stress, Animal:10


title: Muscle-Semimembranosus_Pietrain_Hal-Nn_no-stress_Animal-33

value: Pietrain, Gender:castrated males, Hal genotype:Nn, Treatment:no stress, Animal:33


title: AML [Ulm_CN_xx_xx_61_21aug2009]

description: Not Applicable

value: Validation


title: NR1D1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR1D1 ChIP - Array 6

source_name: NR1D1 ChIP


title: NR1H2-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR1H3 ChIP - Array 6

source_name: NR1H3 ChIP


title: JUND-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
JUND ChIP - Array 6

source_name: JUND ChIP

value: JUND


title: NR2F1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR2F1 ChIP - Array 6

source_name: NR2F1 ChIP


title: NR2F2-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR2F2 ChIP - Array 6


title: AML [Ulm_CN_xx_xx_59_14aug2009]

description: Not Applicable

source_name: AML


title: AML [Ulm_CN_xx_xx_58_11aug2009]

description: Not Applicable

value: NPM1 A


title: JUNB-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
JUNB ChIP - Array 6

source_name: JUNB ChIP

value: JUNB


title: AR-array1

description:
Ch2 input ctrl CEL files: input1-1.CEL, input2-1.CEL, input3-1.CEL
AR ChIP - Array 1

source_name: AR ChIP

value: AR


title: AML [Ulm_CN_xx_xx_57_07aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_55_12aug2009]

description: Not Applicable


title: JUN-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
JUN ChIP - Array 6

source_name: JUN ChIP

value: JUN


title: AML [Ulm_CN_xx_xx_60_14aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_54_19aug2009]

description: Not Applicable


title: GPX4 siRNA 120-3

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: 750ng biotin-labeled sample was hybridized to each HT-12 array using Illumina reagents and standard procedure

scan_protocol: The standard Illumina scanning protocol was used

data_processing: The data were normalised using 'Shift to 75 percentile' method in GeneSpring GX, and a baseline transformation to the median of all samples was performed.

source_name: CACO-2 Cells, GPX4 siRNA 120pmol

label_protocol: Total RNA was amplified and labelled using Ambion Total Prep reagents (Applied Biosystems, Scoresby, Victoria, Australia) according to the manufacturers' instructions.

growth_protocol: Cells were grown in DMEM eagle medium with or without antibiotic (penistrep) (depending on what was required) containing FCS. Cells were subcultured, cell count was carried out and cell were left to grow for 24 hrs before transfection with siRNA after 30-50% confluency. 72 hrs following transfcetion, cells were washed with PBS and total RNA extracted and purified.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Nanodrop and Agilent Bioanalyser.

treatment_protocol: Twenty four hours after cells have been subcultured, cells were incubated with either GPx4 specific siRNA or scrambled control siRNA for seventy two hours.

tag: cell line

value: Caco-2 cells (HTB-37)

value: human colorectal carcinoma


title: Muscle-Semimembranosus_Pietrain_Hal-NN_no-stress_Animal-23

description: Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by the factors breed (Italian Duroc, Italian Large White or Pietrain), Halothane genotype (NN, Nn or nn), and pre-slaughter stress or no stress treatment.

value: Pietrain, Gender:castrated males, Hal genotype:NN, Treatment:no stress, Animal:23

value: 2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 5 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT. The 10 animals used for the extraction from heart muscle were:2 Italian Duroc stressed, genotype at RYR1 locus c.1843CC; 3 Italian Large White stressed, genotype at RYR1 locus c.1843CC; 2 Pietrain stressed, genotype at RYR1 locus c.1843CC; 3 Pietrain stressed, genotype at RYR1 locus c.1843CT.


title: ORE1-IOE-2h+Mock (1st)

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

description: Gene expression data from ORE1-IOE, 2h after Mock treatment

hyb_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

organism: Arabidopsis thaliana

source_name: Arabidopsis ORE1-IOE Seedlings treated with Ethanol (0.1%)

growth_protocol:
IOE: Seeds were surface-sterilized for 1 min in 70% ethanol and then in sterilisation solution (20% sodium hypochlorite) for 30 min. After sterilization, the seeds were sown on half-strength MS medium (Murashige and Skoog, 1962), supplemented with 1% (w/v) sucrose and solidified with 0.7% (w/v) phytoagar and appropriate antibiotics. After imbibition, the seeds were stratified at 4°C for 3 days. The seeds were germinated at 22°C under a 16-h day (140 µmol m-2 s-1) / 8-h night regime. The two-week-old Arabidopsis seedlings were carefully removed from plates  subjected to Est/Mocktreatments.
Plants used for protoplast preparation: Col-0 seeds were directly sown on soil and plants were grown under long day (16 h light / 8 h dark) conditions.

extract_protocol: RNeasy Plant Mini Kit

treatment_protocol: After two weeks, seedlings were transferred to MS liquid medium while shaking.   β-estradiol (Sigma-Aldrich) was added to the medium to a final concentration of 10 μM. Subsequently, seedlings were harvested at 2h after estradiol addition.

tag: tissue

value: Whole seedling

tag: ecotype

tag: genotype

tag: age

value: two-week-old

tag: treatment

value: mock


title: GPX4 siRNA 120-1


title: ORE1-IOE-2h+Est (2nd)

description: Gene expression data from ORE1-IOE, 2h after estradiol treatment

scan_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

source_name: Arabidopsis ORE1-IOE Seedlings treated with Est (10µM)

value: Estradiol


title: AML [Ulm_CN_xx_xx_52_06aug2009]

description: Not Applicable

value: NPM1 B


title: AML [Ulm_CN_xx_xx_53_06aug2009]

description: Not Applicable

value: NPM1 wt


title: ORE1-IOE-2h+Est (1st)

label_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual


title: FOSL1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
FOSL1 ChIP - Array 6

source_name: FOSL1 ChIP

value: transgenic MCF7

value: modified LAP (localization and affinity purification) tag containing GFP

value: Goat anti-GFP


title: Negative Control 120-2

source_name: CACO-2 Cells, scrambled siRNA 120pmol


title: GPX4 siRNA 120-2


title: Negative Control 120-1


title: FOSB-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
FOSB ChIP - Array 6

source_name: FOSB ChIP

value: FOSB


title: Negative Control 120-3


title: NR3C1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
NR3C1 ChIP - Array 6

source_name: NR3C1 ChIP


title: AML [Ulm_CN_xx_xx_51_06aug2009]

description: Not Applicable

value: Validation

value: NPM1 A


title: FOS-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
FOS ChIP - Array 6

source_name: FOS ChIP

value: FOS


title: GPX4 siRNA 60-3

source_name: CACO-2 Cells, GPX4 siRNA 60pmol

value: Caco-2 cells (HTB-37)


title: ORE1-IOE-2h+Mock (2nd)


title: GPX4 siRNA 60-2

value: human colorectal carcinoma


title: FOSL2-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
FOSL2 ChIP - Array 6

source_name: FOSL2 ChIP

source_name: Input DNA


title: 35S:ORE1-protoplast 6h (2nd)

description: Transiently (6h) expressed 35S:ORE1 in Arabidopsis mesophyll cell protoplasts

source_name: mesophyll cell protoplasts

value: mesophyll cell protoplasts

value: five-week-old


title: ELK-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
ELK ChIP - Array 6

source_name: ELK ChIP

value: ELK


title: WT (1st)

description: Arabidopsis mesophyll cell protoplasts

value: WT protoplast


title: GPX4 siRNA 60-1


title: AML [Ulm_CN_xx_xx_50_14aug2009]

description: Not Applicable

source_name: AML


title: 35S:ORE1-protoplast 6h (1st)


title: WT (2nd)

description: Arabidopsis mesophyll cell protoplasts


title: ATF1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
ATF1 ChIP - Array 6

source_name: ATF1 ChIP


title: AR-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
AR ChIP - Array 6

source_name: AR ChIP

value: AR


title: AML [Ulm_CN_xx_xx_48_20aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_49_19aug2009]

description: Not Applicable


title: Negative Control 60-3

source_name: CACO-2 Cells, scrambled siRNA 60pmol


title: AML [Ulm_CN_xx_xx_47_14aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_46_12aug2009]

description: Not Applicable

value: NPM1 non-ABD


title: AML [Ulm_CN_xx_xx_45_21aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_43_07aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_44_20aug2009]

description: Not Applicable


title: Negative Control 60-2


title: AML [Ulm_CN_xx_xx_42_11aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_38_06aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_37_19aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_36_20aug2009]

description: Not Applicable


title: nsrR Mutant rep2

city: Saint-Genès-Champanelle

first: Christine

last: MARTIN

address: Centre de Theix

department: MICA

country: France

institute: INRA

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

organism: Escherichia coli

label_protocol: standard Affymetrix protocol

growth_protocol: growth in LB medium for 6H

extract_protocol: In brief, cells were harvested directly into RNA Protect (QIAGEN), and total RNA was purified using a QIAGEN RNeasy Mini kit.

treatment_protocol: NOR-4 treament or nsrR knockout

value: nsrR KO


title: 5g/d of yeast C3L2

city: Aberystwyth

first: Eric

last: PINLOCHE

address: Cledwyn Building

institute: IBERS

description: Sanger sequencing method

data_processing:
Base-calling and vector sequence trimming were done using Sequence Analysis software (© Beckman Instruments, Inc.)
RSTs were separated using head-tail border 5’-ACGGGTCG-3’ or the complement 5’-CGACCCGT-3’ created by concatemerization using BioEdit = Raw data
Blast filtering to remove Chimera (95% seq ID over 90% sequence length)
Cluster sequences at 100% sequnece identity (CD-Hit-est) and count unique Tags = Processed data
Tab delimited file of the count of unique tags (100% sequence ID) after blast filtering to remove Chimera: tag sequence, count, tag ID.

organism: Bacteria

source_name: Rumen content

extract_protocol: DNA was extracted using Qiagen Stool kit, amplified with 63F and 109R (with Bsg1 restriction site), purifed with phenol/chloroform/ethanol extraction, digested with Bsg1, concatenate, gel purified, inserted in Puc19 and clone in TOPO10.

treatment_protocol: Whole rumen, liquid fraction (filtered through 0.2 mm) and solid fraction (recovered on the thieve after filtration) was sampled 4h after feeding for 2 days at the end of each period. Sample were frozen at -80 and freeze-dried.

value: 5g/d of yeast

tag: sample type

value: cow rumen content

tag: diet

value: acidogenic


title: NO rep2

value: NO donor NOR-4

value: wild type


title: AML [Ulm_CN_xx_xx_132_07aug2009]

description: Not Applicable

value: Validation

value: NPM1 wt


title: AML [Ulm_CN_xx_xx_131_06aug2009]

description: Not Applicable


title: nsrR Mutant rep3


title: UMARY-1867

city: Bethesda

first: J Raphael

last: Gibbs

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

description: Human Brain Tissue: Purkinje Cells

hyb_protocol: Illumina Whole Genome Gene Expression

scan_protocol: Illumina Beadstation

data_processing: Illumina Genome Studio Gene Expression Module v3.2.7, cubic spline normalization

source_name: Human Brain Tissue: Purkinje Cells

label_protocol: Ambion MessageAmp II (two rounds of amplification)

extract_protocol: PicoPure RNA isolation kit

tag: gender

value: female

tag: age (y)

tag: pmi (hr)

tag: tissue bank

value: UMARY

value: E

tag: cell type

value: Cerebellar Purkinje Cells


title: Wild type rep2


title: UMARY-1136

description: Human Brain Tissue: Purkinje Cells


title: Negative Control 60-1

value: Caco-2 cells (HTB-37)

value: human colorectal carcinoma


title: nsrR Mutant rep1


title: UMARY-1037

description: Human Brain Tissue: Purkinje Cells

value: male


title: UMARY-1847

description: Human Brain Tissue: Purkinje Cells


title: 0.5g/d of yeast C3L1

description: Sanger sequencing method

value: 0.5g/d of yeast


title: Control C3L0

description: Sanger sequencing method

value: Control


title: NO rep1


title: NO rep3


title: UMARY-1105

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1907

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_130_20aug2009]

description: Not Applicable

tag: cohort

tag: npm1 status

value: NPM1 A


title: UMARY-1940

description: Human Brain Tissue: Purkinje Cells


title: 5g/d of yeast C2L2

description: Sanger sequencing method

value: 5g/d of yeast


title: UMARY-1260

description: Human Brain Tissue: Purkinje Cells


title: Wild type rep3


title: UMARY-5024

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1170

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1797

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1028

description: Human Brain Tissue: Purkinje Cells


title: Wild type rep1


title: UMARY-1545

description: Human Brain Tissue: Purkinje Cells


title: 0.5g/d of yeast C2L1

description: Sanger sequencing method

value: cow rumen content


title: AML [Ulm_CN_xx_xx_128_20aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_129_18aug2009]

description: Not Applicable


title: Control C2L0

description: Sanger sequencing method

value: acidogenic


title: 5g/d of yeast C1L2

description: Sanger sequencing method


title: AML [Ulm_CN_xx_xx_126_12aug2009]

description: Not Applicable


title: 0.5g/d of yeast C1L1

description: Sanger sequencing method


title: SIDP28_blood_NoVAP_rep7

city: Memphis

first: Joseph

last: Swanson

state: TN

address: 910 Madison Ave., Suite 308

department: Clinical Pharmacy

institute: University of Tennessee

description: Gene expression data from critically-ill trauma patients following admission to the intensive care unit

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G.

data_processing: The data were analyzed with RMA as the normalization method.

source_name: patients without VAP

label_protocol: Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.

extract_protocol: Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times.  Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.

value: blood


title: SIDP31_blood_NoVAP_rep9


title: Control C1L0

description: Sanger sequencing method


title: AML [Ulm_CN_xx_xx_127_12aug2009]

description: Not Applicable


title: SIDP29_blood_NoVAP_rep8


title: UMARY-1230

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_124_07aug2009]

description: Not Applicable


title: UMARY-871

description: Human Brain Tissue: Purkinje Cells


title: SIDP32_blood_NoVAP_rep10


title: AML [Ulm_CN_xx_xx_125_06aug2009]

description: Not Applicable


title: SIDP27_blood_NoVAP_rep6


title: SIDP24_blood_VAP_rep10

source_name: patients with VAP


title: AML [Ulm_CN_xx_xx_123_12aug2009]

description: Not Applicable


title: 20uM-Exp2

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA by software Partek (Version 6.5 (6.11.0321))

organism: Caenorhabditis elegans

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

extract_protocol: Qiagen RNeasy Mini kit for RNA isolation.

tag: agent

value: 20uM Heme

tag: genotype/variation

value: hrg-2 Mutant

tag: developmental stage

value: mid-late L4 stage


title: 20uM-Exp3


title: UMARY-1862

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1454

description: Human Brain Tissue: Purkinje Cells

value: female


title: UMARY-4263

description: Human Brain Tissue: Purkinje Cells

value: UMARY


title: UMARY-1571

description: Human Brain Tissue: Purkinje Cells

value: E


title: SIDP25_blood_NoVAP_rep5

tag: tissue


title: AML [Ulm_CN_xx_xx_121_18aug2009]

description: Not Applicable

value: Validation

value: NPM1 wt


title: AML [Ulm_CN_xx_xx_122_12aug2009]

description: Not Applicable


title: UMARY-1865

description: Human Brain Tissue: Purkinje Cells

value: Cerebellar Purkinje Cells


title: SIDP22_blood_VAP_rep8


title: AML [Ulm_CN_xx_xx_120_11aug2009]

description: Not Applicable


title: SIDP23_blood_VAP_rep9


title: 4uM-Exp3

value: 4uM Heme


title: AML [Ulm_CN_xx_xx_119_11aug2009]

description: Not Applicable


title: UMARY-4543

description: Human Brain Tissue: Purkinje Cells

value: male


title: AML [Ulm_CN_xx_xx_117_06aug2009]

description: Not Applicable


title: SIDP19_blood_VAP_rep6


title: SIDP20_blood_VAP_rep7


title: SIDP21_blood_NoVAP_rep4


title: AML [Ulm_CN_xx_xx_116_19aug2009]

description: Not Applicable


title: SIDP18_blood_VAP_rep5


title: UMARY-1903

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1570

description: Human Brain Tissue: Purkinje Cells

value: D


title: 4uM-Exp2


title: BLSA-1595

description: Human Brain Tissue: Purkinje Cells

value: BLSA


title: UMARY-1465

description: Human Brain Tissue: Purkinje Cells

value: B


title: AML [Ulm_CN_xx_xx_113_14aug2009]

description: Not Applicable

value: NPM1 A


title: 4uM-Exp1


title: 20uM-Con-3

value: wildtype


title: AML [Ulm_CN_xx_xx_112_07aug2009]

description: Not Applicable


title: SIDP17_blood_NoVAP_rep3

value: blood


title: SIDP16_blood_VAP_rep4


title: UMARY-914

description: Human Brain Tissue: Purkinje Cells

value: C


title: 20uM-Con-2

value: 20uM Heme


title: AML [Ulm_CN_xx_xx_111_20aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_114_20aug2009]

description: Not Applicable


title: SIDP14_blood_VAP_rep3


title: 20uM-Con-1

value: mid-late L4 stage


title: 20uM-Exp1

value: hrg-2 Mutant


title: 4uM-Con-3


title: CREB1-array6

description:
Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
CREB1 ChIP - Array 6

source_name: CREB1 ChIP

value: transgenic MCF7

tag: transcription factor

tag: tag

value: modified LAP (localization and affinity purification) tag containing GFP

tag: chip antibody

value: Goat anti-GFP


title: AML [Ulm_CN_xx_xx_110_07aug2009]

description: Not Applicable

value: Validation


title: SIDP12_blood_NoVAP_rep2


title: UMARY-4725

description: Human Brain Tissue: Purkinje Cells

value: female

value: UMARY

value: Cerebellar Purkinje Cells


title: 4uM-Con-2

value: 4uM Heme


title: SIDP13_blood_VAP_rep2


title: BLSA-2093

description: Human Brain Tissue: Purkinje Cells

value: male

value: BLSA

value: D


title: SIDP11_blood_NoVAP_rep1


title: AML [Ulm_CN_xx_xx_109_18aug2009]

description: Not Applicable

value: NPM1 A


title: AML [Ulm_CN_xx_xx_108_11aug2009]

description: Not Applicable

value: NPM1 D


title: LLI 14 (V69)

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1

source_name: Long-lived individual

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and long lived individuals was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). For each blood donor, 5 ml of peripheral blood were obtained. The content of blood sampling tubes of each patient and healthy donor was centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

treatment_protocol: stored at -20 degree

tag: age

value: peripheral blood


title: LLI 15 (V70)


title: AML [Ulm_CN_xx_xx_107_14aug2009]

description: Not Applicable


title: LLI 12 (V67)


title: LLI 13 (V68)


title: UMARY-5078

description: Human Brain Tissue: Purkinje Cells

value: B


title: 4uM-Con-1

value: wildtype

value: mid-late L4 stage


title: UMARY-1209

description: Human Brain Tissue: Purkinje Cells

value: C


title: SIDP10_blood_VAP_rep1

value: blood


title: AML [Ulm_CN_xx_xx_100_20aug2009]

description: Not Applicable

value: NPM1 wt


title: LLI 10 (V65)


title: AML [Ulm_CN_xx_xx_06PB2947_11aug2009]

description: Not Applicable

value: Validation


title: UMARY-4729

description: Human Brain Tissue: Purkinje Cells


title: UMARY-4788

description: Human Brain Tissue: Purkinje Cells

value: female


title: UMARY-4549

description: Human Brain Tissue: Purkinje Cells

value: UMARY


title: Primary Cell Line D7ADIP

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

institute: UCL

description: human sarcoma and primary mesenchymal cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Hgu133av2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: For pre-processing of raw data (background correction, normalisation, and probeset summarisation) we used the Bioconductor affy package for the R prgramming language specifically the 'rma' algorithm

source_name: Gift from Dr. Mark Clements, now at the University of Westminster, London, U.K.

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

growth_protocol: Primary cells and cell lines were grown accrding to standard protocols and used at passage 4-7.

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

treatment_protocol: Undifferentiated human osteoblasts (HOB) were grown to 60% confluency in proliferation medium according to the manufacturer's (Clonetics) instructions. Differentiated HOB were grown for 21 days in differentiation mediua (Clonetics) and test samples were stained for Alakine Phosphatase, Alizarin S and Von Kossa staining to determine levels of differentiation. MSC were grown in adipogenic medium for 7 days.

value: primary cells

tag: sarcoma and primary cell type

value: bone marrow-derived mesenchymal stem cells

tag: other

value: grown in adipogenic medium for 7 days


title: Primary Cell Line SMC

source_name: Clonetics

value: penile smooth muscle cells

value: Full details are available at the Clonetics website


title: UMARY-4727

description: Human Brain Tissue: Purkinje Cells

tag: gender

value: male

value: Cerebellar Purkinje Cells


title: BLSA-1802

description: Human Brain Tissue: Purkinje Cells

tag: age (y)

value: BLSA


title: AML [Ulm_CN_xx_xx_06PB2258_19aug2009]

description: Not Applicable


title: Primary Cell Line NDLF

value: normal lung fibroblasts


title: UMARY-1544

description: Human Brain Tissue: Purkinje Cells

tag: pmi (hr)

value: B


title: AML [Ulm_CN_xx_xx_06PB1677_18aug2009]

description: Not Applicable

value: NPM1 A


title: LLI 6 (V61)

value: peripheral blood


title: LLI 7 (V62)


title: LLI 11 (V66)


title: Primary Cell Line HOB-DIFF

value: differentiated osteoblasts  grown in differentiation medium


title: AML [Ulm_CN_xx_xx_06PB1122_11aug2009]

description: Not Applicable

value: NPM1 wt


title: LLI 9 (V64)


title: LLI 8 (V63)


title: LLI 5 (V60)


title: LLI 4 (V59)


title: AML [Ulm_CN_xx_xx_06PB0963_06aug2009]

description: Not Applicable

value: Validation


title: AML [Ulm_CN_xx_xx_06KM2530_12aug2009]

description: Not Applicable

value: NPM1 B


title: AML [Ulm_CN_xx_xx_06PB0766_19aug2009]

description: Not Applicable


title: UMARY-5079

description: Human Brain Tissue: Purkinje Cells

tag: tissue bank

value: UMARY

value: D


title: AML [Ulm_CN_xx_xx_06PB0966_18aug2009]

description: Not Applicable


title: Sarcoma Cell Line MFH706

source_name: Wolfson Insitute for Biomedical Research Cell bank, UCL, London, U.K.

tag: cell type

value: tumour cell line

value: malignant fibrous histiocytoma (not well recorded)


title: Sarcoma Cell Line SW 982

source_name: ATCC

value: synovial sarcoma

value: Full details are available at the ATCC website


title: UMARY-4924

description: Human Brain Tissue: Purkinje Cells

value: male


title: AML [Ulm_CN_xx_xx_06KM1590_14aug2009]

description: Not Applicable

tag: cohort


title: Primary Cell Line HOB

value: primary cells

value: undifferentiated osteoblasts grown in proliferation medium

value: Full details are available at the Clonetics website


title: LLI 2 (V57)


title: Sarcoma Cell Line SK-PN-DN

value: malignant primitive neuroectodermal tumor


title: UMARY-4640

description: Human Brain Tissue: Purkinje Cells

value: female

value: Cerebellar Purkinje Cells


title: UMARY-1541

description: Human Brain Tissue: Purkinje Cells

value: B


title: UMARY-5086

description: Human Brain Tissue: Purkinje Cells


title: UMARY-4593

description: Human Brain Tissue: Purkinje Cells


title: UMARY-4915

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_06KM1561_20aug2009]

description: Not Applicable

tag: npm1 status

value: NPM1 wt


title: UMARY-4598

description: Human Brain Tissue: Purkinje Cells


title: LLI 3 (V58)

value: peripheral blood


title: Sarcoma Cell Line SW 872

value: liposarcoma


title: AML [Ulm_CN_xx_xx_06KM1485_11aug2009]

description: Not Applicable

value: Validation

value: NPM1 A


title: control 55 (V55)

source_name: younger control


title: Sarcoma Cell Line SK-UT-1B

value: tumour cell line

value: leiomyosarcoma


title: UMARY-4590

description: Human Brain Tissue: Purkinje Cells

value: UMARY

value: D


title: AML [Ulm_CN_xx_xx_06KM1138_19aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05PB4652_19aug2009]

description: Not Applicable


title: LLI 1 (V56)


title: control 54 (V54)


title: Sarcoma Cell Line U-2197

source_name: DSMZ

value: malignant fibrosis histiocytoma

value: Full details are available at the DSMZ website


title: AML [Ulm_CN_xx_xx_05PB3379_14aug2009]

description: Not Applicable


title: control 53 (V53)


title: AML [Ulm_CN_xx_xx_05PB3766_06aug2009]

description: Not Applicable


title: control 51 (V51)


title: control 52 (V52)


title: BLSA-2066

description: Human Brain Tissue: Purkinje Cells

value: male

value: BLSA


title: Sarcoma Cell Line SK-UT-1A

value: leyomyosarcoma

value: Full details are available at the ATCC website


title: AML [Ulm_CN_xx_xx_05PB3358_19aug2009]

description: Not Applicable


title: Sarcoma Cell Line SK-LMS-1


title: UMARY-4545

description: Human Brain Tissue: Purkinje Cells

value: Cerebellar Purkinje Cells


title: UMARY-1902

description: Human Brain Tissue: Purkinje Cells


title: control 49 (V49)


title: control 50 (V50)


title: UMARY-1936

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1866

description: Human Brain Tissue: Purkinje Cells


title: control 48 (V48)


title: Sarcoma Cell Line STA-ET-11

source_name: Gift from Dr H. Kovar Children's Cancer Research Institute, Vienna, Austria.

value: ewing's tumor cell line

value: Expresses EWS-ERG


title: AML [Ulm_CN_xx_xx_05PB306_20aug2009]

description: Not Applicable

source_name: AML


title: AML [Ulm_CN_xx_xx_05PB2838_11aug2009]

description: Not Applicable

value: NPM1 wt


title: UMARY-1076

description: Human Brain Tissue: Purkinje Cells


title: control 47 (V47)

value: peripheral blood


title: UMARY-1825

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1827

description: Human Brain Tissue: Purkinje Cells

value: female


title: AML [Ulm_CN_xx_xx_05PB2577_14aug2009]

description: Not Applicable

value: Validation

value: NPM1 A


title: control 46 (V46)


title: AML [Ulm_CN_xx_xx_05PB3285_19aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05PB2316_14aug2009]

description: Not Applicable


title: UMARY-1795

description: Human Brain Tissue: Purkinje Cells


title: Sarcoma Cell Line GROH1

value: tumour cell line

value: ewing sarcoma


title: control 45 (V45)


title: control 44 (V44)


title: control 43 (V43)


title: AML [Ulm_CN_xx_xx_05KM958_06aug2009]

description: Not Applicable


title: UMARY-1792

description: Human Brain Tissue: Purkinje Cells

value: UMARY

value: D


title: UMARY-1715

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM940_07aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM837_19aug2009]

description: Not Applicable


title: control 41 (V41)


title: AML [Ulm_CN_xx_xx_05KM772_07aug2009]

description: Not Applicable

value: NPM1 non-ABD


title: AML [Ulm_CN_xx_xx_05PB1734_19aug2009]

description: Not Applicable


title: Sarcoma Cell Line SK-N-MC


title: Sarcoma Cell Line MHH-ES-1


title: UMARY-1713

description: Human Brain Tissue: Purkinje Cells

value: male


title: Sarcoma Cell Line RD-ES


title: UMARY-1710

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM4976_07aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM4853_11aug2009]

description: Not Applicable


title: control 42 (V42)


title: Sarcoma Cell Line SK-N-DZ

value: neuroblastoma (metastatic)


title: control 40 (V40)


title: control 39 (V39)


title: control 38 (V38)


title: UMARY-1712

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM552_14aug2009]

description: Not Applicable


title: UMARY-1498

description: Human Brain Tissue: Purkinje Cells


title: control 37 (V37)


title: control 36 (V36)


title: AML [Ulm_CN_xx_xx_05KM4671_06aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM4648_11aug2009]

description: Not Applicable


title: UMARY-1226

description: Human Brain Tissue: Purkinje Cells


title: Sarcoma Cell Line CADO-ES1

value: Full details are available at the DSMZ website


title: AML [Ulm_CN_xx_xx_05KM4646_11aug2009]

description: Not Applicable


title: UMARY-1584

description: Human Brain Tissue: Purkinje Cells


title: control 34 (V34)


title: control 35 (V35)


title: UMARY-1114

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1496

description: Human Brain Tissue: Purkinje Cells


title: control 32 (V32)


title: control 33 (V33)


title: control 30 (V30)


title: UMARY-1846

description: Human Brain Tissue: Purkinje Cells


title: control 31 (V31)


title: AML [Ulm_CN_xx_xx_05KM4589_12aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM4181_18aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM4203_18aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM4607_06aug2009]

description: Not Applicable


title: Sarcoma Cell Line SK-N-FI

value: Full details are available at the ATCC website


title: Sarcoma Cell Line SW 684

value: fibrosarcoma


title: UMARY-1134

description: Human Brain Tissue: Purkinje Cells

value: Cerebellar Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM4062_07aug2009]

description: Not Applicable


title: control 28 (V28)


title: control 29 (V29)


title: AML [Ulm_CN_xx_xx_05KM401_07aug2009]

description: Not Applicable


title: Sarcoma Cell Line RD

value: rhabdomyosarcoma (embryonal)


title: UMARY-933

description: Human Brain Tissue: Purkinje Cells


title: UMARY-880

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1079

description: Human Brain Tissue: Purkinje Cells


title: Sarcoma Cell Line H-EMC-SS

source_name: HPA Cultures

value: chondrosarcoma

value: Full details are available at the HPA cultures website


title: Sarcoma Cell Line SW 1353


title: Sarcoma Cell Line CAL-78


title: UMARY-1502

description: Human Brain Tissue: Purkinje Cells

value: C


title: UMARY-1064

description: Human Brain Tissue: Purkinje Cells

value: female


title: UMARY-927

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM3970_20aug2009]

description: Not Applicable

value: Validation


title: Sarcoma Cell Line OUMS-27

value: tumour cell line


title: control 26 (V26)

value: peripheral blood


title: AML [Ulm_CN_xx_xx_05KM3733_19aug2009]

description: Not Applicable

value: NPM1 A


title: AML [Ulm_CN_xx_xx_05KM3932_18aug2009]

description: Not Applicable


title: control 25 (V25)


title: Sarcoma Cell Line SJRH30

value: rhabdomyosarcoma (alveolar)


title: control 27 (V27)


title: UMARY-142

description: Human Brain Tissue: Purkinje Cells

value: UMARY

value: D


title: AML [Ulm_CN_xx_xx_05KM3038_14aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM3317_12aug2009]

description: Not Applicable

value: NPM1 B


title: AML [Ulm_CN_xx_xx_05KM334_21aug2009]

description: Not Applicable

value: NPM1 wt


title: control 22 (V22)


title: control 23 (V23)


title: control 24 (V24)


title: AML [Ulm_CN_xx_xx_05KM3026_20aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM3022_18aug2009]

description: Not Applicable


title: control 19 (V19)


title: control 21 (V21)


title: control 18 (V18)


title: UMARY-5081

description: Human Brain Tissue: Purkinje Cells

value: male


title: AML [Ulm_CN_xx_xx_05KM2836_07aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM2683_07aug2009]

description: Not Applicable


title: UMARY-4789

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM2315_20aug2009]

description: Not Applicable


title: control 16 (V16)


title: control 20 (V20)


title: AML [Ulm_CN_xx_xx_05KM3006_19aug2009]

description: Not Applicable


title: UMARY-4916

description: Human Brain Tissue: Purkinje Cells


title: control 17 (V17)


title: UMARY-4782

description: Human Brain Tissue: Purkinje Cells


title: UMARY-4636

description: Human Brain Tissue: Purkinje Cells


title: UMARY-4726

description: Human Brain Tissue: Purkinje Cells


title: UMARY-4540

description: Human Brain Tissue: Purkinje Cells


title: BLSA-1924

description: Human Brain Tissue: Purkinje Cells

value: BLSA

value: B


title: UMARY-4542

description: Human Brain Tissue: Purkinje Cells

value: Cerebellar Purkinje Cells


title: UMARY-1830

description: Human Brain Tissue: Purkinje Cells


title: control 14 (V14)


title: BLSA-2102

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1849

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM1684_21aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM204_06aug2009]

description: Not Applicable


title: control 13 (V13)


title: AML [Ulm_CN_xx_xx_05KM2189_06aug2009]

description: Not Applicable


title: control 12 (V12)


title: control 11 (V11)


title: AML [Ulm_CN_xx_xx_05KM1625_14aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM1662_20aug2009]

description: Not Applicable


title: BLSA-1640

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1648

description: Human Brain Tissue: Purkinje Cells


title: control 15 (V15)


title: UMARY-1614

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM1583_07aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_05KM131_18aug2009]

description: Not Applicable


title: UMARY-1611

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1578

description: Human Brain Tissue: Purkinje Cells


title: AML [Ulm_CN_xx_xx_05KM1157_06aug2009]

description: Not Applicable


title: control 10 (V10)


title: UMARY-1535

description: Human Brain Tissue: Purkinje Cells


title: UMARY-1540

description: Human Brain Tissue: Purkinje Cells


title: control 9 (V9)


title: control 7 (V7)


title: control 8 (V8)


title: AML [Ulm_CN_xx_xx_05KM0044_14aug2009]

description: Not Applicable


title: control 6 (V6)


title: AML [Ulm_CN_xx_xx_04KM4292_21aug2009]

description: Not Applicable


title: control 4 (V4)


title: UMARY-879

description: Human Brain Tissue: Purkinje Cells


title: control 5 (V5)


title: control 3 (V3)


title: AML [Ulm_CN_xx_xx_04KM4180_12aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_04KM4258_11aug2009]

description: Not Applicable


title: control 2 (V2)


title: control 1 (V1)


title: AML [Ulm_CN_xx_xx_04KM4087_18aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_04KM3174_12aug2009]

description: Not Applicable


title: UMARY-1158

description: Human Brain Tissue: Purkinje Cells

value: A


title: UMARY-1078

description: Human Brain Tissue: Purkinje Cells


title: AML [7426_21jan09]

description: Not Applicable

value: Training


title: AML [7427_21jan09]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_04KM2657_19aug2009]

description: Not Applicable

value: NPM1 D


title: AML [Ulm_CN_xx_xx_04KM2916_18aug2009]

description: Not Applicable


title: AML [Ulm_CN_xx_xx_04KM3539_11aug2009]

description: Not Applicable


title: UMARY-819

description: Human Brain Tissue: Purkinje Cells


title: AML [7479_21jan09]

description: Not Applicable


title: UMARY-813

description: Human Brain Tissue: Purkinje Cells

value: female


title: UMARY-1133

description: Human Brain Tissue: Purkinje Cells

value: C


title: UMARY-1486

description: Human Brain Tissue: Purkinje Cells


title: Sarcoidosis patient_40

source_name: RNA from peripheral blood

extract_protocol: Blood of patients and volunteers without known disease was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). For each blood donor, 5 ml of peripheral blood were obtained. The content of blood sampling tubes of each patient_and healthy donor was centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

tag: disease state

value: Sarcoidosis


title: AML [7423_21jan09]

description: Not Applicable


title: AML [7421_21jan09]

description: Not Applicable


title: Sarcoidosis patient_42


title: Sarcoidosis patient_41


title: Sarcoidosis patient_43


title: AML [7424_28oct08]

description: Not Applicable


title: Sarcoidosis patient_38


title: Sarcoidosis patient_45


title: AML [7420_21jan09]

description: Not Applicable


title: UMARY-604

description: Human Brain Tissue: Purkinje Cells


title: Sarcoidosis patient_44


title: AML [7419_21jan09]

description: Not Applicable


title: AML [7418_21jan09]

description: Not Applicable


title: fibroblast_K1_0.05%DMSO_48h_rep2

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio software package  (gene expression module version 1.9.0).

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrepAmp Kit for Illumina arrays

growth_protocol: Fibroblasts were cultured from cryo-preserved cells in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% antibiotic/antimycotic solution at 37 oC in a humidified atmosphere of 5% CO2. 10E5 cells were seeded in 6-well plates and grown to a confluence of approximately 80 %.

extract_protocol: Total RNA was extracted from cells using the High Pure RNA Isolation Kit in accordance with the prescribed protocol, quantified with Quant iT RiboGreen Assay Kit

treatment_protocol: The medium was replaced by fresh medium non-supplemented, containing dimethyl sulfooxide (DMSO) added to a final concentration of 0.05%, or genistein at 30, 60 and 100 µM concentrations, with 0.05% DMSO. The experimental treatment was carried out for 1h, 24 h and 48 h period.

tag: cell line

value: HDFa

value: fibroblasts


title: fibroblast_100 µM genistein_48h_rep2

description: replicate 2

source_name: fibroblast_100 µM genistein_48h


title: fibroblast_30 µM genistein_48h_rep2

description: replicate 2

source_name: fibroblast_30 µM genistein_48h


title: Sarcoidosis patient_36


title: Sarcoidosis patient_37


title: fibroblast_K1_0.05%DMSO_24h_rep2

description: replicate 2


title: Sarcoidosis patient_30


title: Sarcoidosis patient_35


title: Sarcoidosis patient_31


title: Sarcoidosis patient_33


title: Sarcoidosis patient_34


title: Sarcoidosis patient_32


title: AML [7417_21jan09]

description: Not Applicable


title: AML [7416_21jan09]

description: Not Applicable


title: AML [7414_28oct08]

description: Not Applicable

value: NPM1 A


title: AML [7410_28oct08]

description: Not Applicable


title: AML [7413_28oct08]

description: Not Applicable


title: AML [7412_28oct08]

description: Not Applicable


title: AML [7411_21jan09]

description: Not Applicable


title: fibroblast_30 µM genistein_24h_rep2

description: replicate 2

source_name: fibroblast_30 µM genistein_24h


title: Sarcoidosis patient_29


title: Sarcoidosis patient_39


title: fibroblast_100 µM genistein_24h_rep2

description: replicate 2

source_name: fibroblast_100 µM genistein_24h


title: Sarcoidosis patient_28


title: AML [7409_21jan09]

description: Not Applicable


title: Sarcoidosis patient_27


title: fibroblast_100 µM genistein_48h_rep1

description: replicate 1


title: fibroblast_K1_0.05%DMSO_48h_rep1

description: replicate 1


title: fibroblast_30 µM genistein_48h_rep1

description: replicate 1


title: fibroblast_30 µM genistein_1h_rep2

description: replicate 2

source_name: fibroblast_30 µM genistein_1h


title: AML [7408_21jan09]

description: Not Applicable


title: fibroblast_K1_0.05%DMSO_1h_rep2

description: replicate 2


title: fibroblast_100 µM genistein_1h_rep2

description: replicate 2

source_name: fibroblast_100 µM genistein_1h


title: Sarcoidosis patient_26


title: AML [7405_20jan09]

description: Not Applicable


title: AML [7407_21jan09]

description: Not Applicable


title: AML [7406_20jan09]

description: Not Applicable


title: Sarcoidosis patient_24


title: AML [7402_28oct08]

description: Not Applicable


title: AML [7328_28oct08]

description: Not Applicable

value: NPM1 non-ABD


title: AML [7403_28oct08]

description: Not Applicable


title: Sarcoidosis patient_23


title: Sarcoidosis patient_22


title: Sarcoidosis patient_25


title: Sarcoidosis patient_21


title: fibroblast_100 µM genistein_24h_rep1

description: replicate 1


title: Sarcoidosis patient_20


title: Sarcoidosis patient_18


title: Sarcoidosis patient_19


title: fibroblast_K1_0.05%DMSO_24h_rep1

description: replicate 1


title: AML [7327_20jan09]

description: Not Applicable


title: AML [7326_20jan09]

description: Not Applicable


title: Sarcoidosis patient_17


title: AML [7325_20jan09]

description: Not Applicable


title: fibroblast_K1_0.05%DMSO_1h_rep1

description: replicate 1


title: fibroblast_100 µM genistein_1h_rep1

description: replicate 1


title: AML [7324_20jan09]

description: Not Applicable


title: AML [7322_20jan09]

description: Not Applicable


title: AML [7321_28oct08]

description: Not Applicable


title: Sarcoidosis patient_14


title: Sarcoidosis patient_16


title: AML [7320_20jan09]

description: Not Applicable


title: Sarcoidosis patient_15


title: fibroblast_30 µM genistein_1h_rep1

description: replicate 1


city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: Sample 24

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 32

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

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

tag: sample type

value: 5 pooled samples, smokers ADCA patients with stage>I

value: normal lung

tag: status

value: smoker


title: Sarcoidosis patient_13


title: fibroblast_30 µM genistein_24h_rep1

description: replicate 1


title: AML [7323_28oct08]

description: Not Applicable


description: Sample 22

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 30

tag: tissue


description: Sample 23

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 31


title: Sarcoidosis patient_12


description: Sample 21

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 29


description: Sample 20

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 28


description: Sample 18

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 26


description: Sample 19

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 27


description: Sample 17

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 25


title: AML [7319_28oct08]

description: Not Applicable

source_name: AML


title: AML [7317_20jan09]

description: Not Applicable

value: NPM1 wt


title: AML [7318_20jan09]

description: Not Applicable


title: Sarcoidosis patient_7


title: Sarcoidosis patient_9


title: Sarcoidosis patient_11


title: Sarcoidosis patient_10


title: AML [7312_16jan09]

description: Not Applicable


title: AML [7315_28oct08]

description: Not Applicable


title: AML [7313_20jan09]

description: Not Applicable


title: AML [7316_28oct08]

description: Not Applicable


title: AML [7314_20jan09]

description: Not Applicable


description: Sample 16

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 24


description: Sample 14

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 22


title: AML [7311_16jan09]

description: Not Applicable


title: Sarcoidosis patient_4

source_name: RNA from peripheral blood


title: Sarcoidosis patient_8


title: Sarcoidosis patient_5


title: Sarcoidosis patient_6


title: AML [7310_28oct08]

description: Not Applicable


description: Sample 15

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 23


title: stage 1 lung adenocarcinoma  pool 20

description: Sample 12

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 20

value: 5 pooled samples, smokers ADCA patients with stage I

value: stage 1 lung adenocarcinoma


title: Sarcoidosis patient_3


description: Sample 13

source_name: stage greater than 1 lung adenocarcinoma  stage greater than 1 lung adenocarcinoma  pool 21


title: stage 1 lung adenocarcinoma  pool 19

description: Sample 11

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 19


title: stage 1 lung adenocarcinoma  pool 17

description: Sample 9

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 17


title: stage 1 lung adenocarcinoma  pool 18

description: Sample 10

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 18


title: stage 1 lung adenocarcinoma  pool 16

description: Sample 8

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 16


title: stage 1 lung adenocarcinoma  pool 15

description: Sample 7

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 15


title: AML [7308_16jan09]

description: Not Applicable


title: AML [7309_16jan09]

description: Not Applicable


title: Sarcoidosis patient_2


title: Sarcoidosis patient_1


title: normal sample_55

value: control


title: AML [7307_16jan09]

description: Not Applicable


title: normal sample_54


title: AML [7306_16jan09]

description: Not Applicable


title: AML [7305_16jan09]

description: Not Applicable


title: normal sample_52


title: stage 1 lung adenocarcinoma  pool 14

description: Sample 6

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 14


title: normal sample_53


title: AML [7303_15jan09]

description: Not Applicable


title: AML [7302_28oct08]

description: Not Applicable


title: normal sample_50


title: normal sample_51


title: stage 1 lung adenocarcinoma  pool 12

description: Sample 4

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 12


title: stage 1 lung adenocarcinoma  pool 13

description: Sample 5

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 13


title: AML [7301_15jan09]

description: Not Applicable


title: AML [7277_28oct08]

description: Not Applicable


title: stage 1 lung adenocarcinoma  pool 11

description: Sample 3

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 11


title: normal sample_48


title: normal sample_49


title: AML [7276_15jan09]

description: Not Applicable


title: normal sample_46


title: normal sample_47


title: AML [7273_23oct08]

description: Not Applicable


title: AML [7274_23oct08]

description: Not Applicable


title: stage 1 lung adenocarcinoma  pool 9

description: Sample 1

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 9


title: AML [7191_15jan09]

description: Not Applicable

source_name: AML


title: AML [7272_23oct08]

description: Not Applicable


title: normal sample_44


title: normal sample_43


title: 60 CD14Cll12_4403827073_L

city: Ulm

first: Nupur

last: Bhattacharya

address: Albert Einstein Allee 23

department: Department of Internal Medicine III

institute: University of Ulm

description: Healthy proband and CLL patient

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: differentiated CD14+ PBMCs from a healthy donor in coculture with CLL cells

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

value: above 50 years

value: peripheral blood mononuclear cells


title: 54 CD14B9_4403827073_F

description: Healthy proband

source_name: differentiated CD14+ PBMCs from a healthy donor in coculture with non-malignant B cells


title: stage 1 lung adenocarcinoma  pool 10

description: Sample 2

source_name: stage 1 lung adenocarcinoma  stage 1 lung adenocarcinoma  pool 10


title: normal sample_45

source_name: RNA from peripheral blood


title: 59 CD14B7_4403827073_K

description: Healthy proband


title: 57 CD14CLL8_4403827073_I

description: Healthy proband and CLL patient


title: 56 CD14CLL4_4403827073_H

description: Healthy proband and CLL patient


title: normal sample_40


title: normal sample_41


title: 55 CD14CLL2_4403827073_G

description: Healthy proband and CLL patient


title: normal sample_39


title: AML [7190_15jan09]

description: Not Applicable

extract_protocol: After thawing, cells were washed once with Hanks’balanced-salt solution. High-quality total RNA was extracted by lysis with guanidinium thiocyanate followed by cesium chloride–gradient purification. RNA levels, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent). None of the samples showed RNA degradation (ratio of 28S ribosomal RNA to 18S ribosomal RNA of at least 2) or contamination by DNA.

value: Training


title: AML [7188_15jan09]

description: Not Applicable