title: control vs inhibitor 10h rep3

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

hyb_protocol: The microarray design consisted of two biological replicates and two dye-swaps. For each biological replicate, RNA samples (1 µg) of three technical replicates were pooled. After 2 h and 10 h of treatment, the germinated and non-germinated achenes were indistinguishable. Therefore, all 50 achenes plated were used for the RNA isolation. For the 24 h samples, the RNA of germinated and non-germinated achenes were isolated separately and equal amounts of their RNA were pooled. All the samples from control experiments (achenes germinated in water and kept in the dark) were compared to samples from KAR1 (0.1 µM), 0.1 µM KAR1/10 µM InhA or InhA-treated (10 µM) achenes.

scan_protocol: Scanning was performed using an Agilent High-Resolution Microarray Scanner with default settings.  The detection of signal intensities and the grid adjustment were accomplished with the Agilent Feature Extraction Software.

data_processing: Raw intensity data were imported into R, version 2.13.0. Data quality was assessed with the arrayQualityMetrics package and further analysis was carried out using the LIMMA package of BIOCONDUCTOR. Background correction was done using the normexp method, and the normalization of the data within arrays was done using the loess method. To normalize the data between arrays, the quantile method was used.

organism: Lactuca sativa

source_name: Lactuca sativa achene, 10h, control

label_protocol: The RNA amplification and labeling procedure was accomplished with the Agilent QuickAmp Labeling Kit according to the manufacturer’s recommendations.

growth_protocol: Achenes (seeds) of Lactuca sativa cv. ‘Grand Rapids’ were used (Stokes,USA). The achenes were stored in a refrigerator at 4°C with silica gel in paper bags until use. In general, the germination time course tests consisted of three independent experiments with three biological replicates (50 achenes in each). The achenes were placed in 90 mm Petri dishes on filter paper moistened with 3 mL water (control), karrikine, inhibitor or the corresponding combination of the germination compounds. The Petri dishes were sealed, and the dark-grown samples were wrapped in two layers of aluminium foil, put into a box and allowed to germinate in a controlled environmental chamber (24°C, 80% RH, and 100 µmol m-2 s-1 light intensity). The germinated achenes were scored at each time point under a green safe-light.

extract_protocol: For the 2 h and 10 h time points, 50 achenes were germinated. For 24 h time point, the number of achenes were scaled up in order to obtain enough (at least 20) germinated achenes after the InhA treatment. Each harvest was repeated three times for three biological replicates. At 24 h, only the achenes with a radicle which had protruded exactly 1 mm were regarded as germinated and achenes with no visible testa rupture were selected as non-germinated. Total RNA was isolated using TRIzol reagent (Invitrogen) and cleaned up with RNeasy Plant Mini Kit (Qiagen). The RNA Integrity Number (RIN) of the samples was determined using the Agilent BioAnalyzer. Only samples with a RIN ≥ 8 were considered for further analysis.

tag: cultivar

value: Grand Rapids

value: achene

value: control

tag: time

source_name: Lactuca sativa achene, 10h, 10 µM inhibitor treated

value: 10 µM inhibitor treated


title: SUM159PT-transfected with LNA-antimiR-1204

status: Public on May 01 2012

type: RNA

city: Portland

first: Laura

middle: M.

last: Heiser

state: OR

address: 3181 SW Sam Jackson Park Rd.

country: USA

institute: OHSU

description: Cell line derived from breast carcinoma

hyb_protocol: RNA was hybridized using the Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The GenePattern suite of tools was employed to visualize the arrays and mask any visible smudges. Probe set based gene expression measurements were normalized using the RMA algorithm in Genepattern (http://www.broad.mit.edu/cancer/software/genepattern/).

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Samples were prepared according to the standard Affymetrix protocol from 3 ug total RNA

growth_protocol: Ham's F12 + 5 % FBS + Insulin (5 ug/ml) + Hydrocortisone (1 ug/ml) + HEPES (10 mM)

extract_protocol: Total RNA was harvested 24 h post-transfection using RNeasy mini kit (Qiagen, Valencia, CA,   USA).

treatment_protocol: Cells transfected with LNA-antimiR-1204 at final concentration of 50nM with Lipofectamine 2000.

tag: tissue

value: Breast

tag: group

value: Case

tag: cell line

tag: transfection


title: WG0041906-DNA_F04_RM4184

type: genomic

city: Toronto

first: Ekaterina

last: Rogaeva

address: 6 Queen’s Park Crescent West

country: Canada

institute: Tanz Centre for Neurodegenerative Diseases

hyb_protocol: Samples were applied to beadchips and the loaded beadchips were incubated overnight in the Illumina Hybridization oven. Unhybridized and non-specifically hybridized DNA was washed away, and beadchips were prepared for staining and extension.

scan_protocol: The beadchips were scanned on the Illumina BeadArray Reader using default settings.

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Blood

label_protocol: 750ng of DNA was denatured and neutralized before amplification. The denatured DNA was isothermally amplified in an overnight step, and the amplified product was them enzymatically fragmented (i.e. End-point fragmentation), precipitated with isopropanol, collected by centrifugation at 4 degrees celciums, and resuspended in hybridization buffer. C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled.

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.

tag: qc status

value: Passed QC

tag: cell type

value: Blood

tag: disease status

value: Unaffected


title: control vs inhibitor 10h rep2

tag: treatment


title: control vs inhibitor 10h rep4


title: SKBR3-transfected with mimic control

description: Cell line derived from breast carcinoma

source_name: SKBR3-transfected with mimic control

treatment_protocol: Cells transfected with mimic control at a final concentration of 50nM.

value: Control

value: miR-1204 control


title: control vs inhibitor 10h rep1


title: SKBR3-transfected with miR-1204 mimic

description: Cell line derived from breast carcinoma

source_name: SKBR3-transfected with miR-1204 mimic

treatment_protocol: Cells transfected with miR-1204 mimic at a final concentration of 50nM.

value: miR-1204 mimic


title: Patient A4: patient with pancreatic cancer and diabetes mellitus

city: Hangzhou

first: Yulian

last: Wu

state: Zhejiang

address: 88 Jiefang Road

department: surgey

country: China

institute: Second Affiliated Hospital, School of Medicine, Zhejiang University

description: peripheral blood samples from pantient with pancreatic cancer and diabetes mellitus,

hyb_protocol: Resulting biotin-labeled cRNA was recovered and purified with the RNeasy mini kit (Qiagen, Hilden, Germany), then hybridized to the human genome U133 plus 2.0 chips at 45℃ overnight.

scan_protocol: arrays were scanned using GeneChip Scanner 3000 according to the manufacture’s protocol.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). A variance stabilization normalization (VSN) was performed to normalize the different arrays using dChip software. Genes assigned in the GCOS software as “Absent” call in all samples were removed before further analysis. For comparison analysis, a two class unpaired method in the Significant Analysis of Microarray software (SAM) was applied to identify significantly differentially expressed genes between the two selected groups.

label_protocol: Biotinylated cRNA were prepared from 2 microg total RNA using the MessageAmpTM II aRNA Amplification Kit (Ambion, Huntingdon, UK).

extract_protocol: 6-8 ml of blood samples were drawn into EDTA vacutainer tubes (Becton Dickinson, Franklin Lakes, NJ) by routine venipuncture, put immediately on ice and transferred to the laboratory within 4 hours for blood processing. Total RNA from nucleated blood cells was following lysis of erythrocytes and removal of cell debris. RNA was then purified with RNeasy mini kit (Qiagen, Hilden, Germany). The quality of purified total RNA was assessed by using the RNA 6000 Nano LabChip kit on a 2100 bioanalyzer (Agilent, Palo Alto, CA) and quantity was assessed by A260/280 absorbance ratios.

tag: patient identifier

tag: sex

value: female

tag: age of patient

value: 58 years

tag: fbs

value: 136 mg/dl

tag: diagnosis

value: pancreatic adenocarcinoma


title: 12hr vs 24hr

city: Madison

first: Christina

last: Hull

state: WI

address: 1300 University Ave, 687 Medical Sciences Center

department: Biomolecular Chemistry

institute: University of Wisconsin-Madison

description:
raw data file: c2008-2-20 (112).gpr
raw data file: c2008-2-20 (113).gpr
raw data file (dye swap): c2008-2-20 (114).gpr
raw data file (dye swap): c2008-2-20 (115).gpr
Note: raw data files consistently report: Cy3 = earlier_timepoint and Cy5 = later_timepoint; vice versa for the raw data files (dye swap).

hyb_protocol: Slides were incubated in pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) for 1 hour at 42ºC. cDNAs were then applied to slides in 1X formamide buffer (25% formamide, 5X SSC, 0.1% SDS) containing 10 µg each sheared salmon sperm DNA (Eppendorf, Westbury, NY) and yeast tRNA (Sigma-Aldrich, St. Louis MO). Hybridizations were incubated at 42ºC for 12 hours. Slides were washed (1x SSC, .05XSSC) and dried before scanning.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner and the data extracted using GenePix Pro 4.0 (Molecular Devices, Sunnyvale CA) at the University of Wisconsin-Madison Gene Expression Center.

data_processing: Extracted data were analyzed using the GeneSpring 10.0 software package (Agilent Technologies, Santa Clara CA). After initial background correction, data were normalized using the LOWESS (locally weighted scatter plot smoothing) algorithm (Quackenbush 2001) and assessed for statistical significance utilizing ANOVA. Genes meeting the criterion p<0.05 were considered statistically significant and used in further analyses. Significant genes meeting the fold-change threshold were clustered using Cluster 3.0 (de Hoon et al. 2004) according to a robust K-means 8 algorithm (1000 iterations)

organism: Cryptococcus deneoformans

source_name: RNA  was harvested from JEC20xJEC21 crosses at the timepoints indicated (see characteristics)

label_protocol: cDNA was synthesized using the SuperScript III Direct Labeling Kit (Invitrogen, Carlsbad CA). The cDNA was purified over a QiaQuick MinElute PCR Purification Kit (Qiagen, Valencia CA), both according to manufacturer’s instructions.

growth_protocol: C. neoformans cells were grown in rich media. JEC20 and JEC21 were mixed in equal amounts (10 OD units each) and plated to solid V8 juice agar media in a small volume (150µl) with beads. Plates were then incbated at room temperature, in the dark, until cells were harvested for RNA  extraction.

extract_protocol: Cells were flash frozen on dry ice and lyophilized. RNA was harvested from lyophilized powder via hot-acid phenol as described in (Ausubel, Current Protocols in Molecular Biology, 1997)

tag: growth protocol

value: Crosses of JEC20xJEC21 on solid V8 juice agar, incubated at room temperature in the dark


title: control vs karrikine 10h rep4

source_name: Lactuca sativa achene, 10h, 0.1 µM karrikin treated

value: Grand Rapids

value: 0.1 µM karrikin treated


title: WG0041906-DNA_F03_RM0487

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

value: AD


title: WG0041906-DNA_E12_RM0463


title: control vs karrikine 10h rep3

value: achene

value: control


title: 24hr vs 48hr

description:
raw data file: d2008-2-22 (116).gpr
raw data file: d2008-2-22 (117).gpr
raw data file (dye swap): d2008-2-22 (118).gpr
raw data file (dye swap): d2008-2-22 (119).gpr
Note: raw data files consistently report: Cy3 = earlier_timepoint and Cy5 = later_timepoint; vice versa for the raw data files (dye swap).


title: WG0041906-DNA_E11_RM4180


title: OVCAR8-transfected with LNA-antimiR-control

description: Cell line derived from ovarian carcinoma

growth_protocol: RPMI, 10% FBS

treatment_protocol: Cells transfected with LNA-antimiR-control at final concentration of 50nM with Lipofectamine 2000.

value: Ovary

value: LNA-antimiR-control


title: Patient A2: patient with pancreatic cancer and diabetes mellitus

hyb_protocol: Resulting biotin-labeled cRNA was recovered and purified with the RNeasy mini kit (Qiagen, Hilden, Germany), then hybridized to the human genome U133 plus 2.0  chips at 45℃ overnight.

source_name: peripheral blood samples from pantient with pancreatic cancer and diabetes mellitus

value: male

value: 63 years

value: 129 mg/dl


title: WG0041906-DNA_F01_RM4073

value: Passed QC

value: Blood


title: 48hr vs 72hr

description:
raw data file: e2008-2-26 (120).gpr
raw data file: e2008-2-26 (121).gpr
raw data file (dye swap): e2008-2-26 (122).gpr
raw data file (dye swap): e2008-2-26 (123).gpr
Note: raw data files consistently report: Cy3 = earlier_timepoint and Cy5 = later_timepoint; vice versa for the raw data files (dye swap).


title: OVCAR8-transfected with LNA-antimiR-1204

value: Case


title: control vs karrikine 10h rep2


title: OV90-transfected with miR-1204 control

source_name: OV90-transfected with miR-1204 control

value: Control

value: miR-1204 control


title: 0.5hr vs 6hr

description:
raw data file: a2008-6-26 (78).gpr
raw data file: a2008-6-26 (80).gpr
raw data file (dye swap): a2008-6-26 (81).gpr
raw data file (dye swap): a2008-7-8 (98).gpr
Note: raw data files consistently report: Cy3 = earlier_timepoint and Cy5 = later_timepoint; vice versa for the raw data files (dye swap).


title: 6hr vs 12hr

description:
raw data file: b2008-7-8 (99).gpr
raw data file (dye swap): b2008-7-8 (101).gpr
raw data file (dye swap): b2008-7-8 (102).gpr
Note: raw data files consistently report: Cy3 = earlier_timepoint and Cy5 = later_timepoint; vice versa for the raw data files (dye swap).


title: OV90-transfected with miR-1204 mimic

source_name: OV90-transfected with miR-1204 mimic

value: miR-1204 mimic


title: control vs karrikine 10h rep1


title: WG0041906-DNA_F02_RM3624


title: WG0041906-DNA_E10_RM3529

value: Failed QC


title: control vs inhibitor 24h rep3

source_name: Lactuca sativa achene, 24h, control

value: Grand Rapids

source_name: Lactuca sativa achene, 24h, 10 µM inhibitor treated

value: 10 µM inhibitor treated


title: MDAMB231-transfected with LNA-antimiR-control

description: Cell line derived from breast carcinoma

value: Breast


title: WG0041906-DNA_E08_RX1153

value: Unaffected


title: MDAMB231-transfected with LNA-antimiR-1204

description: Cell line derived from breast carcinoma


title: Cohyb_P21 vs P0_HypothalamusMethy_B

city: Houston

first: Robert

middle: A

last: Waterland

state: TX

address: 1100 Bates St.,

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and LOWESS normalization.Probe ratios within one SmaI interval were averaged and the median of the P value log10 ratios of the probes within one SmaI interval was calculated.

organism: Mus musculus

source_name: Genomic DNA extracted from hypothalamus of P21 mouse

label_protocol: 2ug of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

extract_protocol:
Hypothalamus was dissected from fresh mouse brain and flash frozen on dry ice
Total DNA was extracted by standard phenol-chloroform isolation

tag: gender

value: Female

tag: strain

value: mixture of C57BL/6J and C3H/HeJ

tag: genotype

value: non-agouti

tag: developmental stage

source_name: Genomic DNA extracted from hypothalamus of P0 mouse


title: HEY-transfected with LNA-antimiR-control

tag: tissue

value: Ovary

tag: group

value: HEY

value: LNA-antimiR-control


title: Cohyb_Hypothalamus_SL vs. C_A

source_name: Genomic DNA extracted from the hypothalami of SL mice at P180

value: FVB/NJ

value: SL (early postnatal overnutrition)

source_name: Genomic DNA extracted from the hypothalami of C mice at P180

value: C (control)


title: control vs inhibitor 24h rep1

tag: cultivar

value: achene

value: control

tag: time


title: HEY-transfected with LNA-antimiR-1204

source_name: HEY-transfected with LNA-antimiR-1204

value: Case

tag: cell line

tag: transfection


title: WG0041906-DNA_E07_RM0450

tag: qc status

value: Passed QC

tag: cell type

value: Blood

tag: disease status


title: Cohyb_P21 vs P0_HypothalamusMethy_A


title: control vs inhibitor karrikine 2h rep4

source_name: Lactuca sativa achene, 2h, 0.1 µM karrikine and 10 µM inhibitor treated

value: Grand Rapids

tag: treatment

value: 2 h

source_name: Lactuca sativa achene, 2h, control


title: BT549-transfected with LNA-antimiR-control

description: Cell line derived from breast carcinoma

value: Breast

value: Control


title: Cohyb_Hypothalamus_SL vs. C_B

value: Female


title: control vs inhibitor karrikine 2h rep3

value: 0.1 µM karrikine and 10 µM inhibitor treated


title: control vs inhibitor 24h rep2

value: 10 µM inhibitor treated


title: WG0041906-DNA_E03_RM4080

source_name: Blood

value: Unaffected


title: control vs inhibitor karrikine 2h rep2


title: control vs inhibitor karrikine 2h rep1


title: WG0041906-DNA_E01_RM3783

value: Failed QC


title: control vs inhibitor 2h rep4

source_name: Lactuca sativa achene, 2h, 10 µM inhibitor treated


title: Pooled GM C1,2,3 vs. GM 50-3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Cells were then treated with either genistein (50 μg/ml) (4’, 5, 7-Trihydroxyisoflavone; Sigma Chemical Company, St. Louis, MO, USA) or the vehicle control [0.3% dimethylsulfoxide (DMSO), Sigma] in phenol red-free, stripped-serum DMEM medium for 24 h. Briefly, total RNA was isolated with TRIzol agent (Invitrogen) from treated UtLM cells and purified using a RNeasy MidiKit (QIAGEN, Valencia, CA, USA), according to the manufacturers’ protocols. Due to the expense of chip printing and the large amount of RNA needed for each of the hybridizations, the samples from the flasks that received the same treatment were pooled, then concentrated to > 9 ìg/ìl by Microcon 30 columns (Amicon:Millipore, Bedford, MA, USA). Gene expression analysis was conducted using Agilent Whole Human Genome arrays (Agilent Technologies, Palo Alto, CA, USA). Total RNA was amplified by using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500 ng of total RNA, cyanine (Cy) 3- or Cy5-labeled cRNAs were produced according to manufacturer's protocol. For each two-color comparison, 750 ng each of Cy3- and Cy5-labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 h in a rotating oven using the Agilent 60-mer Oligo microarray processing protocol. Slides were later washed as indicated in this protocol, and then scanned with an Agilent Scanner. Data were obtained using the Agilent Feature Extraction software (v7.5), employing defaults for all parameters. Images and GEML (gene expression markup language) files, including error and p-values, were exported from the Agilent Feature Extraction software and deposited into Rosetta Resolver (version 4.0, build 4.0.1.0.7.RSPLIT) (Rosetta Biosoftware, Kirkland, WA, USA). Ratio profiles were combined and intensity plots were generated for each ratio experiment. “Signature genes” were identified, as those having a p-value ≤0.001 with a fold-change ≥1.5 in all three biological replicates.

data_processing: Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters and loaded into the Rosetta Resolver® system (v4.0) (Rosetta Biosoftware, Kirkland, WA).

source_name: uterine leiomyoma cells treated with the vehicle control (DMSO)

growth_protocol: Human uterine leiomyoma (UtLM) cells (GM10964) were purchased from Coriell Institute for Medical Research (Camden, NJ, USA), and cultured as previously reported. Briefly, cells were grown in Eagle’s minimum essential medium [Invitrogen (Gibco), Carlsbad, CA, USA] with 19% fetal bovine serum (FBS) (Sigma, St Louis, MO, USA) and supplemented with vitamins, essential and non-essential amino acids and L-glutamine (Invitrogen). All culture maintenance and experiments were performed at 37°C and 5% CO2. UtLM cells were seeded in T175 flasks (at passages 8–1 14 at 80–95% confluence), and twenty-four hours prior to treatment, the media was changed to Dulbecco’s modified Eagle’s medium/nutrient mixture F-12 Ham (DMEM/F-12) (Hyclone Laboratories, Logan, UT, USA) phenol red-free with charcoal dextran treated FBS (Sigma).

value: uterine leiomyoma cells

source_name: uterine leiomyoma cells treated with genistein (50 μg/ml)


title: WG0041906-DNA_E02_RM0433

value: AD


title: control vs inhibitor 2h rep3


title: Pooled GM C1,2,3 vs. GM 50-2

hyb_protocol: For each two-color comparison, 750 ng each of Cy3- and Cy5-labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 h in a rotating oven using the Agilent 60-mer Oligo microarray processing protocol.

scan_protocol: Slides were later washed as indicated in this protocol, and then scanned with an Agilent Scanner.

label_protocol: Total RNA was amplified by using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500 ng of total RNA, cyanine (Cy) 3- or Cy5-labeled cRNAs were produced according to manufacturer's protocol.

extract_protocol: Briefly, total RNA was isolated with TRIzol agent (Invitrogen) from treated UtLM cells and purified using a RNeasy MidiKit (QIAGEN, Valencia, CA, USA), according to the manufacturers’ protocols. Due to the expense of chip printing and the large amount of RNA needed for each of the hybridizations, the samples from the flasks that received the same treatment were pooled, then concentrated to > 9 ìg/ìl by Microcon 30 columns (Amicon:Millipore, Bedford, MA, USA).

treatment_protocol: Cells were then treated with either genistein (50 μg/ml) (4’, 5, 7-Trihydroxyisoflavone; Sigma Chemical Company, St. Louis, MO, USA) or the vehicle control [0.3% dimethylsulfoxide (DMSO), Sigma] in phenol red-free, stripped-serum DMEM medium for 24 h.


title: Pooled GM C1,2,3 vs. GM 50-1


title: WG0041906-DNA_D05_RX1144


title: WG0041906-DNA_E09_RM4172


title: WG0041906-DNA_D10_RX0316


title: control vs inhibitor 2h rep2


title: WG0041906-DNA_D08_RX1135


title: BT549-transfected with LNA-antimiR-1204

description: Cell line derived from breast carcinoma

source_name: BT549-transfected with LNA-antimiR-1204


title: control vs inhibitor 24h rep4


title: WG0041906-DNA_D11_RM3515


title: control vs inhibitor 2h rep1


title: GM 50-1 vs. Pooled GM C1,2,3


title: WG0041906-DNA_F09_RM2194


title: GM 50-2 vs. Pooled GM C1,2,3


title: WG0041906-DNA_D09_RM4301


title: WG0041906-DNA_E04_RM4276


title: control vs karrikine 2h rep4

source_name: Lactuca sativa achene, 2h, 0.1 µM karrikin treated

value: 0.1 µM karrikin treated


title: control vs karrikine 2h rep2

value: achene


title: control vs karrikine 2h rep3

value: control


title: GM 50-3 vs. Pooled GM C1,2,3


title: control vs karrikine 2h rep1


title: control vs karrikine 24h rep2

source_name: Lactuca sativa achene, 24h, 0.1 µM karrikin treated


title: WG0041906-DNA_F06_RM0518


title: WG0041906-DNA_D01_RM3683


title: control vs karrikine 24h rep3


title: control vs karrikine 24h rep4


title: hAd-MSC_rep2

city: Singapore

first: Cheryl

last: Tay

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Biological Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalisation in GeneSpring GX v11.5

label: Biotin

source_name: hAd-MSC Biological Replicate 2

label_protocol: Standard Illumina Whole-Genome Gene Expression for BeadStation protocol

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. The RNA was amplified using the Illumina TotalPrep RNA Amplification Kit, according to manufacturer's instructions.

value: Primary human adipose tissue-derived mesenchymal stromal cells (MSC)

tag: passage number

value: Passage 2


title: WG0041906-DNA_D12_RM3996

value: Passed QC

value: Blood


title: AP2-G KO salivary gland sporozoite 5

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

description: Gene expression  in AP2-G KO salivary gland sporozoites

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custome P. berghei Microarrays 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), then  1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x22k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 031546_D_F_20101207) to obtain background subtracted and spatially detrended Processed Signal intensities (Sample tables).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded (Supplementary file on Series record).

organism: Plasmodium berghei

source_name: AP2-G KO salivary gland sporozoite

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

extract_protocol: RNA was prepared using the total RNA Purification kit (Promega) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Mosquitoes infected with P. berghei were disected 24days after blood meal. Sporozoites were collected from the saivary gland.

tag: Stage

value: sporozoite

value: AP2-G KO


title: WG0041906-DNA_E06_RM0443


title: WG0041906-DNA_D02_RM3641


title: hAd-MSC_rep1

description: Biological Replicate 1

source_name: hAd-MSC Biological Replicate 1

value: Passage 7


title: control vs karrikine 24h rep1

value: Grand Rapids

source_name: Lactuca sativa achene, 24h, control


title: WG0041906-DNA_C12_RM4253


title: Corneal Fibroblasts_rep1

description: Biological Replicate 1

source_name: Corneal Fibroblasts Biological Replicate 1

value: Primary corneal fibroblasts


title: AP2-G KO salivary gland sporozoite 3


title: WG0041906-DNA_D06_RM0338


title: WG0041906-DNA_D04_RM3970


title: WG0041906-DNA_C10_RM2136


title: WG0041906-DNA_D07_RX1157


title: GL261 grown in unconditioned medium versus GL261 grown in NPC medium pair 2 (experiment with dye swap)

city: Lund

first: Ulrike

last: Nuber

address: Klinikgatan 26

country: Sweden

institute: Lund University

description:
Comparison of GL261 cells grown in unconditioned versus NPC-conditioned medium samples pair 2; log ratio > 0: Over-expressed in GL261 cells grown in unconditioned medium in comparison to GL261 cells treated with NPC-conditioned medium
Normalized log ratio sample pair 2 (log.ratio.824-827)

hyb_protocol: Two cDNA samples were pooled and hybridized to the microarrays in a humidified chamber at 42°C for 16 hr. Slides were washed at room temperature in 2× SSC/0.2% SDS for 10 min, 2× SSC for 10 min, and 0.2× SSC for 10 min. Bound cDNA was visualized by hybridization with 3DNA (dendrimers specific for respective capture sequences conjugated to either Cy3 or Cy5) in a humidified chamber at 42°C for 3 hr. Subsequently, slides were washed as before.

scan_protocol: Fluorescence intensities of Cy3 and Cy5 were measured separately at 532 and 635 nm with a laser scanner (Affymetrix 428 Array Scanner, Affymetrix). The resulting 16-bit data files were imported into Microarray Suite image analysis software (version 2.0), which runs as an extension of IPLab Spectrum software (Scanalytics, Fairfax, VA). Raw spot intensities of Cy3 and Cy5 were locally background subtracted by the MicroArray Suite software.

data_processing: Each dye swap experiment was normalized by applying variance stabilization (Huber et al., 2002) using the vsn package of bioconductor (http://www.bioconductor.org). Means of normalized log-products and log-ratios of each dye swap experiment pair were used for further analysis. Normalization procedures were performed using R (http://cran.R-project.org).

label: Cy3, Cy5

source_name: GL261 grown in unconditioned medium

label_protocol: Labeling was performed using the 3DNA Array 50 Expression Array Detection kit (Genisphere, Hatfield, PA) according to the manufacturer's instructions. 20 μg of total RNA of undifferentiated and differentiated cells (24, 48, or 96 hr) was reverse transcribed using primers with a specific capture sequence.

growth_protocol: Conditioned medium from mouse neurospheres was collected by cultivating the neurospheres in neurobasal medium for four days, then media were filtered (0.45 µm filter) and stored (at -20° C) until further use. GL261 cells were subjected to a change of normal cultivation medium (control-group) or were exposed to mouse neurosphere conditioned medium (treated group). The GL261 cells were kept under these conditions for three days and then pelleted by centrifugation. These pellets were frozen in liquid nitrogen and stored. In a next step mRNA was extracted, transcribed into cDNA and used for hybridization on the arrays.

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen)

treatment_protocol: Endoplasmic reticulum stress genes are upregulated in mouse high grade astrocytoma cells (GL261) treated with neural stem/precursor cell (NPC) conditioned medium

value: high grade astrocytoma cells (GL261)

tag: medium

value: non-conditioned medium

label: Cy5, Cy3

source_name: GL261 grown in NPC medium

value: NPC medium


title: GL261 grown in unconditioned medium versus GL261 grown in NPC medium pair 1 (experiment with dye swap)

description:
Comparison of GL261 cells grown in unconditioned versus NPC-conditioned medium samples pair 1; log ratio > 0: Over-expressed in GL261 cells grown in unconditioned medium in comparison to GL261 cells treated with NPC-conditioned medium
Normalized log ratio sample pair 1 (log.ratio.758-761)


title: WG0041906-DNA_C11_RX1119


title: AP2-G KO salivary gland sporozoite 4


title: AP2-G KO salivary gland sporozoite 2


title: Scleral Fibroblasts_rep1

description: Biological Replicate 1

source_name: Scleral Fibroblasts Biological Replicate 1

value: Primary scleral fibroblasts

value: Passage 3


title: TMDC_rep1

description: Biological Replicate 1

source_name: TMDC Biological Replicate 1

value: Trabecular meshwork-derived cells from the human eye

value: Passage 4


title: wild type salivary gland sporozoite 5

description: Gene expression  in wild type salivary gland sporozoites

source_name: wild type salivary gland sporozoite

value: wild type


title: WG0041906-DNA_C08_RM2149

source_name: Blood

value: AD


title: AP2-G KO salivary gland sporozoite 1


title: TMDC_rep2

description: Biological Replicate 2

source_name: TMDC Biological Replicate 2


title: Scleral Fibroblasts_rep2

description: Biological Replicate 2

source_name: Scleral Fibroblasts Biological Replicate 2

value: Passage 2


title: GL261 grown in unconditioned medium versus GL261 grown in NPC medium pair 3 (experiment with dye swap)

description:
Comparison of GL261 cells grown in unconditioned versus NPC-conditioned medium samples pair 3; log ratio > 0: Over-expressed in GL261 cells grown in unconditioned medium in comparison to GL261 cells treated with NPC-conditioned medium
Normalized log ratio sample pair 3 (log.ratio.832-835)


title: WG0041906-DNA_C07_RX1130

value: Passed QC


title: Corneal Stromal Cells_rep1

description: Biological Replicate 1

source_name: Corneal Stromal Cells Biological Replicate 1

value: Primary corneal stromal cells

value: Passage unknown


title: WG0041906-DNA_C09_RM0334

value: Blood

value: Unaffected


title: SRp20 knockdown, biological replicate 3

city: Los Angeles

first: Erik

middle: S

last: Anderson

state: CA

address: 6-567 MRL, 675 Charles E. Young Drive South

department: MBIDP

institute: UCLA

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps

source_name: HEK293 cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HEK293 cells grown in DMEM + 10%FBS + L-glutamine

extract_protocol: All samples were separated for RNA and protein level analysis.  Total RNA was isolated using Trizol reagent (Invitrogen).  RNA samples were treated with Dnase and subsequently phenol-chloroform extracted prior to labeling.

treatment_protocol: shRNA constructs were transiently transfected using Lipofectamine 2000 (Invitrogen), incubated for 4 hours and removed.  Cells grew for 72 hours under knockdown conditions.

tag: length of knockdown

value: 72 hours


title: wild type salivary gland sporozoite 2

value: sporozoite


title: SRp20 knockdown, biological replicate 2


title: Corneal Endothelial Cells_rep1

description: Biological Replicate 1

source_name: Corneal Endothelial Cells Biological Replicate 1

value: Corneal endothelial cell line


title: WG0041906-DNA_C04_RX0278


title: WG0041906-DNA_C06_RM8229


title: WG0041906-DNA_D03_RX0260


title: wild type salivary gland sporozoite 3


title: hAd-MSC_rep3

description: Biological Replicate 3

source_name: hAd-MSC Biological Replicate 3

value: Primary human adipose tissue-derived mesenchymal stromal cells (MSC)


title: RPE_rep1

description: Biological Replicate 1

source_name: RPE Biological Replicate 1

value: Primary retinal pigmented epithelial cells (RPE)

value: Passage 5


title: wild type salivary gland sporozoite 4


title: wild type salivary gland sporozoite 1


title: Tra2-beta knockdown, biological replicate 2


title: Tra2-beta knockdown, biological replicate 3


title: SRp20 knockdown, biological replicate 1


title: WG0041906-DNA_B12_NY0868

value: Failed QC


title: WG0041906-DNA_B10_RM2226


title: WG0041906-DNA_C05_RM0259


title: TMDC_rep6

description: Biological Replicate 6

source_name: TMDC Biological Replicate 6

value: Trabecular meshwork-derived cells from the human eye

value: Passage 6


title: WG0041906-DNA_C02_RM5155


title: hESC-derived Neurons_rep1

description: Biological Replicate 1

source_name: hESC-derived Neurons Biological Replicate 1

value: Neurons derived from hESC line H1


title: WG0041906-DNA_C01_RM8215


title: TPC-1_construct_rep2

city: Columbus

first: Jaroslaw

middle: Piotr

last: Jendrzejewski

state: Ohio

address: 460W. 12th Avenue

department: Comprehensive Cancer Center

institute: The Ohio State University

description:
24C_2
gene_expression_after_24h_from_transfection_expression_vector_(PTCSC3)_2

hyb_protocol: Samples were hybridized to the array for 17 hours at 65°C according to the manufacturer's protocol.

scan_protocol: Slides were scanned with an Agilent G2505C Microarray Scanner.

data_processing: Signal intensities were detected by Agilent DNA Microarray scanner and quantile normalized with R software using  'limma' bioconductor library.

label_protocol: RNA samples were labeled with cyanine-3 (Cy3) using the Agilent Low Input One–Color Labeling kit (Agilent Technologies, CA).

growth_protocol: TPC-1 cells were cultured in DMEM (Gibco) supplemented with 10% fetal calf serum (Gibco) and 1x MEM non-essential amino acids (Gibco) at 37C in 5% CO2.

extract_protocol: At 24 h after transfection the cells were washed once in PBS and total RNA was extracted (Trizol reagent, Invitrogen) and DNase-1 treated (Ambion).

treatment_protocol: TPC-1 cell line cells were plated at 1x10^5 per 12-well dish and after 24 h transfected in quadruplicate with PTCSC3 expression vector and with empty vector (pcDNA3) as control using Lipofectamine2000 reagent (Invitrogen).

value: papillary thyroid carcinoma

tag: transfected with

value: construct (PTCSC3-pcDNA3)


title: Tra2-beta knockdown, biological replicate 1


title: WG0041906-DNA_B11_RM4111

value: AD


title: control knockdown, biological replicate 2

value: control


title: WG0041906-DNA_C03_RX0365

value: Passed QC


title: TPC-1_construct_rep4

description:
24C_4
gene_expression_after_24h_from_transfection_expression_vector_(PTCSC3)_4


title: TPC-1_construct_rep1

description:
24C_1
gene_expression_after_24h_from_transfection_expression_vector_(PTCSC3)_1


title: hESC-derived NPC_rep1

description: Biological Replicate 1

source_name: hESC-derived NPC Biological Replicate 1

value: Neural progenitors derived from hESC line H1

value: Passage unknown


title: WG0041906-DNA_B09_RX1122

value: Blood


title: TPC-1_construct_rep3

description:
24C_3
gene_expression_after_24h_from_transfection_expression_vector_(PTCSC3)_3


title: HUVEC_rep1

description: Biological Replicate 1

source_name: HUVEC Biological Replicate 1

value: Primary human umbilical vein endothelial cells

value: Passage 3


title: hESC_rep1

description: Biological Replicate 1

source_name: hESC Biological Replicate 1

value: Human embryonic stem cell line (hESC) H1


title: TPC-1_empty vector_rep4

description:
24E_4
gene_expression_after_24h_from_transfection_control_(empty vector)_4

source_name: TPC-1_empty vector_24h

value: empty vector (pcDNA3)


title: WG0041906-DNA_B07_RM0176

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

value: Unaffected


title: control knockdown, biological replicate 1

value: 72 hours


title: control knockdown, biological replicate 3


title: TMDC_rep5

description: Biological Replicate 5

source_name: TMDC Biological Replicate 5

value: Trabecular meshwork-derived cells from the human eye

value: Passage 5


title: TPC-1_empty vector_rep3

description:
24E_3
gene_expression_after_24h_from_transfection_control_(empty vector)_3


title: Digitoxin treatment, biological replicate 3

treatment_protocol: Digitoxin was dissolved in DMSO at 100uM and added to HEK293 cells at 1:1000 dilution (final concentration 100nM).  Cells were incubated with drug or equal volume of DMSO as a control for 24 hours.

tag: agent

value: Digitoxin

tag: duration

value: 24 hours


title: TPC-1_empty vector_rep2

description:
24E_2
gene_expression_after_24h_from_transfection_control_(empty vector)_2

value: papillary thyroid carcinoma


title: TMDC_rep4

description: Biological Replicate 4

source_name: TMDC Biological Replicate 4


title: TMDC_rep3

description: Biological Replicate 3

source_name: TMDC Biological Replicate 3

value: Passage 7


title: Digitoxin treatment, biological replicate 2


title: TPC-1_empty vector_rep1

description:
24E_1
gene_expression_after_24h_from_transfection_control_(empty vector)_1


title: WG0041906-DNA_B03_RM3638

source_name: Blood


title: VCaP, 8hr EtOH, siNC

status: Public on Apr 27 2012

first: Kern Rei

last: Chng

address: 60 Biopolis Street #02-01 Genome

department: Cancer Biology and Pharmacology 3

institute: GIS

description:
VCaP, 8hr EtOH, siNC
5957936011A,5957936011 E, 5957936011I

hyb_protocol: standard Illumina protocol

scan_protocol: BeadChips were scanned using the BeadArray Reader.

data_processing:
Raw data was analyzed using GeneSpring GX 11.0 software. Dataset was normalized using percentile shift normalization and baseline transformed to median of control samples.
Triplicates were generated for the experiment and analyses were performed using the average of the triplicates (after normalization). Raw data provided as supplementary file

source_name: VCaP prostate cancer cells

label_protocol: Biotinylated cRNA were prepared from 500ng total RNA using Illumina TotalPrep-96 RNA Amplification Kit (Ambion).

growth_protocol: The human prostate cancer VCaP cells (American Type Culture Collection) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution at 37˚C under 5% CO2. For experiments requiring androgen/vehicle (DHT (Tokyo Chemical Industry) /EtOH) treatment, VCaP cells were grown in phenol red free DMEM supplemented with 10% charcoal stripped fetal bovine serum (CDFBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution for 24 hours prior stimulation unless otherwise stated.

extract_protocol: RNA was harvested using Trizol reagent (Sigma) and purified according to manufacturer protocol in PureLink RNA Mini Kit (Invitrogen).

treatment_protocol: VCaP cells were seeded in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution for 3 days. Prior to ETOH/DHT stimulation, VCaP cells were washed and the medium was replaced with phenol red free DMEM supplemented with 10% charcoal stripped fetal bovine serum (CDFBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution to starve the cells for 24 hours. Hormone-deprived VCaP cells were treated with ETOH/10nM DHT as described above.

value: VCaP prostate cancer cells

value: ETOH, treated with control siRNA


title: VCaP, 8hr 10nM DHT, siERG

description:
VCaP, 8hr 10nM DHT, siERG
5957936011D,5957936011 H, 5957936011L

value: 10nM DHT, treated with siRNA against ERG


title: 5-AZA resistant cell line

status: Public on Apr 28 2012

city: Shimotsuke

first: PIYANUCH

last: SRIPAYAP

state: Tochigi

address: 3311-1 Yakushiji

department: Medicine, Division of Hematology

institute: Jichi Medical University

description:
THP-1/AR
Test

hyb_protocol: Sample was hybridized with a CodeLinkTM Human Whole Genome Bioarray (Filgen, Inc., Nagoya, Japan) representing a total of 57,347 human gene transcripts.

scan_protocol: Hybridization signals were analyzed using a GenePix 4000B confocal laser scanner and Array-Pro Analyzer Ver.4.5 software (Media Cybernetics, Inc., Silver Spring, MD).

data_processing:
Quantile normalized log2 ratio representing test/reference by MicroArray Data Analysis Tool Ver3.0 (Filgen, Inc).  We used net intensity(mean) {test} and net intensity (mean) {control}.
The genes whose expression levels were more than 2.5-fold or less than 0.7-fold in one of the AZA-resistant cells compared with the corresponding parental cells were selected.
Normalized log2ratio table linked as supplementary file on Series record.

source_name: Human myeloid leukemia cell

label_protocol: Labeled antisense RNA was then synthesized using an RNA Transcript SureLABEL Core Kit (TaKaRa, Otsu, Japan) and Cy5-UTP (GE Healthcare UK Ltd., Buckinghamshire, England).

growth_protocol:
All cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, penicillin G, and streptomycin sulfate, and split every 4 days.
Generated AZA-resistant protocol: THP-1 cells were trated with step-wise increasing concentration of AZA (0.2 mM to 1.0 mM) and colonized on a medium containing methylcellulose with 1.0 mM AZA, followed by selection and cloning of individual colonies.
The clones with the highest IC50 values from each cell line were designated as THP-1/AR (TAR).

extract_protocol: Total RNA from THP-1 and TAR cells was prepared using the acid guanidium thiocyanate-phenol chloroform method.

value: THP-1 resistant cell line (TAR; THP-1 were treated with step-wise increasing of concentration of AZA)


title: VCaP, 8hr EtOH, siERG

description:
VCaP, 8hr EtOH, siERG
5957936011C,5957936011 G, 5957936011K

value: ETOH, treated with siRNA against ERG


title: VCaP, 8hr 10nM DHT, siNC

description:
VCaP, 8hr 10nM DHT, siNC
5957936011B,5957936011 F, 5957936011J

value: 10nM DHT, treated with control siRNA


title: control THP-1 cell line

description:
THP-1
Control

value: THP-1 control


title: TF324 6d+DOX replicate1

status: Public on Apr 10 2012

city: Torrance

first: Tsai-Der

last: Chuang

state: California

address: 1124 WEST CARSON STREET

department: OB-GYN

institute: LA Biomed at UCLA medical center

description: TF324 cells transfected with lentivirus expressing miR-106R~25 cluster treated with doxycycline.

hyb_protocol: The arrays were processed at the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) according to manufacturer’s protocol.

data_processing: The expression values were background-subtracted, globally normalized using BeadStudio version 1.5.1.3 (Illumina)

source_name: TF324 cells

growth_protocol: The TF324 cell line is a spontaneously transformed leiomyoma smooth muscle cell line (LSMC) derived from transformation of LSMC at 4th passage in our laboratory.  TF324 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) until reaching confluence with a change of media every 2 to 3 days. All supplies for isolation and culturing of the cell were purchased from Sigma-Aldrich (St. Louis, MO), Invitrogen (Carlsbad, CA) and Fisher Scientific (Atlanta, GA).

extract_protocol: Total RNA was extracted from TF324 cell using Trizol (Invitrogen). The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE)

treatment_protocol: TF324 cells were seeded in 24-well plates and after 24 hrs transfected with DOX-inducible lentiviral construct carrying miR-106b~25 cluster (System Biosciences) according to the manufacturer’s protocol. After 48 hrs of incubation, the cells were either treated with DOX (10µg/ml) or untreated (-DOX).  Total RNA isolated from cells incubated for 6 days was subjected to microarray gene expression profiling.

tag: induction

value: miR-106b~25 cluster

value: spontaneously transformed uterine leiomyoma smooth muscle cells


title: WG0041906-DNA_B02_RM4078

value: Passed QC

value: Blood

value: AD


title: WG0041906-DNA_B05_RX1145

value: Failed QC

value: Unaffected


title: HPF3_7d_R1

status: Public on Apr 08 2012

city: Kiel

first: Franz-Josef

last: Müller

address: Niemannsweg 147

department: Klinik für Psychiatrie und Psychotherapie

country: Germany

institute: Zentrum für Integrative Psychiatrie Kiel

description: fibroblasts after 7 days of  reprogramming

hyb_protocol: standard protocol according to vendor guidlines (www.illumina.com)

data_processing: data was extracted with GenomeStudio 2010 with quantile normalization and no background correction

source_name: in vitro cultures

extract_protocol: mRNA extraction kit (Quiagen)

tag: sample

value: HPF3 d7


title: WG0041906-DNA_B01_RM3682


title: WG0041906-DNA_B04_RM8029


title: HPF3_7d_R2

scan_protocol: standard protocol according to vendor guidlines (www.illumina.com)

value: fibroblasts after 7 days of  reprogramming


title: control DMSO treatment biological replicate 2

source_name: HEK293 cell line

value: DMSO

value: 24 hours


title: HPF3-dox_R2

description: unmodified fibroblasts

label_protocol: standard protocol according to vendor guidlines (www.illumina.com)

value: unmodified fibroblasts

value: HPF3 d0


title: WG0041906-DNA_B08_RM4275


title: HPF2_23d_R2

description: fibroblasts after 23 days of  reprogramming

value: HPF2 d23


title: HPF2_7d_R1

value: HPF2 d7


title: OE-OCT4_2

status: Public on Apr 06 2012

city: New haven

first: Natalia

last: Ivanova

state: ct

address: 10 Amistad

department: genetics

institute: Yale

description: OCT4 overexpression replicate 2.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization.

source_name: H1 hESCs, OE-OCT4

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit according to the manufacturer's protocol.

growth_protocol: Cells were cultured on Matrigel-coated plates in mTeSR medium (Stem Cell Technologies).

extract_protocol: RNA was isolated using Trizol, treated with DNase I (Ambion) to remove genomic DNA, extracted with phenol:chloroform (1:1), precipitated and diluted in water.

treatment_protocol: Cells were transduced with EF1a-control, OE-NANOG, OE-OCT4 or OE-SOX2 lentivirus in the presence of polybrene.

value: human embryonic stem cells (hESCs)


title: HPF3-dox_R1

description: unmodified fibroblasts


title: OE-OCT4_1

description: OCT4 overexpression replicate 1.


title: control DMSO treatment biological replicate 3


title: HPF2_23d_R1

value: fibroblasts after 23 days of  reprogramming


title: OE-SOX2_2

description: SOX2 overexpression replicate 2.

source_name: H1 hESCs, OE-SOX2


title: OE-NANOG_1

description: NANOG overexpression replicate 1.

source_name: H1 hESCs, OE-NANOG

value: OE-NANOG


title: HPF2-dox_R1

description: unmodified fibroblasts

value: HPF2 d0


title: HPF2_4d_R2

description: fibroblasts after 4 days of  reprogramming

value: HPF2 d4


title: WG0041906-DNA_A08_RM4285

value: Passed QC

value: Blood


title: OE-NANOG_2

description: NANOG overexpression replicate 2.


title: OE-SOX2_1

description: SOX2 overexpression replicate 1.


title: HPF2_7d_R2


title: EF1a-control_1

description: Control replicate 1.

source_name: H1 hESCs, EF1a-control


title: TF324 6d-DOX replicate1

description: TF324 cells transfected with lentivirus expressing miR-106R~25 cluster without doxycycline treatment.

scan_protocol: The arrays were processed at the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) according to manufacturer’s protocol.

value: control

value: spontaneously transformed uterine leiomyoma smooth muscle cells


title: HPF2_4d_R1

value: fibroblasts after 4 days of  reprogramming


title: HPF2-dox_R2

description: unmodified fibroblasts


title: shSOX2 clone3

description: shSOX2 clone replicate 3.

source_name: H1 hESCs, SOX2 shRNA

treatment_protocol: Cells were transduced with H1P or shSOX2 lentivirus in the presence of polybrene, pick up the clones with high KD efficiency.

value: SOX2 shRNA


title: WG0041906-DNA_A11_RM4071

value: Failed QC

value: AD


title: shSOX2 clone1

description: shSOX2 clone replicate 1.


title: H1P rep2

description: H1P replicate 2.

source_name: H1 hESCs, control


title: WG0041906-DNA_A06_RM4128

value: Unaffected


title: BMP4_d7

description: BMP4 treated day 7.

source_name: H1 hESCs, BMP4 treated

treatment_protocol: Cells were treated without or with BMP4 (100 ng/ ml) for 8 days.

value: bone morphogenetic protein 4 (BMP4)

value: day 7


title: shSOX2 clone2

description: shSOX2 clone replicate 2.


title: BMP4_d3

description: BMP4 treated day 3.

value: day 3


title: BMP4_d2

description: BMP4 treated day 2.

value: human embryonic stem cells (hESCs)

value: day 2


title: BMP4_d6

description: BMP4 treated day 6.

value: day 6


title: H1_bmp4_ct8_d7

description: BMP4 control day 7.

source_name: H1 hESCs, untreated


title: BMP4_d0

description: BMP4 treated day 0.

value: day 0


title: BMP4_d4

description: BMP4 treated day 4.

value: day 4


title: Digitoxin treatment, biological replicate 1

value: Digitoxin

value: 24 hours


title: WG0041906-DNA_A05_RM8217

value: Passed QC

value: Blood


title: H1_bmp4_ct6_d5

description: BMP4 control day 5.

value: day 5


title: H1_bmp4_ct4_d3

description: BMP4 control day 3.


title: H1P rep1

description: H1P replicate 1.

value: control


title: H1_bmp4_ct3_d2

description: BMP4 control day 2.


title: control DMSO treatment biological replicate 1

value: DMSO


title: H1_bmp4_ct7_d6

description: BMP4 control day 6.


title: BMP4_d5

description: BMP4 treated day 5.


title: H1_bmp4_ct2_d1

description: BMP4 control day 1.

value: day 1


title: H1_bmp4_ct1_d0

description: BMP4 control day 0.


title: WG0041906-DNA_A03_RM0015

value: Unaffected


title: BMP4_d1

description: BMP4 treated day 1.

value: bone morphogenetic protein 4 (BMP4)


title: shOCT4_H9_5

description: OCT4 shRNA knockdown H9 cells day 4.

source_name: H9 hESCs, OCT4 shRNA

treatment_protocol: Cells were transduced with H1P, shNANOG, shOCT4 or shSOX2 lentivirus in the presence of polybrene for 8 days.

value: human embyronic stem cells (hESCs)

value: OCT4 shRNA


title: EF1a-control_2

description: Control replicate 2.

value: human embryonic stem cells (hESCs)


title: shOCT4_H9_7

description: OCT4 shRNA knockdown H9 cells day 6.


title: shOCT4_H9_8

description: OCT4 shRNA knockdown H9 cells day 7.

value: day 7


title: shOCT4_7

description: OCT4 shRNA knockdown day 6.

source_name: H1 hESCs, OCT4 shRNA

value: day 6


title: shOCT4_H9_6

description: OCT4 shRNA knockdown H9 cells day 5.


title: shOCT4_8

description: OCT4 shRNA knockdown day 7.


title: shSOX2_6

description: SOX2 shRNA knockdown day 5.

value: SOX2 shRNA


title: shOCT4_H9_1

description: OCT4 shRNA knockdown H9 cells day 0.

value: day 0


title: shOCT4_6

description: OCT4 shRNA knockdown day 5.


title: shSOX2_5

description: SOX2 shRNA knockdown day 4.

value: day 4


title: shSOX2_1

description: SOX2 shRNA knockdown day 0.


title: shSOX2_7

description: SOX2 shRNA knockdown day 6.


title: shOCT4_H9_2

description: OCT4 shRNA knockdown H9 cells day 1.


title: shSOX2_8

description: SOX2 shRNA knockdown day 7.


title: shOCT4_5

description: OCT4 shRNA knockdown day 4.


title: shSOX2_4

description: SOX2 shRNA knockdown day 3.

value: day 3


title: shOCT4_H9_3

description: OCT4 shRNA knockdown H9 cells day 2.

value: day 2


title: shSOX2_2

description: SOX2 shRNA knockdown day 1.


title: shOCT4_H9_4

description: OCT4 shRNA knockdown H9 cells day 3.


title: shOCT4_4

description: OCT4 shRNA knockdown day 3.


title: WG0041906-DNA_A04_RX0515

value: Passed QC

value: Blood


title: WG0041906-DNA_A02_RM3805

value: Failed QC


title: WG0041906-DNA_A07_RM4150

value: AD


title: WG0041906-DNA_A10_RM0108


title: shNANOG_4

description: NANOG shRNA knockdown day 3.

source_name: H1 hESCs, NANOG shRNA

value: NANOG shRNA


title: shNANOG_8

description: NANOG shRNA knockdown day 7.


title: shOCT4_2

description: OCT4 shRNA knockdown day 1.

value: day 1


title: H1P_8

description: H1p control day 7.

value: control


title: shOCT4_1

description: OCT4 shRNA knockdown day 0.

value: human embyronic stem cells (hESCs)


title: H1P_5

description: H1p control day 4.


title: H1P_3

description: H1p control day 2.


title: shNANOG_2

description: NANOG shRNA knockdown day 1.


title: H1P_7

description: H1p control day 6.


title: shNANOG_3

description: NANOG shRNA knockdown day 2.


title: H1P_6

description: H1p control day 5.

value: day 5


title: H1_bmp4_ct5_d4

description: BMP4 control day 4.

value: human embryonic stem cells (hESCs)


title: Runx-rep3

status: Public on Apr 02 2012

city: Seattle

first: Janet

last: Young

state: WA

address: 1100 Fairview Avenue N., C3-168,  P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Probe intensities were corrected, normalized, and summarized by the Lumi package of Bioconductor (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).
Data was vst transformed and quantile normalized using the Lumi package of Bioconductor (Du et al., 2008).

source_name: myoblasts transduced with lentivirus carrying Runx3

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina arrays

growth_protocol: RD cells were obtained from ATCC (American Type Culture Collection) in approximately 1990, and all analyses have been performed on cells that originated from low passage number frozen aliquots. Cells were maintained in DMEM with 10% bovine calf serum and 1% Pen-Strep (Gibco). Low-serum differentiation media consisted of DMEM with 1% horse serum, 1% Pen-Strep and 10 ug/mL insulin and transferrin.

extract_protocol: RNA was extracted with Qiagen RNeasy kit according to manufacturer's instruction. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: RD cells were infected with titer-matched amounts of either RUNX1-, ZNF238-, miR-206- or GFP-expressing lentiviruses, allowed to recover in growth media for 24 hours, and then shifted to differentiation media for 72 hours. Each condition was performed with 3 independent biological replicates.

value: RD cells


title: RP58-rep3

source_name: myoblasts transduced with lentivirus carrying RP58 (ZNF238)


title: H1P_1

description: H1p control day 0.


title: Runx-rep1

source_name: myoblasts transduced with lentivirus carrying Runx1


title: Runx-rep2

source_name: myoblasts transduced with lentivirus carrying Runx2


title: RP58-rep1


title: shNANOG_7

description: NANOG shRNA knockdown day 6.

value: day 6


title: shNANOG_5

description: NANOG shRNA knockdown day 4.


title: H1P_4

description: H1p control day 3.


title: shNANOG_1

description: NANOG shRNA knockdown day 0.


title: H1P_2

description: H1p control day 1.


title: shOCT4_3

description: OCT4 shRNA knockdown day 2.

value: OCT4 shRNA


title: miR206-rep3

source_name: myoblasts transduced with lentivirus carrying miR-206


title: miR206-rep2


title: RP58-rep2


title: GFP-rep3

source_name: myoblasts transduced with lentivirus carrying GFP


title: J-M2

status: Public on Mar 30 2012

city: PARIS

first: Nicolas

last: DERIAN

address: 15 Avenue Pitié

department: Biotherapy

country: France

hyb_protocol: Labelled cRNA were hybridized overnight to Illumina Human HT-12 V3 BeadChip arrays (Illumina)

scan_protocol: Beadchips were scanned on the Illumina BeadArray 500GX Reader using Illumina BeadScan image data acquisition software (version 2.3.0.13).

data_processing:
Data were process using BeadStudio software and R package Lumi.
Normalized matrix contains expression value normalized by quantiles, transformed by log2 and detection p-values after removing outliers, )merging these data with an other experiment performed on Illumina HT12 V3.0 (GPL6947), 39396 probes remained.

source_name: patient J 2 month after treatment

label_protocol: Total RNA was amplified and converted to biotinylated cRNA according to the manufacturer’s protocol (Illumina TotalPrep RNA Amplification Kit; Ambion).

extract_protocol: RNA was extracted from fresh PBMCs using the NucleoSpin RNA II  kit (Macherey-Nagel, Hoerd, France) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyser showing a quality RNA integrity number of 8–10 (Agilent Technologies). RNA yield was assessed using a NanoDrop 1000 spectrophotometer (NanoDrop Products, Thermo Fisher Scientific).

treatment_protocol: Vitamin D supplementation using 100 000 IU of cholecalciferol per week

tag: tissue

value: PBMC

tag: sample time

value: 2 month after treatment


title: J-M0

source_name: patient J before treatment


title: I-M2

source_name: patient I 2 month after treatment

value: Vitamin D supplementation using 100 000 IU of cholecalciferol per week


title: miR206-rep1

tag: cell line


title: I-M0

source_name: patient I before treatment


title: K-M2

source_name: patient K 2 month after treatment


title: GFP-rep1


title: K-M0

source_name: patient K before treatment


title: H-M2

source_name: patient H 2 month after treatment


title: G-M0

source_name: patient G before treatment


title: MCF7_LTED_E2_highdose_rep1

city: Ann Arbor

first: Viktoriya

last: Strumba

state: MI

address: 109 Zina Pitcher place

institute: University of Michigan

description: Cells were selected in 50pM E2

scan_protocol: standard Illumina protocol

data_processing: Raw expression data were quantile normalized using GenomeStudio software. Log2 transformation and further analyses done in R

source_name: MCF-7: 50pE

label_protocol: standard Illumina protocol

growth_protocol: MCF-7 cells were maintained in phenol red-free Improved Minimum Essential Medium supplemented with 10% charcoal-stripped calf serum and indicated hormones.

extract_protocol: Total RNA was harvested using RNeasy mini columns (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with either 0.05% ethanol (vehicle) , 1pM or 50pM E2 concentrations, or 50pM or 1nM 3βAdiol concentrations.  Prior to microarray, all cells were grown in 10% charcoal stripped serum only.

tag: treatment dose

value: 50 picomolar E2


title: G-M2

source_name: patient G 2 month after treatment


title: H-M0

source_name: patient H before treatment


title: MCF7_LTED_3βAdiol_lowdosel_rep2

description: Cells were selected in 50pM 3βAdiol

value: 50 picomolar 3βAdiol


title: MCF7_LTED_3βAdiol_lowdose_rep3

description: Cells were selected in 50pM 3βAdiol


title: GFP-rep2


title: MCF7_LTED_3βAdiol_highdose_rep3

description: Cells were selected in 1nM 3βAdiol

source_name: MCF-7: 1n3β

value: 1 nanomolar 3βAdiol


title: MCF7_LTED_E2_highdose_rep3

description: Cells were selected in 50pM E4


title: MCF7_LTED_3βAdiol_highdose_rep1

description: Cells were selected in 1nM 3βAdiol


title: MCF7_LTED_3βAdiol_highdose_rep2

description: Cells were selected in 1nM 3βAdiol


title: MCF7_LTED_E2_highdosel_rep2

description: Cells were selected in 50pM E3


title: MCF7_LTED_E2lowdosel_rep3

description: Cells were selected in 1pM E4

source_name: MCF-7: 1pE

value: 1 picomolar E2


title: shSOX2_3

description: SOX2 shRNA knockdown day 2.

source_name: H1 hESCs, SOX2 shRNA

value: SOX2 shRNA

tag: time

value: day 2


title: MCF7_LTED_E2lowdose_rep1

description: Cells were selected in 1pM E2


title: MCF7_LTED_3βAdiol_lowdose_rep1

description: Cells were selected in 50pM 3βAdiol


title: MCF7_LTED_vehicle_rep2

description: Cells were selected in the absence of estrogens

source_name: MCF-7: Veh

value: vehicle


title: MCF7_LTED_vehicle_rep3


title: MCF7_LTED_E2lowdose_rep2

description: Cells were selected in 1pM E3


title: MCF7_LTED_vehicle_rep1


title: shNANOG_6

description: NANOG shRNA knockdown day 5.

source_name: H1 hESCs, NANOG shRNA

tag: cell type

value: NANOG shRNA


title: 638 plaque

status: Public on Mar 28 2012

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

description: Sample from carotid plaque taking during carotid endarterectomy

hyb_protocol: Hybridization was performed according to Affymetrix protocols for HG-U133 plus2 2.0 arrays, at the Bioinformatics and Expression Analysis core facility at the Karolinska Institute.

scan_protocol: Scanning was performed according to Affymetrix protocols for HG-U133 plus2 2.0 arrays, at the Bioinformatics and Expression Analysis core facility at the Karolinska Institute.

data_processing: cel files were preprocessed using RMA normalization, as implemented in the Affymetrix Power Tools 1.10.2 package apt-probeset-summarize. As part of the RMA normalization, all expression measurements were log2-transformed.

source_name: carotid plaque

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

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen) and treatment with the RNase-free DNase set (Qiagen) according to the manufacturer’s instructions. RNA quality was analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies Inc, Palo Alto, Calif), and RNA concentration was measured on a NanoDrop (Thermo Scientific). Low concentration and low quality samples were omitted.

treatment_protocol: Flash frozen directly after sampling.

tag: individual

tag: sample type

value: carotid plaque

tag: age (y)

tag: ischemic time (days)

tag: ischemic event

value: FALSE

value: mixed carotid plaque cells


title: 659 plaque

value: TRUE


title: 625 plaque


title: 645 plaque


title: 664 plaque


title: 629 plaque


title: 677 plaque


title: 654 plaque


title: 680 plaque


title: 675 plaque


title: 591 plaque


title: 678 plaque


title: 630 plaque


title: 635 plaque


title: 646 plaque


title: 651 plaque


title: 642 plaque


title: 681 plaque


title: 618 plaque


title: 624 plaque


title: 605 plaque


title: 606 plaque


title: 686 plaque


title: 603 plaque


title: 669 plaque


title: 627 plaque


title: 588 plaque


title: 597 plaque


title: 619 plaque


title: 571 plaque


title: 551 plaque


title: 558 plaque


title: 561 plaque


title: 521 plaque


title: 541 plaque


title: 514 plaque


title: 587 plaque


title: 564 plaque


title: 544 plaque


title: 554 plaque


title: 550 plaque


title: 528 plaque


title: 531 plaque


title: 532 plaque


title: 502 plaque


title: 538 plaque


title: 481 plaque


title: 519 plaque


title: 492 plaque


title: 509 plaque


title: 466 plaque


title: 520 plaque


title: 477 plaque


title: 497 plaque


title: 454 plaque


title: 458 plaque


title: 479 plaque


title: 489 plaque


title: 442 plaque


title: 439 plaque


title: 433 plaque


title: 425 plaque


title: 420 plaque


title: 414 plaque


title: 404 plaque


title: 400 plaque


title: 431 plaque


title: 429 plaque


title: 427 plaque


title: 421 plaque


title: 411 plaque


title: 446 plaque


title: 392 plaque


title: 406 plaque


title: 430 plaque


title: 412 plaque


title: 398 plaque


title: 397 plaque


title: 388 plaque


title: 383 plaque


title: 408 plaque


title: 384 plaque


title: 378 plaque


title: 372 plaque


title: 371 plaque


title: 440 plaque


title: 391 plaque


title: 366 plaque


title: 367 plaque


title: 345 plaque


title: 365 plaque


title: 359 plaque


title: 355 plaque


title: 346 plaque


title: 364 plaque


title: 356 plaque


title: 327 plaque


title: 360 plaque


title: 337 plaque


title: 306 plaque


title: 333 plaque


title: 322 plaque


title: 300 plaque


title: 302 plaque


title: 311 plaque


title: 313 plaque


title: 334 plaque


title: 340 plaque


title: 363 plaque


title: 298 plaque


title: 318 plaque


title: 297 plaque


title: 324 plaque


title: 370 plaque


title: 316 plaque


title: 301 plaque


title: 292 plaque


title: 286 plaque


title: 282 plaque


title: 285 plaque


title: 279 plaque


title: 296 plaque


title: 284 plaque


title: 288 plaque


title: 281 plaque


title: L852_2_L

status: Public on Mar 27 2012

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: 48 h after electroporation

data_processing: The data were normalised using quantile normalisation with Lumi R package

source_name: L851 patient knock-down

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

growth_protocol: AML blasts from patient L852 were grown in RPMI1640 supplemented with 20% foetal calf serum, 2 mM glutamine, 7 ng/ml GM-CSF and 20% HS-5 supernatant.

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

value: primary AML

tag: disease

value: Acute myeloid leukaemia

value: 48 h after electroporation


title: L852_1_J

description: 24 h after electroporation

source_name: L851 patient control

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

value: 24 h after electroporation


title: siRE_D4_SKNO1_I

description: 96 h after 1st electroporation

source_name: RUNX1/ETO knock-down 96h

growth_protocol: SKNO-1 cells were grown in RPMI1640 supplemented with 20% foetal calf serum, 2 mM glutamine and 7 ng/ml GM-CSF

treatment_protocol: SKNO-1 cells were electroporated with 200 nM of either RUNX1/ETO siRNA (siRE) or mismatch siRNA (siMM) in three to four day intervals.

value: 96 h after 1st electroporation


title: siRE_D2_SKNO1_E

description: 48 h after 1st electroporation

source_name: RUNX1/ETO knock-down 48h

value: 48 h after 1st electroporation


title: siRE_D10_SKNO1_F

description: 72 h after 3rd electroporation

source_name: RUNX1/ETO knock-down 240h

value: 72 h after 3rd electroporation


title: siMM_D4_SKNO1_K

description: 96 h after 1st electroporation

source_name: RUNX1/ETO mismatch control 96h


title: siMM_D10_SKNO1_H

description: 72 h after 3rd electroporation

source_name: RUNX1/ETO mismatch control 240h


title: 5617835176_L

status: Public on Mar 20 2012

city: Seoul

first: Cheol-Keun

last: Park

address: 50 Irwon-dong Kangnam-gu

country: South Korea

institute: Samsung Medical Center

description:
fresh frozen tissue
SAMPLE 433

hyb_protocol: RNA was hybridized to Human HT-12 v4 BeadChips from Illumina.

data_processing: The software package to extract raw data was Genomestudio.

source_name: Liver Hepatocellular Carcinoma

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted using the Rneasy Plus Mini kit - Qiagen.

value: liver tumor

tag: ajcc stage


title: siMM_D2_SKNO1_G

description: 48 h after 1st electroporation

source_name: RUNX1/ETO mismatch control 48h


title: siRE_D7_SKNO1_B

description: 72 h after 2nd electroporation

source_name: RUNX1/ETO knock-down 168h

value: 72 h after 2nd electroporation


title: siMM_D7_SKNO1_D

description: 72 h after 2nd electroporation

source_name: RUNX1/ETO mismatch control 168h


title: 5617835176_G

description:
fresh frozen tissue
SAMPLE 431


title: 552 plaque


title: 5617835176_D

description:
fresh frozen tissue
SAMPLE 430


title: Empty vector transfected sample 2

status: Public on Mar 22 2012

city: Chicago

first: Swati

last: Bhattacharyya

state: IL

address: 240 E Huron st, McGAW, M230

department: Medicine

institute: Northwestern University

description: Empty vector transfected  sample

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Raw signal intensities for each probe were obtained using Illumina Beadstudio data analysis software and imported to the Bioconductor lumi package for data transformation and normalization. Probes with all samples ‘‘absent’’ (near or below background levels) were filtered. To control for multiple testing and reduce the false positive rate (FDR), stringent statistical criteria were used to identify differentially expressed genes with raw p < 0.01 and FDR adjusted p value < 0.05.

source_name: Empty vector transfected sample

label_protocol: cDNA was labeled using an Ambion labeling kit (Ambion).

extract_protocol: RNA was isolated using RNeasy mini kits (Qiagen, Valencia, CA). The integrity of RNA was ascertained using Agilent Bioanalyzer (Santa Clara, CA).

value: skin fibroblasts


title: LPS 6hours treated sample 1

description: LPS 6hours treated sample

source_name: LPS 6hours treated sample


title: LPS 6hours treated sample 3

description: LPS 6hours treated sample


title: Empty vector transfected sample 3

description: Empty vector transfected  sample


title: Empty vector transfected sample 1

description: Empty vector transfected  sample


title: LPS 6hours treated sample 2

description: LPS 6hours treated sample


title: 5617835176_I

description:
fresh frozen tissue
SAMPLE 432


title: 5617835175_C

description:
fresh frozen tissue
SAMPLE 426


title: 5617835176_B

description:
fresh frozen tissue
SAMPLE 429


title: n5958040051_E

description:
fresh frozen tissue
SAMPLE 422


title: n5958040051_K

description:
fresh frozen tissue
SAMPLE 424


title: n5958040051_B

description:
fresh frozen tissue
SAMPLE 420


title: 5617835169_H

description:
fresh frozen tissue
SAMPLE 413


title: 5617835169_K

description:
fresh frozen tissue
SAMPLE 415


title: 5617835175_A

description:
fresh frozen tissue
SAMPLE 425


title: 5617835175_E

description:
fresh frozen tissue
SAMPLE 427


title: 5617835170_B

description:
fresh frozen tissue
SAMPLE 416


title: 5617835170_F

description:
fresh frozen tissue
SAMPLE 417


title: n5958040051_C

description:
fresh frozen tissue
SAMPLE 421


title: 5617835164_A

description:
fresh frozen tissue
SAMPLE 408


title: 5617835163_K

description:
fresh frozen tissue
SAMPLE 407


title: 5617835164_K

description:
fresh frozen tissue
SAMPLE 410


title: 5617835170_L

description:
fresh frozen tissue
SAMPLE 419


title: 5617835164_I

description:
fresh frozen tissue
SAMPLE 409


title: 5617835169_C

description:
fresh frozen tissue
SAMPLE 411


title: 5617835169_D

description:
fresh frozen tissue
SAMPLE 412


title: 5617835175_J

description:
fresh frozen tissue
SAMPLE 428


title: 5617835169_J

description:
fresh frozen tissue
SAMPLE 414


title: 5617835163_E

description:
fresh frozen tissue
SAMPLE 405


title: n5958040051_H

description:
fresh frozen tissue
SAMPLE 423


title: 5617835151_J

description:
fresh frozen tissue
SAMPLE 394


title: 5617835154_F

description:
fresh frozen tissue
SAMPLE 396


title: 5617835151_C

description:
fresh frozen tissue
SAMPLE 390


title: 5617835137_J

description:
fresh frozen tissue
SAMPLE 388


title: 5617835151_G

description:
fresh frozen tissue
SAMPLE 392


title: 5617835163_I

description:
fresh frozen tissue
SAMPLE 406


title: 5617835162_F

description:
fresh frozen tissue
SAMPLE 400


title: 5617835154_J

description:
fresh frozen tissue
SAMPLE 398


title: 5617835137_D

description:
fresh frozen tissue
SAMPLE 386


title: 5617835134_H

description:
fresh frozen tissue
SAMPLE 383


title: 5617835134_E

description:
fresh frozen tissue
SAMPLE 381


title: 5617835162_K

description:
fresh frozen tissue
SAMPLE 402


title: 5617835170_I

description:
fresh frozen tissue
SAMPLE 418


title: 5617835162_I

description:
fresh frozen tissue
SAMPLE 401


title: 5617835134_K

description:
fresh frozen tissue
SAMPLE 385


title: 5617835163_B

description:
fresh frozen tissue
SAMPLE 404


title: 5617835162_A

description:
fresh frozen tissue
SAMPLE 399


title: 5617835151_D

description:
fresh frozen tissue
SAMPLE 391


title: 5617835154_D

description:
fresh frozen tissue
SAMPLE 395


title: 5617835134_F

description:
fresh frozen tissue
SAMPLE 382


title: 5617835137_K

description:
fresh frozen tissue
SAMPLE 389


title: 5617835134_A

description:
fresh frozen tissue
SAMPLE 380


title: 5617835137_G

description:
fresh frozen tissue
SAMPLE 387


title: 5617835151_H

description:
fresh frozen tissue
SAMPLE 393


title: 5617835134_J

description:
fresh frozen tissue
SAMPLE 384


title: 5617835163_A

description:
fresh frozen tissue
SAMPLE 403


title: 5617835154_I

description:
fresh frozen tissue
SAMPLE 397


title: 5617835132_K

description:
fresh frozen tissue
SAMPLE 379


title: 5617835131_K

description:
fresh frozen tissue
SAMPLE 373


title: 5617835085_F

description:
fresh frozen tissue
SAMPLE 359


title: 5617835132_C

description:
fresh frozen tissue
SAMPLE 375


title: 5617835131_J

description:
fresh frozen tissue
SAMPLE 372


title: 5617835085_I

description:
fresh frozen tissue
SAMPLE 362


title: 5617835132_H

description:
fresh frozen tissue
SAMPLE 377


title: 5617835127_A

description:
fresh frozen tissue
SAMPLE 364


title: 5617835126_H

description:
fresh frozen tissue
SAMPLE 356


title: 5617835126_D

description:
fresh frozen tissue
SAMPLE 354


title: 5617835131_H

description:
fresh frozen tissue
SAMPLE 371


title: 5617835085_D

description:
fresh frozen tissue
SAMPLE 358


title: 5617835126_E

description:
fresh frozen tissue
SAMPLE 355


title: 5617835131_C

description:
fresh frozen tissue
SAMPLE 369


title: 5617835085_H

description:
fresh frozen tissue
SAMPLE 361


title: 5617835131_E

description:
fresh frozen tissue
SAMPLE 370


title: 5617835132_A

description:
fresh frozen tissue
SAMPLE 374


title: 5617835085_G

description:
fresh frozen tissue
SAMPLE 360


title: 5617835126_B

description:
fresh frozen tissue
SAMPLE 353


title: 5617835084_K

description:
fresh frozen tissue
SAMPLE 352


title: 5617835132_E

description:
fresh frozen tissue
SAMPLE 376


title: 5617835127_F

description:
fresh frozen tissue
SAMPLE 366


title: 5617835127_J

description:
fresh frozen tissue
SAMPLE 368


title: 5617835127_D

description:
fresh frozen tissue
SAMPLE 365


title: 5617835127_H

description:
fresh frozen tissue
SAMPLE 367


title: 5617835132_J

description:
fresh frozen tissue
SAMPLE 378


title: 5617835085_K

description:
fresh frozen tissue
SAMPLE 363


title: 5617835085_B

description:
fresh frozen tissue
SAMPLE 357


title: 5617835083_E

description:
fresh frozen tissue
SAMPLE 342


title: 5617835084_I

description:
fresh frozen tissue
SAMPLE 351


title: 5617835084_F

description:
fresh frozen tissue
SAMPLE 350


title: 5617835125_B

description:
fresh frozen tissue
SAMPLE 345


title: 5617835124_I

description:
fresh frozen tissue
SAMPLE 341


title: 5617835124_A

description:
fresh frozen tissue
SAMPLE 337


title: 5617835125_C

description:
fresh frozen tissue
SAMPLE 346


title: 5617835120_D

description:
fresh frozen tissue
SAMPLE 331


title: 5617835125_L

description:
fresh frozen tissue
SAMPLE 348


title: 5617835082_C

description:
fresh frozen tissue
SAMPLE 335


title: 5617835120_H

description:
fresh frozen tissue
SAMPLE 333


title: 5617835083_I

description:
fresh frozen tissue
SAMPLE 344


title: 5617835120_K

description:
fresh frozen tissue
SAMPLE 334


title: 5617835124_D

description:
fresh frozen tissue
SAMPLE 338


title: 5617835084_B

description:
fresh frozen tissue
SAMPLE 349


title: 5617835080_J

description:
fresh frozen tissue
SAMPLE 329


title: 5617835082_I

description:
fresh frozen tissue
SAMPLE 336


title: 5617835124_E

description:
fresh frozen tissue
SAMPLE 339


title: 5617835120_B

description:
fresh frozen tissue
SAMPLE 330


title: 5617835080_F

description:
fresh frozen tissue
SAMPLE 327


title: 5617835124_G

description:
fresh frozen tissue
SAMPLE 340


title: 5617835083_F

description:
fresh frozen tissue
SAMPLE 343


title: 5617835125_I

description:
fresh frozen tissue
SAMPLE 347


title: 5617835080_D

description:
fresh frozen tissue
SAMPLE 326


title: 5617835080_A

description:
fresh frozen tissue
SAMPLE 325


title: 5617835120_E

description:
fresh frozen tissue
SAMPLE 332


title: 5617835080_H

description:
fresh frozen tissue
SAMPLE 328


title: 5617835119_L

description:
fresh frozen tissue
SAMPLE 324


title: 5617835119_F

description:
fresh frozen tissue
SAMPLE 322


title: 5617835119_I

description:
fresh frozen tissue
SAMPLE 323


title: 5617835116_K

description:
fresh frozen tissue
SAMPLE 315


title: 5617835078_I

description:
fresh frozen tissue
SAMPLE 319


title: 5617835119_B

description:
fresh frozen tissue
SAMPLE 320


title: 5617835119_E

description:
fresh frozen tissue
SAMPLE 321


title: 5617835077_I

description:
fresh frozen tissue
SAMPLE 309


title: 5617835116_B

description:
fresh frozen tissue
SAMPLE 311


title: 5617835114_G

description:
fresh frozen tissue
SAMPLE 305


title: 5617835077_A

description:
fresh frozen tissue
SAMPLE 306


title: 5617835078_F

description:
fresh frozen tissue
SAMPLE 318


title: 5617835077_F

description:
fresh frozen tissue
SAMPLE 308


title: 5617835116_D

description:
fresh frozen tissue
SAMPLE 312


title: 5617835077_C

description:
fresh frozen tissue
SAMPLE 307


title: 5617835076_E

description:
fresh frozen tissue
SAMPLE 299


title: 5617835078_D

description:
fresh frozen tissue
SAMPLE 317


title: 5617835077_K

description:
fresh frozen tissue
SAMPLE 310


title: 5617835116_G

description:
fresh frozen tissue
SAMPLE 313


title: 5617835114_F

description:
fresh frozen tissue
SAMPLE 304


title: 5617835116_J

description:
fresh frozen tissue
SAMPLE 314


title: 5617835113_I

description:
fresh frozen tissue
SAMPLE 298


title: 5617835076_G

description:
fresh frozen tissue
SAMPLE 300


title: 5617835078_C

description:
fresh frozen tissue
SAMPLE 316


title: 5617835076_K

description:
fresh frozen tissue
SAMPLE 302


title: 5617835114_A

description:
fresh frozen tissue
SAMPLE 303


title: 5617835076_I

description:
fresh frozen tissue
SAMPLE 301


title: 5617835113_E

description:
fresh frozen tissue
SAMPLE 296


title: 5617835075_J

description:
fresh frozen tissue
SAMPLE 293


title: 5617835112_G

description:
fresh frozen tissue
SAMPLE 290


title: 5617835075_A

description:
fresh frozen tissue
SAMPLE 292


title: 5617835113_D

description:
fresh frozen tissue
SAMPLE 295


title: 5617835113_H

description:
fresh frozen tissue
SAMPLE 297


title: 5617835112_B

description:
fresh frozen tissue
SAMPLE 288


title: 5617835074_G

description:
fresh frozen tissue
SAMPLE 287


title: 5617835111_L

description:
fresh frozen tissue
SAMPLE 286


title: 5617835110_L

description:
fresh frozen tissue
SAMPLE 280


title: 5617835110_B

description:
fresh frozen tissue
SAMPLE 276


title: 5617835073_L

description:
fresh frozen tissue
SAMPLE 275


title: 5617835111_D

description:
fresh frozen tissue
SAMPLE 282


title: 5617835111_J

description:
fresh frozen tissue
SAMPLE 285


title: 5617835110_D

description:
fresh frozen tissue
SAMPLE 277


title: 5617835073_E

description:
fresh frozen tissue
SAMPLE 273


title: 5617835111_B

description:
fresh frozen tissue
SAMPLE 281


title: 5617835110_E

description:
fresh frozen tissue
SAMPLE 278


title: 5617835110_H

description:
fresh frozen tissue
SAMPLE 279


title: 5617835111_E

description:
fresh frozen tissue
SAMPLE 283


title: 5617835112_D

description:
fresh frozen tissue
SAMPLE 289


title: 5617835111_G

description:
fresh frozen tissue
SAMPLE 284


title: 5617835073_D

description:
fresh frozen tissue
SAMPLE 272


title: 5617835112_H

description:
fresh frozen tissue
SAMPLE 291


title: 5617835073_J

description:
fresh frozen tissue
SAMPLE 274


title: 5617835109_E

description:
fresh frozen tissue
SAMPLE 268


title: 5617835073_A

description:
fresh frozen tissue
SAMPLE 271


title: 5617835109_H

description:
fresh frozen tissue
SAMPLE 269


title: 5617835109_A

description:
fresh frozen tissue
SAMPLE 266


title: 5617835109_K

description:
fresh frozen tissue
SAMPLE 270


title: n5958040041_K

description:
fresh frozen tissue
SAMPLE 265


title: 5617835109_B

description:
fresh frozen tissue
SAMPLE 267


title: n5958040041_F

description:
fresh frozen tissue
SAMPLE 264


title: 5617835107_D

description:
fresh frozen tissue
SAMPLE 260


title: 5617835107_J

description:
fresh frozen tissue
SAMPLE 262


title: 5617835107_C

description:
fresh frozen tissue
SAMPLE 259


title: 5617835105_F

description:
fresh frozen tissue
SAMPLE 251


title: 5617835070_J

description:
fresh frozen tissue
SAMPLE 248


title: 5617835071_G

description:
fresh frozen tissue
SAMPLE 255


title: n5958040041_C

description:
fresh frozen tissue
SAMPLE 263


title: 5617835105_J

description:
fresh frozen tissue
SAMPLE 253


title: 5617835104_E

description:
fresh frozen tissue
SAMPLE 242


title: 5617835105_C

description:
fresh frozen tissue
SAMPLE 250


title: 5617835071_K

description:
fresh frozen tissue
SAMPLE 257


title: 5617835105_G

description:
fresh frozen tissue
SAMPLE 252


title: 5617835107_A

description:
fresh frozen tissue
SAMPLE 258


title: 5617835070_A

description:
fresh frozen tissue
SAMPLE 245


title: 5617835104_C

description:
fresh frozen tissue
SAMPLE 241


title: 5617835071_A

description:
fresh frozen tissue
SAMPLE 254


title: 5617835070_L

description:
fresh frozen tissue
SAMPLE 249


title: 5617835069_J

description:
fresh frozen tissue
SAMPLE 240


title: 5617835104_J

description:
fresh frozen tissue
SAMPLE 244


title: 5617835107_H

description:
fresh frozen tissue
SAMPLE 261


title: 5617835071_I

description:
fresh frozen tissue
SAMPLE 256


title: 5617835070_E

description:
fresh frozen tissue
SAMPLE 246


title: 5617835070_F

description:
fresh frozen tissue
SAMPLE 247


title: 5617835104_H

description:
fresh frozen tissue
SAMPLE 243


title: 5617835069_F

description:
fresh frozen tissue
SAMPLE 239


title: 5617835069_C

description:
fresh frozen tissue
SAMPLE 238


title: 5617835068_F

description:
fresh frozen tissue
SAMPLE 231


title: 5617835103_J

description:
fresh frozen tissue
SAMPLE 235


title: 5617835069_B

description:
fresh frozen tissue
SAMPLE 237


title: 5617835103_C

description:
fresh frozen tissue
SAMPLE 234


title: 5617835068_D

description:
fresh frozen tissue
SAMPLE 230


title: 5617835075_L

description:
fresh frozen tissue
SAMPLE 294


title: 5617835066_J

description:
fresh frozen tissue
SAMPLE 223


title: 5617835068_K

description:
fresh frozen tissue
SAMPLE 232


title: 5617835093_C

description:
fresh frozen tissue
SAMPLE 225


title: 5617835103_L

description:
fresh frozen tissue
SAMPLE 236


title: 5617835103_B

description:
fresh frozen tissue
SAMPLE 233


title: 5617835066_I

description:
fresh frozen tissue
SAMPLE 222


title: 5617835093_F

description:
fresh frozen tissue
SAMPLE 226


title: 5617835065_L

description:
fresh frozen tissue
SAMPLE 214


title: 5617835093_G

description:
fresh frozen tissue
SAMPLE 227


title: 5617835092_I

description:
fresh frozen tissue
SAMPLE 217


title: 5617835066_F

description:
fresh frozen tissue
SAMPLE 220


title: 5617835093_A

description:
fresh frozen tissue
SAMPLE 224


title: 5617835093_I

description:
fresh frozen tissue
SAMPLE 228


title: 5617835066_G

description:
fresh frozen tissue
SAMPLE 221


title: 5617835068_B

description:
fresh frozen tissue
SAMPLE 229


title: 5617835092_H

description:
fresh frozen tissue
SAMPLE 216


title: 5617835066_B

description:
fresh frozen tissue
SAMPLE 219


title: 5617835092_K

description:
fresh frozen tissue
SAMPLE 218


title: 5617835065_D

description:
fresh frozen tissue
SAMPLE 211


title: 5617835086_F

description:
fresh frozen tissue
SAMPLE 206


title: 5617835065_J

description:
fresh frozen tissue
SAMPLE 213


title: 5617835086_H

description:
fresh frozen tissue
SAMPLE 207


title: 5617835064_A

description:
fresh frozen tissue
SAMPLE 200


title: 5617835086_L

description:
fresh frozen tissue
SAMPLE 209


title: 5617835092_E

description:
fresh frozen tissue
SAMPLE 215


title: 5617835061_D

description:
fresh frozen tissue
SAMPLE 194


title: 5617835179_D

description:
fresh frozen tissue
SAMPLE 199


title: 5617835061_I

description:
fresh frozen tissue
SAMPLE 196


title: 5617835061_K

description:
fresh frozen tissue
SAMPLE 197


title: 5617835064_D

description:
fresh frozen tissue
SAMPLE 201


title: 5617835086_I

description:
fresh frozen tissue
SAMPLE 208


title: 5617835064_I

description:
fresh frozen tissue
SAMPLE 203


title: 5617835064_L

description:
fresh frozen tissue
SAMPLE 204


title: 5617835176_J

description:
fresh frozen tissue
SAMPLE 192

value: adjacent non-tumor liver


title: 5617835176_F

description:
fresh frozen tissue
SAMPLE 191


title: 5617835175_H

description:
fresh frozen tissue
SAMPLE 188


title: 5617835061_G

description:
fresh frozen tissue
SAMPLE 195


title: 5617835065_A

description:
fresh frozen tissue
SAMPLE 210


title: 5617835179_B

description:
fresh frozen tissue
SAMPLE 198


title: 5617835065_I

description:
fresh frozen tissue
SAMPLE 212


title: 5617835064_H

description:
fresh frozen tissue
SAMPLE 202


title: 5617835175_F

description:
fresh frozen tissue
SAMPLE 187


title: 5617835176_A

description:
fresh frozen tissue
SAMPLE 189


title: 5617835175_D

description:
fresh frozen tissue
SAMPLE 186


title: 5617835176_K

description:
fresh frozen tissue
SAMPLE 193


title: 5617835176_E

description:
fresh frozen tissue
SAMPLE 190


title: 5617835175_B

description:
fresh frozen tissue
SAMPLE 185


title: 5617835170_K

description:
fresh frozen tissue
SAMPLE 179


title: 5617835169_I

description:
fresh frozen tissue
SAMPLE 174


title: n5958040051_D

description:
fresh frozen tissue
SAMPLE 181


title: 5617835169_L

description:
fresh frozen tissue
SAMPLE 175


title: n5958040051_G

description:
fresh frozen tissue
SAMPLE 183


title: n5958040051_L

description:
fresh frozen tissue
SAMPLE 184


title: 5617835163_G

description:
fresh frozen tissue
SAMPLE 168


title: 5617835169_E

description:
fresh frozen tissue
SAMPLE 172


title: 5617835169_G

description:
fresh frozen tissue
SAMPLE 173


title: 5617835154_G

description:
fresh frozen tissue
SAMPLE 161


title: n5958040051_F

description:
fresh frozen tissue
SAMPLE 182


title: 5617835170_E

description:
fresh frozen tissue
SAMPLE 177


title: 5617835163_C

description:
fresh frozen tissue
SAMPLE 166


title: 5617835170_A

description:
fresh frozen tissue
SAMPLE 176


title: n5958040051_A

description:
fresh frozen tissue
SAMPLE 180


title: 5617835164_B

description:
fresh frozen tissue
SAMPLE 170


title: 5617835162_J

description:
fresh frozen tissue
SAMPLE 164


title: 5617835162_E

description:
fresh frozen tissue
SAMPLE 163


title: 5617835154_E

description:
fresh frozen tissue
SAMPLE 160


title: 5617835162_L

description:
fresh frozen tissue
SAMPLE 165


title: 5617835151_K

description:
fresh frozen tissue
SAMPLE 159


title: 5617835151_F

description:
fresh frozen tissue
SAMPLE 157


title: 5617835164_J

description:
fresh frozen tissue
SAMPLE 171


title: 5617835163_D

description:
fresh frozen tissue
SAMPLE 167


title: 5617835170_J

description:
fresh frozen tissue
SAMPLE 178


title: 5617835151_I

description:
fresh frozen tissue
SAMPLE 158


title: 5617835154_H

description:
fresh frozen tissue
SAMPLE 162


title: 5617835163_L

description:
fresh frozen tissue
SAMPLE 169


title: 5617835151_E

description:
fresh frozen tissue
SAMPLE 156


title: 5617835132_G

description:
fresh frozen tissue
SAMPLE 149


title: 5617835137_F

description:
fresh frozen tissue
SAMPLE 153


title: 5617835132_I

description:
fresh frozen tissue
SAMPLE 150


title: 5617835134_B

description:
fresh frozen tissue
SAMPLE 151


title: 5617835085_E

description:
fresh frozen tissue
SAMPLE 136


title: 5617835134_D

description:
fresh frozen tissue
SAMPLE 152


title: 5617835127_G

description:
fresh frozen tissue
SAMPLE 142


title: 5617835127_C

description:
fresh frozen tissue
SAMPLE 140


title: 5617835132_D

description:
fresh frozen tissue
SAMPLE 148


title: 5617835085_L

description:
fresh frozen tissue
SAMPLE 138


title: 5617835132_B

description:
fresh frozen tissue
SAMPLE 147


title: 5617835151_B

description:
fresh frozen tissue
SAMPLE 155


title: 5617835127_I

description:
fresh frozen tissue
SAMPLE 143


title: 5617835131_L

description:
fresh frozen tissue
SAMPLE 146


title: 5617835084_H

description:
fresh frozen tissue
SAMPLE 127


title: 5617835126_A

description:
fresh frozen tissue
SAMPLE 129


title: 5617835127_B

description:
fresh frozen tissue
SAMPLE 139


title: 5617835086_A

description:
fresh frozen tissue
SAMPLE 205


title: 5617835131_G

description:
fresh frozen tissue
SAMPLE 144


title: 5617835127_E

description:
fresh frozen tissue
SAMPLE 141


title: 5617835085_A

description:
fresh frozen tissue
SAMPLE 134


title: 5617835137_L

description:
fresh frozen tissue
SAMPLE 154


title: 5617835085_C

description:
fresh frozen tissue
SAMPLE 135


title: 5617835126_C

description:
fresh frozen tissue
SAMPLE 130


title: 5617835126_G

description:
fresh frozen tissue
SAMPLE 132


title: 5617835126_F

description:
fresh frozen tissue
SAMPLE 131


title: 5617835085_J

description:
fresh frozen tissue
SAMPLE 137


title: 5617835084_J

description:
fresh frozen tissue
SAMPLE 128


title: 5617835126_I

description:
fresh frozen tissue
SAMPLE 133


title: 5617835084_G

description:
fresh frozen tissue
SAMPLE 126


title: 5617835131_I

description:
fresh frozen tissue
SAMPLE 145


title: 5617835084_A

description:
fresh frozen tissue
SAMPLE 125


title: 5617835125_K

description:
fresh frozen tissue
SAMPLE 124


title: 5617835124_J

description:
fresh frozen tissue
SAMPLE 118


title: 5617835124_C

description:
fresh frozen tissue
SAMPLE 115


title: 5617835124_F

description:
fresh frozen tissue
SAMPLE 116


title: 5617835083_A

description:
fresh frozen tissue
SAMPLE 119


title: 5617835124_H

description:
fresh frozen tissue
SAMPLE 117


title: 5617835083_G

description:
fresh frozen tissue
SAMPLE 120


title: 5617835119_A

description:
fresh frozen tissue
SAMPLE 100


title: 5617835119_J

description:
fresh frozen tissue
SAMPLE 103


title: 5617835119_K

description:
fresh frozen tissue
SAMPLE 104


title: 5617835082_D

description:
fresh frozen tissue
SAMPLE 112


title: 5617835119_G

description:
fresh frozen tissue
SAMPLE 102


title: 5617835082_J

description:
fresh frozen tissue
SAMPLE 114


title: 5617835078_E

description:
fresh frozen tissue
SAMPLE 98


title: 5617835080_G

description:
fresh frozen tissue
SAMPLE 105


title: 5617835083_J

description:
fresh frozen tissue
SAMPLE 122


title: 5617835078_J

description:
fresh frozen tissue
SAMPLE 99


title: 5617835120_C

description:
fresh frozen tissue
SAMPLE 108


title: 5617835120_G

description:
fresh frozen tissue
SAMPLE 109


title: 5617835080_I

description:
fresh frozen tissue
SAMPLE 106


title: 5617835082_B

description:
fresh frozen tissue
SAMPLE 111


title: 5617835119_D

description:
fresh frozen tissue
SAMPLE 101


title: 5617835083_H

description:
fresh frozen tissue
SAMPLE 121


title: 5617835125_H

description:
fresh frozen tissue
SAMPLE 123


title: 5617835120_A

description:
fresh frozen tissue
SAMPLE 107


title: 5617835116_L

description:
fresh frozen tissue
SAMPLE 96


title: 5617835120_L

description:
fresh frozen tissue
SAMPLE 110


title: 5617835082_G

description:
fresh frozen tissue
SAMPLE 113


title: 5617835116_I

description:
fresh frozen tissue
SAMPLE 95


title: 5617835116_F

description:
fresh frozen tissue
SAMPLE 94


title: 5617835078_B

description:
fresh frozen tissue
SAMPLE 97


title: 5617835112_K

description:
fresh frozen tissue
SAMPLE 76


title: 5617835116_C

description:
fresh frozen tissue
SAMPLE 93


title: 5617835114_E

description:
fresh frozen tissue
SAMPLE 86


title: 5617835077_J

description:
fresh frozen tissue
SAMPLE 91


title: 5617835114_K

description:
fresh frozen tissue
SAMPLE 88


title: 5617835113_J

description:
fresh frozen tissue
SAMPLE 82


title: 5617835113_F

description:
fresh frozen tissue
SAMPLE 80


title: 5617835113_B

description:
fresh frozen tissue
SAMPLE 78


title: 5617835113_G

description:
fresh frozen tissue
SAMPLE 81


title: 5617835076_J

description:
fresh frozen tissue
SAMPLE 84


title: 5617835077_E

description:
fresh frozen tissue
SAMPLE 90


title: 5617835076_D

description:
fresh frozen tissue
SAMPLE 83


title: 5617835113_C

description:
fresh frozen tissue
SAMPLE 79


title: 5617835112_A

description:
fresh frozen tissue
SAMPLE 73


title: 5617835110_C

description:
fresh frozen tissue
SAMPLE 67


title: 5617835112_F

description:
fresh frozen tissue
SAMPLE 75


title: 5617835114_H

description:
fresh frozen tissue
SAMPLE 87


title: 5617835116_A

description:
fresh frozen tissue
SAMPLE 92


title: 5617835110_A

description:
fresh frozen tissue
SAMPLE 66


title: 5617835111_H

description:
fresh frozen tissue
SAMPLE 71


title: 5617835110_F

description:
fresh frozen tissue
SAMPLE 68


title: 5617835111_F

description:
fresh frozen tissue
SAMPLE 70


title: 5617835111_K

description:
fresh frozen tissue
SAMPLE 72


title: 5617835073_I

description:
fresh frozen tissue
SAMPLE 65


title: 5617835075_I

description:
fresh frozen tissue
SAMPLE 77


title: 5617835110_G

description:
fresh frozen tissue
SAMPLE 69


title: 5617835112_C

description:
fresh frozen tissue
SAMPLE 74


title: 5617835114_B

description:
fresh frozen tissue
SAMPLE 85


title: 5617835077_D

description:
fresh frozen tissue
SAMPLE 89


title: 5617835072_G

description:
fresh frozen tissue
SAMPLE 58


title: 5617835109_F

description:
fresh frozen tissue
SAMPLE 61


title: 5617835107_I

description:
fresh frozen tissue
SAMPLE 56


title: 5617835073_F

description:
fresh frozen tissue
SAMPLE 64


title: 5617835109_J

description:
fresh frozen tissue
SAMPLE 62


title: 5617835073_C

description:
fresh frozen tissue
SAMPLE 63


title: 5617835109_C

description:
fresh frozen tissue
SAMPLE 60


title: 5617835071_L

description:
fresh frozen tissue
SAMPLE 54


title: 5617835107_B

description:
fresh frozen tissue
SAMPLE 55