title: sourceC_lineage4_mantled_1_MP

value: Mantled


title: sourceC_lineage5_normal_2_N

status: Public on Sep 09 2015

type: genomic

city: St. Louis

first: Steve

middle: W.

last: smith

state: MO

address: 4041 Forest Park Ave

department: Bioinformatics

country: USA

institute: Orion Genomics

hyb_protocol: Hybridizations were performed by Mogene (St. Louis, MO) following standard Nimblegen conditions.

scan_protocol: Arrays were scanned by Mogene (St. Louis, MO) on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed by Mogene (St. Louis, MO) using Nimblegen's standard protocol for custom Nimblescan data extraction.
For data processing, corrections on spatial non-uniformity of fluorescent signal intensities, done separately for the Cy3 and Cy5 dye channels, were made. Data were then normalized by background subtraction using negative control probes, followed by scaling. After normalization, median log signal of the control probes for each dye of each array is set to zero. MAD (median absolute deviation) log signal of all the probes on an array is a constant for a give treatment (untreated or DNA methylation depleted). DNA methylation was measured as the sample average (over the two pairs of dye-swapped technical replicates) of normalized log2 ratios of untreated over DNA methylation depleted. The raw data files are labeled with "UT" for untreated or "MD" for Methyl-depleted.

molecule: genomic DNA

organism: Elaeis guineensis

source_name: UT (untreated) or MD (methyl-depleted)

label_protocol: For each fraction, 200 ng was used for cyanogen dye labeling (Cy3 or Cy5).  For each sample, four microarrays were hybridized in a duplicated dye swap design to differentially labeled untreated and DNA methylation depleted fractions.  Labeling was performed by MOgene (St. Louis, MO) following standard Nimblegen protocols.

extract_protocol: Genomic DNA was extracted from adult leaf tissue by standard methods.  Genomic DNA (60 µg) was mechanically sheared to 1-4 kb fragments by hydroshearing.  Sheared DNA was divided into four equal portions, two of which were digested with 10 units/µg McrBC (New England Biolabs) under manufacturer’s recommended conditions and the other two were mock treated without adding enzyme.  Following digestion, DNAs were treated with proteinase K (50mg/ml) for 1 hour at 50oC and then precipitated with EtOH under standard conditions.  Resuspended DNAs were resolved by agarose gel electrophoresis, and DNA in the 1-4 kb size range was excised from the gel and extracted.

tag: phenotype

value: Normal

tag: tissue

value: adult leaf


title: Heart-Vehicle-rep3

type: protein

city: Beijing

first: Hao

last: LI

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

country: China

institute: Peking University Third Hospital

hyb_protocol: Antibody arrays were used according to the manufacturer’s instructions. All sample measurements were performed in duplicate. The array glass slides were washed, incubated with a biotin-conjugated anti-cytokine mix for 2 hours, washed again, and developed for 2 hours with HRP-conjugated streptavidin.

scan_protocol: Expose to x-ray film and detect signal using film developer or detect signal directly from membrane using chemiluminescene imaging system.

data_processing: By comparing the signal intensities, relative expression levels of cytokines can be made. The intensities of signals can be quantified by densitometry. Positive control can be used to normalize the results from different membranes being compared.

label: biotin

molecule: protein

organism: Mus musculus

source_name: heart, vehicle

label_protocol: Samples were labeled according to the manufacturer’s instructions

extract_protocol: Weigh out tissue and cut into cubes. Prepare protein extraction reagent containing inhibitors. Add ice-cold Protein Extraction Reagent containing protease inhibitors. Grind in a blender on low power using 30-second bursts until fully homogenized. Allow material to cool for 1 minute between bursts. Centrifuge the lysate at 14,000xg for 15 minutes and transfer the supernatant to a new tube for further analysis.

treatment_protocol: Mice were subcutaneous injected with a single dose of  isoproterenol (ISO, 5 mg/kg body weight) or vehicle saline (10 ml/kg body weight). Hearts were harvested and immediately frozen in liquid nitrogen.

tag: age

value: 10 weeks old

tag: Sex

value: Male

tag: strain

value: Heart


title: sourceC_lineage4_mantled_2_MP


title: sourceC_lineage5_normal_1_N


title: sourceC_lineage5_normal_4_N


title: Heart-Vehicle-rep1


title: Heart-Vehicle-rep2


title: Sample_16

type: RNA

city: Seattle

first: Jamie

last: Guenthoer

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The raw array data were then exported to the R v3.0.3 statistical software Bioconductor lumi package for pre-processing, and the gene expression values were log2 transformed. Probes were identified to be low signal if the log2 expression values were below the median of negative controls for each sample. Probes with more than 1/3 low signal across samples were excluded. A median normalization was carried out. As the data were processed in batches, including the batch effect from FFPE vs. Frozen samples, the ComBat algorithm was used to remove the batch effect before combining data from different batches. Data were then subjected to shorth variance filtering to remove probes that have no or little variation across samples (9). In this filtering, probes with a standard deviation less than the mean of the standard deviations of arrays within the shorth interval were removed from further analysis. Of the starting 29,361 probes in the WG-DASL assay, after preprocessing there were 19,168 probes left for analysis.

molecule: total RNA

organism: Homo sapiens

source_name: Breast Tumor Tissue_7161-16 rep 1

label_protocol: cDNA generation and biotin labeling was performed using the Illumina Whole-Genome DASL HT assay according to manufacturer's recommended protocol.

extract_protocol: RNA was extracted from FFPE tissue sections using Qiagen FFPE RNeasy kit and from fresh or frozen tissue using Qiagen AllPrep DNA/RNA Mini Kit according to manufacturer's recommended protocols. RNA was further cleaned up with DnaseI treatment. RNA quantity and quality was assessed on a Nanodrop Spectrophotometer.

value: breast tumor

tag: specimen preparation

value: FFPE

tag: pre/post treatment

value: Pre

tag: dose cohort

value: Cohort 4


title: sourceC_lineage5_normal_3_N


title: Sample_14X

scan_protocol: Standard Illumina hybridization protocol

source_name: Breast Tumor Tissue_7161-15 rep 2


title: Sample_15

source_name: Breast Tumor Tissue_7161-07 rep 1

value: Cohort 2


title: Sample_14

source_name: Breast Tumor Tissue_7161-15 rep 1


title: Sample_13X

source_name: Breast Tumor Tissue_7161-09 rep 2

value: Cohort 3


title: Sample_09

description: Due to high missing probe rate, sample dropped from final analysis and not included in normalized dataset

source_name: Breast Tumor Tissue_7161-02 rep 1

value: Cohort 1


title: Sample_13

source_name: Breast Tumor Tissue_7161-09 rep 1


title: Sample_11X

source_name: Breast Tumor Tissue_7161-06 rep 2


title: sourceC_lineage4_normal_3_N

description: There are intentionally only 6 raw data files associated with this sample. One of the four arrays for this sample failed QC. When this happens, as a compromise, we use one array twice in the two technical replicates for one way of labeling. In this way we keep dye-bias neutralized with the compromise that signals from one array are weighted twice as much as those from other arrays.


title: Sample_11

source_name: Breast Tumor Tissue_7161-06 rep 1


title: Sample_10

source_name: Breast Tumor Tissue_7161-05 rep 1


title: sourceC_lineage3_mantled_4_MP


title: sourceC_lineage3_mantled_1_MP


title: sourceC_lineage3_mantled_2_MP


title: sourceC_lineage3_mantled_5_MP


title: Sample_8


title: Sample_08X

source_name: Breast Tumor Tissue_7161-02 rep 2


title: K562-FLT3-ITD-2_rep2

city: Isehara-shi

first: Anar

middle: Damdinsuren

last: Damdinsuren

state: Kanagawa

address: 143 Shimokasuya

department: Department of Laboratory Medicine

country: Japan

institute: Tokai University, School of Medicine

description: Gene expression in K562 cell line after stable transfection with pMY-puro-FLT3-ITD-2 plasmid DNA

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 10x Gene Expression Blocking Agent and 25x Fragmentation Buffer, according to the manufacturers instructions. 2x Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Whole Human Genome Microarray 4x44K v2 (G2519F-026652) for 17 hours at 65°C. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 and 1 minute with 37°C Gene Expression Wash buffer 2 and immediately dried.

scan_protocol: Slides were scanned on Agilent DNA Microarray Scanner (G2505A) using one color scan setting.

data_processing:
The scanned images were analyzed with Feature Extraction Software using default parameters (protocol GE1-v5_91_0806 and Grid: 026652_D_F_20100115).
75% tile shift (Genespring GX)

source_name: Cell line culture, replicate 2

label_protocol: 200ng cRNA was labeled with Cyanine-3 (Cy3) using One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions. Labeled cRNA was purified using RNEasy Mini Kit (QIAGEN), and quantified by NanoDrop ND-1000 spectrophotometer.

growth_protocol: Cells were cultured in RPMI-1640 medium (Wako, Osaka, Japan), containing 10% FBS (Wako) and 1% Penicillin/Streptomycin (Sigma–Aldrich, St. Louis, MO, USA) at 37oC and 5% CO2.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturers protocol. RNA quality was confirmed using Agilent Model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cell line

tag: plasmid


title: sourceC_lineage3_normal_2_N


title: K562-FLT3-ITD-1_rep2

description: Gene expression in K562 cell line after stable transfection with pMY-puro-FLT3-ITD-1 plasmid DNA


title: K562-FLT3-ITD-2_rep1

source_name: Cell line culture, replicate 1


title: K562-FLT3-ITD-1_rep3

source_name: Cell line culture, replicate 3


title: Sample_7

source_name: Breast Tumor Tissue_7161-01 rep 1


title: sourceC_lineage3_normal_3_N

source_name: UT (untreated) or MD (methyl-depleted)


title: sourceC_lineage4_normal_1_N


title: K562-FLT3-ITD-1_rep1


title: Sample_6

source_name: Breast Tumor Tissue_7161-33 rep 1

value: Fresh

value: Post

value: Cohort 6


title: Sample_12

source_name: Breast Tumor Tissue_7161-08 rep 1


title: sourceD_lineage15_normal_3_N


title: sourceD_lineage15_normal_1_N


title: sourceC_lineage3_normal_1_N


title: Sample_4

source_name: Breast Tumor Tissue_7161-18 rep 1


title: sourceD_lineage15_normal_2_N


title: Sample_03X

source_name: Breast Tumor Tissue_7161-08 rep 2


title: K562-mock_rep3

description: Gene expression in K562 cell line after stable transfection with pMY-puro plasmid DNA

value: pMY-puro


title: sourceD_lineage11_mantled_3_M

value: Mantled


title: Sample_3


title: sourceC_lineage4_normal_2_N

value: Normal


title: sourceD_lineage11_mantled_1_M

value: adult leaf


title: sourceD_lineage11_mantled_2_M


title: sourceD_lineage11_mantled_4_M


title: Sample_2


title: K562-mock_rep1


title: sourceD_lineage11_normal_2_N


title: Sample_1


title: Sample_02X

source_name: Breast Tumor Tissue_7161-05 rep 2


title: sourceD_lineage11_normal_3_N


title: K562-mock_rep2


title: sourceD_lineage11_normal_1_N


title: MTS 29 (KHR)

city: Chicago

first: Michael

last: Spiotto

state: IL

department: Radiation Oncology

institute: The University of Chicago

description: Biological Replicate 5

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with background subtrations in Genome Studio. Data was exported and analyzed by Partek Genomics Suite 6.

source_name: KHR

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

growth_protocol: Oral tumors were allowed to grow for 21d and were isolated.

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

treatment_protocol: At the time of isolation, tumors were placed in Trizol, snap frozen and stored at -80 C.

value: Oral tumor tissue


title: sourceD_lineage10_mantled_4_M


title: sourceD_lineage10_mantled_3_M


title: Hypoxia treated, CD44hi sorted, biological replicate 3

city: Cambridge

first: Christine

last: Loreth

state: MA

address: 610 Main St

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on the Affymetrix Human U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: SKBR3, 1% oxygen 7 days, sorted CD44hi

label_protocol: Amplified RNA (aRNA) was synthesized and biotin labeled according to the Affymetrix 3'IVT labeling protocol from 200ng total RNA

growth_protocol: SKBR3 cells were maintained in McCoy's 5A with 10% serum, and penicillin/streptomycin

extract_protocol: Cells were harvested in buffer RLT (Qiagen) followed by RNA isolation using the RNeasy kit (#74104, Qiagen).

treatment_protocol: Cells were treated with 60 nM epirubicin for 3 days or incubated at 1% oxygen (hypoxia) for 7 days. Cells were then harvested and flow-sorted (FACS) based on CD44 surface expression.

value: SKBR3 cells


title: Hypoxia treated, CD44hi sorted, biological replicate 4


title: MTS 22 (KHR-N-/-)

description: Biological Replicate 4

source_name: KHR-Notch1 -/-


title: sourceC_lineage3_mantled_3_MP


title: Hypoxia treated, CD44hi sorted, biological replicate 2


title: sourceD_lineage10_mantled_2_M


title: sourceD_lineage10_mantled_1_M


title: MTS 16 (KHR-N+/-)

description: Biological Replicate 4

source_name: KHR-Notch1 +/-


title: MTS 11 (KR-N-/-)

description: Biological Replicate 4

source_name: KR-Notch1 -/-


title: MTS 10 (KR-N-/-)

description: Biological Replicate 3


title: MTS 5 (KR-N+/-)

description: Biological Replicate 5


title: Hypoxia treated, CD44hi sorted, biological replicate 1


title: sourceD_lineage10_normal_2_N


title: sourceD_lineage10_normal_4_N


title: Hypoxia treated, CD44-/lo sorted, biological replicate 3

source_name: SKBR3, 1% oxygen 7 days, sorted CD44-/lo


title: Hypoxia treated, CD44-/lo sorted, biological replicate 4


title: sourceD_lineage10_normal_3_N


title: MTS 27 (KHR)

description: Biological Replicate 3


title: MTS 4 (KR-N+/-)

description: Biological Replicate 4


title: sourceA_lineage9_mantled_1_A


title: MTS 28 (KHR)

description: Biological Replicate 4


title: Hypoxia treated, CD44-/lo sorted, biological replicate 1


title: MTS 20 (KHR-N-/-)

description: Biological Replicate 2


title: MTS 15 (KHR-N+/-)

description: Biological Replicate 3


title: Hypoxia treated, CD44-/lo sorted, biological replicate 2


title: sourceA_lineage9_normal_1_N


title: sourceA_lineage9_normal_3_N


title: Epirubicin treated, CD44hi sorted, biological replicate 3

source_name: SKBR3, 60nM epirubicin 3 days, sorted CD44hi


title: MTS 9 (KR-N-/-)

description: Biological Replicate 2


title: Epirubicin treated, CD44-/lo sorted, biological replicate 4

source_name: SKBR3, 60nM epirubicin 3 days, sorted CD44-/lo


title: sourceA_lineage9_mantled_2_A


title: Epirubicin treated, CD44hi sorted, biological replicate 1


title: MTS 23 (KHR-N-/-)

description: Biological Replicate 5


title: sourceA_lineage8_mantled_2_A


title: Epirubicin treated, CD44hi sorted, biological replicate 4


title: MTS 14 (KHR-N+/-)

description: Biological Replicate 2


title: Epirubicin treated, CD44hi sorted, biological replicate 2


title: MTS 21 (KHR-N-/-)

description: Biological Replicate 3


title: Epirubicin treated, CD44-/lo sorted, biological replicate 3


title: MTS 3 (KR-N+/-)

description: Biological Replicate 3


title: sourceA_lineage8_mantled_3_A


title: sourceA_lineage8_mantled_4_A


title: sourceA_lineage9_normal_2_N


title: sourceA_lineage8_mantled_1_A


title: sourceD_lineage10_normal_1_N


title: sourceA_lineage8_normal_1_N


title: MTS 26 (KHR)

description: Biological Replicate 2


title: sourceA_lineage8_normal_2_N


title: Untreated, biological replicate 1

source_name: SKBR3, untreated


title: Epirubicin treated, CD44-/lo sorted, biological replicate 1


title: Untreated, biological replicate 3


title: MTS 19 (KHR-N-/-)

description: Biological Replicate 1


title: Untreated, biological replicate 2


title: MTS 1 (KR-N+/-)

description: Biological Replicate 1


title: MTS 25 (KHR)

description: Biological Replicate 1


title: Epirubicin treated, CD44-/lo sorted, biological replicate 2


title: MTS 13 (KHR-N+/-)

description: Biological Replicate 1


title: MTS 2 (KR-N+/-)

description: Biological Replicate 2


title: PAN-MeOH3

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

hyb_protocol: Following fragmentation, 10 g of biotinylated cRNA was hybridized to Affymetrix HG-U133_2.0 arrays fro 16 h at 45°C. Arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix hybridization, wash and stain kit

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update

data_processing: CEL files were analyzed with the MAS5 algorithm using default settings and global scaling to a target intensity of 1000

source_name: human immortalized podocyte cell line, puromycin+methanol treated, 48 h

label_protocol: Biotinylated cRNA was prepared unsing the Affymetrix Express kit protocol strating from 200 ng of total RNA

growth_protocol: Cell were grown in RPMI medium supplemented with 10% FCS, 1% Penecillin/Streptomycin and insulin, tranferrin, and selenite

extract_protocol: RNA was extracted after 48 h of treatment using the RNeasy mini kit (QIAGEN) including the DNase I digestion step

treatment_protocol: Everolimus (dissolved in methanol) and puromycin were added at 100 nM and 30 µg/ml final concentration, respectively

tag: treatment

value: puromycin+methanol

tag: cell type

value: podocyte


title: sourceA_lineage13_mantled_3_A


title: MTS21 (KHR-NICD)

description: Biological Replicate 6

source_name: KHR-NICD tumor biological replicate 6


title: MTS 8 (KR-N-/-)

description: Biological Replicate 1


title: sourceA_lineage13_mantled_1_A

source_name: UT (untreated) or MD (methyl-depleted)


title: sourceA_lineage8_normal_3_N


title: MTS20 (KHR-NICD)

description: Biological Replicate 5

source_name: KHR-NICD tumor biological replicate 5


title: PAN-MeOH2


title: PAN-MeOH1


title: MTS8 (KHR)

description: Biological Replicate 6

source_name: KHR tumor biological replicate 6


title: sourceA_lineage13_mantled_2_A


title: MTS19 (KHR-NICD)

description: Biological Replicate 4

source_name: KHR-NICD tumor biological replicate 4


title: PAN-EV3

source_name: human immortalized podocyte cell line, puromycin+everolimus treated, 48 h

value: puromycin+everolimus


title: sourceA_lineage14_mantled_1_A


title: MTS7 (KHR)

description: Biological Replicate 5

source_name: KHR tumor biological replicate 5


title: MTS5 (KHR)

description: Biological Replicate 4

source_name: KHR tumor biological replicate 4


title: PAN-EV2


title: sourceA_lineage13_normal_4_N


title: sourceA_lineage13_normal_2_N


title: MTS24 (KHR-NICD)

description: Biological Replicate 3

source_name: KHR-NICD tumor biological replicate 3


title: MeOH2

source_name: human immortalized podocyte cell line, methanol treated control, 48 h

value: methanol


title: MeOH3


title: sourceA_lineage7_mantled_3_A


title: sourceA_lineage7_mantled_4_A


title: sourceA_lineage13_normal_1_N


title: MTS18 (KHR-NICD)

description: Biological Replicate 2

source_name: KHR-NICD tumor biological replicate 2


title: sourceA_lineage13_normal_3_N


title: Homo sapiens gastric carcinoma cells SGC-7901_LncRNA-SNHG5 l

first: Shi

last: Juan

address: 5 Dong Dan San Tiao

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description: This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with vecotr

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

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

source_name: Homo sapiens gastric carcinoma SGC-7901

label_protocol: Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

growth_protocol: Homo sapiens gastric carcinoma SGC-7901 was grown to Logarithmic phase phase (5% CO2,at 37°C ) in RPMI1640 (Gibco, Eggenstein, Germany) supplemented with 10% (vol) fetal bovine serum (10106078, Gibco) and 100U/ml penicillin,transfected with siRNA control 20nmol/ml for 48 h

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Homo sapiens gastric carcinoma SGC-7901 was grown to Logarithmic phase phase (5% CO2,at 37°C ) in RPMI1640 (Gibco, Eggenstein, Germany) supplemented with 10% (vol) fetal bovine serum (10106078, Gibco) and 1% (vol) penicillin (15140114, Gibco) ,transfected with siRNA negative control or total siRNAs against MTA2 for 48h, or transfected with vector or SNHG5 plasmid

tag: genotype

value: transfected with SNHG5 plasmid(pCDH-CMV-SNHG5-EF1-GreenPuro-CD511B)

value: SNHG5 overexpression

value: gastric cancer


title: Homo sapiens gastric carcinoma cells SGC-7901_vector control

description: This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with vecotr(pCDH-CMV-MCS-EF1-GreenPuro-CD511B-1, SBI, )

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

value: vector control group


title: sourceA_lineage14_normal_1_N


title: Homo sapiens gastric carcinoma cells SGC-7901_MTA2 siRNA total

description: This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with siRNA agianst MTA2 (MTA2-homo-556: Sense：5'-3' CAGCCUGGCUGAUAGUAAUTT, Antisense：5'-3' AUUACUAUCAGCCAGGCUGTT; MTA2-homo-2364:Sense：5'-3' GCACCAAUGAGCCUAUUGUTT, Antisense：5'-3' ACAAUAGGCUCAUUGGUGCTT; MTA2-homo-409:Sense：5'-3' GGUGGGAGAUUACGUCUAUTT, Antisense：5'-3' AUAGACGUAAUCUCCCACCTT)

value: transfected with siRNA against MTA2(Total; MTA2-homo-556 Sense：5'-3' CAGCCUGGCUGAUAGUAAUTT, Antisense：5'-3' AUUACUAUCAGCCAGGCUGTT; MTA2-homo-2364;Sense：5'-3' GCACCAAUGAGCCUAUUGUTT, Antisense：5'-3' ACAAUAGGCUCAUUGGUGCTT;MTA2-homo-409 Sense：5'-3' GGUGGGAGAUUACGUCUAUTT Antisense：5'-3' AUAGACGUAAUCUCCCACCTT

value: MTA2 knock down


title: sourceA_lineage7_mantled_1_A


title: sourceA_lineage7_mantled_2_A


title: MTS3 (KHR)

description: Biological Replicate 3

source_name: KHR tumor biological replicate 3


title: EV1

source_name: human immortalized podocyte cell line, everolimus treated, 48 h

value: everolimus


title: MTS16 (KHR-NICD)

description: Biological Replicate 1

source_name: KHR-NICD tumor biological replicate 1


title: EV3


title: PAN-EV1


title: MTS1 (KHR)

description: Biological Replicate 1

source_name: KHR tumor biological replicate 1


title: MeOH1


title: MTS2 (KHR)

description: Biological Replicate 2

source_name: KHR tumor biological replicate 2


title: Homo sapiens gastric carcinoma cells SGC-7901_siRNA control

description: This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with siRNA normal control (Sense：5'-3'UUCUCC GAA CGU GUC ACGUTT, Antisense：5'-3'ACG UGA CAC GUU CGG AGA ATT). It is the control group

value: transfected with siRNA normal control(Sense：5'-3'UUCUCC GAA CGU GUC ACGUTT, Antisense：5'-3'ACG UGA CAC GUU CGG AGA ATT)

value: control group


title: sourceA_lineage7_normal_2_N

value: Normal


title: sourceA_lineage7_normal_3_N

value: adult leaf


title: sourceA_lineage7_normal_4_N


title: sourceA_lineage13_mantled_4_A

value: Mantled


title: host-Normal-PMNs+Serum+Gb-time-1-rep3

status: Public on Sep 08 2015

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-1-rep3

hyb_protocol: PATHOGEN-Samples were hybridized onto custom Affymetrix GeneChip; HOST-samples were hybridized onto Affymetrix human U133 plus 2.0 arrays according to manufacturer's recommendations

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with EC 1.1 and scaled to 500

label_protocol: PATHOGEN-Life Technologies (Carlsbad, CA) MessageAmp™ II-Bacteria kit was used as recommended to amplify an average of 0.3 mg of G. bethesdensis and human neutrophil RNAs; HOST Five ng of RNA sample was concentrated to 5 μL and processed according to manufacturer’s instructions using WT-Ovation™ Pico system RNA Amplification System (Nugen Inc., San Carlos, CA).

growth_protocol: PATHOGEN-G. bethesdensis was grown to mid-log phase at 37C in YPG medium : HOST-Serum and Percoll-isolated PMN were isolated from venous blood

extract_protocol: RLT cell lysates were homogenized using QIAshredder system and neutrophil and bacterial RNA were simultaneously extracted using an AllPrep DNA/RNA 96 Kit (Qiagen) with on-column DNase I treatment

treatment_protocol: Cultures contained 1 ml of 10% subject autologous serum in RPMI 1640 (Gibco) supplemented with 25 mM HEPES pH 7.2 with or without 1 × 107 PMN with or without 1 × 108 G. bethesdensis.

value: normal-PMNs--infected with Granulibacter bethesdensis

tag: infection

value: Polymorphonuclear leukocytes

tag: disease state

value: normal

tag: time

value: 1 h


title: host-Normal-PMNs+Serum+Gb-time-4-rep1

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-4-rep1

value: infected with Granulibacter bethesdensis

value: 4 h


title: EV2

value: podocyte


title: host-Normal-PMNs+Serum+Gb-time-24-rep1

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-24-rep1


title: host-Normal-PMNs+Serum+Gb-time-24-rep4

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-24-rep4


title: host-Normal-PMNs-time-4-rep1

description: Gene expression data from_host-Normal-PMNs-time-4-rep1

value: normal-PMNs--not infected with Gb

value: not infected with Gb


title: host-Normal-PMNs+Serum+Gb-time-0-rep3

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-0-rep3

value: 0 h


title: host-Normal-PMNs+Serum+Gb-time-0-rep4

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-0-rep4


title: host-Normal-PMNs+Serum+Gb-time-1-rep1

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-1-rep1


title: host-Normal-PMNs+Serum+Gb-time-24-rep2

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-24-rep2


title: host-Normal-PMNs-time-24-rep4

description: Gene expression data from_host-Normal-PMNs-time-24-rep4


title: host-Normal-PMNs+Serum+Gb-time-0-rep1

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-0-rep1


title: host-Normal-PMNs+Serum+Gb-time-4-rep3

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-4-rep3


title: host-Normal-PMNs+Serum+Gb-time-24-rep3

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-24-rep3


title: host-Normal-PMNs-time-24-rep2

description: Gene expression data from_host-Normal-PMNs-time-24-rep2


title: host-Normal-PMNs-time-24-rep1

description: Gene expression data from_host-Normal-PMNs-time-24-rep1


title: host-Normal-PMNs-time-1-rep3

description: Gene expression data from_host-Normal-PMNs-time-1-rep3


title: host-Normal-PMNs+Serum+Gb-time-1-rep2

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-1-rep2


title: host-Normal-PMNs-time-4-rep4

description: Gene expression data from_host-Normal-PMNs-time-4-rep4


title: host-Normal-PMNs-time-24-rep3

description: Gene expression data from_host-Normal-PMNs-time-24-rep3


title: host-Normal-PMNs+Serum+Gb-time-4-rep4

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-4-rep4


title: host-Normal-PMNs+Serum+Gb-time-1-rep4

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-1-rep4


title: host-Normal-PMNs-time-1-rep2

description: Gene expression data from_host-Normal-PMNs-time-1-rep2


title: host-Normal-PMNs+Serum+Gb-time-0-rep2

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-0-rep2


title: host-Normal-PMNs-time-4-rep2

description: Gene expression data from_host-Normal-PMNs-time-4-rep2


title: host-Normal-PMNs+Serum+Gb-time-4-rep2

description: Gene expression data from_host-Normal-PMNs+Serum+Gb-time-4-rep2


title: host-Normal-PMNs-time-4-rep3

description: Gene expression data from_host-Normal-PMNs-time-4-rep3


title: host-Normal-PMNs-time-1-rep4

description: Gene expression data from_host-Normal-PMNs-time-1-rep4


title: host-Normal-PMNs-time-1-rep1

description: Gene expression data from_host-Normal-PMNs-time-1-rep1


title: host-CGD-PMNs+Serum+Gb-time-24-rep4

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-24-rep4

value: CGD-PMNs--infected with Granulibacter bethesdensis

value: CGD


title: host-CGD-PMNs+Serum+Gb-time-24-rep3

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-24-rep3


title: host-Normal-PMNs-time-0-rep1

description: Gene expression data from_host-Normal-PMNs-time-0-rep1


title: host-CGD-PMNs+Serum+Gb-time-1-rep4

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-1-rep4


title: host-CGD-PMNs+Serum+Gb-time-24-rep2

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-24-rep2


title: host-CGD-PMNs+Serum+Gb-time-4-rep1

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-4-rep1


title: sourceA_lineage7_normal_1_N


title: host-Normal-PMNs-time-0-rep2

description: Gene expression data from_host-Normal-PMNs-time-0-rep2


title: host-CGD-PMNs+Serum+Gb-time-4-rep2

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-4-rep2


title: host-CGD-PMNs+Serum+Gb-time-24-rep1

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-24-rep1


title: host-Normal-PMNs-time-0-rep4

description: Gene expression data from_host-Normal-PMNs-time-0-rep4


title: host-CGD-PMNs+Serum+Gb-time-0-rep3

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-0-rep3


title: host-CGD-PMNs-time-24-rep1

description: Gene expression data from_host-CGD-PMNs-time-24-rep1

value: CGD-PMNs--not infected with Gb


title: host-CGD-PMNs+Serum+Gb-time-4-rep4

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-4-rep4


title: host-CGD-PMNs+Serum+Gb-time-1-rep3

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-1-rep3


title: host-CGD-PMNs+Serum+Gb-time-1-rep1

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-1-rep1


title: host-CGD-PMNs+Serum+Gb-time-0-rep2

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-0-rep2


title: host-CGD-PMNs-time-24-rep2

description: Gene expression data from_host-CGD-PMNs-time-24-rep2


title: host-CGD-PMNs+Serum+Gb-time-0-rep1

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-0-rep1


title: host-CGD-PMNs+Serum+Gb-time-0-rep4

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-0-rep4


title: host-CGD-PMNs+Serum+Gb-time-1-rep2

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-1-rep2


title: host-CGD-PMNs-time-4-rep4

description: Gene expression data from_host-CGD-PMNs-time-4-rep4


title: host-Normal-PMNs-time-0-rep3

description: Gene expression data from_host-Normal-PMNs-time-0-rep3


title: host-CGD-PMNs-time-4-rep3

description: Gene expression data from_host-CGD-PMNs-time-4-rep3


title: host-CGD-PMNs-time-24-rep3

description: Gene expression data from_host-CGD-PMNs-time-24-rep3


title: host-CGD-PMNs-time-4-rep1

description: Gene expression data from_host-CGD-PMNs-time-4-rep1


title: host-CGD-PMNs-time-4-rep2

description: Gene expression data from_host-CGD-PMNs-time-4-rep2


title: host-CGD-PMNs-time-24-rep4

description: Gene expression data from_host-CGD-PMNs-time-24-rep4


title: host-CGD-PMNs-time-1-rep4

description: Gene expression data from_host-CGD-PMNs-time-1-rep4


title: host-CGD-PMNs-time-1-rep2

description: Gene expression data from_host-CGD-PMNs-time-1-rep2


title: GBM_EGFRvIIIpos 7

city: Philadelphia

first: Matthew

middle: J

last: Lazzara

address: 220 South 33rd Street

institute: University of Pennsylvania

hyb_protocol: The cRNAs were subjected to hybridization at 45oC for 16 hrs, followed by washing, staining, and scanning of the chip according to the manufacturer’s instructions.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3 μm resolution after excitation at 570 nm.  The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantify expression levels for targeted genes.  The raw data were subjected to quantile normalization to reduce the signal to noise ratio due to tumor heterogeneity.  The default values provided by Affymetrix were applied to all analysis parameters.

source_name: Brain tissue

growth_protocol: From human patients

extract_protocol: Briefly, ~1 μg of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase (Life Technologies) primed by a poly(T) oligomer that incorporated the T7 promoter.  Second-strand cDNA synthesis was followed by in vitro transcription to generate labeled cRNAs.

treatment_protocol: tissue harvested from standard image-guided surgical resections and banked between January 2002 and January 2009 at the Hospital of the University of Pennsylvania

tag: egfrviii statue

value: primary GBM tumor


title: GBM_EGFRvIIIpos 9

label_protocol: The cRNAs were subjected to hybridization at 45oC for 16 hrs, followed by washing, staining, and scanning of the chip according to the manufacturer’s instructions.


title: host-CGD-PMNs-time-0-rep3

description: Gene expression data from_host-CGD-PMNs-time-0-rep3


title: GBM_EGFRvIIIpos 4


title: GBM_EGFRvIIIpos 3


title: GBM_EGFRvIIIpos 12


title: host-CGD-PMNs-time-1-rep3

description: Gene expression data from_host-CGD-PMNs-time-1-rep3


title: GBM_EGFRvIIIneg 38


title: GBM_EGFRvIIIneg 34


title: GBM_EGFRvIIIneg 37


title: GBM_EGFRvIIIneg 36


title: host-CGD-PMNs-time-1-rep1

description: Gene expression data from_host-CGD-PMNs-time-1-rep1


title: host-CGD-PMNs-time-0-rep4

description: Gene expression data from_host-CGD-PMNs-time-0-rep4


title: GBM_EGFRvIIIneg 32


title: GBM_EGFRvIIIneg 35


title: GBM_EGFRvIIIneg 39


title: host-CGD-PMNs-time-0-rep1

description: Gene expression data from_host-CGD-PMNs-time-0-rep1


title: GBM_EGFRvIIIpos 1


title: host-CGD-PMNs-time-0-rep2

description: Gene expression data from_host-CGD-PMNs-time-0-rep2


title: GBM_EGFRvIIIpos 8


title: GBM_EGFRvIIIpos 5


title: GBM_EGFRvIIIpos 2


title: GBM_EGFRvIIIpos 6


title: GBM_EGFRvIIIpos 10


title: GBM_EGFRvIIIpos 13


title: GBM_EGFRvIIIneg 31


title: GBM_EGFRvIIIneg 33


title: GBM_EGFRvIIIneg 29


title: GBM_EGFRvIIIneg 22


title: GBM_EGFRvIIIneg 27


title: GBM_EGFRvIIIneg 26


title: GBM_EGFRvIIIneg 21


title: GBM_EGFRvIIIpos 11


title: GBM_EGFRvIIIneg 28


title: GBM_EGFRvIIIneg 18


title: GBM_EGFRvIIIneg 23


title: GBM_EGFRvIIIneg 15


title: GBM_EGFRvIIIneg 25


title: GBM_EGFRvIIIneg 19


title: GBM_EGFRvIIIneg 24


title: GBM_EGFRvIIIneg 17


title: GBM_EGFRvIIIneg 20


title: GBM_EGFRvIIIneg 8


title: GBM_EGFRvIIIneg 3


title: GBM_EGFRvIIIneg 12


title: GBM_EGFRvIIIneg 30


title: GBM_EGFRvIIIneg 16


title: GBM_EGFRvIIIneg 9


title: GBM_EGFRvIIIneg 11


title: GBM_EGFRvIIIneg 5


title: GBM_EGFRvIIIneg 14


title: GBM_EGFRvIIIneg 13


title: GBM_EGFRvIIIneg 4


title: GBM_EGFRvIIIneg 10


title: GBM_EGFRvIIIneg 7


title: GBM_EGFRvIIIneg 6


title: GBM_EGFRvIIIneg 2


title: Japanese_flounder_polyIC_25C_3h_2

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

hyb_protocol: After hybridization cocktails preparation, the Agilent-034810 8x15 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol.

scan_protocol: The microarray was scanned with an Agilent G2565CA scanner. Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percent.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.5.1 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

organism: Paralichthys olivaceus

source_name: Spleen, PolyIC, 25C, 3 hours

label_protocol: The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. Double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeled cRNA was purified using the RNeasy Mini Kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol.

extract_protocol: Total RNA was extracted from fish spleen using the RNeasy Mini Kit.

treatment_protocol: Fish were treated with polyIC or DEPC-treated water (control), and reared at 15 ºC or 25 ºC for 3 hours or 24 hours.

value: spleen

value: PolyIC

tag: temperature

tag: time course

value: 3 hours


title: Japanese_flounder_polyIC_15C_3h_2

source_name: Spleen, PolyIC, 15C, 3 hours

tag: tissue


title: Japanese_flounder_polyIC_15C_24h_3

source_name: Spleen, PolyIC, 15C, 24 hours

value: 24 hours


title: Japanese_flounder_polyIC_25C_24h_1

source_name: Spleen, PolyIC, 25C, 24 hours


title: Japanese_flounder_polyIC_25C_3h_3


title: Japanese_flounder_polyIC_25C_24h_3


title: Japanese_flounder_dH2O_25C_24h_1

source_name: Spleen, DEPC-treated water, 25C, 24 hours

value: DEPC-treated water


title: Japanese_flounder_dH2O_25C_3h_1

source_name: Spleen, DEPC-treated water, 25C, 3 hours


title: Japanese_flounder_dH2O_15C_24h_1

source_name: Spleen, DEPC-treated water, 15C, 24 hours


title: Japanese_flounder_dH2O_25C_24h_3


title: Japanese_flounder_dH2O_25C_3h_3


title: Japanese_flounder_dH2O_15C_24h_3


title: Japanese_flounder_polyIC_25C_3h_1


title: Japanese_flounder_polyIC_15C_24h_2


title: Japanese_flounder_dH2O_15C_24h_2


title: Japanese_flounder_dH2O_25C_24h_2


title: Japanese_flounder_polyIC_15C_3h_1


title: Japanese_flounder_dH2O_25C_3h_2


title: Japanese_flounder_polyIC_15C_3h_3


title: Japanese_flounder_polyIC_25C_24h_2


title: Japanese_flounder_dH2O_15C_3h_2

source_name: Spleen, DEPC-treated water, 15C, 3 hours


title: GBM_EGFRvIIIneg 1


title: host-CGD-PMNs+Serum+Gb-time-4-rep3

description: Gene expression data from_host-CGD-PMNs+Serum+Gb-time-4-rep3

value: Polymorphonuclear leukocytes


title: Japanese_flounder_polyIC_15C_24h_1


title: Japanese_flounder_dH2O_15C_3h_3


title: Japanese_flounder_dH2O_15C_3h_1


title: Patient 9 S19

city: Changsha

first: sun

last: chuanzheng

address: tongzhipo

institute: The Third Xiangya Hospital of Central South Uiversity

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: normal liver tissue

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: subject status

value: Non-alcoholic fatty liver disease (NAFLD)

tag: patient id

value: Patient 9

tag: gender

value: female

tag: age

value: 28 years

value: normal liver tissue


title: Patient 7 S16

source_name: NAFLD liver tissue

value: Patient 7

value: 55 years

value: NAFLD liver tissue


title: Patient 6 S12

value: Patient 6

value: male

value: 40 years


title: Patient 8 S18

value: Patient 8

value: 45 years


title: Patient 5 S11

value: Patient 5

value: 27 years


title: Patient 10 S20

value: Patient 10

value: 34 years


title: Patient 3 S8

value: Non-alcoholic fatty liver disease (NAFLD)

value: Patient 3

value: 33 years


title: Patient 2 S5

value: Patient 2

value: 51 years


title: Lung_bronchial_biopsy_asthma_SAM629087

city: South San Francisco

first: David

middle: Fong

last: Choy

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

hyb_protocol: A 750-ng weight of the labeled cRNA was fragmented and hybridized to Agilent Whole Human Genome 4 × 44 K arrays.  Samples were hybridized for 17 h at 65 °C.

scan_protocol: Scanned on an Agilent scanner.

data_processing: Test and reference channels calculated by the Agilent Feature Extraction software, protocol GE2-v5_95 (Agilent).

label_protocol: Total RNA sample was converted to double-stranded cDNA and then to Cy dye-labeled cRNA using an Agilent Quick Amp Labeling kit. The labeled cRNA was purified using an RNeasy mini kit (Qiagen). cRNA yield and Cy dye incorporation were determined using the ND-1000 spectrophotometer (Thermo Scientific).

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) per manufacturer's instructions."

value: asthma

value: Bronchial Biopsy

source_name: Pooled human RNA

tag: reference

value: Stratagene Univerisal Human Reference


title: Lung_bronchial_biopsy_asthma_SAM629090


title: Lung_bronchial_biopsy_asthma_SAM629083


title: Lung_bronchial_biopsy_asthma_SAM629088


title: Patient 1 S2

value: Patient 1

value: female

value: normal liver tissue


title: Lung_bronchial_biopsy_asthma_SAM629080


title: Lung_bronchial_biopsy_asthma_SAM629078


title: Lung_bronchial_biopsy_asthma_SAM629089


title: Lung_bronchial_biopsy_asthma_SAM629086


title: Lung_bronchial_biopsy_asthma_SAM629082


title: Lung_bronchial_biopsy_asthma_SAM629064


title: Lung_bronchial_biopsy_asthma_SAM629091


title: Lung_bronchial_biopsy_asthma_SAM629084


title: Lung_bronchial_biopsy_asthma_SAM629081


title: Lung_bronchial_biopsy_asthma_SAM629063


title: Lung_bronchial_biopsy_asthma_SAM629085


title: Lung_bronchial_biopsy_asthma_SAM629079


title: Lung_bronchial_biopsy_asthma_SAM629061


title: Patient 4 S10

value: Patient 4

value: 32 years


title: Lung_bronchial_biopsy_asthma_SAM629060


title: Lung_bronchial_biopsy_asthma_SAM627117


title: Lung_bronchial_biopsy_asthma_SAM627713


title: Lung_bronchial_biopsy_asthma_SAM628742


title: Lung_bronchial_biopsy_asthma_SAM629062


title: Lung_bronchial_biopsy_asthma_SAM629077


title: Lung_bronchial_biopsy_asthma_SAM627116


title: Lung_bronchial_biopsy_asthma_SAM629059


title: Lung_bronchial_biopsy_asthma_SAM627015


title: Lung_bronchial_biopsy_asthma_SAM627296


title: Lung_bronchial_biopsy_asthma_SAM627115


title: Lung_bronchial_biopsy_asthma_SAM627013


title: Lung_bronchial_biopsy_asthma_SAM627295


title: Lung_bronchial_biopsy_asthma_SAM627014


title: Lung_bronchial_biopsy_asthma_SAM627011


title: Lung_bronchial_biopsy_asthma_SAM627009


title: Lung_bronchial_biopsy_asthma_SAM627114


title: Lung_bronchial_biopsy_asthma_SAM620632


title: Lung_bronchial_biopsy_asthma_SAM620633


title: Lung_bronchial_biopsy_asthma_SAM620630


title: Lung_bronchial_biopsy_asthma_SAM627010


title: Lung_bronchial_biopsy_asthma_SAM620629


title: Lung_bronchial_biopsy_asthma_SAM620634


title: Lung_bronchial_biopsy_asthma_SAM620627


title: Lung_bronchial_biopsy_asthma_SAM620626


title: Lung_bronchial_biopsy_asthma_SAM619379


title: Untreated cells vs Decitabine 25 nM

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description:
Decitabine 25 nM on days 1,2,3,4
D25

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Agilent whole genome array (G4112F) that was scanned using the Agilent G2505B scanner.

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for initial data processing. Median fluorescence signals were loess normalized in R using Bioconductor limma and agilp packages.
Package: agilp (Agilent expression array processing package, v.3.4.0)
Depends: R (>= 2.14.0)
Packaged: 2013-10-15 08:07:21 UTC; biocbuild
Built: R 3.0.2; ; 2013-10-15 14:41:19 UTC; windows

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM of Cy5 or Cy3 label.

growth_protocol: The YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum and 100 µg/mL Penicillin-Streptomycin solution.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: The cells were treated with 4 doses of the drugs every 24 hours at days 1-4 and harvested at day 6.

tag: cell line

value: clonal derivative of the SW48 colon cancer cell line

tag: genotype/variation

value: containing a single copy of a GFP reporter silenced by CpG methylation at its CMV promoter.

tag: treated with

value: DMSO (untreated control)

value: Decitabine


title: Lung_bronchial_biopsy_asthma_SAM619195


title: Patient8

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

description: Gene Expression Data from chemonaive breast tumor

hyb_protocol: 6 ug double stranded cDNA were hybridized to HTA2.0 arrays at 47 C, for 17 h, at 60 rpm,   Fluidics Station  FS450 was used for washing and staining.

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

data_processing: RMA was performed in Affymetrix Gene Expression Console

source_name: ER/HER2 Pos Breast Tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (SensationPlus™ FFPE Amplification and WT Labeling Kit P/N 703089 Rev. 3 (2014))

extract_protocol: Eight 10 µm sections were cut from each block and mounted onto plain glass slides. Tumor sections were scraped from the slides for total RNA extraction. RNA was purified using the RecoverAll Total Nucleic Acid Extraction Kits for FFPE tissues (Ambion, Austin, TX) and further purified and concentrated with the RNEasy Minelute Cleanup Kit (Qiagen, Valencia, CA).

value: Breast tumor

tag: er2 status

value: Positive

tag: her status

tag: neoadjuvant chemotherapy response

value: no pCR


title: Patient10

value: pCR


title: Lung_bronchial_biopsy_asthma_SAM619380

tag: disease state


title: Untreated cells vs Decitabine 25 nM + Carboplatin 20 uM

description:
Decitabine 25 nM + Carboplatin 20 uM on days 1,2,3,4
D25C20

tag: cell type

value: Decitabine + Carboplatin


title: U266/s

city: Catanzaro

first: Maria

middle: Teresa

last: Di Martino

state: Catanzaro

address: V.le Europa

department: Experimental and Clinical Medicine

country: Italy

institute: Magna Graecia University

description: gene expression data from U266/s Multiple Myeloma cell line after negative control oligo transfection

hyb_protocol: 0.6 ug of cRNA were hybridized for 17 + 1 hr at 45 C on GeneChip 1.0 ST human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: the generated raw signal intensities were then processed using Affymetrix Expression Console for data quality control after summarization and Robust Multi-array Average (RMA) normalization. Annotation of data was also performed using Affymetrix Provided Libraries and EC version 1.1.

label_protocol: the generated amplified cDNA was processed for fragmentation and labeling using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix Inc.) according to the Affymetrix’s procedures

growth_protocol: U266/LR7 cells were transfected with 100 nM miR-221/222 inhibitors or negative control either in the presence or absence of melphalan 100 µM. U266/S cells untreated and treated with melphalan 100 µM and  transfected with 100 nM miR-221/222 inhibitors or negative control. Twelve hours after treatment, cells were collected for total RNA extraction.

extract_protocol: Biotinylated cRNA were prepared according to the Affymetrix reconmmended protocol from 500 ng total RNA (Ambion® WT Expression Kit (Ambion, Life Techologies)

treatment_protocol: The extraction of tRNA and purification was performend using RLT lysis buffer and RNeasy kit (Qiagen, Hilden) according to the manufacturer instrctions.

tag: transfection

value: negative control

tag: treatment


title: Lung_bronchial_biopsy_asthma_SAM619196

value: asthma

value: Bronchial Biopsy


title: U266/s_miR221/222

description: gene expression data from U266/s Multiple Myeloma cell line after  miR221 and miR222 inhibitors transfetion

value: 100 nM miR-221/222 inhibitors


title: Patient9


title: U266/s_Melphalan

description: gene expression data from U266/s Multiple Myeloma cell line after Melphalan treatment

value: melphalan 100 µM


title: Patient11


title: Untreated cells vs Carboplatin 20 uM

description:
Carboplatin 20 uM on days 1,2,3,4
C20

value: Carboplatin


title: Lung_bronchial_biopsy_asthma_SAM620631

value: Stratagene Univerisal Human Reference


title: Patient7


title: Patient6


title: Lung_bronchial_biopsy_asthma_SAM620628


title: Lung_bronchial_biopsy_asthma_SAM619197


title: Lung_bronchial_biopsy_asthma_SAM620625


title: LR7_Melphalan+miR221/222

description: gene expression data from U266/LR7 Multiple Myeloma cell line after miR221 and miR222 inhibitors transfection and Melphalan treatment

source_name: U266/LR7 Multiple Myeloma cell line after miR221 and miR222 inhibitors transfetion and Melphalan treatment


title: Patient5


title: LR7_miR221/222

description: gene expression data from U266/LR7 Multiple Myeloma cell line after miR221 and miR222 inhibitors transfection

source_name: U266/LR7 Multiple Myeloma cell line after  miR221 and miR222 inhibitors transfetion


title: LR7_Melphalan

description: gene expression data from U266/LR7 Multiple Myeloma cell line after Melphalan treatment


title: Patient3


title: U266/s_Melphalan+miR221/222

description: gene expression data from U266/s Multiple Myeloma cell line after miR221 and miR222 inhibitors transfection and Melphalan treatment

source_name: U266/s Multiple Myeloma cell line after miR221 and miR222 inhibitors transfetion andMelphalan treatment


title: LR7

description: gene expression data from U266/LR7 Multiple Myeloma cell line after negative control oligo transfection


title: 9L.EGFRvIII rat 4

hyb_protocol: The labeled cRNAs were subjected to hybridization on RatRef-12 Expression BeadChip array (Illumina Inc.).

scan_protocol: Chips were imaged using an Illumina BeadArray Reader (two channel, 0.8um resolution confocal laser scanner)

data_processing: Gene identities and expression intensities were determined using Partek Genomic suite (Partek Incorporated).  The raw data were subjected to quantile normalization to reduce signal to noise ratio among biological replicates of each tumor type.

organism: Rattus norvegicus

source_name: tumor tissue, EGFRvIII

growth_protocol: EGFRvIII-expressing 9L rat gliosarcoma cells (Sibenaller et al., 2005) were created by transfection with pcDNA3.1(+) (Life Technologies) with Lipofectamine 2000 (Life Technologies) according to the manufacturer’s recommendations and selected with 600μg/ml zeocin (Life Technologies) for 2-3 weeks.  Twelve syngeneic female Fischer rats (4-6 weeks old, 120–150 g) bearing either 9L.empty vector (EV) (n = 6) or 9L.EGFRvIII (n = 6) tumors were used.  General anesthesia was induced by intraperitoneal injection of a ketamine/acepromazine mixture at a dose of 91/9.1 mg/kg.  A 10 μL suspension of 5 × 104 9L.EV or 9L.EGFRvIII cells in phosphate buffered saline was injected into the cortex at a depth of 2 mm with a Hamilton syringe and a 30-gauge needle using stereotactic apparatus (3 mm lateral and 3 mm posterior to the bregma).

extract_protocol: Three weeks after orthotopic implantation, tumors were removed and stored at -80oC in RNALater (Life Technologies).  RNA was extracted using the TriZol method and purified by RNeasy kit (Qiagen).  The quality of the extracted RNAs was assessed using an Agilent Bioanalyzer.  Approximately 100 ng of RNA was amplified into biotinylated cRNAs using the Illumina TotalPrep RNA amplification kit (Ambion) according to manufacturer recommendations.

treatment_protocol: no treatment

tag: intracranial injection of 9l cells expressing

value: EGFRvIII

tag: strain

value: Fisher

value: female


title: 9L.EGFRvIII rat 5

label_protocol: Approximately 100 ng of RNA was amplified into biotinylated cRNAs using the Illumina TotalPrep RNA amplification kit (Ambion) according to manufacturer recommendations.


title: 9L.EGFRvIII rat 2


title: Patient4

tag: tissue


title: Lung_bronchial_biopsy_asthma_SAM619194


title: 9L.EV rat 6

description: 9LEmpty Vector-K

source_name: tumor tissue, EV

value: EV (empty vector control)


title: 9L.EGFRvIII rat 3


title: Patient1


title: Patient2


title: 9L.EV rat 1

description: 9LEmpty Vector-A


title: 9L.EV rat 4

description: 9LEmpty Vector-G


title: 9L.EV rat 5

description: 9LEmpty Vector-I


title: 9L.EV rat 3

description: 9LEmpty Vector-E


title: 9L.EGFRvIII rat 6


title: 9L.EGFRvIII rat 1


title: 9L.EV rat 2

description: 9LEmpty Vector-C


title: CD39+ CD8 T cells, Chronic HCV, patient 6

city: Boston

first: Jernej

last: Godec

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
1927_CD39_Pos
CD39pos_CD8Tcell_HCVchronic_6

hyb_protocol: Labeled targets were hybridized to Affymetrix Human genome U133 Plus 2.0 arrays on the Affymetrix GeneChip Array Station (GCAS) automation platform

scan_protocol: The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332)

data_processing: The data were processed using GenePattern (RMA), GSEA (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).

source_name: CD39 positive CD8 T cells from a patient with a chronic HCV

label_protocol: cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit,  Nugen Encore Biotin Fragmentation and Label, following the manufacturer's protocol.

extract_protocol: RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined with a Nanodrop spectrophotometer or Ribogreen RNA quantification kits (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified with the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer's instructions

tag: patient id

value: patient 6

tag: hcv infection status

value: chronic

tag: cd39 status

value: positive

value: peripheral blood mononuclear cell (PBMC)

tag: cell subtype

value: CD8+ T cells


title: CD39- CD8 T cells, Resolver HCV, patient 1

description:
515_CD39_Neg
CD39neg_CD8Tcell_HCVresolver_1

source_name: CD39 negative CD8 T cells from a resolver HCV patient

value: patient 1

value: resolver

value: negative


title: CD39- CD8 T cells, Chronic HCV, patient 5

description:
1524_CD39_Neg
CD39neg_CD8Tcell_HCVresolver_5

value: patient 5


title: CD39- CD8 T cells, Chronic HCV, patient 6

description:
1927_CD39_Neg
CD39neg_CD8Tcell_HCVchronic_6

source_name: CD39 negative CD8 T cells from a patient with a chronic HCV


title: CD39- CD8 T cells, Chronic HCV, patient 7

description:
111_CD39_Neg
CD39neg_CD8Tcell_HCVchronic_7

value: patient 7


title: CD39- CD8 T cells, Resolver HCV, patient 4

description:
0327_CD39_Neg
CD39neg_CD8Tcell_HCVresolver_4

value: patient 4


title: CD39- CD8 T cells, Chronic HCV, patient 9

description:
0258_CD39_Neg
CD39neg_CD8Tcell_HCVchronic_9

value: patient 9


title: CD39- CD8 T cells, Resolver HCV, patient 2

description:
3000_CD39_Neg
CD39neg_CD8Tcell_HCVresolver_2

value: patient 2


title: CD39- CD8 T cells, Resolver HCV, patient 3

description:
0329_CD39_Neg
CD39neg_CD8Tcell_HCVresolver_3

value: patient 3


title: CD39+ CD8 T cells, Resolver HCV, patient 3

description:
0329_CD39_Pos
CD39pos_CD8Tcell_HCVresolver_3

source_name: CD39 positive CD8 T cells from a resolver HCV patient


title: CD39+ CD8 T cells, Chronic HCV, patient 8

description:
941_CD39_Pos
CD39pos_CD8Tcell_HCVchronic_8

value: patient 8


title: CD39+ CD8 T cells, Chronic HCV, patient 7

description:
111_CD39_Pos
CD39pos_CD8Tcell_HCVchronic_7


title: pathogen-Normal-PMNs+Serum-time-4-rep2

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-4-rep2

organism: Granulibacter bethesdensis

value: strain CGDNIH1 or ATCC  BAA-1260

tag: time

value: 4 h


title: CD39+ CD8 T cells, Resolver HCV, patient 4

description:
0327_CD39_Pos
CD39pos_CD8Tcell_HCVresolver_4


title: pathogen-Normal-PMNs+Serum-time-1-rep2

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-1-rep2

value: 1 h


title: pathogen-Normal-PMNs+Serum-time-4-rep4

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-4-rep4


title: pathogen-Normal-PMNs+Serum-time-24-rep1

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-24-rep1


title: pathogen-Normal-PMNs+Serum-time-24-rep4

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-24-rep4


title: pathogen-Normal-PMNs+Serum-time-0-rep3

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-0-rep3

value: 0 h


title: pathogen-Normal-PMNs+Serum-time-4-rep1

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-4-rep1


title: pathogen-Normal-PMNs+Serum-time-1-rep3

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-1-rep3


title: pathogen-Normal-PMNs+Serum-time-4-rep3

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-4-rep3


title: CD39+ CD8 T cells, Chronic HCV, patient 9

description:
0258_CD39_Pos
CD39pos_CD8Tcell_HCVchronic_9

value: chronic

value: positive


title: CD39+ CD8 T cells, Resolver HCV, patient 1

description:
515_CD39_Pos
CD39pos_CD8Tcell_HCVresolver_1

value: peripheral blood mononuclear cell (PBMC)

value: CD8+ T cells


title: pathogen-Normal-PMNs+Serum-time-1-rep1

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-1-rep1


title: pathogen-Normal-PMNs+Serum-time-0-rep4

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-0-rep4


title: pathogen-Normal-PMNs+Serum-time-1-rep4

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-1-rep4


title: pathogen-Normal-PMNs+Serum-time-24-rep2

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-24-rep2


title: pathogen-Normal-PMNs+Serum-time-0-rep1

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-0-rep1


title: pathogen-Normal-PMNs-time-24-rep3

description: Gene expression data from_pathogen-Normal-PMNs-time-24-rep3


title: pathogen-Normal-PMNs-time-24-rep1

description: Gene expression data from_pathogen-Normal-PMNs-time-24-rep1


title: pathogen-Normal-PMNs+Serum-time-0-rep2

description: Gene expression data from_pathogen-Normal-PMNs+Serum-time-0-rep2


title: pathogen-Normal-PMNs-time-24-rep2

description: Gene expression data from_pathogen-Normal-PMNs-time-24-rep2


title: pathogen-Normal-PMNs-time-4-rep4

description: Gene expression data from_pathogen-Normal-PMNs-time-4-rep4


title: pathogen-Normal-PMNs-time-4-rep3

description: Gene expression data from_pathogen-Normal-PMNs-time-4-rep3


title: pathogen-Normal-PMNs-time-4-rep2

description: Gene expression data from_pathogen-Normal-PMNs-time-4-rep2


title: pathogen-Normal-PMNs-time-1-rep2

description: Gene expression data from_pathogen-Normal-PMNs-time-1-rep2


title: pathogen-Normal-PMNs-time-1-rep4

description: Gene expression data from_pathogen-Normal-PMNs-time-1-rep4


title: pathogen-Normal-PMNs-time-4-rep1

description: Gene expression data from_pathogen-Normal-PMNs-time-4-rep1


title: pathogen-Normal-PMNs-time-0-rep2

description: Gene expression data from_pathogen-Normal-PMNs-time-0-rep2


title: pathogen-Normal-PMNs-time-0-rep4

description: Gene expression data from_pathogen-Normal-PMNs-time-0-rep4


title: pathogen-Normal-PMNs-time-24-rep4

description: Gene expression data from_pathogen-Normal-PMNs-time-24-rep4


title: pathogen-Normal-PMNs-time-0-rep3

description: Gene expression data from_pathogen-Normal-PMNs-time-0-rep3


title: pathogen-CGD-PMNs+Serum-time-24-rep2

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-24-rep2


title: pathogen-CGD-PMNs+Serum-time-4-rep4

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-4-rep4


title: pathogen-Normal-PMNs-time-1-rep3

description: Gene expression data from_pathogen-Normal-PMNs-time-1-rep3


title: pathogen-CGD-PMNs+Serum-time-24-rep1

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-24-rep1


title: pathogen-Normal-PMNs-time-0-rep1

description: Gene expression data from_pathogen-Normal-PMNs-time-0-rep1


title: pathogen-CGD-PMNs+Serum-time-24-rep4

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-24-rep4


title: pathogen-CGD-PMNs+Serum-time-4-rep3

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-4-rep3


title: pathogen-CGD-PMNs+Serum-time-1-rep4

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-1-rep4


title: pathogen-CGD-PMNs+Serum-time-4-rep2

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-4-rep2


title: pathogen-CGD-PMNs+Serum-time-1-rep2

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-1-rep2


title: pathogen-CGD-PMNs-time-24-rep3

description: Gene expression data from_pathogen-CGD-PMNs-time-24-rep3


title: pathogen-CGD-PMNs+Serum-time-1-rep1

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-1-rep1


title: pathogen-CGD-PMNs-time-24-rep2

description: Gene expression data from_pathogen-CGD-PMNs-time-24-rep2


title: pathogen-CGD-PMNs-time-4-rep2

description: Gene expression data from_pathogen-CGD-PMNs-time-4-rep2


title: pathogen-CGD-PMNs+Serum-time-4-rep1

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-4-rep1


title: pathogen-CGD-PMNs+Serum-time-1-rep3

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-1-rep3


title: pathogen-CGD-PMNs+Serum-time-0-rep2

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-0-rep2


title: pathogen-CGD-PMNs-time-4-rep4

description: Gene expression data from_pathogen-CGD-PMNs-time-4-rep4


title: pathogen-CGD-PMNs+Serum-time-0-rep1

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-0-rep1


title: pathogen-CGD-PMNs-time-24-rep4

description: Gene expression data from_pathogen-CGD-PMNs-time-24-rep4


title: pathogen-CGD-PMNs+Serum-time-0-rep4

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-0-rep4


title: pathogen-CGD-PMNs+Serum-time-0-rep3

description: Gene expression data from_pathogen-CGD-PMNs+Serum-time-0-rep3


title: pathogen-CGD-PMNs-time-24-rep1

description: Gene expression data from_pathogen-CGD-PMNs-time-24-rep1


title: pathogen-CGD-PMNs-time-4-rep1

description: Gene expression data from_pathogen-CGD-PMNs-time-4-rep1


title: pathogen-CGD-PMNs-time-1-rep4

description: Gene expression data from_pathogen-CGD-PMNs-time-1-rep4


title: pathogen-CGD-PMNs-time-1-rep2

description: Gene expression data from_pathogen-CGD-PMNs-time-1-rep2


title: pathogen-CGD-PMNs-time-1-rep1

description: Gene expression data from_pathogen-CGD-PMNs-time-1-rep1


title: pathogen-CGD-PMNs-time-0-rep1

description: Gene expression data from_pathogen-CGD-PMNs-time-0-rep1


title: luminal_CD133_negative_2sort12

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

hyb_protocol: Labeled RNA was hybridized to arrays using the standard Agilent 1-color gene expression hybridization and wash protocol

scan_protocol: Arrays were scanned on an Agilent G2505C Microarray Scanner at 5 micron resolution

data_processing:
Images were processed using the Agilent Feature Extraction software version 10.5.1.1.
Control features and nonuniform array features were removed. Remaining features for each probe were averaged and log base 2 transformed.
Log2 intensities were quantile normalized.

source_name: mouse mammary tumor arising from transplanted epithelial cells

label_protocol: Total RNA was labeled with Cy3 using the Agilent One-Color Quick Amp Labeling Protocol

growth_protocol: Cells were transduced with PyMT-expressing lentivirus, sorted, and transplanted into syngeneic cleared mouse mammary fat pads. RNA was isolated from tumors grown from transplanted cells.

extract_protocol: Total RNA was isolated using the Qiagen RNEasy kit

tag: donor/recipient strain

value: FVB/NJ

tag: source cell type

value: mouse mammary epithelial cells

tag: transduced with

value: PyMT-expressing lentivirus

value: high

value: low

tag: lung metastasis

value: Yes


title: luminal_CD133_negative_2sort36

value: negative


title: pathogen-CGD-PMNs-time-0-rep2

description: Gene expression data from_pathogen-CGD-PMNs-time-0-rep2


title: pathogen-CGD-PMNs-time-1-rep3

description: Gene expression data from_pathogen-CGD-PMNs-time-1-rep3


title: luminal_CD133_negative_3sort8


title: luminal_CD133_negative_3sort1

value: No


title: luminal_CD133_positive_3sort27


title: basal_3sort5

value: basal cells

value: mid


title: pathogen-CGD-PMNs-time-0-rep4

description: Gene expression data from_pathogen-CGD-PMNs-time-0-rep4

value: strain CGDNIH1 or ATCC  BAA-1260


title: luminal_CD133_positive_3sort29


title: luminal_CD133_positive_3sort10


title: Rv1 pLKO.1_rep2

city: Oxford

first: Natasha

last: Sahgal

address: Old Road Campus

department: Ludwig Institute of Cancer Research

country: United Kingdom

institute: University of Oxford

description:
replicate 2
SAMPLE 2

data_processing: The data was background corrected, filtered and normalised using the vsn package in R

source_name: Control Rv1 cells

growth_protocol: Cells were maintained in RPMI1640 media supplemented with 10% FBS and antibiotics.

extract_protocol: RNA mimiprep kit (sigma) was used to extract following the manufacturer's protocol.

tag: cell line

value: prostate cancer cells


title: luminal_CD133_negative_3sort25


title: luminal_CD133_negative_3sort7


title: Rv1 shJMJD1A_rep1

description:
replicate 1
SAMPLE 3

source_name: JMJD1A-knockdown Rv1 cells


title: Rv1 shJMJD1A_rep2

description:
replicate 2
SAMPLE 4


title: stem_3sort31

value: stem cells


title: Rv1 pLKO.1_rep1

description:
replicate 1
SAMPLE 1


title: luminal_CD133_positive_3sort11


title: luminal_CD133_negative_3sort32


title: stem_3sort4


title: stem_3sort18


title: stem_3sort6


title: HCT116

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

hyb_protocol: Manufacturer's instructions

scan_protocol: Manufacturer's instructions

data_processing: Manufacturer's instructions. Nsuma_cgh.txt: Agilent SurePrint G3 Custom CGH+SNP 2x400K (G4883A) results.

source_name: HCT116 Colon-derived cell line

label_protocol: Manufacturer's instructions

growth_protocol: Three colorectal tumors and their paired non-adjacent normal colonic mucosa were used in this analysis. Samples were obtained from the Hospital Universitari de Bellvitge (Barcelona, Spain) following a protocol approved by the Ethics Committee. Human colon cancer cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA), except DKO, generously provided by B. Vogelstein. All cell lines were grown in DMEM:F12 medium plus 10% heat-inactivated FBS, L-glutamine and  pyruvate (Invitrogen)

extract_protocol: Genomic DNA

value: Cell line

source_name: Human reference male

tag: sample type

value: Human reference male


title: DKO

source_name: DKO Colon-derived cell line

tag: cell type

value: DKO


title: basal_2sort9


title: luminal_CD133_negative_2sort16


title: luminal_CD133_negative_3sort24


title: luminal_CD133_positive_2sort22

value: positive


title: basal_3sort16

value: FVB/NJ


title: basal_2sort13

value: mouse mammary epithelial cells


title: luminal_CD133_negative_2sort15

value: PyMT-expressing lentivirus


title: luminal_CD133_positive_2sort3

value: high


title: basal_3sort19

value: low


title: luminal_CD133_positive_2sort7

value: Yes


title: stem_2sort8


title: stem_2sort19


title: basal_2sort2


title: 557

source_name: Normal colon from donnor 557

value: Normal colon

source_name: Matched colon primary tumor

value: Matched colon primary tumor


title: luminal_CD133_negative_2sort6

value: negative


title: luminal_CD133_positive_2sort21


title: 369

source_name: Normal colon from donnor 369


title: basal_3sort21

value: basal cells

value: mid


title: 544

source_name: Normal colon from donnor 544


title: Leaves E2-hexenal treated 24 h, biological rep3

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

country: Netherlands

institute: University of Amsterdam

description: gene expression 24h after E2-hexenal treatment

hyb_protocol: Labelled cRNA was hybridized to whole genome Affymetrix ATH1 GeneChip, according to the manufacturer’s instructions (Affymetrix)

scan_protocol: Affymetrix scanner

data_processing: We performed a set of quality control checks, i.e. visual inspection of the scans, RNA degradation analysis, examination of the consistency among the replicated samples by principal component analysis, checking the arrays for surface anomalies and inspection of MA plots using a pseudo-median reference and examination of the Affymetrix provided QC values. All 18 arrays passed these tests.

organism: Arabidopsis thaliana

source_name: rosette leaves 24h after E-2 hexenal treatment

label_protocol: Labelled cRNA was prepared  according to the manufacturer’s instructions (Affymetrix).

growth_protocol: All experiments were performed with Arabidopsis thaliana plants, ecotype Columbia (Col-0).

extract_protocol: RNA was extracted using the TRIzol (Invitrogen) extraction procedure followed by purification on RNAeasy columns (Qiagen).

treatment_protocol: All chemical treatments were performed on 19 to 21-day old plants, grown in soil at 21 C with 70% humidity and a 11/13 h light (100 u E/m2/s)/dark cycle. For E-2-hexenal treatment, 3 plants were placed into airtight glass desiccators (22 L). E-2-hexenal was diluted in methanol and 50 ul of the diluted solutions were applied to a sterile cotton swab, placed in a 50 ml Erlenmeyer flask, positioned among the plants. For the control treatment only methanol was applied.

tag: ecotype

value: Columbia (Col-0)

value: 24h after E-2 hexenal treatment


title: Leaves mock treated 24 h, biological rep1

description: gene expression 24h after mock treatment

source_name: rosette leaves 24h after mock treatment

tag: treatment

value: 24h after mock treatment


title: Leaves mock treated 3 h, biological rep1

description: gene expression 3h after mock treatment

source_name: rosette leaves 3h after mock treatment

value: 3h after mock treatment


title: Leaves E2-hexenal treated 1 h, biological rep3

description: gene expression 1h after E2-hexenal treatment

source_name: rosette leaves 1h after E2 hexenal treatment

value: 1h after E2-hexenal treatment


title: Leaves mock treated 1 h, biological rep1

description: gene expression 1h after mock treatment

source_name: rosette leaves 1h after mock treatment

value: 1h after mock treatment


title: Leaves E2-hexenal treated 3 h, biological rep3

description: gene expression 3h after E2-hexenal treatment

source_name: rosette leaves 3h after E-2 hexenal treatment

value: 3h after E2-hexenal treatment


title: Leaves mock treated 24 h, biological rep3


title: Leaves mock treated 3 h, biological rep3

description: gene expression 3h after mock treatment


title: Leaves E2-hexenal treated 3 h, biological rep2


title: Leaves mock treated 24 h, biological rep2


title: Leaves mock treated 3 h, biological rep2

description: gene expression 3h after mock treatment


title: Leaves mock treated 1 h, biological rep2

description: gene expression 1h after mock treatment


title: Leaves E2-hexenal treated 1 h, biological rep2


title: Leaves mock treated 1 h, biological rep3

description: gene expression 1h after mock treatment


title: Leaves E2-hexenal treated 24 h, biological rep2


title: Leaves E2-hexenal treated 24 h, biological rep1


title: Leaves E2-hexenal treated 3 h, biological rep1


title: NC_3

status: Public on Sep 07 2015

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

hyb_protocol: RNA was labeled using the Affymetrix IVT Express kit

scan_protocol: Arrays were scanned following manufacturers instructions

data_processing: Microarray CEL files were imported and normalized using RMA function from Partek Genomics Suite 6.0.

source_name: mouse bone marrow samples

label_protocol: biotin

extract_protocol: The total RNA was isolated by use of miRNeasy extraction kit (Qiagen, Valencia, CA).

value: bone marrow

tag: bmt type

value: Normal Control


title: Leaves E2-hexenal treated 1 h, biological rep1


title: NC_1


title: Cpdm unsorted cells

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: Cultured for 10 days in the presence of ascorbic acid and ß-glycerophosphate

hyb_protocol: Following fragmentation the cRNA were hybridized for 16 hr at 45C on the arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software GCOS 1.4 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: Murine bone marrow cells

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

growth_protocol: Bone marrow cells from wildtype and Cpdm mice were cultured for 10 days in the presence of ascorbic acid (50 μg/ml)  and ß-glycerophosphate (10 mM )

extract_protocol: RNA was isolated using the RNeasyMini kit (Qiagen).

treatment_protocol: No treatment of the cells was performed

value: Unsorted bone marrow cells

tag: genotype

value: Cpdm


title: miR-126KO+AE9a-P4_1

tag: tissue

value: miR-126KO+AE9a 4th passage


title: AE9a+miR-126-P4_2

value: AE9a+miR-126 4th passage


title: WT unsorted cells

value: wildtype


title: miR-126KO+AE9a-P4_2


title: miR-126KO+AE9a-P4_3


title: AE9a-P4_2

value: AE9a 4th passage


title: AE9a+miR-126-P4_3


title: AE9a+miR-126-P4_1


title: AE9a-P4_3


title: AE9a-P4_1


title: NC_2


title: miR-126KO+AE9a-P3_3

value: miR-126KO+AE9a 3rd passage


title: miR-126KO+AE9a-P3_1


title: miR-126KO+AE9a-P3_2


title: 56318-Met-Liver

city: Chapel Hill

first: Richard

last: Moffitt

state: NC

address: 450 West Drive

institute: University of North Carolina

hyb_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent G2505C fluorescent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction (v10.5) software.

data_processing: log2 Cy5 signal was analyzed after setting negative values to zero. Probe data were collapsed by gene symbol via mean expression. Samples were quantile normalized to the subset of genes with less than 0.5 standard deviation across primary, metastatic, and normal samples. Data were processed in MATLAB R2013a.

source_name: Human Reference

extract_protocol: Qiagen Rneasy Kit

value: Stratagene Human reference RNA

tag: cell line/tissue

value: Liver

tag: tissue type

value: Metastasis


title: 56524-Met-Liver

label_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]


title: 56315-Met-Liver


title: AE9a+miR-126-P3_3

value: AE9a+miR-126 3rd passage


title: 56328-Met-Liver


title: AE9a+miR-126-P3_2


title: AE9a-P3_3

value: AE9a 3rd passage


title: 56522-Met-Liver


title: 56532-Met-Liver


title: 56381-Met-Peritoneal

value: Peritoneal


title: miR-126KO+AE9a-P2_3

value: miR-126KO+AE9a 2nd passage


title: 56380-Met-AbWall

value: AbWall


title: AE9a-P3_2

value: bone marrow


title: 56376-Met-LymphNode

value: LymphNode


title: 56521-Met-Liver


title: MettL4 KO_vs_MettL4 KO 3

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

description: RNA m6a methylation data from mouse embryos stem cell treated with siRNA for Mettl14

hyb_protocol: RNA was hybridized to Agilent arrays following manufacturers instructions

data_processing: Microarray files were imported and normalized using Bioconductor package limma.

source_name: mESC transfected with siRNA for Mett14

label_protocol: RNA was labeled using Cy5 or Cy3 subject to two-channel Agilent microarray protocol

growth_protocol: Mouse ES cells were maintained on feeder layers of irradiated mouse embryonic fibroblasts (MEFs) in DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM L-glutamine, 0.1 mM non-essential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma) and 500 units/ml leukemia inhibiting factor (LIF, Chemicon). Lentiviral constructs including shRNA were purchased from Sigma. To produce lentivirus, lentiviral constructs and packaging constructs were transfected into 293ft cells by calcium phosphate reagent (Clontech). About 36 hours after transfection, viral supernatants were collected and supplemented with 6 μg/μl polybrene (Millipore). ES cells were incubated with virus-containing medium for 12 h. 3 days after infection, 2 μg/ml puromycin (Sigma) were added to medium for stable cell lines selection.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen).  RNA was treated with RNAse free DNAse I (Roche) to deplete DNA contamination.  PolyA RNA was purified using GenElute™ mRNA Miniprep Kit (Sigma Aldrich) per manufacturer’s instruction.

treatment_protocol: ES cells J1 were seeded 2×105 per well in 6-well plate and transfected with siRNAs by lipofectamine RNAiMAX (Invitrogen) following manufacturer’s protocol. After 48 hours cells were reseeded and transfected with siRNA again. After another 48 hours cells were collected for analysis. Target sequences of siRNA:   Mettl14, CCGGATGTACAGAGGAAAT, GGGAACTCATCAGACTAAA, GCACCTCGGTCATTTATAT  Scramble

tag: genotype/variation

value: Mettl14 knockout (M14)

tag: strain


title: 56378-Met-Liver


title: 56317-Met-Liver


title: DZA_vs_SCR Ctl 3

description: RNA m6a methylation data from mouse embryos stem cell treated with scrambled control or siRNA for DZA

source_name: mESC transfected with siRNA for DZA

value: DZA mutant

source_name: mESC treated with scrambled control

value: Wild type


title: 56543-Met-Liver


title: AE9a+miR-126-P2_2

value: AE9a+miR-126 2nd passage


title: AE9a-P3_1


title: AE9a+miR-126-P2_1


title: 56329-Met-Liver


title: miR-126KO+AE9a-P2_1


title: AE9a-P2_3

value: AE9a 2ndt passage


title: miR-126KO+AE9a-P2_2


title: 56533-Met-Duo

value: Duo


title: MettL4 KO_vs_SCR Ctl 2

description: RNA m6a methylation data from mouse embryos stem cell treated with scrambled control or siRNA for Mettl14


title: 56327-Met-Liver


title: 56324-Met-LymphNode


title: 56323-Met-Lung

value: Lung


title: MettL4 KO_vs_SCR Ctl 3


title: AE9a-P2_2

value: AE9a 2nd passage


title: 56325-Met-Liver

value: Stratagene Human reference RNA

value: Liver


title: AE9a+miR-126-P2_3

value: AE9a+miR-126 2ndt passage


title: MettL4 KO_vs_MettL4 KO 2


title: AE9a-P2_1


title: MettL4 KO_vs_MettL4 KO 1


title: DZA_vs_SCR Ctl 2


title: DZA_vs_SCR Ctl 1


title: MettL4 KO_vs_SCR Ctl 1


title: 49076-Met-Lung

value: Metastasis


title: 48659-Met-Liver


title: miR-126KO+AE9a-P1_3

value: miR-126KO+AE9a 1st passage


title: AE9a+miR-126-P1_1

value: AE9a+miR-126 1st passage


title: miR-126KO+AE9a-P1_1


title: 49066-Met-Liver


title: 49067-Met-LymphNode


title: AE9a+miR-126-P1_2


title: miR-126KO+AE9a-P1_2


title: 49386-Met-Lung


title: AE9a-P1_3

value: AE9a 1st passage


title: 53836-Met-Lung


title: 49065-Met-Liver


title: AE9a-P1_2

value: bone marrow


title: 48638-Met-Diaphragm

value: Diaphragm


title: AE9a-P1_1


title: 49382-Met-Peritoneal

value: Peritoneal


title: 49385-Met-Diaphragm


title: 48653-Met-LymphNode

value: LymphNode


title: 48652-Met-Liver


title: 48648-Met-Liver


title: 49375-Met-Liver


title: 49376-Met-Liver


title: AE9a+miR-126-P1_3


title: AE9a+miR-126-P3_1

value: AE9a+miR-126 3rdt passage


title: 49381-Met-Duo


title: 48639-Met-Peritoneal


title: 49068-Met-Lung


title: 49370-Met-Liver


title: 53863-Met-Peritoneal


title: 48613-Met-Colon

value: Colon


title: 48581-Met-LymphNode


title: 49084-Met-Colon


title: 48577-Met-Fat

value: Fat


title: 49396-Met-Peritoneal


title: 48574-Met-AbWall

value: AbWall


title: 48584-Met-Liver


title: 49363-Met-LymphNode


title: 49086-Met-Liver


title: 53846-Met-Lung

value: Lung


title: 53847-Met-Lung


title: 48591-Met-Liver


title: 49359-Met-AbWall


title: 53844-Met-Fat


title: 49364-Met-LymphNode


title: 49083-Met-Diaphragm


title: 48586-Met-Lung


title: 53841-Met-LymphNode


title: 49085-Met-Liver


title: 54019-CFPAC-CellLine

source_name: CellLine

value: CFPAC


title: 54246-HPAFII-CellLine

value: Stratagene Human reference RNA

value: HPAFII


title: 49362-Met-LymphNode


title: 54277-Capan2-CellLine


title: 54276-Capan1-CellLine


title: 51251-HUPT3-CellLine


title: 54278-Hs766T-CellLine


title: 54023-HPAC-CellLine

value: HPAC


title: 54018-BXPC3-CellLine


title: 56531-Primary-Pancreas

value: Pancreas

value: Primary


title: 56523-Primary-Pancreas


title: 56316-Primary-Pancreas


title: 56320-Primary-Pancreas


title: 56534-Primary-Pancreas


title: 54318-Primary-Pancreas


title: 54300-Primary-Pancreas


title: 54171-Primary-Pancreas


title: 64496-Primary-Pancreas


title: 54295-Primary-Pancreas


title: 56326-Primary-Pancreas


title: 54296-Primary-Pancreas


title: 56322-Primary-Pancreas


title: 54294-Primary-Pancreas


title: 54316-Primary-Pancreas


title: 54174-Primary-Pancreas


title: 54312-Primary-Pancreas


title: 54298-Primary-Pancreas


title: 54025-T3M4-CellLine


title: 54314-Primary-Pancreas


title: 54313-Primary-Pancreas


title: 54299-Primary-Pancreas


title: 54279-SW1990-CellLine


title: 54317-Primary-Pancreas


title: 54297-Primary-Pancreas


title: 54173-Primary-Pancreas


title: 54310-Primary-Pancreas


title: 54315-Primary-Pancreas


title: 54311-Primary-Pancreas


title: 54305-Primary-Pancreas


title: 54307-Primary-Pancreas


title: 54293-Primary-Pancreas


title: 56535-Primary-Pancreas


title: 54309-Primary-Pancreas


title: 54301-Primary-Pancreas


title: 54175-Primary-Pancreas


title: 56529-Primary-Pancreas


title: 54304-Primary-Pancreas


title: 56374-Primary-Pancreas


title: 54172-Primary-Pancreas


title: 54291-Primary-Pancreas


title: 54303-Primary-Pancreas


title: 54292-Primary-Pancreas


title: 54243-Primary-Pancreas


title: 56542-Primary-Pancreas


title: 56373-Primary-Pancreas


title: 54306-Primary-Pancreas


title: 56530-Primary-Pancreas


title: 56375-Primary-Pancreas


title: 56540-Primary-Pancreas


title: 54302-Primary-Pancreas


title: 54308-Primary-Pancreas


title: 56541-Primary-Pancreas


title: 56377-Primary-Pancreas


title: 56528-Primary-Pancreas


title: 56369-Primary-Pancreas


title: 56367-Primary-Pancreas


title: 64510-Primary-Pancreas


title: 56537-Primary-Pancreas


title: 56539-Primary-Pancreas


title: 46647-Primary-Pancreas


title: 64495-Primary-Pancreas


title: 64498-Primary-Pancreas


title: 56536-Primary-Pancreas


title: 64507-Primary-Pancreas


title: 56538-Primary-Pancreas


title: 64509-Primary-Pancreas


title: 64492-Primary-Pancreas


title: 64501-Primary-Pancreas


title: 64505-Primary-Pancreas


title: 56527-Primary-Pancreas


title: 64490-Primary-Pancreas


title: 56525-Primary-Pancreas


title: 64491-Primary-Pancreas


title: 72613-Primary-Pancreas


title: 48569-Primary-Pancreas


title: 64504-Primary-Pancreas


title: 64503-Primary-Pancreas


title: 64508-Primary-Pancreas


title: 64482-Primary-Pancreas


title: 64502-Primary-Pancreas


title: 64500-Primary-Pancreas


title: 64494-Primary-Pancreas


title: 49392-Primary-Pancreas


title: 72616-Primary-Pancreas


title: 46645-Primary-Pancreas


title: 64497-Primary-Pancreas


title: 46646-Primary-Pancreas


title: 46592-Primary-Pancreas


title: 46644-Primary-Pancreas


title: 49390-Primary-Pancreas


title: 47701-Primary-Pancreas


title: 46642-Primary-Pancreas


title: 46587-Primary-Pancreas


title: 47700-Primary-Pancreas


title: 46826-Primary-Pancreas


title: 48550-Primary-Pancreas


title: 46339-Primary-Pancreas


title: 47708-Primary-Pancreas


title: 46460-Primary-Pancreas


title: 46452-Primary-Pancreas


title: 46578-Primary-Pancreas


title: 47983-Primary-Pancreas


title: 46643-Primary-Pancreas


title: 46450-Primary-Pancreas


title: 47695-Primary-Pancreas


title: 46585-Primary-Pancreas


title: 47965-Primary-Pancreas


title: 46337-Primary-Pancreas


title: 46584-Primary-Pancreas


title: 47703-Primary-Pancreas


title: 46582-Primary-Pancreas


title: 46581-Primary-Pancreas


title: 46830-Primary-Pancreas


title: 47969-Primary-Pancreas


title: 46986-Primary-Pancreas


title: 47590-Primary-Pancreas


title: 47702-Primary-Pancreas


title: 47692-Primary-Pancreas


title: 47989-Primary-Pancreas


title: 46987-Primary-Pancreas


title: 46828-Primary-Pancreas


title: 46648-Primary-Pancreas


title: 48562-Primary-Pancreas


title: 46832-Primary-Pancreas


title: 48568-Primary-Pancreas


title: 46650-Primary-Pancreas


title: 46652-Primary-Pancreas


title: 52043-Primary-Pancreas


title: 49388-Primary-Pancreas


title: 48564-Primary-Pancreas


title: 46653-Primary-Pancreas


title: 52042-Primary-Pancreas


title: 49073-Primary-Pancreas


title: 46649-Primary-Pancreas


title: 48556-Primary-Pancreas


title: 48558-Primary-Pancreas


title: 53838-Primary-Pancreas


title: 46831-Primary-Pancreas


title: 46985-Primary-Pancreas


title: 49071-Primary-Pancreas


title: 46651-Primary-Pancreas


title: 48567-Primary-Pancreas


title: 48661-Primary-Pancreas


title: 54249-Primary-Pancreas


title: 49360-Primary-Pancreas


title: 53862-Primary-Pancreas


title: 54248-Panc1005-CellLine


title: 56379-Normal-Liver

value: Liver

value: Normal


title: 53292-Panc1-CellLine


title: 56372-Normal-Pancreas


title: 54247-Panc0327-CellLine


title: 56368-Normal-Pancreas


title: 56370-Normal-Pancreas


title: 56366-Normal-Pancreas


title: 47588-Normal-Pancreas


title: 56371-Normal-Pancreas


title: 46451-Normal-Pancreas


title: 56330-Normal-Pancreas


title: 54275-Normal-Pancreas


title: 53861-Normal-Pancreas


title: 46338-Normal-Pancreas


title: 46336-Normal-Pancreas


title: 47693-Normal-Pancreas


title: 46453-Normal-Pancreas


title: 47589-Normal-Pancreas


title: 46576-Normal-Pancreas


title: 47982-Normal-Pancreas


title: 48112-Normal-Pancreas


title: 47694-Normal-Pancreas


title: 47970-Normal-Pancreas


title: 47968-Normal-Pancreas


title: 56526-Normal-Pancreas


title: 46579-Normal-Pancreas


title: 54242-Panc0203-CellLine


title: 47697-Normal-Pancreas


title: 49391-Normal-Pancreas


title: 47967-Normal-Pancreas


title: 48557-Normal-Pancreas


title: 53265-HPNE-CellLine

value: HPNE


title: 49064-Normal-Liver


title: 49069-Normal-Lung


title: 49072-Normal-Spleen

value: Spleen


title: 48678-Normal-Liver


title: 48664-Normal-Peritoneal

value: Peritoneal


title: 48662-Normal-Spleen


title: 49387-Normal-Pancreas


title: 48663-Normal-LymphNode

value: LymphNode


title: 48654-Normal-Lung


title: 48563-Normal-Pancreas


title: 53835-Normal-Lung


title: 46454-Normal-Pancreas


title: 48660-Normal-Lung


title: 48665-Normal-Pancreas


title: 53837-Normal-Pancreas


title: 49384-Normal-Diaphragm

value: Diaphragm


title: 48656-Normal-Pancreas


title: 48649-Normal-Diaphragm


title: 48651-Normal-Liver


title: 48655-Normal-Lung


title: 48650-Normal-Fat


title: 48640-Normal-Liver


title: 53266-HPNE-CellLine


title: 48641-Normal-Pancreas


title: 48643-Normal-Spleen


title: 48644-Normal-LymphNode


title: 48647-Normal-Pancreas


title: 49379-Normal-Fat


title: 49380-Normal-LymphNode


title: 48642-Normal-Lung


title: 49383-Normal-Diaphragm


title: 49377-Normal-Pancreas


title: 48603-Normal-LymphNode


title: 48599-Normal-Pancreas


title: 48600-Normal-Spleen


title: 49378-Normal-Liver


title: 48596-Normal-Liver


title: 49374-Normal-LymphNode


title: 48604-Normal-Liver


title: 48601-Normal-Lung


title: 48645-Normal-Liver


title: 48614-Normal-Pancreas


title: 49365-Normal-Diaphragm


title: 49367-Normal-Diaphragm


title: 48646-Normal-Liver


title: 48589-Normal-Fat


title: 49368-Normal-Diaphragm