title: BPMV-LRR - rep2

description: treatment=BPMV-LRR rep 2 (May still include original submitter created erros/discrepancies)

source_name: The top fully expanded trifoliolate leaves, petioles and stem segments. (treatment: BPMV-LRR)

value: BPMV-LRR

tag: infection


title: Twin Pair ID 16 A-B

status: Public on Oct 20 2012

type: genomic

city: Kobe-shi

first: Chihchieh

last: Yu

address: 7-5-1 kusunoki-cho, chuo-ku

country: Japan

institute: Kobe University

description: twin pair ID 16 enriched in Higher IQ (compared to Lower IQ)

hyb_protocol: Labeled DNA targets were hybridized for 16 hrs at 45C on Human Promoter 1.0R arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400. GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used.

scan_protocol: Promoter chips were scanned using Genechip Scanner 3000.

data_processing: Data were converted to GCOS format and then normalized and analyzed with MAT software. Candidate regions sized around 600bp with p value less than 0.000001 were extracted. Annotation was done using R.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: twin pair ID 16 A

label_protocol: After amplification using WGA2 kit, 7.5ug dsDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: Genomic DNA was extracted from the blood samples using traditional methods. 1ug of gDNA was fragemeted and subjected to methylated DNA enrichment using MethylMiner Methlyated DNA Enrichment Kit (Invitrogen).

tag: twin pair id

tag: twin a or twin b

value: A

tag: relative iq within twin pair

value: Higher


title: twin pair 12_higher IQ

type: RNA

description:
twin 12B
expression profile from Twin Pair ID12, higher IQ twin

hyb_protocol: Following fragmentation, cRNA were hybridized for 17+/-1 hr at 45C on Human Genechip 1.0st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used.

scan_protocol: Gene chips were scanned using Genechip Scanner 3000.

data_processing: The data were analysed using Partek Genomic Suite 6.5 (Agilent). We normalized the data according to the RMA algorithm.

label: Tdt

molecule: total RNA

source_name: twin 12B_Higher_IQ

label_protocol: 300ng of total RNA was processed using Ambion WT expression Kit (Applied Biosystems) and the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: B-lymphoblastoid cell lines were grown in a RPMI-1640 (WAKO) medium and supplemented with 10% FBS (Gibco) and antibiotics (Wako).

extract_protocol: total RNA was isolated using RNeasy Plus Mini Kit (Qiagen)

tag: cell type

value: B-lymphoblastoid cell


title: BPMV empty vector - rep1

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: treatment=BPMV empty vector (R1) (May still include original submitter created erros/discrepancies)

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy soybean scanning protocol

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Glycine max

source_name: The top fully expanded trifoliolate leaves, petioles and stem segments. (treatment: BPMV empty vector)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: germplasm name

tag: tissue

tag: development stage

value: leaf production ('PO:0007133')

tag: growth media

value: not specified

tag: transfection

value: BPMV empty vector

value: soybean rust


title: Twin Pair ID 16 B-A

description: twin pair ID 16 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 16 B

value: B

value: Lower


title: temperature: 42 - cultivar: Sicot 53 - rep2

description:
Plants were acclimated for 4 d at optimal conditions (32/25 oC day/night) in the growth cabinet before initiation of the temperature treatment. For the control (32 oC), cabinet conditions were left unchanged during the treatment period. Due to limited growth cabinet space, plants of a comparative physiological age were transferred to the controlled environment growth cabinet after the control plants had been removed. Well-watered plants were exposed to heat stress by increasing the ambient air temperature to 42 oC (67% RH) during the photoperiod and 25 oC (40 % RH) during the dark period.
The third youngest fully expanded leaf of plants at the first square physiological age was sampled for all experiments. Three leaf tissue samples were collected for each genotype under the ambient or hot growth cabinet (12 samples total) (May still include original submitter created erros/discrepancies)

hyb_protocol: Affymetrix (AGRF)

scan_protocol: Affymetrix (AGRF)

organism: Gossypium hirsutum

source_name: Third youngest fully expanded leaf (temperature: 42 - cultivar: Sicot 53)

label_protocol: Affymetrix (AGRF)

extract_protocol: hot borate RNA extraction protocol

tag: cultivar

value: Sicot 53

value: Third youngest fully expanded leaf

value: all leaf cells

value: vegetative

value: field soil

tag: treatment


title: twin pair 12_lower IQ

description:
twin 12A
expression profile from Twin Pair ID12, lower IQ twin

source_name: twin 12A_Lower_IQ


title: BPMV empty vector - rep2

description: treatment=BPMV empty vector rep 2 (May still include original submitter created erros/discrepancies)

value: The top fully expanded trifoliolate leaves, petioles and stem segments.


title: Twin Pair ID 15 B-A

description: twin pair ID 15 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 15 B


title: temperature: 42 - cultivar: Sicot 53 - rep1


title: temperature: 42 - cultivar: Sicot 53 - rep3


title: twin pair 11_higher IQ

description:
twin 11B
expression profile from Twin Pair ID11, higher IQ twin

source_name: twin 11B_Higher_IQ


title: Twin Pair ID 14 A-B

description: twin pair ID 14 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 14 A


title: twin pair 14_higher IQ

description:
twin 14A
expression profile from Twin Pair ID14, higher IQ twin

source_name: twin 14A_Higher_IQ


title: twin pair 10_lower IQ

description:
twin 10B
expression profile from Twin Pair ID10, lower IQ twin

source_name: twin 10B_Lower_IQ


title: BPMV-LRR - rep1

description: treatment=BPMV-LRR rep 1 (May still include original submitter created erros/discrepancies)


title: Wild type EDL, sample2

status: Public on Oct 21 2012

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: gene expression data from normal wild-type EDL

hyb_protocol: 15 ug of biotin-labeled cRNA was used in a 300 ul hybridization cocktail which included spiked transcript controls.  200 ul of cocktail was loaded onto Affymetrix MOE430 2.0 microarrays (Santa Clara, CA) and hybridized for 16 hr at 45o C with agitation.  Standard post-hybridization washes and double-stain protocols used an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned using a Hewlett Packard Gene Array scanner.

data_processing: Affymetrix GCOS version 1.4 software

organism: Mus musculus

source_name: Wild type EDL muscle

label_protocol: 8 ug of RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first strand cDNA.  After second strand synthesis, double strand cDNA was used in an in vitro transcription reaction to generate biotinylated cRNA, which was purified and fragmented.

extract_protocol: Total RNA was extracted using Trizol (GibcoBRL, Rockville, MD), and the RNA pellets were resuspended at 1 ug RNA/ul DEPC-treated water.  This was followed by a cleanup protocol with a Qiagen (Valencia, CA) RNeasy Total RNA mini kit.

tag: age

value: 19 weeks

tag: strain

value: FVB

tag: genotype/variation

value: wild type


title: temperature: 42 - cultivar: Sicala 45 - rep2

source_name: Third youngest fully expanded leaf (temperature: 42 - cultivar: Sicala 45)

value: Sicala 45


title: twin pair 10_higher IQ

description:
twin 10A
expression profile from Twin Pair ID10, higher IQ twin

source_name: twin 10A_Higher_IQ

value: Higher

value: B-lymphoblastoid cell


title: temperature: 42 - cultivar: Sicala 45 - rep3


title: Twin Pair ID 13 A-B

description: twin pair ID 13 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 13 A

value: A


title: twin pair 9_lower IQ

description:
twin 9B
expression profile from Twin Pair ID9, lower IQ twin

source_name: twin 9B_Lower_IQ


title: Twin Pair ID 12 A-B

description: twin pair ID 12 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 12 A


title: temperature: 42 - cultivar: Sicala 45 - rep1


title: twin pair 11_lower IQ

description:
twin 11A
expression profile from Twin Pair ID11, lower IQ twin

source_name: twin 11A_Lower_IQ


title: Twin Pair ID 12 B-A

description: twin pair ID 12 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 12 B


title: temperature: 32 C - cultivar: Sicot 53 - rep3

source_name: Third youngest fully expanded leaf (temperature: 32 C - cultivar: Sicot 53)


title: Twin Pair ID 11 A-B

description: twin pair ID 11 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 11 A


title: temperature: 32 C - cultivar: Sicot 53 - rep1

description:
Plants were acclimated for 4 d at optimal conditions (32/25 oC day/night) in the growth cabinet before initiation of the temperature treatment. For the control (32 oC), cabinet conditions were left unchanged during the treatment period. Due to limited growth cabinet space, plants of a comparative physiological age were transferred to the controlled environment growth cabinet after the control plants had been removed. Well-watered plants were exposed to heat stress by increasing the ambient air temperature to 42 oC (67% RH) during the photoperiod and 25 oC (40 % RH) during the dark period.
The third youngest fully expanded leaf of plants at the first square physiological age was sampled for all experiments. Three leaf tissue samples were collected for each genotype under the ambient or hot growth cabinet (12 samples total) (May still include original submitter created erros/discrepancies)


title: Twin Pair ID 14 B-A

description: twin pair ID 14 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 14 B


title: Twin Pair ID 11 B-A

description: twin pair ID 11 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 11 B


title: Twin Pair ID 13 B-A

description: twin pair ID 13 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 13 B


title: Twin Pair ID 9 A-B

description: twin pair ID 9 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 9 A


title: Twin Pair ID 15 A-B

description: twin pair ID 15 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 15 A


title: Twin Pair ID 9 B-A

description: twin pair ID 9 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 9 B


title: Twin Pair ID 10 A-B

description: twin pair ID 10 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 10 A


title: Twin Pair ID 7 A-B

description: twin pair ID 7 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 7 A


title: Twin Pair ID 8 A-B

description: twin pair ID 8 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 8 A


title: temperature: 32 C - cultivar: Sicot 53 - rep2


title: Twin Pair ID 8 B-A

description: twin pair ID 8 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 8 B


title: twin pair 9_higher IQ

description:
twin 9A
expression profile from Twin Pair ID9, higher IQ twin

source_name: twin 9A_Higher_IQ


title: Twin Pair ID 7 B-A

description: twin pair ID 7 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 7 B


title: Twin Pair ID 6 B-A

description: twin pair ID 6 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 6 B


title: twin pair 8_higher IQ

description:
twin 8A
expression profile from Twin Pair ID8, higher IQ twin

source_name: twin 8A_Higher_IQ


title: Twin Pair ID 10 B-A

description: twin pair ID 10 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 10 B


title: temperature: 32 C - cultivar: Sicala 45 - rep2

source_name: Third youngest fully expanded leaf (temperature: 32 C - cultivar: Sicala 45)


title: twin pair 8_lower IQ

description:
twin 8B
expression profile from Twin Pair ID8, lower IQ twin

source_name: twin 8B_Lower_IQ


title: Twin Pair ID 5 A-B

description: twin pair ID 5 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 5 A


title: twin pair 7_lower IQ

description:
twin 7B
expression profile from Twin Pair ID7, lower IQ twin

source_name: twin 7B_Lower_IQ


title: temperature: 32 C - cultivar: Sicala 45 - rep3

description:
Plants were acclimated for 4 d at optimal conditions (32/25 oC day/night) in the growth cabinet before initiation of the temperature treatment. For the control (32 oC), cabinet conditions were left unchanged during the treatment period. Due to limited growth cabinet space, plants of a comparative physiological age were transferred to the controlled environment growth cabinet after the control plants had been removed. Well-watered plants were exposed to heat stress by increasing the ambient air temperature to 42 oC (67% RH) during the photoperiod and 25 oC (40 % RH) during the dark period.
The third youngest fully expanded leaf of plants at the first square physiological age was sampled for all experiments. Three leaf tissue samples were collected for each genotype under the ambient or hot growth cabinet (12 samples total) (May still include original submitter created erros/discrepancies)


title: temperature: 32 C - cultivar: Sicala 45 - rep1


title: Twin Pair ID 5 B-A

description: twin pair ID 5 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 5 B


title: twin pair 6_higher IQ

description:
twin 6B
expression profile from Twin Pair ID6, higher IQ twin

source_name: twin 6B_Higher_IQ


title: twin pair 6_lower IQ

description:
twin 6A
expression profile from Twin Pair ID6, lower IQ twin

source_name: twin 6A_Lower_IQ


title: twin pair 7_higher IQ

description:
twin 7A
expression profile from Twin Pair ID7, higher IQ twin

source_name: twin 7A_Higher_IQ


title: Twin Pair ID 6 A-B

description: twin pair ID 6 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 6 A


title: Twin Pair ID 4 B-A

description: twin pair ID 4 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 4 B


title: twin pair 5_higher IQ

description:
twin 5B
expression profile from Twin Pair ID5, higher IQ twin

source_name: twin 5B_Higher_IQ


title: Adult WT heart 3

city: Madrid

first: Lucas

last: Elisa

state: Madrid

address: Nicolas Cabrera 1

department: Molecular Biology

country: Spain

institute: Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)

description:
WT 3
WT_303.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al., 2006). Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini and Hochberg, 1995; Reiner et al., 2003).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The animals were bred and housed on a 12-hour light/dark cycle with free access to food and water.

extract_protocol: frozen heart tissue was lysed using metal beads (2 min, 30 Hz) in a Tissue Lyser (QUIAGEN), and total mRNA was extracted using Fibrous Tissue RNeasy Mini Kit (QIAGEN).Sampled with an adequate RNA quality (Bioanalyzer, Agilent 2100) were selected for analysis.

treatment_protocol: Mice were anesthetized by inhaling isoflurane and hearts were collected after heart arrest in diastole using cold intracardiac KCl injection. Hearts were rinsed with cold PBS and the third upper part was excised and treated with RNA later (QIAGEN) for 16 hours at 4ºC. Then samples were stored at -70ºC untill RNA extraction.

tag: strain background

value: adult_9 months old

value: heart


title: twin pair 5_lower IQ

description:
twin 5A
expression profile from Twin Pair ID5, lower IQ twin

source_name: twin 5A_Lower_IQ


title: Twin Pair ID 4 A-B

description: twin pair ID 4 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 4 A


title: ID_35%tumor

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
ID.35
The ID patient has mosaic aberrations in chromosome 1.

hyb_protocol: Standard Agilent protocol.

scan_protocol: Standard Agilent protocol.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy3 sample in the ''US22502676_252252210311_S01_CGH_105_Dec08_1_1 file.
Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.

source_name: ID 35% tumor diluted with normal DNA

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al., J Pathol. 2007 Jan;211(1):45-51 (PMID 17117405).

tag: disease state

value: intellectual disability

tag: percent id sample

source_name: Reference DNA

tag: sample type

value: pool of 19 healthy individuals


title: Twin Pair ID 3 B-A

description: twin pair ID 3 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 3 B

tag: twin pair id

tag: twin a or twin b

value: B


title: twin pair 4_higher IQ

description:
twin 4A
expression profile from Twin Pair ID4, higher IQ twin

source_name: twin 4A_Higher_IQ

tag: relative iq within twin pair

tag: cell type


title: twin pair 4_lower IQ

description:
twin 4B
expression profile from Twin Pair ID4, lower IQ twin

source_name: twin 4B_Lower_IQ

value: Lower


title: Adult WT heart 2

description:
WT 2
WT_282.CEL

tag: tissue


title: ID_25%tumor

description:
ID.25
The ID patient has mosaic aberrations in chromosome 1.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy5 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_2.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.

source_name: ID 25% tumor diluted with normal DNA


title: Twin Pair ID 3 A-B

description: twin pair ID 3 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 3 A


title: ID_30%tumor

description:
ID.30
The ID patient has mosaic aberrations in chromosome 1.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy3 sample in the ''US22502676_252252210311_S01_CGH_105_Dec08_1_2.txt file.
Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.

source_name: ID 30% tumor diluted with normal DNA


title: Adult GRK2+/- heart 3

description:
GRK2+/- 3
289.CEL

value: B6.129-Adrbk1tm1Mca/J backcrossed more than 20 generations onto C57BL/6J

value: GRK2 heterozygous (GRK2+/-)


title: CLL patient

data_processing: Median normalization in R/Bioconductor.

source_name: CLL patient with mosaic aberrations

value: chronic lymphocytic leukemia (CLL)


title: twin pair 3_higher IQ

description:
twin 3B
expression profile from Twin Pair ID3,higher IQ twin

source_name: twin 3B_Higher_IQ


title: Adult WT heart 1

description:
WT 1
WT_276.CEL


title: ID_20%tumor

description:
ID.20
The ID patient has mosaic aberrations in chromosome 1.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy3 sample in the ''US22502676_252252210311_S01_CGH_105_Dec08_1_3.txt file.
Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.

source_name: ID 20% tumor diluted with normal DNA


title: twin pair 3_lower IQ

description:
twin 3A
expression profile from Twin Pair ID3, lower IQ twin

source_name: twin 3A_Lower_IQ


title: Twin Pair ID 2 A-B

description: twin pair ID 2 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 2 A


title: Twin Pair ID 2 B-A

description: twin pair ID 2 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 2 B


title: ID_10%tumor

description:
ID.10
The ID patient has mosaic aberrations in chromosome 1.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy5 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.

source_name: ID 10% tumor diluted with normal DNA


title: ID_15%tumor

description:
ID.15
The ID patient has mosaic aberrations in chromosome 1.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy5 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_3.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210311_S01_CGH_105_Dec08_1_4.txt' file.

source_name: ID 15% tumor diluted with normal DNA


title: Adult GRK2+/- heart 2

description:
GRK2+/- 2
280.CEL


title: Twin Pair ID 1 B-A

description: twin pair ID 1 enriched in Lower IQ (compared to Higher IQ)

source_name: twin pair ID 1 B


title: Adult GRK2+/- heart 1

description:
GRK2+/- 1
273.CEL


title: twin pair 2_lower IQ

description:
twin 2B
expression profile from Twin Pair ID2, lower IQ twin

source_name: twin 2B_Lower_IQ


title: Twin Pair ID 1 A-B

description: twin pair ID 1 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 1 A


title: BT474_35%tumor

description:
BT474.35
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy5 sample in the ''US22502676_252252210461_S01_CGH_107_Sep09_1_4.txt file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.

source_name: BT474 35% tumor diluted with normal DNA

tag: cell line

value: breast cancer cells

tag: percent tumor cells

source_name: Reference DNA


title: BT474_30%tumor

description:
BT474.30
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy3 sample in the ''US22502676_252252210461_S01_CGH_107_Sep09_1_2.txt file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.

source_name: BT474 30% tumor diluted with normal DNA


title: twin pair 1_higher IQ

description:
twin 1A
expression profile from Twin Pair ID1, higher IQ twin

source_name: twin 1A_Higher_IQ


title: twin pair 2_higher IQ

description:
twin 2A
expression profile from Twin Pair ID2, higher IQ twin

source_name: twin 2A_Higher_IQ


title: BT474_100%tumor

description:
BT474.100
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy5 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_3.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.

source_name: BT474 100% tumor not diluted


title: twin pair 1_lower IQ

description:
twin 1B
expression profile from Twin Pair ID1, lower IQ twin

source_name: twin 1B_Lower_IQ


title: Wild-type-2

city: Chicago

first: Sean

middle: Pravin

last: Pitroda

state: IL

address: 5841 South Maryland Avenue, MC 1105

department: Radiation and Cellular Oncology

institute: The University of Chicago

description: Tumor-associated endothelial cells derived from B16F1 melanoma tumors grown in C57BL/6 (wild-type) mouse, untreated, technical replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

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 750.

source_name: Tumor-associated endothelial cells from B16F1 melanoma tumor grown in  C57BL/6 mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: B16-F1 murine melanoma cells were cultured in RPMI 1640 medium. Tumor culture media was purchased from Invitrogen (Carlsbad, CA) and supplemented with 10% fetal calf serum (Atlanta Biologicals; Lawrenceville, GA) and 1% penicillin/ streptomycin (Invitrogen). Cell cultures were maintained at 37 °C in a humidified environment containing 5% CO2. C57BL/6 (C57BL/6-NCr) wild-type mice were obtained from FCRI-Taconic (Germantown, NY). TNFR 1, 2 -/- (B6;129S-Tnfrsf1a[tm1Imx]Tnfrsf1b[tm1Imx]/J) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16-F1 tumors were established following subcutaneous injection of 1-2x106 cells in 100 μl of phosphate-buffered saline (PBS) into the right hind limbs of WT and KO mice. At the start of each tumor experiment (day 0 corresponding to 10 days post-injection) the mean tumor volume of B16-F1 tumors was equal in WT and KO mice (mean initial tumor volume (V0) ± S.E.M.; WT: 144 ± 44 mm3; KO: 209 ± 11 mm3; p = 0.19, 2-tailed Student’s t- test). Tumor volume was determined by direct measurement with calipers and estimated by using the formula (length x width x depth/2). Mice were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumor endothelial cells were isolated from day 0 WT (n = 15) and KO (n = 13) tumors when tumor volumes were equal. This process was based on a stepwise immunopurification (Seaman, S. et al. Genes that distinguish physiological and pathological angiogenesis. Cancer Cell 11, 539-54 (2007)) of tumor tissue that had been pooled, minced and dissociated at 37 °C with 2 mg/ml of collagenase A in PBS (Roche; Indianapolis, IN) for 1 hour. Cells were filtered through 100 µm and 25 µm mesh nylon filter fabric and pelleted in PBS with 0.5% bovine serum albumin (BSA) at 1000 x g for 5 minutes at 4 °C. Centrifugation was repeated until the supernatant was transparent (8-12 times). All subsequent steps were carried out on ice or at 4 °C. Samples were cleared of hematopoietic cells by incubation for 30 minutes at 4 °C with a 1:1:1 mixture of biotin anti-CD19, biotin anti-CD45 and biotin anti-F4/80, which had been separately pre-bound to streptavidin-linked dynabeads (Dynal; Lake Success, NY), followed by removal of the bead-bound cells with a Dynal-50 magnet. Fc-Block (anti-CD16/32 antibodies) (BD-Pharmingen; San Diego, CA) was added to the cell suspension to prevent non-specific binding of Fc-receptor containing cells in the positive selection. After an additional 30 minutes of 4 °C incubation, anti-VE cadherin and anti-CD105 antibodies were added to bind the endothelial cells. Following 30 minutes of 4 °C incubation, the cell suspension was washed 5 times with PBS/BSA. Streptavidin-linked dynabeads were added to the cell suspension, rotated for 5 minutes at 4 °C, captured with the Dynal-50 magnet, and washed 5-10 times with PBS/BSA until only bead-bound cells remained. Cells were then washed twice with complete media (RPMI 1640 with 10% FCS) with 1% penicillin/streptomycin and 1 µg/ml Fungizone (E.R. Squibb & Sons; Princeton, NJ) and resuspended in the same media. Cells were rested in culture at 37 °C and 5% CO2 for 1 hour before RNA isolation.

extract_protocol: RNA was collected and purified from confluent WT and KO tumor endothelial cell cultures using TRIzol reagent according to the manufacturer’s recommendations (Invitrogen). The quality of samples was assessed by using gel electrophoresis in 1.8% agarose and spectrophotometry. Samples of high quality were transferred to the Functional Genomics Facility of The University of Chicago for labeling and hybridization in duplicates with Affymetrix GeneChip® Mouse Genome 430 2.0 arrays.

tag: background strain

tag: tumor type

value: B16F1 melanoma

value: tumor endothelial cells


title: BT474_25%tumor

description:
BT474.25
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_3.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.

source_name: BT474 25% tumor diluted with normal DNA


title: Knockout-1

description: Tumor-associated endothelial cells derived from B16F1 melanoma tumors grown in TNFR 1, 2 -/- (knockout) mouse, untreated, technical replicate 1

source_name: Tumor-associated endothelial cells from B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse


title: Mosaic sample of a patient diagnosed with ID

description:
ID_patient
The ID sample has a single copy number gain of 4Mb and a single copy number loss of 7.5Mb.

source_name: Blood from ID patient

value: blood

value: intellectual disability (ID)


title: Knockout-2

description: Tumor-associated endothelial cells derived from B16F1 melanoma tumors grown in TNFR 1, 2 -/- (knockout) mouse, untreated, technical replicate 2


title: Wild-type-1

description: Tumor-associated endothelial cells derived from B16F1 melanoma tumors grown in C57BL/6 (wild-type) mouse, untreated, technical replicate 1

value: wild type


title: BT474_15%tumor

description:
BT474.15
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_4.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.

source_name: BT474 15% tumor diluted with normal DNA


title: BT474_20%tumor

description:
BT474.20
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy5 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_2.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.

source_name: BT474 20% tumor diluted with normal DNA


title: BT474_10%tumor

description:
BT474.10
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.

data_processing:
Median normalization in R/Bioconductor.

Raw data files:
Test: Cy5 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.

source_name: BT474 10% tumor diluted with normal DNA


title: Lung_WT 4_rep1

status: Public on Oct 19 2012

city: Pittsburgh

first: John

middle: F

last: Alcorn

state: PA

address: 4401 Penn Ave

department: Pediatrics

institute: Children's Hospital of Pittsburgh

description: WildType Biological replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was median normalized using Cancer Gene Expression Data Analysis Tool (caGEDA), a software developed by Dr. James Lyons-Weiler [http://www.ncbi.nlm.nih.gov/pubmed/16323966].

label: Biotin

source_name: WildType Biological replicate 4

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit

extract_protocol: RNA was isolated using an Agilent Absolutely RNA Miniprep Kit.

treatment_protocol: Mice were infected with 125 pfu of influenza A/PR/8/34 by oropharyngeal aspiration, lung tissue was harvested 21 days later.

tag: Sex

value: Male

value: Lung


title: Lung_WT 2_rep1

description: WildType Biological replicate 2

source_name: WildType Biological replicate 2


title: Lung_IL-22 KO 3_rep2

description: KO Biological replicate 3

source_name: KO Biological replicate 3

value: IL-22 KO


title: Lung_WT 1_rep1

description: WildType Biological replicate 1

source_name: WildType Biological replicate 1


title: Lung_IL-22 KO 3_rep1

description: KO Biological replicate 3


title: Lung_IL-22 KO 1_rep1

description: KO Biological replicate 1

source_name: KO Biological replicate 1


title: Lung_IL-22 KO 4_rep1

description: KO Biological replicate 4

source_name: KO Biological replicate 4


title: Lung_WT 4_rep2

description: WildType Biological replicate 4


title: Lung_IL-22 KO 2_rep1

description: KO Biological replicate 2

source_name: KO Biological replicate 2


title: Lung_WT 3_rep1

description: WildType Biological replicate 3

source_name: WildType Biological replicate 3


title: Lung_IL-22 KO 1_rep2

description: KO Biological replicate 1


title: Lung_IL-22 KO 2_rep2

description: KO Biological replicate 2


title: Lung_WT 2_rep2

description: WildType Biological replicate 2


title: Lung_WT 1_rep2

description: WildType Biological replicate 1


title: Lung_WT 3_rep2

description: WildType Biological replicate 3


title: Tyrphostin-treated at 24 h

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

hyb_protocol: Labeled cRNA is hybridized to oligonucleotide microarrays using Affymetrix fluidics station.

scan_protocol: Arrays are washed, stained with anti-biotin streptavidin-phycoerythrin labeled antibody and scanned using the GeneChip system (Hewlett-Packard).

data_processing: GeneChip 3.0 software to determine the expression of each gene. Algorithm: ExpressionStat 5.0

source_name: Keratinocytes cultured from foreskin

label_protocol: Five micrograms of total RNA is reverse transcribed, amplified and labeled as described in Affymetrix protocols.

growth_protocol: Keratinocyte SFM Gibco with EGF, bovine pituitary extract, pen/strep

extract_protocol: From a plate of cultured keratinocytes, total RNA was isolated using 10 ml of Triazol (Invitrogen Life Technologies, Carlsbad, CA), which was followed by RNeasy kits procedure (Qiagen, Chatsworth, CA) according to manufacturer's instruction. DNA was removed with on-column DNase digestion using a Qiagen RNAses-free DNase kit. To ensure good RNA quality, 28S and 18S ribosomal bands are visualized on a non-denaturing agarose gel and OD260/280 spectrophotometric ratio of at least 1.8 is ascertained.

treatment_protocol: Addition of AG1478

tag: time point

tag: treatment


title: Tyrphostin-treated at 4 h

value: 4 h


title: Control culture at 24 h


title: Control culture at 48 h


title: Tyrphostin-treated at 48 h


title: seedlings-4.4-5_2w

city: beijing

first: Jinsong

last: Zhang

address: No.1 West Beichen Road,Chaoyang District

country: China

institute: IGDB

description: Gene expression of seedling

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arabidopsis Oligo Microarray (4X44K). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

source_name: seedling, 2 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Col-0 and AtDOF4.4-overexpressing transgenic lines 4.4-1 and 4.4-5 growed for two weeks on MS

extract_protocol: Two-week-old seedlings (aerial part) of Col-0 and AtDOF4.4-overexpressing transgenic lines 4.4-1 and 4.4-5, grown on MS, were used for extraction of total RNA and subjected to chip analysis using Agilent Arabidopsis Oligo Microarray (4X44K) in SHANGHAIBIO CORPORATION (www.ebioservice.com; Shanghai, China).

value: seedling

tag: cultivar

tag: genotype/variation

value: AtDOF4.4-overexpressing transgenic line 4.4-5


title: seedlings-4.4-1_2w

description: Gene expression of seedling

value: AtDOF4.4-overexpressing transgenic line 4.4-1


title: Tyrphostin-treated at 1 h

value: 1 h


title: Lung_IL-22 KO 4 _rep2

description: KO Biological replicate 4

tag: strain


title: seedlings-col-0_2w

description: Gene expression of seedling


title: Control culture at 4 h


title: iPS #3 for individual 03-01

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

hyb_protocol: Standard Illumina hybridization protocol  Standard Illumina scanning protocol

data_processing: The data was  analyzed by GenomeStudio using quantile normalization and background subtraction.

source_name: iPSC

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

growth_protocol: iPSCs and hES were mantained on matrigel coated plates in DMEM/F12 media containing 1% N2 supplement, 2% B27 supplement, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1% penicillin/ streptomycin, 0.5 mg/mL BSA Fraction V, 0.12 mM monothioglycerol and supplemented with 80ng/mL FGF2. Colonies were passed using dispase.

extract_protocol:
Total RNA was isolated using PicoPure RNA
 isolation kit (Arcturus).  Quality control was performed with Agilent Bioanalyser.

value: iPSC

tag: donor's  gender

value: male

tag: donor's age

value: 43 years old

tag: cell passage number


title: iPS #9 for individual 03-02

value: female


title: iPS #9 for individual 03-01


title: iPS #5 for individual 03-02


title: neuronal differentiation at day 50 induced in low FGF for iPS PGP1-1

source_name: neuronal differentiation at day 50

treatment_protocol: Three-dimensional cell aggregates known as SFEBq were generated according to Eiraku et al. (2008) Cell Stem Cell 3(5):519-532; with some modifications as described in the SI Materials and Methods section of Mariani et al. (2012) Proc Natl Acad Sci U S A. 109(31):12770-5

tag: fgf2 concentration

value: 5 ng/mL


title: neuronal differentiation at day 50 induced in high FGF for iPS 03-01#9 replicate 1

value: 20 ng/mL


title: iPS #5 for individual 03-04

value: 6 years old


title: iPSC PGP1-1 replicate 1

value: 80 ng/mL


title: iPS #8 for individual 03-02


title: iPS #2 for individual 03-03

value: 8 years old


title: iPS #3 for individual 03-04


title: neuronal differentiation at day 50 induced in high FGF for iPS PGP1-1


title: iPS #6 for individual 03-04


title: iPS #9 for individual 03-01 (2)


title: iPS #9 for individual S1123-03

value: 16 years old


title: neuronal differentiation at day 50 induced in low FGF for iPS 03-01#9 replicate 2


title: iPS #2B for individual 03-02


title: iPS #4 for individual 03-03


title: iPS #3 for individual 03-03


title: iPS #1 for individual 03-04


title: PGP1-1 replicate 1 (control iPSC)

value: 55 years old


title: neuronal differentiation at day 50 induced in high FGF for iPS 03-01#9 replicate 2


title: iPSC PGP1-1 replicate 2


title: neuronal differentiation at day 50 induced in low FGF for iPS 03-01#9 replicate 1


title: hES H1

source_name: hES

value: hES


title: iPS #2 for individual S1123-02

value: 56 years old


title: iPS #4 for individual 03-01


title: iPS #2 for individual 03-01


title: PGP1-1 replicate 2  (control iPSC)


title: iPS #8 for individual S1123-03


title: Pineal_DD_CT18b

city: Tel Aviv

first: Shahar

last: Alon

address: Tel Aviv University

department: Department of Neurobiology, The George S. Wise Faculty of Life Sciences

country: Israel

institute: Tel Aviv University

description: Gene expression data from zebrafish pineal glands

hyb_protocol: The target cRNA generated from each sample was fragmented and 15 micogram of the fragmented cRNA was added to the hybridization cocktail which includes in addition to the fragmented target, probe array controls (pre-mixed biotin-labeled bioB, bioC, bioD and cre, in staggered concentrations, ready to be added directly to the hybridization cocktail. These controls facilitate monitoring of the hybridization process for troubleshooting), BSA, and herring sperm DNA. It was then hybridized to the probe array during a 16-hour incubation at 45 deg (C). The array was then washed and stained on the Affymetrix fluidic station (using Streptavidin-Phycoerythrin which binds to the biotinylated UTP and CTP incorporated previously in the hybridized cRNA).

scan_protocol: The stained array was scanned on the Affymetrix scanner (450).

data_processing: The GCOS (Gene Operating System) generates the numerical data from the scanned intensities using the MAS 5 software (MicroArray suite 5.0; Affymetrix).

organism: Danio rerio

source_name: pineal glands at CT18b, constant darkness

label_protocol: Double-strand cDNA was generated from 10-100 ng of mRNA by using a T7-linked oligo(dT) primer (Affymetrix). After second-strand synthesis, in vitro transcription was performed with MEGAscript® T7 Kit (Ambion, Inc.). The cRNA (600ng) was then used for second cycle first-strand cDNA (Affymetrix) by using a T7-linked oligo(dT) primer (Affymetrix). After 2nd cycle - second-strand synthesis, in vitro transcription was again performed; this time biotinylated UTP and CTP (Affymetrix) were incorporated in the cRNA, resulting in approximately 1800-fold amplification of labeled RNA.

growth_protocol: Adult zebrafish were raised in a light- and temperature-controlled recirculation water system under a 12-h light/12-h dark cycle at 28 °C and fed twice a day.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, Qiagen).

treatment_protocol: Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. 12 pineal glands were collected and pooled at each time point.

value: pineal gland

tag: gender

value: males and females

tag: age

value: adult (0.5-1.5 years old)

value: Tg(aanat2:EGFP)Y8 transgenic zebrafish


title: Pineal_DD_CT10b

source_name: pineal glands at CT10b, constant darkness

tag: tissue


title: iPS #2 for individual S1123-03

tag: cell type

value: iPSC


title: Pineal_DD_CT22b

source_name: pineal glands at CT22b, constant darkness


title: K3 (control iPS)

value: male

value: newborn


title: Human_Prostate_Cellline_LNCaP_5mikroM_SiomycinA_treatment_48h_1

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

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

data_processing: Data processing was done using open source statistical tool lumi package from Bioconductor. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated. Finally data was transformed using quantile normalization.

label_protocol: Total RNA was prepared for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina) according to manufacturer's recommendations. In brief, 250 ng total RNA was used for cDNA synthesis, followed by the generation of biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion).

growth_protocol: The human prostate cancer cell line PC3 and LNCaP were purchased from ATCC (Manassas) and cultured in RPMI 1640 or HAMs F12 medium, respectively. The medium was supplemented with 50 units/ml penicillin, 50 μg/ml streptomycin sulphate, 1% nonessential amino acids, and 10% FBS (Invitrogen). Multiplex human cell line authentification was done at the DKFZ institute core facility based on specific STR-pattern.

extract_protocol: Total RNA from cell lines was isolated using Rneasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: PC3 and LNCaP cells were cultured overnight in 6 well plates (1.0 x 10^5 cells) , and treated for 24h and 48h with either 0.5 microM Siomycin A or DMSO as control.

tag: cell line

value: LNCaP

value: human prostate cancer cell line


title: iPS #2 for individual S1123-01

value: 53 years old


title: Human_Prostate_Cellline_LNCaP_5mikroM_SiomycinA_treatment_48h_2


title: Pineal_DD_CT2b

source_name: pineal glands at CT2b, constant darkness


title: iPS #5 for individual S1123-02

value: female


title: Pineal_DD_CT6b

source_name: pineal glands at CT6b, constant darkness


title: iPS #1 for individual S1123-03


title: Human_Prostate_Cellline_LNCaP_DMSO_control_24h_2


title: Human_Prostate_Cellline_LNCaP_5mikroM_SiomycinA_treatment_24h_3


title: Human_Prostate_Cellline_LNCaP_DMSO_control_48h_3


title: iPS #1 for individual S1123-01


title: iPS #3 for individual S1123-01


title: hES H1 (control)

value: embryonic


title: Human_Prostate_Cellline_LNCaP_5mikroM_SiomycinA_treatment_24h_1


title: Human_Prostate_Cellline_LNCaP_DMSO_control_48h_2


title: iPS #11 for individual S1123-02


title: Control culture at 1 h

value: 1 h


title: Human_Prostate_Cellline_LNCaP_5mikroM_SiomycinA_treatment_48h_3


title: Human_Prostate_Cellline_LNCaP_DMSO_control_48h_1


title: iPS #17 for individual S1123-02


title: iPS #4 for individual S1123-01


title: Human_Prostate_Cellline_LNCaP_DMSO_control_24h_3


title: Human_Prostate_Cellline_LNCaP_5mikroM_SiomycinA_treatment_24h_2


title: Human_Prostate_Cellline_LNCaP_DMSO_control_24h_1


title: Human_Prostate_Cellline_PC3_5mikroM_SiomycinA_treatment_48h_1


title: Pineal_DD_CT22

source_name: pineal glands at CT22, constant darkness


title: Human_Prostate_Cellline_PC3_5mikroM_SiomycinA_treatment_48h_2


title: Human_Prostate_Cellline_PC3_DMSO_control_48h_3


title: Pineal_DD_CT14

source_name: pineal glands at CT14, constant darkness


title: Pineal_DD_CT6

source_name: pineal glands at CT6, constant darkness


title: Human_Prostate_Cellline_PC3_5mikroM_SiomycinA_treatment_48h_3


title: Human_Prostate_Cellline_PC3_DMSO_control_48h_2


title: Human_Prostate_Cellline_PC3_DMSO_control_24h_3


title: Pineal_DD_CT18

source_name: pineal glands at CT18, constant darkness


title: Human_Prostate_Cellline_PC3_5mikroM_SiomycinA_treatment_24h_3


title: Pineal_DD_CT2

source_name: pineal glands at CT2, constant darkness


title: Human_Prostate_Cellline_PC3_DMSO_control_48h_1


title: Human_Prostate_Cellline_PC3_5mikroM_SiomycinA_treatment_24h_1


title: Human_Prostate_Cellline_PC3_DMSO_control_24h_2


title: Human_Prostate_Cellline_PC3_5mikroM_SiomycinA_treatment_24h_2


title: Human_Prostate_Cellline_PC3_knockdown_UBE2C_2

label_protocol: Total RNA was prepared for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina) according to manufacturer’s recommendations. In brief, 250 ng total RNA was used for cDNA synthesis, followed by the generation of biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion).

treatment_protocol: PC3 and LNCaP cells were cultured overnight in 6 well plates (1.0 x 10^5 cells) , and transfected using HiPerfect (Qiagen) and 50nM siRNA ON-Target pools including four different siRNAs for MELK and UBE2C (Thermo Scientific), and the All Stars negative control siRNA (Qiagen).

value: prostate cancer cells

value: RNAi-based inhibition of UBE2C


title: Human_Prostate_Cellline_PC3_knockdown_UBE2C_3


title: Pineal_DD_CT10

source_name: pineal glands at CT10, constant darkness


title: Human_Prostate_Cellline_PC3_DMSO_control_24h_1


title: Human_Prostate_Cellline_PC3_knockdown_UBE2C_1


title: Human_Prostate_Cellline_PC3_knockdown_MELK_3

value: RNAi-based inhibition of MELK


title: Pineal_DD_CT14b

source_name: pineal glands at CT14b, constant darkness


title: Human_Prostate_Cellline_PC3_knockdown_MELK_2


title: genomic DNA from whole blood 3

city: Los Angeles

first: Steve

last: Horvath

state: CA

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

department: Human Genetics

institute: University of California, Los Angeles

description: normal whole blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2. The raw data (non-normalized Unmethylated and Methylated signal intensities) are not available.

label: Cy3, Cy5

source_name: whole blood 3

label_protocol: Standard Illumina Protocol

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

value: Male

tag: sample type

value: whole blood

tag: plate

value: PLATE A

tag: sentrix barcode

tag: sentrix position

tag: well id

tag: diseasestatus (1=control, 2=scz patient)

value: yes


title: BHI-KO-60-B2b

city: Philadelphia

first: Benjamin

last: Janto

department: Microbiology & Immunology

institute: Drexel University College of Medicine

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

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

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

data_processing: Raw data (.pair file) was edited to remove subclusters (genes) that are not present in Haemophilus influenzae CZ4126/02 by merging it with a list of subclusters known to be present in CZ4126/02. The CZ4126/02-relevant data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Haemophilus influenzae

source_name: H. influenzae CZ4126/02 ΔLsr::Cmr, BHI, 60min after ODA600 0.75

label_protocol: Labeling of cDNA was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Haemophilus influenzae CZ4126/02 and Haemophilus influenzae CZ4126/02ΔLsr::Cmr were grown in either BHI or CDM (Coleman et al. J Clin Microbiol. 41 (9), 4408-10) to various culture densities using an inoculum from an overnight culture grown in BHI. 40 mL cultures were incubated at 37°C with shaking at 200 rpm.

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Plus kit with the standard protocol with gDNA eliminator columns. Eluted RNA (~85 µL) was DNased by adding 10 µL 10X TurboDNase buffer and 5 µL TurboDNase (2 units/µL) (Ambion) and incubating at 37 °C for 1.5 hours. 2 µL more TurboDNase was added and incubation was continued for an additional 1.5 hours. DNased RNA samples were cleaned by passing the samples through the RNeasy protocol a second time (with gDNA eliminator steps). Samples were eluted in nuclease-free (n.f.) water, quantitated on a NanoDrop 1000 spectrophotometer and stored at -80 °C. First- and second-strand cDNA synthesis was performed using a SuperScript® One-Cycle cDNA Kit (Invitrogen) as outlined in the NimbleGen Microarray Experienced User's Guide including RNase A and cDNA precipitation steps.

treatment_protocol: 2 mL of culture was diluted in 4 mL RNAProtect (Qiagen) and stored at RT for 10 minutes, then 4 °C overnight. Samples were pelleted, the supernatant removed and the cell pellets resuspended in 100 µL of 1X Tris-EDTA (TE) + 1 mg/mL lysozyme (Worthington Biochemical) and 1 mg/mL proteinase K (Qiagen).

tag: strain/background

tag: genotype

tag: growth medium

value: brain-heart infusion (BHI)

tag: sampling time

value: 60 minutes after ODA600 0.75

tag: biological replicate

tag: technical replicate

tag: probe set


title: BHI-KO-60-B2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: BHI-KO-60-B1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Cellline_PC3_knockdown_control_Allstar_1

tag: genotype/variation

value: control


title: Human_Prostate_Cellline_PC3_knockdown_control_Allstar_2


title: BHI-KO-60-B1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Cellline_PC3_knockdown_MELK_1


title: Human_Prostate_Cellline_PC3_knockdown_control_Allstar_3


title: BHI-KO-60-A2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: genomic DNA from whole blood 1

description: normal whole blood sample

source_name: whole blood 1

tag: gender

tag: age


title: genomic DNA from whole blood 4

description: normal whole blood sample

source_name: whole blood 4


title: genomic DNA from whole blood 93

description: normal whole blood sample

source_name: whole blood 93

value: Female


title: BHI-WT-60-B1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

source_name: H. influenzae CZ4126/02 wild-type, BHI, 60min after ODA600 0.75

value: wild-type


title: genomic DNA from whole blood 5

description: normal whole blood sample

source_name: whole blood 5


title: genomic DNA from whole blood 94

description: normal whole blood sample

source_name: whole blood 94


title: BHI-WT-60-B1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: BHI-WT-60-A2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: BHI-KO-60-A2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: BHI-WT-60-B2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: genomic DNA from whole blood 95

description: normal whole blood sample

source_name: whole blood 95


title: BHI-WT-60-B2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: BHI-KO-60-A1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: genomic DNA from whole blood 92

description: normal whole blood sample

source_name: whole blood 92


title: genomic DNA from whole blood 84

description: normal whole blood sample

source_name: whole blood 84


title: genomic DNA from whole blood 2

description: normal whole blood sample

source_name: whole blood 2


title: BHI-KO-60-A1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: BHI-WT-60-A2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: genomic DNA from whole blood 88

description: normal whole blood sample

source_name: whole blood 88


title: genomic DNA from whole blood 87

description: normal whole blood sample

source_name: whole blood 87


title: genomic DNA from whole blood 91

description: normal whole blood sample

source_name: whole blood 91


title: genomic DNA from whole blood 90

description: normal whole blood sample

source_name: whole blood 90


title: genomic DNA from whole blood 83

description: normal whole blood sample

source_name: whole blood 83


title: BHI-KO-30-B2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 ΔLsr::Cmr, BHI, 30min after ODA600 0.75

value: 30 minutes after ODA600 0.75


title: BHI-WT-60-A1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: BHI-KO-30-B2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: BHI-KO-30-B1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: BHI-WT-60-A1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: genomic DNA from whole blood 86

description: normal whole blood sample

source_name: whole blood 86


title: genomic DNA from whole blood 85

description: normal whole blood sample

source_name: whole blood 85


title: genomic DNA from whole blood 82

description: normal whole blood sample

source_name: whole blood 82


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_109

growth_protocol: Frozen (n=98) prostate tumor and benign tissue samples were obtained from previously untreated patients, who had undergone radical prostatectomy after tumor diagnosis in a PSA based screening program performed in Tyrol by the Department of Urology, Medical University of Innsbruck (15). The study was approved by the ethics committee at the Medical University of Innsbruck. Immediately after surgery, the prostate specimens were rapidly processed for histopathological analysis and stored as either snap-frozen or fixed, paraffin-embedded tissue. Tissue samples were isolated from a cohort with Gleason scores (GS) between 6 and 10. Two subgroups were defined as low- (GS ≤ 3+4) and high-risk (GS ≥ 4+3). Apart from tumor foci, the corresponding benign tissue was collected from a subset of the same specimens. All tumor and benign areas were assigned by an experienced uropathologist, and tissue samples were isolated by macrodissection from 10µm cryo- or FFPE sections.

extract_protocol: Total RNA from frozen prostate tissues was isolated using EZ1 RNA Mini Kit (Qiagen) according to the manufacturer's instructions, quality checked by the Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified.

tag: tissue

value: prostate

tag: disease stage

value: Benign

tag: gleason pattern group


title: genomic DNA from whole blood 89

description: normal whole blood sample

source_name: whole blood 89

tag: sample type

tag: plate

tag: sentrix barcode


title: genomic DNA from whole blood 81

description: normal whole blood sample

source_name: whole blood 81

tag: sentrix position

tag: well id

tag: diseasestatus (1=control, 2=scz patient)


title: BHI-KO-30-B1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: strain/background

tag: genotype

tag: growth medium


title: BHI-KO-30-A2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: sampling time

tag: biological replicate

tag: technical replicate


title: BHI-KO-30-A2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

tag: probe set


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_105


title: genomic DNA from whole blood 77

description: normal whole blood sample

source_name: whole blood 77

tag: gender

tag: age


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_108

tag: tissue

tag: disease stage

value: Cancer

value: high


title: BHI-KO-30-A1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: genomic DNA from whole blood 76

description: normal whole blood sample

source_name: whole blood 76

tag: sample type


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_107

tag: gleason pattern group


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_104


title: genomic DNA from whole blood 79

description: normal whole blood sample

source_name: whole blood 79

tag: plate

tag: sentrix barcode


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_101

value: low


title: genomic DNA from whole blood 70

description: normal whole blood sample

source_name: whole blood 70

tag: sentrix position

tag: well id


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_106


title: genomic DNA from whole blood 75

description: normal whole blood sample

source_name: whole blood 75

tag: diseasestatus (1=control, 2=scz patient)


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_103


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_102


title: BHI-KO-30-A1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: strain/background

tag: genotype


title: genomic DNA from whole blood 69

description: normal whole blood sample

source_name: whole blood 69


title: genomic DNA from whole blood 73

description: normal whole blood sample

source_name: whole blood 73


title: BHI-WT-30-B2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 wild-type, BHI, 30min after ODA600 0.75

tag: growth medium

tag: sampling time


title: genomic DNA from whole blood 74

description: normal whole blood sample

source_name: whole blood 74


title: BHI-WT-30-B2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: biological replicate

tag: technical replicate


title: genomic DNA from whole blood 78

description: normal whole blood sample

source_name: whole blood 78

tag: gender


title: genomic DNA from whole blood 71

description: normal whole blood sample

source_name: whole blood 71

tag: age


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_100

tag: tissue


title: genomic DNA from whole blood 80

description: normal whole blood sample

source_name: whole blood 80


title: BHI-WT-30-B1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

tag: probe set


title: genomic DNA from whole blood 72

description: normal whole blood sample

source_name: whole blood 72

tag: sample type

value: no


title: genomic DNA from whole blood 68

description: normal whole blood sample

source_name: whole blood 68


title: BHI-WT-30-B1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_93

tag: disease stage

tag: gleason pattern group


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_99


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_97


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_96


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_95


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_94


title: genomic DNA from whole blood 67

description: normal whole blood sample

source_name: whole blood 67

tag: plate

tag: sentrix barcode


title: BHI-WT-30-A2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_92


title: BHI-WT-30-A1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_91


title: BHI-WT-30-A1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: genomic DNA from whole blood 66

description: normal whole blood sample

source_name: whole blood 66

tag: sentrix position

tag: well id


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_87


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_86


title: genomic DNA from whole blood 63

description: normal whole blood sample

source_name: whole blood 63

tag: diseasestatus (1=control, 2=scz patient)


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_89


title: genomic DNA from whole blood 64

description: normal whole blood sample

source_name: whole blood 64


title: genomic DNA from whole blood 60

description: normal whole blood sample

source_name: whole blood 60


title: CDM-KO-60-B2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 ΔLsr::Cmr, CDM, 60min after ODA600 0.75

tag: strain/background

tag: genotype

value: chemically-defined media (CDM)


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_90


title: genomic DNA from whole blood 61

description: normal whole blood sample

source_name: whole blood 61

value: Male


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_84


title: CDM-KO-60-B2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: growth medium

tag: sampling time


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_85


title: genomic DNA from whole blood 65

description: normal whole blood sample

source_name: whole blood 65

value: whole blood


title: genomic DNA from whole blood 62

description: normal whole blood sample

source_name: whole blood 62

value: PLATE A


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_79


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_80


title: CDM-KO-60-B1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

tag: biological replicate

tag: technical replicate


title: CDM-KO-60-B1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_82


title: genomic DNA from whole blood 59

description: normal whole blood sample

source_name: whole blood 59

tag: gender

tag: age

value: yes


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_78

tag: tissue


title: CDM-KO-60-A2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

tag: probe set


title: genomic DNA from whole blood 57

description: normal whole blood sample

source_name: whole blood 57

tag: sample type


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_81

tag: disease stage

tag: gleason pattern group


title: genomic DNA from whole blood 58

description: normal whole blood sample

source_name: whole blood 58

tag: plate

tag: sentrix barcode


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_77


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_75


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_83


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_73


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_76


title: BHI-WT-30-A2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in brain-heart infusion media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 wild-type, BHI, 30min after ODA600 0.75

value: brain-heart infusion (BHI)


title: CDM-KO-60-A1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

value: 60 minutes after ODA600 0.75


title: genomic DNA from whole blood 54

description: normal whole blood sample

source_name: whole blood 54

tag: sentrix position

tag: well id


title: genomic DNA from whole blood 56

description: normal whole blood sample

source_name: whole blood 56

tag: diseasestatus (1=control, 2=scz patient)


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_70


title: CDM-KO-60-A2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: strain/background

tag: genotype


title: genomic DNA from whole blood 55

description: normal whole blood sample

source_name: whole blood 55


title: genomic DNA from whole blood 53

description: normal whole blood sample

source_name: whole blood 53


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_72


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_71


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_98


title: CDM-WT-60-B2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 wild-type, CDM, 60min after ODA600 0.75

tag: growth medium

tag: sampling time


title: CDM-KO-60-A1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 60 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: biological replicate

tag: technical replicate


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_69


title: CDM-WT-60-B2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_67


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_88


title: CDM-WT-60-B1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_65


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_64


title: genomic DNA from whole blood 52

description: normal whole blood sample

source_name: whole blood 52

tag: gender

tag: age


title: genomic DNA from whole blood 51

description: normal whole blood sample

source_name: whole blood 51


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_62

tag: tissue


title: genomic DNA from whole blood 50

description: normal whole blood sample

source_name: whole blood 50

tag: sample type


title: CDM-WT-60-B1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: probe set


title: CDM-WT-60-A2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_61

tag: disease stage

tag: gleason pattern group


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_60


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_68


title: genomic DNA from whole blood 49

description: normal whole blood sample

source_name: whole blood 49

tag: plate

tag: sentrix barcode


title: CDM-WT-60-A2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_56


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_54


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_57


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_58


title: CDM-WT-60-A1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: genomic DNA from whole blood 48

description: normal whole blood sample

source_name: whole blood 48

tag: sentrix position

tag: well id


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_53


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_74


title: genomic DNA from whole blood 46

description: normal whole blood sample

source_name: whole blood 46

tag: diseasestatus (1=control, 2=scz patient)


title: CDM-WT-60-A1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 60 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: strain/background

tag: genotype


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_50


title: CDM-KO-30-B2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 ΔLsr::Cmr, CDM, 30min after ODA600 0.75

tag: growth medium

tag: sampling time


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_52


title: genomic DNA from whole blood 47

description: normal whole blood sample

source_name: whole blood 47


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_51


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_48


title: CDM-KO-30-B2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: biological replicate

tag: technical replicate


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_49


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_63


title: genomic DNA from whole blood 45

description: normal whole blood sample

source_name: whole blood 45

tag: gender

tag: age


title: CDM-KO-30-B1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: CDM-KO-30-A2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_45

tag: tissue


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_44


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_46


title: genomic DNA from whole blood 42

description: normal whole blood sample

source_name: whole blood 42

tag: sample type


title: CDM-KO-30-A2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: probe set


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_40

tag: disease stage

tag: gleason pattern group


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_41


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_39


title: genomic DNA from whole blood 43

description: normal whole blood sample

source_name: whole blood 43

tag: plate

tag: sentrix barcode


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_43


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_37


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_36


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_38


title: CDM-KO-30-A1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_47


title: genomic DNA from whole blood 40

description: normal whole blood sample

source_name: whole blood 40

tag: sentrix position

tag: well id


title: genomic DNA from whole blood 44

description: normal whole blood sample

source_name: whole blood 44

tag: diseasestatus (1=control, 2=scz patient)


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_34


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_35


title: genomic DNA from whole blood 41

description: normal whole blood sample

source_name: whole blood 41


title: CDM-KO-30-A1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: strain/background

tag: genotype


title: CDM-WT-30-B2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 wild-type, CDM, 30min after ODA600 0.75

tag: growth medium

tag: sampling time


title: CDM-WT-30-B2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: biological replicate

tag: technical replicate


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_33


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_31


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_32


title: CDM-WT-30-B1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.