title: High Prot-w50-REP2

city: Sheffield

first: graham

last: stafford

address: School of Clinical Dentistry

country: United Kingdom

institute: University of Sheffield

description: SAMPLE 20

hyb_protocol: The labelled cDNA probe was applied to pre-hybridised P.gingivalis whole genomic microarray slides (Customized by TIGR, USA). The microarray slides were pre-hybridised with pre-hybridisation buffer (detail was described in section 2.5.1.3). Briefly, the array slide was thoroughly washed with distilled water (room temperature), snapped dried on a heat block for 2-3 seconds and UV cross-linked at 250 mJoules. Slides were then hydrated by dipping in pre-warmed 42°C water, centrifuged (7000 g, 5 min) at room temperature to dry the slide and then incubated in a 50-mL coplin jar containing pre-warmed pre-hybridisation buffer for at least 45 min at 42°C. When the hybridisation reaction was ready, the array slide was prepared by dipping in pre-warmed water (42°C) and agitating 2-3 min to remove pre-hybridisation buffer. The array slide was rinsed in isopropanol and centrifuged 5 for min (7000 g, 5 min) at room temperature to dry. The cDNA-labelling probe was prepared for array hybridisation by adding 40 μl of hybridisation buffer (detail as described in section 2.5.1.4) and gently pipetting up and down. The hybridizing probe mixture was then boiled for 5 min, centrifuged (10,000 x g, 5 min), and cooled for 2 min at room temperature. The probe mixture was applied gently to the array slide, carefully covered with a square cover slip (Nugene), and placed in a hybridisation chamber in a water bath (42°C) and incubated 18 h in the dark. After hybridisation, the slides were removed from the chamber taking care not to disturb the cover slip. The cover slip was removed by submerging the slide with the cover slips facing down in a dish containing warm 1x SSC, 0.05 % SDS wash buffer. The cover slips were dislodged by gently moving the slides from side-to-side and the slides placed in a rack in a fresh bath with warm (65°C) 1xSSC 0.05% SDS (First washing buffer, see details in 2.5.1.5). The array slide was agitated for 2-3 min, transferred to a second bath of buffer and re-agitated for 2-3 min and repeated for a third and fourth times (details in section 2.5.1.5 were used to wash). The slides were then blotted on paper towels to remove as much SDS-containing buffer as possible, then transferred to a fresh solution of 0.06 x SSC and agitated for 2-3 min. Finally the slides were centrifuged (700x g, 5 min) at room temperature to dry them and were kept in the dark until scanned.

scan_protocol: The array slide was scanned using a GenePix scanner (supplied by Prof. Robert Poole Department of Molecular Biology and Biotechnology, University of Sheffield) at 532nm (Cy3 channel) and the images were saved as tif picture files prior to analysis.

data_processing: Data from six individual experiments were normalized and then analyzed using the Spotfinder Software (TM4, The Institute of Genomic Research; TIGR, www.tigr.org). The data points with a density below 100,000 were discarded from analysis. A cut off ratio of 1.5:1 was used on all the slides. Significant Analysis of Microarray Software (SAM; TM4, and TIGR) was used to test statistical significance of the results from the microarray experiments. This statistical analysis involved sorting the change in expression of each gene relative to the standard deviation of all replicates for that gene. Therefore, genes with even a small change were not discounted if the ratios were consistent among all the repeats, thus effectively reducing false-negatives. False-positives were avoided when genes had poor reproducibility between replicates. Spot intensities for all channels were entered into SAM as paired, unlogged values. Delta values were chosen according to the lowest false discovery rate, which for this study was 4.7%. In combination with the 1.5 fold change, the genes with expression ratios of ≥3.5 were considered biologically significant.

organism: Porphyromonas gingivalis

source_name: High Prot-w50-REP2

label_protocol: The cDNA was generated using random primers for reverse transcription (Invitrogen). The reverse transcription reaction comprised 16 μg of P.gingivalis , 6 μg of random primer hexamers, the first strand buffer (75 mM KCl, 50 mM Tris-HCl (pH 8.3), 3 mM Mgcl2, 12.5 mM dATP, dCTP, and dGTP; 4.16 mM dTTP; and 8.33 mM amino allyl-dUTP, 800 units of Superscript II and nuclease free water (Qiagen) in a 30 μl final volume in a PCR reaction tube (All reagents in the reverse transcriptase reaction were purchased from the Invitrogen,UK except amino allyl-dUTP which was purchased from Sigma ). The reaction was mixed by inversion.   For cDNA generation the randomized primers were annealed at 70°C for 10 min followed by snap-freezing in a dry ice/ethanol bath for 30 sec and centrifugation for 1 min. The reaction mixture (Superscript II buffer, 0.1M DTT, and aa-dNTP mix)   was then incubated with Superscript II reverse transcriptase (Invitrogen) at 42°C overnight in a DNA Engine DYAD TM thermal cycler.   Residual RNA was removed by alkaline treatment followed by neutralization (The RNA was hydrolyzed by incubation with 10 μl of 0.5 M EDTA and 10 μl 1 M NaOH at 65 °C for 15 min. The sample was neutralized by 1M HCL before purification of the cDNA). The cDNA was purified using a QIAquick PCR purification kit (Qiagen) according to the manufacturers instruction except that the phosphate wash and elution buffers (see details of preparation in section 2.4.1.2) were substituted for the Qiagen supplied buffers because the Qiagen buffers contain free amines, which compete with the Cy dye coupling reaction). Purified cDNAs were labelled with 4.5 μl N-hydroxysuccinimide-Cy3 dye (40 nmol) dissolved in dimethyl sulfoxide (Amersham Biosciences) in the presence of 4.5 μl 0.1 M Na2CO3 buffer, pH 9.0. These cDNA samples were allowed to incubate at room temperature in the dark for 60 min. After incubation, the labelling mixtures were cleaned again using the QIAquick PCR purification Kit (Qiagen) according to the manufacturers instruction to remove uncouple Cy-dye. These cDNAs were then speed dried for 30 min.

growth_protocol: P. gingivalis strains were grown on Fastidious anaerobe (+5% Horse blood) for 48h: Invasive samples were recovered from OSCC cell lines after invasion in antibiotic protection assays according to Suwannakul et al., 2010 (Microbiology, Jun 24.), non-invasive cells were recovered from cell supernatants also as described in Suwannakul et al.,.  Similarly High and low protease samples represent low and high protease isolates grown on FA-blood for 48h. all anaerobically at 37C

extract_protocol: RNA samples used in microarray studies were extracted, purified and quantified as described earlier (section 2.4.2.1) All RNA samples exhibited A260/A280 ratio of at least 1.8 and the concentration was > least 3 mg/ml. RNA samples were checked by RNA gel electrophoresis.


title: High Prot-w50-REP1

status: Public on Aug 31 2010

type: RNA

description: SAMPLE 19

molecule: total RNA

source_name: High Prot-w50-REP1

tag: strain


title: High Prot-w50-REP3

description: SAMPLE 21

source_name: High Prot-w50-REP3


title: C2C12 differentiation condition, rep1

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

country: USA

institute: Northwestern University

description: Cells collected at 24 h after induction of differentiation

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
We used the GC-bin method for background correction and applied quantile normalization. Probe set intensities and gene expression levels were derived from the probe logarithmic intensity error model (PLIER).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

label: biotin

organism: Mus musculus

source_name: C2C12 differentiated day 1

label_protocol: Standard Affymetrix protocol

growth_protocol: C2C12 cells were maintained at 20–70% confluency in Dulbecco’s Modified Eagles Medium (DMEM).  supplemented with 10% fetal bovine serum.

extract_protocol: Standard Affymetrix protocol

treatment_protocol: To induce differentiation, cells were switched to DMEM 2% horse serum (Sigma) after 10 h ( 100% confluency).

tag: media

value: differentiation

tag: cell line


title: C2C12 differentiation condition, rep2


title: Low Prot-w50-REP2

description: SAMPLE 23

source_name: Low Prot-w50-REP2


title: IL6_IL1_1

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

hyb_protocol: stardard affymetrix protocol

scan_protocol: stardard affymetrix protocol

data_processing: Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software and normalized using MAS5 method.

source_name: CD4+ T cell

label_protocol: according to Ambion MessageAmpII-Biotin kit protocol

growth_protocol: CD4+ T cells from spleens and lymph nodes of 6- to 8-week-old mice were purified by negative selection and magnetic separation (Miltenyi Biotec, Germany) followed by sorting of naive CD4+CD62L+CD44-CD25- population using FACSAria II (BD, NJ). Cells were activated by plate-bound anti-CD3/CD28 (both 10 μg ml-1; eBioscience, CA) in serum-free medium for 3-4 days either under neutral conditions or with IL-6 plus IL-1β(each 20 ng ml-1) and either human TGF-β1 (0.5 ng ml-1; Th17(β)) or IL-23 (50 ng ml-1; Th17(23)) (all from R&D Systems, MN). In all cell cultures anti-IFN-γ neutralizing antibodies (10 μg ml-1, BD Pharmingen) were added. IL-12 (20 ng ml-1) was purchased from PeproTech (NJ); huIL-2 was used at 100 U ml-1. TGF-β signaling was inhibited by using neutralizing anti-TGF-β1 and anti-TGF-β2 antibodies (5 μg ml-1, both R&D Systems, MN) or by a TGFβR1 kinase inhibitor (2-(3-(6-Methylpyridin-2-yl)-1H-pyrazol-4-yl)-1,5-naphthyridine, 1 μM; EMD, NJ). Procedures for isolation of lamina propria lymphocytes and CNS-infiltrating lymphocytes are given in the Methods.

extract_protocol: according to Ambion mirVana RNA extraction kit protocol

tag: treatment


title: Low Prot-w50-REP1

description: SAMPLE 22

source_name: Low Prot-w50-REP1


title: IL6_IL1_TGFB_1


title: IL6_IL1_2


title: IL6_IL1_TGFB_2


title: SV40 infected MEFs, biological rep 1

city: Pittsburgh

first: Ulka

last: Sachdev-Ost

address: 300 Halket Street Suite 5414

institute: University of Pittsburgh School of Medicine

description: SV40 infected MEFs, biological rep 1

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 the Agilent GeneArray 3000 with 7G upgrade. This step was done by the Genomics and Proteomics Core Labs at the University of Pittsburgh.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, global scaling as normalization method, and the trimmed mean target intensity of each array was arbitrarily set to 150. RMA was performed using BRB-Array Tools (Rich Simon, National Cancer Institute, http://linus.nci.nih.gov/BRB-ArrayTools.html) and fold change averages were calculated from the biological replicates of each class compared to control MEFs

source_name: SV40 infected MEFs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). This step was done by the Genomics and Proteomics Core Labs at the University of Pittsburgh.

growth_protocol:
DMEM + 10% heat inactivated FBS + Penn/Strep
N/A

extract_protocol: Total RNA was isolated from cells with the RNeasy Kit (Qiagen)

treatment_protocol: Cells were grown to confluence and infected with SV40. After four days, cells were harvested with trypsin, washed 3X with PBS-EDTA and cell pellet was frozen until total RNA isolation.

tag: confluency

value: 4 days post-confluent


title: SV40 infected MEFs, biological rep 2

description: SV40 infected MEFs, biological rep 2


title: Low Prot-w50-REP3

description: SAMPLE 24

source_name: Low Prot-w50-REP3


title: SV40 infected MEFs, biological rep 3

description: SV40 infected MEFs, biological rep 3

treatment_protocol: Cells were grown to confluence and infected with SV40. After three days, cells were harvested with trypsin, washed 3X with PBS-EDTA and cell pellet was frozen until total RNA isolation.

value: 3 days post-confluent


title: Mock infected MEFs, biological rep 3

description: Mock infected MEFs, biological rep 3

source_name: Mock infected MEFs

treatment_protocol: Cells were grown to confluence and fed with fresh medium. After three days, cells were harvested with trypsin, washed 3X with PBS-EDTA and cell pellet was frozen until total RNA isolation.


title: No_Cytokine_2


title: IL6_TGFB_TGFBRi


title: IL6_IL1_IL23_1


title: C2C12 growth condition, rep1

description: Cells collected at 60–70% confluency

source_name: C2C12 growth

value: growth


title: IL6_TGFB


title: IL6_IL1_IL23_2


title: C2C12 growth condition, rep2

description: Cells collected at 60–70% confluency


title: Mock infected MEFs, biological rep 2

description: Mock infected MEFs, biological rep 2

treatment_protocol: Cells were grown to confluence and fed with fresh medium. After four days, cells were harvested with trypsin, washed 3X with PBS-EDTA and cell pellet was frozen until total RNA isolation.


title: Low Prot-11834-REP3

description: SAMPLE 18

source_name: Low Prot-11834-REP3


title: No_Cytokine_1


title: High Prot-11834-REP3

description: SAMPLE 15

source_name: High Prot-11834-REP3


title: High Prot-11834-REP2

description: SAMPLE 14

source_name: High Prot-11834-REP2


title: Low Prot-11834-REP2

description: SAMPLE 17

source_name: Low Prot-11834-REP2


title: High Prot-11834-REP1

description: SAMPLE 13

source_name: High Prot-11834-REP1


title: Mock infected MEFs, biological rep 1

description: Mock infected MEFs, biological rep 1


title: Non-IN-w50-REP3

description: SAMPLE 12


title: D44N expressing MEFs, biological rep 3

description: D44N expressing MEFs, biological rep 3

source_name: D44N expressing MEFs

growth_protocol:
DMEM + 10% heat inactivated FBS + 0.4mg/ml G418 + Penn/Strep
N/A

treatment_protocol: Cells were grown to confluence and fed with fresh medium. After two days, cells were harvested with trypsin, washed 3X with PBS-EDTA and cell pellet was frozen until total RNA isolation.

value: 2 days post-confluent


title: Non-IN-w50-REP2

description: SAMPLE 11


title: Non-IN-w50-REP1

description: SAMPLE 10


title: INVASIVE-w50-REP3

description: SAMPLE 9


title: 3213 expressing MEFs, biological rep 1

description: 3213 expressing MEFs, biological rep 1

source_name: 3213 expressing MEFs


title: D44N expressing MEFs, biological rep 2

description: D44N expressing MEFs, biological rep 2


title: INVASIVE-w50-REP2

description: SAMPLE 8


title: Non-IN--11834-REP3

description: SAMPLE 6


title: INVASIVE-w50-REP1

description: SAMPLE 7


title: 3213 expressing MEFs, biological rep 2

description: 3213 expressing MEFs, biological rep 2


title: D44N expressing MEFs, biological rep 1

description: D44N expressing MEFs, biological rep 1


title: 3213 expressing MEFs, biological rep 3

description: 3213 expressing MEFs, biological rep 3


title: N136 expressing MEFs, biological rep 3

description: N136 expressing MEFs, biological rep 3

source_name: N136 expressing MEFs


title: N136 expressing MEFs, biological rep 2

description: N136 expressing MEFs, biological rep 2


title: Non-IN-11834-REP2

description: SAMPLE 5


title: TAg expressing MEFs, biological rep 3

description: TAg expressing MEFs, biological rep 3

source_name: TAg expressing MEFs


title: Non-IN-11834-REP1

description: SAMPLE 4


title: TAg expressing MEFs, biological rep 2

description: TAg expressing MEFs, biological rep 2


title: Low Prot-11834-REP1

description: SAMPLE 16

source_name: Low Prot-11834-REP1


title: TAg expressing MEFs, biological rep 1

description: TAg expressing MEFs, biological rep 1


title: INVASIVE-11834-REP3

description: SAMPLE 3


title: INVASIVE-11834-REP2

description: SAMPLE 2


title: wild-type MEF, biological rep 2b

description: wild-type MEF, biological rep 2b

source_name: wild-type MEFs


title: Astrocytoma, 56 [aCGH]

type: genomic

city: Cambridge

first: David

middle: T W

last: Jones

address: Box 231, Level 3 Lab Block, Addenbrooke's Hospital

department: Pathology

institute: University of Cambridge

description:
A56
Log2 tumour/reference intensity ratios for analysis of copy number variations

hyb_protocol: The purified DNA from test and reference were pooled and mixed with 45µg of Cot1 DNA and ethanol precipitated. The precipitated DNA was dissolved in 30µl of hybridisation buffer, incubated at 37˚C for 2 hours and applied to the prehybridised microarray. Hybridisation was performed in a humidified Micro Array Hybridisation Chamber (Camlab, Cambridge, UK) at 37˚C for 48 hours under a coverslip. The arrays were then washed successively in 1x PBS/0.05% Tween20 at room temperature for 15 min twice, 50% formamide/2xSSC at 42˚C for 30 min once, 1x PBS/0.05% Tween20 at room temperature for 15min and 1x PBS for 5min twice.

scan_protocol: Scanned on an Axon GenePix 4100A personal scanner. Images were quantified using GenePix Pro version 5.1.

data_processing: The median of the ratio of test/reference spot intensity, after subtraction of local background, of the 5Mb-clones in each subarray was used as the normalization factor. The chromosomal arm on which most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was divided by the normalization factor for each subarray, an average of the duplicate calculated and log2-transformed.

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary tumour sample (test)

label_protocol: 400ng of genomic DNA was labelled with a Bioprime labelling kit (Invitrogen)

extract_protocol: Proteinase K digestion followed by phenol:chloroform extraction

tag: case

tag: gender

value: Female

tag: age

tag: disease state

value: Astrocytoma

tag: tumor grade

value: WHO grade II

source_name: Mixed normal blood from 20 individuals (reference)

label_protocol: 400ng of tumour and reference genomic DNA were labelled with Cy5-dCTP and Cy3-dCTP (GE Healthcare), respectively, using BioPrime kit (Invitrogen) according to the manufacturer’s instruction, except that custom-prepared dNTP (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM) was used. After overnight incubation at 37°C, the labelled DNA were purified using a G-50 spin column (GE Healthcare).

tag: sample type

value: reference (mixture of 20 normal male or female genomic DNA)


title: Astrocytoma, 55 [aCGH]

description:
A55
Log2 tumour/reference intensity ratios for analysis of copy number variations

value: Male


title: wild-type MEF, biological rep 2a

description: wild-type MEF, biological rep 2a


title: Astrocytoma, 54 [aCGH]

description:
A54
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, 50 [aCGH]

description:
A50
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: wild-type MEF, biological rep 1a

description: wild-type MEF, biological rep 1a


title: Astrocytoma, 49 [aCGH]

description:
A49
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, 48 [aCGH]

description:
A48
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: N136 expressing MEFs, biological rep 1

description: N136 expressing MEFs, biological rep 1


title: INVASIVE-11834-REP1

description: SAMPLE 1


title: wild-type MEF, biological rep 1b

description: wild-type MEF, biological rep 1b


title: Astrocytoma, 40 [aCGH]

description:
A40
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, Case 54 [mRNA]

description:
A54
Quantile normalised signal intensity.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered on the detection p-value, such that probes with a p-value > 0.01 in all cases were excluded. The remaining data were transformed using variance stabilisation and normalised using quantile normalisation with lumi and limma in R.

source_name: Primary tumour

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

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


title: Astrocytoma, 42 [aCGH]

description:
A42
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, Case 48 [mRNA]

description:
A48
Quantile normalised signal intensity.


title: Astrocytoma, Case 26 [mRNA]

description:
A26
Quantile normalised signal intensity.


title: Astrocytoma, Case 30 [mRNA]

description:
A30
Quantile normalised signal intensity.


title: Astrocytoma, 25 [aCGH]

description:
A25
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, 35 [aCGH]

description:
A35
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, 30 [aCGH]

description:
A30
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, Case 35 [mRNA]

description:
A35
Quantile normalised signal intensity.


title: Astrocytoma, Case 55 [mRNA]

description:
A55
Quantile normalised signal intensity.


title: Astrocytoma, 23 [aCGH]

description:
A23
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, 27 [aCGH]

description:
A27
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, 26 [aCGH]

description:
A26
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, Case 25 [mRNA]

description:
A25
Quantile normalised signal intensity.


title: Astrocytoma, 22 [aCGH]

description:
A22
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Astrocytoma, Case 9 [mRNA]

description:
A9
Quantile normalised signal intensity.


title: Astrocytoma, Case 22 [mRNA]

description:
A22
Quantile normalised signal intensity.


title: Astrocytoma, Case 7  [mRNA]

description:
A7
Quantile normalised signal intensity.


title: MALTL-9

city: Zürich

first: Vanessa

middle: Jane

last: Craig

address: Winterthurerstrasse 190

country: Switzerland

institute: Institute of molecular cancer research

hyb_protocol: According to the Agilent Human miRNA Microarray Kit protocol version 10.0

growth_protocol: Human patient material was obtained from 5 patients with gastric low-grade MALT lymphoma and 4 archived human tonsil samples were used for miRNA expression analysis

extract_protocol: Total RNA was prepared using the QIAGEN - miRNeasy Mini Kit

tag: tissue

value: MALT lymphoma


title: MALTL-12

scan_protocol: According to the Agilent Human miRNA Microarray Kit protocol version 10.0


title: Astrocytoma, 21 [aCGH]

description:
A21
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Female MI (4218331017_F)

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: replicate 4

data_processing: The data were normalised using quantile normalisation followed by log2 transform with GeneSpring GX11. P/A flag was based on a P>0.95 cut off. Only genes with at least one P flag were used in the analysis

source_name: left ventricular samples (infarct excluded)

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

value: 12-15 weeks

value: left ventricle

tag: stress

value: MI


title: Female MI (4218331018_A)

description: replicate 5


title: MALTL-7

data_processing: According to the Agilent Human miRNA Microarray Kit protocol version 10.0


title: Female Sham (4218331018_B)

description: replicate 5

value: Sham


title: MALTL-3

label_protocol: According to the Agilent Human miRNA Microarray Kit protocol version 10.0


title: Astrocytoma, 10 [aCGH]

description:
A10
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: MALTL-4


title: Female Sham (4218331005_F)

description: replicate 2


title: Female MI (4218331017_B)

description: replicate 2


title: Astrocytoma, 12 [aCGH]

description:
A12
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: To-8

value: Tonsil


title: Female MI (4218331017_A)

description: replicate 1


title: Female MI (4218331017_C)

description: replicate 3


title: Female Sham (4218331017_D)

description: replicate 3


title: To-7


title: To-5


title: Female Sham (4218331005_E)

description: replicate 1


title: Female Sham (4218331017_E)

description: replicate 4


title: Male Sham (4218331005_B)

description: replicate 5


title: Astrocytoma, 6 [aCGH]

description:
A6
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: To-6


title: Male MI (4218331005_C)

description: replicate 4


title: Astrocytoma, 7 [aCGH]

description:
A7
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Cerebellum_NPC_ILM_rep4

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: Gene expression profiling data from cerebellum

hyb_protocol: The biotinylated cRNA target was hybridized to the MouseWG-6 BeadChip according to the manufacturer’s instructions with the addition of a 10-min washing in high-temp wash buffer (Illumina) at 55 ºC in a Hybex Microarray Incubation System (SciGene Corportaion, Sunnyvale, CA) following the overnight hybridization.

scan_protocol: The chips were scanned using a BeadScan 2.3.0.10 (Illumina) at a multiplier setting of “2”.

data_processing: The microarray images were registered and gene expression data were extracted automatically according to the manufacturer’s default settings. After background subtraction, raw microarray intensity data were normalized using the cubic spline normalization method (Illumina). Intensity data were then adjusted to set the minimum intensity of an array equal to 1.

label: Biotin

source_name: cerebellum from Npc1 (BALB/cNctr-Npc1m1N/J) mice

label_protocol: 200 ng of total RNA was labeled using a MessageAmp II-biotin enhanced kit (Applied Biosystems, Foster City, CA). Double stranded cDNA was synthesized using T7-oligo (dT) primers followed by an in vitro transcription (IVT) reaction to amplify antisense-RNA (aRNA), while biotin was incorporated into the synthesized aRNA target.

growth_protocol: Npc1(BALB/cNctr-Npc1m1N/J) heterozygous male and female mice on BALB/c background were purchased from Jackson Laboratory (Bar Harbor, MN) and housed in the vivarium under protocols approved by the local IACUC. Mice had free access to water and food; Npc1-/- mice were produced by in-house breeding.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA) and purified with RNeasy Mini Kit according to the manufacturer instructions (Qiagen, Valencia, CA).

treatment_protocol: Mice were genotyped using tail DNA with PCR methods described by Baudray (Baudray et al., 2003). Cerebelli were collected from 8 mice (4 Npc1+/+mice, and 4 Npc1-/- mice) at 3 weeks postnatal and were snap-frozen in liquid nitrogen.

value: Npc1 (BALB/cNctr-Npc1m1N/J)

tag: genotype/variation

value: cerebellum


title: Male Sham (4218331004_E)

description: replicate 2


title: Cerebellum_NPC_ILM_rep3


title: Male MI (4218331004_D)

description: replicate 3


title: Male Sham (4218331004_F)

description: replicate 3


title: Cerebullum_wild-type control_ILM_rep1

value: wild-type


title: Cerebellum_NPC_ILM_rep2


title: Cerebullum_wild-type control_ILM_rep3


title: Cerebullum_wild-type control_ILM_rep4


title: Astrocytoma, 9 [aCGH]

description:
A9
Log2 tumour/reference intensity ratios for analysis of copy number variations


title: Male Sham (4218331005_A)

description: replicate 4


title: Male MI (4218331004_C)

description: replicate 2


title: MEF_ Med1-/-_rep1

city: Kobe

first: Mitsuhiro

last: Ito

address: 7-10-2 Tomogaoka, Suma-ku

country: Japan

institute: Kobe University Graduate School of Medicine

description:
ITOKOBEU_03_MG430_2_10060303
Med1-/-p53-/- MEFs were established from E10.0 embryos derived from a single crossing of Med1+/-p53-/- male and Med1+/-p53+/- female mice.

hyb_protocol: Labeled probes were used for the GeneChip Mouse Genome 430A 2.0 Array (Affymetrix) according to the manufacturer’s instructions.

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

data_processing: The CEL data were analyzed with dChip software, which can normalize and process multiple datasets simultaneously.

source_name: Mouse embryonic fibroblasts, E10.0, Med1-/-

label_protocol: Fifty nanograms of total RNAs were labeled with biotin by in vitro transcription using the 3' IVT Express Kit (Affymetrix), according to the manufacturer’s instruction.

growth_protocol: MEFs were prepared and cultured in Dulbecco's Modified Eagle's medium (DMEM) with 10 % fetal calf serum.

extract_protocol: Total RNA was prepared using the Isogen reagent (Toyobo, Japan).

tag: genotype

tag: developmental stage

value: E10.0 embryos

tag: cell type

value: fibroblasts


title: Male Sham (4218331004_A)

description: replicate 1

tag: strain


title: Male MI (4218331005_D)

description: replicate 5


title: MEF_ Med1-/-_rep2

description:
ITOKOBEU_04_MG430_2_10060304
Med1-/-p53-/- MEFs were established from E10.0 embryos derived from a single crossing of Med1+/-p53-/- male and Med1+/-p53+/- female mice.


title: YJB9929s_rep1

city: Boston

first: Amnon

last: Koren

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: S vs G1 Replication timing.

hyb_protocol: Standard Agilent protocol.

scan_protocol: Agilent, 5micron, 100%PMT.

data_processing:
Images were analyzed with SpotReader (Niles Scientific). Weak (<2std above control probe mean) and saturated probe reads were removed from further analysis. Data was LOWESS-normalized.
The raw data for this Sample is in the rows with a '1' in the 'Block' column of the linked .srr file.
The fully processed replication timing data is available in the 'GSE17963_final_data.txt' file, which is linked to the Series GSE17963 record as a supplementary file.

organism: Candida albicans

source_name: G1-phase cells, YJB9929s

label_protocol: DNA was digested with DpnII and amplified by four rounds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides and subsequently labeled with Cy dyes.

growth_protocol: Cells were grown in YPAD (1% yeast extract, 2% peptone, 2% dextrose) at 30º to log phase and fixated.

extract_protocol: DNA was extracted using the MasterPure Yeast DNA purification kit (Epicentre).

treatment_protocol: G1- and S-phase cells were sorted by FACS.

source_name: S-phase cells, YJB9929s


title: MEF_ Med1+/+_rep2

description:
ITOKOBEU_02_MG430_2_10060302
Med1+/+p53-/- MEFs were established from E10.0 embryos derived from a single crossing of Med1+/-p53-/- male and Med1+/-p53+/- female mice.

source_name: Mouse embryonic fibroblasts, E10.0, Med1+/+


title: Wild type_rep4

description: S vs G1 Replication timing.

data_processing:
Images were analyzed with SpotReader (Niles Scientific). Weak (<2std above control probe mean) and saturated probe reads were removed from further analysis. Data was LOWESS-normalized.
The raw data for this Sample is in the rows with a '2' in the 'Block' column of the linked .srr file.
The fully processed replication timing data is available in the 'GSE17963_final_data.txt' file, which is linked to the Series GSE17963 record as a supplementary file.

source_name: G1-phase cells, WT

source_name: S-phase cells, WT


title: MEF_ Med1+/+_rep1

description:
ITOKOBEU_01_MG430_2_10060301
Med1+/+p53-/- MEFs were established from E10.0 embryos derived from a single crossing of Med1+/-p53-/- male and Med1+/-p53+/- female mice.


title: YJB9929s_rep2

description: S vs G1 Replication timing.


title: Cerebellum_NPC_ILM_rep1


title: Wild type_rep2

description: S vs G1 Replication timing.


title: HSF1 SOM-rep2

city: Turku

first: Lea

last: Sistonen

address: Tykistokatu 6 B

department: Biology

country: Finland

institute: Åbo Akademi University

description: Mapping of in vivo targets for HSF1 in mouse testis by using a global ChIP-chip promoter screen. A 1.5 kb promoter tiling array (NimbleGen Systems Inc.), covering ~26000 promoters of the mouse genome was used.

hyb_protocol: The labeled ChIP DNA was precipitated and hybridized in buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C and then washed. Hybridizations were performed per manufacturer's protocols http://www.nimblegen.com/products/lit/lit.html

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturers's protocol: http://www.nimblegen.com/products/lit/lit.html

data_processing: The ChIP-chip data was normalized with Lowess normalization method and normalized log2 ratio (HSF1 ChIP/Input DNA) was produced for each biological replicate. The promoter values were calculated as average log2 ratios over all probes for each promoter. To identify the HSF1 target population, we used a non-arbitrary analysis method called RankProd described in Breitling et al. 2004. RankProd has been published as an R/Bioconductor package.

source_name: Amplified HSF1 ChIP DNA from mouse wild-type testis labeled with Cy3.

label_protocol: For NimbleGen arrays, ChIP DNA prepared from testes was directly labeled by klenow random priming with Cy5 or Cy3 nonamers per manufacturer's protocol: http://www.nimblegen.com/products/lit/lit.html

extract_protocol:
Isolated testes were cross-linked with a final concentration of 1% formaldehyde. Quenching was performed with 125 mM glycine. Testes were lysed in 4 ml lysis buffer. Chromatin samples were sonicated with Bioruptor (Diagenode) to an approximate size of 100-500 bp. Immunoprecipitation was performed after preclearing with 50% slurry of
protein G-coated Sepharose beads (Amersham Biosciences), at 4C over night. HSF1 antibody was used for immunoprecipitation and an input sample was obtained after the immunoprecipitation. Immunocomplexes were washed eight times. Cross-links were reversed by incubation of samples over night at 65C and DNA was purified and resuspended in water.
DNA amplification of material obtained from three biological replicates, needed for microarray hybridizations. Whole ChIP samples and 20 ng of the input samples were used for the ligation-mediated PCR (LM-PCR). The DNA was blunted using dNTP mix (Promega) and T4 DNA polymerase (New England Biolabs), purified and dissolved in water.
Purified DNA was ligated using T4 DNA ligase (New England Biolabs) and annealed with linkers made from HPLC-purified oligos; oligo 1: 5’-gcg gtg acc ggg aga tct gaa ttc-3’ and oligo 2: 5’-gaa ttc aga tc-3’. DNA was purified again and dissolved in water. LM-PCR was performed using Taq Polymerase (New England Biolabs) and Pfu Polymerase (Stratagen).

treatment_protocol: Adult (60 days old) wild-type mice were used for isolation of testes

value: Wild-type (C57BL/6J)

value: testis

value: Wild-type (C57BL/6J) adult (60 days old) mice testis used as material

tag: antibody

value: HSF1 polyclonal antibody

tag: antibody vendor

value: Stressgen

tag: antibody catalog #

source_name: Amplified Input DNA from mouse wild-type testis labeled with Cy5.

growth_protocol: Pathogen-free mice were housed under controlled environmental conditions and fed with complete pelleted chow and allowed tap water. The mice were killed by CO2 asphyxiation. All mice were handled in accordance with the institutional animal care policies o

tag: chip antibody

value: none, input DNA


title: Wild type_rep1

description: S vs G1 Replication timing.


title: HSF1 SOM-rep3

source_name: Amplified HSF1 ChIP DNA from mouse wild-type testis labeled with Cy5.

growth_protocol: Pathogen-free mice were housed under controlled environmental conditions and fed with complete pelleted chow and allowed tap water. The mice were killed by CO2 asphyxiation. All mice were handled in accordance with the institutional animal care policies

source_name: Amplified Input DNA from mouse wild-type testis labeled with Cy3.


title: HSF1 SOM-rep1


title: Control_normoxia_ATF2-/-_rep2

status: Public on Aug 30 2010

city: SAN DIEGO

first: Alexey

last: Eroshkin

state: California

address: Alexey Eroshkin, 3803 Ruette San Raphael

department: Bioinformatics Core

institute: SBPMDI

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

source_name: Primary melanocytes were treated with Doxycycline before isolation of total RNA

label_protocol: As suggested by illumina

growth_protocol: Primary melanocytes were isolated and enriched population was maintained under normoxia or hypoxia (1% O2) for 12 h before isolation of total RNA. 500 ng of total RNA was used for synthesis of biotin-labeled cRNA using an RNA amplification kit (Ambion). The biotinylated cRNA is labeled by incubation with streptavidin-Cy3 to generate probe for hybridization with the Mouse-6 Expression BeadChip (Illumina) that represents 48K mouse gene transcripts.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Primary melanocytes


title: Control_normoxia_ATF2+/+_rep2

value: wild type


title: Control_hypoxia_ATF2+/+_rep2


title: Control_hypoxia_ATF2+/+_rep1


title: Tamox_hypoxia_ATF2-/-_rep2

source_name: Primary melanocytes were treated with 4-OHT and Doxycycline before isolation of total RNA


title: Control_normoxia_ATF2+/+_rep1


title: Control_hypoxia_ATF2-/-_rep2


title: Tamox_normoxia_ATF2-/-_rep2


title: Control_hypoxia_ATF2-/-_rep1


title: Tamox_normoxia_ATF2-/-_rep1


title: p0 v. p3 - in vivo - rep1

status: Public on Aug 28 2010

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: C. jejuni growing in host

hyb_protocol: Dyed samples to be compared were combined and resuspended in 196µl Ambion SlideHyb buffer 1. Samples were added to Agilent gasket slides, sandwiched with a UV-crosslinked, blocked microarray slide and sealed inside an Agilent hybridization chamber. This was rotated at 54 degrees celsius for 18 hours to allow hybridization to the array before washing and scanning.

scan_protocol: Slides were scanned using a GenePix scanner and GenePix Pro 4.1 software. PMT values were adjusted to obtain approximately equal levels of signal from both wavelength channels.

data_processing: Done using R/LIMMA. Signal ratios were normalized within arrays using a global loess procedure, and between arrays by scaling. Spots that are on the array that are not in strain 11168 were excluded from the analysis. The ORF for these spots are listed in the matrix as B, to be marked for exclusion in the analysis. A duplicate correlation coefficient was calculated, and a least squares linear model was fit. Using false-discovery rate adjustment, P-values less than 0.05 were considered differentially expressed. The full matrix containing the ORF column is available as a supplementary file on the Series record.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Unpassaged Camylobacter jejuni 11168 RNA

label_protocol: 6µg RNA was reverse transcribed with random hexamer primers and an aminoallyl-dUTP/dNTP mix using Invitrogen SuperScriptIII CyDyes 3 or 5 from GE Biosciences were used to dye aminoallyl-cDNA samples. Reactions were cleaned at each step using a QIAGEN QIAquick kit.

growth_protocol: C. jejuni variants were grown on tryptic soy agar plates with 5% sheep's blood for 24 hours. Cells were resuspended to approximate OD600 0.3, and 100 micoliters was used to prepare 15 spread plates of C. jejuni growth. Cells were harvested into triyptic soy broth and transported on ice to the germ-free mouse colony at the University of Michigan (Ann Arbor). At six weeks of age, male mice were inoculated with approximately 1x1010 CFU of either wild-type or mouse-adapted C. jejuni. Infection was allowed to proceed for 96 hours before euthanasia. The cecum was immediately extracted, submerged in RNAlater (Ambion) and the cecal contents were squeezed out using a sterile cell lifter (Corning). Samples were stored in 50ml conical tubes in RNAlater on ice for approximately 2.5 hours until they were stored at -80°C until RNA extraction. RNAlater has been used successfully with C. jejuni, and in our hands these storage conditions did not alter C. jejuni NCTC11168 gene expression in control microarray experiments (data not shown).

extract_protocol: Cecal contents in RNAlater were thawed on ice, and an equal volume of PBS plus a 1:100 volume of phenol (Invitrogen) was added directly to each tube. Tubes were vortexed before slow-speed centrifugation, supernatant extraction, and then high-speed centrifugation. This resulted in pellets that consisted of only the smallest material in the cecal contents, and C. jejuni cells. RNA was then extracted using TRIzol according to the manufacturer instructions. To remove proteins, fat, polysaccharides, proteoglycans, and insoluble materials, the optional centrifuge after homogenization, and precipitation using a high salt solution and isopropanol was performed was performed as described in the TRIzol reagent protocol. Samples were treated for vigorous DNA contamination with the TURBO DNA-free kit (Ambion) and then precipitated overnight with a 1:10 volume of 3M sodium acetate, pH 5.5, and 3 volumes of 200 proof ethanol.

tag: adaptation status

value: Unadapted (unpassaged in C57 BL/6 IL-10-/- mice)

source_name: Passaged Camylobacter jejuni 11168 RNA

value: Adapted:3 passages in C57 BL/6 IL-10-/- mice


title: p0 v. p3 - in vivo - rep2

description: C. jejuni growing in host

value: Adapted:3 passage in C57 BL/6 IL-10-/- mice


title: 415_spleen_normal

city: Charlestown

first: Martin

last: Aryee

address: 149 13th Street

institute: Massachusetts General Hospital

description: DNA methylation data from human spleen

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software and the charm bioconductor package v1.0.1 using a) quantile and b) subset-quantile normalization.  Percent methylation calculated.

source_name: Input fraction from normal spleen

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

growth_protocol: genomic DNA was isolated from frozen tissue, i.e. not grown in culture

extract_protocol: Genomic DNA (gDNA) were isolated using the MasterPure genomic DNA isolation kit (EpiCentre) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was randomly sheared into 1.6-3kb DNA size fragments using a Hydroshear device (DigiLab), digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the unmethylated (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

treatment_protocol: untreated

value: Input fraction from normal spleen

value: spleen

source_name: Methyl-depleted fraction from normal spleen


title: 428_spleen_normal

description: DNA methylation data from human spleen

value: Methyl-depleted fraction from normal spleen


title: p0 v. p3 - in vivo - rep4

description: C. jejuni growing in host


title: Tamox_hypoxia_ATF2-/-_rep1


title: Hopx-/-

status: Public on Aug 29 2010

city: New Haven

first: Daniel

last: Hawiger

state: CT

address: 300 Cedar St. TAC-S570

institute: Yale University

description: DC-induced regulatory T cells in vivo

hyb_protocol: Peformed by Yale University Keck micoroarray facility using Affymetrix mouse genome 430 2.0  arrays

data_processing: GeneSpring GX 10.0.1

source_name: iTregs

growth_protocol: material obtained ex vivo

extract_protocol: Trizol extraction of total RNA followed by RNA clean-up using QIAGEN reagents was performed according to the manufacturers' instructions.

treatment_protocol: FACS-sorted

value: T cells


title: p0 v. p3 - in vivo - rep3

description: C. jejuni growing in host


title: 625_colon_tumor

description: DNA methylation data from human colon tumor

source_name: Input fraction from colon tumor

value: Input fraction from colon tumor

value: Tumor colon

source_name: Methyl-depleted fraction from colon tumor


title: 415_liver_normal

description: DNA methylation data from human liver

source_name: Input fraction from normal liver

value: Input fraction from normal liver

value: liver

source_name: Methyl-depleted fraction from normal liver


title: 441_liver_normal

description: DNA methylation data from human liver

value: Methyl-depleted fraction from normal liver


title: Colorectal adenoma biopsy specimens

city: Kunming

first: Hui

last: Tang

state: Yunnan

address: No. 157 Jinbi Street

department: The First People’s Hospital of Yunnan Province, Kunhua Affiliated Hospital of Kunming Medical College

institute: Institute of Basic Medicine

description: Human colorectal adenoma

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GeneChip operating software (GCOS 1.2, Affymetrix) using default settings (MAS5)

source_name: Human colorectal adenoma biopsy specimens

label_protocol: Biotinylated complementary RNA targets were prepared with 5 micrograms of total RNA using the IVT Labeling Kit (Affymetrix) according to the manufacture’s protocols.

extract_protocol: Total RNA was extracted from each specimen using TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s specifications.

value: 3 colorectal adenoma biopsy specimens were obtained from patients who underwent endoscopic intervention

tag: mean age (range, yr)

tag: gender (male/female)


title: Normal colorectal mucosa

description: Human normal colorectal mucosa

source_name: Human normal colorectal mucosa

value: four normal colorectal mucosa from several locations throughout the colon were obtained from four chinese individuals undergoing colonoscopy examination


title: Colorectal carcinoma biopsy specimens_stage of Duke's C/D

description: Duke's C/D human colorectal carcinoma

source_name: Human colorectal carcinoma biopsy specimens at stage of Duke's C/D

label_protocol: Biotinylated complementary RNA targets were prepared with 5 micrograms of total RNA using the IVT Labeling Kit (Affymetrix) according to the manufacture's protocols.

extract_protocol: Total RNA was extracted from each specimen using TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's specifications.

value: 2 duke's c/d colorectal carcinoma biopsy specimens were obtained from patients who underwent colorectal resection


title: 432_liver_normal

description: DNA methylation data from human liver


title: 428_liver_normal

description: DNA methylation data from human liver


title: Colorectal carcinoma biopsy specimens_stage of Duke's B

description: Duke's B human colorectal carcinoma

source_name: Human colorectal carcinoma biopsy specimens at stage of Duke's B

value: 3 duke's b colorectal carcinoma biopsy specimens were obtained from patients who underwent colorectal resection


title: 449_liver_normal

description: DNA methylation data from human liver


title: 624_colon_tumor

value: Methyl-depleted fraction from colon tumor


title: 517_colon_tumor


title: 614_colon_tumor


title: 441_spleen_normal

description: DNA methylation data from human spleen


title: 449_spleen_normal

description: DNA methylation data from human spleen


title: Colorectal carcinoma biopsy specimens_stage of Duke's A

description: Duke's A human colorectal carcinoma

source_name: Human colorectal carcinoma biopsy specimens at stage of Duke's A

value: 2 duke's a colorectal carcinoma biopsy specimens were obtained from patients who underwent colorectal resection


title: 432_spleen_normal

description: DNA methylation data from human spleen


title: 441_colon_tumor


title: 625_colon_normal

description: DNA methylation data from human colon

source_name: Input fraction from normal colon

value: Input fraction from normal colon

value: colon

source_name: Methyl-depleted fraction from normal colon


title: Hopx-sufficient

description: DC-induced regulatory T cells in vivo

scan_protocol: Peformed by Yale University Keck micoroarray facility


title: 415_brain_normal

description: DNA methylation data from human brain

source_name: Input fraction from normal brain

value: Input fraction from normal brain

value: frontal cortex

source_name: Methyl-depleted fraction from normal brain


title: 614_colon_normal

description: DNA methylation data from human colon

value: Methyl-depleted fraction from normal colon


title: 624_colon_normal

description: DNA methylation data from human colon


title: Control_normoxia_ATF2-/-_rep1

source_name: Primary melanocytes were treated with Doxycycline before isolation of total RNA

value: Primary melanocytes


title: 449_brain_normal

description: DNA methylation data from human brain

value: Methyl-depleted fraction from normal brain


title: 441_colon_normal

description: DNA methylation data from human colon


title: 517_colon_normal

description: DNA methylation data from human colon


title: 432_brain_normal

description: DNA methylation data from human brain


title: 441_brain_normal

description: DNA methylation data from human brain


title: 428_brain_normal

description: DNA methylation data from human brain


title: 11734

city: Wilrijk

first: Lucia

last: Vergauwen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

hyb_protocol: 300 ng of both Cy3 and Cy5 labelled cRNA were applied onto every microarray. Microarray slides were incubated at 65°C for 17h in a rotating Agilent hybridization chamber. Slides were subsequently washed with Agilent wash buffers and acetonitrile and finally submersed in stabilization and drying solution (Agilent Technologies, Diegem, Belgium) to prevent ozone-induced Cy5-degradation. An A-optimal interwoven loop design was used in which each sample appeared on an array twice in Cy3 and twice in Cy5, resulting in 36 arrays for 18 samples.

scan_protocol: Microarrays were scanned using a Genepix Personal 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 µm. The photomultiplier tube voltages (PMT) for separate wavelengths were adjusted to obtain an overall green/red ratio of 1.

data_processing: Images were processed using GenePix Pro 4.1 software (Axon Instruments, Union City, CA, USA) for spot identification and quantification of the fluorescent signal intensities. Statistical analysis was performed using the R package limma (Linear Models for Microarray Data). Spots for which red or green FG < BG + 2SD on all arrays, were deleted before analysis (FG: median foreground intensity, BG: average local background intensity calculated over the full microarray, SD: standard deviation of local background intensities). Median intensity data were background corrected using a normal-exponential convolution model (function backgroundCorrect with method “normexp”, offset = 50) and loess-normalized (function normalizeWithinArrays, method = “loess”).

organism: Danio rerio

source_name: liver 34°C 28 days replicate 1

label_protocol: Fluorescently labelled cRNA was constructed starting from total RNA extracts, following Agilent’s two-colour microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com) using the Quick Amp kit. Briefly, total RNA was reverse transcribed into first and second strand cDNA, after which first strand cRNA was constructed using the second strand cDNA as a template, in the presence of either Cy3-CTP or Cy5-CTP. The labelled cRNA was purified using the Qiagen RNeasy mini spin column kit (Qiagen, Venlo, The Netherlands). Labelling efficiency was determined at 550 nm (Cy3) and 650 nm (Cy5) using a NanoDrop spectrophotometer (NanoDrop Technologies, Rockland, DE, USA).

growth_protocol: Adult zebrafish (Danio rerio) were obtained from a commercial supplier (Aqua hobby, Heist-op-den-berg, Belgium) and acclimatized to laboratory conditions at 26 ± 0.5°C for one month in a climate chamber (Weiss Technik, Liedekerke, Belgium). Fish were kept in aerated, biologically filtered, medium-hard reconstituted freshwater (OECD 203 annex 2, 1992: CaCl2.2H2O: 294.00 mg/l; MgSO4.7H2O: 123.25 mg/l; NaHCO3: 64.75 mg/l; KCl: 5.75 mg/l), at a 14h/10h light/dark cycle. Total ammonia and nitrite levels were always zero. Water was renewed whenever nitrate concentrations reached 25 mg/l. Fish were fed daily with Sera micro-granuli (Heinsberg, Germany) at a rate of 1% of their mean wet weight.

extract_protocol: Total RNA extraction was performed following the Trizol extraction method (Invitrogen life technologies, Merelbeke, Belgium). RNA extracts were purified using Dnase I and RNAse inhibitor (Fermentas, St. Leon-Rot, Germany) and subsequent phenol/chloroform exctraction. RNA purity and integrity were evaluated by measuring 260/230 nm and 260/280 nm absorbance ratios and by denaturing formaldehyde-agarose gel electrophoresis respectively. 27 liver total RNA samples (3 biological replicates at 3 time points for 3 experimental conditions) were extracted, stored at -80°C and used for microarray analysis.

treatment_protocol: Liver from ten specimens per biological replicate were pooled, snap frozen in liquid nitrogen and stored at -80°C until analysis. Samples were homogenized on liquid nitrogen using mortar and pestle prior to aliquoting for different analyses.

tag: gender

value: female

source_name: liver 26°C 4 days replicate 1


title: 11730

description: An A-optimal interwoven loop design was used in which each sample appeared on an array twice in Cy3 and twice in Cy5, resulting in 36 arrays for 18 samples.

source_name: liver 26°C 4 days replicate 3

source_name: liver 18°C 4 days replicate 3


title: 11731

source_name: liver 34°C 4 days replicate 3


title: 11715

source_name: liver 26°C 28 days replicate 1

source_name: liver 18°C 28 days replicate 1


title: 11736

source_name: liver 18°C 28 days replicate 3

source_name: liver 34°C 4 days replicate 1


title: 11737

source_name: liver 34°C 28 days replicate 3

source_name: liver 26°C 4 days replicate 2


title: 11735

source_name: liver 26°C 28 days replicate 3

source_name: liver 18°C 4 days replicate 1


title: 11719


title: 11738

source_name: liver 26°C 28 days replicate 2

source_name: liver 18°C 4 days replicate 2


title: 11739

source_name: liver 18°C 28 days replicate 2

source_name: liver 34°C 4 days replicate 2


title: 11732


title: 11718


title: 11750


title: 11717

source_name: liver 34°C 28 days replicate 1


title: 11721


title: 11733

source_name: liver 34°C 28 days replicate 2


title: 11723

source_name: liver 26°C 4 days replicate 1


title: 11728


title: 11720


title: ASC_FBS_P2_rep6

city: Mannheim

first: Karen

last: Bieback

address: Ludolf-Krehl-Strasse 13-17

country: Germany

institute: Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University

description: Gene expression of ACS from Passage 2 cultured in FBS

hyb_protocol: An in situ hybridization kit plus (Agilent) was used as a hybridization buffer. After hybridization in a hybridization chamber for 16 h at 65°C, microarrays were washed in washing solution 1+2 (20 × SSC and 10% Triton X-102) for 10 min each and in Agilent stabilization and drying solution.

scan_protocol: Immediately after the washing process, microarrays were scanned by a GMS418 laser scanner (Affymetrix, Eurofins MWG GmbH) at an excitation wavelength of 543 nm (Cy3) and 633 nm (Cy5).

data_processing: Fluorescent intensities of scanned images were quantified by ArrayVision Ver.7 (Imaging research) and normalized applying Loess normalization procedure to adjust the Cy3 and Cy5 channels. Differential gene expression analysis was performed using the One-way ANOVA with the commercial software package SAS JMP7 Genomics 3.1 (SAS Institute). A false positive rate of a=0.05 with FDR correction was taken as the level of significance.

source_name: ASC, Passage 2, FBS

label_protocol: lHSel protocol: RNA from each sample was amplified and labeled using a Low input RNA fluorescent linear amplification kit (Agilent).

extract_protocol: Cells were harvested when reaching at least 80% confluency. At passage 2, extraction of RNA was performed for each sample using the RNeasy Mini Kit (Qiagen). The quality of RNA was confirmed by checking the RNA integrity number using using the RNA 6000 Nano LabChip Kit and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were cultured under three different culture-conditions: basal DMEM, low glucose, supplemented with 10 % fetal bovine serum, 10% human serum or 10% thrombin-activated platelet releasate plasma (for reference Kocaömer et al. Stem Cells. 2007;25(5):1270-8.

value: adipose tissue-derived mesenchymal stem cells

tag: supplement

value: 10% fetal bovine serum (FBS)


title: ASC_tPRP_P2_rep6

department: Institute of Transfusion Medicine and Immunology

description: Gene expression of ACS from Passage 2 cultured in tPRP

source_name: ASC, Passage 2, PRP

value: 10% thrombin-activated platelet releasate plasma (tPRP)


title: Cerebullum_wild-type control_ILM_rep2

source_name: cerebellum from Npc1 (BALB/cNctr-Npc1m1N/J) mice

value: Npc1 (BALB/cNctr-Npc1m1N/J)

value: wild-type

value: cerebellum


title: Wild type_rep3

description: S vs G1 Replication timing.

source_name: G1-phase cells, WT

source_name: S-phase cells, WT


title: 11729

value: liver

source_name: liver 26°C 4 days replicate 3


title: 11722


title: 11726

source_name: liver 34°C 4 days replicate 1


title: ASC_tPRP_P2_rep5


title: 11749

source_name: liver 34°C 4 days replicate 3


title: 11725


title: ASC_HS_P2_rep5

description: Gene expression of ACS from Passage 2 cultured in HS

source_name: ASC, Passage 2, HS

value: 10% human serum (HS)


title: ASC_HS_P2_rep4


title: ASC_HS_P2_rep6


title: Male MI (4218331004_B)

description: replicate 1

source_name: left ventricular samples (infarct excluded)

tag: age

value: 12-15 weeks

value: left ventricle

value: Male

value: MI


title: ASC_FBS_P2_rep5

tag: tissue


title: 11724

source_name: liver 18°C 4 days replicate 1


title: ASC_tPRP_P2_rep4


title: ASC_HS_P2_rep1b


title: ASC_tPRP_P2_rep1b


title: 11727

source_name: liver 26°C 4 days replicate 2

source_name: liver 18°C 4 days replicate 2


title: 11748

source_name: liver 18°C 4 days replicate 3

source_name: liver 34°C 28 days replicate 3


title: ASC_tPRP_P2_rep3


title: ASC_FBS_P2_rep4


title: 11747

source_name: liver 18°C 28 days replicate 3


title: Patient 10

city: Houston

first: Pawel

last: Stankiewicz

state: TX

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

hyb_protocol: 12x135K microarrays (NimbleGen Systems, Madison, WI, USA) were hybridized according to the manufacturer’s protocol.

scan_protocol: Scanning was done on NimbleGen MS 200 Microarray Scanner according to manufacturer's protocol.

data_processing: Scans were processed using NimbleScan v2.5, and analyzed with the SignalMap (NimbleGen Systems).

source_name: blood

label_protocol: 0.5 µg of genomic DNA from a test sample and 0.5 µg of a normal male reference sample were labeled by random priming with Cy3 and Cy5, respectively, using the NimbleGen Dual Color Labeling Kit.

extract_protocol: DNA was prepared from peripheral blood using the Puregene DNA isolation kit (Gentra Systems, Minneapolis, MN, USA).

value: blood

tag: disease state

value: epilepsy, learning difficulties, intellectual disability, and neurobehavioral abnormalities

source_name: Normal control

value: normal


title: Patient 11


title: 11746

source_name: liver 34°C 4 days replicate 2

source_name: liver 26°C 28 days replicate 3


title: ASC_FBS_P2_rep3

source_name: ASC, Passage 2, FBS


title: Patient 9


title: ASC_FBS_P2_rep1b


title: Patient 12


title: Patient 8


title: Patient 7


title: 30wk UPII-SV40Tag biological rep #1

city: Shreveport

first: John

middle: L

last: Clifford

state: LA

address: 1501 Kings Hwy

department: Biochemistry

institute: LSUHSC-Shreveport

description: Urothelial RNA, 30 wks of age

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

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

data_processing: Pixel intensities were measured, expression signals were analyzed and features extracted using GeneChip Operating Software 1.3.  Global scaling with a target intensity of 500 was used for normalization.

source_name: Urothelial RNA, 30 wks of age

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

growth_protocol: WT and UPII-SV40Tag mice were sacrificed at 3, 6, 20, and 30 weeks of age and the bladders immediately removed.  The urothelial lining was removed from the bladder for RNA extraction.

extract_protocol: RNA was purified using TriReagent according to manufacturers instructions.

tag: genetic background

value: FVB parent strain

value: Transgenic, uroplakin II promoter driving expression of SV40Tag

value: urothelium


title: 11745

value: female

source_name: liver 34°C 28 days replicate 1


title: 11744

source_name: liver 18°C 28 days replicate 1


title: 30wk UPII-SV40Tag biological rep #2

description: Urothelial RNA, 30 wks of age

tag: genotype


title: ASC_tPRP_P2_rep2

source_name: ASC, Passage 2, PRP

value: adipose tissue-derived mesenchymal stem cells

value: 10% thrombin-activated platelet releasate plasma (tPRP)


title: ASC_HS_P2_rep2

source_name: ASC, Passage 2, HS


title: ASC_FBS_P2_rep2

value: 10% fetal bovine serum (FBS)


title: 11742

source_name: liver 34°C 4 days replicate 3


title: 30wk Wild type biological rep #2

description: Urothelial RNA, 30 wks of age

value: wild type littermates


title: 11743

source_name: liver 34°C 4 days replicate 1

value: liver

source_name: liver 26°C 28 days replicate 1


title: Patient 6


title: Patient 5


title: Patient 4


title: ASC_HS_P2_rep1

value: 10% human serum (HS)


title: 20wk UPII-SV40Tag biological rep #2

description: Urothelial RNA, 20 wks of age

source_name: Urothelial RNA, 20 wks of age


title: 30wk Wild type biological rep #1

description: Urothelial RNA, 30 wks of age


title: ASC_FBS_P2_rep1


title: Patient 3


title: ASC_tPRP_P2_rep1


title: 11740

source_name: liver 34°C 28 days replicate 2

source_name: liver 26°C 4 days replicate 3


title: 11741

source_name: liver 26°C 4 days replicate 1

source_name: liver 18°C 4 days replicate 3


title: Patient 1

source_name: blood

source_name: Normal control


title: 11716


title: 20wk UPII-SV40Tag biological rep #1

description: Urothelial RNA, 20 wks of age


title: 8146_vehicle control_2

city: Gainesville

first: yanxia

last: liu

state: FL

address: 1600 SW Archer Rd

department: Medicinal Chemistry

institute: University of Florida

description: Gene expression data from solvent control treatment

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

scan_protocol: GeneChips were scanned with a Affymetrix GeneChip® 7G Scanner.

data_processing: The array data were normalized using Affy package in Bioconductor. Raw data were normalized by Robust Multichip Analysis (RMA) approach. A linear modeling approach and the empirical Bayes statistics implemented in the Limma package were employed for differential expression analysis.

source_name: colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human colorectal carcinoma cells HCT116 (ATCC) were grown in DMEM medium supplemented with 10% FBS.

extract_protocol: Total RNA was extractedaccording to the manufacturer's instructions.

treatment_protocol:
Human HCT116 colorectal carcinoma cells (400,000) were seeded per well (6-well dish) and one day later treated with largazole, SAHA, FK228 and vehicle control. The final concentration of largazole and FK228 is 20 nM, and SAHA is 2 uM. After 10 h treatment, total RNA was isolated. Largazole and FK228 were synthesized (1,2).SAHA was obtained from Selleck Chemicals Co. Ltd.
references: 1. Ying Y, Taori K, Kim H, Hong J, Luesch H (2008) Total synthesis and molecular target of largazole, a histone deacetylase inhibitor. J Am Chem Soc 130:8455-8459 and 2. Wen S, Packham G, Ganesan A (2008) Macrolactamization versus macrolactonization: Total synthesis of FK228, the depsipeptide histone deacetylase inhibitor. J Org Chem 73:9353-9361)

tag: cell line

value: colorectal carcinoma

tag: treatment group

value: vehicle control


title: 20wk Wild type biological rep #2

description: Urothelial RNA, 20 wks of age


title: 20wk Wild type biological rep #1

description: Urothelial RNA, 20 wks of age


title: 6wk UPII-SV40Tag biological rep #2

description: Urothelial RNA, 6 wks of age

source_name: Urothelial RNA, 6 wks of age


title: Patient 2


title: 6wk UPII-SV40Tag biological rep #1

description: Urothelial RNA, 6 wks of age


title: 8145_vehicle control_1

tag: cell type


title: 8144_FK228_2

description: Gene expression data from FK228 treatment


title: explants injected with HMM, replicate 1

first: Ian

middle: K

last: Quigley

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

hyb_protocol: 10ug of cRNA was hybridized to Xenopus laevis Affymetrix chips for 16hrs at 45C, then washed and stained using the Affymetrix Fluidics Station

scan_protocol: GeneChip Scanner 3000 7G from Affymetrix

data_processing: Data was processed using Microarray Suite 5.0 software using Affymetrix default settings.  Statistical analysis was later performed using Bullfrog software

organism: Xenopus laevis

source_name: explants from embryos injected with HMM RNA

label_protocol: Biotynylated cRNA was prepared according to standard Affymetrix Protocols

growth_protocol: Xenopus embryos grown in 0.1X MMR until stage 9/10

extract_protocol: Total RNA was extracted using the Proteinase K method

treatment_protocol: Animal caps were cut, explanted and cultured in Danilchik's + 0.1% BSA from stage 9/10 until harvest at stage 22

tag: treatment

value: injected at 2-cell stage

tag: culture

value: explanted at stage 9/10

tag: developmental stage

value: harvested at equivalent of stage 22

tag: agent

value: HMM

value: epithelial explant


title: explants injected with HMM, replicate 2


title: ASC_HS_P2_rep3


title: 6wk Wild type biological rep #1

description: Urothelial RNA, 6 wks of age

value: FVB parent strain


title: Mouse cortex of control mice, biological rep3

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 16 hours of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al., 2003). To identify differentially expressed genes, gene expression intensity was compared using a moderated t-test and a Bayes smoothing approach developed for a low number of replicates (Smyth, 2004). To correct for the effect of multiple testing, the false discovery rate, was estimated from p values derived from the moderated t-test statistics (Benjamini et al., 2001). The analysis was performed using the affylmGUI Graphical User Interface for the Limma microarray package.
MoGene-1_0-st-v1.r3.pgf
MoGene-1_0-st-v1.r3.mps

source_name: littermate controls

label_protocol: Total RNA (200 ng per sample) was labeled using the Affymetrix GeneChip® WT cDNA Synthesis and Amplification Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Mouse mutant phenotypes were identified by genotyping as wild-type or mutants. All brain samples were dissected and snap frozen in liquid N2. All samples were prepared using the miRVana PARIS kit (Ambion). Total RNA (200 ng per sample) was labeled using the Affymetrix GeneChip WT cDNA Synthesis and Amplification Kit (Ambion).

value: adult forebrain cortex

value: CamKII-Cre/+;Dicer flox/+ or +/+;Dicer flox/flox


title: 8143_FK228_1


title: 8142_SAHA_2

description: Gene expression data from SAHA treatment

value: SAHA


title: 3wk UPII-SV40Tag biological rep #2

description: Urothelial RNA, 3 wks of age

source_name: Urothelial RNA, 3 wks of age

value: Transgenic, uroplakin II promoter driving expression of SV40Tag

value: urothelium


title: 3wk UPII-SV40Tag biological rep #1

description: Urothelial RNA, 3 wks of age


title: 8141_SAHA_1


title: explants injected with ICD, replicate 3

source_name: explants from embryos injected with ICD RNA

value: ICD


title: 8140_LZ_2

description: Gene expression data from largazole treatment

value: Largazole


title: Mouse cortex of control mice, biological rep1


title: explants injected with ICD, replicate 1


title: explants injected with ICD, replicate 2


title: 8139_LZ_1


title: Mouse cortex of Dicer KO mice, biological rep2

source_name: Dicer KO

value: CamKII-Cre/+;Dicer flox/flox


title: Mouse cortex of control mice, biological rep2


title: 3wk Wild type biological rep #1

description: Urothelial RNA, 3 wks of age

value: wild type littermates


title: Mouse cortex of Dicer KO mice, biological rep3


title: Healthy control-subj. 15

status: Public on Aug 27 2010

first: Robert

middle: D

last: Beech

address: 34 Park St

department: Psychiatry

description:
Healthy control-subj. 15
HC15

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Peripheral blood

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

extract_protocol: Total RNA was isolated from 10 cc whole blood using the PAXgene Blood RNA Isolation kit (QIAGEN, Valencia, CA) per the manufacturer's instructions, and depleted of globin mRNA message using GLOBINclear hybridization capture technology (Ambion, Austin, TX). Quality control was performed with Agilent Bioanalyser.

value: Healthy control

tag: subject

value: Peripheral blood

value: F

tag: race/ ethnicity

value: W

tag: age (in years)

tag: mood stabilizers, antipsychotic medications

tag: YMRS

tag: HAM-A

tag: MADRS

tag: BPD I

tag: BPD II


title: Healthy control-subj. 12

description:
Healthy control-subj. 12
HC12

tag: disease state

tag: tissue

tag: gender

value: O


title: Healthy control-subj. 14

description:
Healthy control-subj. 14
HC14


title: 3wk Wild type biological rep #2

description: Urothelial RNA, 3 wks of age

tag: genetic background

tag: genotype

tag: age


title: Healthy control-subj. 9

description:
Healthy control-subj. 9
HC9


title: Mouse cortex of Dicer KO mice, biological rep1


title: GAS_NS488_4

city: St Lucia

first: Peter

middle: G

last: Maamary

address: Cooper Road

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: University of Queensland

description:
116 11.14.08.gpr
NS488_4_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

hyb_protocol: Dendrimer-labeled cDNA samples from different pairs of isolates were combined and hybridised to the microarray slide for 16 h. Slides were washed to remove unbound cDNA and labeled with dendrimer-targeted Alexa Fluor 546 and Alexa Fluor 647 dyes (Genisphere) for 5 h. Following a final wash to remove excess fluorescent dye, slides were coated in DyeSaver2 (Genisphere) to preserve the fluorescent signal, and subsequently polished with toluene/acetone (3:1) to minimize background fluorescence immediately prior to scanning .

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner (Axon Instruments, Inc.)

data_processing: All transcriptional and statistical analyses were undertaken in silico using GeneSpring GX 10 (Agilent Technologies). Background-subtracted data were filtered and raw fluoresecene values below 50 were discareded as fold-changes at this level may lead to misinterpretation. Data were normalized to the median and presented in log scale for analysis based on fold-change.

label: Alexa Fluor 546

organism: Streptococcus pyogenes

source_name: strain NS488 mid-log in vitro

label_protocol: Purified RNA was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit according to the manufaturer.

growth_protocol: Overnight  cultures were sub-inoculated 1:10 into fresh pre-warmed Todd-Hewitt broth supplemented with yeast extract and grown to mid-logarithmic phase

extract_protocol: Mid-logarithmic phase in vitro-grown bacteria were harvested by centrifugation and lysed by mechanical disruption. Bacterial RNA for microarray was extracted using the RNeasy Mini Kit (Qiagen) and treated with TURBO DNA-free DNase (Ambion) to remove contaminating DNA.

tag: strain

tag: growth phase and conditions

value: mid-logarithmic phase in vitro

tag: m type

tag: covrs status

value: intact


title: Healthy control-subj. 11

description:
Healthy control-subj. 11
HC11

tag: subject

tag: race/ ethnicity

tag: age (in years)


title: GAS_A20_4

description:
116 11.14.08.gpr
A20_4_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

label: Alexa Fluor 647

source_name: strain A20 mid-log in vitro

value: mutant


title: GAS_5448_4

description:
113 11.13.08.gpr
5448_4_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

source_name: strain 5448 mid-log in vitro


title: GAS_NS488_3

description:
115 11.14.08.gpr
NS488_3_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_ALAB49_4

description:
114 11.13.08.gpr
ALAB49_4_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

source_name: strain ALAB49 mid-log in vitro


title: GAS_NS730_4

description:
115 11.14.08.gpr
NS730_4_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

source_name: strain NS730 mid-log in vitro


title: GAS_NS730_3

description:
114 11.13.08.gpr
NS730_3_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_ALAB49_3

description:
113 11.13.08.gpr
ALAB49_3_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

source_name: strain ALAB4 mid-log in vitro


title: Healthy control-subj. 13

description:
Healthy control-subj. 13
HC13

tag: mood stabilizers, antipsychotic medications

tag: YMRS

tag: HAM-A


title: Healthy control-subj. 7

description:
Healthy control-subj. 7
HC7

tag: MADRS

tag: BPD I

tag: BPD II


title: Healthy control-subj. 8

description:
Healthy control-subj. 8
HC8

tag: disease state

tag: tissue

tag: gender

value: H


title: Healthy control-subj. 6

description:
Healthy control-subj. 6
HC6


title: Pooled Human Maternal Blood Cells Sample 2 with Dye Swap

city: Pittsburgh

first: Tianjiao

last: Chu

state: PA

address: 204 Craft Ave

institute: Magee Womens Research Institute

description: Biological replicate 2 of 2 pooled MBC samples divided into two parts. One part digested with HpaII and labeled with Cy5, the other part not digested, and labeled with Cy3.

hyb_protocol: Hybridization was performed in a mix containing 50µL of human Cot-1, 52µL of Agilent 10x blocking agent, 260µL of Agilent 2x HiRPM hybridization buffer, and 158µL of the labeled DNA. The hybridization mix was heated to 95°C for 3 minutes, then incubated at 37°C for 30 minutes and applied onto the active array area. Hybridization with gentle agitation was carried out at 65°C for 40 hours. After hybridization, the slides were washed in Oligo aCGH Wash Buffer 1 and Oligo aCGH Wash Buffer 2, followed by acetonitrile and Stabilization and Drying Solution (Agilent) per the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505B scanner, using Agilent CGH-v4_95_Feb07 protocol.

data_processing: Data were extracted using Agilent Feature Extraction Software (version 9.5.3.1). The log10 of processed Red signal/processed Green signal ratio was obtained using Agilent software. LOWESS normalization using the normalize.loess function of the affy package of BioCondutor was then used to normalize the ratio.

source_name: Human Maternal Blood Cells

label_protocol: Experimental and reference DNA were labeled with Cy3-dUTP and Cy5-dUTP respectively, and vice versa for dye-swaps, using a BioPrime CGH Genomic Labeling kit per the manufacturer’s protocol (Agilent).

extract_protocol:
All samples used in this study were de-identified discarded tissues. CVS samples were obtained between gestational weeks 11 and 13 from the Magee-Womens Hospital Cytogenetic Laboratory. Samples were dissected under a microscope and separated from any decidua or flecks of blood. The culture media was removed and the tissue placed in 1.5 -2.0mL microcentrifuge tubes before freezing at -80oC until DNA was extracted. To extract the DNA, one 5mm stainless steel bead and 180mL buffer ATL (from Qiagen’s DNeasy Blood and Tissue kit) were added to each CVS sample. The samples were placed in the TissueLyser (Qiagen) Adaptor set 2 x 24, and the TissueLyser was operated for 20 seconds at 30Hz. The DNA was then purified using the DNeasy Blood and Tissue kit as per the manufacturer’s protocol. MBCs were obtained between gestational weeks 11 and 13 from the Magee Women’s Hospital Prenatal Screening lab. DNA was extracted from the MBC’s using a modified protocol previously described by Iovannisci, et al., 2006 (Iovannisci et al., 2006), using reagents from the MasturePure DNA Purification Kit (Epincentre Technologies, Madison, WI, Cat. No. MCD85201). Briefly, clotted blood (approximately 1mL) was mixed with an equal volume (1mL) of 2X Tissue and Cell Lysis Solution, votexed for 10s and combined with 2mL Tissue and Cell Lysis Solution (MasturePure kit) containing 25ng/mL proteinase K. 2mL of MPC Protein Precipitation Reagent was added to the total volume (4mL) of the lysed sample and vortex vigorously for 10-15 sec, after which samples were cooled on ice for 1 hour. Cell debris were then pelleted by centrifugation (x2) for at least 30 min at ³ 2000g and supernatants transferred to a new 50mL conical tube. DNA was precipitated in 2 volumes of isoproponal, purified by phenol/chloroform extraction and resuspended in 50mL DNAse/RNAse free water.
Genomic DNA samples (3mg) were digested for 2 hours at 37oC with 50U HpaII (New England Biolabs [NEB]) in 90mL total reaction volume using NEB buffer 4. A second aliquot of 50U, 1mL of buffer 4, and 4mL water were added and digestion continued overnight (total reaction volume was 100mL). Mock digestion controls were included to monitor digestion efficiency. Following overnight digestion, reactions were digested further with 5uL (50U) of TspRI (NEB) at 65ºC for three hours. Reactions were then incubated further with 75U (0.75ml) Exonuclease III (NEB) and incubated at 30ºC for 1 hour. Enzymatic activity was then nullified by heating at 70oC for 20min after which 50U of RecJF (NEB) were added to remove single stranded DNA. Reactions were incubated for 30min at 37oC and inactivated at 65oC for 20min. Reactions were then phenol-chloroform extracted and the DNA precipitated and resuspended in 21.2mL nuclease-free de-ionized water. Finally, extracted genomic DNA was quantified and assessed for purity using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

value: Human Maternal Blood Cells

tag: hpaii digestion

value: Yes

value: No


title: TEL-AML1 ChIP 1

city: San Francisco

first: Joseph

middle: Leo

last: Wiemels

address: 1450 3rd Street, MC 0520

institute: UCSF

description: TEL-AML1 ChIP chip, microRNA promoter arrays

hyb_protocol: Hybridization was carried out according to Nimblegen's standard protocol

scan_protocol: Tiling Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: ChIP-chip data were normalized using the scatter plot smoother lowess based on all probes.  For analysis of significant “enrichment,” data were first sorted according to genomic locations, and a window of size of 500bp moving along the genome was adopted, centering at each probe.  For each probe, the median log-ratio of neighbor probes residing in the window was calculated; typically with 10 probes within each window.

source_name: TEL-AML1 ChIP DNA

label_protocol: At least 4 ug of ligation-mediated PCR-amplified DNA was used to carry out the labeling step.

growth_protocol: The B-cell precursor leukemic cell line REH was grown in 24-well plates (Nunc, Roskilde, Denmark) at 106 cells/mL and was cultured in 6-well plates in RPMI with 10% fetal bovine serum.

extract_protocol: Cells were harvested, and chromatin was formalin crosslinked and sheared to approximately 200–1000 bp using a Sonic Dismembrator model 550 at settings 1.5, for 2–4 cycles 50 s per cycle on ice. The chromatin DNA complexes were then isolated following the microarray application protocol as described in the kit (EZ-ChIP Kit).

treatment_protocol: ChIP antibody to TEL (Santa Cruz Biotechnology) was used.

tag: cell type

value: REH

tag: chip antibody

value: anti-TEL (Santa Cruz Biotechnology)

source_name: Input DNA

treatment_protocol: The chromatin DNA that was not immunoprecipitated served as the input DNA


title: Healthy control-subj. 10

description:
Healthy control-subj. 10
HC10

value: As


title: Pooled Human Maternal Blood Cells Sample 1 with Dye Swap

description: Biological replicate 1 of 2 pooled MBC samples divided into two parts. One part digested with HpaII and labeled with Cy5, the other part not digested, and labeled with Cy3.


title: GAS_5448AP_4

description:
112 11.13.08.gpr
5448AP_4_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

source_name: strain 5448AP mid-log in vitro

tag: strain

tag: growth phase and conditions

tag: m type


title: GAS_5448_3

description:
112 11.13.08.gpr
5448_3_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

tag: covrs status


title: Healthy control-subj. 5

description:
Healthy control-subj. 5
HC5

tag: subject

value: M

tag: race/ ethnicity

tag: age (in years)


title: GAS_NS88.2rep_4

description:
111 11.13.08.gpr
NS88.2rep_4_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

source_name: strain NS88.2rep mid-log in vitro


title: Healthy control-subj. 4

description:
Healthy control-subj. 4
HC4

tag: mood stabilizers, antipsychotic medications

tag: YMRS

tag: HAM-A


title: GAS_5448AP_3

description:
111 11.13.08.gpr
5448AP_3_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: Pooled Human Chorionic Villus Sample 2

description: Biological replicate 2 of 2 pooled CVS samples divided into two parts. One part digested with HpaII and labeled with Cy3, the other part not digested, and labeled with Cy5.

source_name: Human Chorionic Villus

value: Human Chorionic Villus


title: Pooled Human Maternal Blood Cells Sample 1

description: Biological replicate 1 of 2 pooled MBC samples divided into two parts. One part digested with HpaII and labeled with Cy3, the other part not digested, and labeled with Cy5.


title: GAS_A20_3

description:
109 11.13.08.gpr
A20_3_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_NS88.2_4

description:
110 11.13.08.gpr
NS88.2_4_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

source_name: strain NS88.2 mid-log in vitro


title: Healthy control-subj. 3

description:
Healthy control-subj. 3
HC3

value: Healthy control

tag: MADRS

tag: BPD I

tag: BPD II


title: GAS_NS88.2rep_3

description:
110 11.13.08.gpr
NS88.2rep_3_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: Bipolar depressed-subj. 17

description:
Bipolar depressed-subj. 17
BPD17

tag: disease state

value: Bipolar depressed

tag: tissue

value: Peripheral blood

tag: gender


title: Pooled Human Chorionic Villus Sample 1 with Dye Swap

description: Biological replicate 1 of 2 pooled CVS samples divided into two parts. One part digested with HpaII and labeled with Cy5, the other part not digested, and labeled with Cy3.

tag: hpaii digestion


title: Bipolar depressed-subj. 18

description:
Bipolar depressed-subj. 18
BPD18

value: W

value: Seroquel, Trileptal, Klonopin, Geodon


title: Bipolar depressed-subj. 19

description:
Bipolar depressed-subj. 19
BPD19

value: F


title: Bipolar depressed-subj. 20

description:
Bipolar depressed-subj. 20
BPD20

value: Topamax, Seroquel, Celexa, Risperidone


title: TEL-AML1 ChIP 2

tag: cell type

tag: chip antibody


title: Pooled Human Chorionic Villus Sample 2 with Dye Swap

description: Biological replicate 2 of 2 pooled CVS samples divided into two parts. One part digested with HpaII and labeled with Cy5, the other part not digested, and labeled with Cy3.


title: GAS_NS88.2_3

description:
109 11.13.08.gpr
NS88.2_3_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

tag: strain

tag: growth phase and conditions

value: mid-logarithmic phase in vitro

tag: m type

value: mutant


title: GAS_A20_2

description:
108 11.12.08.gpr
A20_2_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

tag: covrs status


title: Pooled Human Maternal Blood Cells Sample 2

description: Biological replicate 2 of 2 pooled MBC samples divided into two parts. One part digested with HpaII and labeled with Cy3, the other part not digested, and labeled with Cy5.

value: Human Maternal Blood Cells


title: Bipolar depressed-subj. 16

description:
Bipolar depressed-subj. 16
BPD16

tag: subject

tag: race/ ethnicity

tag: age (in years)

value: Seroquel, Risperidone


title: GAS_NS488_2

description:
108 11.12.08.gpr
NS488_1_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

value: intact


title: GAS_NS488_1

description:
107 11.12.08.gpr
NS488_1_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_NS730_2

description:
107 11.12.08.gpr
NS730_2_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_NS730_1

description:
106 11.12.08.gpr
NS730_1_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: Bipolar depressed-subj. 15

description:
Bipolar depressed-subj. 15
BPD15

value: H

tag: mood stabilizers, antipsychotic medications

tag: YMRS

tag: HAM-A


title: GAS_5448_1

description:
104_111108.gpr
5448_1_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_5448_2

description:
105 11.12.08.gpr
5448_2_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_ALAB49_2

description:
106 11.12.08.gpr
ALAB49_2_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: Bipolar depressed-subj. 14

description:
Bipolar depressed-subj. 14
BPD14

value: Zyprexa, Tegretol

tag: MADRS

tag: BPD I

tag: BPD II


title: Bipolar depressed-subj. 13

description:
Bipolar depressed-subj. 13
BPD13

tag: disease state

tag: tissue

tag: gender


title: GAS_ALAB49_1

description:
105 11.12.08.gpr
ALAB49_1_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: Bipolar depressed-subj. 12

description:
Bipolar depressed-subj. 12
BPD12


title: Bipolar depressed-subj. 9

description:
Bipolar depressed-subj. 9
BPD9

value: Zyprexa


title: GAS_5448AP_2

description:
104_111108.gpr
5448AP_2_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: Bipolar depressed-subj. 11

description:
Bipolar depressed-subj. 11
BPD11

value: M

value: Depakote, Seroquel


title: Bipolar depressed-subj. 6

description:
Bipolar depressed-subj. 6
BPD6

value: Seroquel


title: Bipolar depressed-subj. 10

description:
Bipolar depressed-subj. 10
BPD10

value: Bipolar depressed

value: AA


title: Bipolar depressed-subj. 7

description:
Bipolar depressed-subj. 7
BPD7

value: Peripheral blood

value: W


title: Bipolar depressed-subj. 8

description:
Bipolar depressed-subj. 8
BPD8

value: F

value: Seroque, Ativan


title: GAS_5448AP_1

description:
103.2 11.14.08.gpr
5448AP_1_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

value: mid-logarithmic phase in vitro


title: Healthy control-subj. 2

description:
Healthy control-subj. 2
HC2

value: Healthy control


title: GAS_NS88.2rep_2

description:
103.2 11.14.08.gpr
NS88.2rep_2_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_NS88.2rep_1

description:
102_111108.gpr
NS88.2rep_1_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_NS88.2_1

description:
101_111108.gpr
NS88.2_1_green
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit

value: mutant


title: GAS_A20_1

description:
101_111108.gpr
A20_1_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: GAS_NS88.2_2

description:
102_111108.gpr
NS88.2_2_red
RNA from bacteria bacteria grown in vitro to mid-logarithmic phase was converted to dendrimer-labeled cDNA with the Genisphere 3DNA Array 900MPX Kit


title: Bipolar depressed-subj. 4

description:
Bipolar depressed-subj. 4
BPD4


title: Bipolar depressed-subj. 3

description:
Bipolar depressed-subj. 3
BPD3


title: Bipolar depressed-subj. 5

description:
Bipolar depressed-subj. 5
BPD5


title: Bipolar depressed-subj. 2

description:
Bipolar depressed-subj. 2
BPD2


title: SAX1 genotype chr 7 and X

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina

data_processing: Standard Illumina

label: C-Bio and A-DNP

organism:
Homo sapiens
Mus musculus

source_name: Tissue culture cells

label_protocol: Standard Illumina

growth_protocol: Normal cells

extract_protocol: Purification of genomic DNA by phenol chloroform extraction

tag: cell line


title: Healthy control-subj. 1

description:
Healthy control-subj. 1
HC1


title: GIST_28_KIT (expression)

city: Bologna

first: Maria

middle: Abbondanza

last: Pantaleo

state: BO

address: via Massarenti 9

department: Institute of Hematology and Medical Oncology "L.A.Seragnoli"

country: Italy

institute: Policlinico S. Orsola-Malpighi, University of Bologna

description: Gene expression data from GIST with KIT mutation

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

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

data_processing: The data were analyzed with Bioconductor affy package, using RMA algorithm for normalization and summarization.

source_name: GIST tumor, KIT mutated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Extraction of total RNA was performed with RNeasy spin columns on flash frozen tumor specimens, according to the manufacturer's instructions.

value: gastrointestinal stromal tumor

tag: age


title: Pooled Human Chorionic Villus Sample 1

description: Biological replicate 1 of 2 pooled CVS samples divided into two parts. One part digested with HpaII and labeled with Cy3, the other part not digested, and labeled with Cy5.

value: Human Chorionic Villus

tag: hpaii digestion

value: No

value: Yes


title: Bipolar depressed-subj. 1

description:
Bipolar depressed-subj. 1
BPD1


title: GIST_26_PDGFRA (expression)

description: Gene expression data from GIST with PDGFRA mutation

source_name: GIST tumor, PDGFRA mutated


title: Family 5, father of 5.1 (92930)

city: Bergen

first: Torunn

last: Fiskerstrand

address: Jonas Lies vei

department: Center for medical genetics and molecular medicine

country: Norway

institute: Haukeland University Hospital

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
CHP files (generated by Affymetrix GTYPE using the BRLMM algorithm) were processed by the programs Progeny lab and  PLINK to identify possible areas of homozygosity in the affected in each family.
Primary data description: Genotype Call (SNP call): 11, 22, 33, 44, 12, 13 ,14 , 23, 24 and 00 (NoCall). The processed data are for each family (1-5 plus 7), and the genotype calls are sorted according to chromosome and position from pter. cM between markers and position in bp from pter are also given.
Sorted genotype calls data: see Series GSE23151 supplementary files.

source_name: Lymphocytes

label_protocol: Standard Affymetrix procedures

extract_protocol: Genomic DNA was extracted from lymphocytes obtained from peripheral blood using the M48 DNA purification system (Qiagen, Germany).

tag: sample name

tag: family

tag: individual

value: father of 5.1

value: peripheral blood

tag: cell type

value: lymphocyte


title: GIST_25_KIT (expression)

value: M


title: Family 7, affected individual 7.1 (91999)

value: affected individual 7.1


title: Family 5, mother of 5.1 (92931)

value: mother of 5.1


title: GIST_24_WT (expression)

description: Gene expression data from GIST wild type both for KIT and PDGFRA

source_name: GIST tumor, KIT and PDGFRA wild type


title: SATO3 genotype


title: FATO genotype

value: FATO