title: CN_AML Patient 13: Monoallelic CEBPA mutation

description: CN_AML Patient 13


title: HL60-Mnt-ChIP-rep4

status: Public on Nov 24 2009

type: genomic

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: 13440769_ Cy3 Mnt_1Mnt_1IgG_760_630_0635

hyb_protocol: The mixed DNA was resuspended in 5 μL of H2O and mixed with 85 μL hybridization mix (100 μL of DIG Easy Hyb solution (Roche 603 558), 5 μL of 10 mg/mL calf thymus DNA (Sigma D8661), 5 μL of 10 mg/mL yeast tRNA (Invitrogen 15401-029)). The resulting solution was incubated at 65 °C for 2 minutes, then cooled to room temperature and applied to a CpG island array slide (UHN Microarray Centre HCGI12K) and incubated overnight at 42 °C in a hybridization chamber. After hybridization, the microarray slide was washed once with washing buffer 1 (1x SSC, 0.1% SDS) at 50°C for 5 minutes. This was followed by a wash with washing buffer 1 (room temperature for 5 minutes) and 2 washes with washing buffer 2 (0.2x SSC for 5 minutes) and one final wash with washing buffer 3 (0.1x SSC for 5 minutes at room temperature). The slide was then dried by spinning at 700 rpm for 15 minutes. To preserve the Cy5 dye from ozone-dependent degradation, which was observed during the summertime when the hybridization occurred, the slides were then dipped in DyeSaver 2 (Genisphere Q500600) and allowed to air dry.

scan_protocol: The microarray slides were scanned using a Gene Pix 4000B scanner (Axon Instruments) at multiple PMT voltages. Array images were first manually examined for image artifacts, and then quantitated using GenePix Pro (v6.0.1.27). A scan that maximized the dynamic range without saturating high-intensity signals was selected and carried forward for analysis. This scan was quantified using the “circular” segmentation algorithm.

data_processing: All data were pre-processed using the variance-stabilizing normalization algorithm as implemented in the vsn package (v3.8.0) for the BioConductor open-source library for the R statistical environment (v2.8.1). Print-tip groups were used as strata and default parameterization was employed.

molecule: genomic DNA

organism: Homo sapiens

source_name: Growing HL60 Cells, Mnt ChIP

label_protocol: A total of 3 μg of amplified DNA from the antibody sample, no antibody, or IgG sample were vacuum desiccated and resuspended in 2.5 μL of H2O (Sigma W4502). 4.5 μL of 0.1 M NaHCO3 at pH 9 was added. The DNA was resuspended by vortexing several times. 2 μL of Cy3 or Cy5 dye (Amersham, PA23001 and PA25001 respectively) were added to the sample. The mix was incubated for 1.5 hours at room temperature in the dark. After incubation, 35 μL of 100 mM Na-Acetate pH5.2 was added and topped with H2O (Sigma W4502) to a total volume of 100 μL for each sample. The fluorescent labeled probes were purified using QIAquick PCR Purification kit (Qiagen 28106). The DNA was eluted with 50 μL of EB buffer from the kit, heated to 65°C. The 100 μL combined ChIP and no antibody samples were vacuum desiccated using a SpeedVac for 60 minutes at maximum heat.

extract_protocol: Exponentially growing HL60 cells were cross-linked with 1% formaldehyde for 10 minutes at 37 °C. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphatebuffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4 °C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then sonicated using 8 pulses (12-13 Watts, setting 10, 10 seconds per pulse, 45 seconds on ice between pulses) from a Model 60 Sonic Dismembrator (Fisher Scientific 15-338-53) to generate fragments between 600 bp and 1000 bp. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) and precleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmonsperm DNA at a final concentration of 50 μg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 10^6 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours with each of the following antibodies: no-antibody control, 0.7 μg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), Mnt antibody. 50 μL of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 μL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Crosslinks were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 μL of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 μL of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 μL of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was extracted from each sample using phenol:chloroform:isoamyl alcohol (25:24:1), then precipitated with 1/10th volume of 3 M sodium acetate (pH 5.3), 5 μg of glycogen, and 2 volumes of ethanol at -20 °C overnight. Pellets were collected by microcentrifugation and resuspended in 60 μL of H2O.

tag: cell line

tag: antibody

value: Mnt

tag: sample type

value: ChIP

source_name: Growing HL60 Cells, IgG ChIP

value: IgG


title: HL60-Mnt-ChIP-rep10

description: 13441062_Cy5Mnt_IgG11_Mnt11_710_620_0635


title: HL60-Mnt-ChIP-rep7


title: HL60-Mnt-ChIP-rep5


title: HL60-Mnt-ChIP-rep3


title: CN_AML Patient 47: Biallelic CEBPA mutation

status: Public on Dec 31 2009

type: RNA

city: Munich

first: Klaus

middle: H

last: Metzeler

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University of Munich

description: CN_AML Patient 47

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the variance stabilizing normalization algorithm. Custom chip definition files based on the  GeneAnnot database were used for probe-set summarization, and probe set expression values were calculated by the median polish method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set  summarization.

label: biotin

molecule: total RNA

source_name: bone marrow mononuclear cells: AML, normal karyotype

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from bone marrow (BM) or peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow or peripheral blood mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML) with a normal karyotype

tag: tissue

value: bone-marrow mononuclear cells from CN-AML patient

tag: genotype

value: Biallelic CEBPA mutation


title: liver_testosterone-treated for 3 weeks_replicate 1

status: Public on Oct 28 2009

city: Düsseldorf

first: Jürgen

last: Krücken

state: NRW

address: Universitätsstr. 1

department: Division of Molecular Parasitology

institute: Heinrich-Heine-University Düsseldorf

description: Experiment intends to compare short- and long-term effects of testosterone treatment on gene expression in female liver.

hyb_protocol: 15 µg biotin-labeled cRNA was then hybridized to Affymetrix MOE230A GeneChips for 16 h at 45 °C. The Chips were washed on an Affymetrix Fluidics Station 400 and stained with phycoerythrine-streptavidin in the presence of biotinylated anti-streptavidine antibodies according to Affymetrix Fluidics Protocol Midi-euk2v3.

scan_protocol: The fluorescence emmision of the hybridized cRNA array was read with an Affymetrix 3000 Scanner at 570 nm.

data_processing: CEL and CHP files were generated using GCOS software and the MAS5 algorithm. The median of signal intensities was set to 100.

label: Biotin

organism: Mus musculus

source_name: Liver of female mouse treated for three weeks with testosterone in sesame oil (vehicle) by s.c. injection.

label_protocol: Affymetrix OneCycle Kit using 5 µg total RNA according to the manufactures instructions.

extract_protocol: Initial purification with pegGOLD TRifast (Peqlab). Digestion with DNAse, purification via RNeasy clumns (Qiagen).

tag: Strain

tag: Gender

value: female

tag: Treatment

value: treatment with 0.9 mg testosterone in 100 µl sesame oil by s.c. injection for three weeks twice a week.

tag: Tissue

value: liver


title: liver_testosterone-treated for 3 weeks_withdrawal of testosterone for 12 weeks_replicate 3

description: Experiment intends to compare short- and long-term effects of testosterone treatment on gene expression in female liver

source_name: Liver of female mouse treated for three weeks with testosterone in sesame oil (vehicle) by s.c. injection followed by twelve weeks of vehicle withdrawal.

value: treatment with 0.9 mg testosterone in 100 µl sesame oil by s.c. injection for three weeks twice a week followed by 12 weeks of vehicle withdrawal.


title: liver_vehicle-treated for 3 weeks_replicate 2

source_name: Liver of female mouse treated for three weeks with sesame oil (vehicle) by s.c. injection.

value: treatment with 100 µl sesame oil by s.c. injection for three weeks twice a week.


title: P-def_rep1

status: Public on Oct 31 2009

city: Tsukuba

first: Matthias

last: Wissuwa

address: 1-1 Ohwashi

country: Japan

institute: JIRCAS

description:
Keyword: Nipponbare
Keyword: 6-4  (NIL with inserts from cv. Kasalath (indica))
Keyword: Comparison between line
Keyword: Phosphorus deficiency
Keyword: Root

hyb_protocol: Both 1 micro gram labelled cRNA were hybridized on a slide by In-situ Hybridization Kit Plus (Agilent Technologies) according to manufacturer's protocol.

scan_protocol: After hybridization, the slide was washed twice according to manufacturer's protocol. the slide was scanned by DNA microarray scaner according to manufacturer's protocol.

data_processing: Feature Extraction ver 7.1 (Agilent Technologies)

organism: Oryza sativa

label_protocol: Labelled cRNA was synthesized by Low RNA Input Linear Amplification kit (Agilent Technlogies) according to manufacturer's protocol.

growth_protocol: Plants were grown in 12L pots filled with soil (Andosol) without Phosphorus

extract_protocol: Total RNA of root tissues (1.6 g) was collected and purified by RNeasy midi kit according to manufacturer's protocol.

tag: root tissues samples in 40 day-old plants

source_name: 6-4_P-def_rep1; without Phosphorus


title: Control_rep1

description:
Keyword: Nipponbare
Keyword: 6-4  (NIL with inserts from cv. Kasalath (indica))
Keyword: Comparison between line
Keyword: Root

source_name: 6-4_control_rep1; high phosphorus content.

growth_protocol: Plants were grown in 12L pots filled with soil (Andosol) with highly phosphorus content.

tag: Root tissues sampled in 40 day-old plants.

source_name: Nipponbare_control_rep1; high phosphorus content.


title: HL60-Mnt-ChIP-rep1

description: 13435981_Cy5Mnt _2Mnt_2IgG_740_600_0635


title: liver_testosterone-treated for 3 weeks_replicate 3


title: liver_testosterone-treated for 3 weeks_replicate 2


title: P-def_rep2

data_processing: Feature Extraction ver 8.1 (Agilent Technologies)

source_name: 6-4_P-def_rep2; without Phosphorus

tag: root tissues sampled in 40 day-old plants


title: liver_vehicle-treated for 3 weeks_replicate 1


title: liver_vehicle-treated for 3 weeks_withdrawal of vehicle for 12 weeks_replicate 3

source_name: Liver of female mouse treated for three weeks with sesame oil (vehicle) by s.c. injection followed by twelve weeks of vehicle withdrawal.

value: treatment with 100 µl sesame oil by s.c. injection for three weeks twice a week followed by 12 weeks of vehicle withdrawal


title: liver_vehicle-treated for 3 weeks_withdrawal of vehicle for 12 weeks_replicate 2


title: liver_testosterone-treated for 3 weeks_withdrawal of testosterone for 12 weeks_replicate 1


title: liver_testosterone-treated for 3 weeks_withdrawal of testosterone for 12 weeks_replicate 2


title: liver_vehicle-treated for 3 weeks_replicate 3


title: liver_vehicle-treated for 3 weeks_withdrawal of vehicle for 12 weeks_replicate 1


title: P-def_rep3

source_name: 6-4_P-def_rep3; without Phosphorus


title: Control_rep2

source_name: Nipponbare_control_rep2; high phosphorus content.

source_name: 6-4_control_rep2; high phosphorus content.


title: Control_rep3

source_name: 6-4_control_rep3; high phosphorus content.

tag: root tissues samples in 40-day-old plants

source_name: Nipponbare_control_rep3; high phosphorus content.


title: LPS, biological rep3

status: Public on Oct 16 2009

city: Nashville

first: David

middle: W

last: Wright

state: TN

address: SC Stevenson Center 7, Station B 351822

department: Chemistry

country: USA

institute: Vanderbilt University

hyb_protocol: All hybridization reagents, hybridization controls, wash reagents, and chemiluminescent reagents were provided in the ABI CL Detection Kit, part#4342142, and the manufacturer’s protocol was followed.  Briefly, the arrays were equilibrated to room temperature and then pre-hybridized with a 1ml volume for 60’ with agitation (100RPM) at 55C per manufacturer’s protocol.  During the pre-hybridization, the DIG-labelled targets were fragmented and then stored on ice until the pre-hyb was completed.  Once pre-hyb was completed the targets were mixed with the appropriate reagents, including Hybridization controls, and the 0.5ml target was added to the pre-hybridization through the port on the array chamber.  The arrays were immediately returned to the 55C Hybridization oven and agitated exactly 16 hours at 100RPM.  The arrays were then washed and incubated with Anti-Dig-APAntibody for 20 minutes.  Following antibody washes, the arrays were incubated with Chemiluminescence Enhancing Solution, washed a final time and then stored in the last wash buffer at room temperature. Substrate for the chemiluminescence reaction was added to each array individually and then the array was immediately imaged on the 1700 Chemiluminescent Analyzer.

scan_protocol: Following addition of the chemiluminescence reaction substrate, each array was immediately imaged on the 1700 Chemiluminescent Analyzer. Each imaging was completed in approximately 15 minutes and the images were assessed for QC/QA and a primary analysis was completed by the AB1700 Expression Array System Software (v 1.1.1).

data_processing: Signal intensities across microarrays were quantile normalized

label: Digoxigenin

source_name: LPS

label_protocol: All RNA Preps were run on an Agilent 2100 Bioanalyzer to assess RNA integrity. Those samples meeting minimum requirements of RIN value of 7.0 and greater were used to generate targets for hybridization to ABI arrays. One (1) ug of Total RNA (30ng mRNA) was used to generate First Strand cDNA using the NanoAmp RT-IVT labeling kit according to manufacturer’s protocol (ABI, Cat#4365715).  Following first strand synthesis, second strand synthesis was completed.  The resulting cDNA was then purified using an ABI kit provided column and the entire reaction was used in an IVT reaction to generate DIG labeled cRNA.  The cRNA was then purified using a kit provided column and assessed for quality on an Agilent Bioanalyzer.  All reactions meeting ABI criteria in terms of quantity and size of target produced were fragmented and then hybridized to the appropriate array for 16 hours with agitation at 55C.

growth_protocol: Cells were cultured under standard incubation conditions (37 ºC, 5% CO2) and grown in RPMI supplemented with 5% FBS and 1μg/mL P/S

extract_protocol: Cells were harvested at 24 h using Versagene RNA purification and DNase treatment kits. Six wells of a 6-well plate were pooled for each biological replicate.

treatment_protocol: Cells were stimulated with lipopolysaccharide (LPS) at a final concentration of 1 μg/mL


title: LPS, biological rep1


title: LPS, biological rep2


title: 13832954 - W498_M A vs Col0_M A

status: Public on Oct 01 2009

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: We are studying the function of a gene encoding a mitochondrial basic amino acid carrier , BAC2 in Arabdopsis thaliana.This gene is expressed during osmotic and salt stresses, and dark-induced senescence. We wish to determine whether there are transcriptome modifications during osmotic stress in mutant plants (bac2) compared to wild-type plants .

hyb_protocol: Col0_M A Cy5 / W498_M A 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,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,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: Col0_M A

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: leaf - Media : MS1/2 saccharose 1%	 Temperature: 21°C	 Light : continuous

extract_protocol: Col0_M A:10ug.

treatment_protocol: Name:Mannitol - abiotic stress - abiotic stress,mannitol:quantity 400mM time 24hour .

value: wt

tag: age

value: 8 day

tag: developmental stage (boyes et al. plant cell 2001)

tag: gentoype

value: bac2 mutant


title: 13832953 - Col0_M A vs W498_M A

hyb_protocol: W498_M A Cy5 / Col0_M A 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.


title: 13832951 - Col0_control A vs W498_control A

hyb_protocol: W498_control A Cy5 / Col0_control A 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.

source_name: W498_control A

extract_protocol: W498_control A:10ug.

treatment_protocol: no treatment

source_name: Col0_control A

extract_protocol: Col0_control A:10ug.


title: 13832952 - W498_control A vs Col0_control A

hyb_protocol: Col0_control A Cy5 / W498_control A 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.


title: 13832949 - W498_control A vs W498_M A

hyb_protocol: W498_M A Cy5 / W498_control A 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.


title: 13832950 - W498_M A vs W498_control A

hyb_protocol: W498_control A Cy5 / W498_M A 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.


title: 13832955 - Col0_control A vs Col0_M A

hyb_protocol: Col0_M A Cy5 / Col0_control A 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.


title: 13832944 - Col0_M B vs W498_M B

hyb_protocol: W498_M B Cy5 / Col0_M B 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.

source_name: Col0_M B

extract_protocol: Col0_M B:10ug.


title: 13832948 - Col0_M A vs Col0_control A

hyb_protocol: Col0_control A Cy5 / Col0_M A 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.


title: 13832945 - W498_M B vs Col0_M B

hyb_protocol: Col0_M B Cy5 / W498_M B 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.


title: 13832942 - Col0_control B vs W498_control B

hyb_protocol: W498_control B Cy5 / Col0_control B 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.

source_name: W498_control B

extract_protocol: W498_control B:10ug.

source_name: Col0_control B

extract_protocol: Col0_control B:10ug.


title: 13832938 - Col0_M B vs Col0_control B

hyb_protocol: Col0_control B Cy5 / Col0_M B 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.


title: 13832937 - Col0_control B vs Col0_M B

hyb_protocol: Col0_M B Cy5 / Col0_control B 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.


title: 13832943 - W498_control B vs Col0_control B

hyb_protocol: Col0_control B Cy5 / W498_control B 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.


title: 13832939 - W498_control B vs W498_M B

hyb_protocol: W498_M B Cy5 / W498_control B 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.


title: 13832940 - W498_M B vs W498_control B

hyb_protocol: W498_control B Cy5 / W498_M B 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.


title: whole embryo without liver 10w+3d

city: Jerusalem

first: Galit

last: Tzur

address: Kiryat Hadassah

department: Gene Therapy

country: Israel

institute: Hadassah University Hospital

description: Gene expression data from human embryo without a liver tissue.

data_processing: Data was normalized using the GCRMA algorithm, implemented in R and bioconductor.

source_name: whole embryo without liver 10w+3d

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by phenol/chloroform purification using PLG tubes.

treatment_protocol: After identification and separation of the liver tissue, the liver and the rest of the embryo were immediately snap-frozen in liquid nitrogen and then stored at –80°C until analysis.

value: whole embryo without liver

value: 10w (weeks) +3d


title: Embryonic liver 11w+6d

description: Gene expression data from early human embryonic liver tissue

hyb_protocol: according to the standard Affymetrix protocol

source_name: Embryonic liver 11w+6d

value: 11w (weeks) +6d (days) from last menstrual period


title: Embryonic liver 11w+2d

scan_protocol: according to the standard Affymetrix protocol

source_name: Embryonic liver 11w+2d

value: 11w (weeks) +2d (days) from last menstrual period


title: Embryonic liver 10w+3d

source_name: Embryonic liver 10w+3d

value: 10w (weeks) +3d (days) from last menstrual period


title: Embryonic liver 9w+5d

source_name: Embryonic liver 9w+5d

value: 9w (weeks) +5d (days) from last menstrual period


title: Embryonic liver 12w

source_name: Embryonic liver 12w

value: 12w (weeks) from last menstrual period


title: Embryonic liver 9w+3d

source_name: Embryonic liver 9w+3d

value: 9w (weeks) +3d (days) from last menstrual period


title: Transplanted-reperfused liver T2-17

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

country: Italy

institute: Unversity of Naples Federico II

description: Gene expression data from a frozen liver biopsy obtained during transplantation procedure, 2 hours after reperfusion

data_processing: Affymetrix CEL files were imported into GeneSping 7.2 software (Agilent Technologies Inc.) and normalized by RMA algorithm

source_name: Frozen biopsy from transplanted liver, 2 hours after reperfusion

label_protocol: In vitro transcription was performed to obtain biotin labeled cRNA according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

extract_protocol: Total RNA was extract by Trizol

tag: gender

value: female

value: 47 years

tag: protocol

value: cold ischemia_6h 50min; Warm ischemia_50min


title: Transplanted-reperfused liver T2-16

hyb_protocol: according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

value: transplanted liver, 2 hours after reperfusion

value: 48 years

value: cold ischemia_7h 30min; Warm ischemia_40min


title: Transplanted-reperfused liver T2-15

scan_protocol: according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

value: male

value: 53 years

value: cold ischemia_6h 50min; Warm ischemia_40min


title: Transplanted-reperfused liver T2-08

value: cold ischemia_8h 15min; Warm ischemia_60min


title: Transplanted-reperfused liver T2-10

value: 34 years


title: Donor liver T0-17

description: Gene expression data from a frozen liver biopsy obtained from a brain dead donor during explantation

source_name: Frozen biopsy from donor liver

value: donor liver

tag: donor

value: brain dead donor

value: 58 years


title: Donor liver T0-16

value: 38 years


title: Donor liver T0-15

value: 40 years


title: Donor liver T0-08


title: C3Bir.B6-Cdcs1 Il10-/-_stimulated_rep3

city: Hannover

first: Andre

last: Bleich

institute: Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School

description: Bone marrow-derived macrophages were cultured for six days. On the last day of culture, cells were stimulated with Cbir-flagellin (1 µg/mL culture medium) for 4 hours.

hyb_protocol: Biotin-labeled and fragmented cRNA (15 µg) was hybridized onto MOE430v2.0 GeneChip™ arrays (Affymetrix) for 16 hours at 45°C. Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChip™ Scanner 3000 laser confocal slide scanner. The images were quantified using GeneChip(TM) Operating Software (GCOS) v1.2 and expression values summarized using the Robust MultiChip Average function in the R/affy package.

data_processing: An analysis of variance (ANOVA) model was applied and F1, F2, F3 and Fs test statistics were constructed along with their permutation p-values. False discovery rate (FDR) was then assessed using the R/qvalue package to estimate q-values from calculated test statistics.

source_name: Bone marrow-derived macrophages, stimulated

label_protocol: Following reverse transcription with an oligo(dT)-T7 primer (Affymetrix, Santa Clara, CA), double-stranded cDNA was synthesized with the Superscript double-stranded cDNA synthesis custom kit (Invitrogen). The cDNA was linearly amplified and labeled with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY) in an in vitro transcription reaction using T7 RNA polymerase.

growth_protocol: Cells were cultured in polystyrene 6-well culture plates (Corning, Corning, NY) at a density of 3 x 106/mL in RPMI1640 medium plus 10% fetal calf serum for six days. Culture medium was changed every third day.

extract_protocol: Cells from each donor in medium only and medium + flagellin (3 wells each) were harvested and pooled in a total of 2 mL Trizol (Invitrogen, Carlsbad, CA.). After passing the lysate through a 20G needle 5-6 times, RNA was extracted following the manufacturer’s protocol. RNA quality and yield was determined using the Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip assay (Agilent Technologies Inc, Palo Alto, CA).

tag: strain

value: C3Bir.Cg-Il10tm1Cgn Cdcs1

value: Male

tag: cell type

value: Bone marrow-derived macrophages

value: stimulated with flagellin


title: C3Bir.B6-Cdcs1 Il10-/-_stimulated_rep2


title: Donor liver T0-10

tag: tissue

value: 83 years

value: female


title: Normal liver N15_E-AFMX-11-448274667

description: Gene expression data from a frozen liver biopsy obtained from a healthy adult subject who suffered sudden death

source_name: Frozen biopsy from normal liver

value: normal liver

tag: arrayexpress repository sample id

value: data retrieved from arrayexpress database, E-AFMX-11-448274667

value: not available


title: C3Bir.B6-Cdcs1 Il10-/-_unstimulated_rep2

description: Bone marrow-derived macrophages were cultured for six days.

source_name: Bone marrow-derived macrophages, unstimulated

value: unstimulated


title: C3Bir.B6-Cdcs1 Il10-/-_unstimulated_rep3


title: B6.C3Bir-Cdcs1 Il10-/-_stimulated_rep2

value: B6.Cg-Il10tm1Cgn Cdcs1


title: Normal liver N12_E-AFMX-11-448274905

value: data retrieved from arrayexpress database, E-AFMX-11-448274905

value: 29 years

value: male


title: C3Bir.B6-Cdcs1 Il10-/-_unstimulated_rep1


title: B6.C3Bir-Cdcs1 Il10-/-_stimulated_rep1


title: B6.C3Bir-Cdcs1 Il10-/-_unstimulated_rep2


title: B6.C3Bir-Cdcs1 Il10-/-_unstimulated_rep1


title: C3Bir.B6-Cdcs1 Il10-/-_stimulated_rep1


title: B6.C3Bir-Cdcs1 Il10-/-_unstimulated_rep3


title: B6.C3Bir-Cdcs1 Il10-/-_stimulated_rep3


title: Normal liver N11_E-AFMX-11-448274825

value: data retrieved from arrayexpress database, E-AFMX-11-448274825


title: C3Bir-Il10-/-_unstimulated_rep3


title: C3Bir-Il10-/-_stimulated_rep3


title: C3Bir-Il10-/-_stimulated_rep1


title: C3Bir-Il10-/-_unstimulated_rep1


title: C3Bir-Il10-/-_stimulated_rep2


title: C3Bir-Il10-/-_unstimulated_rep2


title: B6-Il10-/-_unstimulated_rep2


title: B6-Il10-/-_unstimulated_rep1


title: B6-Il10-/-_stimulated_rep1


title: B6-Il10-/-_unstimulated_rep3


title: mut cSHMT colon, biological rep2

city: Ithaca

last: Lin

state: NY

address: T2 006A VRT

institute: Cornell University

description: nugen amplified

hyb_protocol: Amplified material was applied to Affymetrix 430A 2.0 chips, hybridized, and washed on a 430A fluidics station as per manufacturer's directions.

scan_protocol: Samples were scanned on an Affymetrix GeneChip 3000 scanner.

data_processing: Raw array data was processed using GCOS software. Signal values were scaled to a default target of 500 and summarized in a pivot table. Further statistical analysis was performed in R. Signal values were log2-transformed after offset by 8, and gene filtering applied to include only the 19871 probe sets having at least one present call. A two sample t-test was applied and an arbitrary p-value of 0.01 was used to identify differentially expressed genes between mutant and wild-type or heterozygote and wild-type.

source_name: proximal colon, cSHMT mutant mouse fed folate-deficient diet

label_protocol: Approximately 50 nanograms of total RNA from each colon sample was amplified using the nugen ovation v2.0 amplification kit as per manufacturer's directions.

growth_protocol: cSHMT mice were first back-crossed to C57 Bl/6 for 10 generations. Wild-type, heterozygote, and mutant mice were weaned at three weeks onto a folate choline-deficient diet (AIN-93G minus folate, choline) and maintained on this diet for five weeks.

extract_protocol: Colon samples were removed from RNALater and total RNA was isolated with Trizol as per manufacturer's directions. This total RNA was then further purified using a Qiagen RNEasy column as per manufacturer's directions.

treatment_protocol: Colons were flushed with PBS, and tissue from the proximal third of each colon was opened longitudinally. Samples were rinsed with PBS and frozen in RNALater at -80C.

value: 9 weeks

tag: diet

value: folate-deficient diet for 6 weeks from weaning


title: B6-Il10-/-_stimulated_rep2


title: Normal liver N10_E-AFMX-11-448274747

value: data retrieved from arrayexpress database, E-AFMX-11-448274747

value: 27 years


title: wt cSHMT colon, biological rep2

description: nugen amplified

source_name: proximal colon, wild-type mouse fed folate-deficient diet


title: wt cSHMT colon, biological rep1

description: nugen amplified


title: het cSHMT colon, biological rep3

description: nugen amplified

source_name: proximal colon, cSHMT heterozygous mouse fed folate-deficient diet


title: mut cSHMT colon, biological rep3

description: nugen amplified


title: het cSHMT colon, biological rep1

description: nugen amplified


title: wt cSHMT colon, biological rep3

description: nugen amplified


title: mut cSHMT colon, biological rep1

description: nugen amplified


title: het cSHMT colon, biological rep2

description: nugen amplified


title: B6-Il10-/-_stimulated_rep3

value: Male

value: Bone marrow-derived macrophages


title: Irradiated rat testes, biological rep 5

status: Public on Sep 30 2009

city: Houston

first: Wei

last: Zhou

state: TX

address: 1515 Holcombe Blvd

department: Department of Experimental Radiation Oncology

institute: M.D.Anderson Cancer Center

description: gene expression data from irradiated rat testes

hyb_protocol: cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner and quantified with Affymetrix GCOS 1.2.

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. After normalization, the expression levels within each chip were divided by the median value for all the probes whose expression was regarded as present on the array, and then log base 2 transformed.

organism: Rattus norvegicus

source_name: rat testes, after irradiation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

extract_protocol: Total RNA extraction by RNeasy Midi Kit (Qiagen, Valencia, CA)

treatment_protocol: 6 Gy irradiation to the lower abdomen of the rats

value: testes

tag: genotype

value: LBNF1 rat

value: 25~27 weeks old


title: Irradiated rat testes, biological rep 1


title: Control rat testes, biological rep 10

description: gene expression data from control rat testes

source_name: rat testes, before irradiation


title: Irradiated rat testes, biological rep 2


title: Irradiated rat testes, biological rep 3


title: Control rat testes, biological rep 8


title: Irradiated rat testes, biological rep 4


title: Control rat testes, biological rep 9


title: Control rat testes, biological rep 4


title: Control rat testes, biological rep 5


title: Control rat testes, biological rep 7


title: Control rat testes, biological rep 3


title: Control rat testes, biological rep 1


title: Control rat testes, biological rep 2


title: C2C12_ctrl_12hr

city: Bologna

first: Alberto

middle: Maria

last: Martelli

address: via Irnerio 48

department: Department of Human Anatomy

institute: University of Bologna

hyb_protocol: According to Affymetrix Expression_analysis_technical_manual

scan_protocol: Affymetrix scanner 7G. GCOS 1.4 acquisition software

data_processing: MAS5.0 Signal and Detection algorithm. Scaling to 500.

source_name: C2C12 cells, untreated, 12 hr

label_protocol: Affymetrix one-cycle labeling protocol (Expression_analysis_technical_manual)

growth_protocol: Mouse C2C12 cells were grown in Dulbecco’s-Modified Minimal Essential Medium (D-MEM) containing 10% heat-inactivated fetal calf serum, and 1% (v/w) penicillin/streptomycin.

extract_protocol: Trizol reagent on cell pellets; followed by RNeasy purification

treatment_protocol: Cells were cultured in 6-well plates for 18 hours prior to transfection. Approximately 3 × 105 cells per well were used for transfection experiments by the FuGene method, according to the manufacturer's protocols.

tag: C2C12 mouse myoblast cells, untreated, collected 12 hours after mock treatment


title: C2C12_DGKzeta_12hr

source_name: C2C12 cells, transfected with DGKzeta, 12 hr

tag: C2C12 mouse myoblast cells, transfected with DGKzeta, collected 12 hours transfection


title: 18 hour PE2.0 embolized rat, lung tissue, biological rep4

status: Public on Sep 01 2009

city: Charlotte

first: John

last: Zagorski

state: NC

address: 1542 Garden Terrace, 301

department: Emergency Medicine

institute: Carolinas Medical Center

description: Gene expression data from total lung RNA after 18 hours of PE2.0 treatment.

hyb_protocol: 25 microg of fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 v2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned twice using an Agilent Gene Array Scanner G2500A

data_processing: The data were generated with Affymetrix GeneChip Operating Software using a scaling target of 500, user defined normalization of 1.0, no probe mask, no baseline, and default "parameter" settings.

source_name: Total lung tissue 18 hours after treatment

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols from 5 microgram total RNA (Carolinas Medical Center-modified Affymetrix "Expression Analysis Technical Manual", 2001 using Superscript II cDNA module, Affymetrix IVT module, Affymetrix/Qiagen sample clean-up module).

growth_protocol: Rat was euthanized 18 hours after PE2.0 treatment. Lungs were excised surgically after bronchoalveloar lavage with 8 ml saline

extract_protocol: Lung tissue was snap frozen in liquid nitrogen and crushed to a fine powder with a mortar and pestle in liquid nitrogen. Aliquots of powders were homogenized in guanidinium isothiocyanate and extracted with acidic phenol/chloroform. Crude RNA was collected by ethanol precipitation and purified using Qiagen RNeasy spin columns.

treatment_protocol: Rat was injected in the right jugular vein with 0.15 ml/100 grams weight of a 10% W/V suspension of 25 micron polystyrene mirospheres in 0.01% Tween-20 as PE2.0 treatment; 2.0 million microspheres/100 gram weight

tag: Sprague Dawley male

tag: Weight

value: approximately 350 grams at time of experiment


title: C2C12_GFP_12hr

source_name: C2C12 cells, transfected with EGFP, 12 hr

tag: C2C12 mouse myoblast cells, EGFP-transfected, collected 12 hours transfection


title: Control rat testes, biological rep 6

tag: age


title: 18 hour PE2.0 embolized rat, lung tissue, biological rep2


title: 18 hour PE2.0 embolized rat, lung tissue, biological rep3


title: 18 hour PE2.0 embolized rat, lung tissue, biological rep1


title: 18 hour PE1.3 embolized rat, lung tissue, biological rep4

description: Gene expression data from total lung RNA after 18 hours of PE1.3 treatment.

growth_protocol: Rat was euthanized 18 hours after PE1.3 treatment. Lungs were excised surgically after bronchoalveloar lavage with 8 ml saline

treatment_protocol: Rat was injected in the right jugular vein with 0.10 ml/100 grams weight of a 10% W/V suspension of 25 micron polystyrene mirospheres in 0.01% Tween-20 as PE1.3 treatment; 1.3 million microspheres/100 gram weight


title: 18 hour PE1.3 embolized rat, lung tissue, biological rep3


title: 18 hour PE1.3 embolized rat, lung tissue, biological rep1


title: 18 hour vehicle control rat, lung tissue, biological rep2

description: Gene expression data from total lung RNA after 18 hours of vehicle treatment.

growth_protocol: Rat was euthanized 18 hours after vehicle treatment. Lungs were excised surgically after bronchoalveloar lavage with 8 ml saline

treatment_protocol: Rat was injected in the right jugular vein with 0.15 ml/100 grams weight of 0.01% Tween-20 as "vehicle" control treatment


title: Soybean Iron Inefficient Iron Sufficient Rep 3

city: Ames

first: Randy

last: Shoemaker

state: IA

address: 100 Osbourne Dr. G401

department: Agronomy

institute: Iowa State University

description: Data was collected from the 2nd trifoliate of Soybean genotypes which differ in their iron stress response grown under either iron sufficient or deficient conditions.

hyb_protocol: Biotin labeled cRNA was hybridized to the Affymetrix soybean genome array as reccomended by Affymetrix (Affymetrix GeneChip Analysis Technical Manual; Affymetrix Inc, Santa Clara, CA) at the iowa State University Gene Chip Facility (http://www.biotech.iastate.edu/facilities/Genechip.htm)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 at the Iowa State University Gene Chip Facility (http://www.biotech.iastate.edu/facilities/Genechip.htm).

data_processing: Results were analyzed usinig the GeneTraffic Microarray Analysis System.  An MBEI transformation of the data was performed according to internal GeneTraffic algorithms.

organism: Glycine max

source_name: 2nd trifoliate of iron sufficient plant

label_protocol: Samples were labeled with the Affymetrix One Cycle labeling kit, following manufacturer's directions

growth_protocol: Seedlings were germinated in sterile vermiculite.  Seven days after planting, seedlings were transplanted to iron limited hydroponics system.  A pH of 7.8 was maintained by an aeration of 3% CO2:Air mixture throughout the hydroponics system.  Plants were grown in hydroponics until 2nd trifoliate stage, approximately 14 days.

extract_protocol: RNA was extracted from leaf tissue using Qiagen's RNeasy RNA extraction kit following the protocol provided by the manufacturer.  RNA integrity was evaluated on an Agilent Bioanalyzer 2100 using an Agilent RNA Nano LabChip (Agilent technologies, Palo Alto, CA)

treatment_protocol: Plant was grown in iron sufficient (100 uM Fe(NO3)3) hydroponics for 14 days prior to harvest of 2nd trifoliate.

value: IsoClark

tag: iron status

value: Iron Sufficient

tag: iron tolerance

value: Iron Inefficient


title: Soybean Iron Inefficient Iron Sufficient Rep 2

tag: Genotype

tag: Iron Status

tag: Iron Tolerance


title: Soybean Iron Inefficient Iron Deficient Rep 3

source_name: 2nd trifoliate of iron deficient plant

treatment_protocol: Plant was grown in iron sufficient (50 uM Fe(NO3)3) hydroponics for 14 days prior to harvest of 2nd trifoliate.

value: Iron Deficient


title: 2 hour PE2.0 embolized rat, lung tissue, biological rep2

description: Gene expression data from total lung RNA after 2 hours of PE2.0 treatment.

source_name: Total lung tissue 2 hours after treatment

growth_protocol: Rat was euthanized 2 hours after PE2.0 treatment. Lungs were excised surgically after bronchoalveloar lavage with 8 ml saline


title: 18 hour vehicle control rat, lung tissue, biological rep3


title: 18 hour PE1.3 embolized rat, lung tissue, biological rep2


title: 18 hour vehicle control rat, lung tissue, biological rep1


title: 2 hour PE2.0 embolized rat, lung tissue, biological rep3


title: Soybean Iron Inefficient Iron Sufficient Rep 1

tag: Iron Tolerane


title: 2 hour PE2.0 embolized rat, lung tissue, biological rep1


title: Soybean Iron Efficient Iron Sufficient Rep 3

value: Clark

value: Iron Efficient


title: Soybean Iron Inefficient Iron Deficient Rep 1


title: 2 hour PE2.0 embolized rat, lung tissue, biological rep4


title: Soybean Iron Efficient Iron Sufficient Rep 2


title: 2 hour PE1.3 embolized rat, lung tissue, biological rep1

description: Gene expression data from total lung RNA after 2 hours of PE1.3 treatment.

growth_protocol: Rat was euthanized 2 hours after PE1.3 treatment. Lungs were excised surgically after bronchoalveloar lavage with 8 ml saline


title: Soybean Iron Efficient Iron Deficient Rep 2

treatment_protocol: Plant was grown in iron deficient (50 uM Fe(NO3)3) hydroponics for 14 days prior to harvest of 2nd trifoliate.


title: 2 hour vehicle control rat, lung tissue, biological rep3

description: Gene expression data from total lung RNA after 2 hours of vehicle treatment.

growth_protocol: Rat was euthanized 2 hours after vehicle treatment. Lungs were excised surgically after bronchoalveloar lavage with 8 ml saline


title: 2 hour PE1.3 embolized rat, lung tissue, biological rep3


title: 2 hour PE1.3 embolized rat, lung tissue, biological rep2


title: Soybean Iron Efficient Iron Deficient Rep 1

tag: Iron Efficient

tag: Iron Deficient Growth Conditions


title: Soybean Iron Inefficient Iron Deficient Rep 2

value: Iron inefficient


title: 2 hour PE1.3 embolized rat, lung tissue, biological rep4


title: Soybean Iron Efficient Iron Sufficient Rep 1


title: 2 hour vehicle control rat, lung tissue, biological rep1


title: 2 hour vehicle control rat, lung tissue, biological rep2


title: Low sulfide, biological replicate 1

status: Public on Aug 18 2009

type: mixed

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

institute: University of Calgary

description: log2 expression for growth of D. vulgaris under Low Sulfide Conditions (1mM)

hyb_protocol: Dried probes from the treatment condition (cDNA) and universal reference (gDNA) were mixed and diluted to 40 µl using a hybridization solution containing 50% (vol/vol) formamide, 5x SSC, 0.1% (wt/vol) SDS and 0.1 mg/ml herring sperm DNA. This solution was then incubated at 98 °C for 5 minutes and then kept at 60 °C. 16 ul of 3x SSC solution was added to the wells at the ends of the microarray slides to maintain proper chamber humidity, and then the hybridization solution was applied to the Corning UltraGAPS microarray slide which had been pre-washed according to manufacturer specification (Corning, New York). The slides were incubated for 17 hours in Corning hybridization chambers and then washed according the manufacturer’s specifications and dried in a centrifuge.

scan_protocol: The hybridized slides were scanned on a PerkinElmer Scanarray 5000 scanner (PerkinElmer, Massachusetts).

data_processing: Spot and background intensities were quantified using TIGR’s Spotfinder software. Raw data from 4 arrays (with duplicate spots) were used to generate 8 columns of data. The gDNA channel was used as the control for spot uniformity and labeling efficiency. Spots were flagged and rejected if the spot was saturated, of irregular size, missing in one channel or had a poor signal to noise ratio (lower than 2 times the median local background). This data underwent a lowpass filter and total intensity normalization in both the RNA and gDNA channels. These normalized data columns were then analyzed with Stanford Tools SAM (Significance Analysis of Microarrays) which median centered the data averaged the duplicate spots and replicate arrays and generated a q-value to represent the probability that the if the spot is included as differentially expressed that it is a false positive (results available on GEO series GSE15073).

label: Alexa fluor 647

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Low Sulfide Condition (cDNA)

label_protocol: Amino modified cDNA was generated from 10 ug of total RNA using indirect cDNA labeling and random hexamers utilizing the Indirect SuperScript labeling kit from invitrogen. Amino-modified gDNA was generated using 1 µg of gDNA using indirect labeling with random hexamers utilizing the Bioprime indirect labeling kit from Invitrogen. The amino-modified cDNA was then coupled with Alexa fluor 647 and the amino-modified gDNA with Alexa fluor 555.

growth_protocol: For Cathode Protectoin (CP) condition D. vulgars was cultured at 30 °C in a biocorrosion reactor with a working volume of 400ml containing defined Widdel-Pfenning (WP) medium containing 3 mM acetate and 28 mM sulfate. The medium was bubbled with oxygen-free mixed gas consisting of 10% CO2 and 90% N2. A negative potential of -1.1V was supplied to the iron working electrode. For 50% hydrogen, 5% hydrogen and lactate growth conditions D. vulgaris was cultured at 30 °C in 1 L Erlenmeyer flasks containing 500 ml of defined Widdel-Pfenning (WP) medium containing 3 mM acetate and 28 mM sulfate. The medium was bubbled with oxygen-free mixed gas consisting of either 0.5% (vol/vol), 5% or 50% hydrogen, 10% CO2 and the balance made up by N2. Alternatively, 65 mM lactate was the sole electron donor in cultures gassed with 10% CO2 and 90% N2. Gas was delivered at 100 ml/min after passing through a heated (325 °C) copper reduction tube for oxygen removal.

extract_protocol: Total RNA was extracted from mid-log phase cells using Invitrogen Trizol and Bacterial Max reagents. The RNA was purified with the Qiagen RNA Easy kit with on column DNase digestion. RNA quality and quantity were assessed using the absorbance ratio at 260 and 280 nm (A260/A280), denaturing agarose gel electrophoresis with ethidium bromide staining and with a Qubit fluorometer. To extract genomic DNA (gDNA) cell pellets were resuspended in NaCl-EDTA with lysozime, SDS, NaCL04, and chloroform:isoamylalcohol. This solution was centrifuged for 3 minutes at 10xg and the supernatant was added to 2 volumes of 95% EtOH to precipitate the DNA. Once the ethanol was removed the DNA is dissolved in TE and DNAse-Free RNAase and Proteinase K are used to remove contaminates. A phenol extraction and ethanol precipitation is then used to isolate the purified DNA. Quantification of DNA was conducted using absorbance ratio at 260 and 280 nm (A260/A280), agrose gel electrophoresis and with a Qubit fluorometer.

tag: strain

value: Hildenborough

label: Alexa fluor 555

source_name: Low Sulfide Condition (gDNA)


title: High sulfide, biological replicate 1

description: log2 expression for growth of D. vulgaris under High Sulfide Conditions (10mM)

source_name: High Sulfide Condition (cDNA)

source_name: High Sulfide Condition (gDNA)


title: COH-exposed RGCs3

status: Public on Aug 20 2009

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Ave

institute: University of Miami

description: Equivalent amounts of reference and experimental aRNAs were hybridized with the Agilent Rat Oligo Microarrays (Agilent, USA) according to the manufacturer’s instructions.

hyb_protocol: Once purified and fragmented, the dye labeled aRNA was used for micro-array hybridization. Labeled and amplified RNA from were hybridized to the Oligo microarray (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned at 5 μm resolution using a GenePix 4100A scanner (Axon Instruments at Molecular Devices) and the resulting images were analyzed with the software package GenePix Pro 5.1 (Axon Instruments at Molecular Devices).

data_processing: Data extracted from the images were transferred to the software package Acuity 4.0 (Axon Instruments) for normalization and statistical analysis. Each array was normalized for signal intensities across the whole array and locally, using Lowess normalization. For further analysis genes were selected according to the following quality criteria: (1) at least 90% of the pixels in the spot had intensity higher than background plus two standard deviations; (2), there were less than 2% saturated pixels in the spot; (3) signal to noise ratio (defined as ratio of the background subtracted mean pixel intensity to standard deviation of background) was 3 or above for each channel; (4) the spot diameter was between 25 and 75 μm; (5) the regression coefficient of ratios of pixel intensity was 0.6 or above.

source_name: Purified COH-exposed RGCs

label_protocol: Target RNA amplification and labeling with Cy5 dye from CyDye Post Labelling Reactive Dye Pack (Amersham, USA) was carried out in two rounds using the Amino Allyl MessageAmp™ aRNA Kit (Ambion, USA) as specified by the manufacturer.

extract_protocol: Purified cells were used for RNA isolation by Stratagene Absolutely RNA Nanoprep kit.

tag: COH-exposed RGCs were isolated according to the two-step immunopanning method reported earlier to yield 95–99% enrichment for RGCs.

source_name: Universal Rat Reference RNA

label_protocol: Target RNA amplification and labeling with Cy3 dye from CyDye Post Labelling Reactive Dye Pack (Amersham, USA) was carried out in two rounds using the Amino Allyl MessageAmp™ aRNA Kit (Ambion, USA) as specified by the manufacturer.

extract_protocol: Cells were used for RNA isolation by Stratagene RNA kit.

tag: Comprised as a collection of RNA pooled from fourteen rat cell lines for broad gene coverage, the Universal Rat Reference RNA provides the ability to cross-compare data sets from multiple experiments as a single, common control.


title: control (normotensive) RGCs1

source_name: Purified control (normotensive) RGCs

tag: RGCs were isolated according to the two-step immunopanning method reported earlier to yield 95–99% enrichment for RGCs.

source_name: Rat Universal Reference RNA

tag: Comprised as a collection of RNA pooled from fourteen rat cell lines for broad gene coverage (Figure 1), the Universal Rat Reference RNA provides the ability to cross-compare data sets from multiple experiments as a single, common control.


title: control (normotensive) RGCs4

tag: Control (normotensive) RGCs were isolated according to the two-step immunopanning method reported earlier to yield 95–99% enrichment for RGCs.


title: Recipient 9 diagnosed as RHC with no ACR

status: Public on Aug 05 2009

city: Suita

first: Tadafumi

last: Asaoka

address: 2-2, Yamadaoka

department: Surgery

institute: Osaka University

description: Liver biopsy samples were collected within 30 minutes from the time of liver biopsy, 2mm width ×5mm length, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).

data_processing: In each sample, the Cy5/Cy3 ratio values were log-transformed and global equalization to remove a deviation of the signal intensity between whole Cy3- and Cy5-fluorescence was performed by subtracting a median of all log (Cy5/Cy3) values from each log (Cy5/Cy3) value. Genes with missing values in more than 10% of samples were excluded from further analysis.

source_name: 21 Total RNAs mixture from normal liver labeled with Cyanine-3 (green).

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion). CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website).

extract_protocol: Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

tag: Mixture of total RNA from human normal liver

source_name: Total RNA from recipient represented the clinicopathological diagnoses for RHC with no ACR

tag: liver biopsy tissue

tag: RHC with no ACR


title: Recipient 10 diagnosed as RHC with no ACR

treatment_protocol: Liver biopsy samples were collected within 30 minutes from the time of liver biopsy, 2mm width ×5mm length, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.


title: Recipient 13 diagnosed as RHC with no ACR


title: control (normotensive) RGCs3


title: control (normotensive) RGCs2


title: COH-exposed RGCs2


title: COH-exposed RGCs4


title: Recipient 11 diagnosed as RHC with no ACR


title: Recipient 12 diagnosed as RHC with no ACR


title: Recipient 7 diagnosed as RHC with no ACR


title: Recipient 4 diagnosed as RHC with no ACR


title: COH-exposed RGCs1


title: Recipient 6 diagnosed as RHC with no ACR


title: Recipient 7 diagnosed as ACR-predominant with superimposed RHC

source_name: Total RNA from recipient represented the clinicopathological diagnoses for ACR-predominant with superimposed RHC

tag: ACR-predominant with superimposed RHC


title: Recipient 8 diagnosed as RHC with no ACR


title: Recipient 1 diagnosed as ACR-predominant with superimposed RHC


title: Recipient 9 diagnosed as ACR-predominant with superimposed RHC


title: Recipient 6 diagnosed as ACR-predominant with superimposed RHC


title: Recipient 5 diagnosed as RHC with no ACR


title: Recipient 5 diagnosed as ACR-predominant with superimposed RHC


title: CpG island methylation in KATOIII

status: Public on Aug 31 2009

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

description: To recover methylated DNA with anti-5-methyl cytidine antibody, DynaBeads protein A (Dynal) was used.

hyb_protocol: Labelled DNA mixed with Cot-1 DNA and Agilent blocking solution was hybridized to arrays for 40 hours at 67C and 10rpm. Arrays were washed as per Agilent protocol.

scan_protocol: Arrays were washed and scanned immediately with Agilent microarray scanner.

data_processing:
Arrays were processed using Agilent Feature Extraction software and normalized (Background subtraction) using Agilent Chip Analytics software.  Our original parameter, "Me value" as a value that linearly correlates with the fraction of methylated DNA molecules in CpG islands in samples with various overall DNA methylation levels, was calculated from subtracted signal log2 ratio and p[Xbar].
Methylation statuses were defined according to Me_Value.  U, <0.4;  M, >0.6;  -, between 0.4 and 0.6. x, Probes that showed Cy3 signal intensities (Input) more than five times average signal intensity. The probes were eliminated as non-functional probes due to high possibility of cross-hybridization.

source_name: Sonicated KATOIII genomic DNA

label_protocol: One µg of DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).

extract_protocol: DNA lysis buffer plus proteinase K.  phenol/chloroform extraction.  Ethernol precipitated.  RNase treated.

tag: cell line

value: gastric cancer cell line, KATOIII

source_name: MeDIP KATOIII

label_protocol: Five µg of genomic DNA fragmented by sonication was immunoprecipitated with five µg of anti-5-methyl cytidine antibody (Diagnode) and solved in 50 µL of buffer.  Immunoprecipitated DNA was checked by real-time PCR to ensure that it was enriched.  Fourty-five µL of DNA immnoprecipitated was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).


title: Recipient 1 diagnosed as RHC with no ACR


title: Recipient 3 diagnosed as RHC with no ACR


title: Recipient 2 diagnosed as RHC with no ACR


title: Recipient 2 diagnosed as ACR-predominant with superimposed RHC


title: Recipient 8 diagnosed as ACR-predominant with superimposed RHC


title: Recipient 3 diagnosed as ACR-predominant with superimposed RHC


title: CpG island methylation in 5-aza-dC-treated AGS

source_name: Sonicated 5-aza-dC-treated AGS genomic DNA

treatment_protocol: AGS cells were seeded at a density of 3 x 10^5 cells/10 cm dish on day 0 and treated with freshly prepared 1 µM 5-aza-dC (Sigma) for 24 hours on days 1, 3, and 5.  After each treatment, the cells were placed in fresh medium and harvested on day 6.

value: gastric cancer cell line, AGS

tag: agent

value: 5-aza-dC treated

source_name: MeDIP 5-aza-dC-treated AGS DNA


title: CpG island methylation in AGS

source_name: Sonicated AGS genomic DNA

source_name: MeDIP AGS


title: CpG island methylation in AGS (2)


title: CpG island methylation in normal stomach

source_name: Sonicated normal stomach genomic DNA

tag: sample

value: pooled genomic DNA from the stomach of three healthy volunteers (Japanease, male, HP(-))

source_name: MeDIP normal stomach DNA


title: Recipient 4 diagnosed as ACR-predominant with superimposed RHC


title: CpG island methylation in HSC57

value: gastric cancer cell line, HSC57

source_name: MeDIP HSC57


title: CpG island methylation in HSC39

source_name: Sonicated HSC39 genomic DNA

value: gastric cancer cell line, HSC39

source_name: MeDIP HSC39


title: Latex-fruit allergic patient 4

status: Public on Jul 30 2009

city: Roma

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

institute: Università Cattolica del Sacro Cuore di Roma

description: Approximately 30-50% of individuals who are allergic to natural rubber latex (NRL) show an associated hypersensitivity to some plant-derived foods, especially freshly consumed fruits. This association of latex allergy and allergy to plant-derived foods is called latex-fruit syndrome. Even if the prevalence of both types of allergy has dramatically increased in the recent years, few information is available about the molecular mechanisms involved in the allergical process. The aim of this study was to identify genes that may be associated with the pathogenesis of allergy to latex and/or vegetable food. For this purpose, PBMCs isolated from patients with allergy to latex, fruit or latex and fruit, and from healthy controls were analyzed by the mean of microarray technology.

hyb_protocol: Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.

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

data_processing:
The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis

CEL file lost in computer crash

source_name: peripheral blood mononuclear cells

label_protocol: Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)

extract_protocol: RNA was isolated from PBMCs using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. A specific DNA digestion step on column was added to remove contaminating DNA.

tag: Patient 4 is a female (38years old), affected with the latex-fruit syndrome.

tag: The diagnosis of latex and fruit allergies were assessed as described for patients with allergy to fruit or latex.


title: Latex-fruit allergic patient 2

tag: Patient 2 is a female (39years old), allergic to latex and some vegetable food.


title: Latex-fruit allergic patient 3

tag: Patient 3 is a male (31years old), allergic to latex and some vegetable food.


title: Latex allergy patient 4

tag: Patient 4 is a female (71years old), allergic to latex.

tag: The diagnosis of latex allergy was assessed by skin prick test with standard latex extract and a 1-cm2 piece of surgical glove latex material (prick-by-prick method). Latex allergy was confirmed by specific provocation test. Furthermore, specific anti-natural rubber latex immunoglobulins IgE were measured by means of fluorescent enzyme immunoassay.


title: Latex allergy patient 6

tag: Patient 6 is a female (30years old), allergic to latex.


title: Latex-fruit allergic patient 1

tag: Patient 1 is a male (40years old), allergic to latex and some vegetable food.


title: Latex-fruit allergic patient 6

tag: Patient 6 is a female (46years old), affected with the latex-fruit syndrome.


title: Latex allergy patient 2

tag: Patient 1 is a male (35years old), allergic to latex.


title: Latex-fruit allergic patient 5

tag: Patient 5 is a male (19years old), suffering from the latex-fruit syndrome.


title: Latex allergy patient 3

tag: Patient 3 is a male (7years old), allergic to latex.


title: Latex allergy patient 5

tag: Patient 5 is a female (25years old), allergic to latex.


title: Latex allergy patient 1

tag: Patient 1 is a male (10years old), allergic to latex.


title: 211T-A3 vs 951T-F44

city: New York

first: Simon

last: Kang'a

address: 341 East 25th Street

department: Medical Parasitology

institute: New York University School of Medicine

description:
4 Replicates comparing T.parva SVSP transcription in cell lines 211T-A3 vs 951T-F44:
Biological replicate 1 of 2:  7681_211TAcy3_951TAcy5_A.txt
Flip-dye of biological replicate 1 of 2:  5922_211TAcy5_951TAcy3_A.txt
Biological replicate 2 of 2:  7682_211TBcy3_951TBcy5_A.txt
Flip-dye of biological replicate 2 of 2: 7678_211TBcy5_951TBcy3_A.txt

hyb_protocol: Microarray glass slides were prehybridized in 1% bovine serum albumin in 5x SSC, 0.1% SDS for 45 min at 42°C, washed with ddH2O and dried by centrifugation at 700 rpm for 10 min. Lyophilized dye-incorporated target aRNA samples were resuspended in 30 μl of filter sterilized hybridization solution consisting of 50% formamide, 5x SSC, 0.1% SDS, 0.6 µg/µl salmon sperm DNA, heat denatured, and 50 μl of a combined Cy3 and Cy5 aRNA pair applied onto an array by pipetting under a lifter slip (Erie Scientific, Portsmouth NH). The microarrays were placed in a sealed, humidified hybridization chamber (Corning Inc, Corning NY) and hybridized at 42°C for 16 to 20 hrs. Reverse dye labeling of samples was employed in separate experiments to account for any bias in dye coupling or emission efficiency of Cy dyes. Following incubation, slides were sequentially washed in 2x SSC, 0.1% SDS for 5 min at 42°C, 0.1x SSC, 0.1% SDS for 5 min at room temperature, 0.1x SSC for 5 min at room temperature, and in ddH2O for 2 min prior to drying by centrifugation at 700 rpm for 10 min.

scan_protocol: Microarray slides were scanned at 10 μm resolution using an Axon 4000B microarray scanner (Axon Instruments, Union City CA), and the data images saved as two independent 16-bit TIFF files corresponding to the Cy3 and Cy5 channels, respectively. The raw intensity data were extracted using Genepix 5.0 (Axon Instruments, Union City CA) software. Genepix automatically flags spots that are undetectable in either channel. In addition, we also flagged spots containing >30% saturated pixels in either channel or with a diameter of < 70 µm or if greater than 50% of the pixels within the spot were less than the median plus two standard deviations (SD) of background intensity.

data_processing: Data analysis was performed using the limma and marray packages from the Bioconductor site (www.bioconductor.org; (Dudoit et al., 2003).  Following data normalization, executed in two steps, first using within-slide loess normalization followed by quantile between–slide normalization, we employed linear models (Smyth, 2004) to rank the differentially expressed genes in order of evidence (i.e., P value) of differentially expressed genes. Briefly, the function lmFit in limma accepts a model matrix, which describes the experimental design and produces an output object of class MarrayLM, which stores the fitted model information for each gene. The fitted model object is further processed by the eBayes function to produce empirical Bayes test statistics for each gene, including moderated t-statistics, P-values and log-odds of differential expression (B).

organism: Theileria parva

source_name: 211T-A3 cell line

label_protocol: The Amino Allyl MessageAMPTM aRNA Kit (Ambion, Austin TX) was used for RNA amplification as per manufacturer’s instruction, starting with 5 μg of the DNA-free total RNA. This kit first prepares cDNA targets from the total RNA by reverse transcription followed by in vitro transcription with simultaneous incorporation of amino-allyl dUTP to produce amplified RNA (aRNA). The aRNA was purified using mini columns, quantified and stored at -80 oC until use. 15 μg of purified aRNA was mixed with either Cytidine (Cy) 3 or Cy5 NHS-ester (Amersham Pharmacia) in a 0.1 M sodium carbonate buffer (pH 9.3) for 1 hr in the dark at room temperature. The Cy3- and Cy5-labeled aRNA targets were purified to remove un-bound dye using either RNeasy Mini columns (Qiagen, Valencia, CA) or aRNA filter cartridges (Ambion, Austin Texas), and eluted in 100 μl of nuclease free ddH2O. The amounts of aRNA and incorporated Cy3 and Cy5 dyes were determined by measuring fluorescence at 600nm, 550 nm and 650 nm respectively, using the NanoDrop (NanoDrop Technologies, Wilmington DE). The dye incorporated aRNA were then lyophilized using a speedvac.

growth_protocol: The schizont-infected cell lines 211T_A3, 211B_A3 and 951T_F44 were established following infection of five animals, 211 and 951 with T. parva Marikebuni (see treatment protocol for details) using established methods Brown et al., 1973 (Brown, C.G., Stagg, D.A., Purnell, R.E., Kanhai, G.K. and Payne, R.C. (1973) Letter: Infection and transformation of bovine lymphoid cells in vitro by infective particles of Theileria parva. Nature, 245, 101-103.)

extract_protocol: Total RNA was extracted from the schizont-infected cell lines using the RNeasy Mini Kit according to the manufacturer’s protocol (QIAGEN). Each infected cell line was represented by two biological replicates. RNA was treated on-column with RNase-free DNase (QIAGEN) to remove contaminating genomic DNA. Conventional end-point PCRs were performed with T. parva actin (5’- CGGGATCCGACCCACAATGTGCCA-3’ and 5’-CGGAATTCACGGTGCACAATATT-3’) and PIM primers (5’-CGAAGCTTGAAAACATGAAGATCTTTCCC-3’ and 5’- TACGCGGCCGCTTAACAACAATCTTCGTTAATGCG-3’) using GoTaq DNA Polymerase (Promega) to detect contamination with genomic DNA. The RNA was considered ‘DNA-free’ when no amplification product was detectable after 30 cycles.

tag: consisting of CD4+ T cells originating from cattle 211 transformed by T. parva (Marikebuni) clone A3

tag: Bovine T cell cell line

source_name: 951T-F44 cell line

tag: consisting of CD4+ T cells derived from animal 951 transformed by T. parva (Marikebuni) clone F44


title: Fruit allergy patient 5

description: Approximately 30-50% of individuals who are allergic to natural rubber latex (NRL) show an associated hypersensitivity to some plant-derived foods, especially freshly consumed fruits. This association of latex allergy and allergy to plant-derived foods is called latex-fruit syndrome. Even if the prevalence of both types of allergy has dramatically increased in the recent years, few information is available about the molecular mechanisms involved in the allergical process. The aim of this study was to identify genes that  may be associated with the pathogenesis of allergy to latex and/or vegetable food. For this purpose, PBMCs isolated from patients with allergy to latex, fruit or latex and fruit, and from healthy controls were analyzed by the mean of microarray technology.

extract_protocol: RNA was isolated from PBMCs using RNeasy  mini kit (Qiagen) according to the manufacturer's instructions. A specific DNA digestion step on column was added to remove contaminating DNA.

tag: Patient 5 is a male (20years old), allergic to peanuts and apple.

tag: The diagnosis of allergy to the fruit was performed using standardized cross-reactive food allergens (ALK Abellò, Spain) and fresh food (prick-by-prick method). Furthermore, specific anti-cross-reactive vegetable food immunoglobulins IgE were measured by means of fluorescent enzyme immunoassay.


title: 211B-A3 vs 951T-F44

description:
4 Replicates comparing T.parva SVSP transcription in cell lines 211B-A3 vs 951T-F44:
Biological replicate 1 of 2:  5924_951TAcy3_211BAcy5_A.txt
Flip-dye of biological replicate 1 of 2:  5919_951TAcy5_211BAcy3_A.txt
Biological replicate 2 of 2:  7680_951TBcy3_211BBcy5_A.txt
Flip-dye of biological replicate 2 of 2: 5942_951TBcy5_211BBcy3_A.txt

source_name: 211B-A3 cell line

tag: consisting of B cells originating from cattle 211 transformed by T. parva (Marikebuni) clone A3

tag: Bovine B cell cell line


title: HEK293 cells overexpressing KLHL29 intronic transcript (antisense orientation), replicate number 1.

city: São Paulo

first: Eduardo

middle: M

last: Reis

address: Av. professor Lineu Prestes, 748

department: Departamento de Bioquímica

country: Brazil

institute: Instituto de Química da Universidade de São Paulo

description: RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) prior to labeling procedures.

hyb_protocol: Equal quantities of two cRNA samples (825 ng), derived from the same HEK293 transfection and labeled with Cy3 or Cy5, were mixed and hybridized to Whole Human Genome Oligo Microarray 4x44K (Agilent Technologies), strictly following the manufacturer protocol. Slides were washed and processed according to the Agilent 60-mer Oligo Microarray Processing protocol.

scan_protocol: Slides were scanned on a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA), using automatic photomultiplier tube voltage in each channel.

data_processing: Data were extracted and pre-processed using Agilent Feature Extraction (v9.5) software. Genes were defined as expressed when their intensity signals were above the average negative control value plus three standard deviations; a set of 153 negative controls (Agilent Technologies) was present on the array. Only genes that were detected as expressed/not expressed in all four replicates of the same HEK293 transfection were used in further analysis. The intensity values between experiments were normalized by the 40% trimmed mean intensity. Measuring the coefficient of variance among the replicates, we have observed that one array experiment out of the four from each construction had a considerably higher number of outlier points, and the entire replicate experiment was excluded from the analyses.

source_name: HEK293 cell line overexpressing KLHL29 intronic transcript.

label_protocol: Cy5- or Cy3-labeled cRNA was obtained from 400 ng total RNA, amplified by in vitro transcription with T7-RNA polymerase, using the Agilent Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies). Two HEK293 replicates for each construct were labeled with Cy5, and another two with Cy3. In vitro synthesized control mRNA (Agilent RNA Spike-In kit) was spiked into the amplification and labeling assay

growth_protocol: Cells were cultured in DMEM, supplemented with 10% fetal bovine serum, in a humidified incubator with 5% CO2, at 37ºC.

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen, Hilden, Germany), treated with DNAse for 30 min, and quantified by measurement of absorption on a NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: Cells were transfected with the linearized pBudCE4.1 expression vector containing KLHL29 intronic S or AS insert, using FuGENE 6 Transfection Reagent (Roche Applied Science, Indianopolis, IN). After transfection, zeocin-resistant cells were selected at 50 µg/ml zeocin for one month. The heterogeneous population of selected transfectants was propagated, and cells were used for RNA extraction. Biological replicates overexpressing S or AS KLHL29 intronic transcript were produced by thawing and propagation of four frozen HEK293 cell populations, derived from the same transfection.

tag: HEK293 cell line obtained from ATCC (http://www.atcc.org/). Organ

value: Fetal kidney. Cell Type transformed with adenovirus 5 DNA.


title: 211T-A3 vs 211B-A3

description:
4 Replicates comparing T.parva SVSP transcription in cell lines 211T-A3 vs 211B-A3:
Biological replicate 1 of 2:  5929_211TAcy3_211BAcy5_A.txt
Flip-dye of biological replicate 1 of 2:  5927_211TAcy5_211BAcy3_A.txt
Biological replicate 2 of 2:  5923_211TBcy3_211BBcy5_A.txt
Flip-dye of biological replicate 2 of 2: 7687_211TBcy5_211BBcy3_A.txt

tag: consisting of CD4+ T cells originating from cattle 211 transformed by T. parva (Marikebuni) clone A3,


title: Fruit allergy patient 4

tag: Patient 4 is a female (15 years old), allergic to peanuts.


title: HEK293 cells overexpressing KLHL29 intronic transcript (antisense orientation), replicate number 2.


title: Fruit allergy patient 3

tag: Patient 3 is a male (19 years old), allergic to apple and spinach.


title: HEK293 cells overexpressing KLHL29 intronic transcript (antisense orientation), replicate number 3.


title: Fruit allergy patient 2

tag: Patient 2 is a male (33 years old), allergic to peanut and peach.


title: Fruit allergy patient 1

tag: Patient 1 was a female (21 years old), allergic to arachide and apple.


title: healthy individual 2

tag: blood mononuclear cells (PBMCs) were isolated on a ficoll gradient from 5ml of blood harvested from a healthy control volunteer


title: healthy individual 3


title: healthy individual 4


title: HEK293 cells overexpressing KLHL29 intronic transcript (sense orientation), replicate number 4.

scan_protocol: RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) prior to labeling procedures.

source_name: HEK293 cell line overexpressing KLHL29 intronic transcript

label_protocol: Cy5- or Cy3-labeled cRNA was obtained from 400 ng total RNA, amplified by in vitro transcription with T7-RNA polymerase, using the Agilent Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies). Two HEK293 replicates for each construct were labeled with Cy5, and another two with Cy3. In vitro synthesized control mRNA (Agilent RNA Spike-In kit) was spiked into the amplification and labeling assay.


title: HEK293 cells overexpressing KLHL29 intronic transcript (antisense orientation), replicate number 4.


title: Pokkali root, salt-treated, biological replicate 3

status: Public on Jul 16 2009

city: Glen Osmond

first: Ute

last: Baumann

state: SA

address: Hartley Grove

department: Australian Centre for Plant Functional Genomics

country: Australia

institute: University of Adelaide

description: Pokkali salt-treated

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: The data were normalized using the Robust Multichip Average method of background correction, quantile normalisation, and summarisation of cell signal intensities (Irrizary et al., 2003).

organism: Oryza sativa Indica Group

source_name: root, Pokkali, salt-treated

label_protocol: Approx. 8 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Plants were grown in sand-filled tanks and irrigated with nutrient solution (for details see Walia et al (2005), Plant Physiol. 139:822-35) for 30 days.

extract_protocol: RNA was extracted using TRIzol and subsequently purified using an RNeasy spin column (Qiagen) and an on-column DNase treatment.

treatment_protocol: On day 22 after germination, salt treatment commenced by adding NaCl and CaCl2 (5:1 molar concentration) in two steps over a period of 3 days to the nutrient solution reservoir. Salinity in the treatment reservoir reached 7.4 dS/m. Plants were harvested on day 30.

tag: salt-tolerant


title: HEK293 cells overexpressing KLHL29 intronic transcript (sense orientation), replicate number 3.


title: HEK293 cells overexpressing KLHL29 intronic transcript (sense orientation), replicate number 2.


title: healthy individual 1


title: HEK293 cells overexpressing KLHL29 intronic transcript (sense orientation), replicate number 1.


title: Pokkali root, control, biological replicate 3

description: Pokkali control

source_name: root, Pokkali, control


title: Pokkali root, control, biological replicate 1

description: Pokkali control


title: Pokkali root, control, biological replicate 2

description: Pokkali control


title: Pokkali root, salt-treated, biological replicate 1

description: Pokkali salt-treated


title: Pokkali root, salt-treated, biological replicate 2

description: Pokkali salt-treated


title: IR63731 root, salt-treated, biological replicate 2

description: IR63731 salt-treated

source_name: root, IR63731, salt-treated


title: IR63731 root, control, biological replicate 3

description: IR63731 control

source_name: root, IR63731, control


title: IR29 root, salt-treated, biological replicate 3

description: IR29 salt-treated

source_name: root, IR29, salt-treated

tag: salt-intolerant


title: IR63731 root, control, biological replicate 2

description: IR63731 control


title: IR63731 root, salt-treated, biological replicate 1

description: IR63731 salt-treated


title: IR63731 root, salt-treated, biological replicate 3

description: IR63731 salt-treated


title: IR63731 root, control, biological replicate 1

description: IR63731 control


title: IR29 root, salt-treated, biological replicate 1

description: IR29 salt-treated


title: IR29 root, salt-treated, biological replicate 2

description: IR29 salt-treated