title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from brain cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 37

status: Public on Jul 28 2007

type: genomic

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

country: USA

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from ES cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: Genome-wide array sets (1-37) for all tissues were loess normalized using the R package limma.

molecule: genomic DNA

organism: Mus musculus

source_name: Chromatin immunoprecipitated DNA from ES cells using Pol2 antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

value: ES immunoprecipitated chromatin

source_name: Input Chromatin ES cells.

extract_protocol: input chromatin

value: ES input chromatin


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from heart cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from heart cells using Pol2 antibody

value: heart immunoprecipitated chromatin

source_name: Input Chromatin heart cells.

value: heart input chromatin


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 37


title: MEFB1 Expression Biological Replicate 2

status: Public on Jul 01 2007

type: mixed

city: Vienna

first: Denise

middle: P.

last: Barlow

address: Dr. Bohrgasse 9/4

department: Austrian Academy of Sciences

country: Austria

institute: Center of Molecular Medicine (CeMM)

description: The input and Poly-A RNA were hybridized to the same microarray. Microarrays were scanned with a Genepix 4000B scanner (Axon Instruments).

data_processing: The unnormalized values represent the 'Ratio of Medians' of each ID on the platform. The average 'Ratio of Medians' was calculated for each PCR_FRAG_ID on the platform and plotted.

label: Alexa 647

molecule: polyA RNA

source_name: Poly-A RNA

tag: 13.5dpc female mouse embryo fibroblast cell line (MEFB1). The cells have a paternal deletion of the imprinted Igf2r cluster.

label: Alexa 555

molecule: other

source_name: Input DNA (whole cell extract)


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from kidney cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from kidney cells using Pol2 antibody

value: kidney immunoprecipitated chromatin

source_name: Input Chromatin kidney cells.

value: kidney input chromatin


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 37


title: MEFF H3K9me3 Biological Replicate 2

type: other

description: The input and ChIP DNA were hybridized to the same microarray. Microarrays were scanned with a Genepix 4000B scanner (Axon Instruments).

data_processing: The unnormalized values represent the log2 transformed 'Ratio of Medians' of each ID on the platform. To display the data, the average 'Ratio of Medians' was calculated for each PCR_FRAG_ID on the platform, then this single value was log2 transformed and plotted.

source_name: H3K9me3 chromatin immunoprecipitation (ChIP)

tag: 13.5dpc female mouse embryo fibroblast cell line (MEFF). The cells have a maternal deletion of the imprinted Igf2r cluster.


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 37


title: MEFB1 H3K9me3 Biological Replicate 2


title: MEFB1 H4K20me1 Biological Replicate 2

source_name: H4K20me1 chromatin immunoprecipitation (ChIP)


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from liver cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from liver cells using Pol2 antibody

value: liver immunoprecipitated chromatin

source_name: Input Chromatin liver cells.

value: liver input chromatin


title: MEFF H3K4me2 Biological Replicate 2

source_name: H3K4me2 chromatin immunoprecipitation (ChIP)


title: MEFF H4K20me1 Biological Replicate 2


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 37


title: MEFB1 H4K20me3 Biological Replicate 2

source_name: H4K20me3 chromatin immunoprecipitation (ChIP)


title: MEFF H3Ac Biological Replicate 1

source_name: H3Ac chromatin immunoprecipitation (ChIP)


title: MEFF H4Ac Biological Replicate 2

source_name: H4Ac chromatin immunoprecipitation (ChIP)


title: MEFF H3K4me3 Biological Replicate 2

source_name: H3K4me3 chromatin immunoprecipitation (ChIP)


title: MEFB1 H3K27me3 Biological Replicate 1

source_name: H3K27me3 chromatin immunoprecipitation (ChIP)


title: MEFB1 H3Ac Biological Replicate 2


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 8 of 37

source_name: Chromatin immunoprecipitated DNA from brain cells using Pol2 antibody

value: brain immunoprecipitated chromatin

source_name: Input Chromatin brain cells.

value: brain input chromatin


title: MEFF H4Ac Biological Replicate 1


title: MEFB1 H3K4me3 Biological Replicate 2


title: MEFB1 H3K9Ac Biological Replicate 2

source_name: H3K9Ac chromatin immunoprecipitation (ChIP)


title: MEFF H3Ac Biological Replicate 2


title: MEFB1 H4Ac Biological Replicate 2


title: MEFF HP1gamma Biological Replicate 1

source_name: HP1gamma chromatin immunoprecipitation (ChIP)


title: MEFF H3K9Ac Biological Replicate 2

source_name: Input DNA (whole cell extract)


title: MEFF H4K20me1 Biological Replicate 1


title: MEFB1 H3Ac Biological Replicate 1


title: MEFF H3K9Ac Biological Replicate 1

extract_protocol: 13.5dpc female mouse embryo fibroblast cell line (MEFF)


title: MEFF H3K4me3 Biological Replicate 1

tag: 13.5dpc female mouse embryo fibroblast cell line (MEFF)


title: MEFF H3K9me3 Biological Replicate 1


title: MEFB1 H3K4me2 Biological Replicate 2


title: MEFF H3K4me2 Biological Replicate 1


title: MEFF H3K27me3 Biological Replicate 1


title: MEFB1 H4K20me1 Biological Replicate 1


title: MEFB1 HP1gamma Biological Replicate 1


title: MEFF H4K20me3 Biological Replicate 1


title: MEFB1 H3K4me3 Biological Replicate 1


title: MEFB1 H3K4me2 Biological Replicate 1


title: MEFB1 H3K9me3 Biological Replicate 1


title: MEFB1 H3K9Ac Biological Replicate 1


title: OvaMPL, biological replicate 2

status: Public on Jun 09 2007

type: RNA

city: Louisville

first: Thomas

middle: Clark

last: Mitchell

state: KY

address: 570 S. Preston St.

department: Microbiology and Immunology

institute: University of Louisville

description: Gene expression data from whole mouse spleen, 6h after injection with OVA peptides plus MPL adjuvant

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on Affymetrix Genechip Mouse Expression array MOE430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Array Assist 3 (Stratagene, La Jolla, CA) using their default algorithm for GC-RMA normalization. Data is displayed in linear space.

label: biotin

molecule: total RNA

source_name: Whole mouse spleen, 6h after immunization with Ova peptides plus MPL adjuvant

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

growth_protocol: B6.SJL female mice were infused with 4.7x10^5 B6.OTI plus 7x10^5 B6.OTII T cells by iv injection.  Two days later, these recipient mice were given the treatments described below.

extract_protocol: Spleens were removed from mice 6h after iv immunization and processed immediately using a Qiagen Rneasy total extraction kit, following the manufacturer's instructions.

treatment_protocol: Three treatments were given, by iv injection. "Ova": 10µg Ova257-264 + 50µg Ova323-339; "OvaLPS": Ova peptides + 10µg LPS from S. minnesota Re595 ('Ultrapure grade', Invivogen); "OvaMPL": ova peptides + 30µg MPL (manufactured from S. minnesota Re595 LPS, Invivogen).  These doses of LPS and MPL were confirmed to have boosted to equal levels the clonal expansion of CD8+ OTI and CD4+ OTII T cells to stimulatory peptide; clonal expansion was tested in replicate mice on days 2.5 through 7 after immunization.

tag: Female B6.SJL mice, 9 weeks old at time of T cell transfer and immunization


title: OvaMPL, biological replicate 3


title: MEFB1 H4K20me3 Biological Replicate 1


title: OvaMPL, biological replicate 1


title: OvaLPS, biological replicate 2

description: Gene expression data from whole mouse spleen, 6h after injection with OVA peptides plus LPS adjuvant

source_name: Whole mouse spleen, 6h after immunization with Ova peptides plus LPS adjuvant


title: Ova, biological replicate 3

description: Gene expression data from whole mouse spleen, 6h after injection with OVA peptides

source_name: Whole mouse spleen, 6h after immunization with Ova peptides


title: Ova, biological replicate 1


title: Ova, biological replicate 2


title: OvaLPS, biological replicate 3


title: Fbx15-null ES (rep2)

status: Public on Jun 07 2007

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: Fbx15 is specifically espressed in ES cells, but Fbx15-null ES cells do not show obvious phenotypes.

hyb_protocol: Manufature's prtocol

scan_protocol: Manufature's prtocol

data_processing: gProcessedSignals

source_name: FBX15-null ES cells grown on STO cells

label_protocol: Manufature's protocol

extract_protocol: Trizao

tag: 129/SVJae, undifferentiated, grown on STO feeder cells


title: OvaLPS, biological replicate 1


title: Nanog-iPS MEF 20D2

description: Nanog-iPS cells

source_name: Nanog-GFP BAC tg mouse

tag: adult chimera competent

tag: male


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 8 of 37

source_name: Chromatin immunoprecipitated DNA from heart cells using Pol2 antibody

source_name: Input Chromatin heart cells.


title: FBX15-iPS MEF4-7 (rep2)

description: Retroviral vectors for the four factors were transfected into Fbx15 bgeo-KI MEF. Cells were cultured with ES cell condition and selected with G418 for 16 days.

source_name: iPS cells from Fbx15-KI MEF

tag: G418 resistant

tag: ES cell-like phenotypes


title: Nanog-iPS MEF 20D16

description: Nanog-iPS cells


title: Fbx15-null MEF (rep2)

description: fibroblasts

source_name: MEF derived from Fbx15-null E13.5 embryos

tag: G418 sensitive


title: Human retina replicate 1 of 3

status: Public on Jun 04 2007

city: Foster City

first: Julie

last: Blake

address: 850 Lincoln Centre Dr

department: SDS/Arrays

institute: Applied Biosystems

description: Human retina replicate 1 of 3

hyb_protocol: Microarray hybridization, chemiluminescence detection, image acquisition, and analysis were performed on the on the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer using the Applied Biosystems Chemiluminescence Detection Kit and kit protocol. Each microarray was pre-hybridized at 55oC for 1 hr in hybridization buffer with a blocking reagent. Next, 15 µg of labeled cRNA targets were fragmented by incubating them at 60oC for 30 min with fragmentation buffer and the internal control target (a 24-mer oligo labeled with the LIZ® fluorescent dye), and then hybridized to each microarray in a 1.5-mL volume at 55oC for 16 hr. After hybridization the arrays were washed with hybridization wash buffer and chemiluminescence rinse buffer. Enhanced chemiluminescent signals were generated by incubating the arrays with anti-digoxigenin-alkaline phosphatase and chemiluminescence enhancing solution, followed by chemiluminescence substrate.

scan_protocol: Images from each microarray were collected on the Applied Biosystems 1700 Microarray Analyzer. The images were auto-gridded and the chemiluminescent signals were quantified, corrected for background and spot quality, and spatially normalized.

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software. The raw data was globally normalized using quantle normalization.

label: Digoxigenin-UTP

organism: Homo sapiens

source_name: Clontech Human retina

label_protocol: Digoxigenin-UTP-labeled cRNA was generated and linearly amplified from 1 µg of total RNA with three replicates per tissue, using the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 2.0 and kit protocol.

extract_protocol: Clontech's Total RNAs are prepared by the methods referenced in the following: Chomczynski & Sacchi (1987) Anal. Biochem. 162:156-159 Guanidinium thiocyanate method in Maniatis, Sambrook, J. et al (1989) Molecular Cloning: A Laboratory Manual, 2nd edition

tag: Human retina


title: Human PBLs replicate 3 of 3

description: Human PBLs replicate 3 of 3

source_name: Clontech Human PBLs

tag: Human PBLs


title: Human retina replicate 3 of 3

description: Human retina replicate 3 of 3


title: Human PBLs replicate 2 of 3

description: Human PBLs replicate 2 of 3


title: Actin ChIP replicate 1

status: Public on Jul 07 2007

city: Bronx

first: Ari

last: Melnick

state: NY

address: 1300 Morris Park Ave - Chanin 302

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

description: Actin ChIP performed in Ramos cells

hyb_protocol: Samples were hybridized by NimbleGen Systems, Reykjavik, Iceland

scan_protocol: Scan protocol 	Arrays were scanned and analyzed by NimbleGen Systems, Reykjavik, Iceland

data_processing: The fold enrichment for each probe was calculated as the ratio of Cy5 vs. Cy3 and  Any peaks involving >5 probes and with > 2.5 fold enrichment were considered potentially positive hits

source_name: Input DNA

label_protocol: Samples were labeled by NimbleGen Systems, Reykjavik, Iceland

extract_protocol:
As described in:
Polo, J.M. et al. Specific peptide interference reveals BCL6 transcriptional and oncogenic mechanisms in B-cell lymphoma cells. Nat Med 10, 1329-35 (2004)

tag: Total DNA extracted from Ramos Cells

tag: Actin ChIP performed in Ramos cells.


title: Nanog-iPS MEF 20D18

description: Nanog-iPS cells

extract_protocol: Trizol


title: Human bone marrow  replicate 1 of 3

description: Human bone marrow  replicate 1 of 3

source_name: Clontech Human bone marrow

tag: Human bone marrow


title: Human bone marrow  replicate 3 of 3

description: Human bone marrow  replicate 3 of 3


title: Human PBLs replicate 1 of 3

description: Human PBLs replicate 1 of 3


title: Human retina replicate 2 of 3

description: Human retina replicate 2 of 3


title: Human adrenal gland replicate 2 of 3

description: Human adrenal gland replicate 2 of 3

source_name: Clontech Human adrenal gland

tag: Human adrenal gland


title: Human adrenal gland replicate 3 of 3

description: Human adrenal gland replicate 3 of 3


title: Human spleen replicate 2 of 3

description: Human spleen replicate 2 of 3

source_name: Clontech Human spleen

tag: Human spleen


title: Human spleen replicate 1 of 3

description: Human spleen replicate 1 of 3


title: Human mammary gland replicate 3 of 3

description: Human mammary gland replicate 3 of 3

source_name: Clontech Human mammary gland

tag: Human mammary gland


title: Human mammary gland replicate 1 of 3

description: Human mammary gland replicate 1 of 3


title: Human bone marrow  replicate 2 of 3

description: Human bone marrow  replicate 2 of 3


title: Human spleen replicate 3 of 3

description: Human spleen replicate 3 of 3


title: Human adrenal gland replicate 1 of 3

description: Human adrenal gland replicate 1 of 3


title: Human mammary gland replicate 2 of 3

description: Human mammary gland replicate 2 of 3


title: Human colon replicate 2 of 3

description: Human colon replicate 2 of 3

source_name: Clontech Human colon

tag: Human colon


title: Human colon replicate 1 of 3

description: Human colon replicate 1 of 3


title: Human thyroid replicate 1 of 3

description: Human thyroid replicate 1 of 3

source_name: Clontech Human thyroid

tag: Human thyroid


title: Human salivary gland replicate 2 of 3

description: Human salivary gland replicate 2 of 3

source_name: Clontech Human salivary gland

tag: Human salivary gland


title: Human thyroid replicate 2 of 3

description: Human thyroid replicate 2 of 3


title: Human thyroid replicate 3 of 3

description: Human thyroid replicate 3 of 3


title: Human salivary gland replicate 1 of 3

description: Human salivary gland replicate 1 of 3


title: Human placenta replicate 2 of 3

description: Human placenta replicate 2 of 3

source_name: Clontech Human placenta

tag: Human placenta


title: Human placenta replicate 1 of 3

description: Human placenta replicate 1 of 3


title: Human placenta replicate 3 of 3

description: Human placenta replicate 3 of 3


title: Human fetal kidney replicate 2 of 3

description: Human fetal kidney replicate 2 of 3

source_name: Clontech Human fetal kidney

tag: Human fetal kidney


title: Human salivary gland replicate 3 of 3

description: Human salivary gland replicate 3 of 3


title: Human fetal kidney replicate 3 of 3

description: Human fetal kidney replicate 3 of 3


title: Human kidney replicate 1 of 3

description: Human kidney replicate 1 of 3

source_name: Clontech Human kidney

tag: Human kidney


title: Human colon replicate 3 of 3

description: Human colon replicate 3 of 3


title: Human kidney replicate 3 of 3

description: Human kidney replicate 3 of 3


title: Human kidney replicate 2 of 3

description: Human kidney replicate 2 of 3


title: Human fetal thymus replicate 3 of 3

description: Human fetal thymus replicate 3 of 3

source_name: Clontech Human fetal thymus

tag: Human fetal thymus


title: Human fetal thymus replicate 1 of 3

description: Human fetal thymus replicate 1 of 3


title: Human fetal thymus replicate 2 of 3

description: Human fetal thymus replicate 2 of 3


title: MEFF H4K20me3 Biological Replicate 2

source_name: H4K20me3 chromatin immunoprecipitation (ChIP)

tag: 13.5dpc female mouse embryo fibroblast cell line (MEFF). The cells have a maternal deletion of the imprinted Igf2r cluster.

source_name: Input DNA (whole cell extract)


title: Human thymus replicate 2 of 3

description: Human thymus replicate 2 of 3

source_name: Clontech Human thymus

tag: Human thymus


title: Human fetal kidney replicate 1 of 3

description: Human fetal kidney replicate 1 of 3


title: Human thymus replicate 1 of 3

description: Human thymus replicate 1 of 3


title: Human pancreas replicate 2 of 3

description: Human pancreas replicate 2 of 3

source_name: Clontech Human pancreas

tag: Human pancreas


title: Human pancreas replicate 1 of 3

description: Human pancreas replicate 1 of 3


title: Human thymus replicate 3 of 3

description: Human thymus replicate 3 of 3


title: Human testis replicate 3 of 3

description: Human testis replicate 3 of 3

source_name: Clontech Human testis

tag: Human testis


title: Human testis replicate 2 of 3

description: Human testis replicate 2 of 3


title: Human testis replicate 1 of 3

description: Human testis replicate 1 of 3


title: Human pancreas replicate 3 of 3

description: Human pancreas replicate 3 of 3


title: Human small intestine replicate 2 of 3

description: Human small intestine replicate 2 of 3

source_name: Clontech Human small intestine

tag: Human small intestine


title: Human ovary replicate 3 of 3

description: Human ovary replicate 3 of 3

source_name: Clontech Human ovary

tag: Human ovary


title: Human trachea replicate 3 of 3

description: Human trachea replicate 3 of 3

source_name: Clontech Human trachea

tag: Human trachea


title: Human uterus replicate 1 of 3

description: Human uterus replicate 1 of 3

source_name: Clontech Human uterus

tag: Human uterus


title: Human skin replicate 3 of 3

description: Human skin replicate 3 of 3

source_name: Clontech Human skin

tag: Human skin


title: Human uterus replicate 2 of 3

description: Human uterus replicate 2 of 3


title: Human skin replicate 2 of 3

description: Human skin replicate 2 of 3


title: Human small intestine replicate 1 of 3

description: Human small intestine replicate 1 of 3


title: Human skin replicate 1 of 3

description: Human skin replicate 1 of 3


title: Human small intestine replicate 3 of 3

description: Human small intestine replicate 3 of 3


title: Human ovary replicate 2 of 3

description: Human ovary replicate 2 of 3


title: Human ovary replicate 1 of 3

description: Human ovary replicate 1 of 3


title: Human trachea replicate 1 of 3

description: Human trachea replicate 1 of 3


title: Human uterus replicate 3 of 3

description: Human uterus replicate 3 of 3


title: Human trachea replicate 2 of 3

description: Human trachea replicate 2 of 3


title: Human tonsil replicate 2 of 3

description: Human tonsil replicate 2 of 3

source_name: Clontech Human tonsil

tag: Human tonsil


title: Human tonsil replicate 3 of 3

description: Human tonsil replicate 3 of 3


title: Human spinal cord replicate 3 of 3

description: Human spinal cord replicate 3 of 3

source_name: Clontech Human spinal cord

tag: Human spinal cord


title: Human spinal cord replicate 2 of 3

description: Human spinal cord replicate 2 of 3


title: Human tonsil replicate 1 of 3

description: Human tonsil replicate 1 of 3


title: Human skeletal muscle replicate 3 of 3

description: Human skeletal muscle replicate 3 of 3

source_name: Clontech Human skeletal muscle

tag: Human skeletal muscle


title: Human heart replicate 1 of 3

description: Human heart replicate 1 of 3

source_name: Clontech Human heart

tag: Human heart


title: Human heart replicate 3 of 3

description: Human heart replicate 3 of 3


title: Human skeletal muscle replicate 1 of 3

description: Human skeletal muscle replicate 1 of 3


title: Human skeletal muscle replicate 2 of 3

description: Human skeletal muscle replicate 2 of 3


title: Human spinal cord replicate 1 of 3

description: Human spinal cord replicate 1 of 3


title: Human prostate replicate 3 of 3

description: Human prostate replicate 3 of 3

source_name: Clontech Human prostate

tag: Human prostate


title: MEFB1 H4Ac Biological Replicate 1

source_name: H4Ac chromatin immunoprecipitation (ChIP)

tag: 13.5dpc female mouse embryo fibroblast cell line (MEFB1). The cells have a paternal deletion of the imprinted Igf2r cluster.


title: Human fetal brain replicate 2 of 3

description: Human fetal brain replicate 2 of 3

source_name: Clontech Human fetal brain

tag: Human fetal brain


title: Human prostate replicate 2 of 3

description: Human prostate replicate 2 of 3


title: Human fetal brain replicate 1 of 3

description: Human fetal brain replicate 1 of 3


title: Human prostate replicate 1 of 3

description: Human prostate replicate 1 of 3


title: Human liver replicate 3 of 3

description: Human liver replicate 3 of 3

source_name: Clontech Human liver

tag: Human liver


title: Human brain replicate 3 of 3

description: Human brain replicate 3 of 3

source_name: Clontech Human brain

tag: Human brain


title: Human fetal liver replicate 3 of 3

description: Human fetal liver replicate 3 of 3

source_name: Clontech Human fetal liver

tag: Human fetal liver


title: Human lung replicate 1 of 3

description: Human lung replicate 1 of 3

source_name: Clontech Human lung

tag: Human lung


title: Recurrent Squamous cell carcinoma 6

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

country: Germany

institute: Medizinische Hochschule Hannover

description: Laser capture lung cancer cells

hyb_protocol: Arrays were prehybridizised for 10 minutes using 140µl MES- hybridization buffer (70,4g MES free acid monohydrate, 193.3g MES Sodium Salt, 800ml accugen water, pH 6.5 – 6.7) and 140µl aqua dest. at 45°C and 60rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix). After removal of the pre-hybridizing solution, the array is loaded with 250 µl of the hybridizing solution (30µl fragmented aRNA, 5µl control-oligo B2, 15µl 20x Eukaryotic hybridizing control, 3µl salmon sperm-DNA, 3µl azetylic BSA, 150µl 2x MES- Hybridizing buffer and 94µl aqua dest.). Following 16-hour incubation at 45°C with permanent rotation, the hybridizing solution is removed. The array is loaded with 280µl of washing buffer A (300ml 20x SSPE, 1ml 10% Tween 20, 698ml accugen water) and a maximum of 4 hybridized arrays are put into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B (83.3ml 12x MES, 5.2ml 5M NaCl, 1ml 10% Tween 20, 910.5ml accugen water) using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus Oligonukleotid- Arrays = Midi-euk2v3). During washing procedure the staining solution is prepared: Staining solution: 600µl 2x Staining Buffer 540µl dH2O 48µl BSA 12µl Streptavidine- Phycoerythrin- Conjugate Array is incubated with 600µl of the staining solution after washing for 40 minutes followed by incubation with the antibody solution for 10 minutes: Antibody solution: 300µl 2x Staining Buffer 266 4µl dH2O 24µl BSA 6µl Goat IgG 3.6µl biotinylated Anti- Streptavidin- AB After removal of the antibody solution 600µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.

scan_protocol: The scanning of the array is performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome phycoerythrin at a wave length of 488nm with an emission at 570nm.

data_processing: Using the affy package of functions of statistical scripting language 'R' integrated into the Bioconductor project data from cel files of each sample were normalized by variance stabilizing transformations (VSN) Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics 2002;18:96-104.

label: Biotin/Streptavidin-PE

source_name: recurrent SCC (stage IIIB or IV)

label_protocol:
Amplification, reverse transcription and labelling of the sample.
For amplification of micro-dissected RNA, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used.
Between 200-500ng of isolated RNA were transcribed into cDNA.
First strand cDNA- Synthesis:
11µl (RNA or RNA and dH2O) Sample
1µl Oligo(dT)Primer
70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
Reaction kit:
2µl 10x First Strand Buffer
1µl Ribonuclease Inhibitor
4µl dNTP Mix
Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
Second strand cDNA- Synthese:
63µl Nuclease-free Water
10µl 10x Second Strand Buffer
4µl dNTP Mix
1µl RNase H
For second strand sythesis 2µl der DNA- Polymerase are added followed by a 2 h incubation at 42°C.
Purification of cDNA:
Final elution volume = 16 µl and storage for 12 h at -20°C
Labelling with in vitro transcription using biotin labelled nucleotides:
Labeling mix:
4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit, Enzo Life Sciences, Farmingdale)
4µl T7 10x reaction buffer
12µl RNase free water
The labelling mix is incubated with the sample and 4µl of the enzyme mix is added followed by an incubation period of 5 hours at 37°C. The amplified RNA is
purified and is eluted in a final volume of 96 µl.
Quality control of aRNA:
The concentration and purity of aRNA is measured using the NanoDrop ND-1000 (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
The OD 260/OD 280 aRNA was between 1.7 and 2. To exclude the possibility of degradation and/or contamination RNA was analyzed again using a Agilent 2100
Bioanalyzer (Agilent Technologies, Palo Alto CA).
Fragmentation:
For optimal hybridization with the complementary oligonucleodid sequences, a fragmentation of the amplified RNA was performed.
24µl of the sample were added to 6µl of fragmentation buffer (200mM TRIS-Acetat, ph 8.2, 500mM KOAc, 150mM MgOAc, Affymetrix) and incubated at 94°C for 35
minutes.

extract_protocol:
RNA of LCM-tumor cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the
kit and were applied according to the manufacturer’s instructions.
In brief:
LCM tumor cells suspended in 350µl lysis buffer were incubated with 350µl 70% ethanol.
700µl suspension was put on RNeasy MinElute- column and spun down for one minute with 10,000 rpm.
DNase- digestion (10µl DNase+70µl RDD buffer-> 80µl) for 15 at 30°C.
2 washing steps with 350µl RW1- buffer and 500µl RPE- buffer.
500µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2 minutes with 10,000 rpm.
Removal of ethanol: column was spun down for 5 minutes with 30,000 rpm.
Elution of RNA with 14µl of RNAse free water.
Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
GmbH, Erlangen). Purified RNA was stored at -80°C.

tag: age

tag: gender

value: w

tag: disease

value: recurrent SCC

tag: received platinum-based therapy with progression

value: yes


title: Recurrent Squamous cell carcinoma 4

description: Laser capture lung cancer cells

value: m


title: Recurrent Squamous cell carcinoma 7

description: Laser capture lung cancer cells


title: Nanog-iPS MEF 20D17

description: Nanog-iPS cells

source_name: Nanog-GFP BAC tg mouse

tag: germ-line competent


title: Recurrent Squamous cell carcinoma 8

description: Laser capture lung cancer cells


title: Human fetal liver replicate 1 of 3

description: Human fetal liver replicate 1 of 3


title: Human UHR replicate 1 of 3

description: Human UHR replicate 1 of 3

source_name: Stratagene Human UHR

tag: Human UHR


title: Human brain replicate 1 of 3

description: Human brain replicate 1 of 3


title: Human liver replicate 2 of 3

description: Human liver replicate 2 of 3


title: Human UHR replicate 3 of 3

description: Human UHR replicate 3 of 3


title: Human fetal brain replicate 3 of 3

description: Human fetal brain replicate 3 of 3


title: Human lung replicate 2 of 3

description: Human lung replicate 2 of 3


title: Human liver replicate 1 of 3

description: Human liver replicate 1 of 3


title: Human lung replicate 3 of 3

description: Human lung replicate 3 of 3


title: Human brain replicate 2 of 3

description: Human brain replicate 2 of 3


title: Human UHR replicate 2 of 3

description: Human UHR replicate 2 of 3


title: Recurrent Squamous cell carcinoma 3

description: Laser capture lung cancer cells


title: Recurrent Squamous cell carcinoma 2

description: Laser capture lung cancer cells


title: Recurrent Squamous cell carcinoma 1

description: Laser capture lung cancer cells


title: Squamous cell carcinoma 9

description: Laser capture lung cancer cells

source_name: primary lung cancer disease

value: SCC

value: no


title: Squamous cell carcinoma 8

description: Laser capture lung cancer cells


title: Squamous cell carcinoma 10

description: Laser capture lung cancer cells


title: Squamous cell carcinoma 3

description: Laser capture lung cancer cells


title: Squamous cell carcinoma 7

description: Laser capture lung cancer cells


title: Squamous cell carcinoma 4

description: Laser capture lung cancer cells


title: Squamous cell carcinoma 6

description: Laser capture lung cancer cells


title: Squamous cell carcinoma 5

description: Laser capture lung cancer cells


title: Human heart replicate 2 of 3

description: Human heart replicate 2 of 3


title: Squamous cell carcinoma 1

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 15

description: Laser capture lung cancer cells

source_name: recurrent AC (stage IIIB or IV)

extract_protocol:
Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the
kit and were applied according to the manufacturer’s instructions.
In brief:
LCM tumor cells suspended in 350µl lysis buffer were incubated with 350µl 70% ethanol.
700µl suspension was put on RNeasy MinElute- column and spun down for one minute with 10,000 rpm.
DNase- digestion (10µl DNase+70µl RDD buffer-> 80µl) for 15 at 30°C.
2 washing steps with 350µl RW1- buffer and 500µl RPE- buffer.
500µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2 minutes with 10,000 rpm.
Removal of ethanol: column was spun down for 5 minutes with 30,000 rpm.
Elution of RNA with 14µl of RNAse free water.
Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
GmbH, Erlangen). Purified RNA was stored at -80°C.

value: recurrent AC


title: Squamous cell carcinoma 2

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 14

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 3

description: Laser capture lung cancer cells

scan_protocol: (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome phycoerythrin at a wave length of 488nm with an emission at 570nm.


title: Recurrent Adenocarcinoma 9

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 12

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 13

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 10

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 4

description: Laser capture lung cancer cells

source_name: recurrent AC (Stage IIIB or IV)


title: Recurrent Adenocarcinoma 11

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 6

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 5

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 1

description: Laser capture lung cancer cells

source_name: recurrent lung cancer disseas (Stage IIIB or IV)

value: recurrent NSCLC


title: Adenocarcinoma 9

description: Laser capture lung cancer cells

value: adenocarcinoma


title: Adenocarcinoma 10

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 8

description: Laser capture lung cancer cells


title: Recurrent Adenocarcinoma 2

description: Laser capture lung cancer cells

source_name: recurrent Adenocarcinoma (Stage IIIB or IV)


title: Adenocarcinoma 8

description: Laser capture lung cancer cells


title: Adenocarcinoma 7

description: Laser capture lung cancer cells


title: Adenocarcinoma 4

description: Laser capture lung cancer cells


title: Adenocarcinoma 6

description: Laser capture lung cancer cells


title: Adenocarcinoma A1

description: Laser capture lung cancer cells

source_name: primary lung cancer samples

value: Adenocarcinoma


title: Adenocarcinoma 5

description: Laser capture lung cancer cells

source_name: primary lung cancer disaese


title: kontrolli_DC_D

status: Public on Jun 01 2007

city: Uppsala

first: Anna

last: Kiialainen

address: University Hospital, Entrance 70

department: Deapartment of Medical Sciences

country: Sweden

institute: Uppsala University

description: control

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: MAS 5.0, scaled to 100

source_name: monocyte derived DCs

label_protocol: Enzo Bioarray High Yield RNA Transcript labeling kit

growth_protocol: IL-4+GM-CSF for seven days

extract_protocol: Trizol + RNeasy

tag: in vitro differentiated DCs


title: kontrolli_DC_C

description: control


title: Adenocarcinoma 3

description: Laser capture lung cancer cells


title: potilas_DC_A


title: kontrolli_DC_A

description: control


title: potilas_DC_E


title: potilas_DC_C


title: potilas_DC_D


title: P536_P_HSPC

city: Tokyo

first: Hidewaki

last: Nakaagwa

state: Tokyo

address: 4-6-1 Shirokanedai, Minato-ku,

department: Institute of Medical Science

institute: The University of Tokyo

description: Human hormone-refractory prostate cancer cells were microdissected from clinical frozen sample and after two-round T7-based amplification, Cy5-labeled cDNA was hybridized competitively on cDNA microarrays with Cy3-labeled cDNA of control mixture of amplified RNA from normal prostate epithelial cells that were also microdissected.

hyb_protocol: Labeled cDNAs were mixed with microarray hybridization solution version 2 (Amersham) and formamide (Sigma) to a final concentration of 50%. After hybridization for 14-16 hours at 42 oC in Automated Slide Processor, the slides were washed in 2xSSC and 1% SDS for 10min at 55 oC, washed in 0.2xSSC and 0.1% SDS for 10min at 55 oC, and washed in 0.1xSSC for 1 min at room temperature in Automated Slide Processor.

scan_protocol: Microarray slides were scanned using  the Array Scanner Generation III (Amersham) after hybridization.

data_processing: Images were gridded and the fluorescent intensity of each spot (Cy5/Cy3) was evaluated photometrically by the ArrayVision computer program (Imaging Research, Inc., St. Catharines, Ontario, Canada) . The fluorescent intensities of Cy5 (tumor) and Cy3 (control) for each target spot were adjusted so that the mean Cy3/Cy5 ratio of the 52 housekeeping genes was equal to one.  Because data derived from low signal intensities are less reliable, we determined a cut-off value on each slide and excluded genes from further analysis when both Cy3 and Cy5 dyes yielded signal intensities lower than the cut-off value. For other genes, we calculated the Cy5/Cy3 ratio using the raw data of each sample.

label_protocol: 2.5 ug aliquots of aRNA from tumor cells or normal cells were annealed with random primer for 10 min at 70oC. They were labeled in a 50ul volume by reverse transcription reaction for 2 hours at 37oC using Superscript II reverse transcriptase (Invitrogen) with 1mM Cy5-dCTP for tumor cells or Cy3-dCTP for normal cells (Amersham) and 25mM each dATP, dGTP, and dTTP. The labeling reaction was stopped by adding 6ul 2.5 N NaOH and incubation for 30 min at 65oC and neutralized by 20ul 1M Tris-HCl (pH7.4) and 7ul 2.5N HCl. The labeled cDNAs were purified by QIAquick PCR Purification Kit (QIAGEN).

extract_protocol: 100,00-200,000 tumor cells or normal cells were isolated selectively using the EZ cut system with a pulsed ultraviolet narrow beam-focus laser (SL Microtest GmbH, Germany) in accordance with the manufacturer’s protocols. Total RNAs were isolated from captured cells with QIAGNE RNAeasy Kit (QIAGEN). After DNAse I treatment, total RNAs were subjected to two rounds of T7-based amplification using Ampliscribe T7 Transcription Kit (Epicentre Technologies), or MEGAscript High Yield Transcription Kit (Ambion), which yielded 50–100 ug of amplified RNA (aRNA) from each sample.

tag: Hormone-sensitive (or-naïve) prostate cancer cells that were microdissected from the radical prostatectomy sample.

source_name: Universal control of normal prostatic epithelial cells

tag: Mixture of normal prostatic epithelial cells from five patients undergoing radical cystectomy for bladder cancer or suprapubic prostatectomy for benign prostatic hyperplasia.


title: potilas_DC_B


title: Recurrent Squamous cell carcinoma 5

description: Laser capture lung cancer cells

tag: disaese


title: P40_P_HSPC


title: P37_P_HSPC


title: P13_P_HSPC


title: Human fetal liver replicate 2 of 3

description: Human fetal liver replicate 2 of 3


title: P1_P_HSPC


title: P4_P_HSPC


title: P38_P_HSPC


title: Adenocarcinoma 2

description: Laser capture lung cancer cells


title: P32_P_HSPC


title: IWP20_P_HSPC


title: OK7_P_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from the prostate, procured by prostate biopsy.


title: OK9_P_HRPC


title: OK11_P_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from the prostate, procured by TUR-P.


title: H3K27Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27Ac and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

data_processing: raw data

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K27Ac antibody

tag: cells

value: K562 Chromatin immunoprecipitated chromatin

source_name: Input Chromatin K562 Chromatin cells.

value: K562 Chromatin input chromatin


title: OK4_P_HRPC


title: OK3_P_HRPC

tag: Mixture of normal prostatic epithelial cells from five patients undergoing radical cystectomy for bladder cancer or suprapubic prostatectomy for benign prostatic hyperplasia


title: H3K27Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K27Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2


title: H3K18Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2

description: Chromatin immunoprecipitation was performed using antibodies against H3K18Ac and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K18Ac antibody


title: H3K4me2 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me2 and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K4me2 antibody


title: H3K4me3 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K4me3 antibody


title: H3K18Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3


title: H3K4me3 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3


title: H3K4me1 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1 and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K4me1 antibody


title: H3K4me1 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3


title: OK2_P_HRPC


title: NG1_B_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from bone metastasis, procured by warm autopsy.


title: H3K18Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K4me1 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2


title: KZ3_P_HRPC


title: KC3_B_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from bone metastasis, procured by bone biopsy.


title: H3K9Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2

description: Chromatin immunoprecipitation was performed using antibodies against H3K9Ac and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K9Ac antibody


title: H3K9Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K4me2 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3


title: IW13_P_HRPC


title: IWP18_P_HSPC


title: H3K4me3 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K9Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 3 ENC1865_H3K9Ac_K562_C.gpr

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: GenePix

scan_protocol: GenePix

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: GenePix

tag: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K9Ac antibody

source_name: Input DNA from K562 Chromatin cells

tag: Input DNA from K562 Chromatin cells


title: IW12_L_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from lymph-node metastasis, procured by warm autopsy.


title: TAFII p250 (6B3) K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3

description: Chromatin immunoprecipitation was performed using antibodies against TAFII p250 (6B3) and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using TAFII p250 (6B3) antibody


title: TAFII p250 (6B3) K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K9Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 1 ENC1863_H3K9Ac_K562_A.gpr


title: IW12_B_HRPC


title: IW10_B_HRPC


title: KZ5_P_HRPC


title: IW10_L_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from lymph-node metastasis, procured by warm autopsy


title: IW7_L_HRPC

scan_protocol: Microarray slides were scanned using  the Array Scanner Generation III (Amersham) after hybridization


title: IW10_P_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from the prostate, procured by warm autopsy.


title: colon mucosa, voluntary exercise, rat

status: Public on May 30 2007

city: Munich

first: Katja

last: Buehlmeyer

state: Bavarian

address: Connollystreet 32

department: Institute of Public Health Research

institute: TU Munich

description: We used a pool of each 8 samples (exercised or sedentary rats). Three independent hybridizations were carried out. Genes were considered as regulated if the expression ratio was more than 2-fold up- or down-regulated, at least two arrays show the same expression pattern and signal value of the gene was 2-fold above background signal intensity.

hyb_protocol: According to the MWG-Array-Application Guide (Revision June 2003).

scan_protocol: Arrays were scanned via Affimetrix 428 Array Scanner, Santa Clara, CA.

data_processing: Data were normalized and analyzed via ImaGene 4.2 software (BioDiscovery, Los Angeles, CA)

organism: Rattus norvegicus

source_name: exercise, colon mucosa, pool of 8 rats

extract_protocol: Total RNA was isolated using the NucleoSpin RNA II-Kit (Macharey-Nagel, Düren, Germany).

treatment_protocol: Rats lasted a period of 12 weeks voluntary running exercise with food and water ad libitum.

tag: Strain

value: Wistar, Gender:male, Age:6 weeks, Tissue:colon mucosa

source_name: sedentary, colon mucosa, pool of 8 rats

treatment_protocol: Rats were sedentary for a period of 12 weeks with food and water ad libitum.


title: colon mucosa, voluntary exercise, rat (2)

label_protocol: According to the MWG-Array-Application Guide (Revision June 2003).


title: EH1_P_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from the prostate, procured by warm autopsy


title: colon mucosa, voluntary exercise, rat (3)


title: IW5_P_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from the prostate, procured by biopsy.


title: IW3_P_HRPC


title: IW7_B_HRPC


title: EH1_B_HRPC

description: Human hormone-refractory prostate cancer cells were microdissected from clinical frozen sample and after two-round T7-based amplification, Cy5-labeled cDNA was hybridized competitively with Cy3-labeled cDNA of control mixture of amplified RNA from normal prostate epithelial cells that were also microdissected.


title: IW7_P_HRPC


title: EH1_H_HRPC

tag: Hormone-refractory prostate cancer cells that were microdissected from liver metastasis, procured by warm autopsy.


title: Staphylococcus aureus_control _45min_replicate1

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

description: Control

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.0

label: Biotin

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_control

label_protocol: Conversion to cDNA and labeling was performed as described in Beenken et al., Journal of Bacteriology, 2004 July, 186(14):4665-4684

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C

extract_protocol: Total bacterial RNA was isolated as described by Beenken et al., 2004 July, 186(14):4665-4684

treatment_protocol: Dimethyl sulfoxide (DMSO, 1% (vol/vol))

tag: Standard strain ATCC25923


title: Staphylococcus aureus_berberine_45min_replicate3

description: berberine chloride treatment

source_name: Staphylococcus aureus_berberine

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. (iii) 500 µl of a 12800 µg /ml berberine chloride stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 1/2× MIC (64 µg/ml), and the final concentration of DMSO was 1% (vol/vol). Then, the bacterial suspensions were further incubated for 45 min at 37°C

treatment_protocol: berberine chloride (64 µg/ml)


title: Staphylococcus aureus_control _45min_replicate3

description: Control

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C


title: Staphylococcus aureus_berberine_45min_replicate1

description: berberine chloride treatment


title: Leukocyte sample (N66)

city: Amsterdam

first: Esther

last: Lips

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: NKI-AVL

description: reference

hyb_protocol: Hybridisation according to the protocol for Affymetrix 10K SNP arrays

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Genotypes were scored with the GDAS software (Affymetrix). Copy numbers were consequently computed with dCHIP SNP and CNAG. Samples were normalized against a set of in-house normal reference samples.

source_name: Leukocyte sample (N66)

label_protocol: Biotinylated DNA wase prepared according to the standard Affymetrix protocol for Affymetrix 10K SNP arrays

extract_protocol: DNA was isolated with the Genomic Wizard Kit (Promega)

tag: gender

tag: tissue

value: normal leukocytes

tag: tumor stage


title: Leukocyte sample (N49)

description: reference

source_name: Leukocyte sample (N49)


title: Leukocyte sample (N106)

description: reference

source_name: Leukocyte sample (N106)


title: Leukocyte sample (N42)

description: reference

source_name: Leukocyte sample (N42)


title: Staphylococcus aureus_berberine_45min_replicate2

description: berberine chloride treatment


title: Leukocyte sample (N44)

description: reference

source_name: Leukocyte sample (N44)


title: Staphylococcus aureus_control _45min_replicate2

description: Control

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C.


title: Leukocyte sample (N30)

description: reference

source_name: Leukocyte sample (N30)


title: Leukocyte sample (N9)

description: reference

source_name: Leukocyte sample (N9)


title: KC5_B_HRPC

source_name: Universal control of normal prostatic epithelial cells


title: Swine_SLA-DRB1_070701-New_repA2

city: Guelph

first: Maria

middle: Isabel

last: Nino-Soto

state: Ontario

address: College Ave. West

department: Pathobiology

country: Canada

institute: University of Guelph

description: Comparison between SLA-DRB1 defined genotype boars, fifth comparison, second replicate (dye-swap for first replicate).

hyb_protocol: Just prior to hybridization, slides were incubated in a solution of 5X standard saline citrate (SSC, Ambion Inc., TX, USA), 0.1% sodium dodecyl sulphate (SDS, Ambion Inc., TX, USA) and 0.1 mg/ml acetylated bovine serum albumin (BSA, Sigma-Aldrich Canada Ltd., Oakville, ON, Canada). Slides were incubated at 42° C for 45 min, washed twice for 5 min in 0.1X SSC and rinsed in milliQ water for 30 sec. Slides were then dried by centrifugation at 700 X g for 2 min and stored in a dust-free environment until hybridization. A total of 23 ul of a hybridization mix consisting of 5 ul of 10 mg/ml lyophilized yeast tRNA (Invitrogen Canada Inc. ON, Canada), 5 ul of 10 mg/ml salmon sperm DNA (Invitrogen Canada Inc., ON, Canada) and 100 ul of DIG easy Hyb (Roche Canada, Mississauga, ON, Canada) were added to the probe mix. All the hybridization mix was placed on the slide and covered with a LifterSlip coverslip (Erie Scientific Co, NH, USA). Hybridization was performed in the dark at 42º C for 20 h in a hybridization oven (Shake 'N' Bake, Boekel Scientific, USA). For washing the slides after hybridization, all solutions were prepared using milliQ water and 45 ml aliquots of each wash solution were filtered before use. Coverslips were removed and slides were washed three times using a solution of 1×SSC, 0.1% SDS and 0.1 mM DTT. Washes were performed at 50ºC for 10 min. Slides were rinsed twice in 1X SSC and 0.1 mM DTT for 2 min and once in 0.1X SSC and 0.1 mM DTT to remove residual SDS. Slides were dried by centrifugation at 700 X g for 2 min. Slides were scanned immediately.

scan_protocol: Slides were scanned in a GenePix 4000B scanner using GenePix Pro 6.0 for image acquisition (Molecular Devices Corporation, Sunnyvale, CA, USA) following the manufacturer protocols. The PMT gains in the scanner were adjusted in order to obtain an average ratio value of 1.0.

data_processing: The log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected intensity medians of channel 1 (635) over channel 2 (532).

organism: Sus scrofa

source_name: SLA-DRB1 potentially new allele

label_protocol: Reverse transcription was performed using SuperScript III (Invitrogen Canada Inc., ON, Canada) and labelling was performed with Alexa Fluor® 647 dye (Invitrogen Canada Inc., Burlington, ON, Canada) as follows. A mix of 3 ug of aRNA in 22 ul of nuclease water and 2 ul of 3 mg/ml random hexamer primers (Invitrogen Canada Inc., ON, Canada) was heated at 65° C for 5 min and snap-chilled in ice for one min. A volume of 14 ul of a master mix containing 8 ul First Strand Buffer, 2 ul of 0.1 M DDT, 2 ul of a dNTP mix containing 5-(3-aminoallyl)-dUTP (Ambion Inc., TX, USA) for post-synthesis labelling of the cDNA (dNTP final concentrations = dATP, dCTP and dGTP – 0.5 mM each; dTTP – 0.15 mM; aa-dUTP – 0.30 mM) and 80 U of 40 U/ul RnaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen Canada Inc., ON, Canada) was added to the reaction, mixed gently and incubated at 25° C for 5 min. After incubation, 400 U of 200 U/ul SuperScript III were added and the reaction was incubated for 3 hrs at 42° C. After incubation, the reaction was heated to 95° C and 0.43 volumes of 1 M NaOH (Sigma-Aldrich Canada Ltd., Oakville, ON, Canada) were added to inactivate the enzyme and denature RNA:cDNA hybrids. The reaction was incubated at 70° C for 10 min and 0.43 volumes of 1 N HCl (Sigma-Aldrich Canada Ltd., Oakville, ON, Canada) were added to neutralize the reaction. Finally, 0.11 volumes of the neutralized reaction of 3 M, pH = 5.5 sodium acetate (Ambion Inc., TX, USA) were added to the reaction. The amino-modified cDNA (aa-cDNA) was purified using the QIAquick PCR purification kit (Qiagen Inc., Mississauga, ON, Canada) according to manufacturer instructions. Final elution of the aa-cDNA was performed twice with 50 ul of nuclease-free water. The EB buffer provided with the QIAquick PCR purification kit was not used for elution as it interferes with the labelling reaction. The aa-cDNA was precipitated using 0.1 volume of 3 M, pH 5.5 sodium acetate, 1 ul of 5 mg/ml linear acrylamide (Ambion Inc., TX, USA) and 2.5 volumes of 100% ethanol. Samples were incubated at – 80° C overnight. Following incubation, the samples were centrifuged at 12,000 X g for 15 min at 4° C, supernatant discarded, pellet washed with 500 ul of 75% ethanol and centrifuged again at 5,000 X g for 5 min at 4° C. Supernatant was removed and samples were left to air dry for 5 min. The aa-cDNA pellet was resuspended in 5 ul of nuclease-free water. All work hereafter was performed in low light conditions to protect the reactive dyes. Three ul of labelling buffer (3 M NaHCO3, pH 9.0) were added to the aa-cDNA aliquot. To prepare the dye, 2 ul of DMSO were added to a vial of Alexa Fluor 647 dye, vortex for 10 sec and added to the aa-cDNA for labelling. The reaction was incubated at room temperature in the dark for 1 hr. The dye labelled cDNA was purified as described before, and elution was performed three times using 50 ul of EB buffer. Purified labelled cDNA was precipitated as described before and after air-drying, the coloured pellet was resuspended in 3 ul of nuclease free water. At this point, the Alexa Fluor 647 labelled cDNA was mixed with its Alexa Fluor 555 counterpart for subsequent hybridization.

extract_protocol:
Total RNA was extracted from isolated BMCs using Trizol reagent (Invitrogen Canada Inc., Burlington, ON, Canada) following the manufacturer's instructions with minor modifications. Briefly, 1 x 10e7 BMCs were aliquoted in 1 ml of PBS, centrifuged at 300 X g for 5 min, supernatant was removed and the cell pellet was lysed by pipetting in 1 ml of Trizol. Cell suspension was stored at – 80° C until further processing. For extraction, the Trizol-cell suspension was thawed to room temperature, 200 ul of chloroform were added and tubes were shaken by hand for 15 seconds. The mix was incubated 3 min in ice and centrifuged at 12,000 X g for 15 min at 4° C. The top clear phase was transferred to a new microcentrifuge tube. Next, 500 ul of isopropanol were added and samples were incubated overnight at – 20° C. After incubation, samples were centrifuged at 12,000 X g for 10 min, at 4° C. Supernatant was removed and the pellet was washed with 500 ul of 75% ethanol. The pellet was carefully dislodged from the tube wall by pipetting. Samples were centrifuged at 7,500 X g for 5 min at 4° C. Supernatant was removed and samples air-dried for 5 – 10 min at room temperature. To resuspend the pellet, 10 – 20 ul of nuclease-free water (Ambion Inc., TX, USA) were added and the pellet was dissolved by pipetting. Samples were incubated for 10 min at 55 – 60° C in a heating block and stored at – 80° C until further processing. RNA was treated with DNA-free (Ambion Inc., TX, USA) following the manufacturer instructions.
Total RNA (3 ug) was used for one round of amplification using the RiboAmp RNA Amplification kit (Molecular Devices Corp, Sunnyvale, CA, USA) according to manufacturer's instructions. No modifications were introduced in the amplification protocol as it is described in the product manual.
Total RNA and amplified RNA (aRNA) concentration and quality were determined in an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Venous blood was collected in EDTA coated BD Vacutainer blood collection tubes (BD – Canada, Oakville, ON, Canada) and BMCs were isolated using a Histopaque-1077 gradient (Sigma-Aldrich Canada Ltd., Oakville, ON, Canada). No further treatment was applied to the isolated cells.

tag: RNA obtained from blood mononuclear cells (BMCs) isolated from Canadian Yorkshire boars

label: Alexa Fluor® 555 dye (Invitrogen Canada Inc., Burlington, ON, Canada)

source_name: SLA-DRB1 allele 070701


title: Swine_SLA-DRB1_070701-New_repB2

description: Comparison between SLA-DRB1 defined genotype boars, sixth comparison, second replicate (dye-swap of first replicate).

label: Alexa Fluor® 647 dye (Invitrogen Canada Inc., Burlington, ON, Canada)


title: Leukocyte sample (N26)

description: reference

source_name: Leukocyte sample (N26)


title: H3K4me2 K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K4me2 antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

source_name: Input Chromatin K562 Chromatin cells.


title: Leukocyte sample (N35)

description: reference

source_name: Leukocyte sample (N35)


title: Leukocyte sample (N25)

description: reference

source_name: Leukocyte sample (N25)


title: Swine_SLA-DRB1_070701-New_repA1

description: Comparison between SLA-DRB1 defined genotype boars, fifth comparison, first replicate.


title: Leukocyte sample (N27)

description: reference

source_name: Leukocyte sample (N27)


title: Leukocyte sample (N23)

description: reference

source_name: Leukocyte sample (N23)


title: Leukocyte sample (N17)

description: reference

source_name: Leukocyte sample (N17)


title: Swine_SLA-DRB1_070701-New_repB1

description: Comparison between SLA-DRB1 defined genotype boars, sixth comparison, first replicate.


title: Leukocyte sample (N7)

description: reference

source_name: Leukocyte sample (N7)


title: Leukocyte sample (N12)

description: reference

source_name: Leukocyte sample (N12)


title: H3K9Ac K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H3K9Ac antibody

extract_protocol: input chromatin


title: Leukocyte sample (N11)

description: reference

source_name: Leukocyte sample (N11)


title: H3K9Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 2 ENC1864_H3K9Ac_K562_B.gpr

source_name: Input DNA from K562 Chromatin cells


title: Swine_SLA-DRB1_050502-New_repB2

description: Comparison between SLA-DRB1 defined genotype boars, fourth comparison, second replicate (dye-swap for first replicate).

data_processing: The log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected intensity medians of channel 1 (635) over channel 2 (532)

source_name: SLA-DRB1 allele 050502


title: Frozen rectal tumor sample (B896)

description: test

source_name: Frozen rectal tumor sample (B896)

value: M

value: rectal carcinoma


title: Leukocyte sample (N10)

description: reference

source_name: Leukocyte sample (N10)


title: Swine_SLA-DRB1_050502-New_repA2

description: Comparison between SLA-DRB1 defined genotype boars, third comparison, second replicate (dye-swap of first replicate).

source_name: SLA-DRB1 potentially new allele


title: Frozen rectal tumor sample (B884)

description: test

source_name: Frozen rectal tumor sample (B884)


title: Leukocyte sample (N18)

description: reference

source_name: Leukocyte sample (N18)


title: Swine_SLA-DRB1_050502-New_repA1

description: Comparison between SLA-DRB1 defined genotype boars, third comparison, first replicate.

treatment_protocol: As described for Channel 1


title: Swine_SLA-DRB1_050502-070701_repB2

description: Comparison between SLA-DRB1 defined genotype boars, second comparison, second replicate (dye swap of first replicate).

source_name: SLA-DRB1 allele 070701


title: Swine_SLA-DRB1_050502-070701_repA2

description: Comparison between SLA-DRB1 defined genotype boars, first comparison, second replicate (dye-swap for first replicate)


title: Frozen rectal tumor sample (B747)

description: test

source_name: Frozen rectal tumor sample (B747)


title: Frozen rectal tumor sample (B772)

description: test

source_name: Frozen rectal tumor sample (B772)


title: Swine_SLA-DRB1_050502-070701_repB1

description: Comparison between SLA-DRB1 defined genotype boars, second comparison, first replicate.


title: Swine_SLA-DRB1_050502-070701_repA1

description: Comparison between SLA-DRB1 defined genotype boars, first comparison, first replicate.


title: Frozen rectal tumor sample (B650)

description: test

source_name: Frozen rectal tumor sample (B650)

value: F


title: Frozen rectal tumor sample (B625)

description: test

source_name: Frozen rectal tumor sample (B625)


title: Frozen rectal tumor sample (B715)

description: test

source_name: Frozen rectal tumor sample (B715)


title: Frozen rectal tumor sample (B593)

description: test

source_name: Frozen rectal tumor sample (B593)


title: TAFII p250 (6B3) K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using TAFII p250 (6B3) antibody

source_name: Input Chromatin K562 Chromatin cells.


title: Frozen rectal tumor sample (B598)

description: test

source_name: Frozen rectal tumor sample (B598)


title: Frozen rectal tumor sample (B674)

description: test

source_name: Frozen rectal tumor sample (B674)


title: Frozen rectal tumor sample (B607)

description: test

source_name: Frozen rectal tumor sample (B607)


title: Frozen rectal tumor sample (B658)

description: test

source_name: Frozen rectal tumor sample (B658)


title: Frozen rectal tumor sample (B498)

description: test

source_name: Frozen rectal tumor sample (B498)


title: Frozen rectal tumor sample (B623)

description: test

source_name: Frozen rectal tumor sample (B623)


title: Frozen rectal tumor sample (B382)

description: test

source_name: Frozen rectal tumor sample (B382)


title: Frozen rectal tumor sample (B385)

description: test

source_name: Frozen rectal tumor sample (B385)


title: Frozen rectal tumor sample (B523)

description: test

source_name: Frozen rectal tumor sample (B523)


title: Frozen rectal tumor sample (B365)

description: test

source_name: Frozen rectal tumor sample (B365)


title: Frozen rectal tumor sample (B338)

description: test

source_name: Frozen rectal tumor sample (B338)


title: Frozen rectal tumor sample (B247)

description: test

source_name: Frozen rectal tumor sample (B247)


title: Swine_SLA-DRB1_050502-New_repB1

description: Comparison between SLA-DRB1 defined genotype boars, fourth comparison, first replicate.

source_name: SLA-DRB1 potentially new allele

treatment_protocol: Venous blood was collected in EDTA coated BD VacutainerÒ blood collection tubes (BD – Canada, Oakville, ON, Canada) and BMCs were isolated using a Histopaque-1077 gradient (Sigma-Aldrich Canada Ltd., Oakville, ON, Canada). No further treatment was applied to the isolated cells.

source_name: SLA-DRB1 allele 050502


title: Frozen rectal tumor sample (B30)

description: test

source_name: Frozen rectal tumor sample (B30)


title: Frozen rectal tumor sample (B209)

description: test

source_name: Frozen rectal tumor sample (B209)

value: rectal adenoma


title: Frozen rectal tumor sample (B1249)

description: test

source_name: Frozen rectal tumor sample (B1249)


title: Frozen rectal tumor sample (B271)

description: test

source_name: Frozen rectal tumor sample (B271)


title: T .rubrum treated with ketoconazole rep2

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

institute: State Key Lab of Virus Gene Engineering

description: Description The cDNA from T.rubrum treated with AMB and T.rubrum treated with DMSO was coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner (Axon Instruments, Inc., CA).

data_processing: Images were processed using GenePix 6.0 (Axon Instruments, Inc., CA) and signals were normalized using a locally weighted scatterplot smoothing regression (LOWESS) algorithm  in the MIDAS software package

organism: Trichophyton rubrum

source_name: T.rubrum_KTZ, labelled with Cy5

tag: T.rubrum treated with KTZ

source_name: T.rubrum_DMSO, labelled with Cy3

tag: T.rubrum treated with DMSO


title: Frozen rectal tumor sample (B321)

description: test

source_name: Frozen rectal tumor sample (B321)


title: Frozen rectal tumor sample (A635)

description: test

source_name: Frozen rectal tumor sample (A635)


title: Frozen rectal tumor sample (B161)

description: test

source_name: Frozen rectal tumor sample (B161)


title: Frozen rectal tumor sample (B1344)

description: test

source_name: Frozen rectal tumor sample (B1344)


title: Frozen rectal tumor sample (B1203)

description: test

source_name: Frozen rectal tumor sample (B1203)


title: T .rubrum treated with amphotericin B rep3

source_name: T.rubrum_AMB, labelled with Cy5

tag: T.rubrum treated with AMB


title: T .rubrum treated with amphotericin B rep1

source_name: T.rubrum_AMB , labelled with Cy5

tag: Trichophyton rubrum treated with AMB

tag: Trichophyton rubrum treated with DMSO


title: T .rubrum treated with amphotericin B rep2


title: Frozen rectal tumor sample (B1208)

description: test

source_name: Frozen rectal tumor sample (B1208)


title: Frozen rectal tumor sample (B122)

description: test

source_name: Frozen rectal tumor sample (B122)


title: T .rubrum treated with ketoconazole rep3


title: Frozen rectal tumor sample (B1183)

description: test

source_name: Frozen rectal tumor sample (B1183)


title: Frozen rectal tumor sample (B1124)

description: test

source_name: Frozen rectal tumor sample (B1124)


title: Frozen rectal tumor sample (A609)

description: test

source_name: Frozen rectal tumor sample (A609)


title: Frozen rectal tumor sample (A626)

description: test

source_name: Frozen rectal tumor sample (A626)


title: T .rubrum treated with ketoconazole rep1


title: Frozen rectal tumor sample (A617)

description: test

source_name: Frozen rectal tumor sample (A617)


title: Leukocyte sample (N108)

description: reference

source_name: Leukocyte sample (N108)


title: Frozen rectal tumor sample (A618)

description: test

source_name: Frozen rectal tumor sample (A618)


title: Frozen rectal tumor sample (A614)

description: test

source_name: Frozen rectal tumor sample (A614)


title: IRI2_36h

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

state: MD

institute: JHU

description: bilateral kidney 2 (36h)

scan_protocol: Agilen

source_name: Whole Lung

label_protocol: Affymetrix

extract_protocol: Affymetrix


title: Frozen rectal tumor sample (A568)

description: test

source_name: Frozen rectal tumor sample (A568)


title: IRI3_36h

description: bilateral kidney 3 (36h)


title: Frozen rectal tumor sample (A572)

description: test

source_name: Frozen rectal tumor sample (A572)


title: BNx1_36h

description: bilateral nephrectomy 1 (36h)


title: Sham5_36h

description: sham laparotomy 5 (36h)


title: Frozen rectal tumor sample (A547)

description: test

source_name: Frozen rectal tumor sample (A547)


title: IRI1_36h

description: bilateral kidney 1 (36h)


title: Frozen rectal tumor sample (A608)

description: test

source_name: Frozen rectal tumor sample (A608)


title: Frozen rectal tumor sample (A575)

description: test

source_name: Frozen rectal tumor sample (A575)


title: Sham4_36h

description: sham laparotomy 4 (36h)


title: BNx2_36h

description: bilateral nephrectomy 2 (36h)


title: Frozen rectal tumor sample (A565)

description: test

source_name: Frozen rectal tumor sample (A565)


title: BNx3_36h

description: bilateral nephrectomy 3 (36h)


title: Frozen rectal tumor sample (A542)

description: test

source_name: Frozen rectal tumor sample (A542)


title: Frozen rectal tumor sample (A528)

description: test

source_name: Frozen rectal tumor sample (A528)


title: Frozen rectal tumor sample (A525)

description: test

source_name: Frozen rectal tumor sample (A525)


title: Sham2_36h

description: sham laparotomy 2 (36h)


title: Sham3_36h

description: sham laparotomy 3 (36h)


title: Frozen rectal tumor sample (A544)

description: test

source_name: Frozen rectal tumor sample (A544)


title: Frozen rectal tumor sample (A571)

description: test

source_name: Frozen rectal tumor sample (A571)


title: Frozen rectal tumor sample (A534)

description: test

source_name: Frozen rectal tumor sample (A534)


title: Frozen rectal tumor sample (A221)

description: test

source_name: Frozen rectal tumor sample (A221)


title: Frozen rectal tumor sample (A515)

description: test

source_name: Frozen rectal tumor sample (A515)


title: Frozen rectal tumor sample (A533)

description: test

source_name: Frozen rectal tumor sample (A533)


title: Frozen rectal tumor sample (B947)

description: test

source_name: Frozen rectal tumor sample (B947)


title: IRI3_6h

description: bilateral kidney 3 (6h)

source_name: Whole Lung


title: Frozen rectal tumor sample (B890)

description: test

source_name: Frozen rectal tumor sample (B890)


title: Frozen rectal tumor sample (A215)

description: test

source_name: Frozen rectal tumor sample (A215)


title: Frozen rectal tumor sample (A209)

description: test

source_name: Frozen rectal tumor sample (A209)


title: Frozen rectal tumor sample (A220)

description: test

source_name: Frozen rectal tumor sample (A220)


title: Frozen rectal tumor sample (A204)

description: test

source_name: Frozen rectal tumor sample (A204)


title: Frozen rectal tumor sample (A160)

description: test

source_name: Frozen rectal tumor sample (A160)


title: Frozen rectal tumor sample (A205)

description: test

source_name: Frozen rectal tumor sample (A205)


title: Sham3_6h

description: sham laparotomy 3 (6h)


title: IRI1_6h

description: bilateral kidney 1 (6h)


title: Frozen rectal tumor sample (A219)

description: test

source_name: Frozen rectal tumor sample (A219)


title: Sham1_36h

description: sham laparotomy 1 (36h)


title: Frozen rectal tumor sample (A168)

description: test

source_name: Frozen rectal tumor sample (A168)


title: IRI2_6h

description: bilateral kidney 2 (6h)


title: Frozen rectal tumor sample (A144)

description: test

source_name: Frozen rectal tumor sample (A144)


title: Frozen rectal tumor sample (A203)

description: test

source_name: Frozen rectal tumor sample (A203)


title: Sham2_6h

description: sham laparotomy 2 (6h)


title: Frozen rectal tumor sample (A156)

description: test

source_name: Frozen rectal tumor sample (A156)


title: Frozen rectal tumor sample (A164)

description: test

source_name: Frozen rectal tumor sample (A164)


title: Frozen rectal tumor sample (A514)

description: test

source_name: Frozen rectal tumor sample (A514)


title: Frozen rectal tumor sample (A140(2))

description: test

source_name: Frozen rectal tumor sample (A140(2))


title: Sham1_6h

description: sham laparotomy 1 (6h)


title: Frozen rectal tumor sample (A140)

description: test

source_name: Frozen rectal tumor sample (A140)


title: BNx3_6h

description: bilateral nephrectomy 3 (6h)

source_name: Whole Lung


title: Frozen rectal tumor sample (A138)

description: test

source_name: Frozen rectal tumor sample (A138)


title: BNx2_6h

description: bilateral nephrectomy 2 (6h)


title: Frozen rectal tumor sample (A137)

description: test

source_name: Frozen rectal tumor sample (A137)


title: BNx1_6h

description: bilateral nephrectomy 1 (6h)

tag: Black 6


title: Frozen rectal tumor sample (A511)

description: test

source_name: Frozen rectal tumor sample (A511)


title: Frozen rectal tumor sample (A510)

description: test

source_name: Frozen rectal tumor sample (A510)


title: Frozen rectal tumor sample (B277)

description: test

source_name: Frozen rectal tumor sample (B277)


title: 71189_#393_A2_420PMT_130706_532median

status: Public on May 29 2007

city: Singapore

first: Christopher

last: Wong

address: 60 Biopolis St #02-01

country: Singapore

institute: Genome Institute of Singapore

description: 71189_#393_A2_420PMT_130706_532median.txt

hyb_protocol: Overnight hybridization - see Wong et al, 2007

scan_protocol: Axon scanners at PMT indicated in the title of data file

data_processing: Apply algorithms described in Wong et al, 2007

organism: Viruses

source_name: human + pathogen; patient #393

label_protocol: Random PCR, end-label with biotin, amplify signal with streptavidin-Cy3 - see Wong et al, 2007

extract_protocol: RNAzol per manufacturer's instructions

tag: pediatric nasal wash specimen


title: 73067_#769_A2_450PMT_280406_532median

source_name: human + pathogen; patient #769


title: 71028_#913_A2_420PMT_230506_532median

source_name: human + pathogen; patient #913


title: 71180_#133_A2_420PMT_300506_532median

source_name: human + pathogen; patient #133


title: 71188_#859_A2_420PMT_130706_532median

description: 71188_#859_A2_420PMT_130706_532median.txt

source_name: human + pathogen; patient #859


title: 71007_#699_A2_450PMT_220506_532median

source_name: human + pathogen; patient #699


title: 71182_#639_A2_420PMT_130706_532median

description: 71182_#639_A2_420PMT_130706_532median.txt

source_name: human + pathogen; patient #639


title: 71006_#321_A2_440PMT_220506_532median

source_name: human + pathogen; patient #321


title: 73070_#841_A2_470PMT_050506_532median

source_name: human + pathogen; patient #841


title: 70927_#818_A2_500PMT_200406_532median

description: 70927_#818_A2_500PMT_200406_532median.txt

source_name: human + pathogen; patient #818


title: 70997_#554_A2_450PMT_220506_532median

source_name: human + pathogen; patient #554


title: 66703_#924_A2_470PMT_190506_532median

source_name: human + pathogen; patient #924


title: 70935_#254_A2_480PMT_280406_532median

source_name: human + pathogen; patient #254


title: 73068_#832_A2_470PMT_050506_532median

source_name: human + pathogen; patient #832


title: 66695_#374_A2_460PMT_150506_532median

source_name: human + pathogen; patient #374


title: 66700_#573_A2_490PMT_170506_532median

source_name: human + pathogen; patient #573


title: 66697_#261_A2_490PMT_170506_532median

source_name: human + pathogen; patient #261


title: 66696_#185_A2_470PMT_170506_532median

source_name: human + pathogen; patient #185


title: 68359_#892_A2_450PMT_190506_532median

source_name: human + pathogen; patient #892


title: 70933_#378_A2_470PMT_110406_532median

description: 70933_#378_A2_470PMT_110406_532median.txt

source_name: human + pathogen; patient #378


title: 71025_#414_A2_440PMT_230506_532median

source_name: human + pathogen; patient #414


title: Frozen rectal tumor sample (A543)

description: test

source_name: Frozen rectal tumor sample (A543)


title: 66698_#331_A2_490PMT_170506_532median

source_name: human + pathogen; patient #331


title: Frozen rectal tumor sample (A539)

description: test

source_name: Frozen rectal tumor sample (A539)


title: 71027_#478_A2_440PMT_230506_532median

source_name: human + pathogen; patient #478


title: 66702_#368_A2_470PMT_190506_532median

source_name: human + pathogen; patient #368


title: 66691_#165_A2_480PMT_150506_532median

source_name: human + pathogen; patient #165


title: 66701_#312_A2_470PMT_190506_532median

source_name: human + pathogen; patient #312


title: 66699_#461_A2_470PMT_170506_532median

source_name: human + pathogen; patient #461


title: 66690_#853_A2_480PMT_150506_532median

source_name: human + pathogen; patient #853


title: 63781_#283_A2_480PMT_150506_532median

source_name: human + pathogen; patient #283


title: Frozen rectal tumor sample (A567)

description: test

source_name: Frozen rectal tumor sample (A567)


title: 35915_#111_210405_400PMT_532median

source_name: human + pathogen; patient #111


title: 36731_#412_092705_400PMT_532median

source_name: human + pathogen; patient #412


title: DH5alphaF_replicate1

city: Koeln

first: Bettina

middle: I

last: Harr

address: Weyertal 121Dept of Genetics

institute: Institut für Genetik

description: E. coli transcriptome analysis

organism: Escherichia coli

source_name: E. coli logarithmic phase


title: DH5alphaF_replicate2

description: E. coli transcriptome analysis


title: MG1655F_replicate2

description: Transcription profile in E. coli


title: 35890#412_051015_400PMT_532median


title: 36042#412_400PMT_532median


title: 36053#483_400PMT_532median

source_name: human + pathogen; patient #483


title: 35887_#122_051015_400PMT_532median

source_name: human + pathogen; patient #122


title: 34959_Dengue_400PMT_532median

description: 34959_Dengue_400PMT median.txt

organism: dengue virus type 1

source_name: Dengue type 1

growth_protocol: per ATCC recommendations

tag: Dengue type 1 viral RNA amplified from cell culture (ATCC #VR-1254) using Dengue type 1-specific PCR primers.


title: 35662_#355_300PMT_532median

source_name: human + pathogen; patient #355


title: 35259_#324_400PMT_532median

source_name: human + pathogen; patient #324


title: DH5alpha_replicate1

description: E. coli transcriptome analysis


title: 32272_SARS_SIN850_300PMT_532median

organism: Severe acute respiratory syndrome-related coronavirus

tag: Severe Acute Respiratory Syndrome (SARS) virus amplified from Vero cell culture as described in Lim PL, Kurup A, Gopalakrishna G, Chan KP, Wong CW, et al

value: Laboratory-Acquired Severe Acute Respiratory Syndrome. N Engl J Med 2004, 350:1740-1745, PMID:15103000, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=15103000


title: MG1655_replicate1

description: Transcription profile in E. coli


title: MG1655F_replicate1

description: Transcription profile in E. coli


title: DH5alpha_replicate2

description: E. coli transcriptome analysis


title: MG1655_replicate2

description: Transcription profile in E. coli


title: Histone H3 actylation K9/K14 mapping asynchronous Exp 1

status: Public on May 26 2007

city: Chicago

first: Isabelle

middle: A

last: Lucas

state: IL

address: 5841 S Maryland

institute: University of Chicago

hyb_protocol: Equal amounts of the nascent strand DNAs (Cy3) and G1 DNA samples (Cy5) were combined and dried down by vacuum centrifugation.  The sample was rehydrated in 39 µl of NimbleGen Hybridization Buffer (NimbleGen Systems Inc.), denatured at 95°C for 5 min and then cooled to 42°C.  Hybridization was carried out for 18 hours at 42°C.  The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems Inc.) and immediately dried down by centrifugation.

scan_protocol: Arrays were scanned at 5 μm resolution using the GenePix4000B scanner (Axon Instruments). Data was extracted from scanned images using NimbleScan 2.1 extraction software (NimbleGen Systems Inc.), which allows for automated grid alignment, extraction and generation of data files.

data_processing: Log2 ratios were computed for each sample pair and scaled using the Tukey bi-weight mean ("Data Analysis and Regression: A Second Course in Statistics", Mosteller and Tukey, Addison-Wesley, 1977) using NimbleScan Version 2.1 software (NimbleGen Systems Inc).

source_name: ChIP DNA

label_protocol: The labeling of dsDNA for oligonucleotide microarray analysis was performed using the method of Selzer et al. (Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer, 2005, 44: pp 305-319).  Briefly, each DNA sample (1 ug) was denatured at 98°C in the presence of 1 O.D. of 5’-Cy3 or Cy5 labeled random nonamer (TriLink Biotechnologies) in 62.5 mM Tris-HCl, pH 7.5, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol. The denatured sample was chilled on ice, and then incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix (6 mM each in TE; Invitrogen) for 2 h at 37°C.  Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. Thirty-fold amplification was typically achieved.

extract_protocol: ChIP was performed according to the protocol provided by Upstate, Inc (http://www.upstate.com) with the following modifications.  Crosslinking of the protein/DNA complexes was done by incubating 5-10 x106 log phase cells with 1% formaldehyde at 37°C for 15 min, and stopped by the addition of glycine (0.125 M, 5 min, room temperature).  Cells were washed twice with ice-cold PBS, and lysed with 500 μl of NP-40 buffer (5 μM PIPES pH 8.0, 85 μM KCl, 0.5% NP-40, and 1% Protease Inhibitor Cocktail, Calbiochem).  Nuclei were lysed with 200 μl of SDS buffer (0.05 M Tris-HCl pH 8.1, 10 μM EDTA, 1% SDS, and 1% Protease Inhibitor Cocktail), and DNA was sheared.  Before the pre-clearing step with salmon sperm DNA/protein A or G agarose beads (32 μg, Upstate), 1% of the nuclear lysate was set aside as the input sample.  The following antibody was used for ChIP: acetylated histone H3 K9/14 (06-599, Upstate, 1:132 dilution).  The antibody/protein/DNA complexes were retrieved by the addition of 24 μg of salmon sperm DNA/protein A or G agarose beads.

tag: Human Epstein Barr Virus-transformed lymphoblastoid cells (cell line 11365) with a normal karyotype (46,XX), asynchronous log phase

source_name: Input DNA


title: Histone H3 actylation K9/K14 mapping asynchronous Exp 2

extract_protocol: ChIP was performed according to the protocol provided by Upstate, Inc (http://www.upstate.com) with the following modifications.  Crosslinking of the protein/DNA complexes was done by incubating 5-10 x106 log phase cells with 1% formaldehyde at 37°C for 15 min, and stopped by the addition of glycine (0.125 M, 5 min, room temperature).  Cells were washed twice with ice-cold PBS, and lysed with 500 μl of NP-40 buffer (5 μM PIPES pH 8.0, 85 μM KCl, 0.5% NP-40, and 1% Protease Inhibitor Cocktail, Calbiochem).  Nuclei were lysed with 200 μl of SDS buffer (0.05 M Tris-HCl pH 8.1, 10 μM EDTA, 1% SDS, and 1% Protease Inhibitor Cocktail), and DNA was sheared.  Before the pre-clearing step with salmon sperm DNA/protein A or G agarose beads (32 μg, Upstate), 1% of the nuclear lysate was set aside as the input sample.


title: 35179_#122_400PMT_532median


title: Origin mapping asynchronous Exp 1

source_name: Nascent strand DNA, 300bp-1kb

extract_protocol: Nascent DNA was isolated according to the method described by Giacca et al (Fine mapping of a replication origin of human DNA. Proc Natl Acad Sci Usa, 1994, 91: pp 7119-7123) with the following modifications.  The sucrose gradient fractions corresponding to the 300 bp-1 kb size range were pooled, and precipitated by adding 1/10 volume of 3M sodium acetate, pH 6.0, and 2.5 volumes of cold ethanol (6-8 μg of nascent DNA were obtained from 100x106 cells).  The size range of the DNA was verified by gel electrophoresis.

source_name: Total genomic DNA, sorted G1 cells

extract_protocol: Cells (50-100 million) in logarithmic phase growth were harvested, fixed at a final concentration of 0.5x106 cells/ml in 30% PBS/70% ethanol, and stored at -20ºC for at least 30 minutes.  For flow cytometry analysis of the cell cycle, the fixed cells were washed twice with ice-cold MgCl2/CaCl2-free PBS (Gibco), resuspended at a final concentration of 1x106 cells/ml in RNaseA solution (Sigma, 0.1mg/ml in MgCl2/CaCl2-free PBS), and incubated at 37ºC for 30 minutes.  The cells were washed twice with ice cold MgCl2/CaCl2-free PBS, resuspended at a final concentration of 1x106 cells/ml in propidium iodide (PI) solution (Sigma, 0.1mg/ml PI in MgCl2/CaCl2-free PBS) and incubated on ice in the dark for at least 30 minutes.  PI-stained cells were analyzed and sorted on a MoFlo (Dako Colorado Inc., Fort Collins, CO). The sorted G1 cells were incubated at 65ºC after adding EDTA (5 mM), Tris pH 8.0 (10 mM), SDS (0.1%) and proteinase K (Roche, 200μg/ml).  This step was followed by phenol-chloroform DNA extraction.  The aqueous phase was dialyzed against water at room temperature for 4 hours.  The DNA was precipitated by adding 1/25 volume of 5M NaCl, and 2.5 volumes of cold ethanol, and then resuspended in water.


title: Origin mapping asynchronous Exp 2


title: SVGR2 subclone 4-F6 GeneChip U133A

status: Public on May 25 2007

city: Providence

first: Kate

last: Manley

state: RI

address: 70 Ship St.

institute: Brown University

description: Gene expression data from SVGR2 glial cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome 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 100.

source_name: SVGR2 glial cells

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

growth_protocol: Cells were cultured in supplemented with 10% fetal calf serum (Mediatech, Inc.) and maintained in a humidified 37°C CO2 incubator.

extract_protocol: Extraction of total RNA was performed using the Qiagen Rneasy midi kit according to the manufacturer's instructions.

treatment_protocol: Cells were left at 100% confluency before RNA was harvested.

tag: VGR2 cells are glial cells which are derived from SVG-A cells. They were created by subjecting SVG-A cells to multiple rounds of lytic infection by the human polyomavirus JCV. SVGR2 cells are the cells that survived this process and are resistant to JCV infection