title: U87 Poly Control_1

source_name: tumor cell line U87; polysomal RNA; untreated

treatment_protocol: No treatment as control grown in the same condition as irradiated U87 cells

tag: Polysome RNA from Human Brain Tumor Cell Line U87 as control


title: U87 Total 7gy7h_1

status: Public on May 21 2008

type: RNA

city: Gaithersburg

first: Shuping

last: Zhao

state: MD

address: 8717 Grovemont Circle

department: Radiation Oncology Branch

country: USA

institute: NCI

description: Tumor cell lines had a biological replicate, and each replicate was run on duplicate slides.

scan_protocol: Hybridized arrays were scanned with 10-Am resolution on a GenePix 4000A scanner (Axon Instruments, Inc., Foster City, CA) at wavelengths 635 and 532 nm for Cy5- and Cy3-labeled probes, respectively. The resulting TIFF images were analyzed by GenePix Pro 4.0 software (Axon Instruments).

data_processing: The ratios of the sample intensity to the reference [green (Cy3)/red (Cy5)] intensity for all targets were determined, and ratio normalization was done to normalize the center of ratio distribution to 1.0.

molecule: total RNA

organism: Homo sapiens

source_name: tumor cell line U87; total RNA; irradiated

label_protocol: Amplified RNA (1.5-3.0 Ag) was labeled with Cy3-dUTP (experimental RNA) or Cy5-dUTP (Stratagene Universal Reference, La Jolla, CA) using Superscript II Reverse Transcriptase (Invitrogen, Carlsbad, CA). Each cDNA microarray chip contained 7680 human cDNA clones (National Cancer Institute ROSP 8K Human Array), and methods for microarray hybridization and washing were described previously (Chuang YY, Chen Y, Gadisetti, et al. Gene expression after treatment with hydrogen peroxide, menadione, or t –butyl hydroperoxide in breast cancer cells. Cancer Res 2002;62:6246–54.16).

growth_protocol: U87 cells were grown in DMEM containing glutamate (5 mmol/L) and 10% fetal bovine serum(FBS)

extract_protocol: Cells were scraped from tissue culture flasks, and total RNA was extracted from each sample using TRIZOL reagent (Invitrogen, Carlsbad, CA) passed through an RNeasy spin column (Qiagen, Valencia, CA) and then amplified using RiboAmp RNA kits (Arcturus, Mountain View, CA) according to manufacturer’s protocol.

treatment_protocol:
Treatment:
Monolayer cultures were irradiated using a Pantak X-ray source at a dose rate of 1.55 Gy/min.

tag: irradiated Human Brain Tumor Cell line U87

source_name: Human Reference RNA

growth_protocol: reference to the manufacturer

extract_protocol:
PROTOCOL
Universal Human Reference RNA is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the Reference RNA for
use as follows:
1. Centrifuge the tube at 12,000 × g for 15 minutes at 4°C.
2. Carefully remove the supernatant.
3. Wash the pellet in 70% ethanol.
4. Centrifuge the tube at 12,000 × g for 15 minutes at 4°C.
5. Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol.
6. Resuspend the pellet in RNase-free water to the desired concentration.

treatment_protocol: no treatment

tag: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to

tag: be used as a reference for microarray gene-profiling experiments.


title: U87 Total 7gy6h_2

hyb_protocol: methods for microarray hybridization and washing were described previously (Chuang YY, Chen Y, Gadisetti, et al. Gene expression after treatment with hydrogen peroxide, menadione, or t –butyl hydroperoxide in breast cancer cells. Cancer Res 2002;62:6246–54.16).

tag: irradiated Human Brain tumor cell line U87


title: U87 Poly Control_2

type: other

molecule: other

extract_protocol: Polysomes were isolated using sucrose-gradient fractionation basically as described by Galban et al. Cells were grown to 80% confluence in 150-mm2 tissue culture dishes and incubated in 100 Ag of cycloheximide/mL for 15 minutes before collection. Cytoplasmic RNA was obtained by lysing cells in 1 mL of polysome buffer [10 mmol/L Tris-HCl (pH 8), 140 mmol/L NaCl, 1.5 mmol/L MgCl2, 0.5% NP40, 10 mmol/L DTT, 100 Ag/mL cycloheximide, 500 Ag/mL heparin, 1 mmol/L phenylmethanesulfonyl fluoride, and 500 units/mL RNasin (Promega, Madison, WI)]. After 10 minutes on ice, lysates were centrifuged (10,000 _ g for 10 minutes), and the resulting cytosolic supernatant was layered onto a 10% to 50% sucrose gradient. Gradients were then centrifuged at 35,000 _ g for 3 hours at 4C and 1-mL fractions collected using an ISCO Density Gradient Fractionation System (ISCO, Lincoln, NE) with continuous monitoring based on A254. The RNA in each fraction was extracted using TRIZOL and used for Northern analysis, or fractions 5 to 11 (corresponding to polysome-bound RNA) were pooled and subjected to microarray analysis.


title: U87 Total Control_2

source_name: tumor cell line U87; total RNA; untreated

treatment_protocol: no treatment as control grown in the same condition as irradiated U87 cells

tag: Human Brain Tumor Cell line U87 as control


title: A549 vs. WI38VA13 (LC-sense 5K original)

city: Gyeongju-si

first: Kyung-Oh

last: Doh

state: Gyeongsangbuk-do

address: 707 Seokjang-dong

department: Physiology

country: South Korea

institute: Dongguk University

description: Spotted by Genocheck (Ansan, Korea)

hyb_protocol: Hybridization was conducted at 66℃ for 16 hours in a humidified chamber. After hybridization, the slides were washed once each in 2xSSC/0.2% SDS for 5 minutes at 55℃, 2xSSC/0.2% SDS for 5 minutes at 65℃, 2xSSC for 5 minutes at room temperature, and 0.05xSSC for 5 minutes at room temperature, then spin-dried in a centrifuge prior to image scanning.

scan_protocol: The slides were scanned by GenePix 4000B (Molecular Devices).

data_processing: Intensity dependent(loess) normalization applied

source_name: WI38VA13 labeded with cy3

label_protocol: Total RNA sample (30 ug) from WI38VA13 cells was reverse-transcribed with oligo-dT primers in the presence of Cy3-dUTP. The labeled cDNA was then purified using a microcon-30 column. The cDNAs from the two samples were combined and precipitated with ethanol; the pellets were resuspended in a hybridization buffer.

extract_protocol: Total RNA preparation was conducted with Welprep RNA isolation reagent (Welgene), in accordance with the protocol recommended by the manufacturer. The quality of purified RNA was verified from the OD 260/280 ratios and via electrophoresis using agarose gels stained with ethidium bromide.

tag: lung fibroblast cell line

source_name: A549 labeled with cy5

label_protocol: Total RNA sample (30 ug) from A549 cells was reverse-transcribed with oligo-dT primers in the presence of Cy5-dUTP. The labeled cDNA was then purified using a microcon-30 column. The cDNAs from the two samples were combined and precipitated with ethanol; the pellets were resuspended in a hybridization buffer.

tag: lung cancer celline


title: Astro Total Control_1

source_name: primary normal astrocytes; total RNA; untreated

growth_protocol: Primary normal human astrocytes were purchased from Cambrex Bioscience and grown in astrocyte Growth Media for no more than three weeks with a change of media every 2 days until cells were 80% confluent. All cultures are maintained at 37 C° in an atmosphere of 5% CO2  and 95% room air.

treatment_protocol: Treatment: no treatment, as a control grown in the same condition as treatment group

tag: Primary normal human astrocytes as control


title: Astro Total 7gy6h_1

source_name: primary normal astrocytes; total RNA; irradiated

tag: total RNA from the irradiated Astrocytes 7gy6h


title: Astro Total 7gy6h_2

tag: total RNA from irradiated Astrocytes 7gy6h


title: Astro Total Control_2

treatment_protocol:
Treatment:
no treatment, as a control grown in the same condition as treatment cells

tag: replicate for Astro Total Control_1


title: Astro Poly Control_2

source_name: primary normal astrocytes; polysomal RNA; untreated

growth_protocol: Primary normal human astrocytes were purchased from Cambrex Bioscience and grown in astrocyte Growth Media for no more than three weeks with a change of media every 2 days until cells were 80% confluent. All cultures are maintained at 37 C° in an atmosphere of 5% CO2 and 95% room air.

tag: polysome RNA from Astrocytes as control


title: Astro Poly Control_1

tag: polysome RNA of normal astrocytes as a control


title: Astro Poly 7gy6h_1

source_name: primary normal astrocytes; polysomal RNA; irradiated

tag: Polysome RNA from Irradiated Astrocytes


title: U87 Total Control_1


title: large_follicle_theca_cell_rep1

status: Public on May 20 2008

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: RNA from theca cell of large follicles

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing:
Auto-scale ON (1-1000).  Scaling = all probe sets, Target Signal 125.  The microarray chip image data were converted to numerical data with GeneChip Operating Software (Affymetrix)  using MAS-5 preprocessing algorithm.
The absolute analysis from MAS was imported into GeneSpring 7.3 software (Silicon Genetics, Redwood City, CA). The developing follicle data were normalized within GeneSpring using the default/recommended normalization methods. These include setting of signal values below 0.01-0.01, total chip normalization to the 50th percentile, and normalization of each gene to the median.

label: biotin

organism: Bos taurus

source_name: theca cells of large follicles (>10 mm)

label_protocol: standard Affymetrix procedures

extract_protocol: Cells from 20-40 follicles of the same size were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).

treatment_protocol: Bovine ovaries were obtained from of young nonpregnant cycling heifers less then 10 min after death. Ovaries were delivered fresh on ice to laboratory. Only follicular stage ovaries were used as assessed by morphological criteria  that include the absence of a corpus luteum and the presence of developing large antral follicles.

tag: theca cells of large follicles (>10 mm) from follicular stage ovaries of young nonpregnant cycling heifers

tag: theca interna layers were dissected away in sheets from the follicle after granulosa cells were removed. Cell preparation have been characterized cytochemically to be greater that 98% pure and contain less than 1% contamination with endothelial cells.


title: large_follicle_theca_cell_rep2

description: RNA from theca cell of large follicles


title: Astro Poly 7gy6h_2

tag: Polysome RNA from irradiated astrocytes 7gy6h


title: medium_follicle_granulosa_cell_rep2

description: RNA from theca cell of medium follicles

tag: granulosa cells of medium follicles (5-10 mm) from follicular stage ovaries of young nonpregnant cycling heifers

tag: granulosa cells were isolated  by dissection (i.e. scraped and flushed) from the fresh tissue as previously described (Skinner and Osteen, 1988). Cell preparations have been characterized cytochemically to be greater that 98% pure and contain less than 1% contamination with endothelial cells.


title: medium_follicle_theca_cell_rep1

description: RNA from theca cell of medium follicles

tag: theca cells of medium follicles (5-10 mm) from follicular stage ovaries of young nonpregnant cycling heifers


title: small_follicle_theca_cell_rep1

description: RNA from theca cell of small follicles

tag: theca cells of small follicles (< or = 5 mm) from follicular stage ovaries of young nonpregnant cycling heifers


title: large_follicle_granulosa_cell_rep1

description: RNA from theca cell of large follicles

tag: granulosa cells of large follicles (>10 mm) from follicular stage ovaries of young nonpregnant cycling heifers


title: large_follicle_granulosa_cell_rep2

description: RNA from theca cell of large follicles

source_name: granulosa cells of large follicles (>10 mm)


title: small_follicle_theca_cell_rep2

description: RNA from theca cell of small follicles

source_name: theca cells of small follicles (< or = 5 mm)


title: OR3 rat

city: shanghai

first: Zhang

last: Qinghua

address: 151# libing road

country: China

institute: Shanghai shbiochip co

description: OR3 rat

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box. Incubate in a hybridization chamber at 42 ℃  for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1×SSC/0.2 SDS(50℃), 0.1×SSC/0.2%SDS(50 ℃) and 0.1×SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Green signal/processed Red signal (high fat diet rat/control rat)

organism: Rattus norvegicus

source_name: obesity-resistant, high fat diet rat

label_protocol: 2 ug of total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ℃ for 10 min, then reversed transcribed at 40℃ for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent). cDNAs were amplified at 40℃for 2 hours in the presence of T7 RNA Polymerase (Agilent) and 4 ul 25mM aaUTP (Ambion).Generated cRNA was purified with RNeasy mini Kit (QIAGEN). Equal amounts of the RNA from four control rats were mixed, and the mixture was labeled with Cy5, while the RNA from OP and OR rats was labeled with Cy3.Mix 4 ug amino allyl-modified cRNA and 100mg Cy3 NHS ester, incubate in the dark at room temperature(~25 ℃) for 1 hour then purified with RNeasy mini Kit (QIAGEN). Equal amounts of the RNA from four control rats were mixed, and the mixture was labeled with Cy5, while the RNA from OP and OR rats was labeled with Cy3.

extract_protocol: Total RNA was prepared from rat livers using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit.

tag: Wistar rats were feed on high fat diet for 16 weeks, in which some of them readily develop into obesity, but the remaining rats resist the development of obesity, termed as obesity-prone(OP) and obesity-resistant(OR) phenotypes respectively.The liver were collected for transcript profiling analysis

source_name: control rat

tag: Wistar rats were feed on standard diet for 16 weeks as control. The liver was collected for transcript profiling analysis


title: medium_follicle_theca_cell_rep2

description: RNA from theca cell of medium follicles

source_name: theca cells of medium follicles (5-10 mm)


title: OR4 rat

description: OR4 rat


title: OR2 rat

description: OR2 rat


title: medium_follicle_granulosa_cell_rep1

description: RNA from theca cell of medium follicles

source_name: granulosa cells of medium follicles (5-10 mm)


title: small_follicle_granulosa_cell_rep1

description: RNA from theca cell of small follicles

tag: granulosa cells of small follicles (< or = 5 mm) from follicular stage ovaries of young nonpregnant cycling heifers


title: small_follicle_granulosa_cell_rep2

description: RNA from theca cell of small follicles

source_name: granulosa cells of small follicles (< or = 5 mm)


title: OP4 rat

description: OP4 rat

source_name: obesity-prone, high fat diet rat


title: OR1 rat

description: OR1 rat


title: OP2 rat

description: OP2 rat


title: OP3 rat

description: OP3 rat


title: ET Patient 19 JAK2 wt. Dye-swap

status: Public on May 19 2008

city: BARCELONA

first: EULÀLIA

last: PUIGDECANET

state: BARCELONA

address: Passeig Marítim, 25-29

department: Patologia

country: Spain

institute: HOSPITAL DEL MAR

description: Technical replicate 2 of 2 of ET patient 19, with dye reversal. 58 year old female compared to healthy control pool.

hyb_protocol: Each microarray was hybridized with 750 ng of each amplified cRNA labelled with Cy5 or Cy3 at a specific activity between 7 and 15 pmoles/ug.  Duplicate hybridizations were performed for each comparison with dye-swapping to control for possible differences in the incorporation rate of the Cy5 and Cy3 fluorochromes. Microarray expression profiles were obtained using Whole Human Genome oligonucleotide microarrays (G4112A, Agilent Technologies, Palo Alto, CA), comprising 41.000 60nt oligonucleotide probes, most represented as single spots, using the protocol recommended by Agilent with SSC based washes.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner. Fluorescence intensity data was extracted and quantified using Genepix 6.0 (Molecular Dynamics). Only spots with signal intensities twice above the local background, not saturated and not flagged as absent by GenePix were considered reliable and used for subsequent analysis.

data_processing:
Normalization method: Loess with parameter span=0.3 downweighting spots with a foreground signal lower than 2-folds the corresponding local background.
Normalized log2ratios were scaled between arrays to make all data comparable. Statistically significant differences in gene expression were determined by computing a Bayesian statistic using all log2ratios from replicate hybridizations. Target genes were considered as differentially expressed when their empirical Bayes statistic B was higher than 15 (B_rank>98%). All quantitative and statistical analyses were performed using MMARGE tool, a web implementation of the Limma package in the R environment. Supervised classification of ET samples into categories according to clinical and biological parameters based on gene expression profiles was performed using standard two-tailed student test using the t-test function from R (cran.r-project.org) and was used to determine statistical significance of differential gene expression. Gene Ontology (GO) terms for annotated genes and common pathways were analyzed using the Ingenuity Pathways Analysis software (Ingenuity Systems, Inc.) and the FATIGO+ gene ontology-based application (fatigo.bioinfo.cnio.es).19 The differentially expressed gene lists were linked to the Internet genome databases (ie. GeneCards, GenBank, Swiss Prot, Online Mendelian Inheritance in Man).

source_name: Peripheral blood granulocytes, essential thrombocythemia

label_protocol: 500 ng of total RNA were reverse transcribed into cDNA and amplified by in vitro transcription in the presence of fluorescently labelled CTP using the Low Input RNA Labelling and Amplification Kit from Agilent following the manufacturer’s instructions.

extract_protocol: Total RNA extracted using a guanidinium thiocyanate-based method (Ultraspec™; Biotecx Laboratories, Houston, TX) following the protocol supplied by the manufacturer.

tag: Gender

value: Female; Age:58

source_name: Peripheral blood granulocytes, healthy donors

tag: Pooled healthy donors, Gender

value: 5 Female/5 Male; Age:ranging from 25 to 58 years


title: ET Patient 20 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 20, with dye reversal. 31 year old female compared to healthy control pool.

value: Female; Age:31


title: ET Patient 18 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 18, with dye reversal. 43 year old male compared to healthy control pool.

value: Male; Age:43


title: ET Patient 20 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 20. 31 year old female compared to healthy control pool.


title: ET Patient 17 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 17. 44 year old female compared to healthy control pool.

value: Female; Age:44


title: OP1 rat

description: OP1 rat


title: ET Patient 16 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 16. 43 year old female compared to healthy control pool.

value: Female; Age:43


title: ET Patient 19 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 19. 58 year old female compared to healthy control pool.


title: ET Patient 15 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 15, with dye reversal. 58 year old female compared to healthy control pool.


title: ET Patient 16 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 16, with dye reversal. 43 year old female compared to healthy control pool.


title: ET Patient 13 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 13. 44 year old female compared to healthy control pool.


title: ET Patient 12 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 12. 71 year old female compared to healthy control pool.

value: Female; Age:71


title: ET Patient 13 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 13, with dye reversal. 44 year old female compared to healthy control pool.


title: ET Patient 10 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 10, with dye reversal. 35 year old male compared to healthy control pool.

value: Male; Age:35


title: ET Patient 14 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 14. 35 year old female compared to healthy control pool.

value: Female;  Age:35


title: ET Patient 12 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 12, with dye reversal. 71 year old female compared to healthy control pool.


title: ET Patient 10 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 10. 35 year old male compared to healthy control pool.


title: ET Patient 8 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 8. 35 year old female compared to healthy control pool.

value: Female; Age:35


title: ET Patient 11 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 11. 50 year old female compared to healthy control pool.

value: Female; Age:50


title: ET Patient 11 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 11, with dye reversal. 50 year old female compared to healthy control pool.


title: ET Patient 8 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 8, with dye reversal. 35 year old female compared to healthy control pool.


title: ET Patient 17 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 17, with dye reversal. 44 year old female compared to healthy control pool.


title: ET Patient 9 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 9. 61 year old male compared to healthy control pool.

value: Male; Age:61


title: ET Patient 14 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 14, with dye reversal. 63 year old female compared to healthy control pool.


title: ET Patient 9 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 9, with dye reversal. 61 year old male compared to healthy control pool.


title: ET Patient 15 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 15. 58 year old female compared to healthy control pool.


title: ET Patient 7 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 7, with dye reversal. 51 year old female compared to healthy control pool.

value: Female; Age:51


title: ET Patient 7 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 7. 51 year old female compared to healthy control pool.


title: rpS11 +/- MPNST

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description: no additional information

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Zebrafish Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (A4 samples) or 450 (A5 and A7 samples).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (A4 samples) or Affymetrix 7G scanner (A5 and A7 samples).

data_processing: Bioconductor Affy package and gcRMA

label: Biotin

organism: Danio rerio

source_name: Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein S11

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

growth_protocol: Zebrafish raised according to standard protocols

extract_protocol: Trizol according to the manufacturer's protocol

treatment_protocol: Tumors were dissected from zebrafish anaesthetized with 0.03% MESAB

tag: Late stage MPNST from zebrafish fish 18-24 months old


title: rpS5 +/- MPNST

description: no additional information

source_name: Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein S5


title: ET Patient 6 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 6. 44 year old male compared to healthy control pool.

value: Male; Age:44


title: ET Patient 5 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 5, with dye reversal. 43 year old female compared to healthy control pool.


title: ET Patient 4 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 4. 36 year old male compared to healthy control pool.

value: Male; Age:36


title: ET Patient 4 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 4, with dye reversal. 36 year old male compared to healthy control pool.


title: ET Patient 18 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 18. 43 year old male compared to healthy control pool.


title: rpL14 +/- MPNST

description: no additional information

source_name: Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein L14


title: Seminoma-17

description: no additional information

source_name: Seminoma

tag: Seminoma from fish 36 months old


title: ET Patient 6 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 6, with dye reversal. 44 year old male compared to healthy control pool.


title: ET Patient 3 JAK2V617F. Dye-swap

description: Technical replicate 2 of 2 of ET patient 3, with dye reversal. 34 year old female compared to healthy control pool.

value: Female; Age:34


title: Slide 4 Spneu D39 wildtype grown in GM17 versus GM17 + 0.25 mM ZnSO4

status: Public on May 17 2008

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: Streptococcus pneumoniae D39 Wild type grown in GM17 versus the same strain grown in GM17 + ZnSO4

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (PMID: 15130795).

organism: Streptococcus pneumoniae

source_name: wild-type D39 GM17 OD 0.3

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

extract_protocol: 50 ml of GM17-broth was inoculated in 4 replicates 1:50 with a frozen stock, and these cultures were statically grown at 37°C. Samples for RNA isolation were taken when the cultures reached an optical density (OD600) of 0.3 (mid-log growth). RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (PMID: 17085554). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures. Synthesis, subsequent labeling of cDNA, and microarray hybridization was performed as described (PMID: 17085554 and 15907200).

tag: wild-type strain D39

source_name: wild-type D39 GM17 + 0.25 mM ZnSO4 OD 0.3


title: p53 M214K/M214K MPNST_73

description: no additional information

source_name: Malignant peripheral nerve sheath tumors from fish homozygous for inactivating mutation in p53


title: ET Patient 3 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 3. 34 year old female compared to healthy control pool.


title: ET Patient 1 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 1. 63 year old female compared to healthy control pool.

value: Female; Age:63


title: ET Patient 1 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 1, with dye reversal. 63 year old female compared to healthy control pool.


title: p53 M214K/M214K MPNST_83

description: no additional information


title: rpL35 +/- MPNST_55

description: no additional information

source_name: Malignant peripheral nerve sheath tumors from fish heterozygous for inactivating mutation in ribosomal protein L35


title: ET Patient 5 JAK2V617F

description: Technical replicate 1 of 2 of ET patient 5. 43 year old female compared to healthy control pool.


title: ET Patient 2 JAK2 wt

description: Technical replicate 1 of 2 of ET patient 2. 47 year old female compared to healthy control pool.

value: Female; Age:47


title: p53 M214K/M214K MPNST_74

description: no additional information


title: RGCs 71

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Ave

institute: University of Miami

description: For each biological replicate we performed two technical subreplicates

hyb_protocol: Once purified and fragmented, the dye labeled aRNA was used for micro-array hybridization. Labeled and amplified RNA from were hybridized to the Oligo microarray (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned at 10 μm resolution using a GenePix 4000A scanner (Axon Instruments at Molecular Devices) and the resulting images were analyzed with the software package GenePix Pro 5.1 (Axon Instruments at Molecular Devices).

data_processing: Data extracted from the images were transferred to the software package Acuity 4.0 (Axon Instruments) for normalization and statistical analysis. Each array was normalized for signal intensities across the whole array and locally, using Lowess normalization. For further analysis genes were selected according to the following quality criteria: (1) at least 90% of the pixels in the spot had intensity higher than background plus two standard deviations; (2), there were less than 2% saturated pixels in the spot; (3) signal to noise ratio (defined as ratio of the background subtracted mean pixel intensity to standard deviation of background) was 3 or above for each channel; (4) the spot diameter was between 110 and 150 μm; (5) the regression coefficient of ratios of pixel intensity was 0.6 or above.

source_name: large RGCs

label_protocol: Target RNA amplification and labeling with Cy5 dye from CyDye Post Labelling Reactive Dye Pack (Amersham, USA) was carried out in two rounds using the Amino Allyl MessageAmp™ aRNA Kit (Ambion, USA) as specified by the manufacturer.

extract_protocol: Purified cells were used for RNA isolation by Stratagene Absolutely RNA Nanoprep kit.

tag: Rat RGCs retrogradely labeled with 4DI-10ASP were purified from freshly dissected retinas and subjected to fluorescent-activated cell sorting (FACS) in order to separate the large RGC sub-population.

source_name: small RGCs

label_protocol: Target RNA amplification and labeling with Cy3 dye from CyDye Post Labelling Reactive Dye Pack (Amersham, USA) was carried out in two rounds using the Amino Allyl MessageAmp™ aRNA Kit (Ambion, USA) as specified by the manufacturer.

tag: Rat RGCs retrogradely labeled with 4DI-10ASP were purified from freshly dissected retinas and subjected to fluorescent-activated cell sorting (FACS) in order to separate the small RGC sub-population.


title: Slide 3 Spneu D39 wildtype grown in GM17 versus GM17 + 0.25 mM ZnSO4


title: rpL35 +/- MPNST_56

description: no additional information


title: RGCs 70


title: RGCs 43


title: rpL35 +/- MPNST_54

description: no additional information


title: ET Patient 2 JAK2 wt. Dye-swap

description: Technical replicate 2 of 2 of ET patient 2, with dye reversal. 47 year old female compared to healthy control pool.

value: 5 Female/5 Male; Age:ranging from 25 to 58 years


title: Slide 2 Spneu D39 wildtype grown in GM17 versus GM17 + 0.25 mM ZnSO4


title: RGCs 41


title: Blood-Mononuclear-cells_low-DTH_cow2_rep3

status: Public on May 16 2008

city: Guelph

first: Maria

middle: Isabel

last: Nino-Soto

state: Ontario

address: College Ave. West

department: Pathobiology

country: Canada

institute: University of Guelph

description: The study explores the genetic basis of high or low antibody (Ab) and cell (DTH)-mediated immune responses in Canadian Holstein cows.

hyb_protocol: Slides were blocked prior to hybridization with incubation in a solution of 5X SSC (Ambion), 0.1% SDS (Ambion) and 0.1 mg/ml acetylated BSA (Sigma-Aldrich) at 42° C (45 min), washed twice for 5 min in 0.1X SSC, rinsed in milliQ water for 30 sec, and dried by centrifugation (700 X g, 2 min). 23 ul of hybridization mix [5 ul-lyophilized yeast tRNA (Invitrogen); 5 ul-salmon sperm DNA (Invitrogen); 100 ul of DIG easy Hyb (Roche) were added to the probe mix. Hybridization mix was placed on the slide and covered with LifterSlip coverslips (Erie Scientific Co). Hybridization took place in the dark at 42º C (20 h). Slides were washed three times using a solution of 1×SSC, 0.1% SDS and 0.1 mM DTT at 50ºC (10 min each). Slides were rinsed twice in 1X SSC and 0.1 mM DTT for 2 min, once in 0.1X SSC and 0.1 mM DTT and dried by centrifugation (700 X g, 2 min). Slides were scanned immediately.

scan_protocol: Slides were scanned in a GenePix 4000B scanner using GenePix Pro 6.0 for image acquisition (Molecular Devices Corporation). PMT gains were adjusted to obtain an average ratio value of 1.0.

data_processing: Log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected LOWESS normalized intensity medians of cow/standard ratios.

source_name: Blood mononuclear cells from cow2

label_protocol: Reverse transcription was performed using SuperScript III (Invitrogen) and labelling with Alexa Fluor (647 or 555) dyes (Invitrogen). aRNA (3 ug) in 22 ul of nuclease water was mixed with 2 ul of random hexamer primers (Invitrogen), heated at 65° C for 5 min, snap-chilled in ice (1 min) and then, 14 ul of master mix [8 ul First Strand Buffer, 2 ul of 0.1 M DDT, 2 ul of dNTP mix with 5-(3-aminoallyl)-dUTP (Ambion) (dNTP final concentrations = dATP, dCTP and dGTP = 0.5 mM each; dTTP = 0.15 mM; aa-dUTP = 0.30 mM) and 80 U of RnaseOUT (Invitrogen)] was added. The mix was incubated at 25° C (5 min) and 400 U of SuperScript III were added.  The reaction was incubated for 3 hrs at 42° C. After incubation, the reaction was heated to 95° C and 0.43 volumes of 1 M NaOH (Sigma-Aldrich) were added. Another incubation at 70° C (10 min) and addition of 0.43 volumes of 1 N HCl (Sigma-Aldrich). Finally, 0.11 volumes (of neutralized reaction) of sodium acetate (Ambion) were added. Amino-modified cDNA (aa-cDNA) was purified using QIAquick PCR purification kit (Qiagen). 100 ul of eluted aa-cDNA in nuclease-free water were obtained. aa-cDNA was precipitated using 0.1 volume of sodium acetate, 1 ul of linear acrylamide (Ambion) and 2.5 volumes of 100% ethanol with two washes with 75% ethanol. The pellet was resuspended in 5 ul of nuclease-free water. All work hereafter was performed in low light. 3 ul of labelling buffer (3 M NaHCO3, pH 9.0) were added to the sample. The corresponding dye aliquot was added to the aa-cDNA. Labelling reactions were incubated at room temperature in the dark (1 hr). Labelled cDNA was cleaned as previously described, with three elutions of 50 ul using EB buffer. Purified labelled cDNA was ethanol precipitated as described before.  The resulting coloured pellet was resuspended in 3 ul of nuclease free water. At this point, matching Alexa647 and Alexa555 labelled samples were mixed.

extract_protocol: Trizol reagent (Invitrogen Canada Inc., Burlington, ON, Canada) following the manufacturer`s instructions with modifications. Briefly, 1 x 10e7 MNCs were aliquoted in 1 ml of PBS, centrifuged at 300 X g (5 min), supernatant removed and the cells lysed in 1 ml of Trizol. Cell suspension was stored at -80° C until further processing. Trizol-cell suspension was thawed, 200 ul chloroform added and suspension thorughly mixed, followed by centrifugation at 12,000 X g (15 min) at 4° C. The clear phase was transferred to a new tube and 500 ul of isopropanol were added. Samples were incubated overnight at -20° C and centrifuged at 12,000 X g (10 min) at 4° C. Supernatant was removed and pellet washed with 500 ul of 75% ethanol followed by centrifugation at 7,500 X g (5 min) at 4° C. Supernatant was removed and samples air-dried for 5-10 min. Pellets were resuspended in nuclease-free water (Ambion Inc., TX, USA), incubated for 10 min at 55-60° C and stored at -80° C. DNase I treatment was performed with DNA-free (Ambion). Total RNA (3 ug) was used for one round of amplification using the RiboAmp RNA Amplification kit (Molecular Devices Corp, Sunnyvale, CA, USA). Total RNA and amplified RNA (aRNA) concentration and quality were determined in an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Cows were immunize with specific antigens to promote antibody and cell-mediated immune responses and samples were collected 6 days post-immunization.  Venous blood was collected in EDTA coated BD Vacutainer blood collection tubes (BD-Canada, Oakville, ON, Canada) and mononuclear cells (MNC) were isolated using Percoll gradient (Sigma-Aldrich Canada Ltd., Oakville, ON, Canada). No further treatment was applied to the isolated cells.

tag: total RNA cow2

value: female, Samples:peripheral blood, Cell type:Mononuclear cells

source_name: Blood mononuclear cells from RNA standard

tag: total RNA standard


title: Spneu D39 zinc slide 1

source_name: wild-type grown in GM17 OD 0.3

tag: strain D39 wild-type

source_name: wild-type grown in GM17 with 0.25 mM ZnSO4 OD 0.3


title: RGCs 42


title: Blood-Mononuclear-cells_low-DTH_cow2_rep4


title: Expression of NB4 cells infected with vector-only control retroviruses

city: Las Vegas

first: Yupo

last: Ma

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

description: NCBI HG18, Build 36, HG18_60mer_expr

hyb_protocol: Hybridization was done according to NimbleGen standard protocols.

scan_protocol: Scanning was done by NimbleGen according to standard protocols using NimbleScan.

data_processing: Data processing was according to NimbleGen standard protocols.

source_name: NB4 cells infected with control retrovirus

label_protocol: Double-strand cDNA was created and labelled according to NimbleGen standard protocols by NimbleGen Inc

growth_protocol: Cells were grown in RPMI supplemented with 10% FBS

extract_protocol: RNA was extracted using the Trizol protocol from Invitrogen.

treatment_protocol: Control cells were infected with a retrovirus containing the shRNA harboring vector only.

tag: Acute promyelocytic leukemia cell line NB4


title: Expression data for Sall4-reduced NB4 cells

description: NCBI HG18, Build 36, HG18_60mer_expr

source_name: Expression of NB4 cells infected with shRNA retrovirus specific for Sall4

treatment_protocol: shRNA treated cells were infected with retrovirus expressing Sall4-specific shRNA.


title: Gene expression data for NB4 cells infected with vector-only control retrovirus

description: NCBI HG18, Build 36, HG18_60mer_expr

label_protocol: Double-strand cDNA was created and labelled according to NimbleGen standard protocols by NimbleGen Inc.

treatment_protocol: Control cells were infected with a retrovirus containing the shRNA harboring vector only.  RNA was extracted using Trizol reagent from Invitrogen.


title: Blood-Mononuclear-cells_low-DTH_cow2_rep1


title: Blood-Mononuclear-cells_low-DTH_cow3_rep2

source_name: Blood mononuclear cells from cow3

tag: total RNA cow3


title: Blood-Mononuclear-cells_low-DTH_cow1_rep4

source_name: Blood mononuclear cells from cow1

tag: total RNA cow1


title: Blood-Mononuclear-cells_low-DTH_cow3_rep1


title: Blood-Mononuclear-cells_low-DTH_cow2_rep2


title: Blood-Mononuclear-cells_low-DTH_cow1_rep3


title: Blood-Mononuclear-cells_low-DTH_cow3_rep3


title: Gene expression data for Sall4-reduced NB4 cells

description: NCBI HG18, Build 36, HG18_60mer_expr

source_name: Gene expression of NB4 cells infected with shRNA retrovirus specific for Sall4


title: Blood-Mononuclear-cells_low-DTH_cow1_rep2


title: RGCs 39


title: RGCs 40

tag: Rat RGCs retrogradely labeled with 4DI-10ASP were purified from freshly dissected retinas and subjected to fluorescent-activated cell sorting (FACS) in order to separate the small RGC sub-population


title: Blood-Mononuclear-cells_low-Ab_cow3_rep4


title: Blood-Mononuclear-cells_low-Ab_cow3_rep3


title: RGCs 69


title: Blood-Mononuclear-cells_low-Ab_cow3_rep1


title: Blood-Mononuclear-cells_low-Ab_cow2_rep4


title: Blood-Mononuclear-cells_low-DTH_cow1_rep1


title: Blood-Mononuclear-cells_low-Ab_cow3_rep2


title: Blood-Mononuclear-cells_low-Ab_cow2_rep3


title: SALL4 ChIP-chip

type: genomic

description: HG18 RefSeq Promoter array tiling array (2.7kb)

hyb_protocol: Standard Nimblegen hybridization kits and protocols were used

scan_protocol: Arrays were scanned by NimbleGen

data_processing: Arrays were processed using Nimblegens standard protocols using NimbleScan for data extraction

molecule: genomic DNA

label_protocol: Standard Nimblegen ChIP labeling protocol

growth_protocol: Grown in RPMI supplemented with 10% FBS

extract_protocol: ChIP-chip was performed starting with 10^9 cells and following the NimbleGen ChIP-chip protocol to extract IP DNA.

treatment_protocol: No treatment of cells prior to ChIP

tag: Acute Promyelocytic Leukemia cell line NB4

growth_protocol: NB4 cells grown in RPMI supplemented with 10% FBS


title: Blood-Mononuclear-cells_low-Ab_cow2_rep2


title: Blood-Mononuclear-cells_low-Ab_cow1_rep2


title: Blood-Mononuclear-cells_low-Ab_cow2_rep1


title: Blood-Mononuclear-cells_low-Ab_cow1_rep4


title: Blood-Mononuclear-cells_high-DTH_cow3_rep4


title: Blood-Mononuclear-cells_low-Ab_cow1_rep3


title: Blood-Mononuclear-cells_high-DTH_cow2_rep5


title: Blood-Mononuclear-cells_high-DTH_cow2_rep4


title: Blood-Mononuclear-cells_high-DTH_cow2_rep3


title: Blood-Mononuclear-cells_high-Ab_cow3_rep4


title: Blood-Mononuclear-cells_high-DTH_cow2_rep2


title: Blood-Mononuclear-cells_high-DTH_cow2_rep1


title: Blood-Mononuclear-cells_low-Ab_cow1_rep1


title: Blood-Mononuclear-cells_high-Ab_cow3_rep3


title: Control mouse kidney, biological rep 3

city: Philadelphia

first: Gideon

last: Dreyfuss

state: PA

address: 415 Curie Blvd

institute: HHMI/ University of Pennsylvania

description: Exon array data from control mouse kidney

hyb_protocol: A hybridization cocktail including 5.5 μg of fragmented, end-labeled ssDNA was applied to GeneChip Mouse Exon 1.0 ST arrays. Hybridization was performed using F450-001 fluidics wash and stain script on the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software (GCOS) to produce .CEL intensity files.

data_processing: Probeset intensities were calculated from the CEL files of the 18 samples using the RMA algorithm with default settings at both the gene level and the probeset level in Partek Genomic Suite 6.3, using the core probe sets as defined by Affymetrix. Probesets with maximum RMA intensity of 3 across all samples were excluded to eliminate probesets with low expression levels.  Alternative splicing multi-way ANOVA was applied using Partek defaults.

organism: Mus musculus

source_name: Control mouse kidney, postnatal day 11

label_protocol: Biotinylated sense-strand DNA targets were prepared using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s directions.  1 μg of total RNA from normal (n=3) and SMA (n=3) mouse spinal cord, brain and kidney was used as input for the first round of amplification. 10 μg of the resulting cRNA was used to proceed to the second round of amplification.

growth_protocol: Littermates of control and SMA mice were provided by Dr. Gordon Lutz (Drexel University, Philadelphia, Pennsylvania,USA). The mice were anesthetized with isoflurane and then sacrificed by cervical dislocation. Tissues were collected by manual dissection.

extract_protocol: Total RNA was isolated using the Ambion mirVana miRNA isolation kit according to the manufacturer's directions.

tag: Phenotype

value: Unaffected, Tissue:kidney


title: Control mouse kidney, biological rep 1


title: SMA mouse kidney, biological rep 2

description: Exon array data from SMA mouse kidney

source_name: SMA mouse kidney, postnatal day 11

value: SMA, Tissue:kidney


title: Control mouse kidney, biological rep 2


title: Blood-Mononuclear-cells_high-Ab_cow3_rep2


title: Blood-Mononuclear-cells_high-DTH_cow3_rep3


title: Blood-Mononuclear-cells_high-DTH_cow3_rep2


title: SMA mouse kidney, biological rep 3

description: Exon array data from SMA mouse kidney


title: Coli-MDS42_del-nusA_rep2

city: New York

first: Christopher

middle: John

last: Cardinale

state: NY

address: 550 1st Avenue

department: Biochemistry

institute: New York University School of Medicine

hyb_protocol: 1 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the PLIER algorithm in the Affymetrix Expression Console. No further adjustments were made to the data in the table.

organism: Escherichia coli

source_name: Reduced genome strain MDS42, deletion of nusA gene, OD600=0.3

label_protocol: Fragmented cDNA labeled with biotin at the 3' terminus by terminal deoxynucleotidyl transferase (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: Overnight culture in LB medium was innoculated from a single colony. The overnight culture was diluted 1/200 into MOPS minimal medium (Neidhardt, J. Bacteriol., 1974) and incubated with shaking at 37 C until OD600=0.5 or OD600=0.3. Total culture volume 10 ml.

extract_protocol: TRI Reagent (Sigma) or Rneasy (QIAGEN) according to manufacturer's protocol. No Rnase treatment.

treatment_protocol: Bicyclomycin (BCM, gift of Schering-Plough Animal Health) was added to the culture at the indicated dose for 20 minutes. Culture was added to 2 volumes of RNAprotect Bacterial Reagent (QIAGEN).

tag: Strain

value: K-12 reduced genome

tag: Isolate

tag: Growth phase

tag: Growth medium

value: MOPS minimal, 0.4% glucose, 0.5% casamino acids

tag: Culture conditions

value: 37 C with shaking at 220 RPM

tag: Drug

tag: Extraction

value: Rneasy


title: Coli-MDS42_del-nusG_rep2

source_name: Reduced genome strain MDS42, deletion of nusG gene, OD600=0.3, overnight culture


title: Coli-MDS42_del-nusG_rep1


title: Coli-MDS42_del-nusA_rep1


title: Blood-Mononuclear-cells_high-Ab_cow3_rep1

tag: Gender


title: Blood-Mononuclear-cells_high-DTH_cow3_rep1


title: SMA mouse kidney, biological rep 1

description: Exon array data from SMA mouse kidney


title: Control mouse brain, biological rep 2

description: Exon array data from control mouse brain

source_name: Control mouse brain, postnatal day 11

value: Unaffected, Tissue:brain


title: Control mouse brain, biological rep 3


title: Control mouse brain, biological rep 1


title: SMA mouse brain, biological rep 3

description: Exon array data from SMA mouse brain

source_name: SMA mouse brain, postnatal day 11

value: SMA, Tissue:brain


title: Coli-MDS42_bcm-100mcg/ml_rep2

source_name: Reduced genome strain MDS42, 100 mcg/ml bicyclomycin 20 min, exponential phase

value: exponential

value: bicyclomycin


title: Blood-Mononuclear-cells_high-Ab_cow2_rep3

tag: total RNA cow2


title: Coli-MDS42_no-drug_rep2

source_name: Reduced genome strain MDS42, control sample, exponential phase


title: Coli-MDS42_no-drug_rep1


title: Blood-Mononuclear-cells_high-Ab_cow2_rep2

tag: total RNA standard

source_name: Blood mononuclear cells from cow2


title: Coli-O157H7_bcm-100mcg/ml_rep1

source_name: O157:H7 strain EDL933, 100 mcg/ml bicyclomycin 20 min, exponential phase

value: TRI Reagent


title: Blood-Mononuclear-cells_high-Ab_cow2_rep1

source_name: Blood mononuclear cells from RNA standard


title: Coli-MDS42_bcm-100mcg/ml_rep1


title: Coli-O157H7_no-drug_rep2

source_name: O157:H7 strain EDL933, control sample, exponential phase


title: Coli-MG1655_bcm-100mcg/ml_rep2

source_name: K12 strain MG1655, 100 mcg/ml bicyclomycin 20 min, exponential phase


title: Coli-MG1655_bcm-100mcg/ml_rep1


title: Coli-O157H7_no-drug_rep1


title: Coli-O157H7_bcm-100mcg/ml_rep2


title: Coli-MG1655_bcm-25mcg/ml_rep2

source_name: K12 strain MG1655, 25 mcg/ml bicyclomycin 20 min, exponential phase


title: Blood-Mononuclear-cells_high-Ab_cow2_rep4


title: SMA mouse brain, biological rep 2

description: Exon array data from SMA mouse brain


title: SMA mouse brain, biological rep 1

description: Exon array data from SMA mouse brain


title: Coli-MG1655_bcm-25mcg/ml_rep1


title: Blood-Mononuclear-cells_high-Ab_and_high-DTH_cow1_rep2


title: Coli-MG1655_bcm-10mcg/ml_rep2

source_name: K12 strain MG1655, 10 mcg/ml bicyclomycin 20 min, exponential phase


title: Coli-MG1655_bcm-10mcg/ml_rep1


title: Control mouse spinal cord, biological rep 3

description: Exon array data from control mouse spinal cord

source_name: Control mouse spinal cord, postnatal day 11

value: Unaffected, Tissue:spinal cord


title: Blood-Mononuclear-cells_high-Ab_and_high-DTH_cow1_rep4

source_name: Blood mononuclear cells from cow1


title: Blood-Mononuclear-cells_high-Ab_and_high-DTH_cow1_rep3


title: Control mouse spinal cord, biological rep 2


title: Coli-MG1655_no-drug_rep2

source_name: K12 strain MG1655, control sample, exponential phase


title: SMA mouse spinal cord, biological rep 2

description: Exon array data from SMA mouse spinal cord

source_name: SMA mouse spinal cord, postnatal day 11

value: SMA, Tissue:spinal cord


title: SMA mouse spinal cord, biological rep 1


title: SMA mouse spinal cord, biological rep 3


title: Coli-MG1655_no-drug_rep1


title: Blood-Mononuclear-cells_high-Ab_and_high-DTH_cow1_rep1

treatment_protocol: Cows were immunize with specific antigens to promote antibody and cell-mediated immune responses and samples were collected 6 days post-immunization.  Venous blood was collected in EDTA coated BD Vacutainer blood collection tubes (BD-Canada, Oakville, ON, Canada) and mononuclear cells (MNC) were isolated using Percoll gradient (Sigma-Aldrich Canada Ltd.,Oakville, ON, Canada). No further treatment was applied to the isolated cells.


title: Tibetan Pig vs Landrace_longissimus dorsi muscle_ Month 2 vs 2

status: Public on May 15 2008

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

description: Breed:Tibetan Pig vs Landrace Tissue:longissimus dorsi muscle Comparison:Month 2 vs 2

hyb_protocol: The hybridization ,blocking and washing were performed by using Pronto!™ Hybridization Kit (Corning,Product #40026) and Pronto!™ cDNA/Long Oligo Hybridization Solution (Corning,Product #40090).

scan_protocol: Imaging screen was scaned at 10μm resolution and stored as 16-bit tiff format file by using ScanArray Express(PerkinElmer Life Sciences).

data_processing: log2-transformed normalized expression ratio (Cy3/Cy5). Backgorund and negative control value subtracted each channel median, then composite loess normalized intensity with positive control genes.

organism: Sus scrofa

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Tibetan Pig _Month 2

label_protocol: The linear amplification procedure and Labeling reaction were performed by using Agilent Low RNA Input Linear Amplification Kit PLUS_two-color ( 5188-5340).

extract_protocol: The porcine longissimus dorsi muscle tissues stored in RNAlater (Qiagen,Cat. No. 76106). The total RNA isolated by using RNeasy Fibrous Tissue Mini Kit (Qiagen, Cat. No. 74704).

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Tibetan pigs（3♀,Month 2）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Landrace_Month 2

extract_protocol: The porcine longissimus dorsi muscle tissues stored in RNAlater (Qiagen,Cat. No. 76106).The total RNA isolated by using RNeasy Fibrous Tissue Mini Kit (Qiagen, Cat. No. 74704).

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Landrace Pig pigs（3♀,Month 2）.


title: Taihu vs Tibetan Pig _longissimus dorsi muscle_ Month 2 vs 2

description: Breed:Taihu Pig vs Tibetan pig Tissue:longissimus dorsi muscle Comparison:Month 2 vs 2

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Taihu Pig _Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Taihu pigs（3♀,Month 2）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_ Tibetan Pig _Month 2


title: Tibetan Pig_longissimus dorsi muscle_ Month 8 vs 6

description: Breed:Tibetan Pig Tissue:longissimus dorsi muscle Comparison:Month 8 vs 6

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Tibetan Pig _Month 8

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Tibetan pigs（3♀,Month 8）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Tibetan Pig_Month 6

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Tibetan Pig pigs（3♀,Month 6）.


title: Tibetan Pig_longissimus dorsi muscle_ Month 6 vs 4

description: Breed:Tibetan Pig Tissue:longissimus dorsi muscle Comparison:Month 6 vs 4

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Tibetan Pig _Month 6

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Tibetan pigs（3♀,Month 6）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Tibetan Pig_Month 4

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Tibetan Pig pigs（3♀,Month 4）.


title: Tibetan Pig_longissimus dorsi muscle_ Month 4 vs 2

description: Breed:Tibetan Pig Tissue:longissimus dorsi muscle Comparison:Month 4 vs 2

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_ Tibetan Pig _Month 4

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Tibetan pigs（3♀,Month 4）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Tibetan Pig_Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 3 Tibetan Pig pigs（3♀,Month 2）.


title: Landrace vs Taihu Pig_longissimus dorsi muscle_ Month 2 vs 2

description: Breed:Landrace vs Taihu Pig Tissue:longissimus dorsi muscle Comparison:Month 2 vs 2

source_name: Cy3 dye_longissimus dorsi muscle_total RNA_Landrace_Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Landrace pigs（2♂2♀,Month 2）.

source_name: Cy5 dye_longissimus dorsi muscle_total RNA_Taihu Pig_Month 2

tag: The total RNA pool of porcine longissimus dorsi muscle from 4 Taihu Pigs（2♂2♀,Month 2）.


title: diseased, biological rep1

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Gene expression data from DMVD tissue, Lhasa apso

hyb_protocol: Std Affymetrix 1 cycle

scan_protocol: Std Affymetrix 1 cycle

organism: Canis lupus familiaris

source_name: affected anterior mitral valve leaflet

label_protocol: Std Affymetrix 1 cycle (ENZO)

extract_protocol: Qiagen RNEasy with on-column DNAse

treatment_protocol: tissue frozen in liq N2 was used

tag: DMVD tissue, Lhasa apso


title: diseased, biological rep3

description: Gene expression data from DMVD tissue, Dachshund

tag: DMVD tissue, Dachshund


title: diseased, biological rep2

description: Gene expression data from DMVD tissue, Miniature poodle

tag: DMVD tissue, Miniature poodle


title: control, biological rep3

description: Gene expression data from control tissue, beagle cross

source_name: control anterior mitral valve leaflet

tag: control tissue, beagle cross


title: Control mouse spinal cord, biological rep 1

source_name: Control mouse spinal cord, postnatal day 11

tag: Phenotype


title: diseased, biological rep4


title: control, biological rep2


title: control, biological rep1


title: control, biological rep4


title: Chondrocyte plus IL-1B replicate 2 - Dye Swap

status: Public on May 14 2008

city: St. Louis

first: Debabrata

last: Patra

state: MO

address: 425 S. Euclid Avenue

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: RNA quality control with Agilent 2100 Bioanalyzer

hyb_protocol: Hybridization was carried out as per recommended protocol in 3DNA Array 900 Expression Array Detection kit (Genisphere).  Briefly, each sample pair (24 µl) is resuspended in formamide-based hybridization buffer (26 µl), and Array 50dT blocker (2 µl, Genisphere).  Two hybridizations were carried out in a sequential manner.  The primary hybridization is performed by adding 48 µl of sample to the microarray under a supported glass coverslip at 43°C for 16 to 20 hours at high humidity in the dark.  Prior to secondary hybridization, slides are gently submerged sequentially in 2X SSC (at 43°C) for 11 min, 2X SSC (at room temperature) for 11 min, and 0.2X SSC (at room temperature) for 11 min and spun dry.  Secondary hybridization is carried out using the complimentary capture reagents provided in the kit.  For each reaction, the following were added: 3DNA capture reagent with Cy3 (2.5 µl), 3DNA capture reagent with Cy5 (2.5 µl), SDS-based hybridization buffer (26 µl), and nuclease-free water (21 µl).  The secondary hybridization solution is incubated in dark at 80°C for 10 min, then 50°C for 15 min.  Hybridization is performed by adding 48 µl secondary hybridization solution to the slide under a supported glass coverslip at 65°C for 4 hours at high humidity in dark.  Arrays were washed gently by submerging sequentially in 2X SSC, 0.2% SDS (at 65 °C)for 11 min, then 2X SSC (at room temperature) for 11 min and finally in 0.2X SSC (at room temperature) for 11 min and spun dry.

scan_protocol: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence. Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

data_processing: Dye swapped between untreated and IL-1B treated samples.  Background substracted and Lowess normalized data.

source_name: chondrocytes treated with IL-1B

label_protocol: First strand cDNA was generated by oligo-dT primed reverse transcription (Superscript II)  and labeled with Cy3 or Cy5 dyes using the 3DNA Array 900 kit (Genisphere) without prior amplication of the RNA.  2 µg of RNA was primed with fluorophore specific oligo-dT primer and incubated at 80°C and then reverse transcribed using Superscript II RNase H-Reverse Transcriptase and 10 mM each dATP, dCTP, dGTP, and dTTP for 2 hours at 42°C. Samples were paired for RNA expression level comparison.

growth_protocol: Chondrocytes were isolated following published protocols and plated at high density in DMEM/F12 media plus 10% FBS, 50 µg/ml ascorbate and 50 units/ml penicillin and 50 µg/ml streptomycin.

extract_protocol: RNA was isolated from chondrocytes using Trizol using protocol recommended by manufacturer.

treatment_protocol: Chondrocytes were allowed to recover for 24 hours and IL-1B (10 ng/ml) was added to experimental cells or PBS containing 0.1% BSA to untreated cells for 24 hours.

tag: Treated with IL-1B

source_name: untreated chondrocytes

tag: Untreated


title: Chondrocyte plus IL-1B replicate 2


title: Chondrocyte plus IL-1B replicate 1 - Dye Swap


title: Chondrocyte plus IL-1B replicate 1


title: ein5-6Xabh1-1_bud_totalRNA_F_2

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: ein5-6Xabh1-1 flower bud total RNA Forward replicate 2

hyb_protocol: The Arabidopsis Tiling 1.0F whole genome tiling array was hybridized for 16 h, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix Scanner G7

data_processing: Gene chip data files were processed using TileMap to identify regions of significant changes in gene expression, with a cutoff of 0.6 pp.

organism: Arabidopsis thaliana

source_name: Immature floral tissue, unopened buds

label_protocol: Fifteen micrograms of total RNA was used to synthesize double-stranded cDNA using the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was generated by in vitro transcription using the GeneChip IVT Labeling Kit (Affymetrix).

growth_protocol: All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23ûC under a 16-hour light/8-hour dark cycle.

extract_protocol: total RNA was isolated from immature floral tissue following instructions from the manufacturer (Qiagen, RNeasy Plant Mini Kit).


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C014

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

hyb_protocol: Finally 2ug of the labeled DNA material was hybridized per chip to Affymetrix Mouse Tiling Array 1.0R Array (16 chip set) for 18 h at 450C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100microg/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

data_processing: Processing of the microarray data to generate graphs representing a plot of intensities of each probe mapping to the genome versus its genomic coordinate was performed in the following steps : (1) All the three independent biological replicas from all four time points (00,12,24,and 168hrs) were quantile normalized together and then scaled to have a median feature intensity of 25 (2) The Perfect match (PM), mismatch (MM) intensities for each probe was then mapped to the genome using exact 25mer matching. For each genomic position to which a probe pair matched a data set was generated containing all PM, MM probes within a window of + 50 base pairs. Using a pseudo-median approach the PM-MM data were calculated in a sliding window across the genome as an estimator of the expression level at each genomic position. In order to extract usable positive probes from this data a pseudo-median threshold corresponding to a false positive rate of 2.9% for each time point was estimated from the bacterial probes tiled on the chip. Probes that are above this threshold were considered as present and the rest were noted as absent. Columns #2 and #3 are obtained from analysis done on mm5.

label: Affymetrix DNA labeling reagent (#900542).

molecule: polyA RNA

label_protocol: The fragmented cDNA was then end-labeled with 2.5mM biotinylated DNA labeling reagent (Affymetrix) by using 100 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 h at 370C.

extract_protocol:
To generate poly(A)+ RNA, R1 Mouse Embryonic Stem (R1mES) cells were cultured over mouse Embryonic Fibroblast (MEF) cells mitotically arrested with gamma-radiation. Cells were maintained in serum-free media supplemented with 15% ES-grade serum (Invitrogen), L-glutamine, Penicillin-streptomycin, beta-marcaptoethanol and leukemia inhibitory factor (Chemicon). All cells were routinely harvested at ~ 70% confluency and Poly(A)+ RNA was enriched from isolated total RNA using the Oligotex Kit (Qiagen) following manufacturer’s recommendation. Three independent samples of Poly(A)+ RNA was prepared from separate cultures of R1mES cells.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 700C for 10 min, and cooled to 150C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 420C and 60-min incubation at 420C. SuperScript II was inactivated at 750C for 15 min.
The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 160C for 2 h.
Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).


title: Col-0_bud_totalRNA_F_2

description: Col-0 flower bud total RNA Forward replicate 2


title: Col-0_bud_totalRNA_F_1

description: Col-0 flower bud total RNA Forward replicate 1


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C014


title: ein5-6Xabh1-1_bud_totalRNA_F_1

description: ein5-6Xabh1-1 flower bud total RNA Forward replicate 1


title: ein5-6_bud_totalRNA_F_1

description: ein5-6 flower bud total RNA Forward replicate 1


title: abh1-1_bud_totalRNA_F_2

description: abh1-1 flower bud total RNA Forward replicate 2


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C013


title: abh1-1_bud_totalRNA_F_1

description: abh1-1 flower bud total RNA Forward replicate 1

growth_protocol: All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23˚C under a 16-hour light/8-hour dark cycle.


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C013


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C012


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C014


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C011


title: ein5-6_bud_totalRNA_F_2

description: ein5-6 flower bud total RNA Forward replicate 2


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C012


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C013


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C013


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C012


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C015


title: T-10

city: Durham

first: Piotr

middle: Andrzej

last: Mieczkowski

state: NC

address: CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-10 strain

hyb_protocol: DNA was hybridized according to Lemoine et al 2005, Cell 120:587.

scan_protocol: Arrays were scanned with a GenePix 4000B scanner. Red and Green PMT gain were manually adjusted to about equal brightness in each channel. Pixel size was 10um and 2 lines were averaged.

data_processing: The data in the VALUE column was obtained by analyzing the data deposited at the University of North Carolina Microarray database (genome.unc.edu). The data from repeated arrays were collapsed to a single value per spot and centered acoording to the median. The VALUE corresponds to the Log2 RED/GREEN Normalized ratio based on the Median.

organism: Saccharomyces cerevisiae

source_name: Reference strain genomic DNA

label_protocol: DNA was prepared according to Lemoine et al 2005, Cell 120:587.

tag: Reference strain genomic DNA

source_name: T-10 isolate genomic DNA

tag: T-10 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C014


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C011


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C015


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C011


title: T-9

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-9 strain

extract_protocol: DNA was prepared according to Lemoine et al 2005, Cell 120:587.

source_name: T-9 isolate genomic DNA

tag: T-9 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C012


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C011


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C015


title: T-8

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-8 strain

source_name: T-8 isolate genomic DNA

tag: T-8 isolate genomic DNA


title: T-7

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-7 strain

source_name: T-7 isolate genomic DNA

tag: T-7 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C015


title: T-6

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-6 strain

source_name: T-6 isolate genomic DNA

tag: T-6 isolate genomic DNA


title: T-4

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-4 strain

source_name: T-4 isolate genomic DNA

tag: T-4 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C010


title: A-8

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and A-8 strain

source_name: A-8 isolate genomic DNA

tag: A-8 isolate genomic DNA


title: T-2

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-2 strain

source_name: T-2 isolate genomic DNA

tag: T-2 isolate genomic DNA


title: T-1

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-1 strain

source_name: T-1 isolate genomic DNA

tag: T-1 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C001


title: A-4

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and A-4 strain

source_name: A-4 isolate genomic DNA

tag: A-4 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C010


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C010


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C008


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C006


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C001


title: A-5

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and A-5 strain

source_name: A-5 isolate genomic DNA

tag: A-5 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C010


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C005


title: A-3

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and A-3 strain

source_name: A-3 isolate genomic DNA

tag: A-3 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C001


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C006


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C005


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C008


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C006


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C006


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C005


title: T-11

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and T-11

source_name: T-11 isolate genomic DNA

tag: T-11 isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C001


title: A-1

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and A-1

tag: Reference genomic DNA

tag: isolate genomic DNA


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C008


title: A-2

description: This is a Comparative Genomic Hybridization between DNA from the reference strain and A-2 strain

source_name: A-2 isolate genomic DNA

tag: A-2 isolate genomic DNA


title: wild type vs ace2 swi5 double gene deletion

status: Public on May 13 2008

city: SALT LAKE CITY

first: David

last: Stillman

state: UT

address: 15 N. Medical Drive East, Room 2100

department: Pathology

institute: University of Utah

description:
Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 8.5.
LOWESS normalized data obtained from log10 of processed Red signal/processed Green signal

hyb_protocol: Agilent Two-color Gene Expression Hyb/Wash protocol

source_name: Wild Type

label_protocol: Agilent Two-Color LRILAK Labeling Protocol

extract_protocol: hot phenol extraction followed by pelleting thru CsCl

tag: DY3419 wild type Saccharomyces cerevisiae

source_name: ace2 swi5 double gene deletion

tag: DY1143 ace2 swi5 double gene deletion Saccharomyces cerevisiae


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C005


title: wild type vs ace2 gene deletion

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 8.5

data_processing: LOWESS normalized data obtained from log10 of processed Red signal/processed Green signal

source_name: ace2 gene deletion

tag: DY1159 ace2 gene deletion Saccharomyces cerevisiae


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C008


title: wild type vs swi5 gene deletion

source_name: swi5 gene deletion

tag: DY408 swi5 gene deletion Saccharomyces cerevisiae


title: Parathyroid tissue cultured with low and high-phosphate medium for 1 day

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

country: Japan

institute: Tokyo Women's Medical University

description: Parathyroid tissues were precultured for 7 days with MEM medium supplemented with 10% fetal calf serum, and then cultured with low (2.0mg/dl) and high (10.4mg/dl) phosphate medium for 1 day

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

scan_protocol: AgilentMicroarray Scanner

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.7.5).
LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: human parathyroid tissue

label_protocol: 0.5 µg of total RNA were primed with 2 µl of 100 µM T16P7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

growth_protocol: Parathyroid tissues obtained from primary or secondary hyperparathyroidism were cultured on collagen coated membrane in low and high phosphate medium.

extract_protocol: Total RNA extracted using Rneasy Fibrous Tissue Minikit (Quigen) following manufacturer's instructions

treatment_protocol: Total RNAwas extracted vigorous shaking with a mixer (Mixer Mill MM 300, Qiagen)

tag: low phosphate

source_name: human parathyriod tissue

tag: high phosphate


title: Parathyroid tissue cultured with low and high-phosphate medium for 4 day

description: Parathyroid tissues were precultured for 7 days with MEM medium supplemented with 10% fetal calf serum, and then cultured with low (2.0mg/dl) and high (10.4mg/dl) phosphate medium for 4days.


title: evolved_temperature_Up_16min

type: mixed

city: Princeton

first: yirchung

last: Liu

state: NJ

address: 220 Carl Icahn Laboratory

department: Molecular Biology

institute: Princeton University

description:
Tn5 transposon mutants (Girgis et al. PLoS Genetics 3(9): e154 (2007))
Sample data table reports condensed data from 2 technical replicates.

hyb_protocol: Cy-dye labeled genomic DNA and RNA-derived cDNA probes were combined with a hybridization buffer (5X SSC, 0.1% SDS, 50% formamide, and 10 μg Salmon sperm DNA) and hybridized for ~ 16 hours at 42 C to a DNA microarray.

scan_protocol: Microarray slides were scanned on a GenePix 4000B scanner (Axon Instruments), and fluorescence data for each of the duplicates on each slide were analyzed using GENEPIX PRO 4.0 software.

data_processing: Elements with poor spot morphology or exhibiting uneven hybridization caused by dust particles or scratches, were flagged manually and excluded from further analyses. After local background  subtraction and global normalization relative to the genomic DNA reference, duplicate measurements on the same array were averaged, yielding a single vector for each time-point across a perturbation. The data from all hybridizations were combined into a matrix and scaled relative to each other using quantile-normalization as implemented in the Matlab Bioinformatics  toolbox. Biological duplicates from all experiments were averaged, leading to a single set of time-series data for each perturbation. Seven time-points were assayed for each perturbation, corresponding to 0, 4, 8, 12, 20, 28, and 44 minutes post transition.

organism: Escherichia coli K-12

source_name: genomic DNA

label_protocol: Fluorescent cDNA was synthesized from total RNA with 15 μg of total RNA serving as template. Cyanine-labeled Cy3 or Cy5-dUTP (Amersham Bioscience) and pdN6 random hexamers (GE healthcare) were used in reverse transcription reactions utilizing SuperScript II (Invitrogen, CA) for cDNA synthesis. Fluorescent genomic DNA was generated as described in (Girgis et al., 2007). Genomic DNA served as a universal reference for all hybridizations. E. coli genomic DNA was fragmented (500 – 2000 bp) using mechanical shearing, and subjected to Cy3 or Cy5-dUTP labeling using the BioPrime DNA labeling system (Invitrogen, CA).

growth_protocol: Bacteria were grown in batch or bioreactor vessels in M9 minimal media supplemented with 0.4% glucose.

extract_protocol: DNA extraction: Genomic DNA was isolated and purified according to standard procedures (Ausubel et al. 1994).  Genomic DNA was fragmented by nebulization as described by Girgis et al. PLoS Genetics 3(9): e154 (2007) and purified by phenol/chloroform extraction and ethanol precipitated.

treatment_protocol: Physiological perturbations were carried out under a controlled environment in the context of bioreactor (Bioflo 110, New Brunswick Scientific) growth. Thermoelectric sensors and heaters were used to shift temperature profiles between 250 C and 370 C, and polarographic dissolved oxygen sensors (Mettler Toledo) and nitrogen gas was used to rapidly change oxygen saturation between anaerobic (0% dissolved oxygen) and aerobic (16-21% dissolved oxygen) condition.

source_name: evolved temperature up shift 16min

extract_protocol: RNA extraction: A hot-phenol procedure was used to extract total RNA. Cell pellets were lysed with 500 μl TE (pH8.0), 50 μl 10% SDS and lysozyme (0.5 mg/ml). Total RNA was extracted sequentially with phenol/chloroform (preheated to 640 C), followed by chloroform/isoamyl alcohol. RNA was precipitated with 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ethanol. After incubating overnight at –200 C, samples were spun down and pellets were washed with ice cold 70% ethanol (prepared with DEPC- H2O). RNA was resuspended in water, DNase treated (RQ1 RNase-free DNase/ Promega, WI) and purified using an RNeasy purification kit (Qiagen, CA).


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C016


title: evolved_temperature_Up_44min

tag: Genomic DNA served as a universal reference

source_name: evolved temperature up shift 44min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C004


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C016


title: parental_temperature_Up_0min

description:
E. coli strain MG1655
Sample data table reports condensed data from 2 technical replicates.

source_name: parental temperature up shift 0min


title: parental_temperature_Up_16min

source_name: parental temperature up shift 16min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C004


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C009


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C004


title: oxygen_Up_44min

description:
E. coli strain MG1655
Sample data table reports condensed data from 2 biological replicates (2 technical_replicates/biological_replicate).
CH1: Cy5-rep1, Cy3-rep2; CH2: Cy3-rep1, Cy5-rep2

label: Cy5, Cy3

label: Cy3, Cy5

source_name: oxygen up shift, 44min


title: evolved_temperature_Up_0min

source_name: evolved temperature up shift 0min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C003


title: parental_temperature_Up_44min

source_name: parental temperature up shift 44min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C003


title: oxygen_Up_28min

source_name: oxygen up shift, 28min


title: oxygen_Up_12min

source_name: oxygen up shift, 12min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C016


title: oxygen_Up_20min

source_name: oxygen up shift, 20min


title: oxygen_Up_4min

source_name: oxygen up shift, 4min


title: oxygen_Up_0min

source_name: oxygen up shift, 0min


title: oxygen_Up_8min

source_name: oxygen up shift, 8min


title: temperature_down_28min

source_name: temperature down shift, 28min


title: temperature_down_12min

source_name: temperature down shift, 12min


title: temperature_down_44min

source_name: temperature down shift, 44min


title: temperature_down_20min

source_name: genomic DNA

source_name: temperature down shift, 20min


title: temperature_down_0min

source_name: temperature down shift, 0min


title: temperature_down_8min

source_name: temperature down shift, 8min


title: temperature_down_4min

source_name: temperature down shift, 4min


title: oxygen_down_44min

source_name: oxygen down shift, 44min


title: oxygen_down_28min

source_name: oxygen down shift, 28min


title: oxygen_down_20min

source_name: oxygen down shift, 20min


title: oxygen_down_8min

source_name: oxygen down shift, 8min


title: oxygen_down_12min

source_name: oxygen down shift, 12min


title: oxygen_down_4min

source_name: oxygen down shift, 4min


title: oxygen_down_0min

source_name: oxygen down shift, 0min


title: Slide 15 P stage (fully penetrated) 4th nymphs by the parasitoid

city: Bet Dagan

first: Murad

last: Ghanim

address: Hamacabim

department: Entomology

country: Israel

institute: Volcani Center

hyb_protocol: standard Aminoallyl

scan_protocol: Agilent automatic scanner

data_processing:
LOWESS normalization method was used for each channel separately.
genepix was used for data acquisition
numerator is a sample from fully penetrated nymphs as the treatment labeled with Cy5.
denominator is a sample from non parasitized nymphs as a control labeled with Cy3.
numbers in the VALUE column are therefore normalized data and the outcome is the Cy5/Cy3 ratio after log2 transformation.

organism: Bemisia tabaci

label_protocol: standard Aminoallyl

extract_protocol: TRIZOL

treatment_protocol: Full penetration by the parasitoid E. mundus

tag: B. tabaci 4th nymphs fully penetrated by the parasitoid

source_name: 4th nymphs control non parasitized

label_protocol: Aminoallyl

treatment_protocol: 4th nymphs non parasitized

tag: 4th B. tabaci nymphs non parasitized as a control


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C009


title: Slide 12 PP stage (pre-penetrated) 4th nymphs by the parasitoid

data_processing:
LOWESS normalization method was used for each channel separately.
genepix was used for data acquisition
numerator is a sample from  pre-penetrated nymphs as the treatment labeled with Cy5.
denominator is a sample from non parasitized nymphs as a control labeled with Cy3.
numbers in the VALUE column are therefore normalized data and the outcome is the Cy5/Cy3 ratio after log2 transformation.

treatment_protocol: pre-penetration by the parasitoid E. mundus

tag: B. tabaci 4th nymphs pre-penetrated by the parasitoid


title: Slide 11 PP stage (pre-penetrated) 4th nymphs by the parasitoid

data_processing:
LOWESS normalization method was used for each channel separately.
genepix was used for data acquisition
numerator is a sample from pre-penetrated nymphs as the treatment labeled with Cy5.
denominator is a sample from non parasitized nymphs as a control labeled with Cy3.
numbers in the VALUE column are therefore normalized data and the outcome is the Cy5/Cy3 ratio after log2 transformation.

source_name: 4th nymphs pre-penetrated by the parasitoid


title: temperature_Up_44min

description:
E. coli strain MG1655
Sample data table reports condensed data from 2 biological replicates (2 technical_replicates/biological_replicate).
CH1: Cy5-rep1, Cy5-rep2; CH2: Cy3-rep1, Cy3-rep2

source_name: temperature up shift, 44min


title: temperature_Up_12min

source_name: temperature up shift, 12min


title: temperature_Up_8min

source_name: temperature up shift, 8min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C009


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C002


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C009


title: Slide 14 P stage (fully penetrated) 4th nymphs by the parasitoid

hyb_protocol: standard aminoallyl

source_name: 4th nymphs fully penetrated by the parasitoid

label_protocol: standard aminoallyl


title: temperature_Up_0min

description:
E. coli strain MG1655
Sample data table reports condensed data from 2 biological replicates (2 technical_replicates/biological_replicate).
CH1: Cy5-rep1, Cy5-rep2; CH2: Cy3-rep1, Cy3-rep2

All PCR products on the related array (GPL6570) were printed in duplicate.  Each GPR file was generated for a single replicate: file name "*_rep1" represents replicate 1 and file name "*_rep2" represents replicate 2.  The biological replicates were indicated by the number preceding _rep1 or _rep2.
For example, files:
GSM275371_12487105_rep1.gpr & GSM275371_12487105_rep2.gpr
= print replicate #1 (rep1) and print replicate #2 (rep2) for experimental treatment 1 (12487105, tmUp1).
and
GSM275371_12493496_a_rep1.gpr & GSM275371_12493496_a_rep2.gpr
= print replicate #1 (rep1) and print replicate #2 (rep2) for experimental treatment 2 (12493496, tmUp2) .

source_name: genomic DNA

source_name: temperature up shift, 0min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 168 hrs - C007


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C004


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C016


title: temperature_Up_28min

source_name: temperature up shift, 28min


title: temperature_Up_20min

source_name: temperature up shift, 20min


title: Slide 10 PP stage (pre-penetrated) 4th nymphs by the parasitoid

hyb_protocol: standard Aminoallyl labeling protocol

source_name: bemisia tabaci nymph parasitized by Eretmocerus mundus (parasitoid)


title: temperature_Up_4min

source_name: temperature up shift, 4min


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C003


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C007


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C007


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 24 hrs - C002


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C007


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C003


title: 3907 mother of the CHD patient 3906

status: Public on May 12 2008

city: Berlin

first: Fikret

last: Erdogan

address: Ihnestr. 73

country: Germany

institute: Max-Planck-Institute

description: Array CGH analysis of a patient with congenital heart disease

hyb_protocol: Hybridization was done overnight at 42?C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner .

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

source_name: DNA isolated from blood

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from peripheral blood by  a salting out procedure  (Grimberg et al.,1989).

tag: DNA isolated from blood of the parent (3907).  Gender

value: female

extract_protocol: DNA was extracted from peripheral blood by  a salting out procedure (Blin and Stafford,1976).

tag: DNA isolated from the blood of a healthy female donor


title: Slide 13 P stage (fully penetrated) 4th nymphs by the parasitoid


title: 3908 father of the CHD patient 3906

tag: DNA isolated from blood of the parent (3908).  Gender

value: male

tag: DNA isolated from the blood of a healthy male donor


title: 1692 father of the CHD patient 1690

tag: DNA isolated from blood of the parent (1692).  Gender


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 12 hrs - C002


title: CHD Patient 1771

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

tag: DNA isolated from blood of a patient with congenital heart disease.  Gender


title: CHD Patient 1799


title: CHD Patient 1789


title: CHD Patient 3148

tag: DNA isolated from blood of a patient with congenital heart disease (Tetralogy of Fallot)   Gender


title: CHD Patient 3189


title: 1609 mother of the CHD patient 1610

tag: DNA isolated from blood of the parent (1609).  Gender


title: CHD Patient 3143

tag: DNA isolated from blood of a patient with congenital heart disease (Ventricular septal defect)   Gender


title: 1671 father of the CHD patient 1669

tag: DNA isolated from blood of the parent (1671).  Gender


title: 2915 father of the CHD patient 2930

tag: DNA isolated from blood of the parent (2915).  Gender


title: CHD Patient 3339


title: CHD Patient 1924


title: CHD Patient 1565


title: 1646 father of the CHD patient 1644

tag: DNA isolated from blood of the parent (1646).  Gender


title: 1691 mother of the CHD patient 1690

tag: DNA isolated from blood of the parent (1691).  Gender


title: 2914 mother of the CHD patient 2930

tag: DNA isolated from blood of the parent (2914).  Gender


title: R1 Mouse Embryonic Stem Cell poly(A)+ RNA at 00 hrs - C002


title: CHD Patient 3139


title: CHD Patient 2686

tag: DNA isolated from blood of a patient with congenital heart disease (Univentricular heart, TAPVC, pulmonary atresia, asplenia syndrome)   Gender


title: CHD Patient 3110


title: CHD Patient 3090


title: CHD Patient 3076

tag: DNA isolated from blood of a patient with congenital heart disease (Atrial Septal Defect)   Gender


title: CHD Patient 2751


title: CHD Patient 3058

tag: DNA isolated from blood of a patient with congenital heart disease (Tricuspid atresia)   Gender


title: CHD Patient 2248

tag: DNA isolated from blood of a patient with congenital heart disease (Aortic insufficiency)   Gender


title: CHD Patient 2896

tag: DNA isolated from blood of a patient with congenital heart disease (Hypoplastic Left Heart Syndrome)   Gender


title: CHD Patient 2930


title: CHD Patient 2332

tag: DNA isolated from blood of a patient with congenital heart disease (Patent Ductus Arteriosus)   Gender

tag: DNA isolated from the blood of a healthy female donor


title: CHD Patient 2238

tag: DNA isolated from the blood of a healthy male donor


title: CHD Patient 2086

tag: DNA isolated from blood of a patient with congenital heart disease (AVSD, ASD)   Gender


title: CHD Patient 2341


title: CHD Patient 2289

tag: DNA isolated from blood of a patient with congenital heart disease (TAPVC, VSD)   Gender


title: CHD Patient 2685


title: CHD Patient 2129

tag: DNA isolated from blood of a patient with congenital heart disease (Tetralogy of Fallot)   Gender


title: CHD Patient 2123

tag: DNA isolated from blood of a patient with congenital heart disease (Ventricular septal defect)   Gender


title: CHD Patient 2178

tag: DNA isolated from blood of a patient with congenital heart disease (Mithral stenosis)   Gender


title: CHD Patient 2287


title: CHD Patient 2148

tag: DNA isolated from blood of a patient with congenital heart disease (VSD, Mitral insufficiency)   Gender


title: CHD Patient 2073


title: CHD Patient 2344


title: CHD Patient 2598


title: CHD Patient 2595


title: CHD Patient 2039


title: CHD Patient 3003


title: CHD Patient 2033

tag: DNA isolated from blood of a patient with congenital heart disease (DORV, HLHS)   Gender


title: CHD Patient 2022

tag: DNA isolated from blood of a patient with congenital heart disease (TA, TGA, PDA)   Gender


title: CHD Patient 2007

tag: DNA isolated from blood of a patient with congenital heart disease (Aortic stenosis)   Gender


title: CHD Patient 4828

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

extract_protocol: DNA was extracted from peripheral blood by a salting out procedure (Grimberg et al.,1989).

tag: DNA isolated from blood of a patient with congenital heart disease (Atrioventricular septum defect). Gender

extract_protocol: DNA was extracted from peripheral blood by a salting out procedure (Blin and Stafford,1976).

tag: DNA isolated from blood of a healthy male donor


title: CHD Patient 4876

tag: DNA isolated from blood of a patient with congenital heart disease (Aortic stenosis). Gender


title: CHD Patient 1994

tag: DNA isolated from blood of a patient with congenital heart disease ( Ventricular septal defect)   Gender


title: CHD Patient 4878

tag: DNA isolated from blood of a patient with congenital heart disease (Ventricular septal defect). Gender


title: CHD Patient 4875

tag: DNA isolated from blood of a patient with congenital heart disease (VSD, PDA). Gender


title: CHD Patient 4771

tag: DNA isolated from blood of a patient with congenital heart disease (Pulmonary stenosis). Gender

tag: DNA isolated from blood of a healthy female donor


title: CHD Patient 4791

tag: DNA isolated from blood of a patient with congenital heart disease (Tetralogy of Fallot). Gender


title: CHD Patient 2018

tag: DNA isolated from the blood of a healthy female donor


title: CHD Patient 3918


title: CHD Patient 4146

tag: DNA isolated from blood of a patient with congenital heart disease (AVSD, ASD, PS). Gender


title: CHD Patient 3431


title: 1670 mother of the CHD patient 1669

tag: DNA isolated from blood of the parent (1670).  Gender


title: CHD Patient 4609

tag: DNA isolated from blood of a patient with congenital heart disease (Hypoplastic Left Heart Syndrome). Gender


title: CHD Patient 4201

tag: DNA isolated from blood of a patient with congenital heart disease (Atrial Septal Defect). Gender


title: CHD Patient 4264


title: CHD Patient 3551


title: CHD Patient 1955


title: CHD Patient 4770

tag: DNA isolated from blood of a patient with congenital heart disease (Aortic coarctation). Gender


title: CHD Patient 1952

tag: DNA isolated from blood of a patient with congenital heart disease (Aortic insufficiency). Gender


title: CHD Patient 1943


title: CHD Patient 3906


title: CHD Patient 1960


title: CHD Patient 3103

tag: DNA isolated from blood of a patient with congenital heart disease (Ventricular septal defect)   Gender


title: CHD Patient 3488


title: CHD Patient 4801


title: CHD Patient 1939

tag: DNA isolated from blood of a patient with congenital heart disease (VSD, right ventriucular hypoplasia, single atrium). Gender


title: CHD Patient 1933


title: CHD Patient 1920

tag: DNA isolated from blood of a healthy male donor


title: CHD Patient 1835


title: CHD Patient 1873

tag: DNA isolated from blood of a patient with congenital heart disease (Ebstein anomaly). Gender


title: CHD Patient 1822


title: CHD Patient 1815


title: CHD Patient 1755


title: CHD Patient 1859


title: CHD Patient 1737


title: CHD Patient 1917


title: CHD Patient 1809


title: CHD Patient 1800


title: Mo9 #06141 Dmo

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Mo9 #06141 Dmo

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: CD14+ cells, Decidual

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

extract_protocol: RNeasy extraction kit

tag: tissue

value: Decidual


title: CHD Patient 1745

tag: DNA isolated from blood of a patient with congenital heart disease (Total abnormal venous connection). Gender