title: human PBMC (adherent fraction), Chlamydia infected, 7 days

city: Hannover

first: Markus

last: Rihl

address: Carl-Neuberg-Str. 1

department: Clinical Immunology and Rheumatology

institute: Hannover Medical School (MHH)

description:
cDNA based microarray
Messenger RNA of C trachomatis infected monocytes of the three healthy donors was compared with the corresponding mock-infected samples. For mock infection, SPG buffer was used instead of the C trachomatis suspension, all other procedures were performed identically. Cells were resuspended in solution D and total RNA was extracted by application of phenol:chloroform 5:1 (pH 4.5, Ambion, Austin, TX) followed by precipitation in isopropanol at -80°C for 1 hr and incubation with RQ1 DNase (Promega, Madison, WI) at 37 °C for 1 hr.
The signal intensity of the G3PDH housekeeping gene on the microarray membrane was used as indirect quality marker for the RNA utilized as only experiments were included in the analysis that revealed a G3PDH signal intensity within 1.5 times the standard deviation of all membranes evaluated in our study. The entire microarray procedure and its analysis has recently been validated and reported in detail. Total RNA of all donors was pooled and for each microarray experiment 150 µg were reverse transcribed and amplified by SMART™-PCR (BD Biosciences Clontech, Palo Alto, CA), a technology that allows reverse transcription of small amounts of total RNA and subsequent amplification of the entire cDNA. Probes were labeled with 32P and subsequently over night hybridized to a filter-based nylon membrane containing immobilized cDNA-specific sequences from a total of 1,184 genes (Human Atlas Array 1.2, BD Biosciences Clontech, Palo Alto, CA). For analysis, we focused solely on the 159 cytokines, chemokines and their receptors as given by the manufacturer. Signal intensities were retrieved by a STORM 860 scanner (Molecular Dynamics, Sunnyvale, CA) in combination with the AtlasImage 2.0 software (BD Biosciences Clontech). Data from all signal intensities were then subtracted by the local background intensity measured around each gene. The local background intensities of all individual genes were subsequently averaged, resulting in the mean background intensity of a particular membrane. Gene expression in our experiments was determined by a spot intensity of a single transcript that exceeded twice the mean background. Normalisation to background and to the G3PDH housekeeping gene was achieved by the global (sum) normalization method. Signal intensity data are given as the ratio of C trachomatis infected vs mock infected probes.

hyb_protocol: probes were over night hybridized to a filter-based nylon membrane (Atlas 1.2 I, Clontech)

scan_protocol: signal intensities were retrieved by phosphoimaging using a STORM 860 scanner

data_processing: data from all signal intensities were subtracted by the local background intensity measured around each gene. The local background intensities of all individual genes were subsequently averaged, resulting in the mean background intensity of a particular membrane. Gene expression in our experiments was determined by a spot intensity of a single transcript that exceeded twice the mean background. Normalisation to background and to the G3PDH housekeeping gene was achieved by the global (sum) normalization method

source_name: human PBMC (adherent fraction) from healthy donors

label_protocol: probes were labeled with 32P using rediprime beats (Amersham)

extract_protocol: cells were resuspended in solution D, total RNA was extracted by application of phenol:chloroform 5:1, followed by precipitation in isopropanol at -80°C for 1 hr and incubation with RQ1 DNase at 37 °C for 1 hr.

tag: Ficoll separated human PBMC from healthy donors, infected with purified Chlamydia trachomatis EB serovar K (UW/31/Cx) and incubated at 37C at 5% CO2 for 7d


title: Laser capture microdissected (LCM) endothelium at the globular stage, biological replicate 2

status: Public on Apr 26 2007

type: RNA

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

description: Endothelium regions from globular stage seeds were microdissected using the LEICA AS LMD system.

hyb_protocol: Following fragmentation, Ten micrograms of cRNA were hybridized for 16 hr at 45?C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.

label: biotin

molecule: total RNA

organism: Glycine max

source_name: Soybean globular stage endothelium captured by LCM

label_protocol: Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22?C.

extract_protocol: Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Pods with lengths between 0.5 and 1.2 cm containing seeds with globular-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from six-micron sections using a Leica AS LMD System.

tag: Soybean cv. Asgrow A3237


title: Laser capture microdissected (LCM) epidermis at the globular stage, biological replicate 2

description: Epidermis regions from globular stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage epidermis captured by LCM


title: Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 3

description: Suspensor regions from globular embryos were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage suspensor captured by LCM


title: Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 2

hyb_protocol: Following fragmentation, fifteen micrograms of cRNA were hybridized for 16 hr at 45?C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.


title: Laser capture microdissected (LCM) endothelium at the globular stage, biological replicate 3

label_protocol: Eight nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.


title: Laser capture microdissected (LCM) endosperm at the globular stage, biological replicate 3

description: Endosperm regions from globular stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage endosperm captured by LCM


title: Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 3

description: Embryo proper regions from globular embryos were microdissected using the LEICA AS LMD system.

hyb_protocol: Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45?C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

source_name: Soybean globular stage embryo proper captured by LCM


title: human PBMC (adherent fraction), Chlamydia infected, 1 day

country: Germany

organism: Homo sapiens

tag: Ficoll separated human PBMC from healthy donors, infected with purified Chlamydia trachomatis EB serovar K (UW/31/Cx) and incubated at 37C at 5% CO2 for 1 d


title: human PBMC (adherent fraction), Chlamydia infected, 4 hours

tag: Ficoll separated human PBMC from healthy donors, infected with purified Chlamydia trachomatis EB serovar K (UW/31/Cx) and incubated at 37C at 5% CO2 for 4 h


title: human PBMC (adherent fraction), mock infected, 1 day

tag: Ficoll separated human PBMC (adherent fraction) from healthy donors, mock-infected (using SPG buffer) and incubated at 37C at 5% CO2 for 1 d


title: human PBMC (adherent fraction), mock infected, 4 hours

tag: Ficoll separated human PBMC (adherent fraction) from healthy donors, mock-infected (using SPG buffer) and incubated at 37C at 5% CO2 for 4 h


title: human PBMC (adherent fraction), mock infected, 7 days

tag: Ficoll separated human PBMC (adherent fraction) from healthy donors, mock-infected (using SPG buffer) and incubated at 37C at 5% CO2 for 7 d


title: Isolate 7876 (7876_070)

status: Public on Apr 27 2007

type: genomic

city: Ames

first: Mike

last: Paustian

state: IA

address: 2300 Dayton Ave

institute: National Animal Disease Center, USDA-ARS

description: Comparative genomic hybridization between Map K-10 and other mycobacteria

hyb_protocol: Labeled cDNA from experimental mycobacterial isolates was purified and mixed with alternately labeled Map K10 cDNA in a final volume of 55 µL containing 3x SSC, 0.22pct SDS, and 34 µg salmon sperm DNA (Invitrogen).  This hybridization solution was incubated at 100C for 2 minutes, applied to the Map K10 microarray, and allowed to hybridize overnight at 65C.  The arrays were washed sequentially for 3 minutes at room temperature in 300 mL volumes of 0.5x SSC/0.01pct SDS, 0.5x SSC, 0.1x SSC, and 0.01x SSC, then dried by centrifugation and scanned.

scan_protocol: Microarray was scanned with a ScanArray 4000 confocal laser scanner (PerkinElmer, Boston, MA).  Laser and PMT power were adjusted to minimize pixel saturation and background fluorescence

data_processing: Raw intensity measurements for each spot on the microarray were extracted from scanned images using ScanArray Express software (PerkinElmer) and adjusted with local background subtraction and LOWESS normalization.  Poorly detected spots were removed by filtering out those in which more than 50pct of the pixels from both samples were within two standard deviations of the local background.  Note that for final analyses, triplicate spots were averaged and ORFs not represented by at least 2 replicate spots were discarded.

label: Alexa 555

molecule: genomic DNA

organism: Mycobacterium avium

label_protocol: Purified genomic DNA was randomly sheared by nebulization on ice at 10 psi for approximately 1.5 min, resulting in an average fragment size of 800 bp.  Aliquots of sheared genomic DNA (4 µg) were labeled with Invitrogen BioPrime Plus Array CGH kit.

extract_protocol: QIAGEN Genomic-tip or QIAamp DNA blood kit

tag: in vitro pure culture

label: Alexa 647


title: Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 1


title: Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 1

label_protocol: Ten nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.


title: SREBP1c vs mock infected, rep3 (dye swap)

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Human Fibroblast cells(AG01518) infected with adenovirus coding for SREBP1c and mock virus as control

hyb_protocol: Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium

scan_protocol: Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction)

data_processing: Normalization and statistical analysis of the data sets were performed using GeneSpring 5.0. A Lowess non-linear normalization was applied, and a statistical analysis of the data based on the global error model of GeneSpring was used

source_name: Human Fibroblasts cells AG01518

label_protocol: total RNA was labeled with Cy5

growth_protocol: AG01518 foreskin fibroblasts from passages 11 to 19 were cultured in Modified Eagle Medium supplemented with 10% foetal calf serum and glutamine

extract_protocol: Total RNA (40 ug) was isolated from cells infected with mock viruses using the RNeasy kit (Qiagen) and used for microarray hybridizations

treatment_protocol: AG01518 fibroblasts were infected with adenoviruses encoding mock virus at 60 virus per cell for 24 h

tag: Human Fibroblasts cells AG01518 infected with mock viruses

label_protocol: total RNA was labeled with Cy3

extract_protocol: Total RNA (40 ug) was isolated from cells infected with SREBP1c encoding viruses using the RNeasy kit (Qiagen) and used for microarray hybridizations

treatment_protocol: AG01518 fibroblasts were infected with adenoviruses encoding SREBP1c at 60 virus per cell for 24 h

tag: Human Fibroblasts cells AG01518 infected with SREBP1c encoding viruses


title: M. tuberculosis_H37Rv_log-phase_rep1

status: Public on Apr 25 2007

city: IRVINE

first: Li

last: Fu

address: 8 Corporate Park, Suite 300

institute: Pacific Tuberculosis and Cancer Research Organization

description:
Quality control of gene expression data is based on expression
of housekeeping genes, spike controls, background values, and
noise levels (pixel-to-pixel variations).

hyb_protocol: The assay utilized reverse transcriptase and random hexamer primers to produce DNA complementary to the RNA. The cDNA products were then fragmented by DNAase I and labeled with terminal transferase and biotinylated GeneChip DNA Labeling Reagent at the 3' terminal. The chip is stained with streptavidin-phycoerythrin after hybridization. A global normalization scheme is applied so that each array's median value is adjusted to a predefine value (500). The scale factor for achieving this transformed median value for an array is uniformly applied to all the probe set values on a specific array to result in the determined Signal value for all the probe sets on the array.

scan_protocol: The chip is scanned using GeneChip Scanner 3000. The images are analyzed using GCOS (GeneChip Operating Software) version 1.4.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis log-phase culture

label_protocol: Standard Affymetrix labeling protocol.

extract_protocol: Cultures were mixed with an equal volume of RNALaterTM (Ambion, Austin, TX) and the bacteria harvested by centrifugation (1 min, 25000 x g, 8°C) and transferred to Fast Prep tubes (Bio 101, Vista, CA) containing Trizol (Life Technologies, Gaithersburg, MD). Mycobacteria were mechanically disrupted in a Fast Prep apparatus (Bio 101). The aqueous phase was recovered, treated with Cleanascite (CPG, Lincoln Park, NJ), and extracted with chloroform-isoamyl alcohol (24:1 v/v). Nucleic acids were ethanol precipitated. DNaseI (Ambion) treatment to digest contaminating DNA was performed in the presence of Prime RNase inhibitor (5’-3’, Boulder, CO). The RNA sample was precipitated and washed in ethanol, and redissolved to make a final concentration of 1 mg/ml.

tag: M. tuberculosis, log phase of growth, standard broth culture


title: SREBP1c vs mock infected, rep2


title: ORF Hst4 Binding map (slide 3 spot1)

status: Public on Apr 24 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

hyb_protocol: Robyr, D. and Grunstein, M. (2003) Genomewide histone acetylation microarrays. Methods, 31, 83-89

scan_protocol: ImaGene 4.2

data_processing: Genespring

organism: Schizosaccharomyces pombe

source_name: ChiP IP of ProtA-Hst4

source_name: ChiP Input

tag: ChiP Input


title: Intestinal adenocarcinoma of cis-Apc/Smad4 compound mutant mouse_3

city: Kyoto

first: Makoto

middle: Mark

last: Taketo

state: Kyoto

address: Yoshida-Konoé-cho, Sakyo

department: Pharmacology

country: Japan

institute: Kyoto University Graduate School of Medicine

description: The Apc (+/–) mice carry a knockout allele of the Apc gene (Apc Delta716), and develop numerous intestinal adenomas (200-500) by loss of heterozygosity (LOH) of the gene. The cis-Apc/Smad4 mice (cis-Apc+/ Delta716 Smad4+/– compound mutant mice) carry a knockout allele of the Smad4 gene on the same chromatid as that of Apc. In the compound mutant, loss of the SMAD4-dependent TGF-beta family signaling turns the intestinal adenomas into adenocarcinomas.

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide spotted with oligonucleotides (65mers) for 16h at 60ºC.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray microarray scanner (Perkin Elmer) and image intensity data were extracted and analyzed with ScanArray Express v3.1 software.

data_processing: Both Cy3 and Cy5 signals were normalized by Lowess method. VALUE is Log (base 10) of the ratio of the mean of Channel 2 (Cy5) to Channel 1 (Cy3).

organism: Mus musculus

source_name: Apc (+/–) #3 small intestinal adenoma

label_protocol: The mRNA was amplified, and 5-(3-aminoallyl)-UTP was incorporated to it using AminoAllyl MessageAmp aRNA Amplification Kit (Ambion). The aminoallyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3.

extract_protocol: Total RNA was isolated from a single polyp in the small intestine by homogenizing in TriReagent (Sigma). The total RNA (150 micro g) was treated with DNase I for 30 min at 37ºC and purified using RNeasy Mini Kit (Qiagen). The mRNA was then extracted from 100 micro g of total RNA using GenElute mRNA Miniprep Kit (Sigma).

tag: Strain

value: C57BL/6, Gender:male, Age:18 weeks, Tissue:polyp adenoma in the small intestine

source_name: cis-Apc/Smad4 #3 small intestinal adenocarcinoma

label_protocol: The mRNA was amplified, and 5-(3-aminoallyl)-UTP was incorporated to it using AminoAllyl MessageAmp aRNA Amplification Kit (Ambion). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy5.

value: C57BL/6, Gender:male, Age:15 weeks, Tissue:adenocarcinoma in the small intestine


title: ORF Hst4 Binding map (slide 3 spot2)

label_protocol: Robyr, D. and Grunstein, M. (2003) Genomewide histone acetylation microarrays. Methods, 31, 83-89


title: ORF Hst4 Binding map (slide 2 spot2)

extract_protocol: Robyr, D. and Grunstein, M. (2003) Genomewide histone acetylation microarrays. Methods, 31, 83-89


title: ORF Hst4 Binding map (slide 1 spot2)


title: ORF Hst4 Binding map (slide 2 spot1)


title: IGR Hst4 Binding map (slide 3 spot1)


title: IGR Hst4 Binding map (slide 1 spot2)


title: M. tuberculosis_capreomycin_4h_rep2

data_processing: A global normalization scheme is applied so that each array's median value is adjusted to a predefine value (500). The scale factor for achieving this transformed median value for an array is uniformly applied to all the probe set values on a specific array to result in the determined Signal value for all the probe sets on the array.

source_name: Standard broth culture

label_protocol: Standard Affymetrix Labeling Protocol

extract_protocol:
Cultures are mixed with an equal volume of RNALaterTM
(Ambion, Austin, TX) and the bacteria harvested by
centrifugation (1 min, 25000 x g, 8°C) and transferred to
Fast Prep tubes (Bio 101, Vista, CA) containing Trizol
(Life Technologies, Gaithersburg, MD). Mycobacteria are
mechanically disrupted in a Fast Prep apparatus (Bio 101).
The aqueous phase is recovered, treated with Cleanascite
(CPG, Lincoln Park, NJ), and extracted with chloroform-isoamyl
alcohol (24:1 v/v). Nucleic acids are ethanol precipitated.
DNaseI (Ambion) treatment to digest contaminating DNA is
performed in the presence of Prime RNase inhibitor
(5’-3’, Boulder, CO). The RNA sample is precipitated and
washed in ethanol, and redissolved to make a final
concentration of 1 mg/ml.

tag: M. tuberculosis H37Rv log-phase culture

tag: in response to capreomycin 10 ug/ml for 4 hours


title: IGR Hst2 Binding map (270F9 spot2)

source_name: ChiP IP of Hst2-myc


title: ORF Hst4 Binding map (slide 1 spot1)


title: Intestinal adenocarcinoma of cis-Apc/Smad4 compound mutant mouse_2

source_name: Apc (+/–) #2 small intestinal adenoma

source_name: cis-Apc/Smad4 #2 small intestinal adenocarcinoma


title: M. tuberculosis_capreomycin_4h_rep1

extract_protocol: Cultures are mixed with an equal volume of RNALaterTM (Ambion, Austin, TX) and the bacteria harvested by centrifugation (1 min, 25000 x g, 8°C) and transferred to Fast Prep tubes (Bio 101, Vista, CA) containing Trizol (Life Technologies, Gaithersburg, MD). Mycobacteria are mechanically disrupted in a Fast Prep apparatus (Bio 101). The aqueous phase is recovered, treated with Cleanascite (CPG, Lincoln Park, NJ), and extracted with chloroform-isoamyl alcohol (24:1 v/v). Nucleic acids are ethanol precipitated. DNaseI (Ambion) treatment to digest contaminating DNA is performed in the presence of Prime RNase inhibitor (5’-3’, Boulder, CO). The RNA sample is precipitated and washed in ethanol, and redissolved to make a final concentration of 1 mg/ml.


title: M. tuberculosis_H37Rv_log-phase_rep2

tag: M. tuberculosis H37Rv, log-phase of growth, in vitro


title: IGR Hst4 Binding map (slide 1 spot1)


title: SREBP1c vs mock infected, rep1


title: Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 2


title: IGR Hst4 Binding map (slide 2 spot1)


title: Intestinal adenocarcinoma of cis-Apc/Smad4 compound mutant mouse_1

source_name: Apc (+/–) #1 small intestinal adenoma

source_name: cis-Apc/Smad4 #1 small intestinal adenocarcinoma


title: IGR Hst2 Binding map (270F8 spot1)


title: IGR Hst4 Binding map (slide 3 spot2)


title: IGR Hst2 Binding map (270F8 spot2)


title: IGR Hst2 Binding map (270F9 spot1)


title: ORF Hst2 Binding map (270F9 spot1)


title: IGR Hst4 Binding map (slide 2 spot2)


title: Hst2 Expression profile (F010D #8 spot1)

hyb_protocol: A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast. 2004 Jan 15;21(1):25-39.

source_name: Hst2 mut. sample

tag: Hst2  mut. sample

source_name: WT sample

tag: WT sample


title: ORF Hst2 Binding map (270F8 spot2)


title: ORF Hst2 Binding map (270F9 spot2)


title: Hst2 Expression profile (F010D #8 spot2)

label_protocol: A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast. 2004 Jan 15;21(1):25-39.


title: GMP001

city: Berlin-Steglitz

first: Dirk

last: Carstanjen

state: Berlin

address: Krahmer Strasse 6

department: Molecular Genetics

institute: Institute for Molecular Pharmacology

description:
Mouse granulocyte/monocyte-macrophage progenitors (GMP) from bone marrow of 10 - 16 weeks old C57/Bl6 - S129Ola (mixed genetic background) purified by flow cytometry.
Lot batch = 3002162

source_name: GMP


title: ORF Hst2 Binding map (270F8 spot1)


title: Hst2 Expression profile (F010D #7 spot2)

extract_protocol: A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast. 2004 Jan 15;21(1):25-39.


title: Hst4 Expression profile (F010D #13 spot1)

source_name: Hst4 mut. sample

tag: Hst4  mut. sample


title: Hst4 Expression profile (K130C #3 spot1)


title: IGR hst2 vs WT H3 cter Lowess

label: median value used from 4 spots

source_name: CHIP IP sample of hst2 using H3 cter antibody

tag: We used the S. pombe ORF and combined IGR+ORF spotted microarrays (Eurogentec, Belgium custom DNA microarray services). For histone acetylation maps, ChIP-CHIP method was used using according to (Robyr and Grunstein, 2003). Specific acetylation antibodies were used against H3K9ac, H3K14ac, H4K5ac, H4K16ac, H4K12ac, (Suka et al., 2002) and H3K56ac (Xu et al., 2005). The histone ?H3cter? antibody was purchased from Upstate and used for ChIP according to manufacturers recommendations.

source_name: CHIP IP sample of wt using H3 cter antibody


title: Hst4 Expression profile (F010D #13 spot2)


title: ORF hst2 vs WT H3 cter Lowess


title: Hst2 Expression profile (F010D #7 spot1)


title: ORF sir2 vs WT H4K12Ac Lowess

source_name: CHIP IP sample of sir2 using H4K12Ac antibody

source_name: CHIP IP sample of wt using H4K12Ac antibody


title: Hst4 Expression profile (K130C #3 spot2)


title: IGR sir2 vs WT H3 cter Lowess

source_name: CHIP IP sample of sir2 using H3 cter antibody


title: ORF sir2 vs WT H4K16Ac Lowess

source_name: CHIP IP sample of sir2 using H4K16Ac antibody

source_name: CHIP IP sample of wt using H4K16Ac antibody


title: ORF sir2 vs WT H3 cter Lowess


title: IGR hst4 vs WT H3 cter Lowess

source_name: CHIP IP sample of hst4 using H3 cter antibody


title: ORF sir2 vs WT H3K14Ac Lowess

source_name: CHIP IP sample of sir2 using H3K14Ac antibody

source_name: CHIP IP sample of wt using H3K14Ac antibody


title: ORF sir2 vs WT H4K5Ac Lowess

source_name: CHIP IP sample of sir2 using H4K5Ac antibody

source_name: CHIP IP sample of wt using H4K5Ac antibody


title: IGR hst2 vs WT H4K12Ac Lowess

source_name: CHIP IP sample of hst2 using H4K12Ac antibody

tag: We used the S. pombe ORF and combined IGR+ORF spotted microarrays (Eurogentec, Belgium custom DNA microarray services). For histone acetylation maps, ChIP-CHIP method was used using according to (Robyr and Grunstein, 2003). Specific acetylation antibodies were used against H3K9ac, H3K14ac, H4K5ac, H4K16ac, H4K12ac, (Suka et al., 2002) and H3K56ac (Xu et al., 2005). The histone �H3cter� antibody was purchased from Upstate and used for ChIP according to manufacturers recommendations.


title: ORF hst4 vs WT H4K16Ac Lowess

source_name: CHIP IP sample of hst4 using H4K16Ac antibody


title: IGR hst2 vs WT H3K9Ac Lowess

source_name: CHIP IP sample of hst2 using H3K9Ac antibody

source_name: CHIP IP sample of wt using H3K9Ac antibody


title: ORF hst4 vs WT H4K12Ac Lowess

source_name: CHIP IP sample of hst4 using H4K12Ac antibody


title: IGR hst2 vs WT H4K5Ac Lowess

source_name: CHIP IP sample of hst2 using H4K5Ac antibody


title: IGR hst4 vs WT H4K12Ac Lowess


title: IGR hst2 vs WT H3K14Ac Lowess

source_name: CHIP IP sample of hst2 using H3K14Ac antibody


title: IGR hst2 vs WT H4K16Ac Lowess

source_name: CHIP IP sample of hst2 using H4K16Ac antibody


title: IGR hst4 vs WT H3K9Ac Lowess

source_name: CHIP IP sample of hst4 using H3K9Ac antibody


title: IGR hst4 vs WT H4K16Ac Lowess


title: IGR hst4 vs WT H4K5Ac Lowess

source_name: CHIP IP sample of hst4 using H4K5Ac antibody


title: ORF hst4 vs WT H4K5Ac Lowess


title: ORF hst4 vs WT H3 cter Lowess

source_name: CHIP IP sample of wt using H3 cter antibody


title: IGR hst4 vs WT H3K14Ac Lowess

source_name: CHIP IP sample of hst4 using H3K14Ac antibody


title: lung_E18_Nmyc9a_nuc_3

type: protein

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: protein profiling of mouse lung organogenesis from embryonic day E13.5 until adulthood

data_processing: filtered for a STATQUEST score of =>95% confidence and at least 2 spectral counts

molecule: protein

source_name: lung E18 nmyc9a nuclear

extract_protocol:
As per: 2. Kislinger T et al. Global survey of organ and or...[PMID: 16615898] and 6. Kislinger T et al. PRISM, a generic large scale ...[PMID: 12644571]

Tissue fractionation
The tissue fractionation was done as described [2]. Briefly, lung tissue was rinsed twice in ice cold phosphate-buffered saline and homogenized in ice cold lysis buffer, containing 250 mM sucrose, 50 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 1 mM DDT, and 1 mM PMSF using a tight fitting Teflon pestle. The lysate was centrifuged in a bench-top centrifuge at 800 g for 15 minutes; the supernatant served as source for cytosol, mitochondria and microsomes. The pellet, which contains the nuclei was re-homogenized in lysis buffer and centrifuged as above. The nuclei were resuspended in 2 molar sucrose buffer (2M sucrose, 50 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 1 mM DDT, and 1 mM PMSF) and pelleted by ultracentrifugation at 80000 g in a SW40Ti (Beckman) for 35 minutes. Mitochondria were isolated from the crude cytoplasmic fraction by bench-top centrifugation at 6000 g for 15 minutes. The mitochondrial pellet was washed and pelleted twice in lysis buffer. The cytosolic fraction was obtained after removal of the microsomal fraction by ultracentrifugation at 100000 g in a SW60Ti (Beckman) for 1 hour.

Organelle protein extraction
Nuclear proteins were extracted by resuspending the isolated nuclei in 5 volumes of 20 mM HEPES (pH 7.9), 1.5 mM MgCl2, 0.42 M NaCl, 0.2 mM EDTA, and 25 % glycerol for 30 minutes with gentle shaking at 4ºC. The nuclei were lysed by 10 passages through an 18-gauge needle, and debris was removed by microcentrifugation at 13000 rpm. The supernatant served as nuclear fraction. Mitochondrial proteins were isolated by incubating the mitochondria in a hypotonic lysis buffer [10 mM HEPES, pH 7.9] for 30 minutes on ice, briefly sonicated and debris pelleted at 13000 rpm for 30 minutes.

tag: mixed male and female mice, homozygous for the Nmyc hypomorphic allele 9a


title: ORF hst2 vs WT H4K5Ac Lowess

tag: We used the S. pombe ORF and combined IGR+ORF spotted microarrays (Eurogentec, Belgium custom DNA microarray services). For histone acetylation maps, ChIP-CHIP method was used using according to (Robyr and Grunstein, 2003). Specific acetylation antibodies were used against H3K9ac, H3K14ac, H4K5ac, H4K16ac, H4K12ac, (Suka et al., 2002) and H3K56ac (Xu et al., 2005). The histone ‘H3cter’ antibody was purchased from Upstate and used for ChIP according to manufacturers recommendations.


title: lung_E18_Nmyc9a_nuc_2

treatment_protocol: As per: 2. Kislinger T et al. Global survey of organ and or...[PMID: 16615898] and 6. Kislinger T et al. PRISM, a generic large scale ...[PMID: 12644571]


title: lung_E18_Nmyc9a_mito_1

source_name: lung E18 nmyc9a mitochondria


title: lung_E18_Nmyc9a_nuc_1


title: lung_E18_Nmyc9a_mito_2


title: ORF hst2 vs WT H3K9Ac Lowess


title: lung_E18_Nmyc9a_cyto_2

source_name: lung E18 nmyc9a cytosol

treatment_protocol:
As per:
2. Kislinger T et al. Global survey of organ and or...[PMID: 16615898] and 6. Kislinger T et al. PRISM, a generic large scale ...[PMID: 12644571]


title: lung_E18_Nmyc9a_cyto_1

source_name: lung E18 nmyc9a cyto 1


title: ORF hst2 vs WT H4K16Ac Lowess

source_name: CHIP IP sample of wt using H4K12Ac antibody


title: ORF hst4 vs WT H3K9Ac Lowess


title: Lung_P14_nuclear_2

tag: ICR mouse, mixed male and female mice


title: lung_p14_mitochondria_1


title: ORF hst4 vs WT H3K14Ac Lowess

source_name: CHIP IP sample of wt using H3K14Ac antibody


title: lung_E18_Nmyc9a_cyto_3


title: Lung_P14_mitochondria_2


title: Lung_P14_nuclear_1


title: ORF hst2 vs WT H3K14Ac Lowess


title: Lung_P2_nuclear_1


title: ORF hst2 vs WT H4K12Ac Lowess

source_name: CHIP IP sample of hst2 using H4K12Ac antibody


title: Lung_P2_nuclear_4


title: lung_p14_cytosol_2


title: lung_p14_cytosol_1


title: Lung_P2_cytosol_4


title: Lung_P2_mitochondria_3


title: Lung_E18_nuclear_4


title: Lung_P2_cytosol_2


title: Lung_E18_nuclear_1


title: Lung_E18_nuclear_2


title: Lung_E18_mitochondria_1


title: Lung_E18_mitochondria_2


title: Lung_E18_cytosol_3


title: Lung_E16_cytosol_1


title: Lung_E18_cytosol_2


title: Lung_E16_nuclear_2


title: Lung_E16_cytosol_2


title: Lung_E16_mitochondria_3


title: Lung_E14_mitochondria_1


title: Lung_E14_nuclear_1


title: Lung_E14_nuclear_4


title: Lung_E14_mitochondria_2


title: Lung_E16_mitochondria_1


title: Lung_E16_nuclear_1


title: Lung_E18_cytosol_1


title: Lung_E18_mitochondria_3


title: Pseudomonas aeruginosa_no treatment_ 20min_replicate4

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: No treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 150)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

label: Biotin

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa_no treatment

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated P. aeruginosa cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.

extract_protocol: Total RNA was isolated at 20 min after OD600 reached 0.8 using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: No treatment

tag: Wild type


title: Lung_adult_mitochondria_3


title: Lung_Adult_nuclear_2

extract_protocol:
As per: 2. Kislinger T et al. Global survey of organ and or...[PMID: 16615898] and 6. Kislinger T et al. PRISM, a generic large scale ...[PMID: 12644571]
Tissue fractionation
The tissue fractionation was done as described [2]. Briefly, lung tissue was rinsed twice in ice cold phosphate-buffered saline and homogenized in ice cold lysis buffer, containing 250 mM sucrose, 50 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 1 mM DDT, and 1 mM PMSF using a tight fitting Teflon pestle. The lysate was centrifuged in a bench-top centrifuge at 800 g for 15 minutes; the supernatant served as source for cytosol, mitochondria and microsomes. The pellet, which contains the nuclei was re-homogenized in lysis buffer and centrifuged as above. The nuclei were resuspended in 2 molar sucrose buffer (2M sucrose, 50 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 1 mM DDT, and 1 mM PMSF) and pelleted by ultracentrifugation at 80000 g in a SW40Ti (Beckman) for 35 minutes. Mitochondria were isolated from the crude cytoplasmic fraction by bench-top centrifugation at 6000 g for 15 minutes. The mitochondrial pellet was washed and pelleted twice in lysis buffer. The cytosolic fraction was obtained after removal of the microsomal fraction by ultracentrifugation at 100000 g in a SW60Ti (Beckman) for 1 hour.
Organelle protein extraction
Nuclear proteins were extracted by resuspending the isolated nuclei in 5 volumes of 20 mM HEPES (pH 7.9), 1.5 mM MgCl2, 0.42 M NaCl, 0.2 mM EDTA, and 25 % glycerol for 30 minutes with gentle shaking at 4ºC. The nuclei were lysed by 10 passages through an 18-gauge needle, and debris was removed by microcentrifugation at 13000 rpm. The supernatant served as nuclear fraction. Mitochondrial proteins were isolated by incubating the mitochondria in a hypotonic lysis buffer [10 mM HEPES, pH 7.9] for 30 minutes on ice, briefly sonicated and debris pelleted at 13000 rpm for 30 minutes.


title: Lung_Adult_nuclear_3


title: Lung_E14_cytosol_2


title: Pseudomonas aeruginosa_no treatment_ 20min_replicate1

description: No treatment


title: Pseudomonas aeruginosa_no treatment_ 20min_replicate3

description: No treatment


title: Pseudomonas aeruginosa_no treatment_ 20min_replicate2

description: No treatment


title: ORF K080D sir2D H3 cter (#10)

description: we used an antibody against histone H3 C-terminal region (H3 cter) to control for nucleosome occupancy.

source_name: CHIP IP sir2D H3 cter

tag: sir2D sample where H3 cter antibody was used

source_name: CHIP Input

tag: CHIP input sir2D H3 cter


title: Lung_E14_cytosol_1


title: ORF K080D sir2D H3 cter (#3)


title: Lung_adult_mitochondria_2


title: Lung_Adult_cytosol_2

source_name: adult lung cytosol


title: Lung_adult_cytosol_1

source_name: lung cytosol from adult


title: Lung_P2_mitochondria_2

source_name: lung mitochrondria from postnatal day 2


title: IGR K080D sir2D H3 cter (#10)


title: IGR J120E hst2 H3 cter #10

description: The normalised value=0 indicates no data.

source_name: CHIP IP sample of hst4D using H3 cter antibody


title: IGR J230C sir2 H3K14Ac

description: A set of five highly specific antibodies for H3K9Ac, H3K14Ac, H4K5Ac, H4K12Ac and H4K16Ac developed and titrated for ChIP (Suka et al., 2001) were used for ChIP of chromatin extracts from wt, hos2?, clr6-1, clr3? and sir2? cells. The mutant alleles were first backcrossed with the standard laboratory strain (972 h-) to ensure isogenic strain backgrounds . Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was labeled with Cy5. The wt control ChIP DNA was labeled with Cy3 and simultaneously hybridized with the Cy5 labeled DNA to the IGR+ORF microarrays to produce genome wide mutant versus wt histone acetylation maps.

source_name: CHIP IP sir2-D H3K14Ac

tag: sir2-D sample where H3K14Ac antibody was used

source_name: CHIP IP sir2-D Wt

tag: Wt sample of sir2-D


title: IGR K080D sir2D H3 cter (#3)


title: IGR J230C sir2 H3K9Ac

source_name: CHIP IP sir2-D H3K9Ac

tag: sir2-D sample where H3K9Ac antibody was used


title: IGR J130C sir2 H3K9Ac

tag: sir2-D sample where H3K9Ac antybody was used

tag: Wt sample od sir2-D


title: IGR J120E hst4 H3 cter #08

source_name: CHIP IP sample of hst2D using H3 cter antibody


title: IGR J130C sir2 H4K12Ac

source_name: CHIP IP sir2-D H4K12Ac

tag: sir2-D sample where H4K5Ac antybody was used


title: ORF I240c sir2 H3K9Ac

description: A set of five highly specific antibodies for H3K9Ac, H3K14Ac, H4K5Ac, H4K12Ac and H4K16Ac developed and titrated for ChIP (Suka et al., 2001) were used for ChIP of chromatin extracts from wt, hos2-D, clr6-1, clr3-D and sir2-D cells. The mutant alleles were first backcrossed with the standard laboratory strain (972 h-) to ensure isogenic strain backgrounds . Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was labeled with Cy5. The wt control ChIP DNA was labeled with Cy3 and simultaneously hybridized with the Cy5 labeled DNA to the IGR+ORF microarrays to produce genome wide mutant versus wt histone acetylation maps.


title: IGR J120E hst2 H3 cter #07


title: IGR J120E hst2 H3 cter #09


title: IGR J130C sir2 H4K5Ac

source_name: CHIP IP sir2-D H4K5Ac


title: IGR J230C sir2 H4K12Ac

tag: sir2-D sample where H4K12Ac antibody was used


title: IGR J130C sir2 H3K14Ac

tag: sir2-D sample where H3K14Ac antybody was used


title: IGR J230C sir2 H4K5Ac

tag: sir2-D sample where H4K5Ac antibody was used


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID134

status: Public on Apr 23 2007

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 24 h time point

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

organism: Rattus norvegicus

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Qiagen Micro RNA kit

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: ul

tag: Ratio

tag: Dilution

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: Good

tag: Sample Preservation

value: Cells resuspended in RNAlater and stored at 4 degrees Centigrade

tag: Strain or Line

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

value: Adult

tag: Sacrifice Method

value: Deep pentobarbital anesthesia followed by exsanguination

tag: Sex

value: Male

tag: Units of Age

value: weeks


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID136


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 5d ID137

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 5 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID132


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 24h ID133


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 8d ID146

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 8 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.07, Units of Dose or Concentration: ppm


title: IGR J230C sir2 H4K16Ac

source_name: CHIP IP sir2-D H4K16Ac

tag: sir2-D sample where H4K16Ac antibody was used

tag: Wt sample of sir2-D


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 19d ID154

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 19 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

tag: Array Type


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 19d ID155

tag: Amount to Core


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 19d ID77

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 19 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: Units of Amount


title: IGR J130C sir2 H4K16Ac

tag: sir2-D sample where H4K16Ac antybody was used

tag: Wt sample od sir2-D


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 19d ID152

tag: Ratio

tag: Dilution

tag: RNA Integrity Number


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 19d ID73

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID58

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 24 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 19d ID156

tag: Sacrifice Method

tag: Sex

tag: Units of Age


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID130

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hour time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

tag: Array Type


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID57

tag: Amount to Core


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 8d ID144

tag: Units of Amount


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 8d ID145


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID54


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 19d ID76


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID52

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID49


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 19d ID75


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID50


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 8d ID143


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 5d ID63

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 5 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 24h ID56


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 5d ID62


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 5d ID61


title: Nasal Epithelium Instilation Formaldehyde 0mM 6h ID354

description:
Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde instilation exposure, vehicle control, single exposure, 6 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Vehicle for Chemical: Water, Amount of Vehicle: 40, Route of Exposure: Instillation (nasal), Units of Amount of Vehicle: ul per nostril, Dose or Concentration: 0, Units of Dose or Concentration: mM


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID325

description:
Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID53


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID323


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID68

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 8 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID66


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 5d ID60


title: Nasal Epithelium Instilation Formaldehyde 0mM 6h ID352


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID67


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID322


title: Nasal Epithelium Inhalation Formaldehyde 07ppm 6h ID131


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID65


title: Nasal Epithelium Inhalation Formaldehyde 15ppm 6h ID337

description:
Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 15 ppm, 6 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 15, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 8d ID64


title: Nasal Epithelium Instilation Formaldehyde 0mM 6h ID356


title: ChIP-Chip with anti-V5 antibody, replicate 1 of 2.

city: Kobe

first: Rikuhiro

middle: G

last: Yamada

state: Hyogo

address: Minatojima-Minamimachi 2-2-3

department: Center for Developmental Biology

institute: RIKEN

description: Data from the chromatin immunoprecipitation with anti-V5 antibody on Drosophila genome tiling array. Replicate no.1 of 2 (Independent sampling).

hyb_protocol: 200 ul Hybridization cocktail was applied to Drosophila genome tiling array (Affymetrix) and hybridized at 45 dC for 18 h with 45 rpm rotation. Stain and wash was executed by Fluidics station 450 with EukGE-WS2 ver.4 program.

scan_protocol: Arrays were scanned by GeneChip Scanner 7G (Affymetrix).

data_processing: Raw data (CEL file) was normalized and analyzed by TileMap (Ji, H. and Wong, W.H. 2005. TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21(18): 3629-3636.) with its default parameters (See suplemental file: TileMap_parameterfiles.zip).

organism: Drosophila melanogaster

source_name: Cultured Drosophila S2 cells

label_protocol: The fragmented DNA was then end-labeled with GeneChip Labeling Reagent (Affymetrix) by using terminal deoxynucleotidyltransferase (Roche) in TdT buffer (Roche) and CoCl2 (Roche). To prepare the hybridization cocktail, 5 ug of labeled DNA fragment was mixed with final 1x MES, 3 M TMAC, 0.02% Triton (SIGMA), 50 pM Oligo B2, 1×Hybridization Control (Affymetrix), and 100 ug/ul Herring Sperm DNA (Promega).

growth_protocol: Drosophila S2 cells were maintained in Schneider′s Drosophila medium (Invitrogen) supplemented with 10% FBS (Bioserum) and antibiotics (12.5 U/ml penicillin, 12.5 mg/ml streptomycin; GIBCO).

extract_protocol: Cells were harvested 24 h after stimulation. ChIP was then performed according to the previously described method(Yamashita, M. et al. 2002. Identification of a conserved GATA3 response element upstream proximal from the interleukin-13 gene locus. J Biol Chem 277(44): 42399-42408) with some modifications. In this report, we employed Chromatin Immunoprecipitation Assay Kits (Upstate Biotechnology), anti-Flag M2 antibody (SIGMA) and anti-V5 antibody (SIGMA). Protein G-Sepharose (Amersham) was used for precipitation of antibody/protein immune complexes. The resulting precipitated DNA was amplified by adaptor-mediated PCR(Cawley et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116(4): 499-509) and then fragmented to 50-150 bp by DNase I (Epicentre) in One-Phor-All buffer (Pharmacia). The distribution of fragmented DNA size was verified on a 2% agarose gel.

treatment_protocol: S2 cells were transfected with pMT-Flag-cwo (1.9 ug) or pMT-Flag (1.9 ug) and pCoHygro (0.1 ug, Invitrogen, for selection) using Effectene (QIAGEN) according to the manufacturer’s instructions. Hygromycin-B (300 ug /ml final concentration, Invitrogen) was added 5 days after transfection. After 3 weeks, the established stable cell lines were used for the ChIP assay. 4×10^7 cells were collected and stimulated by copper sulfate to induce fusion genes.

tag: Cultured Drosophila S2 cells


title: Nasal Epithelium Instilation Formaldehyde 0mM 6h ID355


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 19d ID233

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 19 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 19d ID234


title: ChIP-Chip with anti-V5 antibody, replicate 2 of 2.

description: Data from the chromatin immunoprecipitation with anti-V5 antibody on Drosophila genome tiling array. Replicate no.2 of 2 (Independent sampling).


title: ChIP-Chip with anti-Flag antibody, replicate 2 of 2.

description: Data from the chromatin immunoprecipitation with anti-Flag antibody on Drosophila genome tiling array. Replicate no. 2 of 2 (Independent sampling).


title: Nasal Epithelium Inhalation Formaldehyde 15ppm 6h ID342


title: Nasal Epithelium Inhalation Formaldehyde 15ppm 6h ID341


title: Nasal Epithelium Inhalation Formaldehyde 15ppm 6h ID338


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID216

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 5 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID215


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID212

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hrs per day, 24 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 19d ID232


title: Nasal Epithelium Inhalation Formaldehyde 0ppm 6h ID321


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 19d ID230


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID211


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 6h ID209

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 6h ID206


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 6h ID207


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID213


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID219


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 6h ID205


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID217


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 5d ID218


title: Nasal Epithelium Instilation Formaldehyde 400mM 6h ID374

description:
Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde instilation exposure, 400 mM formaldehyde, single exposure, 6 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Vehicle for Chemical: Water, Amount of Vehicle: 40, Route of Exposure: Instillation (nasal), Units of Amount of Vehicle: ul per nostril, Dose or Concentration: 400, Units of Dose or Concentration: mM


title: Nasal Epithelium Instilation Formaldehyde 400mM 6h ID369


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 19d ID308

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 19 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 8d ID222

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 8 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm


title: pst1-1_vs_WT_4

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, pst1-1 mutant versus wild type expression replicate 4

hyb_protocol: 500 ng of Cy3 labeled cDNA was mixed with 500 ng of Cy5 labeled cDNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted with Agilent Feature Extraction software version 8.1.1.1 and analyzed with the Genespring software.

data_processing: Log ratios of pst1-1 mutant over wild type were obtained by dividing median Cy3 value over its corrresponding normalized Cy5 value

source_name: Schizosaccharomyces pombe pst1-1 mutant RNA

label_protocol: 26 ug total RNA were reverse-transcribed by Invitrogen Superscript Indirect cDNA Labeling System incorporating amino-allyl dUTP. Purified cDNA was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled cDNA was purified by Invitrogen SNAP column.

growth_protocol: Asynchronous growing fission yeast cells at 30 C

extract_protocol: total RNA isolated from asynchronous growing fission yeast cells at 30 C by Epicentre MasterPure Yeast RNA Purification Kit.

tag: cDNA reverse transcribed from total RNA isolated from pst1-1 mutant Schizosaccharomyces pombe cells

source_name: Schizosaccharomyces pombe wild type RNA

label_protocol: 26 ug total RNA were reverse-transcribed by Invitrogen Superscript Indirect cDNA Labeling System incorporating amino-allyl dUTP. Purified cDNA was covalently coupled with Cy5 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled cDNA was purified by Invitrogen SNAP column.

tag: cDNA reverse transcribed from total RNA isolated from wild type Schizosaccharomyces pombe cells


title: ChIP-Chip with anti-Flag antibody, replicate 1 of 2.

description: Data from the chromatin immunoprecipitation with anti-Flag antibody on Drosophila genome tiling array. Replicate no.1 of 2 (Independent sampling).


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 8d ID221

tag: Ratio

tag: Dilution


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 24h ID214

tag: RNA Integrity Number

tag: Bioanalyzer Results


title: pst1-1_vs_WT_3

description: Schizosaccharomyces pombe cells, pst1-1 mutant versus wild type expression replicate 3


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 8d ID220

tag: Sample Preservation

tag: Strain or Line


title: pst1-1_vs_WT_2

description: Schizosaccharomyces pombe cells, pst1-1 mutant versus wild type expression replicate 2

data_processing: Log ratios of pst1-1 mutant over wild type were obtained by dividing median Cy5 value over its corrresponding normalized Cy3 value


title: Nasal Epithelium Instilation Formaldehyde 400mM 6h ID372

tag: NCBI Taxonomy ID

tag: Individual


title: clr6-1_vs_WT_3

description: Schizosaccharomyces pombe cells, clr6-1 mutant versus wild type expression replicate 3

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted with Agilent Feature Extraction software version A7.5.1 and analyzed with the Genespring software.

data_processing: Log ratios of clr6-1 mutant over wild type were obtained by dividing median Cy3 value over its corrresponding normalized Cy5 value

source_name: Schizosaccharomyces pombe clr6-1 mutant RNA

tag: cDNA reverse transcribed from total RNA isolated from clr6-1 mutant Schizosaccharomyces pombe cells


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 24h ID292

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hrs per day, 24 h time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

tag: Developmental State

tag: Sacrifice Method

tag: Sex


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 24h ID290

tag: Array Type

tag: Amount to Core

tag: Units of Age


title: clr6-1_vs_WT_2

description: Schizosaccharomyces pombe cells, clr6-1 mutant versus wild type expression replicate 2

data_processing: Log ratios of clr6-1 mutant over wild type were obtained by dividing median Cy5 value over its corrresponding normalized Cy3 value


title: Nasal Epithelium Inhalation Formaldehyde 2ppm 8d ID223

tag: Units of Amount


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 24h ID288


title: clr6-1_vs_WT_4

description: Schizosaccharomyces pombe cells, clr6-1 mutant versus wild type expression replicate 4

tag: cDNA reverse transcribed from total RNA isolated from wild type Schizosaccharomyces pombe cells


title: pst1-1_vs_WT_1

description: Schizosaccharomyces pombe cells, pst1-1 mutant versus wild type expression replicate 1

tag: cDNA reverse transcribed from total RNA isolated from pst1-1 mutant Schizosaccharomyces pombe cells


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 24h ID289

tag: Ratio

tag: Dilution


title: Nasal Epithelium Instilation Formaldehyde 400mM 6h ID365

tag: RNA Integrity Number

tag: Bioanalyzer Results


title: clr6-1_vs_WT_1

description: Schizosaccharomyces pombe cells, clr6-1 mutant versus wild type expression replicate 1


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 19d ID312

tag: Sample Preservation

tag: Strain or Line


title: alp13D_vs_WT_4

description: Schizosaccharomyces pombe cells, alp13 null versus wild type expression replicate 4

data_processing: Log ratios of alp13 null over wild type were obtained by dividing median Cy3 value over its corrresponding normalized Cy5 value

source_name: Schizosaccharomyces pombe alp13 null RNA

tag: cDNA reverse transcribed from total RNA isolated from alp13 null Schizosaccharomyces pombe cells


title: alp13D_vs_WT_3

description: Schizosaccharomyces pombe cells, alp13 null versus wild type expression replicate 3


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 19d ID310

tag: NCBI Taxonomy ID

tag: Individual


title: Mouse ileum with L.innocua(hly)_B_5556

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

hyb_protocol: Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

scan_protocol: Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

data_processing: MAS5; scaling = 500

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.innocua(hly)_B_5556

label_protocol: In vitro transcription (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) was performed on cRNA derived from 40ug total RNA followed by standard fragmentation.  For detailed protocol see http://pathimm.wustl.edu/~mgacore/protocols.htm

extract_protocol: RNA was purified from ileum of each mouse [Midi RNeasy kit (Qiagen) with on-column DNase digestion]. Equivalent amounts of RNA from mice in each treatment group (n=4/experiment) were pooled and two biotinylated cRNA targets (40 ug/replicate) were independently prepared from each sample.

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.innocua(hly)_B_5556


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 6h ID284

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hour time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

tag: Developmental State

tag: Sacrifice Method

tag: Sex


title: Mouse ileum with L.innocua(inlA)_B_5558

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.innocua(inlA)_B_5558

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.innocua(inlA)_B_5558


title: Mouse ileum with B.thetaiotaomicron_B_5560

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with B.thetaiotaomicron_B_5560

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with B.thetaiotaomicron_B_5560


title: Mouse ileum with L.innocua(inlA)_A_5557

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.innocua(inlA)_A_5557

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.innocua(inlA)_A_5557


title: K9me2_2_control wt

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, control wt replicate 2

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked at 18C with paraformaldehyde for 30 minutes

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformaldehyde at 18C for 30 minutes

tag: Chromatin DNA isolated from paraformaldehyde cross-linked control wt Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID294

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 5 day time point

treatment_protocol: in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

tag: Array Type

tag: Amount to Core

tag: Units of Amount

tag: Ratio

tag: Units of Age


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 19d ID309

description:
Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 19 day time point

tag: Dilution

tag: RNA Integrity Number

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line


title: Mouse ileum with L.innocua(hly)_A_5555

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.innocua(hly)_A_5555

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.innocua(hly)_A_5555


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 6h ID286

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

tag: Sacrifice Method


title: K9me2_1_alp13D rrp6D

description: Schizosaccharomyces pombe cells, K9me2 ChIP(chromatin immunoprecipitation)-on-chip, alp13 rrp6 double mutant replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked alp13 rrp6 double mutant Schizosaccharomyces pombe cells and enriched for K9me2 chromatin with anti-dimethyl H3K9 (07-441, Upstate) antibody.


title: alp13D_vs_WT_1

description: Schizosaccharomyces pombe cells, alp13 null versus wild type expression replicate 1

data_processing: Log ratios of alp13 null over wild type were obtained by dividing median Cy5 value over its corrresponding normalized Cy3 value

tag: cDNA reverse transcribed from total RNA isolated from wild type Schizosaccharomyces pombe cells

tag: cDNA reverse transcribed from total RNA isolated from alp13 null Schizosaccharomyces pombe cells


title: Mouse ileum Germ-free_B_5554

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- Germ-free_B_5554

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_Germ-free_B_5554


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 6h ID283

tag: Array Type

tag: Amount to Core

tag: Units of Amount

tag: Sex


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID297

tag: Ratio

tag: Dilution

tag: RNA Integrity Number

tag: Units of Age


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID296

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line


title: Nasal Epithelium Inhalation Formaldehyde 6ppm 5d ID293

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State