title: epiblast stem cells (EpiSCs), PCR amplified, biological rep1

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

source_name: EpiSCs

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: ES cells were maintained with 2i+LIF, feeder free condition.  EpiLCs were induced from the ES cells.  PGCLCs were induced from day 2 EpiLCs.  EpiSCs were derived from epiblast (embryonic day 5.75).  For detail,  see Hayashi et al., Cell 2011.

extract_protocol: total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction

value: epiblast stem cells (EpiSCs)

tag: amplification

value: 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)


title: hpMSCs, EWS-FLI-1, rep4

status: Public on Aug 05 2011

type: RNA

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

hyb_protocol: Manufacturer's protocol.

scan_protocol: Manufacturer's protocol.

data_processing: Gene expression data were obtained with the RMA method using the Affymetrix Power Tools suite.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: hpMSCs expressing EWS-FLI-1

label_protocol: Manufacturer's protocol.

growth_protocol: hpMSCs were obtained from femoral head bone marrow of four pediatric patients undergoing limb axis correction surgery and cultured as described previously (PMIDs: 14584050, 17786951, 18381423).

extract_protocol: Total RNA was extracted 12 days after infection and selection using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. RNA quality was verified by an Agilent RNA 600 nanoassay and by measuring the 260/280 absorbance ratio.

treatment_protocol: hpMSCs were infected as previously described (PMIDs: 14584050, 17786951, 18381423).

tag: cell type

value: human pediatric mesenchymal stem cells (hpMSCs)


title: primordial germ cell (PGC) like cells (PGCLCs), biological rep2

country: Japan

organism: Mus musculus

source_name: PGCLCs

tag: strain


title: epiblast stem cells (EpiSCs), biological rep2


title: hpMSCs, EWS-FLI-1, rep3


title: epiblast stem cells (EpiSCs), PCR amplified, biological rep2


title: intratumoral HCC, non-lymph node metastasis, patient 40

status: Public on Aug 04 2011

city: Shanghai

first: Zuolin

last: Xiang

address: 136 Yi Xue Yuan Road

country: China

institute: Zhongshan Hospital, Fudan University

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 40
intratumoral tissues NLNM

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Scanned data were uploaded into GenomeStudio for further analysis.

label: Cy3, Cy5

source_name: intratumoral HCC, NLNM, patient 40

label_protocol: RNA with a cycle threshold (Ct) value ≤28 was used for the DASL assay.

extract_protocol: Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit (Roche Diagnostics, Germany) according to the manufacturer’s protocol.Proteinase K digestion time was 12 hours for each sample. RNA samples were stored at -80°C until use.

tag: individual

value: patient 40

tag: disease state

value: hepatocellular carcinoma (HCC)

tag: tissue

value: intratumoral HCC tissues

tag: metastasis type

value: non-lymph node metastasis (NLNM)


title: primordial germ cell (PGC) like cells (PGCLCs), biological rep1


title: peritumoral HCC, non-lymph node metastasis, patient 40

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 40
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 40

value: peritumoral HCC tissues


title: intratumoral HCC, non-lymph node metastasis, patient 38

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 38
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 38

value: patient 38


title: peritumoral HCC, non-lymph node metastasis, patient 38

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 38
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 38


title: peritumoral HCC, non-lymph node metastasis, patient 39

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 39
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 39

value: patient 39


title: intratumoral HCC, non-lymph node metastasis, patient 37

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 37
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 37

value: patient 37


title: peritumoral HCC, non-lymph node metastasis, patient 37

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 37
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 37


title: hpMSCs, empty vector, rep2

source_name: hpMSCs infected with empty vector

value: empty vector


title: epiblast stem cells (EpiSCs), biological rep1


title: hpMSCs, EWS-FLI-1, rep1


title: intratumoral HCC, non-lymph node metastasis, patient 36

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 36
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 36

value: patient 36


title: peritumoral HCC, non-lymph node metastasis, patient 36

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 36
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 36


title: hpMSCs, empty vector, rep3


title: GIF-5 cells: CD-133-positive vs CD-133-negative Replicate 1

city: Bunkyo-ku

first: Hiroshi

last: Fukamachi

state: Tokyo

address: Yushima 5-45-1

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

description: Biological replicate 1 of 2. GIF-5 mouse gastric epithelial cells CD133-positive vs CD133-negative.

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 9.5.3

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: CD133-positive GIF-5 cells

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: GIF-5 cells were cultured with DMEM + 10% bovine serum, and were subcultured by treatment with 0.05% trypsin-0.53mM EDTA solution.

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

treatment_protocol: Single cell suspensions were stained with PE-labeled anti-CD133 antibody (eBioscience), and the cells were sorted by FACS vantage into CD133-positive and CD133-negative cells.

tag: cell line

value: gastric epithelial cells

tag: genotype

source_name: CD133-negative GIF-5 cells


title: 1547LBlog3vs14028sLBlog_14212327_MDS.mev.refIsIA.out

city: Rockville

first: Fatma

last: Onmus-Leone

address: 9704 Medical Center Dr.

country: USA

institute: JCVI

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing:
Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).
Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at
(http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Salmonella enterica

source_name: Salmonella enterica strain 14028 with STM1547 mutation/ LB /log

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Strains were grown in LB broth. Samples were collected at log phase.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manusfacturer.

value: 14028 with STM1547 mutation

tag: media

value: LB

tag: growth phase

value: log

tag: channel

value: IB

source_name: Salmonella enterica strain 14028/ LB /log

value: IA


title: day 1 epiblast like cells (EpiLCs), biological rep2

source_name: day 1 EpiLCs

value: epiblast like cells (EpiLCs)


title: hpMSCs, EWS-FLI-1, rep2

source_name: hpMSCs expressing EWS-FLI-1

value: human pediatric mesenchymal stem cells (hpMSCs)


title: embryonic stem cells (ESCs) (2iLIF, feeder free), biological rep2

source_name: embryonic stem cells with 2i+LIF culture condition, feeder free

value: embryonic stem cells (ESCs)


title: GIF-5 cells: CD-133-positive vs CD-133-negative Replicate 2

description: Biological replicate 2 of 2. GIF-5 mouse gastric epithelial cells CD133-positive vs CD133-negative.


title: hpMSCs, empty vector, rep1


title: intratumoral HCC, non-lymph node metastasis, patient 39

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 39
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 39

value: hepatocellular carcinoma (HCC)

value: intratumoral HCC tissues


title: embryonic stem cells (ESCs) (2iLIF, feeder free), biological rep1


title: day 1 epiblast like cells (EpiLCs), biological rep1


title: intratumoral HCC, non-lymph node metastasis, patient 33

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 33
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 33

value: patient 33

value: non-lymph node metastasis (NLNM)


title: intratumoral HCC, non-lymph node metastasis, patient 35

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 35
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 35

value: patient 35


title: peritumoral HCC, non-lymph node metastasis, patient 35

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 35
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 35

value: peritumoral HCC tissues


title: peritumoral HCC, non-lymph node metastasis, patient 33

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 33
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 33


title: intratumoral HCC, non-lymph node metastasis, patient 34

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 34
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 34

value: patient 34


title: intratumoral HCC, non-lymph node metastasis, patient 31

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 31
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 31

value: patient 31


title: peritumoral HCC, non-lymph node metastasis, patient 32

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 32
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 32

value: patient 32


title: intratumoral HCC, non-lymph node metastasis, patient 32

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 32
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 32


title: peritumoral HCC, non-lymph node metastasis, patient 31

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 31
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 31


title: peritumoral HCC, non-lymph node metastasis, patient 28

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 28
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 28

value: patient 28


title: peritumoral HCC, non-lymph node metastasis, patient 29

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 29
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 29

value: patient 29


title: intratumoral HCC, non-lymph node metastasis, patient 28

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 28
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 28


title: intratumoral HCC, non-lymph node metastasis, patient 27

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 27
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 27

value: patient 27


title: intratumoral HCC, non-lymph node metastasis, patient 29

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 29
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 29


title: intratumoral HCC, non-lymph node metastasis, patient 30

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 30
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 30

value: patient 30


title: peritumoral HCC, non-lymph node metastasis, patient 27

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 27
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 27


title: peritumoral HCC, non-lymph node metastasis, patient 26

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 26
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 26

value: patient 26


title: peritumoral HCC, non-lymph node metastasis, patient 30

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 30
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 30


title: intratumoral HCC, non-lymph node metastasis, patient 25

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 25
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 25

value: patient 25


title: peritumoral HCC, non-lymph node metastasis, patient 34

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 34
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 34


title: intratumoral HCC, non-lymph node metastasis, patient 24

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 24
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 24

value: patient 24


title: intratumoral HCC, non-lymph node metastasis, patient 26

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 26
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 26


title: peritumoral HCC, non-lymph node metastasis, patient 24

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 24
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 24


title: intratumoral HCC, non-lymph node metastasis, patient 22

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 22
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 22

value: patient 22


title: peritumoral HCC, non-lymph node metastasis, patient 22

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 22
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 22

value: hepatocellular carcinoma (HCC)


title: intratumoral HCC, non-lymph node metastasis, patient 23

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 23
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 23

value: patient 23

value: intratumoral HCC tissues


title: intratumoral HCC, non-lymph node metastasis, patient 21

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 21
intratumoral tissues NLNM

source_name: intratumoral HCC, NLNM, patient 21

value: patient 21

value: non-lymph node metastasis (NLNM)


title: peritumoral HCC, non-lymph node metastasis, patient 21

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 21
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 21

value: peritumoral HCC tissues


title: peritumoral HCC, non-lymph node metastasis, patient 23

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 23
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 23


title: intratumoral HCC, lymph node metastasis, patient 20

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 20
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 20

value: patient 20

value: lymph node metastasis (LNM)


title: peritumoral HCC, lymph node metastasis, patient 20

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 20
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 20


title: peritumoral HCC, non-lymph node metastasis, patient 25

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 25
peritumoral tissues NLNM

source_name: peritumoral HCC, NLNM, patient 25


title: peritumoral HCC, lymph node metastasis, patient 19

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 19
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 19

value: patient 19


title: intratumoral HCC, lymph node metastasis, patient 18

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 18
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 18

value: patient 18


title: peritumoral HCC, lymph node metastasis, patient 18

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 18
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 18


title: intratumoral HCC, lymph node metastasis, patient 17

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 17
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 17

value: patient 17


title: peritumoral HCC, lymph node metastasis, patient 14

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 14
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 14

value: patient 14


title: peritumoral HCC, lymph node metastasis, patient 16

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 16
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 16

value: patient 16


title: intratumoral HCC, lymph node metastasis, patient 14

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 14
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 14


title: peritumoral HCC, lymph node metastasis, patient 15

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 15
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 15

value: patient 15


title: intratumoral HCC, lymph node metastasis, patient 16

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 16
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 16


title: intratumoral HCC, lymph node metastasis, patient 11

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 11
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 11

value: patient 11


title: peritumoral HCC, lymph node metastasis, patient 13

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 13
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 13

value: patient 13


title: intratumoral HCC, lymph node metastasis, patient 13

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 13
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 13


title: intratumoral HCC, lymph node metastasis, patient 15

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 15
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 15


title: intratumoral HCC, lymph node metastasis, patient 12

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 12
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 12

value: patient 12


title: peritumoral HCC, lymph node metastasis, patient 17

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 17
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 17

value: hepatocellular carcinoma (HCC)


title: intratumoral HCC, lymph node metastasis, patient 10

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 10
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 10

value: patient 10


title: peritumoral HCC, lymph node metastasis, patient 12

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 12
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 12


title: peritumoral HCC, lymph node metastasis, patient 11

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 11
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 11


title: peritumoral HCC, lymph node metastasis, patient 9

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 9
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 9

value: patient 9


title: intratumoral HCC, lymph node metastasis, patient 9

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 9
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 9

value: intratumoral HCC tissues


title: peritumoral HCC, lymph node metastasis, patient 8

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 8
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 8

value: patient 8


title: intratumoral HCC, lymph node metastasis, patient 8

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 8
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 8


title: intratumoral HCC, lymph node metastasis, patient 7

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 7
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 7

value: patient 7


title: intratumoral HCC, lymph node metastasis, patient 19

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 19
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 19


title: peritumoral HCC, lymph node metastasis, patient 7

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 7
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 7

value: peritumoral HCC tissues


title: intratumoral HCC, lymph node metastasis, patient 6

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 6
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 6

value: patient 6

value: lymph node metastasis (LNM)


title: intratumoral HCC, lymph node metastasis, patient 5

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 5
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 5

value: patient 5


title: peritumoral HCC, lymph node metastasis, patient 6

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 6
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 6


title: peritumoral HCC, lymph node metastasis, patient 3

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 3
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 3

value: patient 3


title: intratumoral HCC, lymph node metastasis, patient 4

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 4
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 4

value: patient 4


title: peritumoral HCC, lymph node metastasis, patient 5

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 5
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 5


title: intratumoral HCC, lymph node metastasis, patient 2

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 2
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 2

value: patient 2


title: peritumoral HCC, lymph node metastasis, patient 2

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 2
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 2


title: peritumoral HCC, lymph node metastasis, patient 4

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 4
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 4


title: peritumoral HCC, lymph node metastasis, patient 10

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 10
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 10


title: intratumoral HCC, lymph node metastasis, patient 3

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 3
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 3


title: peritumoral HCC, lymph node metastasis, patient 1

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 1
peritumoral tissues LNM

source_name: peritumoral HCC, LNM, patient 1

value: patient 1


title: intratumoral HCC, lymph node metastasis, patient 1

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissues of patient 1
intratumoral tissues LNM

source_name: intratumoral HCC, LNM, patient 1


title: THP-1 DMSO 48h sample3

city: Cold Spring Harbor

first: Junwei

last: Shi

state: NY

address: 1 Bungtown Rd

institute: cold spring harbor lab

description: Gene expression pattern under JQ1 treatment

hyb_protocol: Hybridization, washing, and scan protocol were according to the manufacturer's instructions on Mouse Gene ST 1.0 GeneChips

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed by RMA

label: Biotin

source_name: MLL-AF9/NrasG12D human cell line

label_protocol: The cDNA was then fragmented and terminally labeled with biotin, using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: Murine cell lines and human THP-1 cell line were cultured in RPMI1640 supplement with 10% FBS and penicillin/streptomycin

extract_protocol: total RNA was isolated by using RNeasy Mini Kit (QIAGEN, #74104)

treatment_protocol: The sample were treated with DMSO, JQ1 or doxycycline as indicated.

value: MLL-AF9/NrasG12D human cell line

tag: parental cell line

tag: treatment

value: DMSO for 48h


title: THP-1 250nM JQ1 48h sample1

value: 250nM JQ1 for 48h


title: THP-1 DMSO 48h sample1


title: THP-1 250nM JQ1 48h sample3


title: Human Embryonic Fibroblasts 19weeks

city: New York

first: Vladislav

middle: M

last: Sandler

address: 1300 York Ave.

department: Genetic Medicine

institute: Weill Cornell Medical College

description: Gene expression data

hyb_protocol: HuGene-1_0-st were hybridized with labelled probes using standard conditions recommended by the manufacturer

scan_protocol: GeneChip Scanner

data_processing: Data from CEL files were imported into RMA express software and normalized. The results were exported as log values.

source_name: Fetal tissue 19 weeks

label_protocol: total RNA was labelled with a fluorophore using standard Affymetrix procedure (primer extension usig a polydT primer)

growth_protocol: Standard fibroblast medium, step liquid culture for FL and Fused cells

extract_protocol: Direct lysis of cells, DNAse treatment, RNeasy column purification

tag: gender

value: Female

value: Human Embryonic Fibroblasts 19weeks


title: THP-1 250nM JQ1 48h sample2


title: Differentiated Human Fetal Liver CD34+ cells 24 weeks

description: Gene expression data

source_name: Fetal liver 24 weeks


title: MLL-AF9/Nras MSCV Myc DMSO 48h sample3

description: Gene expression pattern of Myc overexpression rescue JQ1 treatment

source_name: MLL-AF9/NrasG12D MSCV vector murine cell line

tag: transfection

value: MSCV Myc

tag: genetic background


title: Differentiated Human Fetal Liver CD34+ cells 19 weeks

description: Gene expression data

source_name: Fetal Liver 19 weeks


title: MLL-AF9/Nras MSCV Myc 100nM JQ1 48h sample1

value: MLL-AF9/NrasG12D MSCV vector murine cell line

value: 100nM JQ1 for 48h


title: MLL-AF9/Nras MSCV Myc 100nM JQ1 48h sample2


title: THP-1 DMSO 48h sample2


title: Differentiated fused HEF19 and FL24 cells

description: Gene expression data

source_name: Fused cells, selected and differentiated cells


title: MLL-AF9/Nras MSCV Myc 100nM JQ1 48h sample3


title: MLL-AF9/Nras MSCV empty 100nM JQ1 48h sample3

value: MSCV empty


title: Human Embryonic Fibroblasts 24weeks

description: Gene expression data

source_name: Fetal tissue 24 weeks

value: Human Embryonic Fibroblasts 24weeks


title: MLL-AF9/Nras MSCV empty DMSO 48h sample2


title: MLL-AF9/Nras MSCV Myc DMSO 48h sample1


title: MLL-AF9/Nras MSCV empty DMSO 48h sample1


title: MLL-AF9/Nras MSCV empty DMSO 48h sample3


title: MLL-AF9/Nras MSCV Myc DMSO 48h sample2


title: MLL-AF9/Nras TtTMPV Rluc dox 72h sample1

description: Gene expression pattern of shRNA knockdown Brd4

source_name: MLL-AF9/NrasG12D TtTMPV murine cell line

value: dox for 72h

value: TtTMPV Rluc


title: MLL-AF9/Nras TtTMPV Rluc dox 72h sample3

value: MLL-AF9/NrasG12D TtTMPV murine cell line


title: MLL-AF9/Nras TtTMPV Brd4sh-552 dox 72h

value: TtTMPV Brd4sh-552


title: MLL-AF9/Nras MSCV empty 100nM JQ1 48h sample1


title: MLL-AF9/Nras TtTMPV Brd4sh-2097 dox 72h

value: TtTMPV Brd4sh-2097


title: MLL-AF9/Nras MSCV empty 100nM JQ1 48h sample2


title: MLL-AF9/Nras 100nM JQ1 48h sample1

source_name: MLL-AF9/NrasG12D murine cell line

value: MLL-AF9/NrasG12D murine cell line


title: MLL-AF9/Nras 100nM JQ1 48h sample3


title: MLL-AF9/Nras DMSO 48h sample2


title: MLL-AF9/Nras DMSO 48h sample3


title: MLL-AF9/Nras TtTMPV Rluc dox 72h sample2


title: MLL-AF9/Nras TtTMPV Brd4sh-1448 dox 72h

value: TtTMPV Brd4sh-1448


title: MLL-AF9/Nras 100nM JQ1 48h sample2


title: Tcf1-expressing Thy1+CD25+ Cells Biological replicate #2

city: Philadelphia

first: Avinash

last: Bhandoola

state: Philadelphia

address: 3620 Hamilton Walk

department: Pathology

institute: University of Pennsylvania

description: day 10 cultured on OP9 stroma

hyb_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression analysis Technical Manual (www.affymetrix.com). Biotinylated targets were heated at 99C for 5 min and hybridized for 16 h at 45C to 9 microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

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

data_processing:
The data were analyzed using Partek Genomics Suite, version 6.5. RMA with default settings was used to normalize data. Heat maps were drawn using the online software Matrix2png (www.bioinformatics.ubc.ca/matrix2png ).
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: murine bone marrow

label_protocol: 250ng of total RNA was amplified using the Ambion WT Expression amplification kit according to manufactors instruction. This was followed by the Affymetrix WT Terminal Labeling kit for fragmentation and biotinylation according to the manufactors instructions.

growth_protocol: Wiltype LMPPs (Lineage marker-Sca+kit+Flt3high) were isolated by a FACSAria cell sorter and retrovirally transduced with a Tcf1-containing (Tcf1-VEX) or control vector (VEX) retrovirus. In brief, hematopoietic progenitors were transduced using Retronectin (Takara). Two wells in a 12-well plate was coated with 20 μg/ml RetroNectin according to the manufacturer’s instructions. High-titer retroviral supernatants were added into wells, centrifuged at 2500 rpm, 25 oC for 1-2 hours, following which viral supernatant was removed. Cell sorted progenitor cells were resuspended in the stimulation cocktails including DMEM-complete medium, 1% pen/strep, 15% Fetal Calf Serum (FCS), L-glutamate (2mM), IL-3 (10ng/ml), IL-6 (10 ng/ml), SCF (20 ng/ml), Flt3-ligand (20 ng/ml), Polybrene (4ug/ml) and added to virus-bound RetroNectin-coated plates. For the input population, LMPPs were also placed into the stimulation cocktail medium above for 48 hours upon which the cells were isolated, wash 2x and resupended in 500ul Trizol. Transduced BM progenitors were sorted 48 hour post-infection as DAPI-VEX+ cells. Tcf1-expressing cells and control-vector expressing cells were then seeded on OP9 stroma or OP9 stroma expressing Notch ligand DL4, respectively in MEMa supplemented with 10% L-glutamate, 10%- pen/strep, and 20% FCS. Cytokines were added at a concentration of IL7 1ng/ml and Flt3L 5ng/ml. Cells were passaged at day 6 and placed onto fresh confluent monolayers of OP9 and OP9-DL4 stroma. On day 10, cells were isolated by vigourously pippetting through a 70um mesh and cell sorted as DAPI-CD45.2+Mac1-Gr1-Thy1+CD25+ T lineage cells from both Tcf1-expressing cells on OP9 and control vector expressing cells on OP9-DL4. Cells were sorted into MEMa medium, spun down at 5000rpm for 5 min and the pellet was resuspended in 500ul of Trizol. Samples were submitted to the University of Pennsylvania Microarray facility and procedures following are listed below.

extract_protocol: Trizol extraction of total RNA was performed according to the manufactors instructions

value: bone marrow

value: Tcf1-expressing Thy1+CD25+ Cells


title: AML with normal karyotype #154

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center (EMC)

description: CEBPAwt

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and targeted intensity values at 100. Intensity values were log2 transformed and mean centered per probe set.

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols.

treatment_protocol: Samples are from untreated patients (de novo AML)

tag: genotype/variation (cebpa single mutant, cebpa double mutant)

value: negative,negative


title: Tcf1-expressing Thy1+CD25+ Cells Biological replicate #1

description: day 10 cultured on OP9 stroma

tag: cell type


title: Pooled wiltype LMPPs (Lineage marker-Sca+kit+Flt3high)

description: freshly isolated LMPPs were placed into culture for 48 hours in retroviral stimulation cocktail medium and the cells were then isolated and resuspended in Trizol

tag: strain

value: LMPPs (Lineage marker-Sca+kit+Flt3high)


title: Tcf1 wildtype Lineage negative cells (Mac1-Gr1-Thy1-CD25-) biological replicate 3

description: gene expression data from Tcf1 wildtype lineage negative (CD45.2+Mac1-Gr1-Thy1-CD25-) progenitors after four days of culture on OP9-DL4 stroma

hyb_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression analysis Technical Manual (www.affymetrix.com).  Biotinylated targets were heated at 99C for 5 min and hybridized for 16 h at 45C to 9 microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

data_processing:
The data were analyzed using Partek Genomics Suite, version 6.5. RMA with default settings was used to normalize data. Heat maps were drawn using the online software Matrix2png (www.bioinformatics.ubc.ca/matrix2png). For Tcf1 wildtype and deficient lineage negative progenitors, the first two representative samples are shown in the heat map.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

label_protocol: 10ng of total RNA was amplified using the NuGEN WTA-Ovation Pico RNA kit according to the manufactor's protocol. ST-cDNA was synthesized using NuGEN WT-Ovation Exon Module, and labeled using the NuGEN Encore Biotin Module.

growth_protocol: Tcf1 wildtype and deficient  lymphoid primed multipotent progenitors (LMPPs, Lineage marker-Sca+kit+Flt3high) were isolated by a FACSAria cell sorter and seeded onto wells containing a confluent OP9-DL4 stromal monolayer in MEMa, supplemented with 10% L-glutamate, 10%P-strep, and 20% FCS. Cytokines were added at a concentration of IL1 1ng/ml and Flt3L 5ng/ml. After four days of culture, Tcf1 wildtype and deficient lineage negative progenitors and Tcf1 wt T lineage cells (Thy1+CD25+) were isolated and visualized as DAPI-CD45.2 and then highly pure populations were cell sorted according to phenotype (Lineage negative: Mac1-Gr1-Thy1-CD25-; T lineage: Thy1+CD25+). Cells were sorted into MEMa medium and spun down and resuspended in Trizol.

extract_protocol: Trizol extraction of total RNA was performed  according to the manufactors instructions

value: Tcf7+/+ mice were generated by H.Clevers and backcrossed approximately 6 generations and was maintained at that mixed background


title: Tcf1 wildtype Lineage negative cells (Mac1-Gr1-Thy1-CD25-) biological replicate 2


title: AML with normal karyotype #152

description: CEBPAwt


title: Tcf1 wildtype Lineage negative cells (Mac1-Gr1-Thy1-CD25-) biological replicate 1

description: gene expression data from Tcf1 wt lineage negative (CD45.2+Mac1-Gr1-Thy1-CD25-) progenitors after four days of culture on OP9-DL4 stroma


title: Tcf1 deficient  Lineage negative cells (Mac1-Gr1-Thy1-CD25-) biological replicate 1

description: gene expression data from Tcf1 deficient lineage negative (CD45.2+Mac1-Gr1-Thy1-CD25-) progenitors after four days of culture on OP9-DL4 stroma

value: Tcf7-/- mice were generated by H.Clevers and backcrossed approximately 6 generations and was maintained at that mixed background


title: Tcf1 deficient  Lineage negative cells (Mac1-Gr1-Thy1-CD25-) biological replicate 3


title: Control vector expressing-Thy1+CD25+ Cells

description: day 10 cultured on OP9-DL4 stroma


title: Tcf1 deficient  Lineage negative cells (Mac1-Gr1-Thy1-CD25-) biological replicate 2


title: AML with normal karyotype #143

description: CEBPAwt


title: AML with normal karyotype #138

description: CEBPAwt


title: Tcf1 wildtype T lineage cells (Thy1+CD25+) biological replicate 2

description: gene expression data from Tcf1 T lineage progenitors (CD25.2+Thy1+CD25+) after four days of culture on OP9-DL4 stroma

value: T lineage cells (Thy1+CD25+)


title: AML with normal karyotype #147

description: CEBPAwt


title: AML with normal karyotype #146

description: CEBPAwt


title: Tcf1 wildtype T lineage cells (Thy1+CD25+) biological replicate 1


title: AML with normal karyotype #148

description: CEBPAwt


title: AML with normal karyotype #153

description: CEBPAwt


title: AML with normal karyotype #140

description: CEBPAwt


title: AML with normal karyotype #136

description: CEBPAwt


title: AML with normal karyotype #144

description: CEBPAwt


title: AML with normal karyotype #151

description: CEBPAwt


title: AML with normal karyotype #139

description: CEBPAwt


title: AML with normal karyotype #145

description: CEBPAwt


title: MLL-AF9/Nras DMSO 48h sample1

value: DMSO for 48h


title: AML with normal karyotype #135

description: CEBPAwt


title: AML with normal karyotype #141

description: CEBPAwt


title: AML with normal karyotype #142

description: CEBPAwt


title: AML with normal karyotype #133

description: CEBPAwt


title: AML with normal karyotype #130

description: CEBPAwt


title: AML with normal karyotype #134

description: CEBPAwt


title: AML with normal karyotype #124

description: CEBPAwt


title: AML with normal karyotype #128

description: CEBPAwt


title: AML with normal karyotype #126

description: CEBPAwt


title: AML with normal karyotype #129

description: CEBPAwt


title: AML with normal karyotype #123

description: CEBPAwt


title: AML with normal karyotype #115

description: CEBPAwt


title: AML with normal karyotype #116

description: CEBPAwt


title: AML with normal karyotype #122

description: CEBPAwt


title: AML with normal karyotype #127

description: CEBPAwt


title: AML with normal karyotype #131

description: CEBPAwt


title: AML with normal karyotype #108

description: CEBPAwt


title: AML with normal karyotype #125

description: CEBPAwt


title: AML with normal karyotype #113

description: CEBPAwt


title: AML with normal karyotype #109

description: CEBPAwt


title: AML with normal karyotype #104

description: CEBPAwt


title: AML with normal karyotype #105

description: CEBPAwt


title: AML with normal karyotype #107

description: CEBPAwt


title: AML with normal karyotype #114

description: CEBPAwt


title: AML with normal karyotype #117

description: CEBPAwt


title: AML with normal karyotype #103

description: CEBPAwt


title: AML with normal karyotype #110

description: CEBPAwt


title: AML with normal karyotype #106

description: CEBPAwt


title: AML with normal karyotype #102

description: CEBPAwt


title: AML with normal karyotype #111

description: CEBPAwt


title: AML with normal karyotype #112

description: CEBPAwt


title: AML with normal karyotype #101

description: CEBPAwt


title: AML with normal karyotype #96

description: CEBPAwt


title: AML with normal karyotype #97

description: CEBPAwt


title: AML with normal karyotype #12

description: CEBPAdm

value: negative,positive


title: AML with normal karyotype #99

description: CEBPAwt


title: AML with normal karyotype #95

description: CEBPAwt


title: AML with normal karyotype #19

description: CEBPAdm


title: AML with normal karyotype #13

description: CEBPAdm


title: AML with normal karyotype #18

description: CEBPAdm


title: Well Watered CCLONE 44686 Replicate 2 [DR vs. WW]

city: Athens

first: Adam

middle: W.

last: Barb

state: GA

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

hyb_protocol: Hybridization was carried out as described previously: Lorenz WW, Yu Y-S, Simões M, Dean JFD: Processing the Loblolly Pine PtGen2 cDNA Microarray. Journal of Visualized Experiments 2009, 25.  50 pmol each of Cy-5 and Cy-3 labeled target was combined in a single tube and dried in a vacuum desiccator at 45oC to a volume of 1-2 L.  cDNAs were resuspended in 60uL hybridization buffer (30% formamide, 5X SSC, 5X Denhardt’s, 1% PolyA RNA, 0.1% SDS), vortexed briefly and heated in a 95oC water bath for 5 min.. Targets were loaded at the bottom edge of the LifterSlip™ by way of capillary action.  Slides were placed in a HybChamber™ (Genomic Solutions, Ann Arbor, MI ) and 20L of 100mM DTT was added to humidity wells located at each end of the chamber.  The chamber was assembled, wrapped in aluminum foil, and incubated in a 48oC shaking water bath set at 50 rpm for 14-16 hr.

scan_protocol: The microarrays were scanned using a ProScanArray™ confocal scanner (Perkin Elmer, Waltham, MA).  Scans were conducted with the 532 nm and 635 nm lasers and data were collected at a 10 m resolution.  Laser power remained constant at 90% and gain settings typically ranged between 55-65%.

data_processing: Raw fluorescence data were processed with an image analysis algorithm in ImaGene software, ver. 7.5 (Bio-Discovery Inc., El Segundo, CA, USA) was used to quantify signal and background intensity.  Probes that had been duplicated on the array as internal controls were flagged to leave a single representative for each duplicated set and signal means were determined without background correction.  An in house Perl script was used to import the raw Imagene signal intensity data, to calculate Wang et al. flags (Wang et al. Bioinformatics 2003,19:1341-1347) and to convert the data into a readily exportable file for downstream BRB array tools statistical analysis.  Normalization and Statistical Analysis  Data was filtered and normalized using BRB-Array Tools, an R-based integrated package for the visualization and statistical analysis of DNA microarray gene expression data (Simon et al.  Cancer Informatics 2007, 3:11-17).  Using the reference design experimental module, raw signal intensity data from all replicates, 72 slides total, were log2 transformed and normalized by the Lowess plus print tip method.  Spot signals were filtered by employing Wang flagging and gene filters were employed to remove any gene with 50% or more missing or filtered data.   Normalized signal intensity ratios were calculated for identification of differentially expressed genes (DEGs) that were determined via paired comparisons among the three treatment groups using the class comparison tool and utilizing a random variance t-test for computation of P-values.  Control of the proportion of false discoveries was accomplished the multivariate permutation test with the number of permutations at the default setting of 1000.  All paired treatment comparison analyses were performed with a false discovery rate (FDR) of 0.01 and a confidence level of 90%.    The list DEGs identified in the WW vs. DS comparison with at least a 1.5-fold difference in expression was used to extract the BRB normalized log mean ratio data identified from all three treatments.

organism: Pinus taeda

label_protocol: First-Strand cDNA Synthesis and Purification  Synthesis of amino-allyl and amino-hexyl modified cDNA and was done with an Invitrogen SuperScriptTM Indirect cDNA Labeling System (Invitrogen Corp., Carlsbad, CA) according to the manufacturer’s protocol with a few modifications.  Briefly, each cDNA synthesis reaction contained 20g of DNase treated total RNA annealed to 2L anchored oligo(dT)20 primer plus 1L random hexamer primer.  Reactions were carried out in a 45oC water bath for 12-14 hr.  Samples were purified on S.N.A.P™ columns supplied with the kit and washed three times with 500L wash buffer.  cDNA was eluted twice with 50L DEPC-water, EtOH precipitated ( 10L of 3M Sodium Acetate, pH5.2, 2L 20mg/mL glycogen, and 300uL -20oC 100% EtOH) at -80oC for 30 min.  Pellets were washed three times with -20oC 70% EtOH followed by resuspending in 5L 2X coupling buffer that had been warmed to 43 oC.     Cy Dye Coupling and Assessment of Labeling Efficiency  Cy-5 and Cy-3 dyes (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), were prepared on the same day as labeling by dissolving each in 80L DMSO.  Five microliters of dye was added to the resuspended cDNA sample and incubated in the dark for 1 hour.   Next, 20uL of 3M sodium acetate, pH5.2 and 500uL loading buffer was added to the dye-coupled cDNA.  The sample was passed over a S.N.A.P. column and washed three times as described above.  Labeled cDNA was eluted in 65L DEPC-water.   Nucleic acid and Cy dye concentrations of labeled target cDNAs were determined using a NanoDrop ND-1000 and concentrations were converted to pmol to calculate a ratio for efficiency of labeling.  Typical ratios were in the range of 20-40 pmol n.t./pmol dye and total dye incorporated typically ranged from 200-400 pmol.

growth_protocol: Tissues samples were isolated from plants grown as described previously:Lorenz WW, Sun F, Liang C, Kolychev D, Wang HM, Zhao X, Cordonnier-Pratt MM, Pratt LH, Dean JFD: Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiology 2006, 26(1):1-16

extract_protocol: RNA Extraction was carried out as described previously:Lorenz WW, Sun F, Liang C, Kolychev D, Wang HM, Zhao X, Cordonnier-Pratt MM, Pratt LH, Dean JFD: Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiology 2006, 26(1):1-16 and Lorenz WW, Yu Y-S, Dean JFD: An Improved Method of RNA Isolation from Loblolly Pine (P. taeda L.) and Other Conifer Species Journal of Visualized Experiments 2010, 36

treatment_protocol: Treatment protocol was as described previously: Lorenz WW, Sun F, Liang C, Kolychev D, Wang HM, Zhao X, Cordonnier-Pratt MM, Pratt LH, Dean JFD: Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiology 2006, 26(1):1-16

value: CCLONE 44686

value: 10 mo. old propagule roots, pooled from 3 individuals

value: Well-Watered (WW)

tag: pre-dawn water potential at harvest

tag: harvest point

value: Day 9, control, harvested at same time as DR

source_name: Reference sample

tag: reference sample components

value: CCLONES 40430, 43680, 41586 first flush candle and needle tissue, 500 mg ea.; CCLONES 41201, 41396, 44686, 45226, drought-stressed, drought recovered, and well-watered roots from each genotype, 250 mg ea.; Genotype 7-56, callus tissue (needle origin), 250 mg.


title: AML with normal karyotype #98

description: CEBPAwt


title: AML with normal karyotype #21

description: CEBPAdm


title: Drought Recovery CCLONE 44686 Replicate 4 [DR vs. WW]

tag: tissue

value: Drought-Stressed + Recovery (DR)

value: Day 9, 48 hrs recovery time


title: Well Watered CCLONE 44686 Replicate 1 [DR vs. WW]


title: Well Watered CCLONE 41369 Replicate 6 [DR vs. WW]

value: CCLONE 41369


title: Well Watered CCLONE 41369 Replicate 3 [DR vs. WW]


title: Well Watered CCLONE 41369 Replicate 4 [DR vs. WW]


title: Drought Recovery CCLONE 44686 Replicate 3 [DR vs. WW]


title: AML with normal karyotype #11

description: CEBPAdm


title: Drought Recovery CCLONE 44686 Replicate 6 [DR vs. WW]


title: Drought Recovery CCLONE 44686 Replicate 2 [DR vs. WW]


title: Well Watered CCLONE 41369 Replicate 5 [DR vs. WW]


title: Drought Recovery CCLONE 44686 Replicate 5 [DR vs. WW]


title: Drought Recovery CCLONE 44686 Replicate 1 [DR vs. WW]


title: AML with normal karyotype #2

description: CEBPAsm

value: positive,negative


title: Well Watered CCLONE 44686 Replicate 3 [DR vs. WW]


title: AML with normal karyotype #132

description: CEBPAwt


title: AML with normal karyotype #3

description: CEBPAsm


title: Well Watered CCLONE 41369 Replicate 2 [DR vs. WW]


title: Well Watered CCLONE 41369 Replicate 1 [DR vs. WW]


title: Drought Recovery CCLONE 41369 Replicate 2 [DR vs. WW]


title: Drought Recovery CCLONE 41369 Replicate 4 [DR vs. WW]


title: Drought Recovery CCLONE 41201 Replicate 6 [DR vs. WW]

value: CCLONE 41201


title: Well Watered CCLONE 41201 Replicate 2 [DR vs. WW]


title: Well Watered CCLONE 41201 Replicate 3 [DR vs. WW]


title: Well Watered CCLONE 41201 Replicate 4 [DR vs. WW]


title: Well Watered CCLONE 41201 Replicate 5 [DR vs. WW]


title: Drought Recovery CCLONE 41369 Replicate 3 [DR vs. WW]


title: Drought Recovery CCLONE 41201 Replicate 5 [DR vs. WW]


title: Well Watered CCLONE 45226 Replicate 6 [DS vs. WW]

value: CCLONE 45226


title: Drought Recovery CCLONE 41369 Replicate 5 [DR vs. WW]


title: AML with normal karyotype #119

description: CEBPAwt

value: negative,negative


title: Well Watered CCLONE 41201 Replicate 6 [DR vs. WW]


title: Drought Recovery CCLONE 41201 Replicate 1 [DR vs. WW]


title: Drought Recovery CCLONE 41369 Replicate 1 [DR vs. WW]


title: Drought Recovery CCLONE 41369 Replicate 6 [DR vs. WW]


title: Well Watered CCLONE 45226 Replicate 3 [DS vs. WW]


title: Well Watered CCLONE 45226 Replicate 5 [DS vs. WW]


title: Well Watered CCLONE 41201 Replicate 1 [DR vs. WW]


title: Drought Stress CCLONE 45226 Replicate 6 [DS vs. WW]

value: Drought-Stressed (DS)

value: Day 7


title: Drought Recovery CCLONE 41201 Replicate 3 [DR vs. WW]


title: Drought Stress CCLONE 45226 Replicate 5 [DS vs. WW]


title: Well Watered CCLONE 45226 Replicate 2 [DS vs. WW]


title: Drought Stress CCLONE 45226 Replicate 4 [DS vs. WW]


title: Drought Stress CCLONE 45226 Replicate 3 [DS vs. WW]


title: Drought Recovery CCLONE 41201 Replicate 4 [DR vs. WW]


title: Well Watered CCLONE 45226 Replicate 4 [DS vs. WW]


title: Drought Stress CCLONE 45226 Replicate 2 [DS vs. WW]


title: Drought Recovery CCLONE 41201 Replicate 2 [DR vs. WW]


title: Well Watered CCLONE 44686 Replicate 1 [DS vs. WW]


title: Well Watered CCLONE 44686 Replicate 6 [DS vs. WW]


title: Drought Stress CCLONE 45226 Replicate 1 [DS vs. WW]


title: Drought Stress CCLONE 44686 Replicate 2 [DS vs. WW]


title: Well Watered CCLONE 44686 Replicate 3 [DS vs. WW]


title: Well Watered CCLONE 41369 Replicate 2 [DS vs. WW]


title: Well Watered CCLONE 41369 Replicate 3 [DS vs. WW]


title: Well Watered CCLONE 44686 Replicate 5 [DS vs. WW]


title: Drought Stress CCLONE 41369 Replicate 6 [DS vs. WW]


title: Drought Stress CCLONE 41369 Replicate 4 [DS vs. WW]


title: Drought Stress CCLONE 44686 Replicate 5 [DS vs. WW]


title: Drought Stress CCLONE 44686 Replicate 1 [DS vs. WW]


title: Drought Stress CCLONE 44686 Replicate 3 [DS vs. WW]


title: Well Watered CCLONE 41369 Replicate 4 [DS vs. WW]


title: Drought Stress CCLONE 44686 Replicate 6 [DS vs. WW]


title: Well Watered CCLONE 41369 Replicate 6 [DS vs. WW]


title: Well Watered CCLONE 44686 Replicate 2 [DS vs. WW]


title: Drought Stress CCLONE 44686 Replicate 4 [DS vs. WW]


title: Drought Stress CCLONE 41369 Replicate 1 [DS vs. WW]


title: Well Watered CCLONE 41369 Replicate 5 [DS vs. WW]


title: Drought Stress CCLONE 41369 Replicate 5 [DS vs. WW]


title: Well Watered CCLONE 41369 Replicate 1 [DS vs. WW]


title: Drought Stress CCLONE 41369 Replicate 3 [DS vs. WW]


title: Drought Stress CCLONE 41369 Replicate 2 [DS vs. WW]


title: Well Watered CCLONE 44686 Replicate 4 [DS vs. WW]


title: Well Watered CCLONE 41201 Replicate 5 [DS vs. WW]


title: Well Watered CCLONE 41201 Replicate 4 [DS vs. WW]


title: Well Watered CCLONE 41201 Replicate 6 [DS vs. WW]


title: Well Watered CCLONE 41201 Replicate 3 [DS vs. WW]


title: Well Watered CCLONE 41201 Replicate 2 [DS vs. WW]


title: Well Watered CCLONE 41201 Replicate 1 [DS vs. WW]


title: Drought Stress CCLONE 41201 Replicate 5 [DS vs. WW]


title: Drought Stress CCLONE 41201 Replicate 3 [DS vs. WW]


title: Drought Stress CCLONE 45226 Replicate 6 [DS vs. DR]


title: Drought Stress CCLONE 41201 Replicate 2 [DS vs. WW]


title: Drought Stress CCLONE 41201 Replicate 4 [DS vs. WW]


title: Drought Stress CCLONE 45226 Replicate 2 [DS vs. DR]


title: Drought Stress CCLONE 45226 Replicate 4 [DS vs. DR]


title: Drought Recovery CCLONE 45226 Replicate 6 [DS vs. DR]


title: Drought Recovery CCLONE 45226 Replicate 3 [DS vs. DR]


title: Drought Stress CCLONE 45226 Replicate 1 [DS vs. DR]


title: Drought Stress CCLONE 45226 Replicate 3 [DS vs. DR]


title: Drought Stress CCLONE 45226 Replicate 5 [DS vs. DR]


title: Drought Recovery CCLONE 45226 Replicate 1 [DS vs. DR]


title: Drought Stress CCLONE 41201 Replicate 6 [DS vs. WW]


title: Drought Recovery CCLONE 45226 Replicate 5 [DS vs. DR]


title: Drought Recovery CCLONE 45226 Replicate 4 [DS vs. DR]


title: Drought Recovery CCLONE 45226 Replicate 2 [DS vs. DR]


title: Drought Stress CCLONE 44686 Replicate 6 [DS vs. DR]


title: Drought Recovery CCLONE 44686 Replicate 4 [DS vs. DR]


title: Drought Stress CCLONE 44686 Replicate 4 [DS vs. DR]


title: Drought Stress CCLONE 44686 Replicate 5 [DS vs. DR]


title: Drought Stress CCLONE 44686 Replicate 3 [DS vs. DR]


title: Drought Recovery CCLONE 44686 Replicate 5 [DS vs. DR]


title: Drought Stress CCLONE 44686 Replicate 2 [DS vs. DR]


title: Drought Stress CCLONE 44686 Replicate 1 [DS vs. DR]


title: Drought Stress CCLONE 41201 Replicate 1 [DS vs. WW]


title: Drought Recovery CCLONE 44686 Replicate 6 [DS vs. DR]


title: Drought Recovery CCLONE 44686 Replicate 1 [DS vs. DR]


title: Drought Stress CCLONE 41369 Replicate 5 [DS vs. DR]


title: Drought Recovery CCLONE 44686 Replicate 2 [DS vs. DR]


title: Drought Stress CCLONE 41369 Replicate 3 [DS vs. DR]


title: Drought Stress CCLONE 41369 Replicate 6 [DS vs. DR]


title: Drought Stress CCLONE 41369 Replicate 4 [DS vs. DR]


title: Drought Stress CCLONE 41369 Replicate 2 [DS vs. DR]


title: Drought Recovery CCLONE 44686 Replicate 3 [DS vs. DR]


title: Drought Recovery CCLONE 41369 Replicate 4 [DS vs. DR]


title: Drought Recovery CCLONE 41369 Replicate 6 [DS vs. DR]


title: Drought Recovery CCLONE 41369 Replicate 3 [DS vs. DR]


title: Drought Stress CCLONE 41369 Replicate 1 [DS vs. DR]


title: Drought Recovery CCLONE 41369 Replicate 5 [DS vs. DR]


title: Drought Recovery CCLONE 41369 Replicate 2 [DS vs. DR]


title: mock_96hpi_3

city: Erlangen

first: Lars

middle: Matthias

last: Voll

address: Staudtstrasse 5

department: Division of Biochemistry

country: Germany

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (Expression Analysis Technical Manual, 2001, Affymetrix)

scan_protocol: Microarrays were scanned on an Affymetrix GSC3000.

data_processing:
Data analysis was performed using the Bioconductor packages "affy", "gcRMA" and "limma" (http://www.bioconductor.org/) within the R environment.
Data were preprocessed using the affy package (Gautier et al., 2004) and normalized by the gcRMA method (Wu et al., 2004). The limma package (Smyth, 2004) was used for analysis of differentially expressed genes. The p-values for the contrasts of interest were adjusted for multiple testing by estimation of the false discovery rate (FDR) using the method introduced by Benjamini and Hochberg (Benjamini and Hochberg, 1995).

organism: Zea mays

source_name: leaf number 4 as counted from the bottom

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

growth_protocol: Maize plants of the cultivar Nathan were grown in a phytochamber in a 15 h / 9 h light-dark cycle; light period started with a  continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28°C and 20°C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plants were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.

extract_protocol: For RNA isolation, material from 10 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer's instructions, respectively.

treatment_protocol: Two hours after transfer from AMM to nitrogen starvation medium (-N), sporidia grown at 28°C were harvested for total RNA extraction.

tag: cultivar

value: Nathan

tag: time point

value: 96 hpi

tag: infection

value: mock


title: Drought Stress CCLONE 41201 Replicate 6 [DS vs. DR]

tag: genotype


title: Cgram_96hpi_2

value: Colletotrichum graminicola strain CgM2


title: Drought Recovery CCLONE 41369 Replicate 1 [DS vs. DR]

value: 10 mo. old propagule roots, pooled from 3 individuals


title: Drought Stress CCLONE 41201 Replicate 4 [DS vs. DR]


title: mock_36hpi_2

value: 36 hpi


title: Drought Stress CCLONE 41201 Replicate 5 [DS vs. DR]


title: mock_96hpi_2


title: Drought Stress CCLONE 41201 Replicate 3 [DS vs. DR]


title: Cgram_96hpi_1


title: mock_36hpi_1


title: Well Watered CCLONE 45226 Replicate 1 [DS vs. WW]

value: Well-Watered (WW)

value: Day 9, control, harvested at same time as DR


title: mock_96hpi_1


title: Drought Stress CCLONE 41201 Replicate 2 [DS vs. DR]

value: CCLONES 40430, 43680, 41586 first flush candle and needle tissue, 500 mg ea.; CCLONES 41201, 41396, 44686, 45226, drought-stressed, drought recovered, and well-watered roots from each genotype, 250 mg ea.; Genotype 7-56, callus tissue (needle origin), 250 mg.


title: Cgram_36hpi_3


title: Cgram_96hpi_3


title: Cgram_36hpi_1


title: Drought Stress CCLONE 41201 Replicate 1 [DS vs. DR]


title: mock_36hpi_3


title: Cgram_36hpi_2


title: Drought Recovery CCLONE 41201 Replicate 4 [DS vs. DR]

value: Drought-Stressed + Recovery (DR)

value: Day 9, 48 hrs recovery time


title: Drought Recovery CCLONE 41201 Replicate 3 [DS vs. DR]


title: Drought Recovery CCLONE 41201 Replicate 1 [DS vs. DR]


title: Drought Recovery CCLONE 41201 Replicate 6 [DS vs. DR]


title: Well Watered CCLONE 45226 Replicate 5 [DR vs. WW]


title: Well Watered CCLONE 45226 Replicate 6 [DR vs. WW]


title: Drought Recovery CCLONE 41201 Replicate 5 [DS vs. DR]


title: KR1: pB

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description: Cancer cells exhibit the ability to proliferate indefinitely, but paradoxically, overexpression of cellular oncogenes in primary cells can result in a rapid and irreversible cell cycle arrest known as oncogene-induced senescence (OIS). However, we have shown that constitutive overexpression of the oncogene c-MYC in primary human foreskin fibroblasts results in a population of cells with unlimited lifespan; these immortalized cells are henceforth referred to as iMYC. Here, in order to further elucidate the mechanisms underlying the immortalization process, a gene expression signature of three independently established iMYC cell lines compared to matched early passage c-MYC overexpressing cells was derived. Network analysis of this "iMYC signature" indicated that a large fraction of the down-regulated genes were functionally connected and major nodes centered around the TGFb, IL-6 and IGF-1 signaling pathways. Here, we focused on the functional validation of the alteration of TGFb response during c-MYC-mediated immortalization. The results demonstrate loss of sensitivity of iMYC cells to activation of TGFb signaling upon ligand addition. Furthermore, we show that aberrant regulation of the p27 tumor suppressor protein in iMYC cells is a key event that contributes to loss of response to TGFb. These findings highlight the potential to reveal key pathways contributing to the self-renewal of cancer cells through functional mining of the unique gene expression signature of cells immortalized by c-MYC.  Cell Cycle. 2011 Aug 1;10(15).

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

source_name: KR1: pB

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: foreskin fibroblast

tag: cell line

tag: genotype/variation

value: pBABE


title: KR2: iMyc

source_name: KR2: iMyc

value: iMyc


title: KR1: iMyc

source_name: KR1: iMyc


title: JAB1: Myc

source_name: JAB1: Myc

value: Myc


title: KR2: Myc

source_name: KR2: Myc


title: JAB1: iMyc

source_name: JAB1: iMyc


title: KR1: Myc

source_name: KR1: Myc


title: JAB1: pB

source_name: JAB1: pB


title: Well Watered CCLONE 45226 Replicate 3 [DR vs. WW]

value: CCLONE 45226

tag: treatment


title: KR2: pB

source_name: KR2: pB


title: Well Watered CCLONE 45226 Replicate 4 [DR vs. WW]


title: Well Watered CCLONE 45226 Replicate 2 [DR vs. WW]


title: Well Watered CCLONE 45226 Replicate 1 [DR vs. WW]


title: Well Watered CCLONE 44686 Replicate 6 [DR vs. WW]

value: CCLONE 44686


title: Well Watered CCLONE 44686 Replicate 5 [DR vs. WW]


title: Drought Recovery CCLONE 45226 Replicate 5 [DR vs. WW]


title: Drought Recovery CCLONE 41201 Replicate 2 [DS vs. DR]

value: CCLONE 41201


title: Drought Recovery CCLONE 45226 Replicate 1 [DR vs. WW]


title: Drought Recovery CCLONE 45226 Replicate 2 [DR vs. WW]


title: K5-M6-BRep2

city: Waipahu

first: Ratnesh

last: Singh

state: HI

address: 94-340 Kunia Rd

institute: Hawaii Agriculture Research Center

description:
66_KA5-MA6
Biological replicate 2 of 3, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.

hyb_protocol: Potato cDNA microarrays were prehybridized for 45 min in prehybridization buffer (5X SSC, 0.1% SDS, 1% BSA) preheated at 42°C. Prehybridized slides were washed twice in miliQ water for 5 min each, then washed for 2 min in isopropanol and air dried. Labelled cDNA probes were dissolved in 45 µl of 1X hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS). 2 µl of EDTA (from 0.5M stock), 2 µl of polyA DNA (from 10 µg/ µl stock) and 0.75 µl of salmon sperm DNA (from 10 µg/µl stock) were added into the probe mix. Heat denatured probes were carefully applied to the microarray slides and incubated in hybridization chamber at 42°C for 16-20h. Hybridized slides were washed for 5 min in a low stringency wash buffer (2X SSC and 0.1% SDS) preheated to 42°C, followed by 10 min wash in a high-stringency wash buffer (0.05X SSC and 0.1% SDS) at room temperature. Slides were washed four times for one min each in 0.05X SSC, and dried using centrifuge.

scan_protocol: Scanned on GenePix Personal 4100A scanner (Molecular Devices Corporation, Sunnyvale, CA). Images were quantified using using GenePix Pro 6.0 (Molecular Devices Corporation, Sunnyvale, CA).

data_processing: Per spot and per chip normalization based on the Lowess method was implemented using GeneSpring 7.0 (Agilent Technologies, Santa Clara, CA). Statistically significant differentially expressed genes were identified by applying one-way ANOVA analysis.

label: Alexa 555

organism: Coffea arabica

source_name: Typica shoot tips including first unopened leaf pair

label_protocol: Total RNA was used to synthesize fluorescently labeled (Alexa Fluor 555 & Alexa Fluor 647) cDNA probes using the SuperScript Indirect cDNA Labeling System (Invitrogen Corporation, Carlsbad, CA) following manufacturers instructions.

growth_protocol: Tall Mokka and Typica trees were clonally propagated and maintained under similar environmental conditions in the fields at the Kunia experimental station of Hawaii Agriculture Research Center (HARC) on Oahu.

extract_protocol: Total RNA extracted using RNeasy Plant mini kit following manufacturers instructions.

treatment_protocol: Shoot tips including unopened leaves were collected from all trees.

value: Typica

label: Alexa 647

source_name: Tall Mokka shoot tip

value: Tall Mokka


title: M5-K6-DSRep2

description:
65_MA5-KA6
Dye swap Replicate of 66_KA5-MA6, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.

source_name: Tall Mokka shoot tip including first unopened leaf pair

source_name: Typica shoot tip


title: Well Watered CCLONE 44686 Replicate 4 [DR vs. WW]


title: K5-M6-BRep1

description:
63_KB5-MA6
Biological replicate 1 of 3, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.


title: Drought Recovery CCLONE 45226 Replicate 6 [DR vs. WW]


title: M9

status: Public on Aug 03 2011

city: Wuhan

first: Xiao-Qin

last: Xia

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

department: Center for Molelcular and Cellular Biology of Aquatic Organisms

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

description:
SOM04P8P
Inversion

hyb_protocol: Performed by Roche Nimblegen Service Group in Iceland.

data_processing: The data in the matrix table are quantile-normalized between arrays for male and female separately.

organism: Drosophila melanogaster

growth_protocol: fly cultures were grown and maintained on dextrose-cornmeal-yeast medium at room temperature

extract_protocol: Total RNA from biological samples was extracted using TRIzol Reagent (Invitrogen) and purified using the Rneasy Mini Kit (Qiagen)

treatment_protocol: Three low-density crosses were set up for the strains REC, INV1, INV2, SIM1, REV1, and REV2.  The resulting virgin progeny was collected, separated by sex, and allowed to age for 5-7 days.  Fifty individuals for each sex were snap frozen in liquid nitrogen at the same time of the day within a 2 hours window, and subsequently stored at -80C.

tag: gender

value: male


title: M12

description:
SOM04P8T
Reversion

scan_protocol: Performed by Roche Nimblegen Service Group in Iceland.


title: F2

description:
SOM04P7W
Recombination

label_protocol: Performed by Roche Nimblegen Service Group in Iceland.

value: female

value: REC


title: M17

description:
SOM04P8Z
Reversion


title: F8

description:
SOM04P82
Inversion


title: F5

description:
SOM04P7Z
Simultaneous control


title: K5-M6-BRep3

description:
77_KB5-MB6
Biological replicate 3 of 3, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.


title: M5-K6-DSRep1

description:
64_MA5-KB6
Dye swap Replicate of 63_KB5-MA6, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.


title: Drought Recovery CCLONE 45226 Replicate 3 [DR vs. WW]

value: 10 mo. old propagule roots, pooled from 3 individuals


title: M5

description:
SOM04P8K
Simultaneous control


title: F7

description:
SOM04P81
Inversion


title: F11

description:
SOM04P85
Reversion


title: M11

description:
SOM04P8S
Reversion


title: M18

description:
SOM04P90
Reversion


title: F4

description:
SOM04P7Y
Simultaneous control


title: M2

description:
SOM04P8G
Recombination


title: F1

description:
SOM04P7V
Recombination


title: M7

description:
SOM04P8M
Inversion


title: F15

description:
SOM04P89
Inversion


title: F14

description:
SOM04P88
Inversion


title: F12

description:
SOM04P86
Reversion


title: F17

description:
SOM04P8C
Reversion


title: M3

description:
SOM04P8H
Recombination


title: F10

description:
SOM04P84
Reversion


title: F3

description:
SOM04P7X
Recombination


title: Drought Recovery CCLONE 45226 Replicate 4 [DR vs. WW]


title: M5-K6-TRep4

description:
69_MA5-KA6
Technical Replicate of 65_MA5-KA6, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.


title: K5-M6-TRep4

description:
67_KA5-MA6
Technical replicate of 66_KA5-MA6, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.


title: F16

description:
SOM04P8E
Reversion


title: F9

description:
SOM04P83
Inversion


title: M1

description:
SOM04P8F
Recombination


title: F18

description:
SOM04P8D
Reversion


title: M15

description:
SOM04P8X
Inversion


title: F6

description:
SOM04P80
Simultaneous control


title: M8

description:
SOM04P8N
Inversion


title: M14

description:
SOM04P8W
Inversion


title: M13

description:
SOM04P8V
Inversion


title: M10

description:
SOM04P8R
Reversion


title: E. coli Polymyxin B treatment at time=60 min, rep 2

first: Bruk

last: Mensa

state: PA

address: 1010 Stellar Chance Building, 422 Curie Blvd.

department: Biochemistry and Biophysics

institute: University of Pennsylvania, School of Medicine

description:
DeGrado2_ (1297) GC17 E. coli_2
Gene expression data from E. coli in late logarithmic growth treated with 0.39 µg/mL Polymyxin B sulfate for 60 minutes

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on E. coli Genome 2.0 Array. The microarrays were then washed and stained.

scan_protocol: Genechips were scanned with a  GCS3000 laser scanner.

data_processing: Data were GC-RMA normalized and processed using SAM (significance analysis of Microarrays)

organism: Escherichia coli

source_name: E. coli T=60 min after 0.39 µg/mL Polymyxin B treatment, rep 2

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

growth_protocol: Cultures of E.coli were grown from dilutions of overnight cultures in LB media at 37C with shaking

extract_protocol: 1 mL of culture was harvested from each sample at indicated times and Qiagen Rneasy mini kit isolation of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: At OD600 = 0.4, the culture of E.coli was split into 9 equal flasks containing prewarmed LB media: three containing 1X volume of LB media with no antimicrobial, three containing 1X volume of LB media + 17.5 µg/mL PMX 10070 (for a final concentration of 8.75 µg/mL PMX 10070) and three containing 1X volume of LB media + 0.78 µg/mL of Polymyxin B sulfate (for a final concentration of 0.39 µg/mL Polymyxin B sulfate)


title: E. coli control at time=60 min, rep 2

description:
DeGrado2_ (1291) GC11 E. coli_2
Gene expression data from E. coli in late logarithmic growth

source_name: E. coli T=60 min, no treatment, rep 2


title: E. coli Polymyxin B treatment at time=60 min, rep 3

description:
DeGrado2_ (1298) GC18 E. coli_2
Gene expression data from E. coli in late logarithmic growth treated with 0.39 µg/mL Polymyxin B sulfate for 60 minutes

source_name: E. coli T=60 min after 0.39 µg/mL Polymyxin B treatment, rep 3


title: M6

description:
SOM04P8L
Simultaneous control


title: E. coli Polymyxin B treatment at time=60 min, rep 1

description:
DeGrado2_ (1296) GC16 E. coli_2
Gene expression data from E. coli in late logarithmic growth treated with 0.39 µg/mL Polymyxin B sulfate for 60 minutes

source_name: E. coli T=60 min after 0.39 µg/mL Polymyxin B treatment, rep 1


title: E. coli control at time=60 min, rep 3

description:
DeGrado2_ (1292) GC12 E. coli_2
Gene expression data from E. coli in late logarithmic growth

source_name: E. coli T=60 min, no treatment, rep 3


title: F13

description:
SOM04P87
Inversion


title: E. coli PMX 10070 treatment at time=60 min, rep 2

description:
DeGrado2_ (1294) GC14 E. coli_2
Gene expression data from E. coli in late logarithmic growth treated with 8.75 µg/mL PMX 10070 for 60 minutes

source_name: E. coli T=60 min after 8.75 µg/mL PMX 10070 treatment, rep 2


title: E. coli PMX 10070 treatment at time=60 min, rep 1

description:
DeGrado2_ (1293) GC13 E. coli_2
Gene expression data from E. coli in late logarithmic growth treated with 8.75 µg/mL PMX 10070 for 60 minutes

source_name: E. coli T=60 min after 8.75 µg/mL PMX 10070 treatment, rep 1


title: E. coli PMX 10070 treatment at time=60 min, rep 3

description:
DeGrado2_ (1295) GC15 E. coli_2
Gene expression data from E. coli in late logarithmic growth treated with 8.75 µg/mL PMX 10070 for 60 minutes

source_name: E. coli T=60 min after 8.75 µg/mL PMX 10070 treatment, rep 3


title: E. coli control at time=60 min, rep 1

description:
DeGrado2_ (1290) GC10 E. coli_2
Gene expression data from E. coli in late logarithmic growth

source_name: E. coli T=60 min, no treatment, rep 1


title: M16

description:
SOM04P8Y
Reversion


title: M4

description:
SOM04P8J
Simultaneous control


title: M5-K6-DSRep3

description:
76_MB5-KB6
Dye swap Replicate of 77_KB5-MB6, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.


title: E. coli Polymyxin B treatment at time=20 min, rep 2

description:
DeGrado2_ (1288) GC8 E. coli_2
Gene expression data from E. coli in early logarithmic growth treated with 0.39 µg/mL Polymyxin B sulfate for 20 minutes

source_name: E. coli T=20 min after 0.39 µg/mL Polymyxin B treatment, rep 2


title: HEF19-SNP

type: genomic

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Data from CEL files were accessed using CLC Genomics Workbench 3. From all the SNPs detected by the array, we retained only the once located within exons, according to the hg18 genome annotation. This was done using Galaxy (http://main.g2.bx.psu.edu/)
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

molecule: genomic DNA

source_name: Genomic DNA from Fibroblasts, 19 weeks

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Standard medium for human fibroblasts.

extract_protocol: DNAeasy Qiagen

tag: sex

value: Female

value: Human Embryonic Fibroblasts 19weeks


title: HEF24-SNP

source_name: Genomic DNA from Fibroblasts, 24 weeks

value: Human Embryonic Fibroblasts 24weeks


title: E. coli Polymyxin B treatment at time=20 min, rep 1

description:
DeGrado2_ (1287) GC7 E. coli_2
Gene expression data from E. coli in early logarithmic growth treated with 0.39 µg/mL Polymyxin B sulfate for 20 minutes

source_name: E. coli T=20 min after 0.39 µg/mL Polymyxin B treatment, rep 1


title: E. coli PMX 10070 treatment at time=20 min, rep 3

description:
DeGrado2_ (1286) GC6 E. coli_2
Gene expression data from E. coli in early logarithmic growth treated with 8.75 µg/mL PMX 10070 for 20 minutes

source_name: E. coli T=20 min after 8.75 µg/mL PMX 10070 treatment, rep 3


title: E. coli Polymyxin B treatment at time=20 min, rep 3

description:
DeGrado2_ (1289) GC9 E. coli_2
Gene expression data from E. coli in early logarithmic growth treated with 0.39 µg/mL Polymyxin B sulfate for 20 minutes

source_name: E. coli T=20 min after 0.39 µg/mL Polymyxin B treatment, rep 3


title: E. coli control at time=20 min, rep 3

description:
DeGrado2_ (1283) GC3 E. coli_2
Gene expression data from E. coli in early logarithmic growth

source_name: E. coli T=20 min, no treatment, rep 3


title: E. coli PMX 10070 treatment at time=20 min, rep 2

description:
DeGrado2_ (1285) GC5 E. coli_2
Gene expression data from E. coli in early logarithmic growth treated with 8.75 µg/mL PMX 10070 for 20 minutes

source_name: E. coli T=20 min after 8.75 µg/mL PMX 10070 treatment, rep 2


title: E. coli PMX 10070 treatment at time=20 min, rep 1

description:
DeGrado2_ (1284) GC4 E. coli_2
Gene expression data from E. coli in early logarithmic growth treated with 8.75 µg/mL PMX 10070 for 20 minutes

source_name: E. coli T=20 min after 8.75 µg/mL PMX 10070 treatment, rep 1


title: CD4+8+ sorted thymocyte double positive

city: jupiter

first: howard

middle: t

last: petrie

state: FL

address: 130 scripps way

department: cancer biology

institute: the scripps research instititute

description: Gene expression data from FACS sorted cortical lymphocytes from C57BL6 male mice 5 weeks old.

hyb_protocol: Fragmentation/hybridization to U74Av2 arrays (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: Imaging was performed on a Hewlett Packard GeneArray Scanner according to standard Affymetrix protocol.

data_processing: The data were analyzed using Affymetrix Expression Console version 1.0 based on Affymetrix MAS 5.0 analysis default settings.  Global scaling was applied and the trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Total thymocytes

label_protocol: Biotin-labeled cRNA probes were prepared as recommended by the manufacturer (Affymetrix), using oligo-dT primers, SuperScript, and BioArray High Yield RNA Transcript kits (Affymetrix).

extract_protocol: RNA was extracted using StrataPrep total RNA kits as recommended by the manufacturer (Stratagene).

tag: cell marker

tag: age

value: 5 wks

value: thymocyte


title: E. coli control at time=20 min, rep 1

description:
DeGrado2_ (1281) GC1 E. coli_2
Gene expression data from E. coli in early logarithmic growth

source_name: E. coli T=20 min, no treatment, rep 1


title: E. coli control at time=20 min, rep 2

description:
DeGrado2_ (1282) GC2 E. coli_2
Gene expression data from E. coli in early logarithmic growth

source_name: E. coli T=20 min, no treatment, rep 2


title: lin- CD24+ CD25+ CD44lo sorted thymocyte double negative DN3

source_name: Blast enriched thymocytes

tag: cell type


title: lin- CD24+ CD25- CD44lo sorted thymocyte pre-double positive


title: Cardiac Ventricle-TG-2

city: Little Rock

first: Jeanne

last: Wei

address: 4301 West Markham Street

department: Geriatrics

institute: University of Arkansas for Medical Sciences

description: Cardiac Ventricle-TG-2

hyb_protocol: Each sample from one group was hybridized to an independent GeneChip MGU74Av2 (Affymetrix). According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: The microarray data analysis and data interpretation were performed using ArrayTrack (Tong et al., 2003).

source_name: Cardiac Ventricle TG

label_protocol: According to Affymetrix protocol

extract_protocol: Total RNA was extraxted using Ultrapec reagent then purified with Qiagen Rneasy Kit according to the manufacturers' instructions.

tag: transgenic status

value: transgenic


title: Cardiac Ventricle-TG-1

description: Cardiac Ventricle-TG-1


title: Control Human Tubuli 160

city: Bronx

first: Karolina

last: Woroniecka

address: 1300 Morris Park Ave

institute: AECOM

description:
HK160T
KS1-HG_U133A_2-6375

hyb_protocol: Biotinylated cRNA was hybridized onto Affymetrix Human Genome U133A 2.0 Arrays (Affymetrix, USA).

scan_protocol: The data were scanned using a GeneChip scanner in accordance with the Affymetrix protocol.

data_processing: Data were normalized in GeneSpring GZ software (Agilent) using the RMA16 summarization algorithm. Baseline is the median of all samples.

source_name: Tubuli of control kidney

label_protocol: Labeling was performed using the Two-Cycle Target Labeling Kit (Affymetrix) as per the manufacturer's protocol. The GeneChip IVT labeling kit performed the final in vitro transcription reaction to produce biotinylated cRNA for the microarray.

extract_protocol: 1mm x 1mm biopsy tissues were placed under an Olympus model SZX12 stereomicroscope using 90x magnification. The biopsy tissue was manually microdissected at 4C in RNALater for glomerular and tubular compartments using fine tip forceps. In general, 5 glomeruli that readily released from the capsule were collected and placed into cold RLT solution (Qiagen RNeasey kit). The corresponding tubulointerstitial and vascular compartment was placed into RLT solution also. For easier designation we called this component tubules. Dissected tissue was homogenized using a Powergen125 (Fisher) homogenizer and stored at -80C. RNA was prepared using RNAeasy mini columns (Qiagen) according to manufacterer's instructions. RNA quality and quantity was determined using a Lab-on-Chip Total RNA PicoKit (Agilent BioAnalyzer).

value: kidney

tag: tissue subregion

value: tubulus

tag: disease state

value: control

tag: individual


title: Control Human Tubuli 82

description:
HK82T
KS1-HG_U133A_2-2922

tag: tissue


title: lin- CD24+ CD25+ CD44hi sorted thymocyte double negative DN2


title: Control Human Tubuli 177

description:
HK177T
KS1-HG_U133A_2-6573


title: Control Human Tubuli 172

description:
HK172T
KS1-HG_U133A_2-6466


title: Control Human Tubuli 70

description:
HK70T
KS1-HG_U133A_2-2906


title: Cardiac Ventricle-nTG-1

description: Cardiac Ventricle-nTG-1

source_name: Cardiac Ventricle n-TG

value: non-transgenic


title: Cardiac Ventricle-nTG-2

description: Cardiac Ventricle-nTG-2


title: Control Human Tubuli 76

description:
HK76T
KS1-HG_U133A_2-2912


title: Control Human Tubuli 64

description:
HK64T
KS1-HG_U133A_2-2903


title: lin- CD24+ CD25- CD44hi sorted thymocyte double negative DN1

value: lin- CD24+CD25-CD44hi


title: Control Human Tubuli 77

description:
HK77T
KS1-HG_U133A_2-2914


title: Control Human Tubuli 81

description:
HK81T
KS1-HG_U133A_2-2920


title: Cardiomyocytes-G, biological rep2

city: Beijing

first: junjie

last: li

address: #5 Dong Dan San Tiao

institute: PUMC

description:
Gene expression data from neonatal rat cardiomyocytes infected with Ad-GFP
Sample name: 4-G

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip rat 230 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with GeneSpring GX 11.0 Software using RMA algorithm.

organism: Rattus norvegicus

source_name: Neonatal rat cardiomyocytes infected with Ad-GFP

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

growth_protocol: Primary cardiomyocytes were prepared by enzymatic disassociation of 1- to 2-day old Sprague-Dawley rats, the isolated cardiomyocytes resuspended in fresh DMEM/F12 (HyClone) containing 10% FBS and 1% penicillin-streptomycin were plated into the Laminin (Sigma) precoated dishes (Corning) and incubated for 24 h at 37 ℃.

extract_protocol: Extraction of total RNA was performed using TRIzol according to the manufacturer's instructions.

treatment_protocol: Cardiomyocytes were infected with GFP control or atrogin-1 adenovirus and cultured with serum-free DMEM/F12 for 24 hours.

tag: strain

value: Sprague-Dawley

value: 1- to 2-days old

tag: developmental stage

value: neonate

value: heart ventricular myocardium

value: cardiomyocyte


title: Cardiomyocytes-A , biological rep2

description:
Gene expression data from neonatal rat cardiomyocytes infected with Ad-atrogin-1-GFP
Sample name: 4-A

source_name: Neonatal rat cardiomyocytes infected with Ad-atrogin-1-GFP

tag: infection

value: atrogin-1 adenovirus


title: Cardiomyocytes-A, biological rep1

description:
Gene expression data from neonatal rat cardiomyocytes infected with Ad-atrogin-1-GFP
Sample name: 3-A


title: Cardiomyocytes-G, biological rep1

description:
Gene expression data from neonatal rat cardiomyocytes infected with Ad-GFP
Sample name: 3-G


title: HN07.356N

first: Levi

last: Waldron

address: 655 Huntington Avenue

department: Biostatistics

institute: Harvard School of Publich Health

description:
U133Plus2_112307W_SKB08_HN07-356

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

hyb_protocol: Labeling and hybridization to arrays were performed by The Centre for Applied Genomics, Medical and Related Sciences Centre (MaRS), Toronto, ON, Canada, using standard Affymetrix procedures.

scan_protocol: Microarray slides were scanned using the GeneArray 2500 scanner (Agilent Technologies).

data_processing: Data were processed using the BrainArray Entrez-gene centric alternative CDF, with GC-RMA background correction and normalization.

source_name: Normal

label_protocol: Amplification and biotin labeling of antisense cRNA was performed using the Enzo BioArray High YieldTM RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY, USA), according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from all tissues using Trizol reagent (Life Technologies, Inc., Burlington, ON, Canada), followed by purification using the Qiagen RNeasy kit/DNase RNase-free set (Qiagen, Valencia, CA, USA), according to manufacturer’s instructions. RNA was quantified by spectrophotometry and its quality was assessed using the 2100 Bioanalyzer (Firmware v.A.01.16, Agilent Technologies, Canada). All samples were of sufficient quantity and quality for arrays and quantitative real-time PCR (QRT-PCR) analyses.

tag: patient identifier

value: squamous cell carcinoma of the tongue

tag: tissue location

value: floor of mouth

tag: Stage

value: unknown

tag: grade

tag: site

value: margin

tag: site detail

value: normal

tag: recurrence

value: no

tag: outcome

value: ANED


title: HN07.358

description:
U133Plus2_112307W_SKB09_HN07-358

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: FOM margin

value: floor of mouth margin


title: Control Human Glomeruli 150

description:
HK150G
KS1-HG_U133A_2-5116

source_name: Glomerulus of control kidney

value: kidney

value: glomerulus

value: control


title: HN04.19N

description:
U133Plus2_112307W_SKB01_HN04-19

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Normal tongue

value: tongue

value: IV

value: invasive poorly diff

value: normal tongue

value: yes

value: distant

value: DOD


title: Control Human Glomeruli 119

description:
HK119G
KS1-HG_U133A_2-3470


title: HN04.20A

description:
U133Plus2_112307W_SKB02_HN04-20

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Posterior margin

value: squamous cell carcinoma of the tongue

value: posterior margin


title: Control Human Tubuli 37

description:
HK37T
KS1-HG_U133A_2-2868

value: tubulus


title: Control Human Tubuli 53

description:
HK53T
KS1-HG_U133A_2-2741


title: HN07.346SG

description:
U133Plus2_091108_SR36_HN07-346SG

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Margin

value: unknown

value: margin

value: local


title: HN07.355P

description:
U133Plus2_112307W_SKB07_HN07-355

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: floor of mouth

value: no

value: ANED


title: Control Human Glomeruli 123

description:
HK123G
KS1-HG_U133A_2-5111

value: kidney

value: glomerulus

value: control


title: Control Human Glomeruli 154

description:
HK154G
KS1-HG_U133A_2-5118


title: Control Human Glomeruli 110

description:
HK110G
KS1-HG_U133A_2-3467


title: Control Human Glomeruli 100

description:
HK100G
KS1-HG_U133A_2-3427


title: HN04.21RL

description:
U133Plus2_112307W_SKB03_HN04-21

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Right lateral margin

value: tongue

value: IV

value: invasive poorly diff

value: Right lateral margin


title: HN04.22LL

description:
U133Plus2_112307W_SKB04_HN04-22

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Left lateral margin

value: left lateral margin

value: yes

value: distant

value: DOD


title: HN07.354T

description:
U133Plus2_112307W_SKB06_HN07-354

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: FOM tumor

value: squamous cell carcinoma of the tongue

value: unknown

value: tumor

value: floor of mouth tumor


title: Control Human Glomeruli 82

description:
HK82G
KS1-HG_U133A_2-2921


title: Control Human Tubuli 17

description:
HK17T
KS1-HG_U133A_2-2898

value: tubulus


title: Control Human Glomeruli 83

description:
HK83G
KS1-HG_U133A_2-2923


title: HN04.176P

description:
U133Plus2_091108_SR32_HN05-176P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: margin

value: posterior margin

value: no

value: ANED


title: Control Human Glomeruli 81

description:
HK81G
KS1-HG_U133A_2-2919

value: kidney

value: glomerulus

value: control


title: Control Human Glomeruli 76

description:
HK76G
KS1-HG_U133A_2-2911


title: HN07.343T

description:
U133Plus2_091108_SR35_HN07-343T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Tumor

value: tongue

value: local


title: HN04.24T

description:
U133Plus2_112307W_SKB05_HN04-24

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Tongue tumor

value: IV

value: invasive poorly diff

value: tongue tumor

value: yes


title: Control Human Glomeruli 77

description:
HK77G
KS1-HG_U133A_2-2913


title: HN07.342N

description:
U133Plus2_091108_SR34_HN07-342N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: squamous cell carcinoma of the tongue

value: unknown

value: normal

value: DOD


title: HN04.177PL

description:
U133Plus2_091108_SR33_HN05-177PL

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Posterior lateral margin

value: margin

value: posterior lateral margin


title: Control Human Glomeruli 34

description:
HK34G
KS1-HG_U133A_2-2784


title: HN04.173T

description:
U133Plus2_091108_SR31_HN05-173T

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tumor

value: no


title: HN04.144S

description:
U133Plus2_091108_SR29_HN05-144S

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

source_name: Superior margin

value: invasive mod diff

value: superior margin

value: regional and distant


title: HN04.137N

description:
U133Plus2_091108_SR25_HN05-137N

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).

value: tongue