title: MseN_MseU15

description:
Cells (DSMZ5348) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mse cells were grown upto mid log phase after which the cells were subjected to U shock and harvested 15 min later. Biological repeats were done for both experimental conditions.

growth_protocol: Mse cells were inoculated into DSMZ sulfolobus medium (with 0.2 wt% Yeast extract) and challenged with 1 mM uranyl acetate in mid log phase at cell density of 1x108 cells/ml

treatment_protocol: Harvest of cells occurred for normal growth and for the U shock cultures at a cell density of 1 x 108 cells/ml

value: heterotrophic growth with 0.2 wt% Yeast extract

value: heterotrophic growth with 1 mM uranyl acetate shock at mid log phase, harvest after 15min


title: NoL_control01

status: Public on Sep 25 2012

type: RNA

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description:
Gene expression data from human clinical samples
xc01_NoL_Exp_U133p2

hyb_protocol: Hybridized to the Human Genome U133 Plus 2.0 microarray, after quality checking on GeneChips Test Arrays.

scan_protocol: Washing and scanning were done using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: The justRMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Labeling and hybridization were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc.).

extract_protocol: Total RNA from cells was extracted by homogenization in TRIZOL (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s protocol, then treated with RQ1 RNAse-Free DNase (Promega, Madison, USA) to eliminate genomic DNA contamination, and finally purified with RNeasy Minikit (Qiagen)

treatment_protocol: Human samples obtained from patients and healthy donors

tag: disease type

tag: disease subtype

tag: cell type

value: bone marrow mononuclear cells (BMNCs)


title: hSF P11

city: Greifswald

first: Joerg

last: Mostertz

address: F.-L.-Jahnstr 15

department: Competence Center Functional Genomics

country: Germany

institute: Greifswald University

hyb_protocol: Biotinylated sense-strand DNA was then hybridized on to the Affymetrix GeneChip® Human Gene 1.0 ST arrays, for 16 h. --> folllowed the protocols of the manufacturer

scan_protocol: The arrays were washed and stained using the Fluidics Station 450 and scanning was performed by Scanner 3000 7G (Affymetrix, High Wycombe, UK).--> folllowed the protocols of the manufacturer

data_processing:
Microarray data analysis was carried out by using the Rosetta Resolver® system for gene expression data analysis (Rosetta Biosoftware, Seattle, WA, USA). In brief, the raw signals of the probes were summarized using RMA thereby generating probe set specific signal intensities. Chips were normalized by using quantile normalization.
To compare RNA expression levels of genes in hCF, hSF and hTF, normalized expression signals of genes from corresponding samples were averaged and fold changes were calculated. To assess differences in mean signal intensities between experimental groups, ANOVA (analysis of variance, with Benjamini Hochberg test correction) and a post-hoc Scheffe test was performed. Rosetta Resolver ratio built statistics to correct for possible signal intensity bias were also considered. Only genes (1) an absolute fold change of ≥ 1.5 together with a Scheffe test p value ≤ 0.05 in at least one of the three pairwise comparisons hCF vs. hTF, hSF vs. hTF and hCF vs. hSF, resp., as well as (2) a ratio built p value ≤ 0.05 were deemed differentially expressed genes (DEG) and considered for further evaluation.

source_name: sclera fibroblasts (hSF)

label_protocol: For each sample, total RNA (200 ng) was reverse transcribed into cDNA,  subsequently amplified and in-vitro transcribed to cRNA. Sense-strand cDNA was generated from 10µg of purified cRNA using random primers, followed by subsequent fragmentation and labeling. Biotinylated sense-strand DNA was then hybridized on to the Affymetrix GeneChip® Human Gene 1.0 ST arrays, for 16 h. The arrays were washed and stained using the Fluidics Station 450 and scanning was performed by Scanner 3000 7G (Affymetrix, High Wycombe, UK). --> folllowed the protocols of the manufacturer

growth_protocol: Each tissue was cut into pieces of approximately 1 mm2 in size, placed in a 12 well cell culture plate in DMEM (Applichem, Darmstadt, Germany) with 50 U/ml of penicillin, 50 μg/ml streptomycin and 10% FCS (PAA, Cölbe, Germany), and incubated at 37° C under 5% CO2 at 95 % humidity. Growth medium was changed three times a week. When outgrowing primary fibroblasts reached a confluent monolayer, cells were trypsinized in 0.25% trypsin/EDTA (PAA, Cölbe, Germany) solution in phosphate buffered saline (PBS) and transferred to a 25 cm2 cell culture flasks (Greiner bio one, Frickenhausen, Germany).

extract_protocol: To the cells harvested in TRIzol®, chloroform (Baker, Deventer, Netherlands) was added (10 %), and cells were vigorously vortexed. The resulting homogenate was centrifuged at 10,000 g for 2 min and the aqueous supernatant was reextracted with TRIzol®/chloroform and centrifuged as above. The aqueous supernatant was adjusted to 35 % enthanol and applied onto an RNeasy column (QIAGEN, Hilden, Germany). After washing the column residual DNA was digested with DNase I (QIAGEN, Hilden, Germany) and after three wash steps total RNA was eluted with 100 µL of RNase free water followed by purification using the RNA Clean-Up and Concentration Micro Kit (Norgen Biotek Corp., Thorold, ON, Canada). RNA quantity and purity was measured at 260/280/230 nm with a Nanodrop photospectrometer (Thermo Scientific, Waltham, MA, USA) and RNA integrity was assessed by using the Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: no differing treatment  in terms of 'control-treatment' settings

value: sclera fibroblasts (hSF)


title: hTF P29

source_name: Tenon’s space fibroblasts (hTF)

value: Tenon’s space fibroblasts (hTF)


title: MprN_MprU3h

city: Raleigh

first: Arpan

last: Mukherjee

state: NC

address: 840 Main Campus Dr. Rm 3304

department: Chemical Engineering

country: USA

institute: North Carolina State University

description:
Cells (DSMZ10039) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mpr cells were grown upto mid log phase after which the cells were subjected to U shock and harvested 3 h later. Biological repeats were done for both experimental conditions. Mpr cDNA was hybridized onto Mse array as all genes in Mpr mapped to Mse gemome.

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC

scan_protocol: Images were aquired with a GenePix 4000B scanner (Molecular Devices) using 532 nm and 635 nm lasers simultaneously. An automatic photomultiplier (PMT) gain adjustment was used to balance the 532 nm and 635 nm channels prior to scanning the whole slide. A pixel size of 10 microns was selected for the image resolution. Separate images were saved for the 532 and 635 nm scans, and analyzed together using  GenePix Pro (v6.0) software.

data_processing: Signals for each channel were obtained using GenePix Pro (v6.0) using circular features and were background substrated using the median local intensity around the spot. Once all the slides were quantitated, data from the dye-flip was analyzed with JMP Genomics 5.0 (SAS, NC), normalized using Lowess then ANOVA to estimate the global fixed effects of dye & treatment and the random effects array and block followed by using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

organism: Metallosphaera sedula

source_name: Cell Pellet

label_protocol: Producing cDNA: In a sterile PCR tube add 20 ug RNA with 6 ug random primers. Then add nuclease free water so the volume is 10 uL. Incubate at 70 degree C for 10 min. Place tube on ice for 1 min. Add 8 uL of RT Master Mix (recipe below) to each tube and swirl to mix. Quick spin before incubation. RT Master Mix: 4uL 5X strand buffer, 1uL 0.1M DTT, 1uL dNTP mix (see below), 2uL superscript III Invitrogen. dNTP mix: 3uL dATP (100mM), 3uL dGTP (100mM), 3uL dCTP(100mM), 1.8uL dTTP (100mM), 2.4uL aa-dUTP(50mM) Ambion, 6.8uL nuclease free water. Incubate at 46 degree C for at least 3 hours. Hydrolyze RNA by adding 10uL 1N NaOH to each tube. To stop reaction add 10 uL 0.5M EDTA to each tube. Mix and incubate at 65 degree C for 15 min. Add 10uL 1N HCl to each tube neutralize reaction mix. Transfer samples into labeled tubes of appropriate sizes. Add five volumes PB Buffer (Qiagen) to each tube and mix well. Add 300 ul of RT product to a labeled Qiagen PCR cleanup column. Spin at 1,000 rpm for 15 sec., empty collection tube, and repeat until all of the solution has passed through the column. Complete wash One, add 750 ul of phosphate wash buffer (recipe below) to column and spin at 13,000 rpm for 1 min., empty tube. Complete wash Two, add 750 ul of phosphate wash buffer to column and spin at 13,000 rpm for 1 min., empty tube. Phosphate wash buffer: 0.1mL 1M KPO4( pH 8.5), 3.05mL autoclaved dH2O and 16.85mL 95% EtOH. Spin an additional 1 min. with the same collection tube and discard the flow through. Transfer to new 1.5 mL tube, add 60uL phosphate elution buffer to the membrane and incubate at room temp. for 1 min. Spin at 13,000 rpm. Phosphate elution buffer: 4mM KPO4. Repeat phosphate elution into same tube using 60uL. Fluorescent Labeling: Dry all RT samples completely in speed vac. Resuspend each dried sample cDNA in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0. Mix up and down with pipette for good mixing. Dissolve and mix thoroughlythe Cy™ dye to be used with 20uL of DMSO. Tpically Cye dyes contain four applications in each vial. Mix 4.5 uL of dye with prepared cDNA sample. Incubate in the dark for 2 hour @ R.T. Mix RT-PCR products with 35uL 100mM NaOAc PH 5.2 and mix by vortexing. Mix with 250uL Qiagen Buffer PB and filter through spin columns (13,000 rpm). Wash spin column with 750 uL of Buffer PE (Qiagen). Spin an additional 1 min. with the same collection tube and discard the flow through. Elute labeled cDNA 2 times with 30 uL of EB Buffer (Qiagen). Combine different labeled probes Speed vacuum sample until dry (not too dry, i.e. don’t leave in speed vacuum for over 1 hour). Combine different labeled probes and speed vacuum sample until dry. Resuspend samples in 29uL sterilized dH2O

growth_protocol: Mpr cells were inoculated into DSMZ sulfolobus medium (with 0.2 wt% Yeast extract) and challenged with 1 mM uranyl acetate in mid log phase at cell density of 1x108 cells/ml

extract_protocol: Cells were cooled to T < 10C using dry ice and ethanol mix and harvested by centrifugation (4800xg, 20 min at 4C) and pellets were stored at -80°C. Total RNA was isolated using a modified Trizol (Invitrogen) protocol in combination with an RNAeasy kit (Qiagen). RNA quality was determined by running it on 1% Agarose gel. The biological replicates were pooled prior to cDNA construction.

treatment_protocol: Harvest of cells occurred for the U shock and normal growth cultures at cell density of 1 x 108 cells/ml

tag: strain

tag: growth media

value: heterotrophic growth with 1 mM uranyl acetate shock at mid log phase, harvest after 3h


title: MseN_MseU3h

description:
Cells (DSMZ5348) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mse cells were grown upto mid log phase after which the cells were subjected to U shock and harvested 3 h later. Biological repeats were done for both experimental conditions.

organism: Metallosphaera sedula DSM 5348

growth_protocol: Mse cells were inoculated into DSMZ sulfolobus medium (with 0.2 wt% Yeast extract) and challenged with 1 mM uranyl acetate (mid log phase) at cell density of 1x108 cells/ml


title: MseU15_MseU60

description:
Cells (DSMZ5348) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mse cells were grown upto mid log phase after which the cells were subjected to U shock and harvested 15 min and 60 min later. Biological repeats were done for both experimental conditions.

treatment_protocol: Harvest of cells occurred for the U shock cultures at a cell density of 1 x 108 cells/ml 15 min and 60 min after U shock.

value: heterotrophic growth with 0.2 wt% Yeast extract with 1 mM uranyl acetate shock at mid log phase, harvest after 15 min

value: heterotrophic growth with 0.2 wt% Yeast extract with 1 mM uranyl acetate shock at mid log phase, harvest after 60 min


title: MseN_MseU60

description:
Cells (DSMZ5348) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mse cells were grown upto mid log phase after which the cells were subjected to U shock and harvested 60 min later. Biological repeats were done for both experimental conditions.

value: heterotrophic growth with 1 mM uranyl acetate shock, harvest after 60min


title: hSF P01


title: hCF P25

source_name: choroidea fibroblasts (hCF)

value: choroidea fibroblasts (hCF)


title: MDS_patient16_RARS

description:
Gene expression data from human clinical samples
p16_mdsRARS_Exp_U133p2

source_name: Low-risk MDS_RARS_BMNCs

value: Low-Risk Myelodysplastic Syndrome (MDS)

value: Refractory anemia with ringed sideroblasts (RARS)


title: A549_24hr_control for CNT-1

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression after 24hr in human alveolar epithelial cell  as cotrol for CNT-1

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_Sep09 and Grid: 026652_D_F_20110819). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data is the average of n=4. VALUE: Normalized signal intensity (log2)

source_name: Alveolar epithelial cell, 24hr, control for CNT-1, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Human alveolar epithelial cell line A549 were seeded into each well of a 96-well plate (Becton, Dickinson and Company, Franklin Lakes, NJ) and grown in the DMEM with 10% heat-inactivated fetal bovine serum medium for 24 hours.

extract_protocol: Total RNA was extracted from the cells using the QIAcube instrument (Qiagen, Tokyo, Japan) following the manufactures instructions. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Each medium were replaced by three kinds of single-wall carbon nanotubes (SWCNTs), CNT-1, CNT-2 or CNT-3 in a 10-fold dilution series. Cell concentrations at this point were approximately 1.3 x 10^5 cells/mL. The cultures were incubated for 24 or 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Alveolar epithelial cell

tag: cell line

tag: treatment

value: untreatment, control for CNT-1

tag: time


title: MprN_MseN

description:
Cells Mpr (DSMZ10039) and Mse(DSMZ5348) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mse and Mpr cells were grown upto mid log phase after which they were harvested at cell density of 1x108 cells/ml. Biological repeats were done for both experimental conditions. Mpr cDNA was hybridized on Mse Array as all genes in Mpr could be mapped to Mse genome

growth_protocol: Mpr and Mse cells were inoculated into DSMZ sulfolobus medium (with 0.2 wt% Yeast extract) and harvested at cell density of 1x108 cells/ml

treatment_protocol: Harvest of cells occurred for both species at cell density of 1 x 108 cells/ml

value: heterotrophic growth with 0.2 wt% yeast extract


title: MDS_patient17_RARS

description:
Gene expression data from human clinical samples
p17_mdsRARS_Exp_U133p2


title: A549_24hr_control for CNT-2

description: Gene expression after 24hr in human alveolar epithelial cell  as cotrol for CNT-2

source_name: Alveolar epithelial cell, 24hr, control for CNT-2, replicate 4

value: untreatment, control for CNT-2


title: hCF P19


title: MDS_patient15

description:
Gene expression data from human clinical samples
p15_mds_Exp_U133p2

source_name: Low-risk MDS_BMNCs


title: GS000000658-ASM

status: Public on Sep 26 2012

type: genomic

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Hybridization was performed under contract by Illumina, Inc. per manufacturer's protocol.

scan_protocol: Scanning were performed under contract by Illumina, Inc. per manufacturer's protocol.

data_processing:
Genotype and normalized signal intensity were computed by Illumina's Genome Studio, V2011.1. A modified version of the PICNIC (PMID 19837654) algorithm computed total copy number and LOH as described previously (PMID 22895193). http://www.illumina.com/documents/products/technotes/technote_topbot.pdf
Segmented_Absolute_Copy_Number; Segmented copy number for this SNP, where 2 is normal. PICNIC segmentation of data in the Absolute_Copy_Number column.
Genotype; Genotype as called by GenomeStudio
GC_SCORE; GenCall Score, genotyping quality from GenomeStudio
Absolute_Copy_Number; Copy number for this SNP, where 2 is normal. Scaling from tumor/normal ratio to absolute copy number takes into account the overall sample ploidy, as estimated by the PICNIC algorithm.
Segmented_Lesser_Parental_Copy_Number; PICNIC determines the copy number state for both parental alleles. For a normal autosome, one would expect one copy from each parent and the Segmented_Lesser_Parental_Copy_Number would then be 1. A value of zero represents LOH and values > 1 represent gain of both alleles.
Raw data file column X; Signal intensity for X allele, as provided by GenomeStudio. Scaled to the same mean across array strips/sections.
Raw data file column Y; Signal intensity for Y allele, as provided by GenomeStudio. Scaled to the same mean across array strips/sections.

molecule: genomic DNA

source_name: Cell line_adenocarcinoma_smoker

label_protocol: Labeling was performed under contract by Illumina, Inc. per manufacturer's protocol.

growth_protocol: Cells were grown in RPMI medium supplemented with 10% fetal calf serum. All cells were grown at 37°c and 5% CO2.

extract_protocol: Extraction was performed under contract by Illumina, Inc. per manufacturer's protocol.

treatment_protocol: No treatments were performed prior to these assays.

tag: cell line name

tag: other name

tag: atcc #

tag: disease state

value: non-small cell lung cancer

tag: tissue diagnosis

value: adenocarcinoma

tag: gender

value: female

tag: age

tag: race

value: Caucasian

tag: smoking history

value: smoker

tag: pack years

tag: cell line initiation date

tag: source of speciment

value: pleural effusion

tag: stage at initial evaluation

tag: death date

tag: initial diagnosis date


title: hCF P07

tag: cell type


title: MprN_MprU60

description:
Cells (DSMZ10039) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.2 wt% yeast extract
Mpr cells were grown upto mid log phase after which the cells were subjected to U shock and harvested 60 min later. Biological repeats were done for both experimental conditions . Mse array was used for Mpr cDNA hybridization since all probes in Mpr mapped to Mse genome

label: Cy3, Cy5

treatment_protocol: Harvest of cells occurred for normal growth and U shock cultures (after 60 min of shock) at a cell density of 1 x 108 cells/ml

tag: strain

tag: growth media

value: heterotrophic growth with 0.2 wt% Yeast extract

value: heterotrophic growth with 1 mM uranyl acetate shock, , harvest after 60min


title: hCF P03


title: hCF P20


title: MDS_patient10_RARS

description:
Gene expression data from human clinical samples
p10_mdsRARS_Exp_U133p2

tag: disease type

tag: disease subtype

value: bone marrow mononuclear cells (BMNCs)


title: MDS_patient13_RA

description:
Gene expression data from human clinical samples
p13_mdsRA_Exp_U133p2

source_name: Low-risk MDS_RA_BMNCs

value: Refractory anemia (RA)


title: MDS_patient12_RA

description:
Gene expression data from human clinical samples
p12_mdsRA_Exp_U133p2


title: MDS_patient14

description:
Gene expression data from human clinical samples
p14_mds_Exp_U133p2


title: MDS_patient11_RA

description:
Gene expression data from human clinical samples
p11_mdsRA_Exp_U133p2


title: MprAU_MseAU

description:
Cells (DSMZ 5348 & DSMZ10039) were grown at 70C in an orbital shaking oil bath at 90 rpm on DSMZ 88 medium (pH 2) with 0.1 wt% U3O8, with a headspace supplemented with CO2. Yeast extract was completed removed before the chemolithoautotrophic experiment.
Mse and Mpr cells growing under heterotrophic conditions were pelleted to remove organic component (yeast extract) and resuspended in fresh DSMZ Sulfolobus medium88. The cells were inoculated in 200 mls of DSMZ medium with 0.1 wt% U3O8 with CO2 supplementation in headspace, initial cell density was 1x108 cells/ml for each culture. Biological repeats were run for each condition (Mse on U3O8 and Mpr on U3O8). The cultures were harvested after 2 days of incubation and RNA was extracted. RNA was pooled from the biological repeats for each condition and reverse transcribed to cDNA. cDNA from each condition was labeled with both cy3 and cy5 dyes. Mse cy3 was mixed with Mprcy5 and hybridized onto Array1 and Msecy5 was mixed with Mprcy3 and hybridized onto Array2. This was done to account for dye effects. Mpr cDNA was also hybridized on Mse array as all genes in Mpr mapped to Mse genome.

growth_protocol: Mse and Mpr cells were inoculated into DSMZ sulfolobus medium without any yeast extract but supplemented with 0.1 wt% U3O8. The initial cell density was 1x108 cells/ml for both species, incubation was done in 70C oil bath with a shaking rate of 90 rpm.

extract_protocol: After incubation with U3O8,cells were cooled down to a temeperature < 10C from the normal growth temperature of 70C to stop transcription (using a mix of dry ice and 95% ethanol), cells were harvested by centrifugation (4800xg, 20 min at 4 oC). Cell pellets were stored at -80°C. Total RNA was isolated using a modified Trizol (Invitrogen) protocol in combination with an RNAeasy kit (Qiagen). RNA quality was determined with an Experion bioanalyzer (Bio-Rad). The biological replicates were pooled prior to cDNA construction.

treatment_protocol: Harvest of cells occurred 2 days after incubation with U3O8

tag: growth conditions

value: Chemolithoautrophy with Triuranium octaoxide


title: detached inflorescences at T24, biological rep2

city: Pisa

first: Alice

last: Trivellini

address: Viale delle Piagge

country: Italy

institute: University of Pisa

description: Gene expression data from 5 week old detached inflorescences after 24h of dark incubation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Genechips were scanned using the Affymetrix 7G Scanner

data_processing: The microarray results were the average of two independent temporally separated biological experiments. The results were analyzed using ArrayStar software, version 3 (DNASTAR®, Madison, WI, USA) as described below. Analyses  were based on two biological replicates per treatment (0 h vs. 24 h). Probe intensity data from the GeneChips were processed in a three-stage procedure using Robust Multichip Average (RMA) and Bolstad’s algorithms (Bolstad, 2004). For this analysis a pre-processing RMA background correction method, a quantile normalization (Irizarry et al., 2003) and RMA’s median polish summarization methods were used. Expression levels are based on log2 values.

organism: Arabidopsis thaliana

source_name: arabidopsis 24h dark detached inflorescence

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

growth_protocol: Seeds of A. thaliana ecotype Ler-0 were germinated and grown in a temperature-regulated growth chamber (20°C to 22°C, 4 AM:16-h light /8-h dark cycle, 100 μmol m-2 s-1 white light and 60% relative humidity)

extract_protocol: Total RNA was isolated from the inflorescences using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions, cleaned using an RNeasy Mini RNA isolation kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Inflorescences were harvested by excising at the junction between the peduncle and the pedicel of the lowest most unopened floret at the base of the inflorescence. Detached inflorescences were harvested at 3:00 PM (11 h into day period), and either immediately snap-frozen in liquid nitrogen and stored at -80°C, or placed at 21°C on blotting paper moistened with 50 mL of nanopure water inside a 2-L black plastic container (0h and 24h).

tag: time

tag: treatment

value: detached dark-held immature inflorescences

tag: ecotype

tag: tissue

value: inflorescences from the primary bolts


title: breast tumor part_MCB_rep1_1681

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0.

scan_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0 with Agilent scanner and Feature Extraction 6.0.

data_processing: Agilent Two-Color Microarray-Based Gene Expression Analysis, version 4.0.

source_name: Metaplastic carcinoma of breast

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0.

growth_protocol: The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit.

treatment_protocol: The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately before RNA extraction.

tag: er/pr/her status

tag: gender

tag: status

value: primary tumor

tag: tumor type

value: metaplastic carcinoma of breast (MCB)

source_name: Commercially available.

tag: reference

value: Stratagene's human common reference RNA


title: detached inflorescences at T0, biological rep2

description: Gene expression data from 5 week old detached inflorescences

source_name: arabidopsis 0h detached inflorescence

value: 0 h

tag: age


title: breast tumor part_MCB_rep1_1763


title: Salinity treated sample

city: Jinan

first: Yuguang

last: Song

state: Shandong

address: South Shanda Road 27

department: School of life sicense

country: China

institute: Shandong University

description: Gene expression data from a mixture of Soybean seedlings that stressed under salinity for different time piont

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000: Affymetrix, P/N 00-00212

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

organism: Glycine max

source_name: 14 days Soybean seedlings stressed under salinity for different time piont

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Seedlings of the soybean cultivar Williams 82 were grown in vermiculite under a 16h photoperiod at 25 ºC for 14 days

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

treatment_protocol: The seedlings were treated with 150 mM NaCl for 1h, 3h, 6h, 12h or 24h; RNA preps were pooled.  Mock treatments (ddH2O only) were included as a control; RNA preps were pooled.

tag: cultivar

value: Williams 82

tag: development stage

value: 14 days old seedling

tag: stress

value: salinity


title: breast tumor part_MCB_rep1_1715

value: female


title: breast tumor part_MCB_rep1_1779


title: MDS_patient09_RARS

description:
Gene expression data from human clinical samples
p09_mdsRARS_Exp_U133p2

value: Low-Risk Myelodysplastic Syndrome (MDS)

value: Refractory anemia with ringed sideroblasts (RARS)

tag: cell type


title: MDS_patient07

description:
Gene expression data from human clinical samples
p07_mds_Exp_U133p2

tag: disease type


title: MDS_patient08_RARS

description:
Gene expression data from human clinical samples
p08_mdsRARS_Exp_U133p2

tag: disease subtype


title: MDS_patient04_RARS

description:
Gene expression data from human clinical samples
p04_mdsRARS_Exp_U133p2


title: detached inflorescences at T0, biological rep1


title: MDS_patient06

description:
Gene expression data from human clinical samples
p06_mds_Exp_U133p2


title: detached inflorescences at T24, biological rep1


title: wild type mature anther, biological rep3

city: Nanjing

first: Zhao

middle: Zhi

last: Gang

state: Jiangsu

address: Tongwei-load

department: Institute of Crop Science

institute: Nanjing Agricultural University

description: Gene expression data from three-week-old wild type seedling

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Oryza sativa Japonica Group

source_name: Wild type mature anthers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Surface-sterilized seeds of the wild type and dao plants were soaked in water for 3 d and then placed in field for flower.

tag: genotype

value: wild type

value: mature anther

value: japonica variety

value: anthesis


title: MDS_patient03_RARS

description:
Gene expression data from human clinical samples
p03_mdsRARS_Exp_U133p2

value: bone marrow mononuclear cells (BMNCs)


title: dao mature anther, biological rep2

description: Gene expression data from three-week-old Epi-df seedling

source_name: dao mature anthers

value: dao mutant


title: MDS_patient02_RA

description:
Gene expression data from human clinical samples
p02_mdsRA_Exp_U133p2

value: Refractory anemia (RA)


title: MDS_patient05

description:
Gene expression data from human clinical samples
p05_mds_Exp_U133p2


title: dao mature anther, biological rep3


title: dao mature anther, biological rep1


title: wild type mature anther, biological rep2


title: breast tumor part_MCB_rep1_4357

value: primary tumor


title: norm2_5

status: Public on Sep 24 2012

city: Singapore

first: Joanna

middle: Dawn

last: Holbrook

address: 30 Medical Drive

department: Growth Development and Metabolism

country: Singapore

institute: Singapore Institute of Clinical Sciences

description: Group: normal2

hyb_protocol: Hybridization performance was assessed by means of 10 proprietary spike-in controls incorporated into the cRNA synthesis procedure. The labelled cRNA was then purified and hybridized onto Agilent SurePrint G3 Human Gene Expression (8 x 60 K) microarrays in a rotating (10 rpm) hybridization oven for 17 h at 65°C, after which they were washed and processed with proprietary buffers and solutions.

scan_protocol: The microarrays were then scanned at a resolution of 3 µm on an Agilent scanner using an extended dynamic range (PMT 10/100). The image data were processed using default values in feature extraction version 10.7.1.1 (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Agilent “.txt” files were outputted from the scanner and loaded into Arraystudio (Omicsoft).  Signal extraction was performed from the gProcessedSignal value incorporating background subtraction.  All expression values were log transformed.  All probes with expression levels less than two standard deviations above background were removed.  Values across replicate probes were averaged.    Data were normalised amongst samples using quantile normalisation.  Two samples with MAD scores <-5 were removed from the analysis.  Duplicate data for the same sample were averaged.

source_name: umbilical cord

label_protocol: Briefly, Cy3-labelled cRNA was generated from 100 ng of total RNA using the Quick Amp Labelling Kit (One-Color) (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: Umbilical cord tissue (300 mg) was first placed in a sterile Dispomix tube and homogenized for 55s for 3 cycles in 3 ml of Trizol using the Dispomix (Medic Tools, AG, Zug, Switzerland). After spinning down the debris, the supernatants were divided equally into three 2ml tubes. 200ul of chloroform were added to each tube, vortexed vigorously and centrifuged for 15min at 4˚C. The aqueous phase was carefully transferred to a new tube containing 1ul of linear acrylamide. An equal amount of isopropanol was added and mixed by inversion. After incubating at -20˚C overnight to precipitate the RNA, the pellet was obtained by centrifuging at 13,200 rpm for 10 min at 4˚C. The RNA pellet was washed twice in 70% (v/v) ethanol, air-dried and resuspended in RNase-free water. The isolated RNA was then purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany). On-column DNase digestion was carried out before the first wash step according to the manufacturer ’s instructions.  The purified RNA was then eluted in 30 µl of RNase-free water and stored at -80 °C. RNA concentration and purity were measured using a nanodrop ND-8000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA), and RNA integrity was determined using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Labchips (Agilent Technologies, Santa Clara, CA, USA).

value: umbilical cord

tag: group

tag: bw

tag: ga

value: Female

tag: ChIP


title: Mock treated sample

description: Gene expression data from a mixture of mock treated Soybean seedlings for different time piont

source_name: 14 days Soybean seedlings for mock treatment

value: control


title: MDS_patient01_RA

description:
Gene expression data from human clinical samples
p01_mdsRA_Exp_U133p2


title: norm2_1

description: Group: normal2

tag: tissue

value: Male


title: norm2_3

description: Group: normal2

tag: gender


title: norm2_6B

description: Group: normal2


title: norm1_7C

description: Group: normal1


title: norm1_7B

description: Group: normal1


title: norm2_6A

description: Group: normal2


title: norm2_2

description: Group: normal2


title: wild type mature anther, biological rep1


title: norm1_7D

description: Group: normal1


title: norm2_7

description: Group: normal2


title: norm2_4

description: Group: normal2


title: norm1_3

description: Group: normal1


title: norm1_5

description: Group: normal1


title: norm1_2

description: Group: normal1


title: norm1_7A

description: Group: normal1


title: norm1_1

description: Group: normal1


title: Control-non-(VPA)-stimulated_rep3

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Non-normalized data: GenomeStudio-computed raw signal intensity.
Normalized data: GeneSpring GX 11.5-computed quantile-normalization was applied on log2-transformed data

organism: Mus musculus

source_name: 24h cultured LSK cells with growth factors only

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s specifications starting with 100 ng total RNA.

growth_protocol: Freshly isolated hematopoietic stem/progenitor cells, defined by L-S+K+ phenotype, were stimulated for 24h in the presence or in the absence of 1mM valproic acid (VPA), in a liquid medium supplemented with fetal calf serum, murine stem cell factor and recombinant murine granulocyte/macrophage-colony stimulating factor. After 24h culture the cells were collected in RNA lysis buffer (Qiagen) for gene expression studies.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol.

tag: strain

value: Bone Marrow

value: hematopoietic stem/progenitor cell (HSPC)

tag: cell phenotype

value: L-S+K+

tag: agent


title: LBW_6

description: Group: LBW

value: LBW


title: norm1_4

description: Group: normal1


title: Control-non-(VPA)-stimulated_rep1


title: Valproic_acid-stimulated_rep2

source_name: 24h cultured LSK cells with Valproic Acid

value: Valproic Acid


title: LBW_3B

description: Group: LBW


title: Control-non-(VPA)-stimulated_rep2


title: HBW_7

description: Group: HBW

value: HBW


title: LBW_8B

description: Group: LBW


title: LBW_4

description: Group: LBW


title: HBW_3

description: Group: HBW


title: HBW_8

description: Group: HBW


title: LBW_1

description: Group: LBW


title: HBW_5

description: Group: HBW


title: HBW_2B

description: Group: HBW


title: HBW_2A

description: Group: HBW


title: LBW_5

description: Group: LBW


title: Valproic_acid-stimulated_rep3


title: HBW_1

description: Group: HBW


title: GM12878 Negative Control RNA

city: Albany

first: Frank

last: Doyle

state: NY

address: 257 Fuller Rd

department: Nanobiology

institute: UAlbany CNSE

description: GM12878 T7 RIP RNA Rep 1-3

hyb_protocol: Affymetrix Standard

scan_protocol: Affymetrix GeneChipScanner 30007G using Affymetrix Gene Chip Command Console v3.1

data_processing:
Further descriptions can be found at http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=296267047&c=chr18&g=wgEncodeSunyAlbanyTiling#TRACK_HTML
CEL file replicates were combined to generate broadpeak (bed6+3) and chp files (chp file metadata is incorrect and does not show each replicate due to a presumed Tiling Array Software (TAS) bug).

source_name: GM12878 T7 control RIP RNA

label_protocol: Affymetrix WT standard

tag: cell line

tag: antibody target


title: GM12878 PABPC1 RIP RNA

description: GM12878 PABP RIP RNA Rep 1-3

source_name: GM12878 PABP RIP RNA

value: PABP


title: GM12878 ELAVL1 RIP RNA

description: GM12878 ELAVL1 RIP RNA Rep 1-3

source_name: GM12878 ELAVL1 RIP RNA


title: K562 PABPC1 RIP RNA

description: K562 PABP RIP RNA Rep 1-3

source_name: K562 PABP RIP RNA


title: HBW_4

description: Group: HBW


title: K562 ELAVL1 RIP RNA

description: K562 ELAVL1 RIP RNA Rep 1-3

source_name: K562 ELAVL1 RIP RNA


title: GM12878 Input(Total) RNA

description: GM12878 input RNA Rep 1-3

source_name: GM12878 RIP input RNA (total)


title: K562 Negative Control RNA

description: K562 T7 RIP RNA Rep 1-3

source_name: K562 T7 control RIP RNA


title: LBW_3C

description: Group: LBW


title: LBW_7

description: Group: LBW


title: Valproic_acid-stimulated_rep1


title: LBW_2

description: Group: LBW


title: LBW_3A

description: Group: LBW


title: HBW_6

description: Group: HBW


title: HBW_2C

description: Group: HBW


title: K562 Input(Total) RNA

description: K562 input RNA Rep 1-3

source_name: K562 RIP input RNA (total)


title: iPSC_donor5 cloneB

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: standard Affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT; version apt-1.12.0) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: iPSC reprogrammed from MSC

label_protocol: standard Affymetrix protocol

growth_protocol: Established iPSC colonies were maintained on MEFs in DMEM/F12 medium supplemented with Glutamax, 20% knockout serum replacer, 1% NAA, 0.1 mM βME and 50 ng/ml bFGF.

extract_protocol: RNeasy kit (Quiagen)

tag: tissue origin

value: bone marrow

tag: cell type origin

value: mesenchymal stromal cells (MSC)

value: induced pluripotent stem cells (iPSC)

tag: passage


title: MESENTERIC_SP467L_3

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

description:
MESENTERIC_SP467L_3.CEL
mesenteric artery from one mouse, not pooled

hyb_protocol: The hybridization procedures were performed at the University of Iowa DNA Core facility using protocols recommended by the manufacturer (Affymetrix).

scan_protocol: The scanning of the arrays was performed at the University of Iowa DNA Core facility using protocols recommended by the manufacturer (Affymetrix).

data_processing:
Affymetrix Power Tools (APT, release apt-1.12.0) was used to process the microarray data files (i.e., *.CEL files) and to normalize the data according to the RMA (robust multiarray average) algorithm to generate gene-level (i.e., transcript) signal values.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: mesenteric artery from transgenic mouse containing dominant negative PPAR gamma (P467L mutation) targeted to vascular smooth muscle

label_protocol: A kit (NuGen, San Carlos, CA) was used to implement a two-step amplification procedure starting with approximately 50 ng of total RNA to generate biotin-labeled RNA fragments.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) and was purified using a column-based kit (Purelink RNA, Invitrogen, Carlsbad, CA) following the manufacturer’s protocol.

value: mesenteric artery

value: PPAR gamma P467L


title: MESENTERIC_SP467L_2

description:
MESENTERIC_SP467L_2.CEL
mesenteric artery from one mouse, not pooled


title: 19 rep1

city: Rehovot

first: Gilad

last: Landan

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Microarrays were scanned using GeneChip scanner 3000 7G

data_processing: Data were log2 transformed and normalized using dChip model-based expression (5th percentile, omitting Affymetrix control probes at filtration/comparison, with one of the duplicate arrays for passage 19 serving as baseline).

source_name: WI-38 cell culture

growth_protocol: Cells were grown in MEM supplemented with 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine, and antibiotics. 100,000 cells were seeded in a 10cm plate during each weekly passaging.

extract_protocol: RNA was extracted with TRI reagent (Molecular Research Center Inc.) according to the manufacturer’s instructions, in biological duplicates. Purified RNA was reverse-transcribed, amplified, and labeled with Affymetrix GeneChip whole transcript sense target labeling kit. Labeled cDNA was analyzed using Affymetrix human Gene ST 1.0 microarrays, according to the manufacturer's instructions.

tag: cell type

value: WI-38 primary human lung fibroblasts


title: A58 rep2

label_protocol: Affymetrix GeneChip whole transcript sense target labeling kit

value: hTERT-immortalized WI-38 primary human lung fibroblasts


title: MESENTERIC_NT_4

description:
MESENTERIC_NT_4.CEL
mesenteric artery from one mouse, not pooled

source_name: mesenteric artery from non-transgenic littermate

value: non-transgenic


title: 19 rep2


title: A67 rep2


title: MESENTERIC_SP467L_1

description:
MESENTERIC_SP467L_1.CEL
mesenteric artery from one mouse, not pooled


title: A58 rep1


title: iPSC_donor2 cloneA


title: iPSC_donor5 cloneA


title: A39 rep1


title: A67 rep1


title: iPSC_donor4 cloneA


title: A95 rep1


title: iPSC_donor4 cloneB


title: MESENTERIC_NT_2

description:
MESENTERIC_NT_2.CEL
mesenteric artery from one mouse, not pooled


title: MESENTERIC_NT_1

description:
MESENTERIC_NT_1.CEL
mesenteric artery from one mouse, not pooled


title: iPSC_donor2 cloneB


title: MESENTERIC_NT_3

description:
MESENTERIC_NT_3.CEL
mesenteric artery from one mouse, not pooled


title: iPSC_donor4 cloneC


title: iPSC_donor2 cloneC


title: A50 rep2


title: B96 rep2


title: A39 rep2


title: A95 rep2


title: B96 rep1


title: A50 rep1


title: LBW_8A

description: Group: LBW

value: umbilical cord

value: Female


title: V9_vehicle_control

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

description: Gene expression data from whole kidneys after 7 days treatment with vehicle

hyb_protocol: cDNA were hybridized for 18 hr at 45C on GeneChip Human ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 7G.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

organism: Rattus norvegicus

label_protocol: Total RNA (200 ng per sample) was amplified and labeled using the Applause WT-Amp ST and Encore Biotin Module kit (NuGEN, San Carlos, CA)

extract_protocol: Qiagen RNAeasy kit were used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Male Wistar rats received sirolimus or vehicle for 7 days (1.5mg/kg) and were placed in individual metabolic cages for eight days allowing a 24 hour adaption period to the metabolic cage environment. At the end of the experiments rats were anesthetized by inhalation of Isoflurane/air and blood samples and kidneys were collected.

value: Wistar

value: male

value: whole kidney


title: S10_sirolimus 1.5mg/kg_treated

description: Gene expression data from whole kidney after 7 days treatment with sirolimus 1.5mg/kg

source_name: sirolimus 1.5mg/kg_7d_treated


title: V10_vehicle_control


title: V8_vehicle_control


title: HaCaT_ZNF750i_ biological rep2

city: Beer Sheva

first: Idan

last: Cohen

address: Ben-Gurion Boulevard

department: Dept. of Molecular Genetics and Virology

institute: Ben Gurion University

description: Gene expression data from HaCaT cells at day 12 of calcium induced in-vitro differentiation

hyb_protocol: Following fragmentation, 5 µg of biotinylated sense strand cDNA were hybridized for 16 hr at 45C on Human gene 1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station450.

scan_protocol: GeneChips were scanned using the Affymetrix G7 scanner.

data_processing: RMA, using Partek genomic suite.

source_name: HaCaT cells at day 12 of in-vitro calcium induced differentiation

label_protocol: Biotinylated sense strand cDNA were prepared according to Affymetrix protocol from 300 ngtotal RNA (GeneChip® Whole Transcript (WT) SenseTarget Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: HaCaT cells (Boukamp et al., 1988) were grown in DMEM (0.06 mM CaCl2) till 90-100% confluence, then media was changed to DMEM (1.8mM CaCl2) for 12 days to induce differentiation.

extract_protocol: Total RNA was isolated using TRI REAGENT (Molecular Research Center, Inc.) and subjected to DNaseI treatment (New England Bio-Labs), followed by Qiagen Rneasy kit cleanup.

treatment_protocol: shRNA knock down

tag: shRNA transfection

value: ZNF750 gene silencing


title: HaCaT_Control_ biological rep2

value: HaCaT cells at day 12 of calcium induced in-vitro differentiation

value: control


title: HaCaT_ZNF750i_ biological rep3


title: HaCaT_ZNF750i_ biological rep1


title: T21_2

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description: CD43+/41+/235+ progenitors generated from T21 iPSC line, biological rep2

hyb_protocol: cRNA was hybridized according to the Affymetrix GeneChip Technical Manual.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The raw intensity values from CEL files were processed using RMA method implemented by the Bioconductor R oligo package. RMA processing resulted in 33,297 probesets, that were then mapped to 19,392 RefSeq genes. In cases where several probesets mapped to one RefSeq gene the expression values were averaged to obtain one value per gene.

source_name: CD43+/41+/235+ progenitors generated from Trisomy 21 iPSCs

label_protocol: Biotinylated cRNA was prepared according to manufacturer instructions for the NuGEN WT-Ovation Pico RNA kt .

growth_protocol: For hematopoietic differentiation, embryoid bodies were generated by culturing small aggregates of feeder-depleted iPSCs in 6 well low-cluster plates in StemPro-34 (Invitrogen) media supplemented with glutamine, ascorbic acid, transferrin, monothioglycerol, and with the following cytokines: bone morphogenic protein 4 (BMP4) 25 ng/ml and vascular endothelial growth factor (VEGF) 50 ng/ml on days 0-2; BMP4 25 ng/ml, VEGF 50 ng/ml, stem cell factor (SCF) 50 ng/ml, thrombopoietin (TPO) 50 ng/ml, Flt3 ligand (FLT3) 50 ng/ml, and fibroblast growth factor (bFGF) 20 ng/ml on days 2-4; VEGF 50 ng/ml, SCF 50 ng/ml, TPO 50 ng/ml, FLT3 50 ng/ml, and bFGF 20 ng/ml on days 4-8.

extract_protocol: Total RNA was extracted with the Qiagen miRneasy kit per manufacturer's instructions.

treatment_protocol: Embryoid bodies were dissociated to single cells by a 1 hour incubation with 0.2% Collagenase B containing 20% serum followed by a 2 minute incubation with trypsin (0.05% trypsin-EDTA) at 37ºC. After enzymatic treatment, 1 ml serum was added and the embryoid bodies were disaggregated to single cells by multiple passages through a 20-gauge needle. Cells were stained with anti-human CD41 and CD235, and flow cytometrically sorted for the double positive population to extract RNA.


title: HaCaT_Control_ biological rep3


title: S7_sirolimus 1.5mg/kg_treated


title: V7_vehicle_control


title: S8_sirolimus 1.5mg/kg_treated


title: T21_4

description: CD43+/41+/235+ progenitors generated from T21 iPSC line, biological rep4

value: CD43+/41+/235+ progenitors generated from Trisomy 21 iPSCs


title: S9_sirolimus 1.5mg/kg_treated


title: WT_3

description: CD43+/41+/235+ progenitors generated from euploid iPSC line, biological rep3

source_name: CD43+/41+/235+ progenitors generated from euploid iPSCs


title: BoneMarrow_5FU_Day4_Animal_3_Rep2

city: New Haven

first: Brian

last: Adams

state: CT

address: 10 Amistad Street; Rm214K

department: Genetics

institute: Yale University

description:
2nd-BA8
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.

hyb_protocol: hyb_1: 1 µg RNA was  directly hybridized to miRNA capture oligos in a 96 well plate format for 1.5hrs at 35°C.  Samples were also spiked with control FPCM oligos as a pre-hybridization control.  Wells were washed in 2xSSC and prepared for ligation and labeling hyb_2:Samples were PCR amplified using the ThermoPCR system from NEB where one primer was biotin-conjugated.  Biotin-labeled PCR products were spiked with post hybridization control oligos in 1.5X TMAX and hybridized to a mixture of carboxylated MagPlex microspheres (Luminex), where each oligo coupled-bead has a unique color combination (referred to as region by the manufacturer).   Hybridizations  occured at 95°C for 10 min and incubating at 53°C overnight.

scan_protocol: Raw barcode signals from each miRNA construct were acquired on a Luminex-FlexMap3D instrument.  The acquired median phycoerythrin fluorescence intensity values were then used in subsequent data analysis.

data_processing: Profiling data was log2 transformed and normalized assuming equal total miRNA expression across samples.  MiRNAs with maximum expression across all samples more than 7.25 on log2 data were considered passing expression threshold.  Differential miRNA expression was analyzed by student’s t-test and then calculated for false discovery rate using the Benjamini and Hochberg method.

source_name: BoneMarrow, 5FU, Day4 Post

label_protocol:
pre-PCR processing protocol: 3' and 5' adaptors were sequentially ligated to RNA samples for subsequent PCR detection.  RNA was reverse-transcribed using a primer specific to the 3' adaptor and M-MLV reverse transcriptase (Promega) according to the manufacturers instructions
Beads coupled to Biotin-labeled PCR products were washed in 1X TMAC, incubated with 10 µg/ml SA-PE (Invitrogen) at 50°C, and washed with 1X TMAC.

extract_protocol:
Total RNA was extracted from whole bone marrow samples using Trizol.  Bone marrow was pharmlyse treated to remove RBC fraction before RNA isolation.
pre-PCR_processing_protocol: 3' and 5' adaptors were sequentially ligated to RNA samples for subsequent PCR detection.  RNA was reverse-transcribed using a primer specific to the 3' adaptor and M-MLV reverse transcriptase (Promega) according to the manufacturers instructions

treatment_protocol: 6 week old female c57bl/6 mice were split into two arms within this study.  Arm 1 was left as an untreated cohort of 5 animals, and the second Arm 2 was treated ip with 5-FU (150mg/kg).  After 4 days of treatment RNA was extracted.

value: Bone Marrow

tag: age

value: 6wk Adult


title: BoneMarrow_5FU_Day4_Animal_2_Rep2

description:
2nd-BA7
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.


title: HaCaT_Control_ biological rep1


title: BoneMarrow_5FU_Day4_Animal_1_Rep2

description:
2nd-BA6
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.


title: BoneMarrow_5FU_Day4_Animal_1_Rep1

description:
1st-BA6
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.


title: WT_2

description: CD43+/41+/235+ progenitors generated from euploid iPSC line, biological rep2

value: CD43+/41+/235+ progenitors generated from euploid iPSCs


title: Neuroblastoma, #105

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description:
inss-st-1
itcc0156

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: gn

label_protocol: 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: ganglioneuroma


title: T21_1

description: CD43+/41+/235+ progenitors generated from T21 iPSC line, biological rep1


title: WT_1

description: CD43+/41+/235+ progenitors generated from euploid iPSC line, biological rep1


title: BoneMarrow_Untreated_Day4_Animal_5_Rep1

description:
1st-BA5
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.

source_name: BoneMarrow, Untreated, Day4


title: MSC donor4 P12

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

source_name: mesenchymal stromal cells (MSC)

label_protocol: standard Illumina labeling protocol

extract_protocol: Genomic DNA extraction

treatment_protocol: MSC were isolated from tibia plateau of patients undergoing orthopaedic surgery. All samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (Permit number: EK128/09). MSC were culture-expanded in standard medium consisting of DMEM (PAA; 1g/L glucose) supplemented with glutamine (PAA), penicillin/streptomycin (PAA) and 10% human platelet lysate (hPL).

tag: donor

value: mesenchymal stromal cells (MSC)


title: Neuroblastoma, #107

description:
inss-st-2
itcc0186

source_name: gnb

value: ganglioneuroblastoma


title: Neuroblastoma, #108

description:
inss-st-1
itcc0222


title: Neuroblastoma, #106

description:
inss-st-3
itcc0166


title: Neuroblastoma, #110

description:
inss-st-4
itcc0363


title: MSC donor6 P14


title: BoneMarrow_Untreated_Day4_Animal_4_Rep1

description:
1st-BA4
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.


title: Neuroblastoma, #104

description:
inss-st-1
itcc0153


title: MSC donor4 P3 15 Gy

growth_protocol: MSC were treated with a blood product irradiator (model IBL-437, Institute for transfusion medicine, Aachen) with 15Gy. DNAm profiles were analyzed 7 days after treatment.

tag: irradiation


title: BoneMarrow_Untreated_Day4_Animal_3_Rep1

description:
1st-BA3
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.


title: MSC donor5 P3 15 Gy


title: MSC donor11 P3 Gy


title: MSC donor5 P16


title: BoneMarrow_Untreated_Day4_Animal_2_Rep1

description:
1st-BA2
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.


title: Neuroblastoma, #109

description:
inss-st-2
itcc0289


title: Neuroblastoma, #103

description:
inss-st-2
itcc0142


title: MSC donor6 P3 15 Gy


title: Neuroblastoma, #101

description:
inss-st-1
itcc0139


title: Neuroblastoma, #102

description:
inss-st-1
itcc0140


title: M. luteus 24hr rep 3

city: Emeryville

first: Ee-Been

last: Goh

address: 5885 Hollis St, 4th Floor

department: Fuels Synthesis Division

institute: Joint BioEnergy Institute

description: This sample is of Micrococcus luteus NCTC2665 at 24 hrs. It is the third of three biological replicates of the test cultures used in this experiment, each from different starter cultures.

hyb_protocol: Hybridization was performed at 50ºC for 20-24 hrs following NimbleGen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed on a Axon GenePix 4200A scanner following NimbleGen's standard operating protocol. See www.nimblegen.com.

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

label: Alex fluor 555

organism: Micrococcus luteus NCTC 2665

label_protocol: Labeling was carried out by reverse transcription of 10 µg of total RNA primed with 5 µg of random hexamers (Roche, Germany) were reverse transcribed using the SuperScript Indirect cDNA labeling kit (Invitrogen). Alexa Fluor 555 dyes (Invitrogen) were then incorporated into amino-allyl-dUTP-labeled cDNA, the fluorescently labeled cDNA was purified with the QiaQuick PCR purification kit (Qiagen) and dried under vacuum (Vacufuge Speed Vac, Eppendorf).

growth_protocol: 15M. l tryptic soy broth media in 30M. l glass conical tubes were seeded with overnight M. luteus cultures at starting OD600 of 0.03 and grown at 30°C with 200rpm agitation.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA concentration was determined on a Nanodrop ND-1000 (Thermo Scientific) and RNA quality was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: Control cultures were harvested after 12 hours and test cultures were harvested after 24 hours for RNA extraction.

tag: time

tag: growth phase

value: stationary


title: Neuroblastoma, #100

description:
inss-st-4
itcc0131

tag: tissue


title: Neuroblastoma, #98

description:
inss-st-2
itcc0124


title: Neuroblastoma, #97

description:
inss-st-1
itcc0116


title: M. luteus 24hr rep 2

description: This sample is of Micrococcus luteus NCTC2665 at 24 hrs. It is the second of three biological replicates of the test cultures used in this experiment, each from different starter cultures.


title: ESC HES2

source_name: embryonic stem cells (ESC)

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Genomic DNA was isolated from 10(6) cells using the Qiagen DNA Blood Midi Kit.

value: ESC


title: MSC donor11 P14 GFP

growth_protocol: The hTERT sequence was cloned into the retroviral expression vector pMIG (pMSCV-IRES-GFP) (Addgene plasmid 9044, Addgene, Cambridge, MA, USA) via EcoRI. For control we used the corresponding empty pMIG vector (IRES-GFP). Transfected MSC were culture expanded in parallel until entering the senescent state.


title: ESC H1


title: Neuroblastoma, #99

description:
inss-st-1
itcc0128


title: ESC H9


title: M. luteus 24hr rep 1

description: This sample is of Micrococcus luteus NCTC2665 at 24 hrs. It is the first of three biological replicates of the test cultures used in this experiment, each from different starter cultures.


title: MSC donor2 P7


title: M. luteus 12hr rep 3

description: This sample is of Micrococcus luteus NCTC2665 at 12 hrs. It is the third of three biological replicates of the control cultures used in this experiment, each from different starter cultures.

value: late exponential


title: iP-MSC donor5 cloneB

source_name: bone marrow-derived MSC (iP-MSC)

growth_protocol: MSC from three donors (passage 3) were infected on two consecutive days with equal amounts of pMXs based retroviruses (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4 and c-MYC genes. On day 3, medium was changed to high glucose DMEM (Gibco), 20% FCS, 1% nonessential amino acids (NAA), 1x penicillin/streptomycin, 1x L-glutamine, 0.1 mM β-mercaptoethanol (βME) and 50 ng/ml basic fibroblast growth factor (bFGF) (Peprotech, Hamburg, Germany). On day 6 the cells were plated on gelatin-coated dishes containing irradiated CF1 murine embryonic fibroblasts (MEFs), and on day 7 the culture medium was supplemented with 20 μg/ml vitamin C (Sigma) and 1mM valproic acid (Sigma). Between days 21–30 the ESC-like colonies were observed and mechanically isolated. Established iP-MSC were maintained on MEFs in DMEM/F12 medium supplemented with Glutamax, 20% knockout serum replacer, 1% NAA, 0.1 mM βME and 50 ng/ml bFGF. Cells were passaged by manual dissection of cell clusters every 5-6 days.

value: donor5, cloneB

value: iPSC


title: MSC donor11 P14 hTERT


title: M. luteus 12hr rep 2

description: This sample is of Micrococcus luteus NCTC2665 at 12 hrs. It is the second of three biological replicates of the control cultures used in this experiment, each from different starter cultures.


title: M. luteus 12hr rep 1

description: This sample is of Micrococcus luteus NCTC2665 at 12 hrs. It is the first of three biological replicates of the control cultures used in this experiment, each from different starter cultures.


title: BoneMarrow_Untreated_Day4_Animal_1_Rep1

description:
1st-BA1
In total RNA from 8 animals were isolated and processed for miRNA profiling, profiling was run in two separate batches and only samples that passed QC were further analyzed, as noted  samples labeled "1st" and "2nd-" originated from the 1st and 2nd batches respectively and are not considered biological replicates.

tag: gender

value: Female


title: iP-MSC donor5 cloneA

value: donor5, cloneA


title: iP-MSC donor4 cloneB

value: donor4, cloneB


title: iP-MSC donor2 cloneB

value: donor2, cloneB


title: Neuroblastoma, #95

description:
inss-st-2
itcc0113


title: MSC donor11

value: MSC


title: iP-MSC donor4 cloneA

value: donor4, cloneA


title: Neuroblastoma, #92

description:
inss-st-2
itcc0108


title: GFPMYC positive GC B cells, Biological replicate 7

city: New York

first: David

last: Dominguez-Sola

address: 1130 Saint Nicholas Ave, ICRC Room 507

department: Institute for Cancer Genetics

institute: Columbia University

description:
Sample name: GFPMYCpos_1G
Gene expression data from MYC positive GC B cell subpopulation, paired to 2G

hyb_protocol: 3.75 micrograms of fragmented, Biotin-labeled amplified cDNA was hybridized using the Affymetrix HWS kit, Standard Array (49 Format), using NuGEN's Encore Biotin kit instructions. Samples were hybridized for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G, connected to Command Console software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500

label: Biotin

source_name: Spleen, SRBC immunized mouse, 12 days post-immunization

label_protocol: Encore Biotin Labeling Kit (NuGEN). Biotin labeled and fragmented amplified cDNA was prepared following manufacturer's instructions.

growth_protocol: 8 week old GFPMYC/C57BL6 mouse, Sheep Red Blood Cell (SRBC) immunization, 12 days

extract_protocol: Sorted GC B cells. Total RNA isolated using Nucleospin RNA XS kit (Macherey Nagel). cDNA was amplified from 5-20 ng of total RNA using the Ovation RNA amplification kit (NuGEN), following manufacturer's instructions.

treatment_protocol: B cell fraction was isolated using magnetic beads (B cell isolation kit, Miltenyi). GC B cells (PNAhi/CD95hi) were sorted based on their relative GFP(=MYC) expression in two pools (MYC+, MYC-) for each mouse

value: Spleen

value: B lymphocytes

tag: gfpmyc status

value: positive


title: GFPMYC positive GC B cells, Biological replicate 5

description:
Sample name: GFPMYCpos_11G
Gene expression data from MYC positive GC B cell subpopulation, paired to 12G


title: Neuroblastoma, #90

description:
inss-st-4
itcc0014

value: ganglioneuroma


title: Neuroblastoma, #89

description:
inss-st-1
itcc0012


title: Neuroblastoma, #91

description:
inss-st-1
itcc0029


title: GFPMYC positive GC B cells, Biological replicate 6

description:
Sample name: GFPMYCpos_9G
Gene expression data from MYC positive GC B cell subpopulation, paired to 10G


title: GFPMYC negative GC B cells, Biological replicate 4

description:
Sample name: GFPMYCneg_2G
Gene expression data from MYC negative GC B cell subpopulation, paired to 1G

value: negative


title: Planktonic III vs. Biofilm III

city: Goyang

first: Jae-Jun

state: Gyeonggi

department: Department of Otorhinolaryngology-Head & Neck Surgery

country: South Korea

institute: Dongguk University Medical center

description:
Differential gene expression profile of Streptococcus pneumoniae early biofilm cells and planktonic cells Rep3
Biological replicate 3 of 3

hyb_protocol: The Cy3 or Cy5-labeled cDNA probes were purified with QIAquick PCR Purification Kit (Qiagen, Valencia, CA). Dried Cy3 or Cy5-labeled cDNA probes were resuspended in hybridization buffer containing 30% formamide, 5X SSC, 0.1% SDS, 0.1mg/ml salmon sperm DNA. The Cy3 or Cy5-labeled cDNA probes were mixed together and hybridized to a microarray slide (Shigella flexneri 2a str. 2457T plus Shigella flexneri 2a str. 301 virulence plasmid pCP301 Oligonucleotide 3x15K microarray) (Mycroarray.com, Ann Arbor, MI). After overnight at 42C, the slide was washed twice with washing solution 1 containing 2X SSC, 0.1% SDS for 5 min at 42C, and once with washing solution 2 containing 0.1X SSC, 0.1% SDS for 10 min at room temperature, and finally four times with 0.1X SSC for 1 min at room temperature. The slide was dried by centrifugation at 650 rpm for 5min.

scan_protocol: Hybridization image on the slide was scanned by Axon 4000B (Axon Instrument, Union City, CA).

data_processing: Hybridization image was analyzed by GenePix Pro 3.0 software (Axon Instrument, Union City, CA) to obtain gene expression ratios (reference vs test sample). Microarray data analysis was carried out by Genowiz 4.0TM (Ocimum Biosolutions, India). Global lowess was used for data analysis with normalization.

organism: Streptococcus pneumoniae R6

source_name: Planktonic cells

label_protocol: cDNA probes for cDNA microarray analysis were prepared by the reverse-transcription of total RNA (25ug) in the presence of aminoallyl-dUTP and 6ug of random primers (Invitrogen, Carlsbad, CA) for 3 hrs. The cDNA probes were cleaned up using Microcon YM-30 column (Millipore, Bedford, MA) and then followed by coupling of Cy3 dye (for reference) or Cy5 dye (for test sample) (Amersham Pharmacia, Uppsala, Sweden).

growth_protocol: 5 mL (1:100 diluted) bacteria cell suspension grown up to mid logarithm phase in TSB medium supplied with 1% glucose in 5% CO2, at 37° C. Thereafter washed 3 time to remove growth medium and RNA was extracted

extract_protocol: After washing cells were treated with 100 µl (3mg/ml) lysozyme and incubation for 4 min. Subsequently, total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions.The integrity of bacterial total RNA was checked by capillary electrophoresis with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and further purified with an RNeasy Mini Kit ( Qiagen, Valencia, CA).

treatment_protocol: Mid-logarithm phase grown cell suspension, centrifuged and washed three time with PBS to remove growth medium

value: Planktonic

source_name: Biofilm cells

growth_protocol: 1.5 mL (1:100 diluted) bacteria cell suspension was inoculated in 24-well microtiter plate and incubated in 5% CO2 for 15 hrs at 37° C. Thereafter plates were washed 3 time to remove plaktonic cells and RNA was extracted

treatment_protocol: 15 hours incubation in 24-well microtiter plate, after 15h incubation period, non-adherent bacteria were removed by three washes with PBS

value: Biofilm


title: Planktonic II vs. Biofilm II

description:
Differential gene expression profile of Streptococcus pneumoniae early biofilm cells and planktonic cells Rep 2
Biological replicate 2 of 3


title: GFPMYC positive GC B cells, Biological replicate 4

description:
Sample name: GFPMYCpos_7G
Gene expression data from MYC positive GC B cell subpopulation, paired to 8G


title: MSC donor5

value: passage 2


title: MSC donor6


title: iP-MSC donor2 cloneA

value: donor2, cloneA


title: MSC donor4


title: MSC donor2


title: Neuroblastoma, #94

description:
inss-st-2
itcc0112


title: IMR32, MEIS1-shRNA, t=96h

description: Neuroblastoma cells were stably transfected with shRNA specific for MEIS1b. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix). The VALUEs in the data table represent log2 MAS5.0 signal intensities.

source_name: IMR32, MEIS1-shRNA, time 96h

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: To induce MEIS1-shRNA in IMR32, doxycycline was addded to the medium. Controls were identically grown but without doxycycline.

value: Neuroblastoma

tag: stable shrna

value: inducible MEIS1-shRNA

tag: doxycycline induction

value: yes

tag: induction time


title: Planktonic I vs. Biofilm I

description:
Differential gene expression profile of Streptococcus pneumoniae early biofilm cells and planktonic cells Rep1
Biological replicate 1 of 3


title: IMR32, MEIS1-shRNA, t=192h

source_name: IMR32, MEIS1-shRNA, time 192h

tag: cell line


title: GFPMYC negative GC B cells, Biological replicate 3

description:
Sample name: GFPMYCneg_10G
Gene expression data from MYC negative GC B cell subpopulation, paired to 9G


title: IMR32, MEIS1-shRNA, t=48h

source_name: IMR32, MEIS1-shRNA, time 48h


title: GFPMYC negative GC B cells, Biological replicate 2

description:
Sample name: GFPMYCneg_12G
Gene expression data from MYC negative GC B cell subpopulation, paired to 11G


title: IMR32, MEIS1-shRNA, t=24h

source_name: IMR32, MEIS1-shRNA, time 24h


title: Neuroblastoma, #93

description:
inss-st-2
itcc0110


title: Neuroblastoma, #96

description:
inss-st-2
itcc0115

value: ganglioneuroblastoma


title: GFPMYC negative GC B cells, Biological replicate 1

description:
Sample name: GFPMYCneg_8G
Gene expression data from MYC negative GC B cell subpopulation, paired to 7G


title: F5305-liver-Chronic [522946A03_532.pair]

status: Public on Sep 22 2012

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

hyb_protocol: Microarrays were hybridized with 6.7 μg Cy3-labelled cDNA for 16-20 hours at 42ºC and were washed and dried according to manufacturer’s instruction. Cy3-labelled cDNA was hybridized to the Woodchuck Gene Expression HX3 Microarray.

scan_protocol: Microarrays were then scanned using a Roche NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution and features were extracted using NimbleScan Software.

data_processing:
Quantile normalization to normalize log2 signal intensities was obtained from scanning.
The gene expression data was normalized by the robust multichip average algorithm implemented in Partek Genomics Suite 6.5 (Partek, St. Louis MO).

organism: Marmota monax

source_name: Woodchuck Liver, Chronic

label_protocol: After precipitation, double-stranded cDNA was labelled with Cy3 by using Roche NimbleGen One-color DNA Labelling Kit (Roche NimbleGen, Inc., Madison, WI).

extract_protocol: Total RNA was isolated from liver tissues using the QIAamp RNA Blood Mini Kit (Qiagen Inc., Valencia, CA). 10 μg of total RNA isolated were reverse-transcribed using SuperScript double-stranded cDNA synthesis kit (Invitrogen, Inc., Calsbad, CA).

value: Liver

tag: status

value: Chronic

tag: age at surgery


title: F5316-liver-Resolved [522946A01_532.pair]

source_name: Woodchuck Liver, Resolved

value: Resolved


title: F5259-liver-Chronic [522946A02_532.pair]


title: F4620-liver-Uninfected [520791A03_532.pair]

source_name: Woodchuck Liver, Uninfected

value: Uninfected


title: F5281-liver-Resolved [520791A02_532.pair]


title: IMR32, MEIS1-shRNA, t=0h

source_name: IMR32, MEIS1-shRNA, time 0h

value: no


title: F5310-liver-Resolved [520519A03_532.pair]


title: F5316-liver-Resolved [520001A03_532.pair]


title: M5311-liver-Resolved [520001A01_532.pair]


title: F5259-liver-Chronic [520519A02_532.pair]


title: M5240-liver-Chronic [519904A03_532.pair]


title: M5240-liver-Chronic [520001A02_532.pair]


title: M5274-liver-Resolved [519904A01_532.pair]


title: M4657-liver-Uninfected [519811A03_532.pair]


title: F5284-liver-Resolved [519811A02_532.pair]


title: M4607-liver-Uninfected [519904A02_532.pair]


title: M5240-liver-Chronic [519811A01_532.pair]


title: M5269-liver-Resolved [519107A03_532.pair]


title: F5227-liver-Chronic [519175A01_532.pair]


title: M5286-liver-Resolved [519078A01_532.pair]


title: F5227-liver-Chronic [519107A02_532.pair]


title: M4640-liver-Uninfected [519078A02_532.pair]


title: F5220-liver-Chronic [518920A03_532.pair]


title: M5306-liver-Resolved [518920A02_532.pair]


title: F5315-liver-Resolved [519175A03_532.pair]


title: F5281-liver-Resolved [518786A03_532.pair]


title: F5220-liver-Chronic [518786A02_532.pair]


title: F5307-liver-Resolved [519175A02_532.pair]


title: M4646-liver-Uninfected [518786A01_532.pair]


title: F5220-liver-Chronic [518890A01_532.pair]


title: F5259-liver-Chronic [520791A01_532.pair]


title: M4679-liver-Uninfected [519107A01_532.pair]


title: F5305-liver-Chronic [518594A02_532.pair]


title: F5243-liver-Resolved [518890A02_532.pair]


title: F5310-liver-Resolved [518594A01_532.pair]


title: M4660-liver-Uninfected [518890A03_532.pair]


title: M5274-liver-Resolved [516119A02_532.pair]


title: M4640-liver-Uninfected [516119A03_532.pair]


title: F5305-liver-Chronic [516841A03_532.pair]


title: F5282-liver-Resolved [518594A03_532.pair]


title: F5227-liver-Chronic [519078A03_532.pair]


title: F5305-liver-Chronic [516119A01_532.pair]


title: M5301-liver-Chronic [516016A01_532.pair]


title: F5284-liver-Resolved [516016A03_532.pair]


title: F5271-liver-Chronic [515608A03_532.pair]


title: M4657-liver-Uninfected [515877A01_532.pair]


title: M5269-liver-Resolved [515756A01_532.pair]


title: M5301-liver-Chronic [515756A03_532.pair]


title: F4630-liver-Uninfected [515756A02_532.pair]


title: M5286-liver-Resolved [515608A02_532.pair]


title: M5277-liver-Resolved [516016A02_532.pair]


title: F5307-liver-Resolved [515877A03_532.pair]


title: M5301-liver-Chronic [515877A02_532.pair]


title: F4666-liver-Uninfected [520519A01_532.pair]


title: F4656-liver-Uninfected [515566A03_532.pair]


title: F5288-liver-Resolved [518920A01_532.pair]


title: F5288-liver-Resolved [515566A02_532.pair]


title: M5260-liver-Resolved [515608A01_532.pair]


title: M5250-liver-Chronic [515413A02_532.pair]


title: F5281-liver-Resolved [515413A01_532.pair]


title: F5271-liver-Chronic [515492A02_532.pair]


title: F4620-liver-Uninfected [515492A01_532.pair]


title: F5221-liver-Resolved [515413A03_532.pair]


title: F5271-liver-Chronic [515566A01_532.pair]


title: F5243-liver-Resolved [515492A03_532.pair]


title: F5316-liver-Resolved [515247A02_532.pair]


title: M4646-liver-Uninfected [515310A02_532.pair]


title: M4607-liver-Uninfected [515247A03_532.pair]


title: M5250-liver-Chronic [515247A01_532.pair]


title: F5282-liver-Resolved [515310A01_532.pair]


title: M5274-liver-Resolved [515076A03_532.pair]


title: M5306-liver-Resolved [515076A02_532.pair]


title: M4660-liver-Uninfected [515041A01_532.pair]


title: F5307-liver-Resolved [514974A01_532.pair]


title: F5211-liver-Chronic [515041A02_532.pair]


title: F5211-liver-Chronic [514974A03_532.pair]


title: F5315-liver-Resolved [515041A03_532.pair]


title: F5315-liver-Resolved [514767A01_532.pair]


title: M4679-liver-Uninfected [514974A02_532.pair]


title: F5211-liver-Chronic [515076A01_532.pair]


title: M5269-liver-Resolved [514767A02_532.pair]


title: M5276-liver-Chronic [514767A03_532.pair]


title: M5260-liver-Resolved [514736A02_532.pair]


title: M5276-liver-Chronic [514736A01_532.pair]


title: M5306-liver-Resolved [514575A03_532.pair]


title: F5288-liver-Resolved [514704A03_532.pair]


title: F5221-liver-Resolved [514492A01_532.pair]


title: M5276-liver-Chronic [514704A02_532.pair]


title: F4666-liver-Uninfected [506776A03_532.pair]


title: F4630-liver-Uninfected [514736A03_532.pair]


title: M4660-liver-Uninfected [514704A01_532.pair]


title: F5243-liver-Resolved [514575A01_532.pair]


title: M5250-liver-Chronic [514575A02_532.pair]


title: M5235-liver-Chronic [506774A02_532.pair]


title: F5252-liver-Chronic [514492A03_532.pair]


title: F5221-liver-Resolved [506774A03_532.pair]


title: M5235-liver-Chronic [506775A01_532.pair]


title: F5252-liver-Chronic [506776A01_532.pair]


title: F5310-liver-Resolved [506775A02_532.pair]


title: F4620-liver-Uninfected [514492A02_532.pair]


title: F5282-liver-Resolved [506776A02_532.pair]


title: M5277-liver-Resolved [506772A01_532.pair]


title: M5239-liver-Chronic [506771A03_532.pair]


title: M4657-liver-Uninfected [506772A02_532.pair]


title: M5277-liver-Resolved [506758A02_532.pair]


title: M4679-liver-Uninfected [506758A03_532.pair]


title: M4607-liver-Uninfected [506774A01_532.pair]


title: F5284-liver-Resolved [506771A01_532.pair]


title: M4640-liver-Uninfected [506771A02_532.pair]


title: M5260-liver-Resolved [506711A03_532.pair]


title: M5235-liver-Chronic [506772A03_532.pair]


title: M5239-liver-Chronic [506758A01_532.pair]


title: M5239-liver-Chronic [506711A02_532.pair]


title: M5311-liver-Resolved [506676A03_532.pair]


title: F5302-liver-Chronic [506711A01_532.pair]


title: F5302-liver-Chronic [506689A02_532.pair]


title: F4630-liver-Uninfected [506689A01_532.pair]


title: M5286-liver-Resolved [506689A03_532.pair]


title: F4656-liver-Uninfected [506676A01_532.pair]


title: M4646-liver-Uninfected [506775A03_532.pair]


title: M5311-liver-Resolved [506660A01_532.pair]


title: F4656-liver-Uninfected [506660A03_532.pair]


title: F4666-liver-Uninfected [506660A02_532.pair]


title: F5302-liver-Chronic [506676A02_532.pair]


title: N2-5 - Normal

status: Public on Sep 21 2012

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: Encore Biotin Module (Nugen) and Ambion

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: fRMA (using frma package from R/Bioconductor)

source_name: skin and blood

label_protocol: Encore Biotin Module (Nugen) and Ambion

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: patient

tag: group

value: Normal

tag: scorad

tag: kit

value: Ambion

tag: cycles


title: N2-3 - Normal


title: PB-EPC_rep2

city: Taipei City

first: Tse-Shun

last: Huang

address: No.155, Sec.2, Linong Street

department: Institute of Microbiology and Immunology

institute: National Yang-Ming University

description: The outgrowth EPC population after 2-4 week culture, enriched from peripheral blood

hyb_protocol: cRNA were hybridized, washed and stained on U133 plus 2.0 chips according to standard Affymetrix protocol.

scan_protocol: Chips are stained on Affymetrix GCS3000 scanner (scanner type M10)

data_processing: The CEL file was loaded to R/Bioconductor software and normalized by GC-RMA with default settings.

source_name: Outgrown EPC, peripheral blood

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

growth_protocol: Mononuclear cells (MNCs) were Histopaque-1077 isolated and plated in endothelial growth medium-2 on fibronectin-coated six-well plates at 37°C. After 3 days of culturing, the medium and nonadherent cells were removed. Thereafter, the medium were replaced every 2 days, and a certain number of LEPCs colonies formed, which emerge 2–4 weeks after the start of MNC culture.

extract_protocol: Total RNA was extracted by Qiagen miRNeasy kit according to the manufacturer's instructions.

treatment_protocol: No pre-treatment

tag: tissue type

value: Peripheral blood

tag: cell type

value: Endothelial progenitor cells


title: N-4 - Normal


title: N-8 - Normal


title: N-3 - Normal


title: N-5 - Normal


title: N2-2 - Normal


title: N-2 - Normal


title: CB-EPC_rep1

description: The outgrowth EPC population after 2-4 week culture, enriched from cord blood

source_name: Outgrown EPC, Cord Blood

value: Cord blood


title: N2-4 - Normal


title: PB-EPC_rep1


title: N2-6 - Normal


title: CB-EPC_rep2


title: N2-1 - Normal


title: N-7 - Normal


title: N-6 - Normal


title: N-10 - Normal


title: P10 - CLS

value: CLS

tag: age

tag: family history of atopy

value: No

tag: elevated ige

value: Yes

tag: eosinophil count

tag: filaggrin mutation

value: Negative


title: P10 - NL

value: NL


title: P116 - ALS

value: ALS

value: Nugen


title: N-1 - Normal


title: P10 - ALS


title: P116 - CLS


title: P116 - NL


title: P115 - ALS


title: F5252-liver-Chronic [515310A03_532.pair]

tag: tissue

value: Liver


title: P114 - CLS


title: P115 - CLS


title: P115 - NL


title: P114 - ALS


title: P113 - ALS


title: P111 - NL


title: P110 - CLS


title: P114 - NL


title: P110 - ALS


title: P112 - ALS


title: P111 - ALS


title: P113 - CLS


title: genomic DNA from whole blood 663

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

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

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

data_processing: BeadStudio software v3.2, the non_normalized data matrix contains unmethylated and methylated signal intensities.

source_name: whole blood_control

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: female

tag: diseasestatus

value: 1; control

value: whole blood

value: yes

tag: dataset

tag: plate

value: PLATE H

tag: sentrixbarcode

tag: sentrixposition

value: H

tag: wellid

tag: trackingsheet

value: HYB-XSTAIN 1-3


title: P113 - NL

tag: patient

tag: group

tag: scorad

value: Normal

tag: kit

tag: cycles


title: P112 - NL

tag: age

tag: family history of atopy

tag: elevated ige


title: P112 - CLS

tag: eosinophil count

tag: filaggrin mutation


title: genomic DNA from whole blood 687

tag: gender

value: male

tag: diseasestatus

tag: tissue

value: L


title: genomic DNA from whole blood 633

tag: dataset

tag: plate

tag: sentrixbarcode

value: K


title: genomic DNA from whole blood 670

tag: sentrixposition

value: F

tag: wellid

tag: trackingsheet


title: genomic DNA from whole blood 645

value: G


title: genomic DNA from whole blood 676

value: I


title: genomic DNA from whole blood 688

value: A


title: P110 - NL

tag: patient

tag: group

value: NL

tag: scorad

value: No

value: Negative

value: Nugen


title: genomic DNA from whole blood 681

value: female

tag: age

value: 1; control

value: whole blood

value: D


title: P111 - CLS

value: CLS

tag: family history of atopy

tag: kit

tag: cycles


title: genomic DNA from whole blood 654

value: yes

value: PLATE H

value: J

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 637

value: male

value: K


title: genomic DNA from whole blood 640

value: E


title: genomic DNA from whole blood 652

value: L


title: genomic DNA from whole blood 642

value: B


title: genomic DNA from whole blood 679

value: C


title: genomic DNA from whole blood 706


title: genomic DNA from whole blood 639

value: H


title: genomic DNA from whole blood 630

value: F


title: genomic DNA from whole blood 643

value: female

value: G


title: genomic DNA from whole blood 666

value: 1; control

value: whole blood

value: I


title: genomic DNA from whole blood 683

value: yes


title: genomic DNA from whole blood 717

value: PLATE H


title: genomic DNA from whole blood 693


title: genomic DNA from whole blood 631

value: J


title: genomic DNA from whole blood 691

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 664

value: male

value: D


title: genomic DNA from whole blood 669

value: K


title: genomic DNA from whole blood 635

value: A


title: genomic DNA from whole blood 628

value: E


title: genomic DNA from whole blood 660


title: genomic DNA from whole blood 673


title: genomic DNA from whole blood 657


title: genomic DNA from whole blood 712

value: L


title: genomic DNA from whole blood 696


title: genomic DNA from whole blood 678

value: C


title: genomic DNA from whole blood 629


title: genomic DNA from whole blood 692


title: genomic DNA from whole blood 632


title: genomic DNA from whole blood 646

value: B


title: genomic DNA from whole blood 675

value: female


title: genomic DNA from whole blood 697

value: H


title: genomic DNA from whole blood 677

value: 1; control


title: genomic DNA from whole blood 638

value: whole blood


title: genomic DNA from whole blood 655

value: G


title: genomic DNA from whole blood 656

value: yes

value: F


title: genomic DNA from whole blood 699

value: PLATE H

value: J


title: genomic DNA from whole blood 649

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 700

value: male


title: genomic DNA from whole blood 636

value: no


title: genomic DNA from whole blood 698


title: genomic DNA from whole blood 651


title: genomic DNA from whole blood 682


title: genomic DNA from whole blood 665


title: genomic DNA from whole blood 667


title: genomic DNA from whole blood 707


title: genomic DNA from whole blood 659

value: K


title: genomic DNA from whole blood 647

value: D


title: genomic DNA from whole blood 641

value: I


title: genomic DNA from whole blood 714


title: genomic DNA from whole blood 709


title: genomic DNA from whole blood 703

value: A


title: genomic DNA from whole blood 625

value: B


title: genomic DNA from whole blood 684

value: female


title: genomic DNA from whole blood 626


title: genomic DNA from whole blood 653

value: H


title: genomic DNA from whole blood 671

value: 1; control


title: genomic DNA from whole blood 668

value: whole blood


title: genomic DNA from whole blood 661


title: genomic DNA from whole blood 627


title: genomic DNA from whole blood 716


title: genomic DNA from whole blood 702

value: C


title: genomic DNA from whole blood 694

value: yes


title: genomic DNA from whole blood 704


title: genomic DNA from whole blood 680


title: genomic DNA from whole blood 650

value: E


title: genomic DNA from whole blood 648

value: PLATE H


title: genomic DNA from whole blood 662

value: F


title: genomic DNA from whole blood 689

value: J

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 710

value: male


title: genomic DNA from whole blood 685


title: genomic DNA from whole blood 708


title: genomic DNA from whole blood 690


title: genomic DNA from whole blood 705

value: L


title: genomic DNA from whole blood 711


title: genomic DNA from whole blood 686


title: genomic DNA from whole blood 713

value: G


title: genomic DNA from whole blood 701


title: genomic DNA from whole blood 672

value: K


title: genomic DNA from whole blood 191

value: PLATE F


title: genomic DNA from whole blood 719

value: D


title: genomic DNA from whole blood 634

value: female

value: I


title: genomic DNA from whole blood 695

value: 1; control


title: genomic DNA from whole blood 508

value: whole blood


title: genomic DNA from whole blood 477


title: genomic DNA from whole blood 507


title: genomic DNA from whole blood 578


title: genomic DNA from whole blood 558


title: genomic DNA from whole blood 718

value: H


title: genomic DNA from whole blood 457

value: yes


title: genomic DNA from whole blood 658

value: B


title: genomic DNA from whole blood 439


title: genomic DNA from whole blood 720

value: PLATE H


title: genomic DNA from whole blood 612

source_name: whole blood_schizophrenia patient

value: 2; schizophrenia patient

value: PLATE G


title: genomic DNA from whole blood 608

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 644


title: genomic DNA from whole blood 476

value: A


title: genomic DNA from whole blood 621

value: male

value: no


title: genomic DNA from whole blood 715


title: genomic DNA from whole blood 614

value: L


title: genomic DNA from whole blood 607

value: G


title: genomic DNA from whole blood 105

value: PLATE F


title: genomic DNA from whole blood 609

value: K


title: genomic DNA from whole blood 490

value: female


title: genomic DNA from whole blood 611

value: F


title: genomic DNA from whole blood 489

value: 1; control

value: whole blood

value: C


title: genomic DNA from whole blood 613

value: yes

value: J


title: genomic DNA from whole blood 602

value: 2; schizophrenia patient

value: E


title: genomic DNA from whole blood 610

value: PLATE G

value: B

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 110

value: male

value: no

value: PLATE E

value: I


title: genomic DNA from whole blood 600


title: genomic DNA from whole blood 575


title: genomic DNA from whole blood 574


title: genomic DNA from whole blood 598

value: L


title: genomic DNA from whole blood 599

value: A


title: genomic DNA from whole blood 562

value: H


title: genomic DNA from whole blood 605

value: female

value: G


title: genomic DNA from whole blood 674

value: 1; control

value: whole blood

value: PLATE H

value: C


title: genomic DNA from whole blood 506

value: 2; schizophrenia patient

value: yes


title: genomic DNA from whole blood 104


title: genomic DNA from whole blood 532

value: D


title: genomic DNA from whole blood 572

value: J

value: HYB-XSTAIN 1-3


title: genomic DNA from whole blood 438

value: male

value: no

value: K


title: genomic DNA from whole blood 561

value: PLATE E


title: genomic DNA from whole blood 544

value: F


title: genomic DNA from whole blood 158


title: genomic DNA from whole blood 555

value: A


title: genomic DNA from whole blood 553

value: H


title: genomic DNA from whole blood 554


title: genomic DNA from whole blood 470

value: female

value: L


title: genomic DNA from whole blood 542

value: whole blood