title: 13832786 - R H2O 7h 1 vs R DFO 7h 1

hyb_protocol: R DFO 7h 1 Cy5 / R H2O 7h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: R DFO 7h 1:10ug.


title: AGA2 lung_rep1

status: Public on Jun 01 2010

type: RNA

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

molecule: total RNA

organism: Mus musculus

source_name: mouse ID: L1

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: female, age

value: 11 days

source_name: Wt RNA pool lung

tag: RNA pool; female, age


title: AGA2 lung_rep2


title: AGA2 heart_rep9

source_name: mouse ID: H5

value: 10 days

source_name: Wt RNA pool heart


title: AGA2 heart_rep10


title: AGA2 lung_rep4

source_name: mouse ID: L2


title: BYU_Adams_H_bacteriophora_L5M4

city: Provo

first: Chin-Yo

last: Lin

state: UT

address: 753 WIDB

department: Microbiology and Molecular Biology

country: USA

institute: Brigham Young University

description:
Genome not available
This sample is the second of four biological replicates of the L5M in-bred strain of H. bacteriophora.

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

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

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

organism: Heterorhabditis bacteriophora

source_name: Heterorhabditis bacteriophora LM5

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

growth_protocol:
An isolate of Heterorhabditis bacteriophora was created by sub-culturing different experimental lines of nematode-bacterium complex over 20 passages in Galleria mellonella . The original parental strain (OHB) was maintained in ringer's solution without sub-culturing while the inbred line (L5M) was continuously cultured in G. mellonella.
Both OHB and L5M were cultured in G. mellonella larvae and emerging infective juveniles (IJs) were collected using white traps. The IJs were stored in ringer's solution at 16ºC until used for experiments.

extract_protocol: Total RNA was isolated from four biological replicates of IJs of each strain. The IJs (~8-10,000) were transferred to 10 volumes of Trizol Reagent (Molecular Research Center Inc., Cincinnati, OH) and RNA extracted according to manufacturer's protocol.

tag: genotype

value: In-bred laboratory strain L5M

tag: phenotype

value: entamopathogenic traits deteriorated


title: AGA2 heart_rep6

source_name: mouse ID: H3


title: AGA2 heart_rep5


title: AGA2 heart_rep7

source_name: mouse ID: H4


title: AGA2 heart_rep4

source_name: mouse ID: H2


title: AGA2 lung_rep7

source_name: mouse ID: L4


title: AGA2 heart_rep2

source_name: mouse ID: H1


title: AGA2 bone_rep10

source_name: mouse ID: B5

source_name: Wt RNA pool bone


title: BYU_Adams_H_bacteriophora_OHB5

description:
Genome not available
This sample is the third of four biological replicates of the OHB parental strain of H. bacteriophora.

source_name: Heterorhabditis bacteriophora OHB

value: Parental strain OHB

value: normal


title: AGA2 bone_rep8

source_name: mouse ID: B4


title: AGA2 heart_rep3


title: PN1-Hepatocytes_REP2

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Primary post-natal day 1 hepatocytes.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalized using cubic Spline normalization with the Illumina GenomeStudio software.

Non-normalized data is available in the 'GSE19044_non-normalized.txt' file, which is linked to the GSE19044 Series record as a supplementary file.

label: biotin

source_name: Primary post-natal (day1) hepatocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays starting from 500ng of total RNA.

growth_protocol: Standard growth protocol for each cell type.

extract_protocol: Total RNA extraction was performed using the miRNeasy kit (Qiagen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: Culture in embryoid bodies with hepatic differentiation cocktail (details in the manuscript).

tag: tissue

value: liver

tag: cell type

value: primary hepatocyte

tag: developmental stage


title: AGA2 bone_rep6

source_name: mouse ID: B3


title: 13832787 - R DFO 7h 1 vs R H2O 7h 1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the effects of the siderophore deferoxamine on Arabidopsis leaves and roots?

hyb_protocol: R H2O 7h 1 Cy5 / R DFO 7h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: R H2O 7h

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

growth_protocol: root - Media=hydropony (Segond et al. 2009 10.1111/j.1365-313X.2008.03775.x )	 hygrometry=70%	 Temperature=21°C (day)/19°C (night)	 Light=8h

treatment_protocol: Name:H2O 7h - control buffer - control,h2o:time 7hour . Leaves or roots of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves or roots were harvested 7 and 24 h.p.i.

value: roots

tag: ecotype

value: Columbia

tag: harvest date

source_name: R DFO 7h

treatment_protocol: Name:DFO 7h - compound based treatment - compound addition,dfo:quantity 1mM time 7hour . Leaves or roots of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves or roots were harvested 7 and 24 h.p.i.


title: AGA2 bone_rep7


title: E16-Hepatocytes_REP1

description: Primary hepatocytes from E16 embryo.

source_name: Primary hepatocytes from E16 embryo


title: PN1-Hepatocytes_REP3

description: Primary post-natal day 1 hepatocytes.


title: E16-Hepatocytes_REP3

description: Primary hepatocytes from E16 embryo.


title: AGA2 heart_rep8

source_name: Wt RNA pool heart


title: AGA2 heart_rep1


title: AGA2 bone_rep9


title: GPSC-B_EB-28d_REP2

description: GPSC-B cells, EB culture for 28 days.

source_name: GPSC-B cells, EB culture for 28 days

value: germline cell-derived pluripotent stem cells (GPSCs), Lot B

tag: differentiation time

value: 28 days


title: AGA2 bone_rep5


title: E16-Hepatocytes_REP2

description: Primary hepatocytes from E16 embryo.


title: GPSC-B_EB-28d_REP1

description: GPSC-B cells, EB culture for 28 days.


title: GPSC-B_EB-21d_REP1

description: GPSC-B cells, EB culture for 21 days.

source_name: GPSC-B cells, EB culture for 21 days

value: 21 days


title: AGA2 bone_rep4

source_name: mouse ID: B2


title: GPSC-B_EB-7d_REP2

description: GPSC-B cells, EB culture for 7 days.

source_name: GPSC-B cells, EB culture for 7 days

value: 7 days


title: GPSC-B_EB-14d_REP1

description: GPSC-B cells, EB culture for 14 days.

source_name: GPSC-B cells, EB culture for 14 days

value: 14 days


title: GPSC-B_EB-7d_REP1

description: GPSC-B cells, EB culture for 7 days.


title: GPSC-B_EB-14d_REP2

description: GPSC-B cells, EB culture for 14 days.


title: PN1-Hepatocytes_REP1

description: Primary post-natal day 1 hepatocytes.


title: GPSC-B_EB-2d_REP2

description: GPSC-B cells, EB culture for 2 days.

source_name: GPSC-B cells, EB culture for 2 days

value: 2 days


title: GPSC-B_EB-21d_REP2

description: GPSC-B cells, EB culture for 21 days.


title: AGA2 bone_rep3

source_name: mouse ID:B2


title: AGA2 bone_rep1

source_name: mouse ID: B1


title: GPSC-B_EB-2d_REP1

description: GPSC-B cells, EB culture for 2 days.


title: AGA2 bone_rep2

source_name: mouse ID:B1

source_name: Wt RNA pool bone


title: GPSC-A_EB-7d_REP2

description: GPSC-A cells, EB culture for 7 days.

source_name: GPSC-A cells, EB culture for 7 days

value: germline cell-derived pluripotent stem cells (GPSCs), Lot A


title: GPSC-A_EB-28d_REP1

description: GPSC-A cells, EB culture for 28 days.

source_name: GPSC-A cells, EB culture for 28 days


title: GPSC-A_EB-21d_REP1

description: GPSC-A cells, EB culture for 21 days.

source_name: GPSC-A cells, EB culture for 21 days


title: GPSC-B_NT_REP2

description: GPSC-B cells, not treated.

source_name: GPSC-B cells, not treated

value: 0 days


title: GPSC-A_EB-7d_REP1

description: GPSC-A cells, EB culture for 7 days.


title: GPSC-A_EB-14d_REP2

description: GPSC-A cells, EB culture for 14 days.

source_name: GPSC-A cells, EB culture for 14 days


title: GPSC-B_NT_REP1

description: GPSC-B cells, not treated.


title: GPSC-A_EB-28d_REP2

description: GPSC-A cells, EB culture for 28 days.


title: GPSC-A_EB-2d_REP1

description: GPSC-A cells, EB culture for 2 days.

source_name: GPSC-A cells, EB culture for 2 days


title: GPSC-A_EB-21d_REP2

description: GPSC-A cells, EB culture for 21 days.


title: GPSC-A_EB-2d_REP2

description: GPSC-A cells, EB culture for 2 days.


title: ES_EB-28d_REP1

description: ES cells, EB culture for 28 days.

source_name: ES cells, EB culture for 28 days

value: embryonic stem (ES) cells


title: GPSC-A_EB-14d_REP1

description: GPSC-A cells, EB culture for 14 days.


title: GPSC-A_NT_REP2

description: GPSC-A cells, not treated.

source_name: GPSC-A cells, not treated


title: ES_EB-28d_REP2

description: ES cells, EB culture for 28 days.


title: ES_EB-21d_REP1

description: ES cells, EB culture for 21 days.

source_name: ES cells, EB culture for 21 days


title: GPSC-A_NT_REP1

description: GPSC-A cells, not treated.


title: ES_EB-14d_REP1

description: ES cells, EB culture for 14 days.

source_name: ES cells, EB culture for 14 days


title: JB2_MMara_5h_2

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

description: 5h time point of arabinose induced gene expression, experiment serves as baseline control

hyb_protocol: EukGE-WS2 protocol on a GeneChip Fluidics Station 400

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: U. maydis strain JB2 grown for 5h in array medium/arabinose

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labelling kit, except for a reaction temperature of 50°C for first-strand cDNA synthesis

growth_protocol: Strain JB2 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized).  Induction for 5 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer's instructions. RNA samples were further column purified (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

tag: time

value: 5h in array medium/arabinose

tag: strain

value: JB2 is a FB2 (a2b2) derivative in which the b mating type locus was replaced by a hygromycin resistance cassette.


title: AB31_Drbf1_MMara_12h_2

description: 12h time point of crg1P controlled bE1/bW2 gene induction in a Drbf1 background

scan_protocol: Agilent G2500A

source_name: U. maydis strain AB31 grown for 12h in array medium/arabinose

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labelling kit, except for a reaction temperature of 50°C for first-strand cDNA synthesis.

growth_protocol: Strain AB31Drbf1 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 12 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: 12h in array medium/arabinose

value: AB31Drbf1 is a FB2 (a2 b2) derivative in which the induction of the bE1 and bW2 genes is under control of the arabinose-inducible crg1 promoter and the rbf1 gene is replaced by a hygromycin resistance cassette.


title: JB2_MMara_5h_1


title: CP27_MMara_5h_2

description: 5h time point of crg1P controlled rbf1 gene induction

source_name: U. maydis strain CP27 grown for 5h in array medium/arabinose

growth_protocol: Strain CP27 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). rbf1 was induced for 5 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: CP27 is a FB2 (a2b2) derivative in which the b mating type locus was replaced by a copy of rbf1 under control of the arabinose-inducible crg1 promoter.


title: CP27_MMara_5h_1


title: ES_EB-21d_REP2

description: ES cells, EB culture for 21 days.


title: ES_EB-7d_REP2

description: ES cells, EB culture for 7 days.

source_name: ES cells, EB culture for 7 days


title: ES_EB-2d_REP2

description: ES cells, EB culture for 2 days.

source_name: ES cells, EB culture for 2 days


title: AB31_Drbf1_MMara_5h_1

description: 5h time point of crg1P controlled bE1/bW2 gene induction in a Drbf1 background

source_name: U. maydis strain AB31Drbf1 grown for 5h in array medium/arabinose

growth_protocol: Strain AB31Drbf1 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 5 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: AB34_WT_MMnit_12h_2

description: 12h time point of nar1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB34 grown for 12h in array medium/nitrate

growth_protocol: Strain AB34 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 12 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.

value: 12h in array medium/nitrate

value: AB34 is a FB2 (a2 b2) derivative in which the induction of the bE2 and bW2 genes is under control of the nitrate-inducible nar1 promoter.


title: ES_NT_REP2

description: ES cells, not treated.

source_name: ES cells, not treated


title: ES_EB-2d_REP1

description: ES cells, EB culture for 2 days.


title: AB31_Drbf1_MMara_3h_2

description: 3h time point of crg1P controlled bE1/bW2 gene induction in a Drbf1 background

source_name: U. maydis strain AB31Drbf1 grown for 3h in array medium/arabinose

growth_protocol: Strain AB31Drbf1 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 3 hour in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: 3h in array medium/arabinose


title: AB31_Drbf1_MMara_12h_1

source_name: U. maydis strain AB31Drbf1 grown for 12h in array medium/arabinose


title: AB31_Drbf1_MMara_5h_2


title: AB31_Drbf1_MMara_3h_1

growth_protocol: Strain AB31Drbf1 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 3 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: AB34_WT_MMnit_12h_1


title: ES_EB-14d_REP2

description: ES cells, EB culture for 14 days.


title: ES_NT_REP1

description: ES cells, not treated.


title: AB34_WT_MMnit_5h_1

description: 5h time point of nar1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB34 grown for 5h in array medium/nitrate

growth_protocol: Strain AB34 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 5 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.

value: 5h in array medium/nitrate


title: ES_EB-7d_REP1

description: ES cells, EB culture for 7 days.


title: AB34_WT_MMnit_3h_2

description: 3h time point of nar1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB34 grown for 3h in array medium/nitrate

growth_protocol: Strain AB34 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 3 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.

value: 3h in array medium/nitrate


title: AB34_WT_MMnit_2h_2

description: 2h time point of nar1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB34 grown for 2h in array medium/nitrate

growth_protocol: Strain AB34 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 2 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.

value: 2h in array medium/nitrate


title: AB34_WT_MMnit_0h_2

description: 0h time point of nar1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB34 grown for 0h in array medium/nitrate

growth_protocol: Strain AB34 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 0 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.

value: 0h in array medium/nitrate


title: AB34_WT_MMnit_2h_1


title: AB33_WT_MMnit_0h_2

description: 0h time point of nar1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB33 grown for 0h in array medium/nitrate

growth_protocol: Strain AB33 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 0 hours in liquid array medium containing 3g/L nitrate instead of gluatmine as a nitrogen source.

value: AB33 is a FB2 (a2 b2) derivative in which the induction of the bE1 and bW2 genes is under control of the nitrate-inducible nar1 promoter


title: AB34_WT_MMnit_5h_2


title: AB33_WT_MMnit_12h_1

description: 12h time point of nar1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB33 grown for 12h in array medium/nitrate

growth_protocol: Strain AB33 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 12 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.

value: AB33 is a FB2 (a2 b2) derivative in which the induction of the bE1 and bW2 genes is under control of the nitrate-inducible nar1 promoter.


title: AB34_WT_MMnit_3h_1


title: AB33_WT_MMnit_2h_2

description: 2h time point of nar1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB33 grown for 2h in array medium/nitrate

growth_protocol: Strain AB33 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 2 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.


title: AB33_WT_MMnit_12h_2


title: AB34_WT_MMnit_1h_1

description: 1h time point of nar1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB34 grown for 1h in array medium/nitrate

growth_protocol: Strain AB34 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 1 hour in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.

value: 1h in array medium/nitrate


title: AB34_WT_MMnit_0h_1


title: AB34_WT_MMnit_1h_2

growth_protocol: Strain AB34 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 1 hour in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrate source.


title: AB33_WT_MMnit_1h_1

description: 1h time point of nar1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB33 grown for 1h in array medium/nitrate

growth_protocol: Strain AB33 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 1 hour in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.


title: AB33_WT_MMnit_1h_2


title: AB33_WT_MMnit_2h_1


title: AB33_WT_MMnit_5h_1

description: 5h time point of nar1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB33 grown for 5h in array medium/nitrate

growth_protocol: Strain AB33 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 5 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.


title: AB33_WT_MMnit_3h_2

description: 3h time point of nar1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB33 grown for 3h in array medium/nitrate

growth_protocol: Strain AB33 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 3 hours in liquid array medium containing 3g/L nitrate instead of glutamine as a nitrogen source.


title: AB33_WT_MMnit_5h_2


title: AB32_WT_MMara_12h_2

description: 12h time point of crg1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB32 grown for 12h in array medium/arabinose

growth_protocol: Strain AB32 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 12 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: AB31 is a FB2 (a2 b2) derivative in which the induction of the bE1 and bW2 genes is under control of the arabinose-inducible crg1 promoter.


title: AB33_WT_MMnit_0h_1


title: AB33_WT_MMnit_3h_1


title: AB32_WT_MMara_1h_2

description: 1h time point of crg1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB32 grown for 1h in array medium/arabinose

growth_protocol: Strain AB32 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 1 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: 1h in array medium/arabinose

value: AB32 is a FB2 (a2 b2) derivative in which the induction of the bE2 and bW2 genes is under control of the arabinose-inducible crg1 promoter.


title: AB32_WT_MMara_3h_2

description: 3h time point of crg1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB32 grown for 3h in array medium/arabinose

growth_protocol: Strain AB32 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 3 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: AB32_WT_MMara_3h_1

value: AB32 is a FB2 (a2 b2) derivative in which the induction of the bE1 and bW2 genes is under control of the arabinose-inducible crg1 promoter.


title: AB31_WT_MMara_3h_2

description: 3h time point of crg1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB31 grown for 3h in array medium/arabinose

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 3 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: AB31 is a FB2 (a2 b2) derivative in which the induction of the bE1 and bW2 genes is under control of the arabinose-inducible crg1 promoter


title: AB32_WT_MMara_1h_1


title: AB32_WT_MMara_5h_2

description: 5h time point of crg1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB32 grown for 5h in array medium/arabinose

growth_protocol: Strain AB32 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 5 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: 5h in array medium/arabinose


title: AB31_WT_MMara_5h_1

description: 5h time point of crg1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB31 grown for 5h in array medium/arabinose

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 5 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: AB32_WT_MMara_0h_1

description: 0h time point of crg1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB32 grown for 0h in array medium/arabinose

growth_protocol: Strain AB32 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 0 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: 0h in array medium/arabinose

value: AB32 is a FB2 (a2 b2) derivative in which the induction of the bE2 and bW2 genes is under control of the arabinose-inducible crg1 promoter


title: AB32_WT_MMara_12h_1

value: 12h in array medium/arabinose


title: AB31_WT_MMara_5h_2


title: AB32_WT_MMara_0h_2


title: AB32_WT_MMara_2h_2

description: 2h time point of crg1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB32 grown for 2h in array medium/arabinose

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 2 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: 2h in array medium/arabinose


title: AB31_WT_MMara_12h_1

description: 12h time point of crg1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB31 grown for 12h in array medium/arabinose

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 12 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: AB31_WT_MMara_12h_2


title: AB32_WT_MMara_2h_1


title: AB31_WT_MMara_2h_2

description: 2h time point of crg1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB31 grown for 2h in array medium/arabinose

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 2 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: AB31_WT_MMara_2h_1


title: At_prmt5_rep2

city: Buenos Aires

first: Marcelo

middle: Javier

last: Yanovsky

state: Capital Federal

address: Av. San Martín 4453

department: Applied Biology

country: Argentina

institute: IFEVA

description: accession: Columbia with mutation at prmt5

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G GeneChip Operating Software Version 1.6 (GCOS)

data_processing: Probe intensity is spatially corrected, log intensity for probes within annotated exon and intron regions were quantile normalized, and transformed back to natural scale

label: biotin end labeling

molecule: polyA RNA

source_name: A.thaliana tissues

label_protocol: affy

extract_protocol: Qiagen RNeasy Plant Mini Kit

value: aerial (leaves plus apical meristem)

tag: accession

value: Columbia with mutation at prmt5


title: AB31_WT_MMara_1h_1

description: 1h time point of crg1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB31 grown for 1h in array medium/arabinose

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 1 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: AB31_WT_MMara_1h_2


title: AB31_WT_MMara_0h_2

description: 0h time point of crg1P controlled bE1/bW2 gene induction

source_name: U. maydis strain AB31 grown for 0h in array medium/arabinose

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 0 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.


title: At_prmt5_rep1


title: At_wildtype_rep2

description: accession: Columbia

value: Columbia


title: At_wildtype_rep3

description: accession: Columbia


title: AB31_WT_MMara_3h_1

value: 3h in array medium/arabinose


title: At_wildtype_rep1

description: accession: Columbia


title: Dm_dart5_rep2

description: D.melanogaster with mutation at dart5

organism: Drosophila melanogaster

source_name: D.melanogaster tissues

value: heads

value: mutation at dart5


title: Dm_dart5_rep1

description: D.melanogaster with mutation at dart5


title: At_prmt5_rep3


title: Dm_wildtype_rep2

description: wild type D.melanogaster

value: wild type


title: Dm_wildtype_rep3

description: wild type D.melanogaster


title: Dm_wildtype_rep1

description: wild type D.melanogaster


title: 26824202

status: Public on May 01 2010

type: genomic

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

hyb_protocol: samples were co-hybridized with a MAUI hybridization system (BioMicro Systems)

scan_protocol: The arrays were scanned using a 5 µm scanner, and Nimblescan software (Roche Nimblegen, Madison, WI) was used to retrieve fluorescent intensity raw data from the scanned images of the oligonucleotide tiling arrays.

data_processing: First, spatial correction was applied to adjust position-dependent non-uniformity of signals across the array. Specifically, locally weighted polynomial regression (loess) was used to adjust signal intensities based on X,Y feature position. Normalization was then performed using the q-spline method, followed by segmentation using the segMNT CNV calling algorithm.

molecule: genomic DNA

organism: Sus scrofa

source_name: genomic DNA from pig

label_protocol: According with manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Genomic DNA was purified from blood by salt precipitation. The precipitation was performed by adding 2.36volumes of cold 96% ethanol and 0.16volumes of 3M sodium acetate (pH 4.8). After 20 minutes of centrifugation at 4 degrees Celsius and 13.000 rpm, the precipitated DNA was washed with 70% ethanol, re-precipitated by 5 minutes of centrifugation at 4 degrees Celsius and 13.000 rpm. After precipitation, the isolated DNA was resuspended in 16TE-buffer. Following the isolation of the genomic DNA samples, the DNA quality was assessed by measuring the concentration and the purity on the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). DNA integrity and purity were also assessed by gel electrophoresis on a 1% agarose gel (SeaKemH GTGH Agarose, Cambrex Bio Science, and 16TBE buffer, Invitrogen) containing 0.15 mg/mL ethidium bromide.

value: Blood

tag: sex

value: Female

tag: family relation

value: Daughter number 2 of family D

tag: id

value: blood

value: Daughter number 1 of family D


title: Dm_dart5_rep3

description: D.melanogaster with mutation at dart5


title: 25691702

value: Mother of family C

value: Daughter number 2 of family C


title: 25651502

value: Male

value: Father

value: F

value: Mother of family D


title: 25637002

value: Son number 2 of family D


title: 26800602


title: 25634102

value: Mother of family B


title: 25636302


title: 26800902

value: Daughter number 1 of family C

value: Son number 2 of family C


title: 25638502

value: Son number 1 of family B


title: 26388602

value: Son number 1 of family D


title: 25753102

value: Blood


title: 25636602

value: Female

value: Daughter number 2 of family B


title: 25635402

value: blood

value: Daughter number 1 of family B


title: 25926302

value: Son number 2 of family B


title: 25643902


title: 25636002

value: Mother of family A

value: Daughter number 2 of family A


title: 25644202

value: Male


title: 25638202

value: Son number 1 of family C


title: 25642302

value: Daughter number 1 of family A


title: 25637602

value: Father

value: F


title: 25920302


title: 25637902

value: Son number 2 of family A


title: 24111202

value: Daughter number 2 of family D

value: Mother of family D


title: 25641402

value: Son number 1 of family A


title: 19476502

value: Blood


title: 26805002


title: G_2 with array type wheat from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

description: Study gene expression during the grain developmental -The aim of the study is to identify the genes that are differentially expressed during the grain development in wheat.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Triticum aestivum

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: seed - Media : Greenhouse Hygrometry : 60 per cent Temperature: 15.8 per cent

treatment_protocol: no treatment

tag: dev. stage

value: :500 degrees days (dd)


title: C_2 with array type wheat from Affymetrix

value: :200 degrees days (dd)


title: B_2 with array type wheat from Affymetrix

value: :100 degrees days (dd)


title: D_2 with array type wheat from Affymetrix

value: :250 degrees days (dd)


title: 21970302

value: Female

value: Daughter number 1 of family D

value: blood


title: 19499702

value: Male

value: Son number 1 of family D

value: Son number 2 of family D


title: 21966102

value: Father


title: 19508302

value: Daughter number 2 of family C

value: Mother of family C


title: 19545302

value: Daughter number 1 of family C


title: E_2 with array type wheat from Affymetrix

value: :300  degrees days (dd)


title: 19713802

value: F

value: Son number 1 of family C


title: 19476202

value: Blood


title: G_1 with array type wheat from Affymetrix

value: :490 degrees days (dd)


title: C_1 with array type wheat from Affymetrix

value: :185 degrees days (dd)


title: 19482402


title: E_1 with array type wheat from Affymetrix

value: :290  degrees days (dd)


title: MOH12ko 02

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: MOH12ko 02

hyb_protocol: Agilent Gene Expression kit for oligo microarrays (Agilent, order number 5188-5242, protocol G4140-90050).

scan_protocol: Agilent Feature Extraction software 9.5.3.1.

data_processing: GeneSpring GX10 default loading and analysis.

source_name: Cecum, PARP1 KO, infected, 6h

label_protocol: 1.6 - 5 μg of total RNA were reverse transcribed to cDNA, and amplified and labeled to cRNA with the Agilent Low RNA Input Linear Amplification Kit PLUS (order number 5184-3525, Agilent).

growth_protocol: Wildtype and isogenic PARP1 knockout mice were bred in a C57Bl/6J background. Regular back-crossings were performed to maintain isogenicity. All mice were bred and kept in a specified pathogen-free area.

extract_protocol: The intestinal tract was excised and the cecum was isolated. The cecum was then cut into four slices. Slices 1 and 3 were washed in cold PBS to remove cecum content and afterwards frozen in liquid nitrogen in 300 μl RLT-buffer (RNeasy Mini Kit, Qiagen) with 1% β-Mercaptoethanol and stored at -80°C till RNA-extraction. Frozen tissue was homogenized in RLT for 3 minutes at 25 Hz using a Tissue Lyser (Qiagen). RNA was processed using the RNeasy Mini Kit (Qiagen) and the RNase-Free DNase Set (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: Streptomycin-pretreated mice (20 mg/animal) were infected by gavage (5 x 10E7 cfu) as published previously. Live bacterial loads in cecal content were determined by plating. Experiments were approved and performed as legally required (Licence 201/2007).

value: cecum

value: PARP1 knockout

tag: treatment

value: Salmonella SB300 infection

tag: infection duration


title: B_1 with array type wheat from Affymetrix

value: :130 degrees days (dd)


title: MOH2wt 03

description: MOH2wt 03

source_name: Cecum, WT, infected, 6h

tag: genotype

value: wildtype


title: MOH12ko 03

description: MOH12ko 03


title: 19500602

value: Male

value: Son number 1 of family B

value: blood

value: Son number 2 of family B


title: MOH2wt 01

description: MOH2wt 01


title: MOH12ko 01

description: MOH12ko 01


title: MOH2wt 02

description: MOH2wt 02


title: 19501702

value: Female

value: Mother of family B

value: Father


title: 19501402

value: Son number 1 of family C

value: Son number 2 of family C


title: MOH2wt Sm_SB161_control 02

description: MOH2wt Sm_SB161_control 02

source_name: Cecum, WT, control infection, 10h

value: Salmonella SB161 infection


title: MOH2wt Sm_infected 03

description: MOH2wt Sm_infected 03

source_name: Cecum, WT, infected, 10h


title: MOH2wt Sm_infected 02

description: MOH2wt Sm_infected 02


title: swr1-3

city: Sendai

first: Masahiko

last: Harata

address: Tsutsumidori-Amamiyamachi 1-1

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

description: swr1 deletion mutant vs. control strain.

hyb_protocol: Hybridized for 16-18 h at 65 C.

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning.

data_processing: Detected signals for each ORF were normalized by the intensity-dependent (LOWESS) method in the GeneSpring Analysis Platform (GeneSpring ver 7.3.1, Agilent Technologies Inc.).

organism: Saccharomyces cerevisiae

source_name: swr1 deletion mutant

label_protocol: Cyscribe first-strand cDNA labelling kit (Amersham Biosciences). Hybridized for 16-18 h at 65 C.

growth_protocol: Saccharomyces cerevisiae strains were grown in 50 ml YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking into OD=1 (exponential growing) culture.

extract_protocol: Hot-phenol and oligotex dt mRNA purification kit (TaKaRa).

treatment_protocol: None.

tag: mutation

value: swr1 deletion

source_name: control strain

value: wild-type


title: 19719802

value: Blood

value: Daughter number 1 of family B


title: MOH2wt Sm_infected 01

description: MOH2wt Sm_infected 01

tag: tissue

value: cecum

value: Salmonella SB300 infection


title: 19503302

tag: cell type

value: Son number 2 of family A

value: Daughter number 1 of family A


title: 19503002

value: Daughter number 2 of family B


title: D_1 with array type wheat from Affymetrix

value: :230 degrees days (dd)


title: swr1-1


title: arp6-4

description: arp6 deletion mutant vs. control strain.

source_name: arp6 deletion mutant

value: arp6 deletion


title: swr1-2


title: Thp-1-Rv-90Hr-Rep2

city: New Delhi

first: Aanchal

last: Chopra

address: Aruna Asaf Ali Marg

country: India

institute: International Centre for Genetic Engineering and Biotechnology(ICGEB)

hyb_protocol: 1. Mix Cy3 labled linearly amplified cRNA, 10X blocking agent, nuclease free water and 25X fragmentation buffer in recommended proportion.  2. Incubate at 60 degree centigrade for exactly 30 min.  3. Add 2X GEx hybridization buffer to stop the fragmentation.  4. Mix well by gently pipeting, avoid bubbles.  5.  Spin for 1 min at 13000 RPM and place the sample onto the array as soon as possible   6. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  7. Slowly dispense the volume of hybridization sample (see Table 8) onto the gasket well in a “drag and dispense” manner.  8. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned  9. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  10. Hand-tighten the clamp onto the chamber.  11. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. If necessary, tap the assembly on a hard surface to move stationary bubbles.  12. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm when using 2x GEx Hybridization Buffer HI-RPM.  13. Hybridize at 65°C for 17 hours.

scan_protocol: Slides were scanned using agilent microarray scanner (G2565BA) followed by data extraction by agilent feature extraction software version 9.5.3.

data_processing: The normalization was done using GeneSpring GX 10 using the recommended Percentile Shift Normalization. It is a global normalization, where the locations of all the spot intensities in an array are adjusted. This normalization takes each column in an experiment independently, and computes the percentile of the expression values for this array, across all spots (where n has a range from 0-100 and n=50 is the median). It subtracts this value from the expression value of each entity.

organism: Homo sapiens

source_name: PMA differentiated Thp-1 Cells, H37Rv infected (90hHr) Replicate 2

label_protocol: Labeling was Agilent's Quick Amp Labeling Kit. It generates fluorescent cRNA (complimentary RNA) with a sample input RNA range between 200 ng and 1 μg of total RNA or a minimum of 10 ng of poly A+ RNA for one-color processing. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP. There is routinely at least a 100-fold RNA amplification with use of this kit.

growth_protocol: Thp-1 cells were cultured in RPMI supplemented with 10% FCS and were maintained between 2-10 x 105 cells/ml at 370C in a humidified, 5% CO2 atmosphere. Before infection cells were differentiated by treating them with PMA (5ng/ml) for a poeriod of 24 h.

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen) following the exact protocol recommended by the manufacturer.

treatment_protocol: Differentiated cells were then washed of excess PMA and left overnight. Cells were then infected with freshly prepared single cell suspension H37Rv in RPMI and infected with an MOI of 1:10.

value: Macrophages

tag: agent

tag: time point


title: 19508002

value: Female

value: Mother of family A

value: blood

value: Male

value: F


title: Thp-1-Rv-90Hr-Rep1

source_name: PMA differentiated Thp-1 Cells, H37Rv infected (90Hr) Replicate 1


title: arp6-3


title: arp6-2


title: 19507702

value: Daughter number 2 of family A


title: arp6-1

value: wild-type


title: Thp-1-Rv-48Hr-Rep2

source_name: PMA differentiated Thp-1 Cells, H37Rv infected (48Hr) Replicate 2


title: Thp-1-Un-Rep1

source_name: PMA differentiated Thp-1 Cells, H37Rv Un-infected

value: control


title: Thp-1-Rv-48Hr-Rep1

source_name: PMA differentiated Thp-1 Cells, H37Rv infected (48Hr) Replicate 1


title: 19509302

value: Blood


title: Thp-1-Rv-16Hr-Rep2

source_name: PMA differentiated Thp-1 Cells, H37Rv infected (16hr) Replicate 2


title: 19508702

value: Father

value: Son number 1 of family B


title: Thp-1-Un-Rep2


title: Thp-1-Rv-16Hr-Rep1

source_name: PMA differentiated Thp-1 Cells, H37Rv infected (16hr) Replicate1


title: 19513002

value: Son number 1 of family A


title: Akt-sphere #42

status: Public on Apr 30 2010

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Akt-spheres derived from ESC#42 +4OHT

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Red signal.

source_name: Akt-spheres induced by 4OHT treatment upon OP9 feeder cells #42

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: The feeder-free mouse ES cells, E14tg2a and the derivatives were maintained as described (Niwa et al., 1998).  The ES cells which expressed myr-Akt-Mer described in (Watanabe et al., 2006) were used.  OP9 stromal cells were cultured in Minimum Essential Medium-Alpha (Gibco, Gaithersburg, MD, USA), supplemented with 20% fetal bovine serum (FBS) (JRH, 5M0161, Lenexa, KS, USA), 1% MEM non-essential amino acids solution (Gibco), 2.2 g/L sodium bicarbonate, 2 mM L-Glutamine (Gibco), 75 mg/L penicillin G and 50 mg/L streptomycin.  The hematopoietic differentiation induction of ES cells on OP9 stromal cells has been described (Nakano et al., 1994; Nakano et al., 1996).  Akt-spheres were produced by the same protocol as hematopoietic differentiation induction on OP9 cells in OP9 culture medium with 4OHT (Sigma-Aldrich, St Louis, MO, USA). 4OHT treatments of ES cells were started 3 days before the induction.  Akt-spheres were expanded in OP9 culture medium with 4OHT on OP9 layer. Akt-spheres were passed onto freshly prepared OP9 cells after gentle pipetting or dissociation by trypsinization every 4 days and the medium was half changed every 2 days.  The Akt-spheres were used for analysis after OP9 cells were removed by culturing on 90 mm dish (Nunc, Roskilde, Denmark) for 30 minutes. The MEFs were treated with 10 ug/mL mitomycin C in phosphate-buffered saline (PBS) for 2.5 hours and plated at 1.2×105 cells/well in 24 well plates or at 6×105 cells/well in 6 well plates.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: 4OHT, which conditionally activates the kinase activity of Akt-Mer fusion protein, was used at 1 microM in culture.

tag: gender

value: male

value: PGC-like sphere cells derived from ESC line #42

tag: cell line


title: 19714102

value: Daughter number 1 of family B

value: Daughter number 2 of family B


title: Akt-sphere #21

description: Akt-spheres derived from ESC#21 +4OHT

source_name: Akt-spheres induced by 4OHT treatment upon OP9 feeder cells #21

value: PGC-like sphere cells derived from ESC line #21


title: ES#21-4OHT

description: Akt-Mer ESC#21 -4OHT

source_name: Akt-Mer ESC#21under ESC culture condition

value: embryonic stem cells (ESC)


title: 19710402

source_name: genomic DNA from pig

value: Son number 2 of family C

value: Female

value: Daughter number 1 of family C


title: Whole Blood Chamber Control 3 (5527)

status: Public on Apr 25 2010

city: Tübingen

first: Gabriel

last: Willmann

address: Schleichstrasse 12-16

institute: University Eye Hospital and Centre for Ophthalmology Tübingen

description: Whole Blood was drawn from V. Cava.

hyb_protocol: 15 micrograms of labeled cRNA from whole blood was fragmented, and 10ug was hybridized to Affymetrix Mouse 430 2.0 Gene Chip arrays for 18-24h (Affymetrix Inc.). Gene chip was washed and stained with streptavidin-phycoerythrin.

scan_protocol: The chip was scanned at 6um resolution with Agilant model G2500A Gene Array scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

data_processing: Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip operating system 1.1 (Affymetrix) for GC-RMA analysis in PARTEK software later on.

source_name: Whole Blood

label_protocol: Three microliter total RNA was used for each sample to obtain linearly amplified labeled cRNA by using GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA, USA) as described by manufacturer. Briefly, total RNA was used to generate double-stranded cDNA with the T7-oligo (dT) primer. This double-stranded cDNA was used in vitro transcription and biotin labeling steps. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280nm. All the cRNA 260/280 ratios were between 1.9 and 2.1. Quality control of the labeled cRNA products was assessed by performing 1µg labeled cRNA on 2% agarose gel to see similar RNA smear type.

extract_protocol: Total RNA was isolated and purified from 100ul of whole blood with the Mouse Ribopure-Blood RNA Isolation Kit (Ambion, Austin, Texas, USA) according to manufacturers instructions.

tag: stress


title: Whole Blood Chemical Hypoxic 2_8806

description: Whole Blood was drawn from V. Cava.

treatment_protocol: At the beginning of the experiment mice were divided into two groups, control (room condition) and chemical hypoxic (room condition). For conditioning, the chemical hypoxic group was supplemented with 200ng of CoCl2 per 100ml/day. Animal’s weight and food intake were monitored daily. Food and water were changed daily during the course of the experiment. Before and after the experiments the hematocrit was monitored by taking blood from the tail vein of control and hypoxic animals. After 15 days animals were euthanized using CO2 after whole blood extraction from V. Cava for further analysis.

value: chemical hypoxia


title: Whole Blood Everest Control 3_8460

description: Whole Blood was drawn from V. Cava.

hyb_protocol: 15 micrograms of labeled cRNA from whole blood was fragmented, and 10ug was hybridized to Affymetrix Mouse genome 430 2.0 Gene Chip arrays for 18-24h (Affymetrix Inc.). Gene chip was washed and stained with streptavidin-phycoerythrin.

treatment_protocol: At the beginning of the experiment mice were divided into two groups, control (room condition, Kathmandu, Nepal) and hypoxic (hypoxic condition). For conditioning, the hypoxic group was exposed to lower levels of hypobaric hypoxia during our mountaineering expedition to Mt Everest. The oxygen level was decreased according to our climbing protocol from 21% to about 7% over a period of 15 days. Food and water were changed daily during the course of the experiment. After 15 days animals were euthanized after whole blood extraction from V. Cava for further analysis.


title: Whole Blood Chemical Hypoxic 4_8808

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Chamber Control 4 (5529)

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Chamber Control 2 (5526)

description: Whole Blood was drawn from V. Cava.


title: 21970002

value: Male

value: blood

value: Son number 2 of family A


title: ES#21+4OHT

description: Akt-Mer ESC#21 +4OHT

source_name: Akt-Mer ESC#21treated with 4OHT under ESC culture condition

tag: strain


title: MOH2wt Sm_SB161_control 01

description: MOH2wt Sm_SB161_control 01

source_name: Cecum, WT, control infection, 10h

value: cecum

value: wildtype

value: Salmonella SB161 infection


title: Whole Blood chamber Control 1 (5525)

description: Whole Blood was drawn from V. Cava.

value: control


title: Whole Blood Everest Hypoxic 2_8453

description: Whole Blood was drawn from V. Cava.

value: hypobaric hypoxia


title: Whole Blood Chemical Hypoxic 3_8807

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Everest Control 2_8459

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Chemical Hypoxic 1_8804

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Everest Hypoxic 3_8456

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Everest Hypoxic 4_8457

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Everest Hypoxic 1_8452

description: Whole Blood was drawn from V. Cava.


title: xpa-1_2

status: Public on Apr 12 2010

city: Oslo

first: Jessica

middle: Margareta

last: Lindvall

address: Gaustadallee 24

country: Norway

institute: University of Oslo

hyb_protocol: hybridization protocol recommended by Affymetrix

scan_protocol: scanning protocol recommended by Affymetrix

data_processing: dChip was used for the processing of the data. The invariant set normalization method was used.

organism: Caenorhabditis elegans

source_name: xpa-1 mutant

label_protocol: GeneChip eukaryotic target labeling kit

extract_protocol: TRIZOL following RNA extraction with chloroform and isopropanol

value: xpa-1 mutant


title: ES like reverted #21

description: ESC-like cells derived by transient treatment with 4OHT on MEFs

source_name: ESC-like cells derived by 4OHT treatment on MEFs

value: male

value: ESC-like cells reverted from #21 PGC-like sphere cells


title: Whole Blood Everest Control 4_8463

description: Whole Blood was drawn from V. Cava.


title: N2_1

source_name: wild-type, N2_1

value: wild-type, N2


title: nth-1;xpa-1_2

source_name: nth-1;xpa-1 mutant

value: nth-1;xpa-1 mutant


title: N2_2

source_name: wild-type, N2_2


title: xpa-1_1


title: Whole Blood Everest Control 1_8458

description: Whole Blood was drawn from V. Cava.


title: nth-1;xpa-1_1


title: nth-1_3

source_name: nth-1 mutant

value: nth-1 mutant


title: nth-1_1


title: nth-1_2


title: Mouse liver LT ApoErtTA:TRE2-TAg_430B

status: Public on Apr 01 2010

city: New York

first: Nikolaus

last: Schultz

state: NY

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0, target value = 250, Tau = 0.015

label: standard Affymetrix protocol

source_name: Livers from ApoErtTA:TRE2-TAg transgenic mice provided with drinking water containing 25 micrograms/ml doxycycline plus 2.5% sucrose to induce expression of SV40 LT and st oncoproteins for 4 days

label_protocol: standard Affymetrix protocol

extract_protocol: RNA STAT-60 (Tel-Test)

tag: genetic background

value: Hybrid B6SJL

tag: age

value: 32-37 days old

value: Liver

value: LT ApoertTA:TRE2-TAg transgenic


title: mp_IAA_REP2

city: Wageningen

first: Dolf

last: Weijers

address: Dreijenlaan 3

department: Laboratory of Biochemistry

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 15ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA

source_name: 9 day-old mp-B4149 seedlings, DEX/IAA-treated, replica 2

label_protocol: cRNA synthesis and labeling was done according to Schmid et al., Nature Genetics [2005] 37, 501-506

growth_protocol: Seedlings were grown on half-strength Murashige-Skoog (MS) media containing 1% sucrose and 0.8% Daichin Agar in a 16 hour light / 8 hour dark cycle at 23 degrees.

extract_protocol: Purified total RNA was isolated using Qiagen RNEasy columns

treatment_protocol: Seedlings were treated with 10 micromolar Dexamethasone during one hour in liquid MS medium, and during 1 more hour with 50 micromolar IAA.

tag: Total seedling


title: mp_IAA_REP1

source_name: 9 day-old mp-B4149 seedlings, DEX/IAA-treated, replica 1


title: GR-bdl_IAA_REP2

source_name: 9 day-old pRPS5A-Myc-GR-bdl seedlings, IAA-treated, replica 2


title: recurrence bone marrow 4

city: Beppu

first: Takehiko

last: Yokobori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

institute: Kyushu university

description: no additional information

hyb_protocol: According to the Agilent protocol.

scan_protocol: According to the Agilent protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent Technologies) with protocol miRNA-v1_95_May07 and Grid: 019118_D_20080214.

source_name: recurrence bone marrow 4

label_protocol: Total RNA (100 ng) was directly labeled with cyanine 3-CTP (Cy3), without fractionation or amplification.

extract_protocol: ISOGEN, reagent for RNA extraction manufactured by Nippon Gene Co. Ltd.

value: bone marrow

tag: size of tumor (t factor)

tag: number of lymph node metastasis

tag: stage of disease

tag: recurrence and site

value: lymph node

tag: clinical outcome

value: cancer death

tag: disease free interval (months)

tag: follow up period (months)


title: Sox17 Sox17-induced mES cells_ChIP_expt1

status: Public on Mar 31 2010

city: Cambridge

first: Kathy

last: Niakan

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: Sox17 ChIP-chip in Sox17-overexpressing mES

hyb_protocol: Approximately 7.5μg of DNA was hybridized per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: results file descriptions: fc.bar and ma.bar are generated by CisGenome software. fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe.

source_name: Sox17 ChIP DNA from Sox17-induced mouse ES cell

label_protocol: Samples (approximately 35μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: Sox17-inducible ES cells and XEN cells were grown for 48 hours prior to harvesting. XEN media consists of: 85% KO-DMEM (Invitrogen); 15% fetal bovine serum (Hyclone); 1% L-glutamine (Invitrogen); 1% β-mercaptoethanol (Invitrogen); 1% Penicillin/Streptomycin. ES media consists of: 85% KO-DMEM; 15% fetal bovine serum (Hyclone); 1% L-glutamine (Invitrogen); 1% β-mercaptoethanol (Invitrogen); 1% Penicillin/Streptomycin (Invitrogen) 103IU of LIF (Chemicon). No MEFs were used in these experiments.

extract_protocol: Mouse XEN cells or Sox17-inducible mouse embryonic stem cells were grown to approximately 5x10^7 cells under routine culture conditions. The cells were trypsinized for 5 minutes at 37ºC, inactivated by adding serum containing medium, and cross-linked with cross-linking buffer containing 1% formaldehyde for 30 minutes. ChIP and LMPCR was performed according to a previously published protocol (Vokes et al., 2007). Chromatin was sonicated in 2ml of buffer 3 using 10x30 second pulses on a Branson 450 Sonifier (3 pulses on setting 4, then 7 on setting 6). For whole genome arrays, two or three ChIP reactions were set up in parallel with 500μl each (with 15μl of each biological sample reserved for an input control) – single promoter arrays used a single ChIP sample. At the final step, the samples were pooled and enrichment was validated using qPCR. For LMPCR, the pooled samples were divided into three and processed in parallel using 0.25mM dATP, dCTP, dGTP, 0.2mM dTTP and 0.05mM dUTP with 27 total cycles and then re-pooled after PCR cleanup. Each pooled set of reaction yielded >38μg of amplified sample. The linearity of amplification was confirmed by comparing qPCR values with the values from the unamplified samples.

treatment_protocol: Sox17-inducible ES cells were treated with 1μg/mL of doxycycline for 48 hours prior to harvesting.

tag: antibody

value: Sox17 goat polyclonal

value: ES

source_name: Input DNA from Sox17-inducible mouse ES cell line


title: FLAG Sox17-induced mES cells_ChIP_expt2

description: Sox17-FLAG ChIP-chip in Sox17-overexpressing mES

source_name: FLAG ChIP DNA from Sox17-induced mouse ES cell

value: FLAG M2 mouse monoclonal


title: Sox17 XEN cells_ChIP_expt1 and expt2

description: Sox17 ChIP-chip in XEN

source_name: Sox17 ChIP DNA from extraembryonic endoderm cell line

value: XEN

source_name: Input DNA from extraembryonic endoderm (XEN) cell line


title: recurrence bone marrow 3

description: no additional information

source_name: recurrence bone marrow 3

tag: tissue

value: liver


title: recurrence bone marrow 2

description: no additional information

source_name: recurrence bone marrow 2

value: skin

value: alive


title: Mouse liver 17kT ApoErtTA:TRE2-TAg_430A

source_name: Livers from ApoertTA:TRE2-TAg transgenic mice provided with drinking water containing 25 micrograms/ml doxycycline plus 2.5% sucrose to induce expression of SV40 17kT and st oncoproteins for 4 days

value: Male

tag: genotype

value: 17kT ApoErtTA:TRE2-TA transgenic


title: recurrence bone marrow 1

description: no additional information

source_name: recurrence bone marrow 1


title: no recurrence bone marrow 2

description: no additional information

source_name: no recurrence bone marrow 2


title: Mouse liver WT_430B

source_name: Livers from non-transgenic, wild-type mice provided with drinking water containing 25 micrograms/ml doxycycline plus 2.5% sucrose for 4 days

tag: gender

value: wild type


title: Mouse liver LT ApoErtTA:TRE2-TAg_430A

source_name: Livers from ApoertTA:TRE2-TAg transgenic mice provided with drinking water containing 25 micrograms/ml doxycycline plus 2.5% sucrose to induce expression of SV40 LT and st oncoproteins for 4 days

value: Hybrid B6SJL


title: GR-bdl_DEX_IAA_REP1

source_name: 9 day-old pRPS5A-Myc-GR-bdl seedlings, DEX/IAA-treated, replica 1


title: no recurrence bone marrow 1

description: no additional information

source_name: no recurrence bone marrow 1


title: no recurrence bone marrow 3

description: no additional information

source_name: no recurrence bone marrow 3


title: GR-bdl_IAA_REP1

source_name: 9 day-old pRPS5A-Myc-GR-bdl seedlings, IAA-treated, replica 1


title: no recurrence bone marrow 4

description: no additional information

source_name: no recurrence bone marrow 4


title: Mouse liver 17kT ApoErtTA:TRE2-TAg_430B

value: 32-37 days old


title: GR-bdl_DEX_IAA_REP2

source_name: 9 day-old pRPS5A-Myc-GR-bdl seedlings, DEX/IAA-treated, replica 2


title: Mouse liver WT_430A

value: Liver


title: Sox17-inducible-line 2 ES cells treated with doxycyline

description:
Sox17-inducible mouse embryonic stem cell_line 2
4592728087_E

hyb_protocol: Illumina BeadStation (Illumina)

scan_protocol: Illumina BeadStation (Illumina)

data_processing: Illumina BeadStudio (Illumina); rank invariant normalization, background subtraction using Illumina BeadStudio (Illumina)

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Sox17-inducible ES cells were grown for 5days prior to harvesting. ES media consists of: 85% KO-DMEM; 15% fetal bovine serum (Hyclone); 1% L-glutamine (Invitrogen); 1% β-mercaptoethanol (Invitrogen); 1% Penicillin/Streptomycin (Invitrogen) 103IU of LIF (Chemicon). No MEFs were used in these experiments.

extract_protocol: Trizol (Invitrogen)

treatment_protocol: Sox17-inducible ES cells were treated with 1μg/mL of doxycycline for 5days prior to harvesting.

tag: cell type

value: Mouse embryonic stem cell


title: Control KH2 cells treated with doxycycline

description:
Control KH2 mouse embryonic stem cell
4592728087_A


title: Untreated Sox17-inducible ES cells

description:
Sox17-inducible mouse embryonic stem cell
4592728087_D

source_name: Untreated Sox17-inducible ES cells


title: Embryos at Carnegie Stage 13 (E28-30d), Replicate 1

status: Public on Mar 18 2010

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

country: United Kingdom

institute: University of Bristol

description:
Human embryos with Carnegie Stage 13 (E28-30d), Replicate 1
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.

hyb_protocol: The fragmented, biotinylated cRNA were used for hybridization at 45℃ for 17 hours with Affymetrix HG-U133A GeneChip microarrays (Affymetrix, Santa Clara, CA)

scan_protocol: An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays

data_processing: Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: carnegie stage

tag: embryonic day

value: embryo


title: Embryos at Carnegie Stage 13 (E28-30d), Replicate 3

description:
Human embryos with Carnegie Stage 13 (E28-30d), Replicate 3
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Untreated Sox17-inducible-line 2 ES cells

description:
Sox17-inducible mouse embryonic stem cell_line 2
4592728087_F


title: Embryos at Carnegie Stage 12 (E26-27d), Replicate 3

description:
Human embryos with Carnegie Stage 12 (E26-27d), Replicate 3
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Sox17-inducible ES cells treated with doxycycline

description:
Sox17-inducible mouse embryonic stem cell
4592728087_C


title: Embryos at Carnegie Stage 12 (E26-27d), Replicate 1

description:
Human embryos with Carnegie Stage 12 (E26-27d), Replicate 1
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Control untreated KH2 cells

description:
Control KH2 mouse embryonic stem cell
4592728087_B

source_name: Control untreated KH2 cells


title: Embryos at Carnegie Stage 14 (E31-32d), Replicate 1

description:
Human embryos with Carnegie Stage 14 (E31-32d), Replicate 1
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 14 (E31-32d), Replicate 3

description:
Human embryos with Carnegie Stage 14 (E31-32d), Replicate 3
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 11 (E24-25d), Replicate 3

description:
Human embryos with Carnegie Stage 11 (E24-25d), Replicate 3
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 10 (E22-23d), Replicate 1

description:
Human embryos with Carnegie Stage 10 (E22-23d), Replicate 1
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 12 (E26-27d), Replicate 2

description:
Human embryos with Carnegie Stage 12 (E26-27d), Replicate 2
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 9 (E20-21d), Replicate 3

description:
Human embryos with Carnegie Stage 9 (E20-21d), Replicate 3
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 13 (E28-30d), Replicate 2

description:
Human embryos with Carnegie Stage 13 (E28-30d), Replicate 2
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 11 (E24-25d), Replicate 2

description:
Human embryos with Carnegie Stage 11 (E24-25d), Replicate 2
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 10 (E22-23d), Replicate 2

description:
Human embryos with Carnegie Stage 10 (E22-23d), Replicate 2
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 9 (E20-21d), Replicate 2

description:
Human embryos with Carnegie Stage 9 (E20-21d), Replicate 2
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 11 (E24-25d), Replicate 1

description:
Human embryos with Carnegie Stage 11 (E24-25d), Replicate 1
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 10 (E22-23d), Replicate 3

description:
Human embryos with Carnegie Stage 10 (E22-23d), Replicate 3
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: NK-cell line_replicate

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description:
Gene expression data from NK cell lines.
YT-N

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Scanning Protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis (e.g., clustering, classification) was carried out using BRB-ArrayTools version (3.7.0).

source_name: NK-cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All the tissues used in the study were fresh frozen and stored below -70 degree C.

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

value: NK

value: male


title: Gamma-delta T-cell line SNT8

description:
Gene expression data from gamma-delta T-cell line.
SNT8

source_name: Gamma-delta T-cell line

value: gamma-delta T-cell

value: female


title: Gamma-delta T-cell line SNT15

description:
Gene expression data from gamma-delta T-cell line.
SNT15


title: NK-cell line SNK10_replicate

description:
Gene expression data from NK cell lines.
SNK10B


title: Embryos at Carnegie Stage 14 (E31-32d), Replicate 2

description:
Human embryos with Carnegie Stage 14 (E31-32d), Replicate 2
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Embryos at Carnegie Stage 9 (E20-21d), Replicate 1

description:
Human embryos with Carnegie Stage 9 (E20-21d), Replicate 1
The protocol for collecting human embryos was reviewed and approved by the Ethics Committee of Xinhua Hospital. The experimental procedures involving human embryos conformed to the National Ethical Guideline on Human Embryo Research issued by the Committee on Bioethics, Chinese National Human Genome Center (Southern Headquarter). Human embryos were obtained from the Department of Obstetrics and Gynecology at Xinhua Hospital during clinical drug abortion. All donors signed informed consent forms. The age of the embryo was estimated by standard clinical parameters. Great care was taken to remove contaminating extraembryonic tissues surrounding the embryo, and the embryo was frozen immediately in liquid nitrogen after washing with diethylpyrocarbonate (DEPC)-treated cold PBS. Samples were stored at -80℃ until use.


title: Gamma-delta T-cell line SNT13

description:
Gene expression data from gamma-delta T-cell line.
SNT13


title: NK-cell line NKYS

description:
Gene expression data from NK cell lines.
NKYS


title: NK-cell line SNK1

description:
Gene expression data from NK cell lines.
SNK1


title: NK/T lymphoma 20

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-57

source_name: Pre-treated fresh frozen biopsy, ENK/T

value: ENK/T


title: NK-cell line KAI3

description:
Gene expression data from NK cell lines.
KAI3


title: NK/T lymphoma 1

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-25


title: NK lymphoma_unclassifiable 7

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-47


title: NK-cell line  HANK

description:
Gene expression data from NK cell lines.
HANK


title: NK-cell line NK92

description:
Gene expression data from NK cell lines.
NK92


title: NK/T lymphoma 19

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-55


title: NK/T lymphoma 21

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-50


title: NK/T lymphoma 18

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-54


title: NK/T lymphoma 17

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-171


title: NK/T lymphoma 3

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-49


title: NK/T lymphoma 11

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-165

value: not available


title: NK/T lymphoma 4

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-162


title: NK/T lymphoma 14

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-168


title: NK lymphoma_unclassifiable 6

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-45


title: NK/T lymphoma 10

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-161


title: Enteropathy-associated T-cell lymphoma 2

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-156

source_name: Pre-treated fresh frozen biopsy, PTCL

value: PTCL


title: NK/T lymphoma 13

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-167


title: NK/T lymphoma 15

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-169


title: NK/T lymphoma 12

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-166


title: NK-cell line SNK10

description:
Gene expression data from NK cell lines.
SNK10


title: Blastic NK-cell lymphoma

description:
Gene expression data from Blastic NK-cell lymphoma pre-treated biopsy.
CLN-164

source_name: Pre-treated fresh frozen biopsy, blastic NK-cell lymphoma

value: blastic NK-cell lymphoma


title: NK/T lymphoma 16

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-170


title: NK/T lymphoma 8

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-151


title: Hepatosplenic T-cell lymphoma 3

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-145


title: NK/T lymphoma 5

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-163


title: Hepatosplenic T-cell lymphoma 4

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-150


title: Hepatosplenic T-cell lymphoma 2

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-141


title: NK/T lymphoma 9

description:
Gene expression data from ENK/T pre-treated biopsy.
CLN-119