title: Cutaneous melanoma cell line MCF7

description: Array CGH data for EST70 melanoma cells


title: BEAS-2B(B)

status: Public on Mar 07 2007

type: RNA

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

country: USA

institute: UT Southwestern Medical Center

description: Immortalized with SV40 Large T antigen

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: 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 250

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Bronchial Epithelial Cell

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol from 5 microgram total RNA

growth_protocol: RPMI 5% BFS

extract_protocol: Qiagen RNeasy kit including DNase1 treatment

tag: Histology

value: immortalized normal

tag: Age:

tag: Sex

value: M

tag: Race:


title: Cutaneous melanoma cell line EST69

status: Public on Mar 06 2007

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description: Array CGH data for EST69 melanoma cells

hyb_protocol: Hybridized and washed as described in J÷nsson et al. (Oncogene 2007)

scan_protocol: Scanned in Agilent Microarray scanner

data_processing: Image analysis was performed using Genepix v4.0. Resultsfile were uploaded into BASE where they were filtered and pin-based lowess normalized

molecule: genomic DNA

label_protocol: Samples were labeled using the Invitrogen BioPrime array CGH labeling module

growth_protocol: Cells were grown according to suppliers recommendations

extract_protocol: Genomic DNA was extracted using a Machery-Nagel exctraction kit

source_name: Promega reference male DNA

tag: pooled lymphoblastoid genomic DNA from ten male individuals


title: Cutaneous melanoma cell line EST135

description: Array CGH data for EST135 melanoma cells


title: Cutaneous melanoma cell line EST84

description: Array CGH data for EST84 melanoma cells


title: Cutaneous melanoma cell line FM69

description: Array CGH data for FM69 melanoma cells


title: Cutaneous melanoma cell line FM6

description: Array CGH data for FM6 melanoma cells


title: Cutaneous melanoma cell line EST81

description: Array CGH data for EST81 melanoma cells


title: Cutaneous melanoma cell line EST73

description: Array CGH data for EST73 melanoma cells


title: Cutaneous melanoma cell line EST50

description: Array CGH data for EST50 melanoma cells


title: Cutaneous melanoma cell line FM66

description: Array CGH data for FM66 melanoma cells


title: Cutaneous melanoma cell line EST74

description: Array CGH data for EST74 melanoma cells


title: Cutaneous melanoma cell line FM95

description: Array CGH data for the FM95 melanoma cells


title: Cutaneous melanoma cell line FM74

description: Array CGH data for FM74 melanoma cells


title: Cutaneous melanoma cell line EST94

description: Array CGH data for EST94 melanoma cells


title: S1P3-KO-hippocampus, biological rep1 (male)

status: Public on Mar 09 2007

city: Maebashi

first: Noriyuki

last: Akahoshi

state: Gunma

address: 3-39-22 Showa-machi

department: Molecular and Cellular Neurobiology

country: Japan

institute: Gunma University Graduate School of Medicine

description: Gene expression data from the hippocampus of S1P3-knockout mouse

hyb_protocol: Following fragmentation, 10 microgram of cRNA was hybridized at 45C for 16 hr on GeneChip Murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned by using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Mus musculus

source_name: hippocampus

label_protocol: Biotinylated cRNA was prepared  from 12 microgram of total RNA according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: C57BL/6N, adult, male


title: Cutaneous melanoma cell line EST57

description: Array CGH data for EST57 melanoma cells


title: Cutaneous melanoma cell line EST75

description: Array CGH data for EST75 melanoma cells


title: 20 min aerated vs anaerobic control

city: Randwick

first: Anthony

middle: G.

last: Beckhouse

state: NSW

address: High St

department: BABS

country: Australia

institute: Ramaciotti Centre for Gene Function Analysis

description: This is one of the technical replicates for the 20 minute aeration period after the shift from anaerobic growth

hyb_protocol: Labelled samples were mixed and added to DIG Easy Hyb solution (Roche Diagnostics, Basel, Switzerland with 0.5mg/ml E.coli tRNA and 0.5mg/ml denatured herring sperm DNA added. The hyb mix was then added to the slide, a coverslip was added and the hyb was done overnight at 37 degrees C. Once hybridised, slides were washed three times for 20 min in SSC (3M NaCl, 300 mM tri-sodium citrate pH 7.5), 0.1% (w/v) sodium dodecyl sulphate at 50 degrees C, followed by rinsing several times in SSC at the same temperature.The slides were dried by centrifugation and scanned immediately.

data_processing: Data from the scanner was uploaded to the GenePix Pro 3.0 (Axon Instruments) and each spot was assessed visually to determine its validity. VALUE column reports the genelist data derived from GeneSpring. GeneSpring data processing involved condensing duplicate spots from duplicate (dye-swap) arrays.

label: Cy3, Cy5

organism: Saccharomyces cerevisiae

source_name: 20 minute aeration sample

label_protocol: Labelling was performed as per the protocol of Alic et. al. Free Radical Biology and Medicine 2004 37: 23-35

growth_protocol: Strains were grown in anaerobic bottles (100ml) containing a deoxygenated (purged with high purity nitrogen) synthetic complete medium supplemented with anaerobic growth requirements ergosterol and unsaturated fatty acids and also amino acids. The bottles were reduced chemically using sodium dithionite to remove any traces of oxygen. Cells were grown in anaerobic conditions (bottles) until exponential phase (OD600=1.0).

extract_protocol: A 50 ml aliquot was treated with 20 min of aeration and placed into pre-cooled falcon tubes and spun at 4 degrees to pellet cells. The supernatant was removed, the pellets were snap frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer's protocol and the RNA was further purified using a QIAGEN RNeasy column with a DNaseI digestion

treatment_protocol: This is the sample that was treated to a period of aeration for 20 min prior to extraction.

tag: S.cerevisiae strain BY4743 homozygous diploid

source_name: anaerobic control

extract_protocol: A 50 ml aliquot was removed prior to treatment (aeration) and placed into pre-cooled falcon tubes and spun at 4 degrees to pellet cells. The supernatant was removed, the pellets were snap frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer's protocol and the RNA was further purified using a QIAGEN RNeasy column with a DNaseI digestion

treatment_protocol: This is the control sample where all time-points had a 0 min anaerobic aliquot of cells removed prior to treatment. The RNA was pooled and hybridised.


title: Fallopian Tube Carcinoma T10107

city: San Francisco

first: Antoine

last: Snijders

state: CA

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

description: Fallopian tube carcinoma (FTC) is a rare, poorly studied and aggressive cancer, associated with poor survival.  Since tumorigenesis is related to acquisition of genetic changes, we used genome-wide array CGH to analyze copy number aberrations occurring in FTC in order to obtain a better understanding of FTC carcinogenesis and to identify prognostic events and targets for therapy.  We used arrays of 2464 genomic clones, providing ~1.4 Mb resolution across the genome to quantitatively map genomic DNA copy number aberrations from fourteen FTC onto the human genome sequence.

hyb_protocol: The test and reference DNAs together with 100 g human Cot-1 DNA were hybridized to the BAC arrays for ~48 hrs at 37C.  After post-hybridization washes, the arrays were mounted in a solution containing 90% glycerol, 10% PBS and 1 M DAPI and sealed with a cover slip.

scan_protocol: A custom built CCD camera system was used to acquire 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images (Pinkel et al., 1998).  Image analysis was carried out using UCSF SPOT software (Jain et al., 2002).

data_processing: The log2ratio of the total integrated Cy3 and Cy5 intensities for each spot after background subtraction was calculated, normalized to the median log2ratio of all the clones on the array and the average of the triplicates calculated using a second custom program, SPROC.  Automatic data filtering to reject data points based on low DAPI intensity, low correlation between Cy3 and Cy5 within each segmented spot and low reference/DAPI signal intensity was also carried out using SPROC.  Data files were subsequently manually edited by rejecting clones for which only one spot of the triplicate survived after SPROC analysis and for which the standard deviation of the log2ratio of the triplicate was >0.2.   For each tumor, the data are plotted as the mean log2ratio of the triplicate spots for each clone normalized to the genome median log2ratio.  The clones are ordered by position in the genome (UCSC draft genome sequence, August 2001 freeze) beginning at 1p and ending with Xq.

source_name: fallopian tube carcinoma

label_protocol: The tumor genomic DNA and normal female reference DNA (300 ng each) were labeled by random priming in separate 50 l reactions to incorporate Cy3 and Cy5, respectively.

extract_protocol: Tumor DNAs were extracted from 20 microdissected consecutive 10µm formaldehyde fixed paraffin embedded sections (Zweemer et al., 2001) using a QIAmp DNA mini kit following a modification of the manufacturer’s protocol (Weiss et al., 1999).

tag: DNA isolated from paraffin embedded fallopian tube carcinoma

source_name: normal female genomic DNA

extract_protocol:
1. If desired, combine partial bags of male blood into one bag. If reference DNA from a
single donor is desired keep individual bags separate. Repeat with female blood and place
back into refrigerator. The following steps should be performed on only male blood until
complete, then with female blood to prevent inadvertent cross-contamination.
2. Place approximately 50 mL aliquots of the male blood into clean 50 mL tubes.
3. Centrifuge the blood at 4,000 rpm at 4°C for 10 minutes.
4. The blood will separate into serum and solids. Aspirate off and discard the top layer of
serum.
5. Using a 10 mL serological pipet, remove the top 1/4-inch of red blood cells from the
remaining dark brown blood and place this into new 50 mL centrifuge tubes. This layer
is called the buffy coat and this is where most white blood cells will be found. Discard
the remaining red blood cells. Combine the buffy coats from 2-3 tubes to a volume of
approximately 10 mL.
6. Combine the approximately 10 mL of red and white blood cell mix with 3-5 volumes
(fill the 50 mL tube to the top with Lysis Buffer) of Erythrocyte Lysis Buffer preheated
to 37 °C. This should lyse the red blood cells and hopefully not the white blood cells.
Incubate for 5 minutes at 37°C.
7. Centrifuge the lysate for 10 minutes at 4,000 rpm at 4°C.
8. Remove all but 4-5 mL of the supernatant above the loose dark brown pellet that
contains the white blood cells.
Page 3 of 4
9. Add 25 mL of the wash solution (NaCl and EDTA) and resuspend the pellet by
vigorously shaking with the lid on tight. Centrifuge again at 4,000 rpm and 4°C for 10
minutes. Aspirate off all but 4-5 mL of wash solution above the pellet.
10. Repeat step 9. Repeat the wash step until the pellet has turned white.
11. Resuspend the pellet in 10 mL of Nuclei Lysis Buffer. Be sure the pellet is broken up
so that the SDS and Protease K can get to the cells.
12. Add 330 μL of 20% SDS solution and 500 μg of Protease K (resuspended at 20 ug/uL
for a total of 25 uL) and vortex to mix well. The combination of nuclei lysis buffer
and SDS and Protease K should lyse the outer cell membrane and the internal nuclear
membrane and free the white blood cell DNA to solution.
13. Incubate at 37°C overnight or until the solution is clear.
14. Add 3.3 mL of supersaturated NaCl (6 M) to the clear solution. Vortex for 15
seconds. This “salting out” step precipitates proteins and leaves DNA in solution.
15. Centrifuge at 4,000 rpm at 4°C for 10 minutes. Transfer supernatant to a new 50 mL
tube. The supernatant may look like an opaque, viscous blob (like snot) with a
yellowish tinge at the bottom. It can be hard to work with.
16. Add 25 mL x 100% EtOH to the tube and invert the tube several times to mix well.
The DNA should readily precipitate out from solution and float to the surface, if it
hasn’t already done so.
17. Spool the floating DNA blob into a new 1.5 mL Centrifuge tube. Fill the tube with
70% EtOH and vortex for 1 minute.
18. Let stand for 15 minutes. Pour out EtOH and wipe excess EtOH out of the tube with a
rolled chem-wipe.
19. Air dry the DNA for 10 - 20 minutes to insure all excess EtOH has evaporated.
20. Resuspend the pellet in dH2O. (see note 1.)
21. Using a 1000 μL pipet followed by a 200 μL pipet, pipet the liquid up and down to
shear the DNA and to make the solutions less viscous.
22. Using a Fluorometer, determine DNA concentration. Aliquot DNA into new 1.5 mL
tubes and dilute to a concentration of 600 ng/ μL (0.6 μg/ μL). Label and store
aliquots at -20°C.
3.0 Notes
1. Tris/EDTA is sometimes used to resuspend the DNA. It may take an hour or two to
fully resuspend the DNA.

tag: Genomic DNA isolated from human blood


title: Cutaneous melanoma cell line EST79

description: Array CGH data for EST79 melanoma cells


title: Fallopian Tube Carcinoma T10102c


title: 120 min aerated vs anaerobic control

description: This is one of the technical replicates for the 120 minute aeration period after the shift from anaerobic growth

scan_protocol: Labelled samples were mixed and added to DIG Easy Hyb solution (Roche Diagnostics, Basel, Switzerland with 0.5mg/ml E.coli tRNA and 0.5mg/ml denatured herring sperm DNA added. The hyb mix was then added to the slide, a coverslip was added and the hyb was done overnight at 37 degrees C. Once hybridised, slides were washed three times for 20 min in SSC (3M NaCl, 300 mM tri-sodium citrate pH 7.5), 0.1% (w/v) sodium dodecyl sulphate at 50 degrees C, followed by rinsing several times in SSC at the same temperature.The slides were dried by centrifugation and scanned immediately.

source_name: 120 minute aeration sample

extract_protocol: A 50 ml aliquot was treated with 120 min of aeration and placed into pre-cooled falcon tubes and spun at 4 degrees to pellet cells. The supernatant was removed, the pellets were snap frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer's protocol and the RNA was further purified using a QIAGEN RNeasy column with a DNaseI digestion

treatment_protocol: This is the sample that was treated to a period of aeration for 120 min prior to extraction.


title: Fallopian Tube Carcinoma T10117


title: Cutaneous melanoma cell line EST45

description: Array CGH data for EST45 melanoma cells


title: Ocular melanoma cell line EST128

description: Array CGH data for EST128 ocular melanoma cells


title: Cutaneous melanoma cell line FM62

description: Array CGH data for FM62 melanoma cells


title: S. cerevisiae shift from anaerobic to aerobic growth

description: This particular slide is the self hybridization control for the pooled anaerobic growth sample (0min)

scan_protocol: Slides were scanned on an ArrayWoRx E Biochip Reader (Applied Precision, WA, USA) after pre-scanning to determine the correct setting to reduce saturation of spots.

data_processing: Data from the scanner was uploaded to the GenePix Pro 3.0 (Axon Instruments) and each spot was assessed visually to determine its validity. VALUE column reports the genelist data derived from GeneSpring. GeneSpring data processing involved condensing duplicate spots on the array.

source_name: Pooled total RNA grown anaerobically for the 0min time-point

growth_protocol: Strains were grown in anaerobic bottles (100ml) containing a deoxygenated (purged with high purity nitrogen) synthetic complete medium supplemented with anaerobic growth requirements ergosterol and unsaturated fatty acids and also amino acids. The bottles were reduced chemically using sodium dithionite to remove any traces of oxygen. Cells were grown in anaerobic conditions (bottles) until exponential phase (OD600=1.0)

extract_protocol: 50 ml aliquots were removed prior to treatment (aeration) into and placed into pre-cooled falcon tubes and spun at 4 degrees to pellet cells. The supernatant was removed, the pellets were snap frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer's protocol and the RNA was further purified using a QIAGEN RNeasy column with a DNaseI digestion


title: 60 min aerated vs anaerobic control

description: This is one of the technical replicates for the 60 minute aeration period after the shift from anaerobic growth

source_name: 60 minute aeration sample

treatment_protocol: This is the sample that was treated to a period of aeration for 60 min prior to extraction.


title: 10 min aerated vs anaerobic control

description: This is one of the technical replicates for the 10 minute aeration period after the shift from anaerobic growth

data_processing: Data from the scanner was uploaded to the GenePix Pro 3.0 (Axon Instruments) and each spot was assessed visually to determine its validity.  VALUE column reports the genelist data derived from GeneSpring. GeneSpring data processing involved condensing duplicate spots from duplicate (dye-swap) arrays.

source_name: 10 minute aeration sample

extract_protocol: A 50 ml aliquot was treated with 10 min of aeration and placed into pre-cooled falcon tubes and spun at 4 degrees to pellet cells. The supernatant was removed, the pellets were snap frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer's protocol and the RNA was further purified using a QIAGEN RNeasy column with a DNaseI digestion

treatment_protocol: This is the sample that was treated to a period of aeration for 10 min prior to extraction.


title: 5 min aerated vs anaerobic control

treatment_protocol: This is the anaerobic 0 min control.

source_name: 5 minute aeration sample

growth_protocol: Strains were grown in anaerobic bottles (100ml) containing a deoxygenated (purged with high purity nitrogen) synthetic complete medium supplemented with anaerobic growth requirements ergosterol and unsaturated fatty acids and also amino acids. The bottles were reduced chemically using sodium dithionite to remove any traces of oxygen. Cells were grown in anaerobic conditions (bottles) until exponential phase (OD600=1.0). The control sample was taken and then the remaining cells were aerated for 5 min prior to extraction

extract_protocol: A 50 ml aliquot was removed and treated (aeration for 5 min)  and placed into pre-cooled falcon tubes and spun at 4 degrees to pellet cells. The supernatant was removed, the pellets were snap frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer's protocol and the RNA was further purified using a QIAGEN RNeasy column with a DNaseI digestion

treatment_protocol: This is the treatment sample where cells were aerated for 5 min prior to extraction.


title: Cutaneous melanoma cell line EST97

description: Array CGH data for EST97 melanoma cells


title: Fallopian Tube Carcinoma T10125


title: Fallopian Tube Carcinoma T10131a


title: Fallopian Tube Carcinoma T10126


title: Cutaneous melanoma cell line EST133

description: Array CGH data for EST133 melanoma cells


title: Fallopian Tube Carcinoma T10109


title: Veins normal malformed rep4

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = malformed veins

hyb_protocol: - hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 micro gram labeled DNA per channel were mixed no fractionation probes were denatured for 3 min at 98 degree celcius hybridization at 60 degree celcius SSPE washes as recommended slides were dipped in acetonitril (10 s) then dried

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: “Automic Imageprocessing for Microarrays” (for details please see the cDNA Microarray Image processing webpage (Applied Computer Science Projects) at the University of Bielefeld

data_processing:
- dye swap design
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- afterwards we did a scaling procedure by division of each value with the standard deviation of the normalized log2-ratios
- as statistical software we use 'R'

source_name: malformed veins

label_protocol:
- totalRNA was transcribed, amplified and labeled according to BD Atlas SMART fluorescent probe amplification kit with following modifications:
- RNA template was hydrolized after transcription (high pH, 30 min/70 degree celcius)
- PCR amplification progress was monitored and stopped before reaching saturation

extract_protocol:
- Veins grinded under liquid nitrogen
- Trizol (Invitrogen) isolation according to the manufactures standard protocol
- Subsequent DNase I treatment

tag: Malformed veins from 3 adult human patients

tag: We used 1-2 cm segments of veins from 3 patients suffering from slow-flow venous malformation. The segments contained tunica interna, media and externa. Control veins also contained all three layers.

source_name: normal veins

tag: Normal human saphenous vein from 3 adults

tag: We use 1-2 cm segments of veins. The segments contained tunica interna, media and externa. Control veins also contained all three layers.


title: Veins normal malformed rep3


title: Cutaneous melanoma cell line SK-MEL-3

description: Array CGH data for SK-MEL-3 melanoma cells


title: Fallopian Tube Carcinoma T10121


title: Fallopian Tube Carcinoma T10129


title: p53-/- Dnmt1-/- TSA 24

city: Jerusalem

first: Laura

last: Lande-Diner

address: Ein Kerem

department: Cell Biochemistry and Human Genetics

country: Israel

institute: Hebrew University Medical School

description: p53-/- Dnmt1-/- TSA 24

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Microarray Suite version 5.0

label: affy

label_protocol: standard Affymetrix protocol

extract_protocol: TriZol  RNA purification

tag: p53 defficient,Dnmt1-/- defficient Embryonic Fibroblasts


title: p53-/- Dnmt1-/- TSA 48

description: p53-/- Dnmt1-/- treated with TSA for 48 hours

tag: p53 defficient, Dnmt1 defficient Embryonic Fibroblasts


title: p53-/- 24 hrs TSA treatment

description: p53-/- treated with TSA for 24 hours

tag: p53 defficient, Embryonic Fibroblasts


title: Veins normal malformed rep1

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keyword = malformed veins

data_processing:
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- afterwards we did a scaling procedure by division of each value with the standard deviation of the normalized log2-ratios
- as statistical software we use 'R'

tag: - Normal human saphenous vein from 3 adults

tag: We used 1 –2 cm segments of veins. The segments contained tunica interna, media and externa.

tag: - Malformed veins from 3 adult human patients

tag: We used 1 –2 cm segments of veins from 3 patients suffering from slow-flow venous malformation. The segments contained tunica interna, media and externa.


title: Fallopian Tube Carcinoma T10116


title: Fallopian Tube Carcinoma T10118


title: Fallopian Tube Carcinoma T10101b


title: p53-/- untreated (control)

description: p53-/- untreated (control)


title: Fallopian Tube Carcinoma T10112


title: p53-/- and Dnmt1-/-  two weeks after  TSA removal

tag: p53 defficient,Dnmt1 defficient  Embryonic Fibroblasts


title: Fallopian tube carcinoma T10119

tag: normal female genomic DNA isolated from human blood


title: p53-/- Dnmt1-/- untreated (control)

description: p53-/- Dnmt1-/-  untreated (control)

tag: p53 defficient, Dnmt1 defficient  Embryonic Fibroblasts


title: DNA from G2/M arrested cell

status: Public on Mar 05 2007

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

description: BrdU incoporation profile

hyb_protocol: Standard protocol provided by Affymetrix

data_processing: Previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol.409,chapter 23,389-410 in “DNA Repair” (edited by J.Campbell) (2006)

organism: Schizosaccharomyces pombe

source_name: Genomic DNA

label_protocol: End labeling by terminal transferase

extract_protocol: Growing cdc25-22 cells expressing Thymidine Kinase were arrested at G2/M boundary and released in the presence of BrdU and HU. BrdU was incorporated in nascent DNA in following S phase. The genomic DNA was digested by HaeIII and BrdU-labeled DNA was purified in CsCl density gradient centrifugation.

tag: WCE fraction for the normalization of BrdU incorporation data.


title: p53-/- TSA 48 hours

description: p53-/- cells treated with TSA for 48 hours


title: DNA prepared from asynchronous cells

description: Orc4 binding profile

scan_protocol: Standard protocol provided by Affymetrix

extract_protocol: Chromatin immunoprecipitation (ChIP) in asynchronous cells was performed as previously described (Takahashi et al., 2003, EMBO).

tag: WCE fraction for the normalization of Orc4 binding data.


title: Veins normal malformed rep2


title: FVB/NJ pituitary gland rep2 (430 2.0 Array)

city: La Jolla

first: Carrolee

last: Barlow

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

description: Wild type 8 wk old male FVB/NJ mouse pituitary gland

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Lockhart-Barlow expression analysis algorithm

source_name: pituitary gland

label_protocol: 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: pituitary glands  were dissected from five FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).

tag: Wild type 8 wk old male


title: FVB/NJ pituitary gland rep1 (430 2.0 Array)

extract_protocol: pituitary glands  were dissected from five FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: WCE fraction

description: WCE fraction used for the normalization of Orp1 and Mcm6.

hyb_protocol: Standard protocol by Affymetrix.

scan_protocol: Standard protocol by Affymetrix.

data_processing: As previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol.409,chapter 23,389-410 in “DNA Repair” (edited by J.Campbell) (2006)

source_name: Whole cell extract

label_protocol: End labbeling by terminal transferase.

extract_protocol: Chromatin immunoprecipitation (ChIP) in G1 arrested cells or asynchronous cells were performed as previously described (Takahashi et al., 2003, EMBO).


title: DNA prepared from G2/M arrested cell

description: BrdU incorporation profile

tag: Mutant strain (cdc25-22) was used


title: DBA/2J pituitary gland rep1 (430 2.0 Array)

description: Wild type 8 wk old male DBA/2J mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: Binding profile of Orc4

description: Orc4 binding profile

source_name: Chromatin-immunoprecipitated DNA

tag: Wild type strain (972) was used.


title: C3H/HeJ pituitary gland rep2 (430 2.0 Array)

description: Wild type 8 wk old male C3H/HeJ mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ pituitary gland rep1 (430 2.0 Array)


title: DBA/2J pituitary gland rep2 (430 2.0 Array)


title: 129S6/SvEvTac pituitary gland rep2 (430 2.0 Array)

description: Wild type 8 wk old male 129S6/SvEvTac mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J pituitary gland rep1 (430 2.0 Array)

description: Wild type 8 wk old male C57BL/6J mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J pituitary gland rep2 (430 2.0 Array)


title: DBA/2J periaqueductal gray rep1 (430 2.0 Array)

description: Wild type 8 wk old male DBA/2J mouse periaqueductal gray

source_name: periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ periaqueductal gray rep2 (430 2.0 Array)

description: Wild type 8 wk old male FVB/NJ mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J pituitary gland rep1 (430 2.0 Array)

description: Wild type 8 wk old male A/J mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J periaqueductal gray rep2 (430 2.0 Array)


title: BrdU incorporation at 90min. after HU treatment.

description: BrdU incorporation profile

source_name: BrdU-labeled DNA


title: C3H/HeJ periaqueductal gray rep2 (430 2.0 Array)

description: Wild type 8 wk old male C3H/HeJ mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ periaqueductal gray rep1 (430 2.0 Array)


title: Orp1 profile in G1

description: Orp1 binding sites along chromosomes were determined based on this profile.

tag: Mutant strain (cdc10-129) expressing FLAG tagged Orp1 protein.


title: BrdU incorporation at 150min in HU in delta cds1 cells

description: BrdU incorporation profile

tag: Mutant strain (cdc25-22 deltacds1) was used.


title: 129S6/SvEvTac pituitary gland rep1 (430 2.0 Array)


title: C57BL/6J periaqueductal gray rep1 (430 2.0 Array)

description: Wild type 8 wk old male C57BL/6J mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J periaqueductal gray rep2 (430 2.0 Array)

description: Wild type 8 wk old male A/J mouse periaqueductal gray

extract_protocol: periaqueductal gray was dissected from one A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: Binding profile of Mcm6

description: Mcm6 binding profile

label_protocol: End labbeling by terminal transferase

tag: Mutant strain (cdc10-129) was used.


title: 129S6/SvEvTac periaqueductal gray rep2 (430 2.0 Array)

description: Wild type 8 wk old male 129S6/SvEvTac mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J periaqueductal gray rep2 (430 2.0 Array)


title: A/J periaqueductal gray rep1 (430 2.0 Array)

extract_protocol: periaqueductal gray regions were dissected from two A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ hypothalamus rep2 (430 2.0 Array)

description: Wild type 8 wk old male FVB/NJ mouse hypothalamus

source_name: hypothalamus

extract_protocol: hypothalami were dissected from one FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ hypothalamus rep1 (430 2.0 Array)

extract_protocol: hypothalami were dissected from two FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J pituitary gland rep2 (430 2.0 Array)

extract_protocol: pituitary glands was dissected from five A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J hypothalamus rep1 (430 2.0 Array)

description: Wild type 8 wk old male DBA/2J mouse hypothalamus

extract_protocol: hypothalami were dissected from two DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J hypothalamus rep1 (430 2.0 Array)

description: Wild type 8 wk old male C57BL/6J mouse hypothalamus

extract_protocol: hypothalami were dissected from two C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J hypothalamus rep2 (430 2.0 Array)


title: C3H/HeJ hypothalamus rep1 (430 2.0 Array)

description: Wild type 8 wk old male C3H/HeJ mouse hypothalamus

extract_protocol: hypothalami were dissected from two C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J hypothalamus rep2 (430 2.0 Array)


title: A/J hypothalamus rep1 (430 2.0 Array)

description: Wild type 8 wk old male A/J mouse hypothalamus

extract_protocol: hypothalami were dissected from two A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: BrdU incorporation at 150min. after HU treatment.

description: BrdU incoporation profile

source_name: BrdU labeled DNA

extract_protocol: Growing cdc25-22 cells expressing Thymidine Kinase were arrested at G2/M boundary and released in the presence of BrdU and HU. BrdU was incorporated in nascent DNA in following S phase. The genomic DNA was digested by HaeIII and BrdU-labeled DNA was purified in CsCl density gradient centrifugation.

tag: Mutant strain (cdc25-22) was used.


title: 129S6/SvEvTac periaqueductal gray rep1 (430 2.0 Array)


title: 129S6/SvEvTac hypothalamus rep1 (430 2.0 Array)

description: Wild type 8 wk old male 129S6/SvEvTac mouse hypothalamus

extract_protocol: hypothalami were dissected from two 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J hypothalamus rep2 (430 2.0 Array)


title: FVB/NJ periaqueductal gray rep1 (430 2.0 Array)

extract_protocol: periaqueductal gray regions were dissected from two FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ hippocampus rep1 (430 2.0 Array)

description: Wild type 8 wk old male FVB/NJ mouse hippocampus

source_name: hippocampus

extract_protocol: Hippocampi were dissected from one FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J bed nucleus of the stria terminalis rep2 (430 2.0 Array)

description: Wild type 8 wk old male DBA/2J mouse bed nucleus of the stria terminalis

source_name: bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac hippocampus rep2 (430 2.0 Array)

description: Wild type 8 wk old male 129S6/SvEvTac mouse hippocampus

extract_protocol: Hippocampi were dissected from one 129S6/SvEvTac mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J hippocampus rep1 (430 2.0 Array)

description: Wild type 8 wk old male C57BL/6J mouse hippocampus

extract_protocol: Hippocampi were dissected from one C57BL/6J mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ bed nucleus of the stria terminalis rep2 (430 2.0 Array)

description: Wild type 8 wk old male FVB/NJ mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J hippocampus rep1 (430 2.0 Array)

description: Wild type 8 wk old male DBA/2J mouse hippocampus

extract_protocol: Hippocampi were dissected from one DBA/2J mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J hippocampus rep2 (430 2.0 Array)


title: DBA/2J hippocampus rep2 (430 2.0 Array)


title: FVB/NJ hippocampus rep2 (430 2.0 Array)


title: 129S6/SvEvTac hippocampus rep1 (430 2.0 Array)


title: 129S6/SvEvTac hypothalamus rep2 (430 2.0 Array)


title: C57BL/6J bed nucleus of the stria terminalis rep1 (430 2.0 Array)

description: Wild type 8 wk old male C57BL/6J mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from two C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ hippocampus rep1 (430 2.0 Array)

description: Wild type 8 wk old male C3H/HeJ mouse hippocampus

extract_protocol: Hippocampi were dissected from one C3H/HeJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J hippocampus rep1 (430 2.0 Array)

description: Wild type 8 wk old male A/J mouse hippocampus

extract_protocol: Hippocampi were dissected from one A/J mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J bed nucleus of the stria terminalis rep1 (430 2.0 Array)

extract_protocol: bed nuclei of the stria terminalis were dissected from two DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ bed nucleus of the stria terminalis rep3 (430 2.0 Array)

description: Wild type 8 wk old male C3H/HeJ mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from two C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ bed nucleus of the stria terminalis rep1 (430 2.0 Array)

extract_protocol: bed nuclei of the stria terminalis were dissected from two FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J hippocampus rep2 (430 2.0 Array)


title: C3H/HeJ bed nucleus of the stria terminalis rep1 (430 2.0 Array)


title: A/J bed nucleus of the stria terminalis rep1 (430 2.0 Array)

description: Wild type 8 wk old male A/J mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from two A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J bed nucleus of the stria terminalis rep2 (430 2.0 Array)

extract_protocol: bed nuclei of the stria terminalis were dissected from three C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ hippocampus rep2 (430 2.0 Array)


title: C3H/HeJ bed nucleus of the stria terminalis rep2 (430 2.0 Array)

extract_protocol: bed nuclei of the stria terminalis were dissected from three C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: p12 spcord right 4

status: Public on Mar 03 2007

city: Baltimore

first: Svetlana

middle: I

last: Novikova

state: MD

address: 666 W. Baltimore st

department: Biomedical Sciences

institute: University of Maryland

description:
Neonatal noxious insult produces a long-term effect on pain processing in adults. Rats subjected to
carrageenan (CAR) injection in one hindpaw within the sensitive period develop bilateral
hypoalgesia as adults. In the same rats, inflammation of the hindpaw, which was the site of the
neonatal injury, induces a localized enhanced hyperalgesia limited to this paw. To gain an insight
into the long-term molecular changes involved in the above-described long-term nociceptive effects
of neonatal noxious insult at the spinal level, we performed DNA microarray analysis (using
microarrays containing oligo-probes for 205 genes encoding receptors and transporters for
glutamate, GABA, and amine neurotransmitters, precursors and receptors for neuropeptides, and
neurotrophins, cytokines and their receptors) to compare gene expression profiles in male rats that received neonatal CAR treatment within (at postnatal day 3; P3) and outside (at postnatal 12; P12) of the sensitive period.

hyb_protocol: The resultant cDNA was then hybridized to oligonucleotide microarrays custom designed and printed for us by TeleChem International (Sunnyvale, CA). The cDNA hybridization was performed at 55°C for 16 h in 2 × SDS-Based Hybridization Buffer (3DNA Array Detection Kit, Genesphere, Hartfield, PA). The hybridization was followed by washing with 2 × SSC and 0.2% SDS at 42°C, 2 × SSC at room temperature, and 0.2 × SSC at room temperature, 10 min each. Washed slides were air-dried for 30 sec. For fluorescent labeling of microarray-bound cDNA, the slides were incubated for 3 h at 65°C with a Capture Reagent Hybridization Mixture from a 3DNA Array Detection Kit (Genesphere Inc, Hatfield, PA).The labeling reaction was terminated by washing the microarray slides at room temperature for 10 min with 0.005% Triton in 2 × SSC and for another 10 min in 0.2 × SSC. After that, the slides were air-dried for 30 sec.

scan_protocol: The processed microarray slides were scanned on a GenePix 4100A scanner (Axon Instrument, Union City, CA) with the laser excitation at 532 nm [emission filter 575DF35 (green); photomultiplier voltage 550] for Alexa 546 (control samples) and the laser excitation at 635 nm [emission filter 670DF40 (red); photomultiplier voltage 695] for Alexa 647 (experimental samples). The densitometry was performed with GenePix Pro 4.1 (Axon Instruments, Union City, CA). Background was subtracted using the 'Local Background Correction' procedure and quality control was achieved by 'Quality Control' feature of the GenePix software.

data_processing:
For each
array, the data were normalized with GenePix 4.0 (Axon
Instruments, Union City, CA) and by Ratio of Median of Internal features standards, GAPDH, beta-actin, ubiquitin and βIII-tubulin.

label: Alexa 647

organism: Rattus norvegicus

source_name: lumbar region of the spinal dorsal horn (LDH), right side, carrageenan

label_protocol:
The resultant cDNA was
then hybridized to oligonucleotide microarrays custom
designed and printed for us by TeleChem International
(Sunnyvale, CA). For fluorescent
labeling of microarray-bound cDNA, the slides
were incubated for 3 h at 65°C with a Capture Reagent
Hybridization Mixture from a 3DNA 300 Array Detection Kit
(Genesphere Inc, Hatfield, PA).

extract_protocol:
For the analysis, the total sample RNA was isolated with
TRIzol protocol (Invitrogen, Carsbad, CA). The RNA yield
was determined using a DU 640 Spectrophotometer
(Beckman, Coulter, Fullerton, CA). The 260/280 nm
ratios of the samples were 1.8. The RNA isolated from a
specific pairs of samples (5 μg RNA per sample) was
reverse transcribed utilizing a 3DNA Array Detection Kit
(Genesphere, Hartfield, PA); with primers containing different
capture sequences for CONT and experimental
(CAR-P3 and CARP-12] tissue

treatment_protocol:
Litters with ≥10
pups were selected for this study. They were divided into
three groups. In the CAR-P3 and CAR-P12 groups, the
pups received a single injection of 0.25% CAR in sterile
0.9% saline (1 μl/g) in to the plantar surface of their left
hindpaw at 9:00 pm on either P3 or P12 respectively. The
injection was conducted with a microliter syringe with a
31-gauge needle.

tag: male, right side LDH, at P12 rats were injected in their left hind paws with 0.25 % carrageenan

label: Alexa 546

source_name: lumbar region of the spinal dorsal horn (LDH), right side, control

label_protocol: same with Alexa 546

extract_protocol: same as Channel 1

treatment_protocol: same as Channel 1

tag: P12 male, right side LDH, intact


title: p12 spcord left 4

source_name: lumbar region of the spinal dorsal horn (LDH), left side, carrageenan

tag: male, left side LDH, at P12 rats were injected in their left hind paws with 0.25 % carrageenan

source_name: lumbar region of the spinal dorsal horn (LDH), left side, control

tag: P12 male, left side LDH, intact


title: A/J bed nucleus of the stria terminalis rep2 (430 2.0 Array)

extract_protocol: bed nuclei of the stria terminalis were dissected from three A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: p12 brain 5

source_name: brain carrageenan

tag: male, brain, at P12 rats were injected in their left hind paws with 0.25 % carrageenan

source_name: brain intact

tag: male, brain intact


title: C3H/HeJ hypothalamus rep2 (430 2.0 Array)

extract_protocol: hypothalami were dissected from two C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: p12 brain2

tag: male, brain, at p12 rats were injected in their left hind paws with 0.25 % carrageenan

tag: p12 brain, intact, control


title: Neonatal pain_P3-spcright6

extract_protocol:
For the analysis, the total sample RNA was isolated with
TRIzol protocol (Invitrogen, Carsbad, CA). The RNA yield
was determined using a DU 640 Spectrophotometer
(Beckman, Coulter, Fullerton, CA). The 260/280 nm
ratios of the samples were 1.8. The RNA isolated from a
specific pairs of samples (5 μg RNA per sample) was
reverse transcribed utilizing a 3DNA Array Detection Kit
(Genesphere, Hartfield, PA); with primers containing different
capture sequences for CONT and experimental
(CAR-P3 and CARP-12] tissue.

tag: P3 male, right side LDH, at P0  rats were injected in their left hind paws with 0.25 % carrageenan

tag: P3 male, right side LDH, intact


title: 129S6/SvEvTac bed nucleus of the stria terminalis rep2 (430 2.0 Array)

description: Wild type 8 wk old male 129S6/SvEvTac mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).

tag: Wild type 8 wk old male


title: Neonatal pain_P3-spcright5


title: 129S6/SvEvTac bed nucleus of the stria terminalis rep1 (430 2.0 Array)

extract_protocol: bed nuclei of the stria terminalis were dissected from two 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: Neonatal pain_P3-spcright4


title: p12 spcordleft 1


title: P12brain1

source_name: p12 brain carrageenan

tag: P12 male, brain, at P12 rats were injected in their left hind paws with 0.25 % carrageenan

source_name: brain, control

tag: P12 male, brain, intact


title: p12 spcord left 3


title: Neonatal pain_P3-spcright3


title: p12 brain 3

tag: p12 brain intact


title: p12 spcord right 3


title: p12 spcrodleft 2


title: Neonatal pain_P3-spcright2


title: p12 brain 4

tag: male brain intact


title: Neonatal pain_P3-spcright1


title: p12 spcord left 5


title: p12 spcord right 5


title: p12 spcord right 2


title: p12 spcord right 1


title: Neonatal pain_P3-spcleft6

tag: P3 male, left side LDH, at P0  rats were injected in their left hind paws with 0.25 % carrageenan

tag: P3 male, left side LDH, intact


title: ND-4

first: Xin

last: Chen

institute: UCSF

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44931.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: SRF

tag: SRF

source_name: ND-4, H9p31 primitive anterior neuroepithelia (day 10)


title: Neonatal pain_P3-spcleft1


title: Neonatal pain_P3-spcleft4


title: ND-9

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44924.gif; format: GIF

source_name: ND-9, H9p37 hESCs (day 0)

tag: ND-9, H9p37 hESCs (day 0)


title: Neonatal pain_P3-brain1

source_name: brain tissue, carrageenan

tag: P3, brain,male, at P0  rat was injected in  left hind paws with 0.25 % carrageenan

source_name: brain tissue control

tag: intact, P3, brain,male


title: Neonatal pain_P3-spcleft3


title: Neonatal pain_P3-brain4

source_name: brain, carrageenan

tag: P3 male, brain, at P0 rats were injected in their left hind paws with 0.25 % carrageenan

tag: P3 male, brain, intact


title: Neonatal pain_P3-brain6


title: Neonatal pain_P3-brain3


title: ND-1

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44928.gif; format: GIF

source_name: ND-1, H9p34 hESCs (day 0)

tag: ND-1, H9p34 hESCs (day 0)


title: Neonatal pain_P3-brain2

source_name: brain control


title: ND-8

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44922.gif; format: GIF

source_name: ND-8, H1p36 aggregates (day 6)

tag: ND-8, H1p36 aggregates (day 6)


title: ND-6

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44932.gif; format: GIF

source_name: ND-6, H9p31 definitive neuroepithelia (day 17)


title: Neonatal pain_P3-brain5

tag: 3 male, brain, at P0 rats were injected in their left hind paws with 0.25 % carrageenan


title: Monkey 3337 at baseline (VL_3337_baseline)

status: Public on Mar 02 2007

city: Rockville

first: Maryanne

last: Vahey

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

description: The monkey 3337 at baseline

hyb_protocol: According to Affymetrix's protocol

scan_protocol: Affymetrix 3000 series scanner

data_processing: The data were analyzed with MAS5.0 using Affymetrix default settings

organism: Macaca fascicularis

source_name: Cyno monkey PBMC in vivo

label_protocol: According to Affymetrix's protocol

extract_protocol: According to Affymetrix's protocol

tag: SIV, cyno monkey, PBMC, in vivo


title: Monkey 3337 at time point week 26 (VL_3337_wk_26)

description: The monkey 3337 at time point week26


title: Monkey 3336 at time point week 20 (VL_3336_wk_20)

description: The monkey 3336 at time point week20


title: Monkey 3337 at time point week 20 (VL_3337_wk_20)

description: The monkey 3337 at time point week20


title: ND-5

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44923.gif; format: GIF

source_name: ND-5, H1p34 primitive anterior neuroepithelia (day 10)


title: ND-7

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44933.gif; format: GIF

source_name: ND-7, H9p29 definitive neuroepithelia (day 17)


title: Monkey 3337 at time point week 2 (VL_3337_wk_2)

description: The monkey 3337 at time point week2


title: ND-2

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44929.gif; format: GIF

source_name: ND-2, H1p36 hESCs (day 0)

tag: ND-2, H1p36 hESCs (day 0)


title: Monkey 3336 at time point week 2 (VL_3336_wk_2)

description: The monkey 3336 at time point week2


title: Monkey 3336 at baseline (VL_3336_baseline)

description: The monkey 3336 at baseline


title: ND-3

description:
Simple annotation: ES cells, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44930.gif; format: GIF

source_name: ND-3, H9p31 aggregates (day 6)

tag: ND-3, H9p31 aggregates (day 6)


title: Monkey 3336 at time point week 26 (VL_3336_wk_26)

description: The monkey 3336 at time point week26


title: Monkey 3334 at time point week 26 (VL_3334_wk_26)

description: The monkey 3334 at time point week26


title: Monkey 3334 at baseline (VL_3334_baseline)

description: The monkey 3334 at baseline


title: Monkey 3334 at time point week 20 (VL_3334_wk_20)

description: The monkey 3334 at time point week20


title: Monkey 3334 at time point week 2 (VL_3334_wk_2)

description: The monkey 3334 at time point week2


title: Monkey 3333 at time point week 2 (VL_3333_wk_2)

description: The monkey 3333 at time point week2


title: Monkey 3333 at time point week 20 (VL_3333_wk_20)

description: The monkey 3333 at time point week20


title: Monkey 3324 at time point week 26 (VL_3324_wk_26)

description: The monkey 3324 at time point week26


title: Monkey 3324 at time point week 20 (VL_3324_wk_20)

description: The monkey 3324 at time point week20


title: Microarray profile of Cervical Cancer Cell Line- SiHa

city: Navi Mumbai

first: Chandan

last: Kumar

state: Maharashtra

address: Kharghar Node

department: ACTREC

country: India

institute: Tata Memorial Center

hyb_protocol: Hybridization in 2XHyb buffer containing 50%formamide, 10X SSC and 0.2%SDS (adapted from Quackenbush protocol) in a 42 degrees Centigrade waterbath overnight in a Hyb chamber, with the probe under a coverslip, as described by Pat Brown Lab http://cmgm.stanford.edu/pbrown/protocols/index.html

scan_protocol: Scanned in Axon 4200A Professional according to the manufacturer's instructions.

data_processing: Slides have been scanned by Axon scanner 4200A and data analyzed by GenePix Version 5.0. 'Value' column represents normalized, log transformed, ratio of medians of CH1/CH2. Normalization has been carried out with respect to 'all normalization features' using GenePix software. Normalization features meet the following criteria:[F532 Median]>= 250 And [F635 Median]>= 250 And [F Pixels]>=30 And [Dia.]>=50 And[% >B635+1SD]>55 And[% >B532+1SD]>55

source_name: Cervical Cancer Cell Line

label_protocol: Amino-allyl dUTP based indirect labelling protocol described by Pat Brown Lab, available at http://cmgm.stanford.edu/pbrown/protocols/index.html

growth_protocol:
Dulbecco's Minimum essential medium with 10%
fetal bovine serum, Temperature: 37.0C

extract_protocol: TriZol Extraction protocol with an additional chloroform extraction step followed by quantitation in spectrophotometer and checking on formaldehyde-agarose gel. RNA stored in 10mM Sodium Citrate Buffer (Ambion).

treatment_protocol: No treatment, Grown in prescribed media till subconfluent.

tag: This line was established from fragments of a primary tissue sample obtained after surgery from a Japanese patient. Electron microscopic observations revealed presence of typical desmosomes at the cell junctions and an abundance of tonofilaments in the cytoplasm.

tag: The line is reported to contain an integrated human papillomavirus type 16 genome (HPV-16, 1 to 2 copies per cell). {Information obtained from

source_name: Human Universal Reference RNA

extract_protocol: Commercial RNA

tag: Purchased from (Stratagene, Cat No. 740000),the Human Universal Reference RNA comprises of a pool of RNA made from 10 different human cell lines including

value: Adenocarcinoma, mammary gland Melanoma, Hepatoblastoma, liver Liposarcoma Adenocarcinoma, cervix Histiocytic lymphoma; macrophage; histocyte, Embryonal carcinoma, testis Lymphoblastic leukemia, T lymphoblast, Glioblastoma, brain, Plasmacytoma; myeloma; B lymphocyte


title: Monkey 3333 at baseline (VL_3333_baseline)

description: The monkey 3333 at baseline


title: Microarray profile of Cervical Cancer Cell Line- HeLa

tag: Source

value: Organ:cervix, Cell type:epithelial, Disease:adenocarcinoma , Cellular Products:keratin The cells are positive for keratin by immunoperoxidase staining.HeLa cells have been reported to contain human papilloma virus 18 (HPV-18) sequences.P53 expression was reported to be low, and normal levels of pRB (retinoblastoma suppressor) were found.


title: Monkey 3324 at time point week 2 (VL_3324_wk_2)

description: The monkey 3324 at time point week2


title: Monkey 3319 at time point week 26 (VL_3319_wk_26)

description: The monkey 3319 at time point week26


title: Monkey 3319 at baseline (VL_3319_baseline)

description: The monkey 3319 at baseline


title: Monkey 3324 at baseline (VL_3324_baseline)

description: The monkey 3324 at baseline


title: Microarray profile of Cervical Cancer Cell Line- Ca Ski

source_name: Cervical cancer Cell Line Ca Ski

tag: Information from ATCC website (http://www.atcc.org/common/catalog/numSearch/numResults.cfm?atccNum=CRL-1550 ):The line was established from cells from a metastasis in the small bowel mesentery. The cells are reported to contain an integrated human papillomavirus type 16 genome (HPV-16, about 600 copies per cell) as well as sequences related to HPV-18.


title: Microarray profile of the human keratinocyte cell line HaCaT

source_name: human keratinocyte cell line HaCaT

tag: human keratinocyte cell line HaCaT


title: Monkey 3318 at time point week 2 (VL_3318_wk_2)

description: The monkey 3318 at time point week2


title: Monkey 3333 at time point week 26 (VL_3333_wk_26)

description: The monkey 3333 at time point week26


title: Monkey 3319 at time point week 20 (VL_3319_wk_20)

description: The monkey 3319 at time point week20


title: Monkey 3319 at time point week 2 (VL_3319_wk_2)

description: The monkey 3319 at time point week2


title: Monkey 3318 at time point week 26 (VL_3318_wk_26)

description: The monkey 3318 at time point week26


title: Monkey 3318 at time point week 20 (VL_3318_wk_20)

description: The monkey 3318 at time point week20


title: Monkey 3318 at baseline (VL_3318_baseline)

description: The monkey 3318 at baseline


title: Lasseter SA-treated 27 hpt

status: Public on Mar 01 2007

city: Raleigh

first: Tristan

last: Coram

state: NC

address: 4118 Williams Hall, NC State University

institute: USDA-ARS, NC State University

description: The data submitted represents the mean data from three biological replications that inlcuded dye swaps between control and treatment samples

hyb_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127107/suppl/GSM127107 Lasseter 27h SA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127107/suppl/GSM127107 Lasseter 27h SA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127107/suppl/GSM127107 Lasseter 27h SA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127107/suppl/GSM127107 Lasseter 27h SA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127107/suppl/GSM127107 Lasseter 27h SA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127107/suppl/GSM127107 Lasseter 27h SA treated (cy5) rep1 TXT.txt.gz

organism: Cicer arietinum

source_name: Control

tag: Genotype

value: Lasseter

tag: Age

value: 14 days (seedling)

tag: Tissue

value: Shoot (stem and leaf)

source_name: Treatment


title: Microarray profile of Cervical Cancer Cell Line- C33A

tag: Cervical Cancer Cell Line. The C-33 A cell line is one of a series of lines derived by N. Auersperg from cervical cancer biopsies. The retinoblastoma protein (pRB) is present but abnormal in size. Expression of p53 is elevated, and there is a point mutation at codon 273 resulting in a Arg -> Cys substitution. The cells are negative for human papillomavirus DNA and RNA. {Information obtained from


title: ICC3996 SA-treated 27 hpt

scan_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127105/suppl/GSM127105 ICC3996 27h SA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127105/suppl/GSM127105 ICC3996 27h SA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127105/suppl/GSM127105 ICC3996 27h SA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127105/suppl/GSM127105 ICC3996 27h SA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127105/suppl/GSM127105 ICC3996 27h SA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127105/suppl/GSM127105 ICC3996 27h SA treated (cy5) rep1 TXT.txt.gz


title: Lasseter SA-treated 03 hpt

data_processing: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127106/suppl/GSM127106 Lasseter 03h SA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127106/suppl/GSM127106 Lasseter 03h SA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127106/suppl/GSM127106 Lasseter 03h SA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127106/suppl/GSM127106 Lasseter 03h SA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127106/suppl/GSM127106 Lasseter 03h SA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127106/suppl/GSM127106 Lasseter 03h SA treated (cy5) rep1 TXT.txt.gz


title: Cervical cancer tissue (India: CaCx36)

description: This sample is the only one in this series with direct comparison between cancer and normal cervical tissues. All other samples in the series have been compared against universal human reference RNA (Stratagene)

source_name: Cervical cancer tissue

treatment_protocol: snap frozen in Liquid nitrogen

tag: Lab ID

tag: Gender

value: Female

value: cervical cancer biopsy

tag: Tumor Stage

value: IIIB

source_name: Normal (non-malignant) Cervical Tissue

value: Non-malignant cervical tissue obtained from radical hysteractomy


title: Neonatal pain_P3-spcleft2

source_name: lumbar region of the spinal dorsal horn (LDH), left side, carrageenan

tag: P3 male, left side LDH, at P0  rats were injected in their left hind paws with 0.25 % carrageenan

source_name: lumbar region of the spinal dorsal horn (LDH), left side, control

tag: P3 male, left side LDH, intact


title: FLIP94-508C SA-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127102/suppl/GSM127102 FLIP94-508C 03h SA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127102/suppl/GSM127102 FLIP94-508C 03h SA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127102/suppl/GSM127102 FLIP94-508C 03h SA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127102/suppl/GSM127102 FLIP94-508C 03h SA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127102/suppl/GSM127102 FLIP94-508C 03h SA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127102/suppl/GSM127102 FLIP94-508C 03h SA treated (cy5) rep1 TXT.txt.gz

label_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted


title: FLIP94-508C SA-treated 27 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127103/suppl/GSM127103 FLIP94-508C 27h SA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127103/suppl/GSM127103 FLIP94-508C 27h SA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127103/suppl/GSM127103 FLIP94-508C 27h SA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127103/suppl/GSM127103 FLIP94-508C 27h SA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127103/suppl/GSM127103 FLIP94-508C 27h SA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127103/suppl/GSM127103 FLIP94-508C 27h SA treated (cy5) rep1 TXT.txt.gz

growth_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted


title: ICC3996 MeJA-treated 27 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127099/suppl/GSM127099 ICC3996 27h MeJA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127099/suppl/GSM127099 ICC3996 27h MeJA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127099/suppl/GSM127099 ICC3996 27h MeJA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127099/suppl/GSM127099 ICC3996 27h MeJA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127099/suppl/GSM127099 ICC3996 27h MeJA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127099/suppl/GSM127099 ICC3996 27h MeJA treated (cy5) rep1 TXT.txt.gz

extract_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted


title: Lasseter MeJA-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127100/suppl/GSM127100 Lasseter 03h MeJA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127100/suppl/GSM127100 Lasseter 03h MeJA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127100/suppl/GSM127100 Lasseter 03h MeJA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127100/suppl/GSM127100 Lasseter 03h MeJA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127100/suppl/GSM127100 Lasseter 03h MeJA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127100/suppl/GSM127100 Lasseter 03h MeJA treated (cy5) rep1 TXT.txt.gz

treatment_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated by salicylic acid, methyl jasmonate, and aminocyclopropane carboxylic acid to reveal pathways of defence-related gene regulation. Plant Biotechnology Journal. Submitted


title: Lasseter MeJA-treated 27 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127101/suppl/GSM127101 Lasseter 27h MeJA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127101/suppl/GSM127101 Lasseter 27h MeJA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127101/suppl/GSM127101 Lasseter 27h MeJA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127101/suppl/GSM127101 Lasseter 27h MeJA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127101/suppl/GSM127101 Lasseter 27h MeJA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127101/suppl/GSM127101 Lasseter 27h MeJA treated (cy5) rep1 TXT.txt.gz


title: ICC3996 MeJA-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127098/suppl/GSM127098 ICC3996 03h MeJA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127098/suppl/GSM127098 ICC3996 03h MeJA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127098/suppl/GSM127098 ICC3996 03h MeJA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127098/suppl/GSM127098 ICC3996 03h MeJA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127098/suppl/GSM127098 ICC3996 03h MeJA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127098/suppl/GSM127098 ICC3996 03h MeJA treated (cy5) rep1 TXT.txt.gz


title: ICC3996 ACC-treated 27 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127045/suppl/GSM127045 ICC3996 27h ACC control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127045/suppl/GSM127045 ICC3996 27h ACC control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127045/suppl/GSM127045 ICC3996 27h ACC control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127045/suppl/GSM127045 ICC3996 27h ACC treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127045/suppl/GSM127045 ICC3996 27h ACC treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127045/suppl/GSM127045 ICC3996 27h ACC treated (cy5) rep1 TXT.txt.gz


title: ICC3996 ACC-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127026/suppl/GSM127026 ICC3996 03h ACC control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127026/suppl/GSM127026 ICC3996 03h ACC control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127026/suppl/GSM127026 ICC3996 03h ACC control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127026/suppl/GSM127026 ICC3996 03h ACC treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127026/suppl/GSM127026 ICC3996 03h ACC treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127026/suppl/GSM127026 ICC3996 03h ACC treated (cy5) rep1 TXT.txt.gz


title: FLIP94-508C MeJA-treated 27 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127097/suppl/GSM127097 FLIP94-508C 27h MeJA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127097/suppl/GSM127097 FLIP94-508C 27h MeJA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127097/suppl/GSM127097 FLIP94-508C 27h MeJA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127097/suppl/GSM127097 FLIP94-508C 27h MeJA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127097/suppl/GSM127097 FLIP94-508C 27h MeJA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127097/suppl/GSM127097 FLIP94-508C 27h MeJA treated (cy5) rep1 TXT.txt.gz


title: FLIP94-508C MeJA-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127089/suppl/GSM127089 FLIP94-508C 03h MeJA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127089/suppl/GSM127089 FLIP94-508C 03h MeJA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127089/suppl/GSM127089 FLIP94-508C 03h MeJA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127089/suppl/GSM127089 FLIP94-508C 03h MeJA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127089/suppl/GSM127089 FLIP94-508C 03h MeJA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127089/suppl/GSM127089 FLIP94-508C 03h MeJA treated (cy5) rep1 TXT.txt.gz


title: Neonatal pain_P3-spcleft5


title: FLIP94-508C ACC-treated 27 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127014/suppl/GSM127014 FLIP94-508C 27h ACC control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127014/suppl/GSM127014 FLIP94-508C 27h ACC control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127014/suppl/GSM127014 FLIP94-508C 27h ACC control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127014/suppl/GSM127014 FLIP94-508C 27h ACC treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127014/suppl/GSM127014 FLIP94-508C 27h ACC treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127014/suppl/GSM127014 FLIP94-508C 27h ACC treated (cy5) rep1 TXT.txt.gz


title: Lasseter ACC-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127046/suppl/GSM127046 Lasseter 03h ACC control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127046/suppl/GSM127046 Lasseter 03h ACC control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127046/suppl/GSM127046 Lasseter 03h ACC control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127046/suppl/GSM127046 Lasseter 03h ACC treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127046/suppl/GSM127046 Lasseter 03h ACC treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127046/suppl/GSM127046 Lasseter 03h ACC treated (cy5) rep1 TXT.txt.gz


title: 240 MIN SERUM STIMULATED MCF10A cells

city: Rehovot

first: Tal

last: Shay

address: Herzel

department: Physics of Complex Systems

institute: Weizmann Institute of Science

description: Gene expression data from 240 MIN SERUM STIMULATED MCF10A cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U!33A2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using laser confocal scanner.

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

source_name: MCF-10A cells  spontaneously immortalized normal human mammary epithelial cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: extraction of total RNA was performed using Versagene's RNA isolation kit according to the manufacture's protocol.

treatment_protocol: MCF10A cells were grown in DME:F12 medium supplemented with antibiotics, [10 mg/ml insulin, 0.1 mg/ml cholera toxin, 0.5 mg/ml hydrocortisone, heat-inactivated horse serum (5%); defined as 'serum' in the text] and 10ng/ml EGF. Cells were serum deprived for 24 hours.

tag: MCF10A cells


title: ICC3996 SA-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127104/suppl/GSM127104 ICC3996 03h SA control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127104/suppl/GSM127104 ICC3996 03h SA control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127104/suppl/GSM127104 ICC3996 03h SA control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127104/suppl/GSM127104 ICC3996 03h SA treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127104/suppl/GSM127104 ICC3996 03h SA treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127104/suppl/GSM127104 ICC3996 03h SA treated (cy5) rep1 TXT.txt.gz


title: 480 MIN SERUM STIMULATED MCF10A cells

description: Gene expression data from 480 MIN SERUM STIMULATED MCF10A cells.


title: FLIP94-508C ACC-treated 03 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127013/suppl/GSM127013 FLIP94-508C 03h ACC control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127013/suppl/GSM127013 FLIP94-508C 03h ACC control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127013/suppl/GSM127013 FLIP94-508C 03h ACC control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127013/suppl/GSM127013 FLIP94-508C 03h ACC treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127013/suppl/GSM127013 FLIP94-508C 03h ACC treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127013/suppl/GSM127013 FLIP94-508C 03h ACC treated (cy5) rep1 TXT.txt.gz


title: Lasseter ACC-treated 27 hpt

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127047/suppl/GSM127047 Lasseter 27h ACC control (cy3) rep1 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127047/suppl/GSM127047 Lasseter 27h ACC control (cy5) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127047/suppl/GSM127047 Lasseter 27h ACC control (cy5) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127047/suppl/GSM127047 Lasseter 27h ACC treated (cy3) rep2 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127047/suppl/GSM127047 Lasseter 27h ACC treated (cy3) rep3 TXT.txt.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM127nnn/GSM127047/suppl/GSM127047 Lasseter 27h ACC treated (cy5) rep1 TXT.txt.gz


title: 40 MIN SERUM STIMULATED MCF10A cells

description: Gene expression data from 40 MIN SERUM STIMULATED MCF10A cells.


title: 60 MIN SERUM STIMULATED MCF10A cells

description: Gene expression data from 60 MIN SERUM STIMULATED MCF10A cells.


title: 480 MIN EGF STIMULATED MCF10A cells

description: Gene expression data from 480 MIN EGF STIMULATED MCF10A cells.


title: 120 MIN SERUM STIMULATED MCF10A cells

description: Gene expression data from 120 MIN SERUM STIMULATED MCF10A cells.


title: 240 MIN EGF STIMULATED MCF10A cells

description: Gene expression data from 240 MIN EGF STIMULATED MCF10A cells.


title: 20 MIN EGF STIMULATED MCF10A cells

description: Gene expression data from 40 MIN EGF STIMULATED MCF10A cells.


title: 120 MIN EGF STIMULATED MCF10A cells

description: Gene expression data from 120 MIN EGF STIMULATED MCF10A cells.


title: 60 MIN EGF STIMULATED MCF10A cells

description: Gene expression data from 60 MIN EGF STIMULATED MCF10A cells.


title: 40 MIN EGF STIMULATED MCF10A cells


title: 20 MIN SERUM STIMULATED MCF10A cells

description: Gene expression data from 20 MIN SERUM STIMULATED MCF10A cells.


title: Unstimulated MCF10A cells

description: Gene expression data from unstimulated MCF10A cells.


title: HELA cells stimulated with EGF for 480 minutes

description: Gene expression data from unstimulated HELA cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U!33A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Human cervical carcinoma cell line

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

treatment_protocol: HELA cells were grown in DMEM supplemented with 10% FCS and antibiotics. Cells were serum deprived for 24 hours. Following stimulation with 10 ng/ml EGF for 480 minutes.

tag: HeLa cells


title: HELA cells stimulated with EGF for 240 minutes

treatment_protocol: HELA cells were grown in DMEM supplemented with 10% FCS and antibiotics. Cells were serum deprived for 24 hours. Following stimulation with 10 ng/ml EGF for 240 minutes.


title: HELA cells stimulated with EGF for 120 minutes

treatment_protocol: HELA cells were grown in DMEM supplemented with 10% FCS and antibiotics. Cells were serum deprived for 24 hours. Following stimulation with 10 ng/ml EGF for 120 minutes.


title: HELA cells stimulated with EGF for 60 minutes

treatment_protocol: HELA cells were grown in DMEM supplemented with 10% FCS and antibiotics. Cells were serum deprived for 24 hours. Following stimulation with 10 ng/ml EGF for 60 minutes.


title: HELA cells stimulated with EGF for 40 minutes

treatment_protocol: HELA cells were grown in DMEM supplemented with 10% FCS and antibiotics. Cells were serum deprived for 24 hours. Following stimulation with 10 ng/ml EGF for 40 minutes.


title: HELA cells stimulated with EGF for 20 minutes

treatment_protocol: HELA cells were grown in DMEM supplemented with 10% FCS and antibiotics. Cells were serum deprived for 24 hours. Following stimulation with 10 ng/ml EGF for 20 minutes.


title: Normal (non-malignant) cervical tissue (India: NCx128)

description: It is important to note that the data provides comparison of test sample against the universal reference RNA, and not cancer versus normal ratios.

source_name: Normal (non-malignant) cervical tissue

value: Non-malignant cervical tissue obtained from radical hysterectomy


title: Unstimulated HELA cells

treatment_protocol: HELA cells were grown in DMEM supplemented with 10% FCS and antibiotics. Cells were serum deprived for 24 hours.


title: Cervical cancer tissue (India: CaCx100)

description: Pathology: keratinising squamous carcinoma

value: IIIB/IVA


title: Cervical cancer tissue (India: CaCx03)

description: Pathology: A tiny focus of superficially invasive sqamous carcinoma seen at the edge of the biopsy

value: IIB


title: Normal (non-malignant) cervical tissue (India: NCx126)


title: Cervical cancer tissue (India: CaCx109)

description: Pathology: Squamous Carcinoma


title: Normal (non-malignant) cervical tissue (India: NCx207)


title: Cervical cancer tissue (India: CaCx99)

description: Pathology: Squamous carcinoma

scan_protocol: Scanned in Axon 4200A Professional according to the manufacturer's instructions


title: Cervical cancer tissue (India: CaCx102)

description: Pathology: Squamous Carcinoma


title: Normal (non-malignant) cervical tissue (India: NCx 207)


title: Cervical cancer tissue (India: CaCx05)

description: Pathology: Poorly Differentiated Squamous carcinoma


title: Normal (non-malignant) cervical tissue (India: NCx1)

description: It is important to note that the data  provides comparison of test sample against the universal reference RNA, and not cancer versus normal ratios.

tag: Tissue:Non-malignant cervical tissue obtained from radical hysteractomy


title: Cervical cancer tissue (India: CaCx04)


title: Normal (non-malignant) Cervical Tissue (India: NCx2)


title: egy wt sibling embryos at d5, biological rep2

status: Public on Jan 31 2007

city: Boston

first: Gerhard

middle: J

last: Weber

state: MA

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Children's Hospital Boston, Harvard Medical School

description: Gene expression data from zebrafish wt embryos at day 5 post fertilization.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

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

organism: Danio rerio

source_name: earl grey embryos at day 4 post fertilization

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Embryos were obtained by pairwise matings of adult egy heterozygote fish, raised at 28 ºC

treatment_protocol: egy mutant embryos and wild-type siblings were collected in triplicates at the 72 and 120hpf stage and separately processed. After homogenization (Tekmar Tissumizer, Cincinnati, OH), total RNA was extracted by using TRIzol reagent (Invitrogen) and purified on RNeasy resins (Qiagen) according to the manufacturer’s recommendations.

tag: strain background

value: AB/WIK, Genotype:egy, Allele:cz3,  isolated wt sibling embryos.

value: 5 days post fertilization


title: Cervical cancer tissue (India: CaCx84)

description: Pathology: Large cell non keratinising squamous carcinoma

value: IIB/IB

tag: Purchased from (Stratagene, Cat No. 740000),the Human Universal Reference RNA comprises of a pool of RNA made from 10 different human cell lines including


title: Cervical cancer tissue (India: CaCx01)


title: egy mut sibling embryos at d3, biological rep1

description: Gene expression data from zebrafish wt embryos at day 3 post fertilization.

source_name: earl grey embryos at day 3 post fertilization

value: AB/WIK, Genotype:egy, Allele:cz3,  isolated mut sibling embryos.

value: 3 days post fertilization


title: egy wt sibling embryos at d3, biological rep2


title: egy mut sibling embryos at d5, biological rep3


title: egy mut sibling embryos at d5, biological rep1

source_name: earl grey embryos at day 5 post fertilization


title: egy mut sibling embryos at d3, biological rep2


title: Cervical cancer tissue (India: CaCx97)

description: Pathology: Suspected adenocarcinoma

value: IB

value: Adenocarcinoma, mammary gland Melanoma, Hepatoblastoma, liver Liposarcoma Adenocarcinoma, cervix Histiocytic lymphoma; macrophage; histocyte, Embryonal carcinoma, testis Lymphoblastic leukemia, T lymphoblast, Glioblastoma, brain, Plasmacytoma; myeloma; B lymphocyte


title: egy wt sibling embryos at d5, biological rep1


title: egy wt sibling embryos at d3, biological rep1


title: liver_ABCA1-TG, biological replicate 3

status: Public on Aug 10 2006

city: Bethesda

first: Eric

last: Billings

address: 10 Center Drive

institute: NHLBI

description: Gene expression data comparing ABCA1 over-expression in LDL receptor +/- genetic background

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix (HP) GeneArray Scanner G2500A.

data_processing: RMA-normalization

source_name: liver, ABCA1-TG

label_protocol: Samples prepared with Arcturus RiboAmp protocol from 2 ug of total RNA

growth_protocol: Male mice were sacrificed at 5 to 6 months old

extract_protocol: Trizol extraction, Qiagen RNEasy clean-up with on-column DNAse treatment

treatment_protocol: Diet: NIH36, livers were snap-frozen and stored at -80C

tag: Strain


title: egy mut sibling embryos at d5, biological rep2


title: liver_LDLr-KO, biological replicate 4

source_name: liver, LDLr-KO


title: liver_ABCA1-TG, biological replicate 2


title: liver_ABCA1-TG, biological replicate 4


title: liver_ABCA1-TG, biological replicate 1


title: liver_LDLr-KO, biological replicate 1


title: Lung_exposure 600µgTPM/l_6hrec B

status: Public on Jul 28 2006

city: Hannover

first: Jürgen

last: Borlak

address: Nikolai-Fuchs-Straße 1

institute: Fraunhofer Institut für Toxikologie und Experimentelle Medizin

description: Gene expression data from rat lungs, dissection occured after 13 weeks of exposition and 6hrs after last treatment

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Expression Array 230 A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: lung tissue from rats exposed to 600µgTPM/l

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8-11 microg total RNA (Expression Analysis Technical Manual, 701021 rev1, Affymetrix).

extract_protocol: Extraction of total RNA was performed with an additional second clean-up (Qiagen RNeasy Mini Kit)

value: Sprague-Dawley

value: male

value: lung

tag: Exposition

value: 13weeks, 5d/week, 2h/day 600µgTPM/l


title: Lung_control_6hrec B

source_name: lung tissue from rats exposed to sham

value: 13weeks, 5d/week, 2h/day sham


title: Lung_exposure 600µgTPM/l_20hrec B

description: Gene expression data from rat lungs, dissection occured after 13 weeks of exposition and 20hrs after last treatment


title: Lung_exposure 300µgTPM/l_6hrec B

source_name: lung tissue from rats exposed to 300µgTPM/l

value: 13weeks, 5d/week, 2h/day 300µgTPM/l


title: Lung_control_20hrec A


title: Lung_exposure 300µgTPM/l_20hrec A


title: Lung_control_20hrec B


title: liver_LDLr-KO, biological replicate 3


title: Lung_exposure 600µgTPM/l_20hrec A


title: Lung_exposure 600µgTPM/l_2hrec B

description: Gene expression data from rat lungs, dissection occured after 13 weeks of exposition and 2hrs after last treatment

source_name: lung tissue from rats exposed to 600µg TPM/l


title: Lung_exposure 300µgTPM/l_20hrec B


title: Lung_control_6hrec A


title: Lung_exposure 300µgTPM/l_2hrec B


title: Lung_exposure 300µgTPM/l_6hrec A


title: Lung_control_2hrec B


title: Lung_exposure 300µgTPM/l_2hrec	A


title: Lung_exposure 600µgTPM/l_6hrec A


title: naive vs. influenza A virus d2

status: Public on Jul 12 2006

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: Microarray experiments were done as two-color hybridizations. RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 4 µg of total RNA (derived from five lungs in each group and time point, respectively) with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with either cyanine 3-CTP (Cy3-CTP) or cyanine 5-CTP (Cy5-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was precipitated overnight with LiCl, ethanol washed and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP and A650nm for Cy5-CTP. Before hybridization, 1.25 µg labeled cRNA of each product were fragmented and mixed with control targets and hybridization buffer according to the supplier's protocol (Agilent Technologies). Hybridizations were done overnight for approximately 17 h at 60°C. The slides were washed according to the manufacturer's manual and scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies). In order to compensate dye specific effects, and to ensure statistically relevant data, a color swap was performed. The RNA samples were labeled vice verse with the two fluorescent dyes (fluorescence reversal).

data_processing: Agilent FE 6.1.1.1 / Rosetta Resolver Built 3.2.2

source_name: naive

tag: C57Bl/6 naive control mice received virus-free allantoic fluid intranasally

source_name: influenza A virus strain HKx31(x31; H3N2) infected d2

tag: C57BL/6 mice were intranasally infected with a sublethal dose (360 hemagglutinating units) in 30 µl allantoic fluid


title: Lung_control_2hrec A


title: Lung_exposure 600µgTPM/l_2hrec A