title: Ovary, Carcinoma, NOS (12934081)

description: Ovary; Carcinoma, NOS; University of Pennsylvania; 8/13/2004

growth_protocol: Ovary; Carcinoma, NOS

tag: Cell Line PE04


title: Ovary, Carcinoma, NOS (12934079)

status: Public on May 08 2007

type: genomic

city: King of Prussia

first: Joel

last: Greshock

state: PA

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

country: USA

institute: GlaxoSmithKline

hyb_protocol: DNA was resuspended and hybridized to the array for 72h at 37oC on a rotating platform. Additional details are found in: Greshock, J, Naylor, TL, Margolin, A, et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004; 14: 179-87

scan_protocol: Images were scanned with an Axon 4500 microarray scanner (Axon, Union City, CA) and analyzed with GenePix 3.0 software (Axon).

data_processing: All spots were subjected to a pin-tip normalization.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA).  Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.

extract_protocol: Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.

tag: Cell Line PE01

source_name: pooled reference

tag: pooled reference


title: Ovary, Carcinoma, NOS (12934076)

tag: Cell Line OVCAR8


title: Bone, NOS, Osteosarcoma, NOS (C40._, C41._) (12735806)

description: "Bone, NOS"; Osteosarcoma, NOS (C40._, C41._); University of Pennsylvania; 10/13/2003

tag: Cell Line Saos-2


title: Ovary, Carcinoma, NOS (12934080)


title: Bone, NOS, Osteosarcoma, NOS (C40._, C41._) (12735454)

growth_protocol: "Bone, NOS"; Osteosarcoma, NOS (C40._, C41._)


title: Ovary, Carcinoma, NOS (12933771)


title: Ovary, Carcinoma, NOS (12934077)


title: Ovary, Cancer (13078290)

description: Ovary; Cancer; University of Pennsylvania; 12/10/2004

growth_protocol: Ovary; Cancer

tag: Cell Line OVCAR7


title: Ovary, Carcinoma, NOS (12933770)

tag: Cell Line OVCAR5


title: Ovary, Cancer (13078289)


title: Ovary, Carcinoma, NOS (12933768)

tag: Cell Line OVCAR4


title: Ovary, Carcinoma, NOS (12933769)


title: Ovary, Carcinoma, NOS (12933732)

tag: Cell Line OVCAR2


title: Ovary, Carcinoma, NOS (12933767)


title: Ovary, Cancer (13078389)

tag: Cell Line OV68 ASC


title: Ovary, Cancer (13078386)


title: Ovary, Cancer (13078385)

tag: Cell Line OV55-2


title: Ovary, Carcinoma, NOS (12993880)

description: Ovary; Carcinoma, NOS; University of Pennsylvania; 10/7/2004

tag: Cell Line OVCAR10


title: Ovary, Carcinoma, NOS (12933736)

tag: Cell Line OVCAR3


title: Ovary, Cancer (13078296)


title: Ovary, Carcinoma, NOS (12993191)


title: Ovary, Cancer (13078292)

tag: Cell Line OV55-1


title: Ovary, Carcinoma, NOS (12993882)

tag: Cell Line OV7


title: Ovary, Cancer (13078295)


title: Ovary, Carcinoma, NOS (12933734)


title: Ovary, Carcinoma, NOS (12993885)

tag: Cell Line OV684


title: Ovary, Carcinoma, NOS (12993883)


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12993784)

description: "Breast, NOS (excludes Skin of breast C44.5)"; Carcinoma, NOS; University of Pennsylvania; 11/9/2004

tag: Cell Line MDA-MB-468


title: Breast, NOS (excludes Skin of breast C44.5), Adenocarcinoma, NOS (12933705)

description: "Breast, NOS (excludes Skin of breast C44.5)"; Adenocarcinoma, NOS; University of Pennsylvania; 9/3/2004

tag: Cell Line MCF7


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12993783)

growth_protocol: "Breast, NOS (excludes Skin of breast C44.5)"; Carcinoma, NOS


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12933421)

description: "Breast, NOS (excludes Skin of breast C44.5)"; Carcinoma, NOS; University of Pennsylvania; 9/3/2004

tag: Cell Line MDA-MB-231


title: Breast, NOS (excludes Skin of breast C44.5), Adenocarcinoma, NOS (12933704)

growth_protocol: "Breast, NOS (excludes Skin of breast C44.5)"; Adenocarcinoma, NOS

tag: pooled reference


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12933423)


title: Unknown primary site, Fibrosarcoma, NOS (12430055)

description: Unknown primary site; Fibrosarcoma, NOS; University of Pennsylvania; 11/19/2002

growth_protocol: Unknown primary site; Fibrosarcoma, NOS

tag: Cell Line HT 1080

source_name: pooled male

tag: pooled male


title: Bone, NOS, Osteosarcoma, NOS (C40._, C41._) (12462411)

description: "Bone, NOS"; Osteosarcoma, NOS (C40._, C41._); University of Pennsylvania; 12/6/2002

tag: Cell Line HOS


title: Unknown primary site, Fibrosarcoma, NOS (12457584)

description: Unknown primary site; Fibrosarcoma, NOS; University of Pennsylvania; 12/6/2002


title: Bone, NOS, Osteosarcoma, NOS (C40._, C41._) (12429852)

description: "Bone, NOS"; Osteosarcoma, NOS (C40._, C41._); University of Pennsylvania; 11/19/2002


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12462636)

description: "Breast, NOS (excludes Skin of breast C44.5)"; Carcinoma, NOS; University of Pennsylvania; 12/8/2002

tag: Cell Line HCC38


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457602)

tag: Cell Line HCC2218


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457527)

tag: Cell Line HCC1954


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457583)


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457844)


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457771)


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457604)

tag: Cell Line HCC1187


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457864)

tag: Cell Line HCC1937


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457866)


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457865)


title: Ovary, Carcinoma, NOS (12988058)

description: Ovary; Carcinoma, NOS; University of Pennsylvania; 10/1/2004

tag: Cell Line CP70


title: Unknown primary site, Rhabdomyosarcoma, NOS (12552874)

description: Unknown primary site; Rhabdomyosarcoma, NOS; University of Pennsylvania; 6/3/2003

tag: Cell Line GCT


title: Ovary, Cancer (13074625)

tag: Cell Line C200


title: Ovary, Carcinoma, NOS (12988012)

tag: Cell Line C30


title: Ovary, Carcinoma, NOS (12988013)


title: Ovary, Carcinoma, NOS (12409514)

description: Ovary; Carcinoma, NOS; University of Pennsylvania; 8/27/2002

tag: Cell Line CaOv-3

source_name: Pooled Male

tag: Pooled Male


title: Ovary, Carcinoma, NOS (12405857)


title: Breast, NOS (excludes Skin of breast C44.5), Infiltrating duct carcinoma (C50._) (12987602)

description: "Breast, NOS (excludes Skin of breast C44.5)"; Infiltrating duct carcinoma (C50._); University of Pennsylvania; 11/9/2004

tag: Cell Line BT-474


title: Ovary, Carcinoma, NOS (12988059)


title: Unknown primary site, Rhabdomyosarcoma, NOS (12602230)

description: Unknown primary site; Rhabdomyosarcoma, NOS; University of Pennsylvania; 6/13/2003

source_name: pooled female

tag: pooled female


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457441)

tag: Cell Line HCC1143


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12457526)


title: Ovary, Cancer (13074624)

tag: pooled reference


title: Breast, NOS (excludes Skin of breast C44.5), Infiltrating duct carcinoma (C50._) (12987601)

growth_protocol: "Breast, NOS (excludes Skin of breast C44.5)"; Infiltrating duct carcinoma (C50._)


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12430323)

description: "Breast, NOS (excludes Skin of breast C44.5)"; Carcinoma, NOS; University of Pennsylvania; 9/28/2002

tag: Cell Line BT-20

tag: pooled male


title: Tumor samples from patient No.16 PT16U95B

type: RNA

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

institute: The Methodist Hospital

description: Gene expression data from primary prostate cancer

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95B array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned 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 normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

label: biotin

molecule: total RNA

source_name: PT16, tumor samples from patient No.16

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

extract_protocol: Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.

tag: Tissue:primary prostate tumor

tag: Tumor stage

tag: Gleason Grade


title: Tumor samples from patient No.20 PT20U95B

source_name: PT20, tumor samples from patient No.20


title: Breast, NOS (excludes Skin of breast C44.5), Carcinoma, NOS (12429833)


title: Tumor samples from patient No.10 PT10U95B

source_name: PT10, tumor samples from patient No.10


title: Tumor samples from patient No.13 PT13U95B

source_name: PT13, tumor samples from patient No.13


title: Ovary, Carcinoma, NOS (12993190)

tag: Cell Line A2780


title: Ovary, Carcinoma, NOS (12993189)


title: Unknown primary site, Fibrosarcoma, NOS (12533085)

description: Unknown primary site; Fibrosarcoma, NOS; University of Pennsylvania; 6/13/2003

tag: Cell Line A204


title: Ovary, Carcinoma, NOS (12988015)

tag: Cell Line A2008


title: Ovary, Carcinoma, NOS (12988014)


title: Unknown primary site, Fibrosarcoma, NOS (12556270)

description: Unknown primary site; Fibrosarcoma, NOS; University of Pennsylvania; 6/3/2003


title: Tumor samples from patient No.20 PT20U95C

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95C array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: Tumor samples from patient No.10 PT10U95C


title: Tumor samples from patient No.13 PT13U95C


title: Ovary, Carcinoma, NOS (12993889)

description: Ovary; Carcinoma, NOS; University of Pennsylvania; 10/7/2004

tag: Cell Line OV684


title: Ovary, Carcinoma, NOS (12988057)

tag: Cell Line A1847


title: Tumor samples from patient No.16 PT16U95C


title: Ovary, Carcinoma, NOS (12933733)

description: Ovary; Carcinoma, NOS; University of Pennsylvania; 8/13/2004

tag: Cell Line OVCAR2


title: NHGRI_SKBR3_02-06-06Slide29T

status: Public on May 07 2007

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: Human Breast cell line

hyb_protocol: The test and reference labeled DNAs were mixed with 75 microgram of Cot I DNA and precipitated with alcohol. The pellet is resuspended in35 micro liter of hybridization solution (50% Formamide, 10% Dextran sulfate, 4% SDS and 2xSSC). The hybridization is performed under a cover slip in a humid chamber at 37 degree for 48 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray

source_name: HMEC

label_protocol: 600 nanogram of genomic DNA was labeld with random hexamers in the presence of Cy5 dUTPs using the Bioprime DNA labeling system from Invitrogen( cat#18094-011)

extract_protocol: DNA was extracted with Phenol/Chloroform/ Isoamyl alcohol method according to manufacturer protocol (Invitrogen#15593-031) and the DNA is further purified by ethanol precipitation.

tag: Human Mammary Epithelial cells

label_protocol: 600 nanogram of genomic DNA was labeld with random hexamers in the presence of Cy3 dUTPs using the Bioprime DNA labeling system from Invitrogen( cat#18094-011)

extract_protocol: DNA was extracted with Phenol/Chloroform/ Isoamyl alcohoil method according to manifecturer protocol (Invitro#15593-031) and the DNA is further purified by the Alcohol precipitation.

tag: Human Breast cell line


title: NHGRI_MDA-MB-436_02-06-06Slide95T

description: Human Breast cell line


title: Ovary, Carcinoma, NOS (13174046)

description: Ovary; Carcinoma, NOS; University of Pennsylvania; 4/8/2005


title: NHGRI_HCC38_02-06-06Slide30T

description: Human Breast cell line


title: NHGRI_MDA-MB-415_02-06-06Slide33T

description: Human Breast cell line


title: Ovary, Carcinoma, NOS (12988016)


title: NHGRI_HCC-1419_02-06-06Slide93T

description: Human Breast cell line


title: NHGRI_HCC-1419_02-06-06Slide35T

description: Human Breast cell line


title: NHGRI_BT-474_02-06-06Slide32T

description: Human Breast cell line


title: NHGRI_MDA-MB-436_02-06-06Slide37T

description: Human Breast cell line


title: Ovary, Carcinoma, NOS (13174048)


title: NHGRI_MDA-MB-435S_02-06-06Slide92T

description: Human Breast cell line


title: NHGRI_BT-474_02-06-06Slide90T

description: Human Breast cell line


title: NHGRI_MDA-MB-435S_02-06-06Slide34T

description: Human Breast cell line


title: NHGRI_T-47D_02-06-06Slide31T

description: Human Breast cell line


title: NHGRI_MDA-MB-415_02-06-06Slide91T

description: Human Breast cell line


title: NHGRI_T-47_02-06-06Slide89T

description: Human Breast cell line


title: NHGRI_HCC38_DyeSwap_HB7-30

description: Human Breast cell line

hyb_protocol: The combined Cy3 and Cy5 labeled cDNAs in 30 ul DEPC H20 are denatured for 2 minutes. 15 ul 20X SSC, 5 ul 100% Formamide, 0.5 ul 10% SDS, and 4 ul DEPC H20 are added and the mixture hybridized on the array slide under a coverslip at 65 degre for 16 hours.

label_protocol: 15-25 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Fluoro dUTP (Cy3/Cy5), after NaOH RNA hydrolysis, the labeled cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104)

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns


title: NHGRI_HCC38_HB7-87

description: Human Breast cell line


title: NHGRI_MDA-MB-436_01-31-06Slide83T

description: Human Breast cell line


title: NHGRI_SKBR3_02-06-06Slide8T

description: Human Breast cell line


title: NHGRI_MDA-MB-435S_01-31-06Slide80T

description: Human Breast cell line


title: NHGRI_HCC1419_DyeSwap_HB7-28

description: Human Breast cell line


title: Biofilm vs planktonic gene expression (3)

city: Jerusalem

first: Moshe

last: Shemesh

address: Hebrew University-Hadassah POB 12272

department: Institute of Dental Sciences

country: Israel

institute: Hebrew University-Hadassah

description: S. mutans UA159 was grown in Brain Heart Infusion Broth (BHI, Difco Labs, Detroit, USA) at 37 ºC in 95 % air/5 % CO2 (v/v). Culture of S. mutans was diluted 1:50, inoculated into fresh BHI media and grown in polystyrene tubes (37 ºC, 5 95 % air/5 % CO2 (v/v)). For biofilm generation, 20 μl of S. mutans culture grown as described above was seeded in 20-mm-diameter, 15-mm-deep sterile polystyrene multidishes.

hyb_protocol: Hybridization was performed basically according to TIGR protocol (http://pfgrc.tigr.org/protocols/M008.pdf). The samples were resuspended in hybridization buffer containing: 50 % formamide, 5 x SSC, 0.1 % SDS and 20 µg yeast tRNA, and heated at 90 °C for 10 min. following a quick centrifugation, the Cy dye-coupled probes were applied to microarray slides and incubated over-night at 42 °C. The hybridization was carried out in corning hybridization chambers submerged in a water bath.

scan_protocol: The hybridized slides were then washed and scanned by using Axon GenePix 4000B Scanner (Axon Instruments, Foster City, CA) with adjusted settings in order to obtain a similar green and red overall intensity. The hybridization patterns and intensities were quantitatively analyzed using the GenePix Pro 4.0 software (Axon) on scanned microarray images. This software localizes every spot with a programmed grid to obtain an averaged signal density of each spot and background (offset) of the area surrounding the spot.

data_processing: The result files (gpr) produced by GenePix have been imported into R and analyzed utilizing LIMMA (Smyth, 2004) software package for R, available from CRAN site (http://www.r-project.org). Spots flagged as not found or absent in GenePix were removed by filtering. Another filter was applied for saturated spots. After filtering, the data within the same slide was normalized using global loess normalization with the default smoothing span of 0.3 (Smyth & Speed, 2003) To identify differentially expressed genes a parametric empirical Bayesian approach implemented in LIMMA (Lonnstedt & Speed, 2002) was used. A moderated t test was performed in parallel, with the use of a false discovery rate (Reiner et al., 2003) correction for multiple testing. TIGR arrays include four replicates for each gene. Instead of just taking the average of replicate spots, we used the duplicate Correlation function (Smyth et al., 2005) available in LIMMA to acquire an approximation of gene-by-gene variance. This method greatly improves the precision with which the gene-wise variances are estimated and thereby maximize inference methods designed to identify differentially expressed genes. P <0.05 confidence level has been used to pinpoint those significantly differentiated genes. Genes had to have an A-value (average expression level for the gene across all arrays and channels) of more than 7.5, leaving out genes with an average intensity in both channels less than 200.

organism: Streptococcus mutans

source_name: Biofilm of S. mutans

label_protocol: cDNA was generated with random hexamers (6 µg) from 2 µg total RNA using the superscript III reverse transcriptase (Invitrogen, Life Technologies, Carlsbad, California, USA). The reverse transcription reaction was carried out at 42 °C overnight with aminoallyl labeled dUTP. Removal of unincorporated aa-dUTP and free amines was carried out using Microcon YM-30 (Millipore) filters according to manufacturer recommendations. Coupling of aminoallyl-labelled cDNA to Cy-dye esters was preformed in 0.1 M sodium carbonate buffer pH 8.6 for 1hr at room temperature. Removal of free dyes was accomplished with QIAquick PCR purification columns (QIAGEN). The labeling level was the quantified using a spectrophotometer ND-100 (Nanodrop Technologies, Wilmington, DE, USA). Each Cy3-labeled sample was mixed with equal amount of Cy5-labeled sample, and the mixtures were allowed to dry in a speed vacuum for about 1 hour.

extract_protocol: For extraction of the total RNA Biofilm-grown S. mutans cells were suspended in TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) and dislodged by scraping into a 2-ml microcentrifuge tube containing 0.4 ml 1-mm-diameter glass beads (Sigma-Aldrich, St. Louis, MO, USA). The cells were disrupted with the aid of a Fast Prep Cell Disrupter (Bio 101, Savant Instruments, Inc., NY, USA), centrifuged and the RNA containing supernatant was supplemented with 1-Bromo-3-Chloropropane (BCP) (Molecular Research Center, Cincinnati, OH, USA). The upper aqueous phase was precipitated with isopropanol. After centrifugation, the resulting RNA pellet was washed with ethanol and resuspended in diethyl pyrocarbonate (DEPC)-treated water. Because of the sensitivity of the PCR, residual contaminating DNA was eliminated by incubation of the sample with RNase-free DNase (Promega, Madison, WI, USA). The DNase was then inactivated by incubation at 65 °C for 10 minutes, and the RNA was precipitated with ethanol and suspended in diethyl pyrocarbonate (DEPC)-treated water. The RNA concentration was determined spectrophotometrically using the Nanodrop Instrument (ND-1000, Nanodrop Technologies, Wilmington, DE, USA). The integrity of the RNA was assessed by agarose-gel electrophoresis.

tag: Biofilm generated on polystyrene multidishes of S. mutans UA159

source_name: Planktonic bacteria

extract_protocol: For RNA extraction from planktonic cells, which were collected after centrifugation (4,500 g, 4 ºC) and immediately resuspended in TRI Reagent into a 2-ml microcentrifuge tube containing 0.4 ml 1-mm-diameter glass beads (Sigma-Aldrich, St. Louis, MO, USA). The cells were disrupted with the aid of a Fast Prep Cell Disrupter (Bio 101, Savant Instruments, Inc., NY, USA), centrifuged and the RNA containing supernatant was supplemented with 1-Bromo-3-Chloropropane (BCP) (Molecular Research Center, Cincinnati, OH, USA). The upper aqueous phase was precipitated with isopropanol. After centrifugation, the resulting RNA pellet was washed with ethanol and resuspended in diethyl pyrocarbonate (DEPC)-treated water. Because of the sensitivity of the PCR, residual contaminating DNA was eliminated by incubation of the sample with RNase-free DNase (Promega, Madison, WI, USA). The DNase was then inactivated by incubation at 65 °C for 10 minutes, and the RNA was precipitated with ethanol and suspended in diethyl pyrocarbonate (DEPC)-treated water. The RNA concentration was determined spectrophotometrically using the Nanodrop Instrument (ND-1000, Nanodrop Technologies, Wilmington, DE, USA). The integrity of the RNA was assessed by agarose-gel electrophoresis.

tag: Planktonic Streptococcus mutans grown to stationary phase


title: NHGRI_MDA-MB-415_01-31-06Slide79T

description: Human Breast cell line


title: NHGRI_HCC-1419_01-31-06Slide81T

description: Human Breast cell line


title: NHGRI_BT-474_01-31-06Slide78T

description: Human Breast cell line


title: NHGRI_MDA-MB415_DyeSwap_HB7-86

description: Human Breast cell line


title: NHGRI_SKBR3_DyeSwap_HB7-29

description: Human Breast cell line


title: Biofilm vs planktonic gene expression (2)

hyb_protocol: The samples were resuspended in hybridization buffer containing: 50 % formamide, 5 x SSC, 0.1 % SDS and 20 µg yeast tRNA, and heated at 90 °C for 10 min. following a quick centrifugation, the Cy dye-coupled probes were applied to microarray slides and incubated over-night at 42 °C. The hybridization was carried out in corning hybridization chambers submerged in a water bath.

scan_protocol: The hybridized slides were then washed and scanned by using Axon GenePix 4000B Scanner (Axon Instruments, Foster City, CA) with adjusted settings in order to obtain a similar green and red overall intensity.  The hybridization patterns and intensities were quantitatively analyzed using the GenePix Pro 4.0 software (Axon) on scanned microarray images. This software localizes every spot with a programmed grid to obtain an averaged signal density of each spot and background (offset) of the area surrounding the spot.

label_protocol: cDNA was generated with random hexamers (6 µg) from 2 µg total RNA using the superscript III reverse transcriptase (Invitrogen, Life Technologies, Carlsbad, California, USA). The reverse transcription reaction was carried out at 42 °C overnight with aminoallyl labeled dUTP. Removal of unincorporated aa-dUTP and free amines was carried out using Microcon YM-30 (Millipore) filters according to manufacturer recommendations. Coupling of aminoallyl-labelled cDNA to Cy-dye esters was preformed in 0.1 M sodium carbonate buffer pH 8.6 for 1hr at room temperature. Removal of free dyes was accomplished with QIAquick PCR purification columns (QIAGEN). The labeling level was the quantified using a spectrophotometer ND-100 (Nanodrop Technologies, Wilmington, DE, USA). Each Cy3-labeled sample was mixed with equal amount of Cy5-labeled sample, and the mixtures were allowed to dry in a speed vacuum for about 1 hour. Hybridization was performed basically according to TIGR protocol (http://pfgrc.tigr.org/protocols/M008.pdf).

extract_protocol: For extraction of the total RNA Biofilm-grown S. mutans cells were suspended in TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) and dislodged by scraping into a 2-ml microcentrifuge tube containing 0.4 ml 1-mm-diameter glass beads (Sigma-Aldrich, St. Louis, MO, USA). The cells were disrupted with the aid of a Fast Prep Cell Disrupter (Bio 101, Savant Instruments, Inc., NY, USA), centrifuged and the RNA containing supernatant was supplemented with 1-Bromo-3-Chloropropane (BCP) (Molecular Research Center, Cincinnati, OH, USA). The upper aqueous phase was precipitated with isopropanol. After centrifugation, the resulting RNA pellet was washed with ethanol and resuspended in diethyl pyrocarbonate (DEPC)-treated water. Because of the sensitivity of the PCR, residual contaminating DNA was eliminated by incubation of the sample with RNase-free DNase (Promega, Madison, WI, USA). The DNase was then inactivated by incubation at 65 °C for 10 minutes, and the RNA was precipitated with ethanol and suspended in diethyl pyrocarbonate (DEPC)-treated water. The RNA concentration was determined spectrophotometrically using the Nanodrop Instrument (ND-1000, Nanodrop Technologies, Wilmington, DE, USA). The integrity of the RNA was assessed by agarose-gel electrophoresis. The same procedure was conducted for RNA extraction from planktonic cells, which were collected after centrifugation (4,500 g, 4 ºC) and immediately resuspended in TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA).

tag: Streptococcus mutans UA159 biofilm generation on polystyrene multidishes for 24h

source_name: S. mutans planktoniccaly grown cells

label_protocol: cDNA was generated with random hexamers (6 µg) from 2 µg total RNA using the superscript III reverse transcriptase (Invitrogen, Life Technologies, Carlsbad, California, USA). The reverse transcription reaction was carried out at 42 °C overnight with aminoallyl labeled dUTP. Removal of unincorporated aa-dUTP and free amines was carried out using Microcon YM-30 (Millipore) filters according to manufacturer recommendations. Coupling of aminoallyl-labelled cDNA to Cy-dye esters was preformed in 0.1 M sodium carbonate buffer pH 8•6 for 1hr at room temperature. Removal of free dyes was accomplished with QIAquick PCR purification columns (QIAGEN). The labeling level was the quantified using a spectrophotometer ND-100 (Nanodrop Technologies, Wilmington, DE, USA). Each Cy3-labeled sample was mixed with equal amount of Cy5-labeled sample, and the mixtures were allowed to dry in a speed vacuum for about 1 hour. Hybridization was performed basically according to TIGR protocol (http://pfgrc.tigr.org/protocols/M008.pdf).

tag: Planktonic Streptococcus mutans UA159 growth to stationary phase


title: NHGRI_HCC38_01-31-06Slide76T

description: Human Breast cell line


title: NHGRI_BT474_DyeSwap_HB7-24

description: Human Breast cell line


title: NHGRI_MDA436_DyeSwap_HB7-27

description: Human Breast cell line


title: NHGRI_MDA-MB415_HB7-88

description: Human Breast cell line


title: NHGRI_MDA435_DyeSwap_HB7-25

description: Human Breast cell line


title: NHGRI_T-47D_01-31-06Slide77T

description: Human Breast cell line


title: NHGRI_MCF10A_DyeSwap_HB7-27

description: Human Breast cell line


title: Biofilm vs planktonic gene expression (1)

description: The hybridized slides were then washed and scanned by using Axon GenePix 4000B Scanner (Axon Instruments, Foster City, CA) with adjusted settings in order to obtain a similar green and red overall intensity.  The results represent the common findings of three independent biological replicate arrays performed with three different RNA samples. In two of the arrays the biofilm RNA sample was labeled with Cy5 and the planktonic with Cy3, while the third array was dye swapped. The hybridization patterns and intensities were quantitatively analyzed using the GenePix Pro 4.0 software (Axon) on scanned microarray images. This software localizes every spot with a programmed grid to obtain an averaged signal density of each spot and background (offset) of the area surrounding the spot.

source_name: S. mutans UA159 planktonic cells

extract_protocol: For extraction of the total RNA Biofilm-grown S. mutans cells were suspended in TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) and dislodged by scraping into a 2-ml microcentrifuge tube containing 0•4 ml 1-mm-diameter glass beads (Sigma-Aldrich, St. Louis, MO, USA). The cells were disrupted with the aid of a Fast Prep Cell Disrupter (Bio 101, Savant Instruments, Inc., NY, USA), centrifuged and the RNA containing supernatant was supplemented with 1-Bromo-3-Chloropropane (BCP) (Molecular Research Center, Cincinnati, OH, USA). The upper aqueous phase was precipitated with isopropanol. After centrifugation, the resulting RNA pellet was washed with ethanol and resuspended in diethyl pyrocarbonate (DEPC)-treated water. Because of the sensitivity of the PCR, residual contaminating DNA was eliminated by incubation of the sample with RNase-free DNase (Promega, Madison, WI, USA). The DNase was then inactivated by incubation at 65 °C for 10 minutes, and the RNA was precipitated with ethanol and suspended in diethyl pyrocarbonate (DEPC)-treated water. The RNA concentration was determined spectrophotometrically using the Nanodrop Instrument (ND-1000, Nanodrop Technologies, Wilmington, DE, USA). The integrity of the RNA was assessed by agarose-gel electrophoresis. The same procedure was conducted for RNA extraction from planktonic cells, which were collected after centrifugation (4,500 g, 4 ºC) and immediately resuspended in TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA).

tag: Planktonic bacteria of Streptococcus mutans UA159 growth to stationary phase

source_name: S. mutans UA159 Biofilm

tag: S. mutans UA159 Biofilm grown 24 h on polystyrene multidishes


title: NHGRI_HCC38_02-06-06Slide88T

description: Human Breast cell line


title: NHGRI_SKBR3_01-31-06Slide75T

description: Human Breast cell line


title: NHGRI_T47D_DyeSwap_HB7-23

description: Human Breast cell line


title: NHGRI_MDA436_HB7-20

description: Human Breast cell line


title: Total Population 2Gy 3h (ASP017)

status: Public on May 05 2007

city: Evry

first: Walid

last: Rachidi

address: 2 rue Gaston Crémieux

country: France

institute: CEA

description: Hybridization irradiated Total population vs control Total population

hyb_protocol: Direct hybridization sample (Cy3 vs Cy5)

scan_protocol: Genpix 4000B

data_processing: Normalized ration Bioconductor (method : prinTipLoess, span : 0,4)

molecule: polyA RNA

source_name: Total Population_2Gy_3h

label_protocol: Ambion / Amino Allyl MessageAmp II aRNA kit

extract_protocol: Qiagen / microRNAeasy kit

tag: Human Foreskin

tag: Gender Male

source_name: Total Population_0Gy_3h

tag: Gender male


title: Progenitors 2Gy 3h (ASP019)

description: Hybridization irradiated progenitors vs control progenitors


title: DFVF1_pig5_lung_healthy

status: Public on May 04 2007

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: RNA from lung tissue was extracted from healthy pig lung tissue and from lung tissue infected with Actinobacillus pleuropneumoniae, reverse transcribed and labeled with Alexa 594. A common reference (equal amounts of RNA from all samples) was reverse transcribed and labeled with Alexa 488. Samples and reference were hybridized simultaneously to DIAS_PIG_27K2_v2 slides and fluorescence in the Alexa 594 and Alexa 488 channels was acquired using a microarray scanner.

hyb_protocol: The slides were pre-hybridized (5 x SSC, 0.1 % SDS, 1 mg/mL BSA, 0.22 µm filtrated) at 42 ºC for 45 min and washed (2x5 dips in water) followed by a dip in isopropanol and centrifugation (300 x g). mSeries LifterSlip (25x60 mm, Erie Scientific Company) were cleaned by dipping in water followed by several dips in ethanol and left for drying. A lifterslip was placed on each slide and incubated at 42 ºC to preheat. The hybridization chamber, a 6x17x22 cm lidded plastic box with a stainless steel “table” and a napkin wetted with hybridization buffer, was placed at 42 ºC to preheat. The purified labeled cDNA were combined pair wise and 20 µg Poly-dA (Invitrogen), 25 µg yeast tRNA (Invitrogen) and 20 µg pig CoT-DNA was added. The samples were speedvaced until dry (medium heat, app. 30 min), resuspended in 70 µL hybridization buffer (50 % formamide, 5x SSC, 0.1 % SDS), incubated at 95 ºC for 3 min, snap cooled on ice and centrifuged. The samples were applied to the pre-heated slides and placed in the hybridization chamber which was sealed and incubated at 42ºC for 12 to 16 hours. Following hybridization, each array was immersed in 100 mL wash-1 (2x SSC, 0.1% SDS, 0.22 µm filtrated) at 42ºC until the lifterslip moves freely away from the slide. The arrays were transferred to a mBox (Erie Scientific Company) and immersed in wash-1 (2x SSC, 0.1% SDS, 0.22 µm filtrated) at 42ºC for 5 min., in wash-2 (0.1x SSC, 0.1% SDS, 0.22 µm filtrated) at ambient temperature for 10 min., 4 times in wash-3 (0.1x SSC, 0.22 µm filtrated) at ambient temperature for 1 min., rinsed in wash-4 (0.01x SSC, 0.22 µm filtrated) for 5 to 10 sec., dipped 5 times in water and dried by centrifugation (300 x g).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 10 µm resolution, 100 % LP and PMT adjusted individually for each channel. Image analysis software: ScanArray Express, ver. 3.0 (Perkin Elmer) using the histogram method with default settings.

data_processing: Statistical analysis was carried out in the R computing environment (ver 2.3.0, developmental version, for Windows) using the package Linear Models for Microarray Analysis (Limma, ver 2.4.11) which is part of the Bioconductor project. The log2-transformed ratios of Alexa-594 to Alexa-488 (not background corrected) were normalized within-slide using printtip-loess with default parameters as implemented in Limma and can be found in the “Value” column.

label: Alexa 594

organism: Sus scrofa

source_name: Lung tissue, healthy

label_protocol: Superscript Indirect cDNA Labeling System (Invitrogen) and ARES cDNA labeling kit (Molecular Probes/Invitrogen)

extract_protocol: RNeasy Maxi Kit with DNase treatment (Qiagen)

tag: Animal

value: 10-12 week old castrate of Danish Landrace/Yorkshire/Duroc from a high health herd (Specific Pathogen Free)

tag: Tissue

value: lung

tag: State

value: healthy

label: Alexa 488

source_name: Common reference

tag: Mixture of total RNA purified from infected and healthy pig lung tissue


title: Progenitors 2Gy 3h (ASP018)

tag: Human foreskin


title: Progenitors 2Gy 3h (ASP020)


title: DFVF1_pig5_lung_infected

source_name: Lung tissue, infected

value: infected with Actinobacillus pleuropneumoniae


title: Total Population 2Gy 3h (ASP016)

source_name: Total Population-2Gy-3h

tag: Human Forskin

source_name: Total population_0Gy-3h


title: Total Population 2Gy 3h (ASP015)

source_name: Total Population-0Gy_3h


title: DFVF1_pig4_lung_healthy


title: Total Population 2Gy 3h (ASP014)

hyb_protocol: Direct hybridization sample (Cy5 vs Cy3)


title: NHGRI_MDA435_HB7-18

description: Human Breast cell line

tag: Human Mammary Epithelial cells


title: NHGRI_T47D_HB7-16

description: Human Breast cell line

tag: Human Breast cell line


title: NHGRI_HCC1419_HB7-21

description: Human Breast cell line


title: DFVF1_pig3_lung_healthy

tag: Common reference


title: NHGRI_SKBR3_HB7-22

description: Human Breast cell line


title: DFVF1_pig3_lung_infected


title: NHGRI_BT474_HB7-17

description: Human Breast cell line


title: DFVF1_pig4_lung_lymph_node_challenged

description: RNA from lung lymph node tissue was extracted from healthy pigs and from pigs challenged with Actinobacillus pleuropneumoniae, reverse transcribed and labeled with Alexa 594. A common reference (equal amounts of RNA from all samples) was reverse transcribed and labeled with Alexa 488. Samples and reference were hybridized simultaneously to DIAS_PIG_55K2_v1 slides and fluorescence in the Alexa 594 and Alexa 488 channels was acquired using a microarray scanner.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL ) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press “button” on the machine which then prepare the slides for hybridization. When the message appears apply the samples onto the slides and press “button” and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % LP and PMT adjusted individually for each channel. Image analysis software: ScanArray Express, ver. 3.0 (Perkin Elmer) using the histogram method with default settings.

source_name: Lung lymph node tissue, challenged

label_protocol: Superscript Indirect cDNA Labeling System (Invitrogen) and ARES cDNA labeling kit (Molecular Probes/Invitrogen). Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. “Green” spike-in RNA was added to the common reference samples and “red” spike-in RNA was added to the samples.

value: lung lymph node

tag: Mixture of total RNA purified from challenged and healthy pig lung lymph node tissue


title: DFVF1_pig4_lung_infected


title: DFVF1_pig3_lung_lymph_node_challenged

value: challenged with Actinobacillus pleuropneumoniae


title: H3K36me2 ChIP in jhd1 KO strain #2

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

description: H3K36me2 ChIP in jhd1 KO (knockout) strain #2

hyb_protocol: Labeled DNA was purified over Zymo columns and eluted using water. Cy5- and Cy3-labeled samples were pooled, and 20x SSC and 10% SDS were added (final: 4x SSC, 0.2% SDS).  Samples were denatured at 95 degrees, spun down, and all but 3 microliters were added to the array. Samples were hybridized under a glass coverslip in a chamber prepared with 3x SSC at both ends. The chamber was submerged in a 65 degree water bath for incubation overnight.  After incubation, the coverslip was removed in a wash containing SSC and SDS. Arrays were then washed in consecutively more strigent solutions containing lower amounts of SSC. Arrays were centrifuged to dry and immediately scanned.

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

data_processing: Data were uploaded to the UNC Microarray Database and retrieved as the log2 normalized ratio of (median intensity of sample pixels / median intensity of reference pixels). Only spots with a regression correlation >0.6 (i.e. those comprised of pixels with consistent ratio values). Spots that either failed from PCR or that were flagged in Genepix were not retrieved. Data were then z-score transformed such that the mean of all spots became 0 and the standard deviation became 1. Dye swap experiments were inverted.

organism: Saccharomyces cerevisiae

source_name: input from jhd1 KO strain

label_protocol: samples and references were amplified using a random primed PCR-based method (see Bohlander et al., 1992)

extract_protocol: Genomic DNA from whole-cell extract was reversed crosslinked, purified, and used as input.

tag: input from jhd1 KO strain

source_name: H3K36me2 ChIP DNA from jhd1 KO strain

extract_protocol: The H3K36me2 rabbit polyclonal antibody was previously described (Tsukada Y. et al., 2006 Nature 439:811-6); the H3K36me2 antibody was generated in rabbits by injection of a synthetic peptide (STGGVKKPHRY-C), in which the first lysine was dimethylated. ChIP assays were performed as described previously (Rao et al., Mol Cell Biol 2005 Nov;25(21):9447-59). Briefly, whole-cell extracts were prepared from 1% formaldehyde-fixed yeast cells using lysis buffer (50 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X, and 0.1% sodium deoxycholate) and sonicated to shear the chromatin. Immunoprecipitation was performed using the H3K36me2 antibody. Crosslinking was reversed at 65°C, and DNA was extracted using a Qiagen PCR purification kit according to the manufacturer's instructions.

tag: H3K36me2 ChIP DNA from jhd1 KO strain


title: DFVF1_pig5_lung_lymph_node_challenged


title: H3K36me2 ChIP in wild type strain #3

description: H3K36me2 ChIP in wild type strain #3

source_name: input from BY4741

tag: input from BY4741

source_name: H3K36me2 ChIP DNA from BY4741

tag: H3K36me2 ChIP DNA from BY4741


title: DFVF1_pig2_lung_lymph_node_control

source_name: Lung lymph node tissue, healthy


title: DFVF1_pig1_liver_control

description: RNA from liver tissue was extracted from healthy pigs and from pigs challenged with Actinobacillus pleuropneumoniae, reverse transcribed and labeled with Alexa 594. A common reference (equal amounts of RNA from all samples) was reverse transcribed and labeled with Alexa 488. Samples and reference were hybridized simultaneously to DIAS_PIG_55K2_v1 slides and fluorescence in the Alexa 594 and Alexa 488 channels was acquired using a microarray scanner.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL ) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press “button” on the machine which then prepare the slides for hybridization. When the message appears apply the samples onto the slides and press “button” and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox)

source_name: Liver tissue, healthy

value: liver

tag: Mixture of total RNA purified from challenged and healthy pig liver tissue


title: H3K36me2 ChIP in JHD1 OE strain #3 (dye swap)

description: H3K36me2 ChIP in JHD1 overexpression (OE) strain #3 (dye swap)

source_name: H3K36me2 ChIP DNA from JHD1 OE strain

tag: H3K36me2 ChIP DNA from JHD1 OE strain

source_name: input from JHD1 OE strain

tag: input from JHD1 OE strain


title: Progenitors 2Gy 3h (ASP021)

tag: Human Foreskin

tag: Genedr Male

tag: Gender male


title: DFVF1_pig4_liver_challenged

source_name: Liver tissue, challenged

tag: Animal

tag: Tissue

tag: State


title: H3K36me2 ChIP in wild type strain #1

description: H3K36me2 ChIP in wild type strain #1

source_name: input from flag-JHD1 strain

tag: input from flag-JHD1 strain

source_name: H3K36me2 ChIP DNA from flag-JHD1 strain

tag: H3K36me2 ChIP DNA from flag-JHD1 strain


title: Ketogenic diet (21C9)

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Hepatic gene expression data of C57BL/6 animals on Ketogenic diet

hyb_protocol: Hybridization protocol Standard Affymetrix

scan_protocol: Scan protocol Standard Affymetrix

data_processing: Data processing GCOS,MAS5

label: Label biotin

organism: Mus musculus

source_name: livers from C57BL/6 animals on Ketogenic diet

label_protocol: Label protocol one cycle (Affymetrix standard protocol)

extract_protocol: Extraction protocol RNA Midi Kit from Qiagen


title: NHGRI_MCF10A_HB7-19

description: Human Breast cell line

source_name: HMEC

tag: Human Mammary Epithelial cells

tag: Human Breast cell line


title: DFVF1_pig5_liver_challenged

source_name: Common reference


title: DFVF1_pig2_liver_control


title: DFVF1_pig1_lung_lymph_node_control

tag: Mixture of total RNA purified from challenged and healthy pig lung lymph node tissue


title: H3K36me2 ChIP in jhd1 KO strain #1

description: H3K36me2 ChIP in jhd1 KO (knockout) strain #1

tag: input from jhd1 KO strain

tag: H3K36me2 ChIP DNA from jhd1 KO strain


title: H3K36me2 ChIP in jhd1 KO strain #1 (dye swap)

description: H3K36me2 ChIP in jhd1 KO (knockout) strain #1 (dye swap)


title: Ketogenic diet (21D1)

source_name: livers from C57BL/6 animals on ketogenic diet

tag: Hepatic gene expression data of C57BL/6 animals on Ketogenic diet


title: H3K36me2 ChIP in jhd1 KO strain #3

description: H3K36me2 ChIP in jhd1 KO (knockout) strain #3


title: DFVF1_pig3_liver_challenged

tag: Mixture of total RNA purified from challenged and healthy pig liver tissue


title: H3K36me2 ChIP in wild type strain #2

description: H3K36me2 ChIP in wild type strain #2


title: H3K36me2 ChIP in wild type strain #1 (dye swap)


title: Chow diet (21C1)

description: Hepatic gene expression data of C57BL/6 animals on chow diet

source_name: livers from C57BL/6 animals


title: MGMA591 post

status: Public on May 03 2007

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

description: 2 blood samples were collected for each dolphin 1) immediately after the capture event (*pre*) and 2) just before the animal was released (*post*).

hyb_protocol: the solution: 33% formamide, 2.6X SSPE, 2.4% SDS, 1.7X Denhardts,  blocking agent: poly dA (1 mg/ml), mouse cot-1 DNA (1 mg/ml),  wash procedure: 2XSSC-0.1% SDS (5 min, 1X), 0.2XSSC-0.1% SDS (5 min, 2X), 0.2XSSC (5 min, 2X), 0.1XSSC (5 min, 1X), water (10 sec, 1X),  quantity of labelled target used: 10 micrograms,  time, concentration, volume, temperature: 18 hours, 0.11 mg/ml, 90 microliters, 50 C,  description of the hybridization instruments: SlideOut oven model 241000, Boekel

scan_protocol: scanning hardware: ScanArray Express,  scanning software: ScanArray Express

data_processing: Ch1 Intensity

label: NSH ester Cy3 (Ambion)

organism: Tursiops truncatus

source_name: blood cells (PBL)

label_protocol: amount of nucleic acids labled: 10 micrograms, lable used: NSH ester Cy3 (Ambion), lable incorperation method: chemical conjugation

extract_protocol: extraction method: PAXgene Blood RNA kit, sample molecule: total RNA, amplification: cDNA tagged with T7 promoter followed by linear amplification of antisense RNA in the presence of amino allyl UTP (MessageAmp II, Ambion)

tag: sex

value: male

tag: age

tag: growth conditions

value: wild animal

tag: development stage

value: sampled in 2004

tag: organism part(tissue)

value: blood

tag: animal/plant strain or line

value: Indian River Lagoon, FL

tag: treatment type

value: post bleeding

tag: sampling data processing

value: Ch1 Intensity


title: Chow diet (21B9)

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

label_protocol: one cycle (Affymetrix standard protocol)

extract_protocol: RNA Midi Kit from Qiagen

treatment_protocol: chow diet

tag: Hepatic gene expression data of C57BL/6 animals on chow diet


title: Chow diet (21B8)

description: heptic gene expression profile of mouse on chow diet.

data_processing: GCOS, MAS5

treatment_protocol: Animals on Chow Diet

tag: Animals on Chow Diet


title: H3K36me2 ChIP in JHD1 OE strain #1 (dye swap)

description: H3K36me2 ChIP in JHD1 overexpression (OE) strain #1 (dye swap)

tag: H3K36me2 ChIP DNA from JHD1 OE strain

tag: input from JHD1 OE strain


title: Ketogenic diet (21C8)


title: MGMA594 pre

value: pre bleeding


title: MGMA589 post


title: MGMA593 post


title: MGMA602 post

value: sampled in 2003


title: MGMA590 pre


title: MGMA592 pre


title: MGMA588 pre

value: female


title: MGMA585 post

value: sampled 2003

value: Charleston Harbor


title: MGMA605 pre


title: H3K36me2 ChIP in JHD1 OE strain #2

description: H3K36me2 ChIP in JHD1 overexpression (OE) strain #2


title: MGMA583 pre


title: MGMA603 post


title: MGMA580 post

value: xxx


title: MGMA600 pre


title: MDA-MB-231 + DTX 100 nM 48h A

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

description:
Spotted cDNA microarrays.
CNIO Oncochip contains about 11,500 cDNA clones representing 9,300 genes (UniGene clusters) plus several hundred not included in UniGene.

hyb_protocol: Hybridization was performed in 4× standard saline citrate, 1× bovine serum albumin, 2 g/ml DNAs and 0.1% sodium dodecyl sulphate at 42°C for 15 hr.

scan_protocol: Slides were washed, dried and then scanned in a Scanarray 5000 XL scanner (GSI Lumonics Kanata, Ontario, Canada) at wavelengths of 635 and 532 nm for Cy5 and Cy3 dyes, respectively.

data_processing:
10-um resolution images were quantified using the GenePix Pro 6.0 program (Axon Instruments, Union City, CA).

DNMAD Normalization

Layout information:
Main grid (12 rows X 4 columns)
Sub-grid  (24 rows X 24 columns)

Layout normalization options:
Use negative flags
Return negative flagged points as NA
Use background correction

source_name: Reference

label_protocol: Cy5-dUTP fluorochrome (Amersham, Uppsala, Sweden)

extract_protocol: Total RNA and T7-(deoxythymidine)24 oligo primer were used to amplify the double-strand cDNA by the Superscript Choice System (Life Technologies, Gaithersburg, MD). In vitro transcription was carried out with MegascriptTM T7 (Ambion, Austin, TX).

tag: Universal Human Reference RNA

source_name: MDA-MB-231 + DTX 100 nM 48h

label_protocol: Cy3-dUTP fluorochrome (Amersham, Uppsala, Sweden)

tag: MDA-MB-231 cells after 48 hours of exposure to 100 nM docetaxel


title: MDA-MB-231 Control C

source_name: MDA-MB-231 Control C

tag: MDA-MB-231 human breast carcinoma cell line.

tag: No treatment.


title: MDA-MB-231 + DTX 100 nM 24h A

source_name: MDA-MB-231 + DTX 100 nM 24h

tag: MDA-MB-231 cells after 24 hours of exposure to 100 nM docetaxel


title: MGMA587 post

tag: sex


title: MGMA581 pre

tag: age


title: MGMA577 post

tag: growth conditions


title: MGMA601 pre

tag: development stage


title: MGMA595 post

tag: organism part(tissue)


title: MGMA599 post

tag: animal/plant strain or line


title: MGMA572 pre

tag: treatment type


title: MDA-MB-231 + DTX 100 nM 48h B


title: MGMA576 pre

tag: sampling data processing


title: MDA-MB-231 + DTX 100 nM 24h B


title: MGMA573 post


title: MGMA596 post


title: MGMA582 post


title: MGMA569 post

value: charleston harbor


title: MGMA575 post

value: sampled  in 2004


title: MGMA597 pre


title: MDA-MB-231 + DTX 100 nM 8h A

source_name: MDA-MB-231 + DTX 100 nM 8h

tag: MDA-MB-231 cells after 8 hours of exposure to 100 nM docetaxel


title: Gastrin-CCK double Knockout replicate 2

city: ANN ARBOR

first: Linda

last: Samuelson

state: MI

address: MED SCI II, # 7761, 1150 W. MEDICAL CENTER DRIVE

department: Molecular and Integrative Physiology

institute: University of Michigan

description: Gastrin-CCK double Knockout fundic RNA

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Probe-set signal intensity from Ann Arbor Suite. See http://dot.ped.med.umich.edu:2000/ourimage/pub/shared/Affymethods.html or Affymethods.pdf supplementary file associated with GSE4810.

source_name: Gastrin-CCK double Knockout fundus

label_protocol: Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: gastrin-CCK double knockout mice were dissected and the fundus was used to isolate RNA from fundic mucosal scrapings. Total RNA was extracted by Trizol followed by an RNeasy kit (Qiagen).

tag: Gastrin-CCK double Knockout, 2 month old male mice fundic mucosal scraping


title: MGMA604 pre


title: MGMA586 pre


title: MGMA598 pre

value: Female

value: sample in 2004


title: MGMA570 pre


title: MGMA574 pre

value: male


title: MGMA571 post

value: wild animal


title: MDA-MB-231 Control D

source_name: MDA-MB-231 Control 0h


title: Gastrin-CCK double Knockout replicate 3

description: Gastrin-CCK double Knockout fundic RNA


title: MGMA566 post


title: MGMA568 pre


title: MGMA563 pre

value: Charleston harbor


title: wild type fundus replicate 2

description: Wild type fundic RNA

source_name: WT fundus

extract_protocol: Approximately 2-4 wild-type mice were dissected and the fundus was used to isolate RNA from fundic mucosal scrapings. Total RNA was extracted by Trizol followed by an RNeasy kit (Qiagen).

tag: Wild type, 2 month old male mice fundic mucosal scrapings


title: Gastrin infused gastrin Knockout replicate 2

description: Gastrin Knockout infused with gastrin fundic RNA

source_name: Gastrin infused gastrin Knockout fundus

extract_protocol: gastrin knockout mice were infused with gastrin for 1 week and the fundus was used to isolate RNA from fundic mucosal scrapings. Total RNA was extracted by Trizol followed by an RNeasy kit (Qiagen).

tag: Gastrin Knockout infused with gastrin, 2 month old male mice fundic mucosal scraping


title: MDA-MB-231 Control A

tag: Universal Human Reference RNA


title: MDA-MB-231 + DTX 2 nM 8h A

source_name: MDA-MB-231 + DTX 2 nM 8h

tag: MDA-MB-231 cells after 8 hours of exposure to 2 nM docetaxel


title: Gastrin infused gastrin Knockout replicate 3


title: MDA-MB-231 + DTX 2 nM 48h A

source_name: MDA-MB-231 + DTX 2 nM 48h

tag: MDA-MB-231 cells after 48 hours of exposure to 2 nM docetaxel


title: wild type fundus replicate 3

description: Wild type fundic RNA


title: MDA-MB-231 Control B

tag: MDA-MB-231 human breast carcinoma cell line.

tag: No treatment.


title: Gastrin Knockout fundus replicate 3

description: Gastrin Knockout infused with saline fundic RNA

source_name: Gastrin Knockout fundus

extract_protocol: gastrin knockout mice were infused with saline for 1 week and the fundus was used to isolate RNA from fundic mucosal scrapings. Total RNA was extracted by Trizol followed by an RNeasy kit (Qiagen).

tag: Gastrin Knockout, 2 month old male mice infused with saline

value: fundic mucosal scraping


title: MDA-MB-231 + DTX 2 nM 24h A

source_name: MDA-MB-231 + DTX 2 nM 24h

tag: MDA-MB-231 cells after 24 hours of exposure to 2 nM docetaxel


title: Gastrin-CCK double Knockout replicate 1

description: Gastrin-CCK double Knockout fundic RNA


title: MGMA565 pre

tag: sex

value: femaile

tag: age

tag: growth conditions

value: blood


title: AR2-HT-24-1-603

status: Public on May 02 2007

city: Ciudad de Buenos Aires

first: Mariano

middle: Cesar

last: Salibe

address: Av. Patricias Argentinas 435

country: Argentina

institute: Gentron LLC

description: hypothalamus of male DBA/1 mice

hyb_protocol: Slides were prehybridised at 42°C in 2X SSC, 0.1% SDS, 1% BSA. Labeled probes were mixed with hybridization buffer containing 30% formamide and hybridized overnight at 42°C

scan_protocol: Images were obtained with a VersArray ChipReader system (BioRad) at 10 um resolution and 16bit depth. Each slide was scanned three times, each time with a 5% increment in the sensitivity of the scanner. The data integration for multipole scanning were calculated by M = log2(cy3 / cy2) and A = 0.5 * log2(cy2 * cy3) values for all the possible combinations between channels among the three scannings. Quality score for each couple of channels was calculated as QS = min(QScy2, QScy3). The resulting 9 sets of A and M values were averaged using the QS as weights to obtain the integrated A and M sets.

data_processing: Data was log2 transformed and normalizaed with an intensity- and location-dependent loess fit

source_name: hypothalamus (collagen)

label_protocol: RNA was reversed transcribed using Superscript II RT (Invitrogen) with oligo dT primers and random primers, both in the presence of aa-dUTP (Sigma). The cDNA was labeled with Cy3 or Cy5 dyes (Amersham), resuspended in DMSO, and incubated for 1 hr at room temperature in the dark. The probes were purified using the SNAP Gel Purification Kit (Invitrogen) following manufacturer instructions with the following modification: at the initial step, 500 ul of loading buffer (2.25 M guanidinium HCl in 70% isopropanol) were added to the sample, placed in a SNAP column and incubated for 4 min before the first centrifugation

growth_protocol: Mice were housed in HEPA filtered air racks (Tecniplast, Italy) with food and water ad libitum

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen)

treatment_protocol: Eight week old DBA/1 male mice were injected i.d. with 100 ul type II Collagen in 100 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

tag: Hypothalamus from male DBA/1 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant

source_name: hypothalamus (control)

treatment_protocol: Eight week old DBA/1 male mice were injected i.d. with 200 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

tag: hypothalamus from male DBA/1 mice 31 d after i.d. injection of Complete Freunds adjuvant


title: wild type fundus replicate 1

description: Wild type fundic RNA


title: AR2-HT-24-3-699

description: Hypothalamus of male DBA/1 mice

tag: hypothalamus from male DBA/1 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant


title: AR2-HT-24-3-700

description: hypothalamus of male DBA/1 mice


title: AR2-HT-24-2-608

description: Hypothalamus of male DBA/1 mice


title: AR2-HT-24-2-609

description: hypothalamus of male DBA/1 mice


title: Gastrin Knockout fundus replicate 1


title: Gastrin infused gastrin Knockout replicate 1


title: MGMA562 post

tag: development stage

tag: organism part(tissue)

tag: animal/plant strain or line

tag: treatment type

value: post bleeding

tag: sampling data processing

value: Ch1 Intensity


title: Gastrin Knockout fundus replicate 2


title: AR2-HT-24-1-602

description: Hypothalamus of male DBA/1 mice


title: AR2-MB-24-2-740

description: Mid Brain of male DBA/1 mice

source_name: midbrain (control)

tag: Mid Brain from male DBA/1 mice 31 d after i.d. injection of Complete Freunds adjuvant

source_name: midbrain (collagen)

tag: Mid Brain from male DBA/1 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant


title: AR2-MB-24-2-741

description: Mid Brain of male DBA/1 mice


title: AR2-MB-24-1-737

description: Mid Brain of male DBA/1 mice


title: AR2-MB-24-2-610

description: Mid Brain of male DBA/1 mice


title: AR2-MB-24-3-702

description: Mid Brain of male DBA/1 mice


title: AR2-MB-24-1-605

description: Mid Brain of male DBA/1 mice


title: P-LI-192-3-778

description: Liver of male c57Bl/6 mice

source_name: liver (control)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 192 h

tag: Liver from male C57Bl/6 mice 192 h after s.c. injection of PBS

source_name: liver (192 h after injected with lung cancer cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 192 h

tag: Liver from male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-LI-72-3-763

description: Liver of male C57Bl/6 mice

source_name: liver (72 h after injected with lung cancer cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 72 h

tag: Liver from male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h

tag: Liver from male C57Bl/6 mice 72 h after s.c. injection of PBS


title: P-LI-192-4-781

description: Liver of male C57Bl/6 mice

tag: Liver from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: AR2-MB-24-2-611

description: Mid Brain of male DBA/1 mice


title: P-LI-18-3-754

description: Liver of male c57Bl/6 mice

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 18 h

tag: Liver from male C57Bl/6 mice 18 h after s.c. injection of PBS

source_name: liver (18 h after injected with lung cancer cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 18 h

tag: Liver from male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-LI-72-4-764

description: Liver of male c57Bl/6 mice

tag: Liver from male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-LI-72-2-753

description: Liver of male C57Bl/6 mice


title: P-LI-72-3-762

description: Liver of male c57Bl/6 mice


title: AR2-MB-24-3-701

description: Mid Brain of male DBA/1 mice


title: P-LI-72-2-752

description: Liver of male c57Bl/6 mice


title: AR2-MB-24-1-604

description: Mid Brain of male DBA/1 mice


title: P-LI-18-4-756

description: Liver of male c57Bl/6 mice


title: P-LI-192-4-780

description: Liver of male c57Bl/6 mice


title: P-LI-18-3-755

description: Liver of male C57Bl/6 mice

tag: Liver from male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: MGMA564 post

source_name: blood cells (PBL)

tag: sex

tag: age

tag: growth conditions

value: sampled in 2003


title: P-LI-192-3-779

description: Liver of male C57Bl/6 mice


title: AR2-MB-24-1-736

description: Mid Brain of male DBA/1 mice


title: P-LI-72-1-751

description: Liver of male C57Bl/6 mice


title: P-LI-18-4-757

description: Liver of male C57Bl/6 mice


title: P-LI-72-4-765

description: Liver of male C57Bl/6 mice


title: P-LI-192-2-749

description: Liver of male C57Bl/6 mice


title: P-LI-192-1-746

description: Liver of male c57Bl/6 mice


title: P-LI-18-2-745

description: Liver of male C57Bl/6 mice


title: P-LI-192-2-748

description: Liver of male c57Bl/6 mice


title: P-LI-72-1-750

description: Liver of male c57Bl/6 mice


title: P-LI-192-1-747

description: Liver of male C57Bl/6 mice


title: P-LI-18-1-742

description: Liver of male c57Bl/6 mice


title: P-LI-18-2-744

description: Liver of male c57Bl/6 mice

source_name: liver (18 h afterinjected with lung cancer cells)


title: P-CO-72-7-774

description: Pre-frontal cortex of male c57Bl/6 mice

source_name: prefrontal cortex (control)

tag: Pre-frontal cortex from male C57Bl/6 mice 72 h after s.c. injection of PBS

source_name: prefrontal cortex (72 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: AR-HT-24-2-552

description: hypothalamus of male c57Bl/6 mice

treatment_protocol: Eight week old C57Bl/6 male mice were injected i.d. with 100 ul type II Collagen in 100 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

tag: Hypothalamus from male C57Bl/6 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant

treatment_protocol: Eight week old C57Bl/6 male mice were injected i.d. with 200 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

tag: Hypothalamus from male C57Bl/6 mice 31 d after i.d. injection of Complete Freunds adjuvant


title: P-CO-18-7-772

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex from male C57Bl/6 mice 18 h after s.c. injection of PBS

source_name: prefrontal cortex (18 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex form male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: AR2-CO-24-1-735

description: Pre-frontal cortex of male DBA/1 mice

source_name: prefrontal cortex (collagen)

tag: Pre-frontal cortex from male DBA/1 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant

tag: Pre-frontal cortex from male DBA/1 mice 31 d after i.d. injection of Complete Freunds adjuvant


title: P-CO-72-7-775

description: Pre-frontal cortex of male C57Bl/6 mice

tag: Pre-frontal cortex from male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: P-LI-18-1-743

description: Liver of male C57Bl/6 mice


title: AR-HT-24-1-544

description: hypothalamus of male c57Bl/6 mice


title: AR-HT-24-3-573

description: hypothalamus of male c57Bl/6 mice


title: P-CO-18-7-773

description: Pre-frontal cortex of male C57Bl/6 mice

tag: Pre-frontal cortex from male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: AR2-CO-24-2-738

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-2-606

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-2-739

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-1-734

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-3-697

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-1-600

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-3-698

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-2-607

description: Pre-frontal cortex of male DBA/1 mice


title: AR2-CO-24-1-601

description: Pre-frontal cortex of male DBA/1 mice


title: P-CO-192-7-777

description: Pre-frontal cortex of male C57Bl/6 mice

source_name: prefrontal cortex (192 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Pre-frontal cortex from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: AR-HT-24-2-550

description: hypothalamus of male c57Bl/6 mice


title: P-CO-192-7-776

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: AR-HT-24-3-572

description: hypothalamus of male c57Bl/6 mice


title: AR-HT-24-1-543

description: hypothalamus of male c57Bl/6 mice


title: M-MB-18-4-508

description: Mid brain of female balb/c mice

source_name: midbrain (18 h after injection of 4T-1 mammary cancer cells)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 18 h

tag: Mid Brain from female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 18 h

tag: Mid Brain from female Balb/c mice 18 h after s.c. injection of PBS


title: M-MB-18-5-536

description: Mid brain of female balb/c mice


title: M-MB-18-4-507

description: Mid Brain of female balb/c mice


title: P-MB-192-6-560

description: Mid Brain of male C57Bl/6 mice

source_name: midbrain (192 h after injection of LL/2(LLC1) lung cancer cell)

tag: Mid Brain from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Mid Brain from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: M-MB-192-3-473

description: Mid Brain of female balb/c mice

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 192 h

tag: Mid Brain from female Balb/c mice 192 h after s.c. injection of PBS

source_name: midbrain (192 h after injection of 4T-1 mammary cancer cells)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 192 h

tag: Mid Brain from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: P-MB-192-5-529

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain  from male C57Bl/6 mice 192 h after s.c. injection of PBS

tag: Mid Brain from male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-MB-72-4-489

description: Mid Brain of female balb/c mice

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 72 h

tag: Mid Brain from female Balb/c mice 72 h after s.c. injection of PBS

source_name: midbrain (72 h after injection of 4T-1 mammary cancer cells)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 72 h

tag: Mid Brain from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: M-MB-18-5-535

description: Mid Brain of female balb/c mice

source_name: midbrain (control)


title: P-MB-18-3-478

description: Mid Brain of male C57Bl/6 mice

source_name: midbrain (18 h after injection of LL/2(LLC1) lung cancer cell)

tag: Mid Brain from male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Mid Brain from male C57Bl/6 mice 18 h after s.c. injection of PBS


title: M-MB-192-3-474

description: Mid brain of female balb/c mice


title: M-MB-72-4-490

description: Mid brain of female balb/c mice


title: M-MB-18-3-472

description: Mid brain of female balb/c mice


title: M-MB-72-3-462

description: Mid Brain of female balb/c mice


title: M-MB-192-4-483

description: Mid brain of female balb/c mice


title: P-MB-192-3-469

description: Mid Brain of male C57Bl/6 mice


title: P-MB-192-5-530

description: Mid Brain of male C57Bl/6 mice


title: P-MB-72-4-496

description: Mid Brain of male C57Bl/6 mice

source_name: midbrain (72 h after injection of LL/2(LLC1) lung cancer cell)

tag: Mid Brain from male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Mid Brain from male C57Bl/6 mice 72 h after s.c. injection of PBS


title: M-MB-192-4-482

description: Mid Brain of female balb/c mice


title: P-MB-192-4-468

description: Mid Brain of male c57Bl/6 mice


title: P-MB-192-6-559

description: Mid Brain of male c57Bl/6 mice


title: P-MB-192-4-467

description: Mid Brain of male C57Bl/6 mice


title: P-MB-72-3-465

description: Mid Brain of male C57Bl/6 mice


title: P-MB-192-3-466

description: Mid Brain of male c57Bl/6 mice


title: P-MB-72-4-495

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain  from male C57Bl/6 mice 72 h after s.c. injection of PBS

tag: Mid Brain from male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-MB-18-3-477

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain  from male C57Bl/6 mice 18 h after s.c. injection of PBS

tag: Mid Brain from male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-MB-72-3-463

description: Mid brain of female balb/c mice


title: M-MB-18-3-470

description: Mid Brain of female balb/c mice

tag: Mid Brain from female Balb/c mice 18 h after s.c. injection of PBS

tag: Mid Brain from female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells


title: P-MB-18-4-442

description: Mid Brain of male C57Bl/6 mice


title: C-MB-18-3-515

description: midbrain of male balb/c mice

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 18 h

tag: Midbrain from male Balb/c mice 18 h after s.c. injection of PBS

source_name: midbrain (18 h after injection of CT26 colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 18 h

tag: Midbrain form male Balb/c mice 18 h after s.c. injection of CT26 colon carcinoma cells


title: P-MB-72-3-464

description: Mid Brain of male c57Bl/6 mice


title: C-MB-72-4-456

description: midbrain of male balb/c mice

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h

tag: Midbrain from male Balb/c mice 72 h after s.c. injection of PBS

source_name: midbrain (72 h after injection of CT26 colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 72 h

tag: Midbrain from male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells


title: AR-MB-24-2-555

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain from male C57Bl/6 mice 31 d after i.d. injection of Complete Freunds adjuvant

source_name: midbrain (collagen)

tag: Mid Brain from male C57Bl/6 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant


title: C-MB-18-4-523

description: midbrain of male balb/c mice


title: C-MB-192-3-475

description: midbrain of male balb/c mice

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 192 h

tag: Midbrain from male Balb/c mice 192 h after s.c. injection of PBS

source_name: midbrain (192 h after injection of CT26 colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 192 h

tag: Midbrain from male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: AR-MB-24-2-556

description: Mid Brain of male c57Bl/6 mice


title: AR-MB-24-1-546

description: Mid Brain of male c57Bl/6 mice


title: C-MB-192-3-476

description: midbrain of male balb/c mice

tag: Midbrain form male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: P-MB-18-4-441

description: Mid Brain of male c57Bl/6 mice


title: C-MB-18-5-566

description: midbrain of male balb/c mice


title: C-MB-72-3-447

description: midbrain of male balb/c mice

tag: Midbrain from male Balb/c mice 72 h after subcutaneous injection of PBS


title: AR-MB-24-1-545

description: Mid Brain of male c57Bl/6 mice


title: C-MB-18-3-516

description: midbrain of male balb/c mice


title: AR-MB-24-3-575

description: Mid Brain of male c57Bl/6 mice


title: C-MB-18-4-524

description: midbrain of male balb/c mice


title: C-MB-192-4-510

description: midbrain of male balb/c mice


title: AR-MB-24-3-574

description: Mid Brain of male c57Bl/6 mice


title: M-HT-18-5-534

description: hypothalamus of female balb/c mice

source_name: hypothalamus (18 h after injection of 4T-1 mammary cancer cell)

tag: Hypothalamus form female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells

source_name: hypothalamus (control)

tag: Hypothalamus from female Balb/c mice 18 h after s.c. injection of PBS


title: M-MB-192-1-241

description: Mid Brain of female balb/c mice

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen). Poly A+ RNA was obtained from total RNA using the MicroPoly(A) Pure kit (Ambion)

tag: Mid Brain from female Balb/c mice 192 h after s.c. injection of PBS

tag: Mid Brain from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: M-HT-18-4-505

description: hypothalamus of female balb/c mice

tag: Hypothalamus from female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells


title: C-MB-72-3-445

description: midbrain of male balb/c mice


title: M-HT-18-5-533

description: hypothalamus of female balb/c mice


title: C-MB-18-5-567

description: midbrain of male balb/c mice


title: M-MB-192-2-224

description: Mid brain of female balb/c mice


title: P-MB-192-2-261

description: Mid Brain of male C57Bl/6 mice

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 192 h

tag: Mid Brain from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 192 h

tag: Mid Brain from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: M-HT-18-4-506

description: hypothalamus of female balb/c mice


title: M-MB-192-1-221

description: Mid Brain of female balb/c mice


title: P-MB-192-1-215

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain  from male C57Bl/6 mice 192 h after s.c. injection of PBS

tag: Mid Brain from male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-MB-192-2-252

description: Mid brain of female balb/c mice


title: C-MB-192-1-272

description: midbrain of male balb/c mice


title: P-MB-192-2-257

description: Mid Brain of male C57Bl/6 mice


title: C-MB-192-4-509

description: midbrain of male balb/c mice


title: P-MB-192-1-238

description: Mid Brain of male c57Bl/6 mice


title: M-HT-72-3-461

description: hypothalamus of female balb/c mice

source_name: hypothalamus (72 h after injection of 4T-1 mammary cancer cell)

tag: Hypothalamus form female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of PBS


title: P-HT-192-6-558

description: hypothalamus of male C57Bl/6 mice

source_name: hypothalamus (192 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Hypothalamus form male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Hypothalamus from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: P-HT-192-5-528

description: hypothalamus of male C57Bl/6 mice


title: M-HT-192-2-223

description: hypothalamus of female balb/c mice

source_name: hypothalamus (192 h after injection of 4T-1 mammary cancer cell)

tag: Hypothalamus form female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells

tag: Hypothalamus from female Balb/c mice 192 h after s.c. injection of PBS


title: M-HT-192-1-220

description: hypothalamus of female balb/c mice

tag: Hypothalamus from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: M-HT-18-3-444

description: hypothalamus of female balb/c mice


title: M-HT-72-4-488

description: hypothalamus of female balb/c mice


title: M-HT-192-2-253

description: hypothalamus of female balb/c mice


title: M-HT-18-3-443

description: hypothalamus of female balb/c mice


title: M-HT-192-4-480

description: hypothalamus of female balb/c mice


title: M-HT-192-4-481

description: hypothalamus of female balb/c mice


title: P-HT-192-2-256

description: hypothalamus of male C57Bl/6 mice


title: M-HT-72-4-487

description: hypothalamus of female balb/c mice

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: P-HT-192-2-260

description: hypothalamus of male C57Bl/6 mice


title: C-MB-72-4-457

description: midbrain of male balb/c mice

tag: Midbrain from male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells

tag: Midbrain from male Balb/c mice 72 h after subcutaneous injection of PBS


title: M-HT-192-1-240

description: hypothalamus of female balb/c mice


title: P-HT-192-5-527

description: hypothalamus of male c57Bl/6 mice

tag: Hypothalamus form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-HT-72-3-460

description: hypothalamus of female balb/c mice


title: P-HT-72-4-493

description: hypothalamus of male c57Bl/6 mice

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus from male C57Bl/6 mice 72 h after s.c. injection of PBS

source_name: hypothalamus (72 h after injection of  LL/2(LLC1) lung tumor cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-HT-72-4-494

description: hypothalamus of male C57Bl/6 mice

tag: Hypothalamus form male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: P-HT-18-4-440

description: hypothalamus of male C57Bl/6 mice

source_name: hypothalamus (18 h after injection of  LL/2(LLC1) lung tumor cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 18 h

tag: Hypothalamus form male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 18 h

tag: Hypothalamus from male C57Bl/6 mice 18 h after s.c. injection of PBS


title: P-HT-192-1-237

description: hypothalamus of male c57Bl/6 mice


title: C-HT-192-1-271

description: hypothalamus of male balb/c mice

tag: Hypothalamus from male Balb/c mice 192 h after s.c. injection of PBS

source_name: hypothalamus (192 h after injection of colon carcinoma cells)

tag: Hypothalamus form male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: P-HT-18-4-439

description: hypothalamus of male c57Bl/6 mice

tag: Hypothalamus form male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-CO-192-2-258

description: Pre-frontal cortex of male C57Bl/6 mice

source_name: prefrontal cortex (192 h after injection of LL/2(LLC1) lung cancer cell)

tag: Pre-frontal cortex from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

source_name: prefrontal cortex (control)

tag: Pre-frontal cortex from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: C-HT-18-5-563

description: hypothalamus of male balb/c mice

tag: Hypothalamus from male Balb/c mice 18 h after s.c. injection of PBS

source_name: hypothalamus (18 h after injection of colon carcinoma cells)

tag: Hypothalamus form male Balb/c mice 18 h after s.c. injection of CT26 colon carcinoma cells


title: C-CO-192-1-262

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal Cortex from male Balb/c mice 192 h after s.c. injection of PBS

source_name: prefrontal cortex (192 h after injection of CT26 colon carcinoma cells)

tag: Pre-frontal cortex from male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: M-MB-18-2-186

description: Mid Brain of female balb/c mice

source_name: midbrain (control)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 18 h

tag: Mid Brain from female Balb/c mice 18 h after s.c. injection of PBS

source_name: midbrain (18 h after injection of 4T-1 mammary cancer cells)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 18 h

tag: Mid Brain from female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells


title: C-HT-18-3-513

description: hypothalamus of male balb/c mice


title: P-CO-192-2-254

description: Pre-frontal cortex of male C57Bl/6 mice


title: P-HT-192-1-217

description: hypothalamus of male c57Bl/6 mice

tag: Hypothalamus from male C57Bl/6 mice 192 h after s.c. injection of PBS

tag: Hypothalamus form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-HT-192-6-557

description: hypothalamus of male c57Bl/6 mice


title: M-MB-72-2-164

description: Mid Brain of female balb/c mice

tag: Mid Brain from female Balb/c mice 72 h after s.c. injection of PBS

source_name: midbrain (72 h after injection of 4T-1 mammary cancer cells)

tag: Mid Brain from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: C-HT-18-5-564

description: hypothalamus of male balb/c mice


title: C-HT-18-3-514

description: hypothalamus of male balb/c mice


title: M-MB-72-1-196

description: Mid brain of female balb/c mice


title: M-CO-192-1-239

description: Pre-frontal cortex of female balb/c mice

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 192 h

tag: Pre-frontal cortex from female Balb/c mice 192 h after s.c. injection of PBS

source_name: prefrontal cortex (192 h after injection of mammary cancer cells)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 192 h

tag: Pre-frontal cortex from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: C-HT-18-4-522

description: hypothalamus of male balb/c mice


title: C-HT-72-4-455

description: hypothalamus of male balb/c mice

source_name: hypothalamus (72 h after injection of colon carcinoma cells)

tag: Hypothalamus form male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells

tag: Hypothalamus from male Balb/c mice 72 h after s.c. injection of PBS


title: P-CO-192-1-235

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-CO-192-1-219


title: C-HT-192-4-499

description: hypothalamus of male balb/c mice

tag: Hypothalamus from male Balb/c mice 192 h after s.c. injection of PBS

tag: Hypothalamus form male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: C-HT-192-4-500

description: hypothalamus of male balb/c mice


title: C-HT-18-4-521

description: hypothalamus of male balb/c mice

tag: Hypothalamus from male Balb/c mice 18 h after s.c. injection of PBS


title: P-CO-192-1-222

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: M-MB-18-2-155

description: Mid Brain of female balb/c mice


title: M-MB-18-1-151

description: Mid Brain of female balb/c mice


title: C-HT-72-4-454

description: hypothalamus of male balb/c mice


title: M-MB-18-1-154

description: Mid Brain of female balb/c mice


title: M-MB-72-1-110

description: Mid Brain of female balb/c mice

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 72 h

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 72 h


title: M-MB-72-1-105

description: Mid Brain of female balb/c mice


title: C-HT-72-3-450

description: hypothalamus of male balb/c mice


title: M-MB-72-2-111

description: Mid Brain of female balb/c mice


title: C-HT-72-3-451

description: hypothalamus of male balb/c mice


title: C-CO-18-4-520

description: Pre-frontal cortex of male balb/c mice

source_name: prefrontal cortex (18 h after injection of CT26 colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 18 h

tag: Pre-frontal cortex from male Balb/c mice 18 h after s.c. injection of CT26 colon carcinoma cells

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 18 h

tag: Pre-frontal cortex from male Balb/c mice 18 h after s.c. injection of PBS


title: C-CO-18-5-561

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal Cortex from male Balb/c mice 18 h after s.c. injection of PBS


title: C-CO-18-3-511

description: Pre-frontal cortex of male balb/c mice


title: C-CO-18-5-562

description: Pre-frontal cortex of male balb/c mice


title: C-CO-18-3-512

description: Pre-frontal cortex of male balb/c mice


title: C-CO-192-4-498

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal cortex from male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells

tag: Pre-frontal cortex from male Balb/c mice 192 h after s.c. injection of PBS


title: P-MB-72-2-199

description: Mid Brain of male C57Bl/6 mice

source_name: midbrain (72 h after injection of LL/2(LLC1) lung cancer cell)

tag: Mid Brain from male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Mid Brain from male C57Bl/6 mice 72 h after s.c. injection of PBS


title: M-MB-72-2-102

description: Mid Brain of female balb/c mice

tag: Mid Brain from female Balb/c mice 72 h after s.c. injection of PBS

tag: Mid Brain from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: C-CO-18-4-519

description: Pre-frontal cortex of male balb/c mice


title: P-MB-72-1-197

description: Mid Brain of male C57Bl/6 mice


title: P-MB-18-2-185

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain  from male C57Bl/6 mice 18 h after s.c. injection of PBS

source_name: midbrain (18 h after injection of LL/2(LLC1) lung cancer cell)

tag: Mid Brain from male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-MB-18-1-184

description: Mid Brain of male c57Bl/6 mice


title: C-CO-192-4-497

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal Cortex from male Balb/c mice 192 h after s.c. injection of PBS


title: P-MB-72-2-113

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain  from male C57Bl/6 mice 72 h after s.c. injection of PBS

tag: Mid Brain from male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-MB-18-2-157

description: Mid Brain of male c57Bl/6 mice


title: P-MB-18-1-156

description: Mid Brain of male c57Bl/6 mice


title: C-CO-72-3-448

description: Pre-frontal cortex of male balb/c mice

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h

tag: Pre-frontal Cortex from male Balb/c mice 72 h after s.c. injection of PBS

source_name: prefrontal cortex (72 h after injection of CT26 colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 72 h

tag: Pre-frontal cortex from male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells


title: P-MB-72-1-112

description: Mid Brain of male c57Bl/6 mice


title: C-CO-72-4-452

description: Pre-frontal cortex of male balb/c mice


title: C-CO-72-4-453

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal cortex from male Balb/c mice 72 h after s.c. injection of PBS


title: C-CO-72-3-449

description: Pre-frontal cortex of male balb/c mice


title: P-MB-72-1-107

description: Mid Brain of male c57Bl/6 mice


title: C-MB-72-1-165

description: midbrain of male balb/c mice

tag: Midbrain from male Balb/c mice 72 h after s.c. injection of PBS

source_name: midbrain (72 h after injection of CT26 colon carcinoma cells)

tag: Midbrain from male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells


title: M-CO-18-5-531

tag: Pre-frontal cortex from female Balb/c mice 18 h after s.c. injection of PBS

source_name: prefrontal cortex (18 h after injection of mammary cancer cells)

tag: Pre-frontal cortex from female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells


title: C-MB-72-1-103

description: midbrain of male balb/c mice


title: P-MB-72-2-106

description: Mid Brain of male c57Bl/6 mice


title: C-MB-72-2-115

description: midbrain of male balb/c mice


title: C-MB-72-1-114

description: midbrain of male balb/c mice


title: M-CO-18-5-532


title: M-CO-18-4-504


title: M-CO-192-4-484

tag: Pre-frontal cortex from female Balb/c mice 192 h after s.c. injection of PBS

tag: Pre-frontal cortex from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: M-CO-18-6-540


title: M-CO-18-4-503


title: M-CO-72-4-485

tag: Pre-frontal cortex from female Balb/c mice 72 h after s.c. injection of PBS

source_name: prefrontal cortex (72 h after injection of mammary cancer cells)

tag: Pre-frontal cortex from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: C-MB-72-2-101

description: midbrain of male balb/c mice


title: C-MB-72-2-198

description: midbrain of male balb/c mice

tag: Midbrain from male Balb/c mice 72 h after subcutaneous injection of PBS


title: M-CO-18-6-539


title: M-CO-72-4-486


title: M-CO-192-4-479


title: M-HT-18-2-189

description: hypothalamus of female balb/c mice

source_name: hypothalamus (control)

tag: Hypothalamus from female Balb/c mice 18 h after s.c. injection of PBS

source_name: hypothalamus (18 h after injection of 4T-1 mammary cancer cell)

tag: Hypothalamus from female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells


title: M-CO-72-3-459

source_name: prefrontal cortex (control)


title: M-HT-72-2-195

description: hypothalamus of female balb/c mice

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of PBS

source_name: hypothalamus (72 h after injection of 4T-1 mammary cancer cell)

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: M-HT-18-2-183

description: hypothalamus of female balb/c mice


title: P-CO-192-6-554

description: Pre-frontal cortex of male C57Bl/6 mice

source_name: prefrontal cortex (192 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Pre-frontal cortex from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: P-CO-192-6-553

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-HT-72-2-150

description: hypothalamus of female balb/c mice


title: M-CO-72-3-458


title: M-HT-18-1-158

description: hypothalamus of female balb/c mice


title: P-CO-192-5-526

description: Pre-frontal cortex of male C57Bl/6 mice


title: M-HT-18-1-178

description: hypothalamus of female balb/c mice


title: P-CO-72-4-492

description: Pre-frontal cortex of male C57Bl/6 mice

source_name: prefrontal cortex (72 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex from male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Pre-frontal cortex from male C57Bl/6 mice 72 h after s.c. injection of PBS


title: P-HT-72-2-194

description: hypothalamus of male c57Bl/6 mice

tag: Hypothalamus from male C57Bl/6 mice 72 h after s.c. injection of PBS

source_name: hypothalamus (72 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Hypothalamus form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-CO-18-4-438

description: Pre-frontal cortex of male C57Bl/6 mice

source_name: prefrontal cortex (18 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex from male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Pre-frontal cortex from male C57Bl/6 mice 18 h after s.c. injection of PBS


title: P-CO-72-4-491

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-HT-72-2-144

description: hypothalamus of female balb/c mice


title: P-CO-18-4-437

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex form male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell