title: Gastrointestinal stromal sarcoma 04-326H FFPE sample with WGA (Qiagen platform), SNP

description:
11N_04-326HFFPEWGAQiagen
Hybridized to 250K_Nsp.

source_name: GISS 04-326H FFPE sample with WGA (Qiagen platform)

value: formalin-fixed paraffin-embedded (FFPE)

value: Qiagen isothermal protocol


title: Secondary EA infection-2dpi

status: Public on Aug 15 2011

type: RNA

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

country: USA

institute: USDA, ARS

description: Secondary EA infected IEL, 2dpi, Biological replicate 1 of 2

hyb_protocol: Hybridizations were performed overnight at 50°C using HybIt hybridization buffer (TeleChem, Sunnyvale, CA) in ArrayIt reaction cassettes.  Following hybridization, the slides were rinsed in 0.5 X SSC, 0.01% SDS and washed once for 15 min at room temperature in 0.2 X SSC, 0.2% SDS at 50°C, 3 times for 1 min at room temperature in 0.2 X SSC, and 3 times for 1 min at room temperature in distilled water.

scan_protocol: Images were scanned on a ScanArray Lite microarray analysis system (Perkin-Elmer, Boston, MA) at a resolution of 10 µm.  The scanned images for each channel were quantified using ScanArray Express version 3.0 software (Perkin-Elmer).

data_processing: The MIDAS 2.19 of the TM4 package (http://www.tigr.org) was used to qualify and normalize the array data.  Two-step normalization, total intensity, and global LOWESS plot methods were applied followed by standard deviation (SD) regularization between blocks and slides.

molecule: total RNA

organism: Gallus gallus

source_name: IEL from non-infected control

label_protocol: Aminoallyl-labeled RNA from IELs was prepared using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion, Austin, TX).  Two of 20 μg aliquots of each aminoallyl-RNA sample were fluorescently labeled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen).  RNA concentrations and labeling efficiencies were determined spectrophotometrically.

growth_protocol: One week-old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of EA, EM, or ET.  One week later, the infected chickens were challenged with an identical inoculum of the homologous parasite.  Intestinal samples were collected daily from 5 birds in a treatment group at from 1 to 6 dpi following primary and secondary infections.  Cecum, duodenum, and jejunum were collected from the birds challenged with EA, EM, and ET, respectively.

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

treatment_protocol: Intestines were cut longitudinally and washed three times with ice-cold Hanks’ balanced salt solution (HBSS) containing 100 U/ml of penicillin and 100 mg/ml of streptomycin (Sigma, St. Louis, MO).  The mucosal layer of intestine was carefully scraped using a cell scraper and IELs were isolated by Percoll density gradient centrifugation.

tag: tissue

value: Duodena, Jejuna, Ceca

tag: cell type

value: Intestinal Intraepithelial lymphocytes (IEL)

source_name: IEL from secondary EA infection at 2dpi

value: Duodena

tag: parasite

value: EA

tag: infection

value: secondary

tag: time

value: 2 dpi


title: Gastrointestinal stromal sarcoma 04-326H FFPE sample, SNP

type: genomic

city: Taipei

first: Cher-wei

last: Liang

address: 7 Chung-Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University Hospital

description:
10N_04-326HFFPE
Hybridized to 250K_Nsp.

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 washed using Affymetrix fluidics stations, and scanned using the GeneChip Scanner 3000.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St. Jude and described in Mullighan et al. Nature 2007;446:758.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: GISS 04-326H FFPE sample

label_protocol: As per the manufacturer (Affymetrix).

growth_protocol: Genomic DNAs were obtained from fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tumor samples.

extract_protocol: Genomic DNA was extracted from fresh-frozen and FFPE mesenchymal tumor samples using the QIAamp DNA Mini Kit and QIAamp DNA FFPE Tissue Kit, respectively. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: WGA was performed using the REPLI-g® FFPE kit (Qiagen, Valencia, CA, USA) and GenomePlex® Tissue Whole Genome Amplification WGA5 kit (Sigma, Saint Louis, MO, USA) in parallel in accordance with the manufacturers’ protocols.

value: gastrointestinal stromal sarcoma (GISS)

tag: tumor identifier

tag: tissue preparation

tag: wga platform_id


title: Gastrointestinal stromal sarcoma 04-326H FFPE sample with WGA (Sigma platform), SNP

description:
12N_04-326HFFPEWGASigma
Hybridized to 250K_Nsp.

source_name: GISS 04-326H FFPE sample with WGA (Sigma platform)

value: Sigma thermocycling protocol


title: Gastrointestinal stromal sarcoma 04-403H FFPE sample with WGA (Sigma platform), SNP

description:
6N_04-403HFFPEWGASigma
Hybridized to 250K_Nsp.

source_name: GISS 04-403H FFPE sample with WGA (Sigma platform)


title: Gastrointestinal stromal sarcoma 04-326H fresh-frozen sample with WGA (Qiagen platform), SNP

description:
8N_04-326HFreshWGAQiagen
Hybridized to 250K_Nsp.

source_name: GISS 04-326H fresh-frozen sample with WGA (Qiagen platform)

value: fresh-frozen


title: Secondary EA infection-1dpi

description: Secondary EA infected IEL, 1dpi, Biological replicate 1 of 2

source_name: IEL from secondary EA infection at 1dpi

value: 1 dpi


title: Primary EA infection-6dpi

description: Primary EA infected IEL, 6dpi, Biological replicate 1 of 2

source_name: IEL from primary EA infection at 6dpi

value: primary

value: 6 dpi


title: Primary EA infection-6dpi-dye swap

description: Primary EA infected IEL, 6dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Secondary EA infection-1dpi-dye swap

description: Secondary EA infected IEL, 1dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Gastrointestinal stromal sarcoma 04-403H FFPE sample with WGA (Qiagen platform), SNP

description:
5N_04-403HFFPEWGAQiagen
Hybridized to 250K_Nsp.

source_name: GISS 04-403H FFPE sample with WGA (Qiagen platform)


title: Primary EA infection-5dpi

description: Primary EA infected IEL, 5dpi, Biological replicate 1 of 2

source_name: IEL from primary EA infection at 5dpi

value: 5 dpi


title: Gastrointestinal stromal sarcoma 04-403H fresh-frozen sample with WGA (Sigma platform), SNP

description:
3N_04-403H Fresh1WGASigma
Hybridized to 250K_Nsp.

source_name: GISS 04-403H fresh-frozen sample with WGA (Sigma platform)


title: Gastrointestinal stromal sarcoma 04-403H fresh-frozen sample, SNP

description:
1N_04-403H Fresh
Hybridized to 250K_Nsp.

source_name: GISS 04-403H fresh-frozen sample


title: Gastrointestinal stromal sarcoma 04-326H fresh-frozen sample, SNP

description:
7N_04-326HFresh
Hybridized to 250K_Nsp.

source_name: GISS 04-326H fresh-frozen sample


title: Gastrointestinal stromal sarcoma 04-403H fresh-frozen sample with WGA (Qiagen platform), SNP

description:
2N_04-403H Fresh1WGAQiagen_REDO
Hybridized to 250K_Nsp.

source_name: GISS 04-403H fresh-frozen sample with WGA (Qiagen platform)


title: Secondary EA infection-2dpi-dye swap

description: Secondary EA infected IEL, 2dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Primary EA infection-3dpi-dye swap

description: Primary EA infected IEL, 3dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from primary EA infection at 3dpi

value: 3 dpi


title: Primary EA infection-3dpi

description: Primary EA infected IEL, 3dpi, Biological replicate 1 of 2


title: Primary EA infection-2dpi

description: Primary EA infected IEL, 2dpi, Biological replicate 1 of 2

source_name: IEL from primary EA infection at 2dpi


title: Primary EA infection-4dpi

description: Primary EA infected IEL, 4dpi, Biological replicate 1 of 2

source_name: IEL from primary EA infection at 4dpi

value: 4 dpi


title: Gastrointestinal stromal sarcoma 04-403H FFPE sample, SNP

description:
4N_04-403HFFPE
Hybridized to 250K_Nsp.

source_name: GISS 04-403H FFPE sample

value: formalin-fixed paraffin-embedded (FFPE)


title: Primary EA infection-4dpi-dye swap

description: Primary EA infected IEL, 4dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from non-infected control


title: Bowel, normal, copy number

description:
28N-98-676
Hybridized to 250K_Nsp.

source_name: Bowel, normal

value: bowel

tag: disease state

value: normal

tag: developmental stage

value: adult

tag: sample type

value: reference


title: Primary EA infection-2dpi-dye swap

description: Primary EA infected IEL, 2dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Duodena, Jejuna, Ceca

value: Intestinal Intraepithelial lymphocytes (IEL)

value: Duodena

value: EA


title: Primary EA infection-5dpi-dye swap

description: Primary EA infected IEL, 5dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Primary EA infection-1dpi

description: Primary EA infected IEL, 1dpi, Biological replicate 1 of 2

source_name: IEL from primary EA infection at 1dpi


title: Adipose tissue, normal, copy number

description:
26N-98-525
Hybridized to 250K_Nsp.

source_name: Adipose tissue, normal

value: adipose


title: Stomach, 24N-97-520, normal, copy number

description:
24N-97-520
Hybridized to 250K_Nsp.

source_name: Stomach, normal

value: stomach

value: fresh-frozen


title: fresh-frozen tissue_3ep7

city: Heidelberg

first: Hendrik

last: Witt

state: BW

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

hyb_protocol: Agilent hybridization protocol following the manufacturer’s instructions.

scan_protocol: Scanned on Agilent Scanner G25505B

data_processing: Array raw data were generated using Feature Extraction 9.1 Software. Normalization of raw signals was performed using vsn (Huber et al., 2002).

source_name: brain

label_protocol: Agilent labling protocol following the manufacturer’s instructions.

extract_protocol: RNA was extracted from biopsy samples using Trizol and RNeasy mini columns following the manufacturer’s instructions.

treatment_protocol: Fresh frozen material was milled in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

tag: gender

value: m

tag: age

tag: localization

value: posterior fossa

source_name: 5xpool brain

value: total brain


title: Gastrointestinal stromal sarcoma 04-326H FFPE sample with WGA (Qiagen platform), copy number

description:
11N_04-326HFFPEWGAQiagen
Hybridized to 250K_Nsp.

source_name: GISS 04-326H FFPE sample with WGA (Qiagen platform)

value: gastrointestinal stromal sarcoma (GISS)

value: Qiagen isothermal protocol


title: Gastrointestinal stromal sarcoma 04-326H FFPE sample, copy number

description:
10N_04-326HFFPE
Hybridized to 250K_Nsp.

source_name: GISS 04-326H FFPE sample

value: formalin-fixed paraffin-embedded (FFPE)


title: fresh-frozen tissue_3ep69

value: f

value: supra


title: fresh-frozen tissue_3ep55


title: fresh-frozen tissue_3ep48


title: Gastrointestinal stromal sarcoma 04-326H FFPE sample with WGA (Sigma platform), copy number

description:
12N_04-326HFFPEWGASigma
Hybridized to 250K_Nsp.

source_name: GISS 04-326H FFPE sample with WGA (Sigma platform)

value: Sigma thermocycling protocol


title: fresh-frozen tissue_3ep65


title: fresh-frozen tissue_3ep49


title: Liver, normal, copy number

description:
22N-96-911
Hybridized to 250K_Nsp.

source_name: Liver, normal

value: liver

value: normal

value: adult

value: reference


title: fresh-frozen tissue_3ep67


title: fresh-frozen tissue_3ep54


title: Gastrointestinal stromal sarcoma 04-326H fresh-frozen sample with WGA (Qiagen platform), copy number

description:
8N_04-326HFreshWGAQiagen
Hybridized to 250K_Nsp.

source_name: GISS 04-326H fresh-frozen sample with WGA (Qiagen platform)


title: Gastrointestinal stromal sarcoma 04-326H fresh-frozen sample with WGA (Sigma platform), copy number

description:
9N_04-326HFreshWGASigma
Hybridized to 250K_Nsp.

source_name: GISS 04-326H fresh-frozen sample with WGA (Sigma platform)


title: fresh-frozen tissue_3ep32


title: Gastrointestinal stromal sarcoma 04-326H fresh-frozen sample, copy number

description:
7N_04-326HFresh
Hybridized to 250K_Nsp.

source_name: GISS 04-326H fresh-frozen sample


title: fresh-frozen tissue_3ep15


title: fresh-frozen tissue_3ep40


title: fresh-frozen tissue_3ep18


title: fresh-frozen tissue_2ep9

value: spinal


title: fresh-frozen tissue_3ep29


title: fresh-frozen tissue_3ep46


title: Gastrointestinal stromal sarcoma 04-403H FFPE sample with WGA (Qiagen platform), copy number

description:
5N_04-403HFFPEWGAQiagen
Hybridized to 250K_Nsp.

source_name: GISS 04-403H FFPE sample with WGA (Qiagen platform)


title: fresh-frozen tissue_3ep25


title: Gastrointestinal stromal sarcoma 04-403H FFPE sample with WGA (Sigma platform), copy number

description:
6N_04-403HFFPEWGASigma
Hybridized to 250K_Nsp.

source_name: GISS 04-403H FFPE sample with WGA (Sigma platform)


title: fresh-frozen tissue_3ep10


title: Stomach, 17N-91-150, normal, copy number

description:
17N-91-150
Hybridized to 250K_Nsp.


title: fresh-frozen tissue_2ep7


title: Mtb_whiB5_3 hours_rep4

city: Padova

first: Stefano

last: Casonato

address: via A. Gabelli, 63

department: Histology, microbiology and medical biotechnologies

country: Italy

institute: University of Padova

description: Biological replicate 1 of 4. 3hrs induction

hyb_protocol: Competitive hybridizations with equal amounts of purified Cy3/Cy5-labelled cDNA were performed in duplicate with both dye arrangements, as previously described (Provvedi et al., 2009).

scan_protocol: Microarrays were scanned using an Agilent G2565CA Microarray Scanner System (Scan Control Software 8.1) (Agilent technologies) and fluorescence intensities of the two channels at each spot were quantified using the Agilent Feature Extraction Software 10.1 (Agilent technologies).

data_processing: Data were normalized with a web-based tool for Diagnosis and Normalization of spotted cDNA MicroArrayData (DNMAD) (http://dnmad.bioinfo.cnio.es/) (Vaquerizas et al., 2005) using the print-tip lowess method after background subtraction. Genes significantly differentially expressed were identified using the Significance Analysis of Microarrays (SAM) tool (Tusher et al., 2001). Differentially expressed genes were defined by a q-value equal to 0% and a minimum fold difference of ±2 between the two samples. SAM is part of the TigerMultiExperiment Viewer package version 4.6 (TMeV) available at http://www.tm4.org/mev/

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb TB84 3hrs induction

label_protocol: Fluorescently labeled cDNA copies of total RNA were prepared by direct incorporation of fluorescent nucleotide analogues during a first-strand reverse transcription reaction as previously described (Provvedi et al., 2009).

growth_protocol: Bacteria were grown in Middlebrook 7H9 broth or 7H10 agar medium supplemented with 0.05% Tween 80, 0.2% glycerol and 10% ADN (Albumin, Dextrose, NaCl) at 37°C.  When necessary streptomycin was added at 20 mg/ml. The inducer Pristinamycin I (Sanofi-Aventis, Paris, France) was dissolved in DMSO (50 mg/ml) and used at 1mg/ml. Liquid cultures were incubated in rolling bottles with gentle rotation.

extract_protocol: RNA extraction from in vitro cultured M. tuberculosis was performed as previously described (Maciag et al., 2007) and analysed using the Agilent Bioanalyser 2100 system (Agilent Technologies) according to the manufacturer's instructions.

treatment_protocol: MTb strains TB84 (containing the plasmid for whiB5 overexpression) and TB60 (containing the empty plasmid) were grown at 37°C in the presence of pristinamycin I 1 mg/ml for 15’ or 3 h and compared on whole genome DNA microarrays

tag: strain

source_name: Mtb TB60 3hrs induction


title: fresh-frozen tissue_2ep6


title: Mtb_whiB5_3 hours_rep3


title: Gastrointestinal stromal sarcoma 04-403H fresh-frozen sample with WGA (Qiagen platform), copy number

description:
2N_04-403H Fresh1WGAQiagen_REDO
Hybridized to 250K_Nsp.

source_name: GISS 04-403H fresh-frozen sample with WGA (Qiagen platform)


title: Gastrointestinal stromal sarcoma 04-403H fresh-frozen sample with WGA (Sigma platform), copy number

description:
3N_04-403H Fresh1WGASigma
Hybridized to 250K_Nsp.

source_name: GISS 04-403H fresh-frozen sample with WGA (Sigma platform)


title: Gastrointestinal stromal sarcoma 04-403H FFPE sample, copy number

description:
4N_04-403HFFPE
Hybridized to 250K_Nsp.

source_name: GISS 04-403H FFPE sample


title: Mtb_whiB5_3 hours_rep2


title: Mtb_whiB5_15'_rep4

description: Biological replicate 1 of 4. 15' induction

source_name: Mtb TB84 15' induction

source_name: Mtb TB60 15' induction


title: Mtb_whiB5_15'_rep3


title: Mtb_whiB5_15'_rep2


title: Mtb_whiB5_3 hours_rep1


title: fresh-frozen tissue_2ep4

source_name: brain

source_name: 5xpool brain


title: fresh-frozen tissue_2ep36


title: Mtb_whiB5_15'_rep1


title: fresh-frozen tissue_2ep5


title: fresh-frozen tissue_2ep30


title: fresh-frozen tissue_2ep27


title: fresh-frozen tissue_2ep23


title: Gastrointestinal stromal sarcoma 04-403H fresh-frozen sample, copy number

description:
1N_04-403H Fresh
Hybridized to 250K_Nsp.

source_name: GISS 04-403H fresh-frozen sample


title: fresh-frozen tissue_2ep25


title: fresh-frozen tissue_2ep31


title: fresh-frozen tissue_2ep29


title: fresh-frozen tissue_2ep33


title: fresh-frozen tissue_2ep35


title: fresh-frozen tissue_2ep34


title: fresh-frozen tissue_2ep22


title: fresh-frozen tissue_2ep3


title: Primary EA infection-1dpi-dye swap

description: Primary EA infected IEL, 1dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from non-infected control

value: Duodena, Jejuna, Ceca

value: Intestinal Intraepithelial lymphocytes (IEL)

source_name: IEL from primary EA infection at 1dpi

value: Duodena

value: EA

value: primary

value: 1 dpi


title: fresh-frozen tissue_2ep19

value: total brain


title: fresh-frozen tissue_2ep16


title: fresh-frozen tissue_2ep10

value: posterior fossa


title: fresh-frozen tissue_1ep7

value: m


title: fresh-frozen tissue_2ep20

value: f


title: fresh-frozen tissue_2ep2


title: fresh-frozen tissue_2ep21

value: supra


title: fresh-frozen tissue_2ep17


title: fresh-frozen tissue_1ep4


title: fresh-frozen tissue_2ep14


title: oral_severedysplasia_1599

type: SAGE

anchor: NlaIII

city: Vancouver

first: Ewan

last: Gibb

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Agency Research Centre

data_processing: Raw SAGE tags, excluding linker and ditags.

source_name: oral biopsy, left ventral tongue

extract_protocol: RNA was isolated by guanidium isothiocyanate and phenol/chloroform extraction.

value: left ventral tongue

tag: dysplasia

value: severe

value: female

tag: smoking status

value: never smoker


title: fresh-frozen tissue_1ep37


title: fresh-frozen tissue_1ep36


title: fresh-frozen tissue_1ep33


title: fresh-frozen tissue_1ep6


title: fresh-frozen tissue_2ep1


title: fresh-frozen tissue_1ep38


title: fresh-frozen tissue_1ep31


title: fresh-frozen tissue_1ep32


title: fresh-frozen tissue_1ep8


title: fresh-frozen tissue_1ep27


title: oral_moderatedysplasia_1427

source_name: oral biopsy, left lateral tongue

tag: tissue

value: moderate


title: fresh-frozen tissue_1ep28


title: fresh-frozen tissue_1ep5


title: fresh-frozen tissue_1ep34


title: fresh-frozen tissue_1ep3


title: fresh-frozen tissue_2ep11

value: spinal


title: fresh-frozen tissue_1ep29


title: oral_milddysplasia_1460

source_name: oral biopsy, right buccal mucosa

value: right buccal mucosa

value: mild

value: male

value: smoker


title: fresh-frozen tissue_1ep30


title: fresh-frozen tissue_1ep26


title: fresh-frozen tissue_1ep25


title: fresh-frozen tissue_1ep23


title: oral_severedysplasia_1444

source_name: oral biopsy, right posterior trigone

value: right posterior trigone

value: severe / CIS


title: oral_moderatedysplasia_1404

source_name: oral biopsy, right ventral tongue

value: right ventral tongue

value: former smoker


title: fresh-frozen tissue_1ep24

value: m

value: total brain


title: oral_severedysplasia_1404


title: oral_milddysplasia_1434

source_name: oral biopsy, left floor of mouth

value: Left floor of mouth


title: fresh-frozen tissue_1ep21

value: f

value: supra


title: oral_moderatedysplasia2_1028

source_name: oral biopsy, right lateral tongue

value: right lateral tongue

value: female


title: fresh-frozen tissue_1ep17


title: TIG1B_MFP_24hr_rep3

city: Sindian City

first: Shun-Yuan

last: Jiang

state: Taipei county

address: 289 Jianguo Rd

department: Department of Research

institute: Buddhist Tzu Chi General Hospital, Taipei Branch

description:
cells: Inducible TIG1B stable clone established from HCT116 colon cancer cells using the GeneSwitch system.
stably integrated plasmids: pSwitch (Invitrogen, Carlsbad, CA, USA), inducible TIG1B expression plasmid (pTIG1B-V5).
inducible protein: Recombinant TIG1B (RARRES1) Isoform containing 228 amino acids of TIG1B fragment at the N-terminus and Myc and His tags at the C-terminus.
inducer: mifepristone (5 nM), 24 hr

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.

label: biotin

source_name: TIG1B stable cells, mifepristone (5 nM) treatment, 24 hr.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol:
culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
culture conduction: at 37ºC with 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.

treatment_protocol: Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.

tag: cell line

value: colon cancer cell line HCT116

tag: clone

value: TIG1B stable clone

tag: agent

value: mifepristone

tag: dose

value: 5 nM

value: 24 hr


title: oral_severedysplasia_1028

value: Severe

value: never smoker


title: TIG1A_MFP_24hr_rep3

description:
cells: Inducible TIG1A stable clone established from HCT116 colon cancer cells using the GeneSwitch system.
stably integrated plasmids: pSwitch (Invitrogen, Carlsbad, CA, USA), inducible TIG1A expression plasmid (pTIG1A-V5).
inducible protein: Recombinant TIG1A (RARRES1) isoform containing 294 amino acids of TIG1A fragment at the N-terminus and Myc and His tags at the C-terminus.
inducer: mifepristone (5 nM), 24 hr

source_name: TIG1A stable cells, mifepristone (5 nM) treatment, 24 hr.

value: TIG1A stable clone

tag: time


title: TIG1B_MFP_24hr_rep2


title: fresh-frozen tissue_1ep16

value: posterior fossa


title: fresh-frozen tissue_1ep15


title: oral_moderatedysplasia_1028

value: moderate


title: fresh-frozen tissue_1ep13

value: m


title: fresh-frozen tissue_1ep11

value: total brain


title: fresh-frozen tissue_1ep19


title: Control_MFP_24hr_rep3

description:
cells: Inducible control stable clone established from HCT116 colon cancer cells using the GeneSwitch system.
stably integrated plasmids: pSwitch (Invitrogen, Carlsbad, CA, USA), pGene/V5 (Invitrogen)
inducible protein: None.
inducer: mifepristone (5 nM), 24 hr

source_name: Control stable cells, mifepristone (5 nM) treatment, 24 hr.

value: Control stable clone


title: TIG1B_MFP_24hr_rep1


title: fresh-frozen tissue_1ep14

value: spinal


title: fresh-frozen tissue_1ep18


title: Control_MFP_24hr_rep2


title: TIG1A_MFP_24hr_rep2


title: Control_MFP_24hr_rep1

source_name: Control stable cells, mifepristone (5 nM) treatment, 24 hr


title: fresh-frozen tissue_1ep1

value: f

value: supra


title: fresh-frozen tissue_1ep12


title: TIG1A_MFP_24hr_rep1


title: HSC normal 11

status: Public on Aug 14 2011

city: New York

first: Christopher

last: Park

state: NY

address: 1275 York Avenue

institute: MSKCC

description: Ribosomal protein gene expression data from age-matched control individual.

hyb_protocol: Following fragmentation, 15μg of cRNA from each sample was hybridized to Affymetrix HG U133 Plus 2.0 microarrays with GeneChip Hybridization Oven 640 overnight for 16 hours.

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

data_processing: The data were analyzed using Affymetrix Expression Console Software Version 1.0. Normalization was performed with the RMA algorithm using default analysis parameters.

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 11

label_protocol: Biotinylated cRNA were prepared according to the  Affymetrix two cycle kit and protocol.

growth_protocol: Mononuclear cells from control and MDS patients were prepared using Ficoll-Paque Plus (GE Healthcare). CD34-positive cells were enriched using magnetic beads (StemCell Technologies) and stained with fluorochrome-conjugated antibodies.  Cells were stained on ice and dead cells were excluded by propidium iodide staining.

extract_protocol: Total RNA was extracted using Ambion RNA Isolation Kit (Applied Biosystems) and treated with DNAseI (Qiagen).

treatment_protocol: 1000-10000 Lin-CD34+CD38-CD90+CD45RA- were sorted (>90% purity by FACS analysis).

value: sorted hematopoietic stem cells

tag: genotype

value: normal cytogenetics

value: age matched


title: Adrenocortical cell_knockout_replicate 4

city: Tokyo

first: Tomohiro

last: Ishii

address: 35 Shinanomachi, Shinjuku-ku

department: Pediatrics

country: Japan

institute: School of Medicine, Keio University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer(HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with at room temperature GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 or 10.7.3.1(Agilent) using default parameters (protocol GE1-v5_10_Apr08 or GE1_105_Dec08 and Grid: 014868_D_F_20070820 or 20090416, respectively) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Adrenocortical cells, knockout mouse

label_protocol: Transcription profiles were determined by microarrays with Cy3-labeled cRNA using the One-Color Quick Amp Labeling kit (Agilent Technologies). Dye incorporation and cRNA yield were checked with the Nanodrop ND1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from FACS-sorted cell populations with TRIzol reagent (Invitrogen Corp., Carlsbad, CA) and subsequent NucleoSpin RNA XS (Macherey-Nagel GmbH & Co. KG, Duren, Germany), according to the manufacturer's instructions, and quantified using the Nanodrop ND1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). RNA quality was inspected on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA), confirming RNA integrity number equal to 7.0 or greater.   mRNA was linearly amplified from 1 ng total RNA of each mouse by the MessageAmp II aRNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX). In brief, double-strand cDNA was synthesized with an oligo(dT) primer bearing a T7 promoter using ArrayScript reverse transcriptase, and was applied as a template for in vitro transcription with T7 RNA polymerase to generate multiple copies of amplified mRNA. Amplified mRNA was purified by the RNAeasy column (QIAGEN, Valencia, CA), and 200 ng of the mRNA was reverse transcribed to generate double-strand cDNA template for cRNA probes of microarray analysis by the SuperScript® II RT (Invitrogen Corp.) with oligo-dT primers.

treatment_protocol: Adrenal glands were dissected from embryos at E17.5 or E18.5. Single cell suspensions were prepared by enzymatical dissociation in phosphate buffered saline (PBS) containing 0.125% trypsin, 0.5% EDTA, and 5% DNase I type IV (Sigma) for 30-60 min at 37°C while gentle shaking. Cells were spun down and resuspended with ice-cold PBS containing 3% fetal calf serum and passed through 40 mm cell strainers (Falcon BD Biosciences). eGFP-positive cells were resolved selectively by fluorescent-activated cell sorting (FACS) (Vantage SE, Becton Dickinson, Franklin Lakes, NJ).

value: Male

tag: genotype/variation

value: Star-/-


title: HSC normal 8

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 8


title: HSC normal 9

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 9


title: HSC normal 10

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 10


title: Adrenocortical cell_knockout_replicate 1


title: HSC normal 3

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 3


title: HSC normal 5

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 5


title: Adrenocortical cell_knockout_replicate 3


title: Adrenocortical cell_wild-type_replicate 5

source_name: Adrenocortical cells, wild-type mouse

value: Female

value: Star+/+


title: HSC normal 6

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 6


title: Adrenocortical cell_wild-type_replicate 7


title: Adrenocortical cell_wild-type_replicate 6


title: HSC normal 7

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 7


title: HSC normal 1

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 1


title: Adrenocortical cell_knockout_replicate 2


title: HSC patient 6, RCMD-RS, IPSS low risk

description: Ribosomal protein gene expression data from human patients with low risk myelodysplastic syndrome.

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 6


title: Adrenocortical cell_wild-type_replicate 4


title: HSC normal 4

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 4


title: HSC patient 7, RCMD-RS, IPSS low risk

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 7


title: HSC normal 2

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Normal age-matched control 2


title: Adrenocortical cell_wild-type_replicate 3


title: HSC patient 2, RCMD-RS, IPSS low risk

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 2


title: HSC patient 5, RARS, IPSS low risk

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 5


title: HSC patient 3, RCMD, IPSS INT-1 risk

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 3

value: monosomy 7


title: HSC patient 8, RCMD, IPSS low risk

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 8


title: HSC patient 4, RCMD, IPSS low risk

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 4


title: HSC patient 1, RCMD, IPSS low risk

source_name: Lin-CD34+CD38-CD90+CD45RA- cells sorted from bone marrow, Patient 1


title: Adrenocortical cell_wild-type_replicate 2


title: Adrenocortical cell_wild-type_replicate 1


title: parental strain_in the presence of multi-inhibitors_biological replicate 2

status: Public on Aug 13 2011

city: Tianjin

first: Bing-Zhi

last: Li

address: Weijin Road 92#

country: China

institute: Tianjin University

description: gene expression at exponential phase

hyb_protocol: The biotin-labeled cRNA was hybridized to the GeneChip® Yeast Genome 2.0 Array from Affymetrix (California, US) after dilution and fragmentation according to Affymetrix’s protocol

scan_protocol: Microarrays were scanned with the Genechip Scanner 3000

data_processing: The data were analyzed with GeneChip Operation System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Saccharomyces cerevisiae

source_name: parental strain, in the presence of multi-inhibitors, at the exponential stage

label_protocol: Total RNA labeling was conducted according to the Affymetrix GeneChip Expression analysis technical manual (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The fermentations of both parental and tolerant yeasts were carried out in 3 L YPD medium (100 g/L glucose, 10 g/L yeast extract and 20 g/L peptone) in a 5 L fermentor without aeration.

extract_protocol: Total RNA was isolated according to the hot phenol method

treatment_protocol: Cultures for microarray analysis were collected at mid-exponential phase

value: angel yeast

tag: growth phase

value: exponential


title: tolerant strain_in the presence of multi-inhibitors_biological replicate 1

description: gene expression at exponential phase

source_name: tolerant strain, in the presence of multi-inhibitors, at the exponential stage

value: CGMCC 2757


title: tolerant strain_in the presence of multi-inhibitors_biological replicate 2

description: gene expression at exponential phase


title: tolerant strain_in the absence of inhibitors_biological replicate 2

description: gene expression at exponential phase

source_name: tolerant strain, in the absence of inhibitors, at the exponential stage


title: tolerant strain_in the absence of inhibitors_biological replicate 1

description: gene expression at exponential phase


title: parental strain_in the presence of multi-inhibitors_biological replicate 1

description: gene expression at exponential phase


title: parental strain_in the absence of inhibitors_biological replicate 2

description: gene expression at exponential phase

source_name: parental strain, in the absence of inhibitors, at the exponential stage


title: NC-NMuMG

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description: Gene expression data from resting epithelial cells

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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

source_name: Mammary gland epithelial cells

label_protocol: Biotin-labelled.

growth_protocol: Seeded in six-well plates (1x105 cells/well) and incubated overnight in DMEM containing 10% FCS, after which the medium was replaced with modified K-1 medium (50:50 Ham's F-12/DMEM with 5μg/ml transferrin and 5μg/ml insulin), and the cells were incubated for further 24 hours.

extract_protocol: Total RNA was extracted by using RNeasy mini-kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Treated with or without rhTGF-b1 3.0 ng/mL and rhEGF 3.0 ng/mL in K-1 medium for 24 hours.

value: Mammary gland

tag: treatment

value: resting epithelial cells


title: parental strain_in the absence of inhibitors_biological replicate 1

description: gene expression at exponential phase


title: EMT-MCT

description: Gene expression data from epithelial cells stimulated with TGF-b1/EGF

source_name: EMT-induced renal tubular epithelial cells

value: Kidney


title: NC-MCT

source_name: Renal tubular epithelial cells


title: EMT-mProx

source_name: EMT-induced proximal renal tubular epithelial cells

value: epithelial cells stimulated with TGF-b1/EGF


title: ND6

city: Rijeka

first: Ivana

last: Ratkaj

address: Trga brace Mazuranica 10

department: Department of Biotechnology

country: Croatia

institute: University of Rijeka

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner Affimetrix.

source_name: patient matched healthy (ND) tissue

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

growth_protocol: Primary DC cells were obtained from affected palmar fascia localized in palmodigital and digital area (D) along with the patient-matched healthy, macroscopically unaffected fascia tissue from the edge of primary incision (ND). All patients were male between 54 and 75 years in the last stage of the disease.Cells were isolated according to previously established protocols (Tse et al. 2004, Kraljevic Pavelic et al. 2009). Briefly, tissues were immediately submerged in phosphate buffered saline (PBS) supplemented with 100 U/ml penicillin and 100 ug/mL streptomycin, and kept at +4C. Each harvested sample was rinsed twice in PBS, cut into pieces (2 x 2 x 2 mm), placed in culture dishes, and cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100ug/mL streptomycin in a humidified atmosphere with 5% CO2 at 37 C for 10-14 days. Tissues were removed after 10 days and cells were further grown until they reached 80-90% confluence.

extract_protocol: Total RNA was isolated by RNeasy mini kit (Qiagen)

value: male

tag: tissue origin

tag: cell type

value: Primary DC cells


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 91

status: Public on Aug 12 2011

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

hyb_protocol: Fluorescently labeled cDNA was hybridized to CombiMatrix arrays as previously described (Mol. Biol. Cell 16:4792).

scan_protocol: Images of the hybridized arrays were acquired with a GenePix 4000B scanner (Axon Instruments) controlled by the GenePix 4.0 program (Molecular Devices). Each array was scanned using the following PMT settings of 400 and 350 for the 635 and 532 nm lasers respectively.

data_processing: Images were gridded with GenePix 4.0 and the median foreground intensity from the Cy5 channel for each feature was used as the input for subsequent analysis and is reported in the VALUE column (the Cy3 channel was not analyzed due to low signal). Background intensity was estimated based on the median intensities of a control set of known antisense and intergenic regions, a method similar to the use of median intensities of known introns in the analysis of rice tiling data (Nat. Genet. 38:124). Specifically, the background intensity was estimated as the median intensity of the positive control probes corresponding to the intergenic (untranscribed) regions flanking CBP1 and TYR1 and the antisense (untranscribed) probes for CBP1, TYR1, and TEF1. A tiling probe was considered detected if it had intensity greater than the background intensity estimated for the corresponding array.

molecule: polyA RNA

organism: Histoplasma capsulatum

source_name: Pooled yeast conditions

label_protocol: Cy5-labeled cDNA was prepared from individual RNA samples as previously described (Mol. Biol. Cell 16:4792), and an equal mass of cDNA was pooled from each sample and hybridized to individual tiling arrays.

extract_protocol: We prepared RNA from yeast-form Histoplasma capsulatum strain G217B (ATCC 26032; a kind gift of William Goldman, Washington University, St. Louis, MO) under a variety of conditions (including early, middle, and late logarithmic growth, stationary phase, heat shock (42C for 30 min), oxidative stress (1 mM menadione), sulfhydryl reducing stress (10mM DTT), and a range of media (HMM (J. Med. Vet. Mycol. 26:137), 3M (J. Med. Vet. Mycol. 26:137), YPD (Meth. Enz. 194:3), and SD complete (Meth. Enz. 194:3). PolyA RNA were prepared as previously described (Mol. Biol. Cell 14:2314, Mol. Biol. Cell 16:4792).

source_name: Pooled mycelial conditions

label_protocol: Cy3-labeled cDNA was prepared from individual RNA samples as previously described (Mol. Biol. Cell 16:4792), and an equal mass of cDNA was pooled from each sample and hybridized to individual tiling arrays.

extract_protocol: We prepared RNA from mycelial-form Histoplasma capsulatum strain G217B (ATCC 26032; a kind gift of William Goldman, Washington University, St. Louis, MO) in Saboraud or HMM (J. Med. Vet. Mycol. 26:137) shaking liquid cultures or HMM still liquid culture. Total RNA were prepared as previously described (Mol. Biol. Cell 14:2314, Mol. Biol. Cell 16:4792).


title: D6

source_name: diseased (D)  tissue

tag: gender

value: palmar fascia localized in palmodigital and digital area (D)


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 90


title: ND2

value: macroscopically unaffected fascia tissue from the edge of primary incision (ND)


title: EMT-EpH4

source_name: EMT-induced mammary gland epithelial cells (EMT resistance)


title: NC-EpH4

source_name: Mammary gland epithelial cells (EMT resistance)


title: D2


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 89


title: D18


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 72


title: ND18


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 71


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 88


title: EMT-NMuMG

source_name: EMT-induced mammary gland epithelial cells


title: NC-mProx

source_name: Proximal renal tubular epithelial cells


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 73


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 56


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 74


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 57


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 55


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 41


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 54


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 24


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 23


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 22


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 21


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 40


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 6


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 7


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 5


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 4


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 39


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 38


title: ES_Suz12KO_rep1

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

institute: European Institute of Oncology

hyb_protocol: Performed at the Affymetrix microarray unit at the Institute of Molecular Oncology of the Italian Foundation for Cancer Research-European Institute of Oncology campus, Milan, Italy, according to the manufacturer’s instructions.

data_processing: Data were processed using standard procedures: Programmatic identifier: GeneChip.CallGEBaseCall.1; Algorithm: ExpressionStat 5.0

source_name: ES cell RNA

label_protocol: Targets for microarray hybridization were synthesized according to the supplier’s instructions (Affymetrix).

extract_protocol: Total RNA was extracted independently from three Suz12 and three Suz12 ES cell clones. RNA was quantified, and equal amounts fromthe three Suz12 WT and the three Suz12 KO samples were pooled into one sample to reduce the experimental variation.

value: Embryonic Stem Cells


title: ES_WT_rep1

scan_protocol: Performed at the Affymetrix microarray unit at the Institute of Molecular Oncology of the Italian Foundation for Cancer Research-European Institute of Oncology campus, Milan, Italy, according to the manufacturer’s instructions.

value: WT


title: Ovarian cancer sample 57

city: Boston

first: Dimitrios

last: Spentzos

state: MA

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

hyb_protocol: The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing:
Full details provided in published manuscript http://jco.ascopubs.org/content/23/31/7911.long
normalization algorithm: dChip

source_name: Ovarian cancer

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.

extract_protocol: RNA was isolated using the trizol protocol

tag: overall survival (months)

tag: overall survival (censored 1=event))


title: Ovarian cancer sample 52


title: Ovarian cancer sample 51


title: Ovarian cancer sample 58


title: Ovarian cancer sample 53


title: Ovarian cancer sample 56


title: Ovarian cancer sample 55


title: Ovarian cancer sample 54


title: ES_Suz12KO_rep2


title: ES_WT_rep2


title: Ovarian cancer sample 49


title: Ovarian cancer sample 50


title: Ovarian cancer sample 48


title: Ovarian cancer sample 47


title: Ovarian cancer sample 42


title: Ovarian cancer sample 43


title: Ovarian cancer sample 37


title: Ovarian cancer sample 40


title: Ovarian cancer sample 41


title: Ovarian cancer sample 44


title: Ovarian cancer sample 45


title: Ovarian cancer sample 46


title: Ovarian cancer sample 35


title: Ovarian cancer sample 31


title: Ovarian cancer sample 30


title: Ovarian cancer sample 33


title: Ovarian cancer sample 38


title: Ovarian cancer sample 32


title: Ovarian cancer sample 36


title: Ovarian cancer sample 39


title: Ovarian cancer sample 34


title: Ovarian cancer sample 28


title: Ovarian cancer sample 25


title: Ovarian cancer sample 22


title: Ovarian cancer sample 29


title: Ovarian cancer sample 26


title: Ovarian cancer sample 27


title: Ovarian cancer sample 23


title: Ovarian cancer sample 24


title: Ovarian cancer sample 19


title: Ovarian cancer sample 18


title: Ovarian cancer sample 16


title: Ovarian cancer sample 20


title: Ovarian cancer sample 21


title: Ovarian cancer sample 17


title: Ovarian cancer sample 13


title: Ovarian cancer sample 15


title: Ovarian cancer sample 7


title: Ovarian cancer sample 14


title: Ovarian cancer sample 5


title: Ovarian cancer sample 9


title: Ovarian cancer sample 6


title: Ovarian cancer sample 8


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 92

tag: strain


title: Ovarian cancer sample 12


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 87


title: Ovarian cancer sample 4


title: Ovarian cancer sample 11


title: Ovarian cancer sample 3


title: Ovarian cancer sample 10


title: Ovarian cancer sample 1


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 83


title: Ovarian cancer sample 2


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 78


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 93


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 82


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 84


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 86


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 81


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 85


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 76


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 79


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 65


title: BA1107

city: la jolla

first: jonathan

last: sebat

state: CALIFORNIA

address: 9500 gilman drive

department: Psychiatry

institute: University of California San Diego

hyb_protocol: Hybridization was performed according to Nimblegen Inc. protocol guidelines for 2.1M probe arrays.

scan_protocol: Arrays were scanned on an Axon 4000B scanner at 5µm resolution as per manufacturer's protocol using a standard reference genome.

data_processing: Data were normalized in a two-step process as described in McCarthy et al Nat Genet. 2009 Nov;41(11):1223-7: First, a ‘spatial’ normalization of probes was performed to adjust for regional differences in intensities across the surface of the array; second,the Cy5 and Cy3 intensities were adjusted to a fitting curve by invariant set normalization, preserving the variability in the data. The log2ratio for each probe was then estimated using the geometric mean of normalized and raw intensity data. The linear scale normalized data are provided as a supplementary file on the Series record.

source_name: Human genomic DNA from fibroblast cell culture

label_protocol: Labelling reaction was performed according to Nimblegen Inc. protocol guidelines as follows: 1 µg Test and Reference genomic DNA was amplified in parallel with Cy3 and Cy5 random 9-mer primers respectively in presence of Klenow Fragment (3’->5’ exo-). Following reaction termination with EDTA and ethanol purification, Cy-labeled DNA was dried and re-hydrated in deionized water.

extract_protocol: Fibrioblast cells were lysed in DNA lysis solution (100 mM Tris, pH 8.5, 5 mM EDTA, 200 mM NaCl, 0.2% (w/v) sarcosyl and 100 mg ml 21 fresh proteinase K) overnight at 50 uC. DNA was precipitated by the addition of an equal volume of NaCl-ethanol mixture (150 ml of 5 M NaCl in 10 ml cold 95% ethanol) and then washed three times in 70% ethanol before resuspension in water with RNase A overnight at 4 C.

tag: diagnosis

value: Schizophrenia

value: Normal


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 62


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 69


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 61


title: BA1106


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 58


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 75


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 77


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 53


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 80


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 64


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 66


title: BA1108


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 70


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 68


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 49


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 59


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 60


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 44


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 63


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 67


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 50


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 52


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 48


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 51


title: BA1105


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 42


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 37


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 47


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 45


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 36


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 43


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 46


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 34


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 31


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 29


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 30


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 32


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 17


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 15


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 35


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 11


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 9


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 18


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 8


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 14


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 20


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 27


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 26


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 25


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 19


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 16


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 10


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 33


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 28


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 13


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 3


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 12


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 2


title: test set_Urethane_long_biological rep3

status: Public on Aug 11 2011

city: Seoul

first: seulji

last: lee

address: 599 Gwanak-ro, Gwanak-gu

department: collage of pharmacy

country: South Korea

institute: Seoul Nat'l Univ.

description: Urethane (3X500)_3

hyb_protocol: For each array, 15 µg of amplified biotin-cDNA was fragmented and hybridized to the Affymetrix Rat Genome 2302.0 GeneChip array (Affymetrix, Santa Clara, CA) for 16 h at 45°C in a rotating hybridization oven. Slides were stained with streptavidin/phycoerythrin and washed for antibody amplification.

scan_protocol: Arrays with hybridized targets were scanned using an Affymetrix GeneChip Analysis System (GC450 Fluidics Stations, a Hybridization Oven 640, a GC3000 7G scanner), and the scanned images were analyzed using GeneChip® Operating Software v1.4 (GCOS) (Affymetrix). Spots of poor quality, as determined by visual inspection, were excluded from further analysis.

data_processing: Forty-one data were obtained for the training compounds in this study. We treated rats with one of three compounds or a control for each GTX and NGTX experimental group and measured 2 time points for each group. All experimental procedures were repeated three times. We excluded 1 file that was found to be a failure. Each ‘.CEL’ file obtained as a raw data file was standardized using the RMA (Robust Multi-array Average) algorithm. Filtering was based on the expressed values of the raw data; probes with one or more expression values in the percentile range of 20-100% (27,458 of 31,099 total chip probes) were selected.

organism: Rattus norvegicus

source_name: liver, test compound treated,72 hours

label_protocol: Biotin-labeling following standard Affymetrix protocols.

growth_protocol: The animals were housed in polycarbonate cages, with hardwood chips, in a room with 12/12 h light/dark cycles at a controlled temperature. They were given food and water ad libitum. All procedures were approved by the Institutional Animal Care and Use Committee of NIFDS.

extract_protocol: Liver specimens were processed for RNA extraction. RNA was isolated using TRIzol (Invitrogen, MO), and quality control was performed using RNA 6000 Nano chips on an Agilent 2001 Bioanalyzer. Total RNA was extracted from frozen tissue using TRIzol (Invitrogen, Carlsbad, CA) and was purified with an RNeasy mini kit (QIAGEN, Hilden, Germany). Total RNA (1 µg) was amplified using the Affymetrix one-cycle cDNA synthesis protocol. (Agilent Technologies, Germany). Total RNA was extracted from frozen tissue using TRIzol (Invitrogen, Carlsbad, CA) and was purified with an RNeasy mini kit (QIAGEN, Hilden, Germany).

treatment_protocol: Each experimental compound was administered to three SD rats. In the repeated administration groups, the compounds were administered three times after three hours and again after 24 hours. The rats were autopsied after 24 hours, and RNA was isolated from liver tissue

value: Sprague-Dawley

tag: age

value: 6-week old

tag: tissue

value: liver

tag: carcinogen

value: test compound


title: test set_SN_long_biological rep3


title: Histoplasma capsulatum pooled yeast polyA RNA vs. pooled mycelia total RNA, array 1


title: test set_Urethane_long_biological rep2

description: Urethane (3X500)_2


title: test set_Urethane_short_biological rep2

description: Urethane (1X500)_2

source_name: liver, test compound treated,3 hours


title: test set_ME_long_biological rep3


title: test set_SN_short_biological rep1


title: s (cy5) / r (cy3) replicate 4

city: Harpenden

first: Nikos

last: Karatolos

state: Herts

address: West Common

country: United Kingdom

institute: Rothamsted Research

description: Analysis used total RNA from a susceptible strain (s) as control samples for comparison to the experimental resistant strain r

hyb_protocol: Labelled cRNAs were hybridized to arrays and these were washed and scanned as described in Agilent’s Quick Amp Labeling Protocol (Version 6.5).

scan_protocol: Microarrays were scanned with an Agilent G2505C US10020348 scanner, and fluorescent intensities of individual spots were obtained using the Agilent Feature Extraction software with default Agilent parameters.

data_processing: Data normalization, filtering, dye flipping and statistical analysis were performed using the GeneSpring GX suit. For statistical analysis, a t-test against zero using the Benjamini-Hochberg false discovery rate (FDR) method for multiple testing corrections was used to detect significantly differentially expressed genes. Genes meeting a p value cut-off of 0.01 and showing a transcription ratio > 2 fold in either direction were considered to be differentially transcribed between the two strains.

organism: Trialeurodes vaporariorum

source_name: [experiment] Strain r

label_protocol: 830 ng of each total RNA was used to generate labelled cRNA following the Agilent's Quick Amp Labelling Protocol (Version 6.5)

extract_protocol: Total RNA extracted from 500 whitefly eggs, using the Isolate RNA Mini Kit (Bioline) according to the manufacturer’s protocol.

source_name: [control] Strain s


title: test set_SN_short_biological rep3


title: test set_SN_short_biological rep2


title: test set_ME_long_biological rep2


title: NGTX_control_biological rep3

source_name: liver, untreated(control)

value: control


title: test set_SN_long_biological rep2


title: test set_Urethane_short_biological rep1

description: Urethane (1X500)_1


title: test set_SN_long_biological rep1


title: s (cy5) / r (cy3) replicate 2


title: NGTX_control_biological rep1


title: s (cy5) / r (cy3) replicate 3


title: NGTX_control_biological rep2


title: test set_ME_long_biological rep1


title: test set_Urethane_long_biological rep1

description: Urethane (3X500)_1


title: s (cy3) / r (cy5) replicate 3


title: test set_ME_short_biological rep3


title: test set_ME_short_biological rep2


title: s (cy3) / r (cy5) replicate 2


title: s (cy3) / r (cy5) replicate 4


title: s (cy5) / r (cy3) replicate 1


title: s (cy3) / r (cy5) replicate 1


title: test set_Urethane_short_biological rep3

description: Urethane (1X500)_3


title: test set_ME_short_biological rep1


title: GTX_control_biological rep3


title: GTX_control_biological rep2


title: NGTX_DL-Ethionine_short_biological rep2

source_name: liver, NGTX treated,3 hours

value: nongenotoxic carcinogen


title: GTX_control_biological rep1


title: NGTX_DL-Ethionine_long_biological rep1

source_name: liver, NGTX treated,72 hours


title: GTX_DEN_short_biological rep3

source_name: liver, GTX treated,3 hours

value: genotoxic carcinogen


title: GTX_DEN_long_biological rep3

source_name: liver, GTX treated,72 hours


title: GTX_DEN_long_biological rep1


title: NGTX_DL-Ethionine_short_biological rep1


title: GTX_DEN_long_biological rep2


title: NGTX_DL-Ethionine_long_biological rep3


title: test set_DCP_short_biological rep3


title: test set_DCP_long_biological rep1


title: Monocytes vs monocytes + CSF-1

city: Dijon

first: Laurent

last: Delva

address: 7 boulevard Jeanne d'Arc

country: France

institute: Inserm U866

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump. Hybridization solution consisted of 100 µL of 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. After hybridization, the miRNAs were detected by fluorescence labeling using tag-specific Cy3 and Cy5 dyes.

scan_protocol: Scanned on a GenePix 4000B (Molecular Device) laser scanner Images were quantified using Array-Pro image analysis software (Media Cybernetics). Images were quantified using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).
Data disregarded if p-value > 0.01.

source_name: Untreated monocytes (Sample A)

label_protocol: The assay started with 5 µg of total RNA sample. The RNA was size-fractionated using a YM-100 Microcon centrifugal filter (GE Millipore), and the 3′ ends of the small RNAs (<300 nt) were extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in the dual-sample experiments.

growth_protocol: The human monocytes CD14+ obtained after MACS separation were grown at a concentration of 0.5x 106 cells/ml in RPMI 1640 Glutamax medium (Bio Whittaker) supplemented with 10% fetal calf serum (Bio Whittaker), penicillin (100 U/mL), streptomycin (100 µg/mL), and amphotericin B (0.25 µg/mL) (Bio Whittaker) for 12 hours.

extract_protocol: Material was isolated using the mirVana miRNA isolation kit (Ambion) following manufacturer's instructions.

treatment_protocol: CD14+ monocytes were untreated or treated with 100ng/ml of CSF-1.

value: Peripheral blood

source_name: CSF-1 treated monocytes at day 6 (Sample B)


title: GTX_DEN_short_biological rep2


title: test set_DCP_long_biological rep2


title: test set_DCP_short_biological rep1


title: test set_DCP_long_biological rep3


title: NGTX_Clofibrate_long_biological rep2


title: NGTX_Clofibrate_long_biological rep3


title: NGTX_DL-Ethionine_long_biological rep2


title: NGTX_Clofibrate_short_biological rep1


title: chicken eye, +15 diopter lens, 3 days, biological replicate 5_Chicken_437e

city: Philadelphia

first: Alice

middle: M

last: McGlinn

state: PA

address: 602D Richards Building 3700 Hamilton Walk

department: Ophthalmology

institute: University of Pennsylvania School of Medicine

description: Gene expression data from contralateral eye, (+) lens, 3 days

hyb_protocol: 3.75ug of labeled cDNA were hybridized to an Affymetrix  Chicken Genome Array for 16 hours at 45°C.  Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Gene Chips were scanned using the Affymetrix 7G Scanner.

data_processing: Affymetrix Command Console was used to quantify expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.  CEL files were imported into Partek Genomic Suite(v.6.4) where RMA was applied yielding normalized, log2 transformed signal intensities.   All resultiing p-values were corrected for multiple comparisons using the Benjamini-Hochberg step-up method to yield False Discovery Rates (FDR) as implemented in Partek.  An FDR of <10% was considered significant

source_name: retina/RPE, +15 diopter lens, 3 days

label_protocol: Fragmented, biotinylated cDNA was prepared from 100ng of total RNA according to the Nugen Ovation Kit protocol.

growth_protocol: One day old chicks were maintained under a 12 hour light:dark cycle.

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

treatment_protocol: At one week of age,  either a (+) or a (-) 15 diopter lens was adhered to one eye of each chick for a period of either 6 hours or 3 days.

value: retina/RPE

tag: breed

value: White Leghorn

value: less than 2 weeks


title: NGTX_Clofibrate_short_biological rep2

value: male


title: GTX_3MeDAB_short_biological rep3


title: NGTX_Clofibrate_short_biological rep3


title: NGTX_Clofibrate_long_biological rep1


title: chicken eye, +15 diopter lens, 3 days, biological replicate 6_Chicken_438e


title: chicken eye, control, 3 days, biological replicate 6_Chicken_438c

description: Gene expression data from control eye, no lens

source_name: retina/RPE, control, 3 days


title: test set_DCP_short_biological rep2


title: GTX_3MeDAB_long_biological rep1


title: chicken eye, +15 diopter lens, 3 days, biological replicate 4_Chicken_436e


title: GTX_3MeDAB_short_biological rep2


title: GTX_2-AAF_long_biological rep3


title: GTX_3MeDAB_short_biological rep1


title: chicken eye, control, 3 days, biological replicate 4_Chicken_436c


title: GTX_3MeDAB_long_biological rep2


title: GTX_3MeDAB_long_biological rep3


title: chicken eye, +15 diopter lens, 3 days, biological replicate 2_Chicken_434e


title: chicken eye, +15 diopter lens, 3 days, biological replicate 3_Chicken_435e


title: NGTX_1,4-Dioxane_short_biological rep2


title: GTX_2-AAF_short_biological rep2


title: chicken eye, control, 3 days, biological replicate 5_Chicken_437c


title: GTX_2-AAF_short_biological rep1


title: GTX_2-AAF_long_biological rep2


title: chicken eye, control, 3 days, biological replicate 1_Chicken_433c


title: NGTX_1,4-Dioxane_short_biological rep1


title: chicken eye, control, 3 days, biological replicate 3_Chicken_435c


title: NGTX_1,4-Dioxane_short_biological rep3


title: chicken eye, -15 diopter lens, 3 days, biological replicate 6_Chicken_411e

description: Gene expression data from contralateral eye,(-) lens, 3 days

source_name: retina/RPE, -15 diopter lens, 3 days


title: NGTX_1,4-Dioxane_long_biological rep1


title: chicken eye, control, 3 days, biological replicate 2_Chicken_434c


title: GTX_2-AAF_short_biological rep3


title: NGTX_1,4-Dioxane_long_biological rep2


title: dermal papilla cultured used to generate agDP1

first: Manabu

last: Ohyama

address: 6-20-2 Shinkawa Mitaka-shi

department: Department of Dermatology

institute: Kyorin University School of Medicine

description: Gene expression data from primarily cultured human dermal papilla cells used for the generation of agDP1 (cDPforagDP1 and cDPforagDP2; derived from respective donors other than those of fDP1-4).

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Genechips were scanned by GeneChip Scanner 3000 7G (Affymetirix Inc.) following the manufacturer's protocol.

data_processing: The data was analyzed with Gene Chip Operating Software (GCOS) ver. 1.4. CHP files were generated using follwing parameters: target signal scaling 500, Alpha1 0.05, Alpha2 0.065, Tau 0.015

label_protocol: Three to 10ng of isolated total RNA was amplified and biotin-labeled by T7-primer based GeneChip® Two-Cycle cDNA Synthesis kit and IVT labeling kit (Affymetirix Inc.).

growth_protocol: The cells (except fDPs) were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen, Carlsbad, CA, USA) containing penicillin and streptomycin (Roche, Basel, Switzerland) and 10% fetal bovine serum (FBS) at 37°C/5% CO2.

extract_protocol: Extraction of total RNA was performed using RNeasy Micro Kit (QIAGEN, Hilden, Germany) following the manufacturer's instructions.

treatment_protocol: For fDP chips, DPs were microdissected from the bulbar portion of hair follicles under a dissection microscope using fine needles. For cultured cells (cDP, Fibro, cDPforagDP chips), the cells were detached from culture dishes with 2% trypsin for 2 minutes when confluent. DP cell aggregation (agDPs), cultured DP cells were transferred into low cell-binding 96 well plates filled with 10%FBS-DMEM at the density of 8,000 cells per well. The plates were centrifuged for several seconds to spin down DP cells and incubated at 37°C/5% CO2 overnight.

tag: source tissue

value: anagen hair follicles

value: dermal papilla

value: female


title: GTX_2-AAF_long_biological rep1


title: dermal papilla cultured used to generate  agDP2

description: Gene expression data from primarily cultured human dermal papilla cells used for the generation of agDP2 (cDPforagDP1 and cDPforagDP2; derived from respective donors other than those of fDP1-4).


title: chicken eye, +15 diopter lens, 3 days, biological replicate 1_Chicken_433e


title: NGTX_1,4-Dioxane_long_biological rep3


title: dermal papilla aggregated agDP2 rep2

description: Gene expression data from DP cell aggregates generated from primarily cultured human dermal papilla cells (cDPforagDP2).

source_name: dermal papilla aggregated agDP2

value: dermal papilla aggregated agDP2


title: dermal papilla freshly-microdissected rep4

description: Gene expression data from whole human dermal papilla microdissected from anagen hair follicles (each fDP chips derived from respecitve volunteer).

source_name: dermal papilla freshly-microdissected

value: dermal papilla freshly-microdissected


title: dermal papilla cultured rep2

description: Gene expression data from primarily cultured human dermal papilla cells (fDPs).

source_name: dermal papilla cultured

value: dermal papilla cultured


title: dermal papilla cultured rep4


title: fibroblasts cultured rep4

description: Gene expression data from primarily cultured human dermal fibroblasts (derived from same donors of fDPs indicated by respective numbers).

source_name: fibroblasts cultured

value: fibroblasts cultured

value: dermis

value: dermal fibroblast


title: dermal papilla cultured rep3


title: dermal papilla aggregated agDP1 rep1

description: Gene expression data from DP cell aggregates generated from primarily cultured human dermal papilla cells (cDPforagDP1).

source_name: dermal papilla aggregated agDP1

value: dermal papilla aggregated agDP1


title: fibroblasts cultured rep2


title: fibroblasts cultured rep1


title: fibroblasts cultured rep3

description: Gene expression data from primarily cultured human dermal fibroblasts (derived from same donors of fDPs indicated by respective numbers)


title: chicken eye, control, 3 days, biological replicate 4_Chicken_409c


title: dermal papilla cultured rep1


title: chicken eye, -15 diopter lens, 3 days, biological replicate 5_Chicken_410e


title: dermal papilla freshly-microdissected rep3


title: chicken eye, control, 3 days, biological replicate 6_Chicken_411c


title: chicken eye, -15 diopter lens, 3 days, biological replicate 1_Chicken_406e


title: chicken eye, -15 diopter lens, 3 days, biological replicate 4_Chicken_409e


title: dermal papilla freshly-microdissected rep2


title: chicken eye, control, 6 hours, biological replicate 6_Chicken_426c

source_name: retina/RPE, control, 6 hours


title: chicken eye, control, 3 days, biological replicate 5_Chicken_410c


title: dermal papilla freshly-microdissected rep1


title: chicken eye, -15 diopter lens, 3 days, biological replicate 2_Chicken_407e


title: chicken eye, +15 diopter lens, 6 hours, biological replicate 6_Chicken_426e

description: Gene expression data from contralateral eye, (+) lens, 6 hours

source_name: retina/RPE, +15 diopter lens, 6 hours


title: chicken eye, control, 6 hours, biological replicate 5_Chicken_425c


title: chicken eye, control, 3 days, biological replicate 2_Chicken_407c


title: NGTX_DL-Ethionine_short_biological rep3

value: Sprague-Dawley

value: 6-week old

value: liver

value: nongenotoxic carcinogen


title: chicken eye, control, 3 days, biological replicate 3_Chicken_408c

value: retina/RPE

value: White Leghorn


title: chicken eye, -15 diopter lens, 3 days, biological replicate 3_Chicken_408e

value: less than 2 weeks


title: chicken eye, control, 3 days, biological replicate 1_Chicken_406c


title: chicken eye, +15 diopter lens, 6 hours, biological replicate 5_Chicken_425e


title: chicken eye, +15 diopter lens, 6 hours, biological replicate 4_Chicken_424e


title: chicken eye, control, 6 hours, biological replicate 1_Chicken_421c


title: chicken eye, +15 diopter lens, 6 hours, biological replicate 2_Chicken_422e


title: chicken eye, control, 6 hours, biological replicate 4_Chicken_424c


title: chicken eye, +15 diopter lens, 6 hours, biological replicate 3_Chicken_423e


title: GFP overexpression control, biological replicate 3

city: Iowa City

first: Pamela

last: Wernett

state: IA

address: 500 Newton Rd., MEB

institute: University of Iowa

description: Nuclear localized GFP into pcDNA5/TO

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials with a Model 640 hybridization oven and Model 450 GeneChip fluidics station.

scan_protocol: Affymetrix® GeneChip® Scanner 3000

data_processing:
Partek® Genomics SuiteTM (Partek) was used for downstream analysis of the microarray data.  The data were normalized with the Robust Multichip Average (RMA) and analyzed with ANOVA.  All data were corrected for genome-wide comparisons using the Benjamini and Hochberg Step-up FDR method.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: GFP overexpression control

label_protocol: Samples were labeled with the FL-OvationTM cDNA Biotin Module V2 (NuGEN).

growth_protocol: HEK293 cells were plated at 70-80% confluency in 60mm dishes and allowed to grow for 24 hrs

extract_protocol: Total RNA was purified from the cells using the RNeasy® Mini Kit (Qiagen) and DNase treated as specified by the manufacturer.  RNA integrity and concentration was assessed utilizing the Agilent 2100 Bioanalyzer.  WT-OvationTM Pico RNA Amplification System V1.0 (NuGEN) and WT-OvationTM Exon Module V1.0 (NuGEN) were used as described by the manufacturer.

treatment_protocol: Transfected with Lipofectamine 2000 (Invitrogen) and 48 hrs after transfection, the supernatant along with any floating cells were discarded and adherent cells were gently washed with H2O and harvested by trypsinization.  Cells were sedimented by centrifugation, resuspended to a density of ~7 x 106 cells/mL, filtered with a 70µm mesh and sorted for cell viability and detection of GFP with a Becton Dickinson FACSAriaTM II machine.  Viable cells with detectable GFP were sorted for exactly 20 minutes into cyrotubes for each sample (n=3) and placed immediately into liquid N2.  Cells were thawed, sedimented by centrifugation and the supernatant was removed.

tag: cell line


title: chicken eye, control, 6 hours, biological replicate 2_Chicken_422c


title: chicken eye, -15 diopter lens, 6 hours, biological replicate 6_Chicken_401e

description: Gene expression data from contralateral eye, (-) lens, 6 hours

source_name: retina/RPE, -15 diopter lens, 6 hours


title: chicken eye, -15 diopter lens, 6 hours,biological replicate 5_Chicken_400e


title: chicken eye, control, 6 hours, biological replicate 3_Chicken_423c


title: GFP overexpression control, biological replicate 2

description: Nuclear localized GFP into pcDNA5/TO


title: MED12 shRNA 5 RNAi knockdown, biological replicate 2

description: MED12 endogenous knockdown via shRNA RNAi technology powered by H1 promoter in peGFP-C1

source_name: MED12 shRNA 5 RNAi knockdown


title: MED12 shRNA 5 RNAi knockdown, biological replicate 3


title: chicken eye, -15 diopter lens, 6 hours, biological replicate 4_Chicken_399e


title: MED12 PQL/Opa domain deletion overexpression, biological replicate 3

description: MED12 with C-terminal domains PQL and Opa deleted with engineered Kozak consensus sequence and N-terminally tagged nuclear localized GFP into pcDNA5/TO


title: chicken eye, control, 6 hours, biological replicate 5_Chicken_400c


title: MED12 PQL/Opa domain deletion overexpression, biological replicate 2


title: chicken eye, control, 6 hours, biological replicate 6_Chicken_401c


title: VSMC AngII+CsA rep3

city: Madrid

first: Vanesa

last: Esteban

state: Madrid

address: Melchor Fernández Almagro, 3.

department: Department of Vascular Biology and Inflammation

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

hyb_protocol: 1.65 micrograms of Cy3-labeled aRNA were hybridized for 17 hours at 65ºC in a Agilent hybridization oven (G2545A, Agilent Technologies) set to 10 rpm in a final concentration of 1x GEx Hybridization Buffer HI-RPM (Agilent Technologies). Arrays were washed and dried out using a centrifuge according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays.

data_processing: Raw data files from Feature Extraction were preprocessed with GeneSpring v10 (Agilent) : Raw signal values (in log2) were thresholded to 1 and arrays were normalized using quantiles (Bolstad et al. 2003).

source_name: Primary VSMC_AngII+CsA

label_protocol: 600 ng of total RNA, were reverse transcribed using T7 promoter primer and the Moloney murine leukemia virus (MMLV) reverse transcriptase (RT). cDNA was then converted to anti-sense RNA (aRNA) by using T7 RNA polymerase that amplifies target material and incorporates cyanine 3 (Cy3)-labeled CTP simultaneously.

extract_protocol: Total RNA was obtained with Trizol and Quiagen columns.

treatment_protocol: Mouse VSMC were growth in DMEM  medium supplemented with 20% heat-inactivated fetal bovine serum.   The cultures were incubated with AngII with or without  CsA  at 37 ºC in a humidified incubator with 5% CO2.

tag: strain background

value: aorta

value: Primary vascular smooth muscle cells


title: chicken eye, -15 diopter lens, 6 hours, biological replicate 3_Chicken_398e


title: MED12 full-length overexpression, biological replicate 2

description: full-length MED12 with engineered Kozak consensus sequence and N-terminally tagged nuclear localized GFP into pcDNA5/TO

source_name: MED12 full-length overexpression


title: VSMC AngII+CsA rep2


title: chicken eye, +15 diopter lens, 6 hours, biological replicate 1_Chicken_421e


title: GFP overexpression control, biological replicate 1

description: Nuclear localized GFP into pcDNA5/TO


title: chicken eye, control, 6 hours, biological replicate 3_Chicken_398c


title: chicken eye, -15 diopter lens, 6 hours,biological replicate 2_Chicken_397e


title: MED12 full-length overexpression, biological replicate 3


title: VSMC AngII rep4

source_name: Primary VSMC_AngII


title: VSMC AngII+CsA rep4


title: MED12 shRNA 5 RNAi knockdown, biological replicate 1


title: MED12 PQL/Opa domain deletion overexpression, biological replicate 1


title: chicken eye, control, 6 hours, biological replicate 4_Chicken_399c


title: VSMC AngII rep1


title: chicken eye, control, 6 hours, biological replicate 2_Chicken_397c


title: VSMC AngII rep3


title: chicken eye, -15 diopter lens, 6 hours,biological replicate 1_Chicken_396e


title: MED12 full-length overexpression, biological replicate 1


title: VSMC AngII+CsA rep1


title: chicken eye, control, 6 hours, biological replicate 1_Chicken_396c


title: Blastomere-embryo 8-cell a

status: Public on Aug 10 2011

city: Leuven

first: Jiqiu

last: Cheng

address: Kasteelpark Arenberg 10

department: Electrical Engineering

country: Belgium

institute: Katholieke Universiteit Leuven

hyb_protocol: According to genome-wide Agilent 244K array manual

scan_protocol: Agilent protocol CGH-v4_10_Apr_08

data_processing: background subtraction, channel clone normalization

source_name: Blastomere-embryo 8-cell

extract_protocol: Genomi Phi V2-amplified single cell DNA

value: single cell from a 4-day-old human IVF embryo

tag: developmental stage

value: Blastomere-embryo 8-cell

source_name: non-amplified genomic DNA from blood

extract_protocol: non-amplified genomic DNA

value: blood

tag: genotype

value: Klinefelter patient (XXY)

tag: sample type

value: non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY)


title: VSMC AngII rep2

tag: tissue origin


title: Blastomere-embryo 16-cell f

source_name: Blastomere-embryo 16-cell

label_protocol: According to genome-wide Agilent 244K array manual

tag: cell type

value: Blastomere-embryo 16-cell


title: P90TE_cRNA

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Standard Illumina hybridzation protocol

scan_protocol: Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Data extraction was done for all beads individually, and outliers with > 2.5 MAD (median absolute deviation) were removed. The data were normalised in BeadStudio using quantile normalisation without background subtraction

source_name: Patient no 90, Tumor epithelium

label_protocol: Biotinylated cRNA were prepared with the TargetAmp 2-Round Biotin-aRNA amplification kit 3.0 (Epicentre Biotechnologies, Madison, USA)

extract_protocol: RNeasy mini and microkits(Qiagen) for whole tissue and laser microdissected samples, respectively according to the specified protocols. Microdissected samples were pooled prior to RNA isolation

value: Colorectal cancer

tag: tissue sub-type

value: Tumor epithelium

tag: patient no

value: Patient no 90


title: P9Tm_T_2

source_name: Patient no 9, Tumor whole tissue

value: Tumor whole tissue

value: Patient no 9


title: Blastomere-embryo 20-cell g

source_name: Blastomere-embryo 20-cell

value: Blastomere-embryo 20-cell


title: Blastomere-embryo 20-cell h


title: Blastomere-embryo 7-cell f

source_name: Blastomere-embryo 7-cell

value: Blastomere-embryo 7-cell


title: P90Nm_T

source_name: Patient no 90, Normal whole tissue

value: Normal whole tissue


title: P90TS_cRNA

source_name: Patient no 90, Tumor stroma

value: Tumor stroma


title: P90Tm_T

source_name: Patient no 90, Tumor whole tissue


title: P90NE

source_name: Patient no 90, Normal epithelium

value: Normal epithelium


title: Blastomere-embryo 7-cell e


title: P90NS_cRNA

source_name: Patient no 90, Normal stroma

value: Normal stroma


title: P9Nm_T_2

source_name: Patient no 9, Normal whole tissue


title: Blastomere-embryo 20-cell f

value: single cell from a 4-day-old human IVF embryo


title: Blastomere-embryo 20-cell e


title: P8Tm_T

source_name: Patient no 8, Tumor whole tissue

value: Patient no 8


title: Blastomere-embryo 15-cell e

source_name: Blastomere-embryo 15-cell

value: Blastomere-embryo 15-cell

value: blood


title: Blastomere-embryo 20-cell d

value: Klinefelter patient (XXY)

value: non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY)


title: P88Nm_T

source_name: Patient no 88, Normal whole tissue

value: Colorectal cancer

value: Patient no 88


title: P88TS

source_name: Patient no 88, Tumor stroma


title: P88Tm_T

source_name: Patient no 88, Tumor whole tissue


title: P84TE

source_name: Patient no 84, Tumor epithelium

value: Tumor epithelium

value: Patient no 84


title: P84TS_2

source_name: Patient no 84, Tumor stroma


title: EBV Cell 617

source_name: EBV Cell 617

extract_protocol: Single cells were transferred to a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (MidAtlantic Diagnostics, Mount Laurel, USA). An aliquot from the last washing droplet was taken as a negative control per cell line. The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with Genomi Phi V2 (GE Healthcare, Piscataway, NJ). The MDA products were purified and resuspended in 50 µl of elution buffer (High Pure PCR Product Purification Kit, Roche, Basel, Switzerland). All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies, Rockland, DE). SC-amplifications yielding less than 2 µg DNA were not further used.

value: single lymphoblastoid cell of the EBV-cell line

tag: genotype/variation

source_name: non-amplified genomic DNA from Klinefelter patient

tag: tissue type

value: XXY


title: Blastomere-embryo 15-cell d

source_name: non-amplified genomic DNA from blood


title: P87TS

source_name: Patient no 87, Tumor stroma

value: Patient no 87


title: P87Nm_T

source_name: Patient no 87, Normal whole tissue

value: Normal whole tissue


title: P88NS_cRNA

source_name: Patient no 88, Normal stroma


title: P87Tm_T

source_name: Patient no 87, Tumor whole tissue

value: Tumor whole tissue


title: P84Tm_T

source_name: Patient no 84, Tumor whole tissue


title: EBV Cell 1160

source_name: EBV Cell 1160


title: P84Nm_T

source_name: Patient no 84, Normal whole tissue


title: P84NS

source_name: Patient no 84, Normal stroma


title: Blastomere-embryo 15-cell a

source_name: Blastomere-embryo 15-cell


title: EBV Cell 1162

source_name: EBV Cell 1162


title: Blastomere-embryo 20-cell a

source_name: Blastomere-embryo 20-cell

value: Blastomere-embryo 20-cell


title: P87NS_cRNA

source_name: Patient no 87, Normal stroma

value: Normal stroma


title: EBV Cell 614

source_name: EBV Cell 614


title: EBV Cell 1151

source_name: EBV Cell 1151


title: EBV Cell 1013

source_name: EBV Cell 1013


title: EBV Cell 1168

source_name: EBV Cell 1168

source_name: non-amplified genomic DNA from Klinefelter patient


title: P82Tm_T

source_name: Patient no 82, Tumor whole tissue

value: Patient no 82


title: P82TS_cRNA

source_name: Patient no 82, Tumor stroma

value: Tumor stroma


title: P82NE

source_name: Patient no 82, Normal epithelium

value: Normal epithelium


title: P82NS

source_name: Patient no 82, Normal stroma


title: P82Nm_T

source_name: Patient no 82, Normal whole tissue


title: P80TE

source_name: Patient no 80, Tumor epithelium

value: Patient no 80


title: P80NE

source_name: Patient no 80, Normal epithelium


title: P80TS_cRNA

source_name: Patient no 80, Tumor stroma


title: P7T

source_name: Patient no 7, Tumor whole tissue

value: Patient no 7


title: P82TE

source_name: Patient no 82, Tumor epithelium


title: P84NE

source_name: Patient no 84, Normal epithelium


title: P74Tm_T

source_name: Patient no 74, Tumor whole tissue

value: Patient no 74


title: P7N

source_name: Patient no 7, Normal whole tissue

value: Colorectal cancer


title: P80Tm_T


title: P80NS

source_name: Patient no 80, Normal stroma


title: P74TE2

source_name: Patient no 74, Tumor epithelium


title: P6M

description: Liver Metastasis

source_name: Patient no 6, Metastasis

value: Metastasis

tag: metastatic site

value: Liver Metastasis

value: Patient no 6


title: P74TS

source_name: Patient no 74, Tumor stroma


title: P74Nm_T

source_name: Patient no 74, Normal whole tissue


title: P74NE2

source_name: Patient no 74, Normal epithelium


title: P67Nm_T

source_name: Patient no 67, Normal whole tissue

value: Patient no 67


title: P74NS

source_name: Patient no 74, Normal stroma


title: P68Tm_T

source_name: Patient no 68, Tumor whole tissue

value: Patient no 68


title: P7M

description: Liver Metastasis

source_name: Patient no 7, Metastasis


title: P67Tm_T

source_name: Patient no 67, Tumor whole tissue


title: P68Nm_T

source_name: Patient no 68, Normal whole tissue


title: P80Nm_T

source_name: Patient no 80, Normal whole tissue


title: P66Tm_T

source_name: Patient no 66, Tumor whole tissue

value: Patient no 66


title: P65Nm_T

source_name: Patient no 65, Normal whole tissue

value: Normal whole tissue

value: Patient no 65


title: P65Tm_T

source_name: Patient no 65, Tumor whole tissue

value: Tumor whole tissue


title: P47Tm_T

source_name: Patient no 47, Tumor whole tissue

value: Patient no 47


title: P47Nm_T

source_name: Patient no 47, Normal whole tissue


title: P46Tm_T

source_name: Patient no 46, Tumor whole tissue

value: Patient no 46


title: P8Nm_T

source_name: Patient no 8, Normal whole tissue

value: Patient no 8


title: P66Nm_T

source_name: Patient no 66, Normal whole tissue


title: P4Tm_T

source_name: Patient no 4, Tumor whole tissue

value: Patient no 4


title: Blastomere-embryo 19-cell c

source_name: Blastomere-embryo 19-cell

value: single cell from a 4-day-old human IVF embryo

value: Blastomere-embryo 19-cell

source_name: non-amplified genomic DNA from blood

value: blood

value: Klinefelter patient (XXY)

value: non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY)


title: P49Tm_T

source_name: Patient no 49, Tumor whole tissue

value: Colorectal cancer

value: Patient no 49


title: P4T

source_name: Patient no 4N, Tumor whole tissue

value: Patient no 4N


title: P4N

source_name: Patient no 4N, Normal whole tissue


title: P4Nm_T


title: P49Nm_T

source_name: Patient no 49, Normal whole tissue


title: P43Tm_T

source_name: Patient no 43, Tumor whole tissue

value: Patient no 43


title: P43NS

source_name: Patient no 43, Normal stroma

value: Normal stroma


title: P43TE

source_name: Patient no 43, Tumor epithelium

value: Tumor epithelium


title: P43Nm

source_name: Patient no 43, Normal whole tissue

value: Normal whole tissue


title: P43TS

source_name: Patient no 43, Tumor stroma

value: Tumor stroma


title: P46Nm_T

source_name: Patient no 46, Normal whole tissue


title: P3Tm_T

source_name: Patient no 3, Tumor whole tissue

value: Tumor whole tissue

value: Patient no 3


title: P3Nm_T

source_name: Patient no 3, Normal whole tissue


title: P34Tm_T

source_name: Patient no 34, Tumor whole tissue

value: Patient no 34


title: P32Tm_T

source_name: Patient no 32, Tumor whole tissue

value: Patient no 32


title: P34Nm_T

source_name: Patient no 34, Normal whole tissue


title: P43NE2

source_name: Patient no 43, Normal epithelium

value: Normal epithelium


title: P35Nm_T

source_name: Patient no 35, Normal whole tissue

value: Patient no 35


title: P32Nm_T

source_name: Patient no 32, Normal whole tissue


title: P35Tm_T

source_name: Patient no 35, Tumor whole tissue


title: P30Nm_T

source_name: Patient no 30, Normal whole tissue

value: Patient no 30


title: P31Nm_T

source_name: Patient no 31, Normal whole tissue

value: Patient no 31


title: P31Tm_T

source_name: Patient no 31, Tumor whole tissue


title: P1M

description: Liver Metastasis

source_name: Patient no 1, Metastasis

value: Metastasis

value: Liver Metastasis

value: Patient no 1


title: P30Tm_T

source_name: Patient no 30, Tumor whole tissue

value: Colorectal cancer


title: P103NS

source_name: Patient no 103, Normal stroma

value: Patient no 103


title: P103TE_cRNA

source_name: Patient no 103, Tumor epithelium


title: P102Tm_T

source_name: Patient no 102, Tumor whole tissue

value: Patient no 102


title: P10Nm_T

source_name: Patient no 10, Normal whole tissue

value: Patient no 10


title: P2M

description: Liver Metastasis

source_name: Patient no 2, Metastasis

value: Patient no 2


title: P28Tm_T

source_name: Patient no 28, Tumor whole tissue

value: Patient no 28


title: P2Tm_T_2

source_name: Patient no 2, Tumor whole tissue

value: Tumor whole tissue