title: Brn3a Wildtype DRG e13.5 430A v2.0 replicate

tag: Brn3a wildtype dorsal root ganglia pooled from e13.5 mouse embryos.


title: Cornea Sample 2

status: Public on Feb 10 2007

type: RNA

city: New York

first: Jose

middle: Mario

last: Wolosin

state: NY

address: 1 Gustave L. Levy Place

department: Ophthalmology

country: USA

institute: Mount Sinai School of Medicine

description: Standard Affymetrix protocols performed

hyb_protocol: Hybridization cocktail made according to Affymetrix protocols. Heated to 99C and then heat block for 5 mins at 45oC. Incubate probe array with 1X hybridization buffer (MES, 1M [Na], 20mM EDTA, 0.01% Tween) for 10 mins 45oC. Hybridize for 16 h 45oC using final volume of 200ul. For washing use GeneChip Fluidics Station 450 using fluidics protocol EukGE-WS2v4. Hybridized microarrays were stained with a strepavidin-phycoerythrin (SAPE) reagent.

scan_protocol: Hybridized microarrays were stained with a strepavidin-phycoerythrin (SAPE) reagent and fluorescence images were captured using an Agilent G2500A laser scanner.

data_processing: Microarray Analysis Suite, version 5.0 (MAS 5.0; Affymetrix)

label: Biotin-labled cRNA

molecule: total RNA

organism: Homo sapiens

source_name: Fresh human cornea

label_protocol: Biotin labeled cRNA using the ENZO RNA transcript labeling Kit 9 (BioArray High Yeald Labeling Kit, P/N 900182). IVT cRNA cleanup and quantitation, cRNA fragmentation, control targets performed according to Affymetrix protocols. Synthesis of cDNA using T7-(dT)24 Primer (Genset Corp) and Superscript Choice System (Gibco BRL Life technologies).

growth_protocol: N/A Fresh tissue

extract_protocol: Epithelial sheets were manually transferred from the Dispase solution directly into lysis buffer, total RNA was isolated using the RNeasy minikit (Qiagen Inc., Valencia, CA) and was further purified using RNeasy (Qiagen) spin columns. RNA was suspended in RNase-Free water at a concentration of 1.5 ug/ul

treatment_protocol: None. Fresh tissue from donor, post mortem

tag: This sample comprises of RNA isolated from human cornea pooled from a mixed population of (age, sex and cause of death identified). Tissue was send to us by the National Disease Resource Center (NDRI); http://www.ndriresource.org/


title: Hoxb1a-deficient r4 Replicate 3

status: Public on Jan 01 2007

city: Chicago

first: Victoria

middle: Emma

last: Prince

state: IL

department: Organismal Biology & Anatomy

institute: University of Chicago

hyb_protocol: Biotin-labeled cRNA, 10 µg of each target was used for hybridization on each KCC/TJU 17K Zebrafish oligo expression microarray on a TECAN HS4800 Hybridization Station. The microarrays were hybridized in 6X SSPE with 50% formamide at 37°C for 20 hours, washed in 0.75X TNT at 46 degC for 1 hour, followed by blocking in TNB at RT for 30 min., and then processed by using direct detection method of the biotin-containing transcripts by Streptavidin-Alexa 647 conjugate in TNB buffer (1:500) at RT for 30 min. Stained chips were washed in 1X TNT wash buffer at room temperature for 60 minutes with changing fresh TNT buffer every 15 minutes.

scan_protocol: Processed chips were scanned by using a Perkin Elmer ScanArray XL5000 Scanner, software version 3.1 with the laser set to 635 nm, at power 90 and PMT 70-50 setting (see tiff files), and a scan resolution of 10 microns. Images were quantified by PerkinElmer QuantArray Software 3.0. Quantitation method used was fixed circle and quantification output were total intensities. Confidence calculation was weighted average.

data_processing: Raw data were normalized and analyzed using GeneSprin software (Version 7.2). After data transformation (to convert any negative to 0.01), normalization was performed by using a per-chip 50th percentile method that normalizes each chip on its median, allowing comparison among chips.

label: Biotin

organism: Danio rerio

source_name: Danio rerio embryonic hindbrain

label_protocol: RNA was amplified and labelled using the Arcturus RiboAmp HS RNA Amplification Kit according to manufacturer's protocol, including biotin-labeling of aRNA (Appendix F) using BioArray HighYield RNA Transcript Labeling Kit [Affymetrix].

extract_protocol: RNA was extracted using a modification of the manufacturer's instructions for the Arcturus PicoPure RNA Isolation Kit: RNA Extraction from Cell Pellets.  The tissue in 50μl solution XB was incubated at 42 degC for 30 minutes, centrifuged at 3000 x g for 2 minutes, the supernatant transferred to a clean tube, and 50μl EtOH added.  The RNA Isolation was carried out according to the manufacturer's protocol, including the optional DNAse treatment from Appendix A.

treatment_protocol:
Rhombomere 4 was dissected from Hoxb1a-deficient (Morpholino injected; McClintock et al. Development. 2002. 129:2339-54.) islet-1 GFP transgenic zebrafish embryos embryos at 19-20 hpf.
8-10 embryos were dechorionated and placed in Ca/Mg-free PBS with tricaine, hindbrain tissue was dissected to produce a thick transverse section that encompassed the rhombomere of interest.  Tissue was dissociated in Ca/Mg-free PBS supplemented with 0.025% trypsin by brief trituration followed by addition of fetal calf serum.

tag: Strain

value: islet1-GFP transgenics

tag: Stage

value: 19-20 hour post fertilization embryos

tag: Tissue

value: Hindbrain rhombomere 4


title: Normal r2 replicate 3b

treatment_protocol:
Rhombomere 2 was dissected from untreated islet-1 GFP transgenic zebrafish embryos embryos at 19-20 hpf.
8-10 embryos were dechorionated and placed in Ca/Mg-free PBS with tricaine, hindbrain tissue was dissected to produce a thick transverse section that encompassed the rhombomere of interest.  Tissue was dissociated in Ca/Mg-free PBS supplemented with 0.025% trypsin by brief trituration followed by addition of fetal calf serum.

value: Hindbrain rhombomere 2


title: Conjunctiva Sample 1

description: This data was collected approx. 2 years ago. Affymetrix protocols described.

label: Biotin-labeled cRNA

source_name: Fresh Human Conjunctiva

growth_protocol: N/A. Fresh tissue

tag: This sample comprises of RNA isolated from human conjunctivae pooled from a mixed population of (age, sex and cause of death identified). Only Tissue was send to us by the National Disease Resource Center (NDRI).


title: Hoxb1a-deficient r4 Replicate 2

hyb_protocol: Biotin-labeled cRNA, 10 µg of each target was used for hybridization on each KCC/TJU 17K Zebrafish oligo expression microarray on a TECAN HS4800 Hybridization Station. The microarrays were hybridized in 6X SSPE with 50% formamide at 37°C for 20 hours, washed in 0.75X TNT at 46°C for 1 hour, followed by blocking in TNB at RT for 30 min., and then processed by using direct detection method of the biotin-containing transcripts by Streptavidin-Alexa 647 conjugate in TNB buffer (1:500) at RT for 30 min. Stained chips were washed in 1X TNT wash buffer at room temperature for 60 minutes with changing fresh TNT buffer every 15 minutes.

scan_protocol: Processed chips were scanned by using a Perkin Elmer ScanArray® XL5000 Scanner, software version 3.1 with the laser set to 635 nm, at power 90 and PMT 70-50 setting (see tiff files), and a scan resolution of 10 microns. Images were quantified by PerkinElmer QuantArray® Software 3.0. Quantitation method used was fixed circle and quantification output were total intensities. Confidence calculation was weighted average.

extract_protocol: RNA was extracted using a modification of the manufacturer's instructions for the Arcturus PicoPure RNA Isolation Kit: RNA Extraction from Cell Pellets.  The tissue in 50μl solution XB was incubated at 42°C for 30 minutes, centrifuged at 3000 x g for 2 minutes, the supernatant transferred to a clean tube, and 50μl EtOH added.  The RNA Isolation was carried out according to the manufacturer's protocol, including the optional DNAse treatment from Appendix A.

value: Hindbrain rhombomere 4 from Hoxb1a-defient embryo


title: Normal r4 Replicate 3

treatment_protocol:
Rhombomere 4 was dissected from untreated islet-1 GFP transgenic zebrafish embryos embryos at 19-20 hpf.
8-10 embryos were dechorionated and placed in Ca/Mg-free PBS with tricaine, hindbrain tissue was dissected to produce a thick transverse section that encompassed the rhombomere of interest.  Tissue was dissociated in Ca/Mg-free PBS supplemented with 0.025% trypsin by brief trituration followed by addition of fetal calf serum.

tag: Organism

value: Zebrafish (Danio rerio)


title: Normal r2 replicate 3a


title: Brn3a Knockout DRG e13.5 430A v2.0 replicate

status: Public on Jan 28 2007

city: La Jolla

first: Eric

last: Turner

state: CA

address: 9500 Gilman Dr., BSB 2077

department: Psychiatry

institute: University of California San Diego

description: Approximately 10 pairs of the most anterior dorsal root ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until sufficient tissue was harvested to be pooled by genotype. Ganglia from 5 embryos were pooled for a single analysis and RNA extracted using the RNeasy system (Qiagen).

data_processing: Gene Chip Operating Software

label: Affymetrix

organism: Mus musculus

source_name: e13.5 Dorsal Root Ganglia

tag: Brn3a mutant dorsal root ganglia pooled from e13.5 mouse embryos.


title: Normal r4 Replicate 1

treatment_protocol:
Rhombomere 4 was dissected from untreated islet-1 GFP transgenic zebrafish embryos embryos at 19-20 hpf.
8-10 embryos were dechorionated and placed in Ca/Mg-free PBS with tricaine, hindbrain tissue was dissected to produce a thick transverse section that encompassed the rhombomere of interest.  Tissue was dissociated in Ca/Mg-free PBS
supplemented with 0.025% trypsin by brief trituration followed by addition of fetal calf serum.


title: Conjunctiva Sample 3

description: Standard Affymetrix protocols performed

tag: This sample comprises of RNA isolated from human conjunctivae pooled from a mixed population of (age, sex and cause of death identified). Tissue was send to us by the National Disease Resource Center (NDRI); http://www.ndriresource.org/


title: Cornea Sample 3

description: Standard Affymetrix protocols performed


title: Normal r4 replicate 2


title: Normal r2 replicate 2

tag: Rhombomere 2 was dissected from untreated islet-1 GFP transgenic zebrafish embryos embryos at 19-20 hpf.


title: Brn3a Heterozygote DRG e13.5 430A v2.0

tag: Brn3a heterozygote dorsal root ganglia pooled from e13.5 mouse embryos.


title: slr0473_WT_1

city: Meguro

first: Mitsunori

last: Katayama

state: Tokyo

address: 3-8-1 Komaba

country: Japan

institute: University of Tokyo

description: 16S and 23S rRNA data was excluded from the analysis.

hyb_protocol: 65oC, overnight

scan_protocol: ScanArray 4000 (PerkinElmer, Inc., MA, USA)

data_processing: Signal of each individual spot was subtracted by background (average signal of corners of each spot) and divided by average value of all spot.

organism: Synechocystis sp. PCC 6803

source_name: slr0473 mutant

label_protocol: RNA Fluorescence labeling core kit, M-MLV version Ver.2.0 (Takara Bio Inc.)

growth_protocol: 0.5% CO2 at 30oC in BG-11

extract_protocol: RNeasy midi kit (Qiagen)

tag: slr1473 mutant

source_name: Wild type strain

tag: Wild type strain


title: slr1805_WT_2

source_name: slr1805 mutant

tag: slr1805 mutant


title: slr1212_WT_2

source_name: slr1212 mutant

tag: slr1212 mutant


title: Hoxb1a-deficient r4 Replicate 1

treatment_protocol:
Rhombomere 4 was dissected from Hoxb1a-deficient (Morpholino injected; McClintock et al. Development. 2002. 129:2339-54.) islet-1 GFP transgenic zebrafish embryos embryos at 19-20 hpf.
8-10 embryos were dechorionated and placed in Ca/Mg-free PBS with tricaine, hindbrain tissue was dissected to produce a thick transverse section that encompassed the rhombomere of interest.  Tissue was dissociated in Ca/Mg-free PBS
supplemented with 0.025% trypsin by brief trituration followed by addition of fetal calf serum.

value: Hindbrain rhombomere 4 from Hoxb1a-deficient embryo


title: TIP-chip hybridization with L27-10, #3

type: genomic

city: Baltimore

first: Sarah

last: Wheelan

state: MD

address: 550 N. Broadway

department: Oncology

institute: Johns Hopkins University School of Medicine

description: See above.

hyb_protocol: The microarrays were hybridized overnight in a humid chamber at 65C. We use a fishing tackle box with six compartments, each of which perfectly fits one slide, and we put damp paper towels in the unused compartments. The whole box is then wrapped in damp paper towels and sealed inside a large plastic bag. Finally, we wrap everything in a paper cloth backed with blue plastic, so that the hybridization is done in the dark. In the morning, the arrays were washed in 2x SSC, 0.03% SDS for 5 minutes at 65C (we pre pare the first wash solution the night before and place it in the hybridization chamber all night to achieve this temperature), then in 1x SSC for 5 minutes at room temperature, and finally in 0.2x SSC for 5 minutes at room temperature. All washes are done in 50mL conical ubes and are done with agitation; we blot the sides and backs of the arrays between washes.

data_processing: The VALUE provided is simply the log (base 2) of the subtracted intensity; we did a complicated analysis of this data that did not require normalization and do not think it is appropriate to normalize it here. GPR files and the code necessary to repeat our analysis is available upon request.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Ty1 high-copy yeast strain

label_protocol: The genomic DNA fragments were pooled and digested in three parallel reactions with MseI, MspI, and HpyCH4V for one hour at 37 C. The fragments were heat inactivated at 65C for 20 min, pooled and labeled for use on the microarray as follows: 200 ng DNA was incubated with 36 microg random hexamer in a 23 microl reaction at 100C for 2 minutes, then 4C for 4 minutes. The labeling reaction then proceeded with the addition of 5 microl 10x dNTP (8 mM dATP, dCTP, dGTP, 4 mM dUTP), 5 microl 10x Klenow buffer, 7 microl Klenow large fragment (5U/microl), 7 microl H2O, and 2 microl Cy5 dUTP, and incubation at 37C for 2 hours. The reaction was stopped with 5 microl 0.5 M EDTA pH 8.0. The products were purified with 450 microl TE and concentrated on a Microcon column (Amicon): after adding TE to the reaction, the reaction was decanted into a Microcon column, spun for 10 minutes at 8000g, then the column was inverted on a new tube and spun for 1 minute at 8000g. The products were washed again with 450 microl TE and 10 microl sheared salmon sperm DNA (10 mg/ml), and concentrated again on a Microcon column, as before except spinning for 15 minutes instead of 10. The resulting volume was adjusted to 26 microl with the addition of H2O, and SDS and SSC were added to final concentrations of 3X SSC and 0.3% SDS, in a total volume of 32.5 microl. After incubation at 100C for 90 seconds and 37C for 30 minutes, the products were spotted onto microarrays and covered with coverslips.

extract_protocol: described in detail in Yuan et al (PubMed ID 15994458)

tag: L27-10 was derived from GRF167 after undergoing ten cycles of Ty1 retrotransposition, so that it is identical to GRF167 exctept for numberous additional copies of Ty1 elements in its genome (PubMed ID 1664403).


title: TIP-chip hybridization with L27-10, #2

description: See above.


title: Brn3a Wildtype DRG e13.5 430A v2.0


title: TIP-chip hybridization with FY2, #2

description: See above.

source_name: control for S288C comparison

tag: See PubMed ID 9483801 (BY4743) for a complete description of the strain background. Basically, this strain is derived from S288C and for our purposes differs from S288C in that it harbors some extra Ty1 elements.


title: TIP-Chip hybridization with GRF167, #2

description: See above.

tag: GRF167, a strain related to S288C but MAT-alpha, ura3-167, his3(delta)200


title: TIP-chip hybridization with L27-10, #1

description: See above.


title: CTCF-IMR90 Nimblegen Nimblegen Condensed array of hg17 v1.0

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using monoclonal antibodies against CTCF and formaldehyde crosslinked chromatin from primary human fibroblast, IMR90 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a condensed array 742,156 oligonucleotides to represent the 15,221 putative CTCF binding sequences plus 44 ENCODE regions, each ranging in size from 500 Kbp to 1.9 Mbp at 100 bp resolution. Each of the 15,221 binding sites were extended at both ends by 2.5 Kbp upstream and downstream of the site.

data_processing: raw data

source_name: Chromatin immunoprecipitated DNA from IMR90 cells using CTCF antibody

tag: cells

source_name: input chromatin DNA


title: U937_NONE_CTCF_ENC13152512

description: For the PCR genome tiling ENCODE arrays, three independent CTCF ChIP-on-chip experiments were performed with U937 chromatin.

data_processing: The resulting array data were normalized by intensity-dependent loess (Dudoit et al.) and averaged, and probability statistics was calculated for each probe based on a single-error model described previously (Li et al., 2003).  A stringent statistical threshold (P<1X10-6) was set to obtain a similar number of CTCF binding sites as detected in IMR90 cells to facilitate comparison between the two cell types.  The resulting list of target sites were converted to NCBI35 (hg17) build of the human genome using the batch liftOver function available from the UCSC genome browser (Kent et al., 2002).  A total of 257 CTCF binding sites were identified within the ENCODE region in U937 cells.

source_name: Chromatin immunoprecipitated DNA from U937 cells using CTCF antibody


title: U937_NONE_CTCF_ENC13152631


title: TIP-chip hybridization with GRF167, #1

description: See above.

source_name: control for comparison to L27-10 Ty1 high copy strain


title: TIP-chip hybridization with FY2, #1

description: See above.


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 18 of 38

description: Chromatin immunoprecipitation was performed using monoclonal antibodies against CTCF and formaldehyde crosslinked chromatin from primary human fibroblast, IMR90 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 33 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 20 of 38


title: U937_NONE_CTCF_ENC12855092


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 01 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 07 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 30 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 19 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 09 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 37 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 17 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 32 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 34 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 08 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 36 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 21 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 06 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 14 of 38


title: Mouse_Retina_P7_Rs1h_KO 2

status: Public on Dec 31 2006

city: Regensburg

first: Bernhard

last: Weber

address: Franz-Josef-Strauss-Allee 11

country: Germany

institute: Institute of Human Genetics, University of Regensburg

description: Standard Affymetrix Protocol

source_name: Mouse Retina at P7

extract_protocol: Qiagen RNeasy Kit

treatment_protocol: Retina extraction

tag: Strain

value: C57BL/6 Rs1h knockout P7


title: Mouse_Retina_P7_Rs1h_KO 3

description: Standard Affymetrix Protocol


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 28 of 38


title: Mouse_Retina_P7_Control 2

description: Standard Affymetrix Protocol

value: C57BL/6 wildtype P7


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 02 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 26 of 38


title: Mouse_Retina_P7_Rs1h_KO 1

description: Standard Affymetrix Protocol


title: Mouse_Retina_P7_Control 3

description: Standard Affymetrix Protocol


title: Mouse_Retina_P7_Control 1

description: Standard Affymetrix Protocol

value: C57BL/6 wildtype


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 16 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 04 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 12 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 27 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 25 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 35 of 38


title: eosinophils_activation_signature

status: Public on Dec 30 2006

city: San Francisco

first: David

last: Voehringer

address: 521, Parnassus Ave

department: Medicine, Infectious diseases

institute: HHMI

description: Activated eosinophils isolated from the lung of parasite infected mice were compared to resting eosinophils isolated from the spleen of IL-5 transgenic mice to identify genes associated with the activation of eosinophils in vivo.

hyb_protocol: protocol can be found here: http://arrays.ucsf.edu/protocols/cdna_transcription_and_coupling.pdf

scan_protocol: Axon scanner 3000B

data_processing: data was normalized using the lowess normalization without background subtraction.

source_name: eosinophils isolated from the spleen of IL-5tg mice

label_protocol: amplified RNA was labeled with Cy3 reactive dye from Amersham Pharmacia.

extract_protocol: Total RNA was isolated using the Fluka Total RNA isolation kit. RNA was then amplified using the aminoallyl mRNA amplification kit from Ambion.

value: IL-4 reporter mice (4get mice) crossed with IL-5 transgenic mice (NJ.1638) on BALB/c background.

value: sorted CCR3+ eosinophils from the spleen of 4-6 week old mice.

source_name: eosinophils isolated from the lung of N. brasiliensis infected mice

label_protocol: amplified RNA was labeled with Cy5 reactive dye from Amersham Pharmacia.

value: IL-4 reporter mice (4get mice) on BALB/c background.

value: Single cell suspension of total lung tissue isolated on day 9 after Nippostrongylus brasiliensis infection. Eosinophils were sorted on a MoFlo high speed cell sorter.


title: eosinophil_maturation_signature

description: Immature (CCR3-) and mature (CCR3+) eosinophils were isolated from the bone marrow and the gene expression profile was compared to identify gene associated with the maturation of eosinophils

source_name: CCR3- sorted eosinophils from the bone marrow

treatment_protocol: CCR3- eosinophils were isolated from the bone marrow by staining eosinophils for FIRE and CCR3 and sorting FIRE+CCR3- cells with a MoFlo high speed cell sorter (DAKO Cytomation).

tag: Age

value: 4-6 weeks old

value: bone marrow

source_name: CCR3+ sorted eosinophils from the bone marrow

treatment_protocol: CCR3+ eosinophils were isolated from the bone marrow by staining eosinophils for FIRE and CCR3 and sorting FIRE+CCR3+ cells with a MoFlo high speed cell sorter (DAKO Cytomation).


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 22 of 38


title: TIGR4 over-expression of RR06 rep 6

status: Public on Dec 17 2006

city: Adelaide

first: Alistair

last: Standish

address: North Terrace

department: School of Molecular and Biomedical Sciences

country: Australia

institute: University of Adelaide

description: Effect of over-expression of response regulator RR06 on gene expression in TIGR4 S. pneumoniae

hyb_protocol: As described in Genisphere Array 900 MPX Kit

scan_protocol: Axon GenePix 4000B scanner

data_processing: SPOT software

label: Alexa 555

organism: Streptococcus pneumoniae

label_protocol: Genisphere Array 900 MPX Kit

extract_protocol: Acid/Phenol.

tag: TIGR4 transformed with pLS1RGFP.

label: Alexa 647

extract_protocol: Acid/Phenol

tag: TIGR4 transformed with prr06


title: TIGR4 over-expression of RR06 rep 5

tag: TIGR4 transformed with prr06.


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 23 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 11 of 38


title: TIGR4 over-expression of RR06 rep 3


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 03 of 38


title: H3K4 trimethylation ChIP - wild-type replicate 2

status: Public on Dec 01 2006

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Genome-wide location analysis of H3K4 trimethylation in wild-type strain

hyb_protocol: 50 degrees C for 20-24 hours

scan_protocol: Scan Array software

data_processing: QuantArray software

source_name: WY171 (wild-type)

label_protocol: Genomic DNA was amplified by ligation-mediated PCR to produce Cy3-labeled DNA.

extract_protocol: Cells were grown to mid-log phase (OD600=0.4-0.5) in rich media (YPD) and crosslinked with formaldehyde.  Cells were lysed with glass beads and sonicated to generate 150-400 bp DNA fragments.  A sample of cross-linked DNA from the whole cell extract was treated to reverse the crosslinks and was PCR amplified by ligation-mediated PCR with Cy3 Dye.

tag: Whole Cell Extract DNA

label_protocol: Genomic DNA was amplified by ligation-mediated PCR to produce Cy5-labeled DNA.

extract_protocol: Cells were grown to mid-log phase (OD600=0.4-0.5) in rich media (YPD) and crosslinked with formaldehyde.  Cells were lysed with glass beads and sonicated to generate 150-400 bp DNA fragments.  Crosslinked DNA was immunoprecipitated with anti-histone H3 trimethyl K4 antibody.  Beads were washed, eluted and crosslinks were reversed.  DNA was precipitated and amplified by ligation-mediated PCR with Cy5 dye.

tag: Immunoprecipitated DNA


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 05 of 38


title: TIGR4 over-expression of RR06 rep 4


title: H3K4 trimethylation ChIP - wild-type replicate 1


title: TIGR4 over-expression of RR06 rep 2


title: vastus lateralis biopsy, 76 year-old trained COPD patient (male #40).

city: Irvine

first: Shlomit

last: Radom-Aizik

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

description:
Needle biopsies were obtained from the vastus lateralis muscle of 6 COPD patients,72±2 year-old males before and after 3 months of training.  RNA was extracted using Trizol. Targets were produced using standard Affymetrix procedures from about 4ug of total RNA.
Keywords = COPD, microarray, exercise, skeletal muscle, training effect

source_name: vastus lateralis biopsy


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 10 of 38


title: vastus lateralis biopsy, 76* year-old trained COPD patient (male #38).


title: vastus lateralis biopsy, 76* year-old sedentary COPD patient (male #7).


title: H3K4 trimethylation ChIP - ctk1 deletion replicate 1

description: Genome-wide location analysis of H3K4 trimethylation in ctk1 deletion strain

source_name: WY173 (ctk1 deletion)


title: H3K4 trimethylation ChIP - ctk1 deletion replicate 3


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 31 of 38


title: H3K4 trimethylation ChIP - ctk1 deletion replicate 2


title: vastus lateralis biopsy, 76 year-old sedentary COPD patient (male #13).


title: vastus lateralis biopsy, 71 year-old trained COPD patient (male #35).


title: TIGR4 over-expression of RR06 rep 1


title: vastus lateralis biopsy, 71 year-old sedentary COPD patient (male #1).


title: H3K4 trimethylation ChIP - wild-type replicate 3


title: vastus lateralis biopsy, 80 year-old trained COPD patient (male #42).


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 15 of 38


title: vastus lateralis biopsy, 80 year-old sedentary COPD patient (male #24).


title: vastus lateralis biopsy, 65 year-old trained COPD patient (male #76).


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 24 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 13 of 38


title: vastus lateralis biopsy, 63 year-old trained COPD patient (male #64).


title: vastus lateralis biopsy,65 year-old sedentary COPD patient (male #48).


title: vastus lateralis biopsy,63 year-old sedentary COPD patient (male #20).


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 29 of 38


title: CTCF-IMR90 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 38 of 38


title: H3K4me3 in WT ChIP chip replicate 3

status: Public on Nov 01 2006

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

description: Replicate 3 _array 098

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysi

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median normalized

source_name: Genomic DNA

label_protocol: Genomic DNA was labeled using Cy3

growth_protocol: BY4741 strain cells were grown to OD of 0.8-1, fixed and DNA was purified after reversing crosslinks

tag: Genomic DNA

source_name: H3K4me3 ChIP DNA in WT

tag: ChIP DNA


title: H3K4me3 in WT ChIP chip replicate 2

description: Replicate 2 _array 033


title: H3K4me3 in WT ChIP chip replicate 1

description: Replicate 1 _array 093


title: H3K4me3 in Ctk1deletion ChIP chip replicate 3

description: Replicate 3 _array 090

source_name: Ctk1deletion Genomic DNA

tag: Ctk1deletion Genomic DNA

source_name: H3K4me3 ChIP DNA in Ctk1deletion


title: H3 in Ctk1deletion ChIP chip replicate 1

description: Replicate 1 _array 050

source_name: H3 ChIP DNA in Ctk2deletion


title: H3 in Ctk1deletion ChIP chip replicate 2

description: Replicate 2 _array 062


title: H3K36Ac in WT vs genomic DNA replicate 1

description: Replicate 1 _array 088

source_name: H3K36Ac in WT ChIP DNA


title: H3K4me3 in Ctk1deletion ChIP chip replicate 2

description: Replicate 2 _array 081


title: H3K36Ac in WT vs H3K36Ac in K36A ChIP chip replicate 3

description: Replicate 3 _array 072

source_name: H3K36Ac in K36A ChIP DNA

label_protocol: ChIP DNA was labeled using Cy3


title: H3 in Ctk1deletion ChIP chip replicate 3

description: Replicate 3 _array 092


title: H3K4me3 in Ctk1deletion ChIP chip replicate 1

description: Replicate 1 _array 061


title: HE cells, poliovirus, 16h

status: Public on Oct 16 2006

city: Oslo

first: Bjorn

last: Grinde

state: Oslo

address: Geitmyrsveien 75

department: Infectious Disease Control

country: Norway

institute: Norwegian Institute of Public Health

description: Experiment to find the effect of poliovirus

data_processing: Quality control of the scanned images (tiff-files) and conversion to numerical values were performed using the GenePix Pro 4.1 (Axon Instruments). The gpr-files obtained were further analyzed using J-Express pro2.7 (http://www.molmine.com). Mean FG intensities were used as input values. Spots with less than 60 % of the pixels (in either Cy5 or Cy3) below background + 2 SD were removed. Controls as well as flagged or empty spots were also filtered away before Global Lowess Normalization. Further quality control was performed using the various Plot and Spot Image View options in J-Express. Reporters for which at least two of the three parallels complied with the above filtering were considered expressed, and the relevant data transferred to Excel. The average ratios, as well as average red and green intensities, for the three parallels were calculated.

source_name: Human embryonic fibroblasts incubated for 16 h with poliovirus

tag: The cells were synchronously infected with enough virus to infect a majority of the cells

source_name: Control cells

tag: Mock infected cells incubated for 16h


title: H3K36Ac vs H3 ChIP chip replicate 4

description: Replicate 4 _array 060

source_name: H3 ChIP DNA

source_name: H3K36Ac ChIP DNA


title: H3K36Ac vs H3 ChIP chip replicate 2

description: Replicate 2 _array 016


title: HE cells, interferon+poliovirus, 16h

source_name: Human embryonic fibroblasts incubated for 16 h with poliovirus and intereferon-alpha

tag: Cells synchronously infected with enough virus to infect a majority of the cells

tag: Mock infected cells


title: H3K36Ac in WT vs genomic DNA replicate 2

description: Replicate 2 _array 023


title: Bacteriophage BFK 20 gene expression - 120 min vs. 0 min

status: Public on Oct 13 2006

city: Bratislava 45

first: Tomas

last: Majtan

address: Dubravska cesta 21

department: Department of Molecular Genomics

country: Slovakia

institute: Institute of Molecular Biology SAS

description: Gene expression microarray analysis of bacteriophage BFK 20 during host infection

data_processing: background subtracted, flagged values adjusted to 1, normalized according to controls, without between-array transformation according to proposed loop

organism: Corynebacterium phage BFK20

source_name: 0 min post infection

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 0 min post infection

source_name: 120 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 120 min post infection


title: Bacteriophage BFK 20 gene expression - 80 min vs. 120 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 120 min post infection

source_name: 80 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 80 min post infection


title: HE cells, vacciniavirus, 4h

description: Experiment to find the effect of vacciniavirus

source_name: Human embryonic fibroblasts incubated for 4 h with vacciniavirus

tag: Cells synchronously infected with enough virus to infect a majority of cells


title: H3K9K14Ac vs H3K36me2 ChIP chip replicate 3

description: Replicate 3 _array 106

source_name: H3K36me2 ChIP DNA

source_name: H3K9K14Ac ChIP DNA


title: H3K36Ac in WT vs H3K36Ac in K36A ChIP chip replicate 2

description: Replicate 2 _array 089


title: H3K36Ac in WT vs H3K36Ac in K36A ChIP chip replicate 1

description: Replicate 1 _array 043


title: H3K36Ac vs H3 ChIP chip replicate 3

description: Replicate 3 _array 019

growth_protocol: BY4741 strain cells were grown to OD of 0.8-1, fixed and DNA was purified after reversing crosslinks"


title: Bacteriophage BFK 20 gene expression - 60 min vs. 80 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 80 min post infection

source_name: 60 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 60 min post infection


title: HE cells, interferon, 16h

description: Experiment to find the effect of interferon-alpha

source_name: Human embryonic fibroblasts incubated with interferon-alpha

tag: HE cells incubated with interferon-alpha

tag: Controll cells incubated without interferon


title: H3K9K14Ac vs H3K36me2 ChIP chip replicate 2

description: Replicate 2 _array 105


title: HE cells, interferon, 8h

source_name: HE cells incubated with interferon

tag: Human embryonic fibroblasts incubated with interferon-alpha for 8h

tag: Control cells


title: Bacteriophage BFK 20 gene expression - 50 min vs. 60 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 60 min post infection

source_name: 50 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 50 min post infection


title: HE cells, poliovirus, 8h

source_name: Human embyronic fibroblasts incubated with poliovirus for 8h

tag: The cells were synchronously infected with enough virus to infect a majority of the cells.

tag: Mock infected cells incubated for 8h


title: H3K36Ac vs H3K36me2 ChIP chip replicate 2

description: Replicate 2 _array 049

scan_protocol: Fluorescent array images

data_processing: After background correc

label_protocol: ChIP DNA was labeled

growth_protocol: BY4741 strain cells

tag: ChIP DNA


title: HE cells, interferon+poliovirus, 8h

source_name: Human embryonic fibroblasts incubated for 8 h with both interferon-alpha and poliovirus

tag: Cells synchronously infected with poliovirus and given interferon


title: Bacteriophage BFK 20 gene expression - 40 min vs. 50 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 50 min post infection

source_name: 40 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 40 min post infection


title: Bacteriophage BFK 20 gene expression - 30 min vs. 40 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 40 min post infection

source_name: 30 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 30 min post infection


title: H3K36Ac in WT vs genomic DNA replicate 3

description: Replicate 3 _array 099

source_name: Genomic DNA

tag: Genomic DNA

source_name: H3K36Ac in WT ChIP DNA


title: H3K9K14Ac vs H3 ChIP chip replicate 1

description: Replicate 1 _array 015

source_name: H3 ChIP DNA


title: Bacteriophage BFK 20 gene expression - 20 min vs. 30 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 30 min post infection

source_name: 20 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 20 min post infection


title: H3K9K14Ac vs H3 ChIP chip replicate 2

description: Replicate 3 _array 054


title: Bacteriophage BFK 20 gene expression - 15 min vs. 20 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 20 min post infection

source_name: 15 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 15 min post infection


title: Bacteriophage BFK 20 gene expression - 10 min vs. 15 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 15 min post infection

source_name: 10 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 10 min post infection


title: H3K9K14Ac vs H3K36me2 ChIP chip replicate 1

description: Replicate 1 _array 063


title: Bacteriophage BFK 20 gene expression - 5 min vs. 7 min

source_name: 7 min post infection

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 7 min post infection

source_name: 5 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 5 min post infection


title: Bacteriophage BFK 20 gene expression - 3 min vs. 5 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 5 min post infection

source_name: 3 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 3 min post infection


title: Bacteriophage BFK 20 gene expression - 7 min vs. 10 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 10 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 7 min post infection


title: Bacteriophage BFK 20 gene expression - 0 min vs. 1 min

source_name: 1 min post infection

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 1 min post infection

source_name: 0 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 0 min post infection


title: Bacteriophage BFK 20 gene expression - 1 min vs. 3 min

tag: Cy5 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 3 min post infection

tag: Cy3 labeled cDNA generated from total RNA isolated from host Brevibacterium flavum CCM 251 after phage BFK 20 infection - 1 min post infection


title: skin_lesional atopic dermatitis skin_LAD5 (U133A)

status: Public on Oct 01 2006

city: Rochester

first: Douglas

middle: A

last: Plager

state: MN

address: 200 First Street SW

department: Dermatology

institute: Mayo Clinic Rochester

description: no additional information

hyb_protocol: Following fragmentation, cRNA was hybridized overnight at 45C on Affymetrix Human Genome U133A GeneChip.  GeneChips were washed and stained with phycoerythrin-labelled streptavidin in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) to quantify and scale the fluorescence data.

label: biotin

source_name: skin(dermis and epidermis)_mid arm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Not applicable

extract_protocol: see Materials and Methods section of DA Plager, AA Leontovich, et al. Experimental Dermatology 2006 article; Trizol extraction of total RNA followed by RNeasy clean-up of total RNA was performed according to the manufacturers' instructions.

treatment_protocol: see Materials and Methods section of DA Plager, AA Leontovich, et al. Experimental Dermatology 2006 article; all therapeutic treatments or confounding exposures were avoided

tag: Tissue:skin(dermis and epidermis)_Source:mid arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:lesional_Age:32years_Gender:female_Race:asian


title: skin_lesional atopic dermatitis skin_LAD4 (U133A)

description: no additional information

source_name: skin(dermis and epidermis)_upper back

tag: Tissue:skin(dermis and epidermis)_Source:upper back_Health status:atopic dermatitis_Disease Severity:severe_Skin status:lesional_Age:38years_Gender:male_Race:white


title: skin_lesional atopic dermatitis skin_LAD3 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:mid arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:lesional_Age:18years_Gender:male_Race:asian


title: skin_Lesional atopic dermatitis skin_LAD1 (U133A)

description: no additional information

source_name: skin(dermis and epidermis)_upper arm

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:atopic dermatitis_Disease Severity:severe_Skin status:lesional_Age:44years_Gender:female_Race:black


title: skin_lesional atopic dermatitis skin_LAD2 (U133A)

description: no additional information

source_name: skin(dermis and epidermis)_upper leg

tag: Tissue:skin(dermis and epidermis)_Source:upper leg_Health status:atopic dermatitis_Disease Severity:severe_Skin status:lesional_Age:19years_Gender:male_Race:hispanic


title: skin_nonlesional atopic dermatitis skin_NLAD3 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:mid arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:nonlesional_Age:18years_Gender:male_Race:asian


title: skin_nonlesional atopic dermatitis skin_NLAD4 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper back_Health status:atopic dermatitis_Disease Severity:severe_Skin status:nonlesional_Age:38years_Gender:male_Race:white


title: skin_normal_Healthy5 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper leg_Health status:normal_Age:32years_Gender:male_Race:white


title: skin_nonlesional atopic dermatitis skin_NLAD1 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:atopic dermatitis_Disease Severity:severe_Skin status:nonlesional_Age:44years_Gender:female_Race:black


title: skin_nonlesional atopic dermatitis skin_NLAD2 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper leg_Health status:atopic dermatitis_Disease Severity:severe_Skin status:nonlesional_Age:19years_Gender:male_Race:hispanic


title: skin_lesional atopic dermatitis skin_LAD6 (U133A)

description: no additional information

source_name: skin(dermis and epidermis)_lower arm

tag: Tissue:skin(dermis and epidermis)_Source:lower arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:lesional_Age:39years_Gender:male_Race:white


title: skin_nonlesional atopic dermatitis skin_NLAD5 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:mid arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:nonlesional_Age:32years_Gender:female_Race:asian


title: skin_nonlesional atopic dermatitis skin_NLAD6 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:lower arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:nonlesional_Age:39years_Gender:male_Race:white


title: H3K36Ac vs H3K36me2 ChIP chip replicate 1

description: Replicate 1 _array 091

source_name: H3K36me2 ChIP DNA

tag: ChIP DNA

source_name: H3K36Ac ChIP DNA


title: skin_normal_Healthy4 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:normal_Age:22years_Gender:female_Race:white


title: skin_normal_Healthy1 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:normal_Age:35years_Gender:female_Race:white


title: skin_normal_Healthy2 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:normal_Age:26years_Gender:male_Race:white


title: 21hvsRef

city: Singapore

first: Fiona

last: Rodrigues

address: 60 Biopolis Street, #02-01 Genome

department: Cell and Medical Biology

country: Singapore

institute: Genome Institute of Singapore

description: Series of 47 timed samples

hyb_protocol: J. David Gladstone Institutes Genomic Core Laboratory SOP

data_processing: GeneData Expressionist

organism: Burkholderia pseudomallei K96243

source_name: 21 hour

label_protocol: Approximately 1.5ug of mRNA was processed to produce amino-allyl labelled cDNA

extract_protocol: Trizol total RNA extraction, Megaclear Ambion purification of total RNA, MICROBexpress Ambion Bacterial Messenger RNA extraction Kit"

tag: Strain

source_name: Reference


title: 22hvsRef

description: Series of 47 timed samples

scan_protocol: J. David Gladstone Institutes Genomic Core Laboratory SOP

source_name: 22 hour


title: skin_normal_Healthy3 (U133A)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:normal_Age:28years_Gender:male_Race:white


title: 21.5hvsRef

description: Series of 47 timed samples

source_name: 21.5 hour


title: 20.5hvsRef

description: Series of 47 timed samples

source_name: 20.5 hour


title: 23hvsRef

description: Series of 47 timed samples

source_name: 23 hour


title: 24hvsRef

description: Series of 47 timed samples

source_name: 24 hour


title: 23.5hvsRef

description: Series of 47 timed samples

source_name: 23.5 hour


title: 20hvsRef

description: Series of 47 timed samples

source_name: 20 hour


title: 22.5hvsRef

description: Series of 47 timed samples

source_name: 22.5 hour


title: 19.5hvsRef

description: Series of 47 timed samples

source_name: 19.5 hour


title: 18.5hvsRef

description: Series of 47 timed samples

source_name: 18.5 hour


title: 18hvsRef

description: Series of 47 timed samples

source_name: 18 hour


title: 17hvsRef

description: Series of 47 timed samples

source_name: 17 hour


title: 17.5hvsRef

description: Series of 47 timed samples

source_name: 17.5 hour


title: 19hvsRef

description: Series of 47 timed samples

source_name: 19 hour


title: 16.5hvsRef

description: Series of 47 timed samples

source_name: 16.5 hour


title: 16hvsRef

description: Series of 47 timed samples

source_name: 16 hour


title: 15hvsRef

description: Series of 47 timed samples

source_name: 15 hour

source_name: Reference


title: 15.5hvsRef

description: Series of 47 timed samples

source_name: 15.5 hour


title: 12.5hvsRef

description: Series of 47 timed samples

source_name: 12.5 hour


title: 11.5hvsRef

description: Series of 47 timed samples

source_name: 11.5 hour


title: 14.5hvsRef

description: Series of 47 timed samples

source_name: 14.5 hour


title: 14hvsRef

description: Series of 47 timed samples

source_name: 14 hour


title: 12hvsRef

description: Series of 47 timed samples

source_name: 12 hour


title: 13.5hvsRef

description: Series of 47 timed samples

source_name: 13.5 hour


title: 13hvsRef

description: Series of 47 timed samples

source_name: 13 hour


title: 10.5hvsRef

description: Series of 47 timed samples

source_name: 10.5 hour


title: 11hvsRef

description: Series of 47 timed samples

source_name: 11 hour


title: 10hvsRef

description: Series of 47 timed samples

source_name: 10 hour


title: 8hvsRef

description: Series of 47 timed samples

source_name: 8 hour


title: 6.5hvsRef

description: Series of 47 timed samples

source_name: 6.5 hour


title: 9.5hvsRef

description: Series of 47 timed samples

source_name: 9.5 hour


title: 7.5hvsRef

description: Series of 47 timed samples

source_name: 7.5 hour


title: 8.5hvsRef

description: Series of 47 timed samples

source_name: 8.5 hour


title: 7hvsRef

description: Series of 47 timed samples

source_name: 7 hour

source_name: Reference


title: 9hvsRef

description: Series of 47 timed samples

source_name: 9 hour


title: 5.5hvsRef

description: Series of 47 timed samples

source_name: 5.5 hour


title: 6hvsRef

description: Series of 47 timed samples

source_name: 6 hour


title: 5hvsRef

description: Series of 47 timed samples

source_name: 5 hour


title: 4hvsRef

description: Series of 47 timed samples

source_name: 4 hour


title: 4.5hvsRef

description: Series of 47 timed samples

source_name: 4.5 hour


title: 3hvsRef

description: Series of 47 timed samples

source_name: 3 hour


title: 3.5hvsRef

description: Series of 47 timed samples

source_name: 3.5 hour


title: 2.5hvsRef

description: Series of 47 timed samples

source_name: 2.5 hour


title: 2hvsRef

description: Series of 47 timed samples

source_name: 2 hour


title: 1.5hvsRef

description: Series of 47 timed samples

source_name: 1.5 hour


title: 1hvsRef

description: Series of 47 timed samples

source_name: 1 hour


title: skin_lesional atopic dermatitis skin_LAD3 (U133B)

description: no additional information

hyb_protocol: Following fragmentation, cRNA was hybridized overnight at 45C on Affymetrix Human Genome U133B GeneChip.  GeneChips were washed and stained with phycoerythrin-labelled streptavidin in the Affymetrix Fluidics Station.

source_name: skin(dermis and epidermis)_mid arm

tag: Tissue:skin(dermis and epidermis)_Source:mid arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:lesional_Age:18years_Gender:male_Race:asian


title: skin_lesional atopic dermatitis skin_LAD5 (U133B)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:mid arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:lesional_Age:32years_Gender:female_Race:asian


title: skin_lesional atopic dermatitis skin_LAD4 (U133B)

description: no additional information

source_name: skin(dermis and epidermis)_upper back

tag: Tissue:skin(dermis and epidermis)_Source:upper back_Health status:atopic dermatitis_Disease Severity:severe_Skin status:lesional_Age:38years_Gender:male_Race:white


title: skin_lesional atopic dermatitis skin_LAD6 (U133B)

description: no additional information

source_name: skin(dermis and epidermis)_lower arm


title: skin_Lesional atopic dermatitis skin_LAD1 (U133B)

description: no additional information

source_name: skin(dermis and epidermis)_upper arm

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:atopic dermatitis_Disease Severity:severe_Skin status:lesional_Age:44years_Gender:female_Race:black


title: skin_lesional atopic dermatitis skin_LAD2 (U133B)

description: no additional information

source_name: skin(dermis and epidermis)_upper leg

tag: Tissue:skin(dermis and epidermis)_Source:upper leg_Health status:atopic dermatitis_Disease Severity:severe_Skin status:lesional_Age:19years_Gender:male_Race:hispanic


title: skin_nonlesional atopic dermatitis skin_NLAD5 (U133B)

description: no additional information


title: skin_nonlesional atopic dermatitis skin_NLAD4 (U133B)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper back_Health status:atopic dermatitis_Disease Severity:severe_Skin status:nonlesional_Age:38years_Gender:male_Race:white


title: skin_nonlesional atopic dermatitis skin_NLAD6 (U133B)

description: no additional information


title: skin_nonlesional atopic dermatitis skin_NLAD1 (U133B)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper arm_Health status:atopic dermatitis_Disease Severity:severe_Skin status:nonlesional_Age:44years_Gender:female_Race:black


title: skin_nonlesional atopic dermatitis skin_NLAD2 (U133B)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper leg_Health status:atopic dermatitis_Disease Severity:severe_Skin status:nonlesional_Age:19years_Gender:male_Race:hispanic


title: skin_nonlesional atopic dermatitis skin_NLAD3 (U133B)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:mid arm_Health status:atopic dermatitis_Disease Severity:mild/moderate_Skin status:nonlesional_Age:18years_Gender:male_Race:asian


title: skin_normal_Healthy4 (U133B)

description: no additional information


title: skin_normal_Healthy5 (U133B)

description: no additional information

tag: Tissue:skin(dermis and epidermis)_Source:upper leg_Health status:normal_Age:32years_Gender:male_Race:white


title: skin_normal_Healthy3 (U133B)

description: no additional information


title: skin_normal_Healthy1 (U133B)

description: no additional information


title: skin_normal_Healthy2 (U133B)

description: no additional information


title: wsb 8510

status: Public on Sep 24 2006

city: Amsterdam

first: Bas

last: Kreike

address: Plesmanlaan 121

department: Radiotherapy

country: Netherlands

institute: Netherlands Cancer Institute

description:
all our samples are co-hybridized with a reference of pooled RNA from over 100 breast cancer samples.
We perform a dye-swap experiment and the VALUE-ratios are the ratios after normalisation and combining the two experiments.
The ratios are log2 transformed.

data_processing: For detailed information see: http://microarrays.nki.nl/

source_name: breast carcinoma

tag: female, <51years at diagnosis, breastcancer, diameter <5cm, terated by breast conserving therapy

tag: Co-hybridized with reference pool of over 100 breast cancer samples


title: wsb 8317


title: wsb 8175


title: wsb 7922


title: VREI_F049_10-03-04

status: Public on Sep 30 2006

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: mes-4(bn85) vs N2 #2

data_processing: log base 2 ratio of cy5 to cy3

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: EXP

tag: mes-4(bn85) mRNA

source_name: REF

tag: N2 mRNA


title: wsb 7185


title: wsb 6725


title: wsb 6583


title: VREI_F045_10-31-04

description: mes-4(bn85) vs N2 #3


title: VREI_F041_11-02-04

description: mes-4(bn85) vs N2 #4


title: VREI_F049_10-07-04

description: mes-4(bn85) vs N2 #1


title: wsb 6539


title: wsb 10923


title: wsb 6423


title: wsb 5887


title: wsb 5044


title: wsb 10622


title: wsb 3814


title: wsb 5287


title: wsb 4380


title: wsb 10492


title: wsb 3551


title: wsb 3685


title: wsb 3532


title: wsb 3434


title: wsb 3809


title: wsb 3494


title: wsb 3442


title: wsb 3376


title: wsb 3483


title: wsb 3319


title: wsb 3269


title: wsb 3116


title: wsb 2976


title: wsb 2787


title: wsb 3346


title: wsb 2852


title: wsb 2618


title: wsb 2596


title: wsb 2495


title: wsb 2422


title: wsb 2572


title: wsb 2406


title: wsb 2463


title: wsb 1717


title: wsb 2201


title: wsb 2121


title: wsb 1896


title: wsb 2338


title: wsb 862


title: wsb 1694


title: wsb 701


title: Profiling of altered gene expression induced by 6 hr of zinc in human prostate cancer cells

first: Shufei

last: Lin

address: 666 W. Baltimore Street

department: Biomedical Sciences

institute: University of Maryland at Baltimore

description: Zinc effect on gene expression of HPR-1 cells was evaluated using Applied Biosystems (Foster City, CA) human genomewise microarray chips V2.0. For each chip, 2 microgram total RNA from each sample was used for converting to cRNA. The synthesis of cRNA and a subsequent hybridization were completed by the Core Facility at UMBI (University of Maryland Biotechnology Institute, Baltimore, MD) according to the ABI standard protocol.

hyb_protocol: Applied Biosystems Protocol

scan_protocol: Applied Biosystems Protocol

data_processing: Applied Biosystems 1700 Chemiluminescent Microarray Analyzer and 1700 Gene Expression Microarray System

label: Chemiluminescent Fluorescence

source_name: PC-3 cell line

label_protocol: Applied Biosystems Protocol

growth_protocol: Cells were maintained in RPMI 1640 medium (GIBCO BRL) with 10% fetal bovine serum plus 1U/ mL penicillin-streptomycin in a 5% CO2 atmosphere at 37oC

extract_protocol: Total RNA was extracted with the Qiagen (Valencia, CA) RNeasy Mini kit according to the manufacturer?s protocol.

treatment_protocol: PC-3 cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion. Serum-free media were refreshed following starving process and zinc (1,500 ng /mL) was introduced for 6 hrs. Both media and Cells were collected concurrently. Cell pellets were immediately frozen and stored at -80 oC pending for RNA isolation.

tag: Androgen-independent prostate carcinoma (PC-3) cell line


title: wsb 1642


title: wsb 1428


title: wsb 1319


title: wsb 10343


title: Profiling of gene expression in human prostate cancer cells

source_name: PC-3 cell ine

growth_protocol: Cells were maintained in RPMI 1640 medium (GIBCO BRL) with 5% fetal bovine serum (10% for LNCaP and PC-3) plus 1U/ mL penicillin-streptomycin in a 5% CO2 atmosphere at 37oC

treatment_protocol: PC-3 cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion. Serum-free media were refreshed following starving process and both media and Cells were collected concurrently after 6 more hours. Cell pellets were immediately frozen and stored at -80 oC pending for RNA isolation.


title: wsb 1281


title: wsb 10167

description:
All our samples are co-hybridized with a reference of pooled RNA from over 100 breast cancer samples.
We perform a dye-swap experiment and the VALUE-ratios are the ratios after normalisation and combining the two experiments.
The ratios are log2 transformed.

tag: female, <51years at diagnosis, breastcancer, diameter <5cm, treated by breast conserving therapy.

tag: Co-hybridized with reference pool of over 100 breast cancer samples.


title: wsb 2523


title: wsb 2402


title: Profiling of gene expression in human prostate cells

description: Zinc effect on gene expression of HPR-1 cells was evaluated using Applied Biosystems (Foster City, CA) human genomewise microarray chips V2.0. For each chip, 2µg total RNA from each sample was used for converting to cRNA. The synthesis of cRNA and a subsequent hybridization were completed by the Core Facility at UMBI (University of Maryland Biotechnology Institute, Baltimore, MD) according to the ABI standard protocol.

growth_protocol: Cells were maintained and propagated in Keratinocyte-SFM supplemented with 1U/mL penicillin and streptomycin sulfate, EGF 0.005 mg/mL, and bovine pituitary extract 0.05 mg/mL in a 5% CO2 atmosphere at 37oC.

extract_protocol: Total RNA was extracted with the Qiagen (Valencia, CA) RNeasy Mini kit according to the manufacturer’s protocol.

treatment_protocol: HPR-1 cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion. Hormone-free media were refreshed following starving process and both media and Cells were collected concurrently. Cell pellets were immediately frozen and stored at -80 oC pending for RNA isolation.

tag: Human prostatic cell line derived from normal prostate epithelial tissue (HPR-1)


title: 2-11-Vector

status: Public on Sep 15 2006

type: other

first: Ronald

middle: B

last: Gartenhaus

address: 655 W Baltimore st

department: Greenbaum Cancer Center

institute: University of Maryland

description: The mRNAs that were actively recruited to the polysomes by vector expressing cells were used for this array.

hyb_protocol: The cRNA probe was hybridized to GEArray-human apoptosis and cell cycle gene arrays (SuperArray, Frederick, MD) and the hybridization signal was detected with Chemiluminescent Detection Kit according to the manufacturers protocol.

scan_protocol: The developed films were scanned using AlphaDigiDoc gel documentation system (AlphaInnotech, San Leandro, CA). GEArray Expression Analysis Suite (SuperArray,Frederick, MD) was used for data extraction and analysis.

data_processing: The values given here are non normalized.

molecule: other

label_protocol: The polysome-associated RNA were used to generate cDNA and thereafter generate cRNA probes labeled with Biotin-16-UTP (Roche Molecular Biochemicals) using the AmpoLabeling-LPR kit (SuperArray) according to the user manual.

growth_protocol: Growen in DMEM with 10%FBS

extract_protocol: Thirty-six hours after transfedtion the cells  were collected and washed with PBS containing 100 μg/ml cycloheximide. The cells were lysed in a buffer containing 0.3M KCl, 5mM MgCl2. 10mM Tris pH 7.4, 0.5% NP-40, 5mM DTT, proteinase-K inhibitors, RNase inhibitors and 1 mg of heparin per ml at 4°C. Centrifugation was performed to pellet nuclei and unlysed cells. The supernatant was centrifuged through a 10-50% sucrose gradient. Polysome associated RNA from vector and MCT-1 transfected cells were purified by RNeasy mini kit (Qiagen) and separately pooled.

treatment_protocol: Transfection was done using Lipofectamine (Invitrogen) according to manufacturers protocol.


title: wsb 575


title: wsb 565


title: Profiling of altered gene expression induced by 1 hr of zinc in human prostate cells

source_name: Human prostatic cell line derived from normal prostate epithelial tissue (HPR-1)

treatment_protocol: Zinc effect was initiated with cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion before the introduction of zinc treatments. Hormone-free media were refreshed following starving process and zinc (1,500 ng /mL) was introduced for 1 hr. Both media and Cells from various treatments were collected concurrently. Pellets were immediately frozen and stored at -80 oC pending for RNA isolation.


title: 2-11-MCT1

description: The mRNAs that were actively recruited to the polysomes by MCT-1 expressing cells were used for this array.

scan_protocol: The developed films were scanned using AlphaDigiDoc gel documentation system (AlphaInnotech, San Leandro, CA). GEArray Expression Analysis Suite (SuperArray) was used for data extraction and analysis.


title: 11-8-MCT-1


title: 11-8-Vector


title: 1-9-Vector

description:
The mRNAs that were actively recruited to the polysomes by vector expressing cells were used for this array.
The values given here are non normalized.

tag: 293 HEK cells transfected with V5-Empty-vector


title: P5L

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description:
circulating whole white blood cells, isolated T cells and Monocytes
Data for Inflamation and Host Reponse to Injury, NIH Glue Grant, Study or Experiment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GCOS version 1.2

source_name: Patient 5 leukocytes

tag: Human trauma patients with documented multiple organ failure and healthy volunteers


title: 1-9-MCT-1

description:
The mRNAs that were actively recruited to the polysomes in MCT-1 expressing cells were used for this array.
The values given here are non normalized.

data_processing: The data here is not yet normalized.

growth_protocol: Growen in DMEM with 10% FBS

extract_protocol: Thirty-six hours after transfection the cells  were collected and washed with PBS containing 100 μg/ml cycloheximide. The cells were lysed in a buffer containing 0.3M KCl, 5mM MgCl2. 10mM Tris pH 7.4, 0.5% NP-40, 5mM DTT, proteinase-K inhibitors, RNase inhibitors and 1 mg of heparin per ml at 4°C. Centrifugation was performed to pellet nuclei and unlysed cells. The supernatant was centrifuged through a 10-50% sucrose gradient. Polysome associated RNA from vector and MCT-1 transfected cells were purified by RNeasy mini kit (Qiagen) and separately pooled.

tag: 293 HEK cells transfected with V5-MCT-1.


title: Profiling of altered gene expression induced by 3 hr of zinc in human prostate cancer cells

treatment_protocol: PC-3 cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion. Serum-free media were refreshed following starving process and zinc (1,500 ng /mL) was introduced for 3 hrs. Both media and Cells were collected concurrently. Cell pellets were immediately frozen and stored at -80 oC pending for RNA isolation.


title: Airway epithelial cells, infected with rsmA mutant of P. aeruginosa, rep1, MOI 50:1, 1.5 h

city: Cork

first: Fergal

last: O'Gara

address: College Road

department: Microbiology

country: Ireland

institute: University College Cork

description: Briefly, 8.5µg of RNA was converted to double stranded cDNA by reverse transcription, using a Superscript cDNA synthesis kit (Invitrogen), with an oligo dT primer containing a T7 RNA polymerase site added 3’ of the poly (T) (Affymetrix). After second strand synthesis, cDNA was converted to biotin-labelled cRNA by in vitro transcription (Enzo). The labelled cRNA was purified using Genechip clean up module (Qiagen). Total cRNA quality and yield was measured using a GeneQuant spectrophotometer and 20 µg of cRNA was fragmented at 94ºC for 35 mins in fragmentation buffer (40 mM tris acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate). Full length and fragmented cRNA sample integrity was assessed by electrophoresis on a 1% agarose-TBE gel visualized by staining with SyBr green. Fragmented cRNA was sent to MRC geneservice (Cambridge, UK) for assessment of RNA quality using a Bioanalyzer (Agilent) before hybridization and scanning. The arrays were washed and stained in a fluidics station and scanned according to the manufacturer’s protocols (Affymetrix).

tag: rsmA mutant of Pseudomonas aeruginosa PAO1

tag: Immortalised, Cystic Fibrosis Tracheal Epithelial (CFTE) cells, Delta F508 mutation of CFTR (Gruenert et al. 2004)

tag: For epithelial cell infection studies, cells were washed twice with sterile phosphate-buffered saline (PBS), detached and seeded in antibiotic-free media into newly-coated plastic vessels 24h prior to infection so as to achieve 80% confluency at the time of infection. Bacterial strains were cultured aerobically for 16-18 h in the described cell culture medium without antibiotics (infection medium) at 37°C. Bacteria were sub-cultured in infection medium for an additional 4 h using the growth conditions described so that bacterial strains were in the exponential phase of growth. Following three rounds of centrifugation and PBS washing to remove extracellular components, bacterial densities were adjusted so as to infect cells at a multiplicity of infection (MOI) of 50:1. Serial dilutions were plated onto Luria-Bertani agar to confirm the MOI used. At the indicated times postinfection, cells which were already detached from the plastic were collected by centrifugation and those cells remaining attached were treated with trypsin-EDTA prior to collection by centrifugation. Harvested cells were immediately frozen at -70°C for subsequent RNA isolation.

tag: RNA isolation and microarray sample preparation

tag: Biological samples from two independent infection experiments were used in two independent microarray experiments as outlined below. Total RNA was isolated from epithelial cells using an RNeasy Kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed using DNA-free (Ambion) and confirmed by PCR to be free of DNA, prior to cDNA synthesis. Isolated RNA was used in the preparation of fragmented cRNA for microarray hybridization according to the manufacturer’s protocol (Affymetrix). Briefly, 8.5µg of RNA was converted to double stranded cDNA by reverse transcription, using a Superscript cDNA synthesis kit (Invitrogen), with an oligo dT primer containing a T7 RNA polymerase site added 3’ of the poly (T) (Affymetrix). After second strand synthesis, cDNA was converted to biotin-labelled cRNA by in vitro transcription (Enzo). The labelled cRNA was purified using Genechip clean up module (Qiagen). Total cRNA quality and yield was measured using a GeneQuant spectrophotometer and 20 µg of cRNA was fragmented at 94ºC for 35 mins in fragmentation buffer (40 mM tris acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate). Full length and fragmented cRNA sample integrity was assessed by electrophoresis on a 1% agarose-TBE gel visualized by staining with SyBr green. Fragmented cRNA was sent to MRC geneservice (Cambridge, UK) for assessment of RNA quality using a Bioanalyzer (Agilent) before hybridization to Human Genome U133A array (Affymetrix). The arrays were washed and stained in a fluidics station and scanned according to the manufacturer’s protocols (Affymetrix).


title: wsb 1631


title: Airway epithelial cells, infected with P. aeruginosa PAO1, rep1, MOI 50:1, 1.5 h

tag: Pseudomonas aeruginosa PAO1


title: AM223

status: Public on Sep 09 2006

first: Boris

last: Bastian

department: Laboratory Medicine

institute: UCSF Cancer Center

description: Use Spot files  "HA3.1_clonepos_May04.20060811.txt " & "HA3.1_spotclone.20060807.txt" to analyse the raw images for this sample and refer to the Sample platform GPL2024 for the clone name

data_processing: Data processing is described in Curtin et al. NEJM, 2005, (353), 2135-3147. Briefly: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system and carried out image and data analysis using UCSF SPOT. The arrays contain 2462 clones printed as triplicate spots. Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. No other computational adjustments were applied to the data. We used the SPROC software to automatically filter the data based on quality criteria, average the log2 ratios of the replicate spots, and assign genome position. Only clones for which two or more spots passed quality criteria and for which the standard deviation of the replicates was less than 0.2 were included in the subsequent analysis. Data were normalized to set the median log2 ratio to zero. We used only clones that were mapped on the genome sequence and which did not detect copy number polymorphisms in normal samples. Data from submission GSE2631 and submission GSE4747 were derived from three different versions of arrays termed HumArray1-3. For compatibility, only data from clones represented on all three versions of the BAC Arrays and that stem from clones that conform to the above criteria are presented in this table.

source_name: normal mucosal melanoma

extract_protocol: paraffin embedded formalin fixed tumor

tag: BRAF & NRAS wt

source_name: reference DNA

tag: normal DNA


title: Profiling of altered gene expression induced by 6 hrs of zinc in human prostate cells

treatment_protocol: Zinc effect was initiated with cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion before the introduction of zinc treatments. Hormone-free media were refreshed following starving process and zinc (1,500 ng /mL) was introduced for 6 hrs. Both media and Cells were collected concurrently. Pellets were immediately frozen and stored at -80 oC pending for RNA isolation.


title: AM220

source_name: primary mucosal melanoma


title: Profiling of altered gene expression induced by 3 hrs zinc in human prostate cells

source_name: HPR-1 cell line

treatment_protocol: Zinc effect was initiated with cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion before the introduction of zinc treatments. Hormone-free media were refreshed following starving process and zinc (1,500 ng /mL) was introduced for 3 hrs. Both media and Cells were collected concurrently. Pellets were immediately frozen and stored at -80 oC pending for RNA isolation.


title: AM211

tag: BRAF wt & NRAS na


title: AM212


title: Profiling of altered gene expression induced by 1 hr of zinc in human prostate cancer cells

treatment_protocol: PC-3 cells at 70-80% confluence in T-75 flasks (Corning, Corning, NY) which were synchronized by 24 hrs hormone-depletion. Serum-free media were refreshed following starving process and zinc (1,500 ng /mL) was introduced for 1 hr. Both media and Cells were collected concurrently. Cell pellets were immediately frozen and stored at -80 oC pending for RNA isolation.


title: AM208


title: Airway epithelial cells, infected with the rsmA mutant of P. aeruginosa, rep2, MOI 50:1, 1.5 h


title: am203

source_name: primary acral melanoma


title: AM157

description: Use Spot files  HA114_clonepos_Jul03_v1_2a.txt  & HA114_spotclone_Aug01_0_95_spotnum.txt to analyse the raw images for this sample and refer to the Sample platform GPL2024 for the clone name

source_name: Primary mucosal melanoma


title: AM205


title: Airway epithelial cells, infected with P. aeruginosa PAO1, rep2, MOI 50:1, 1.5 h


title: AM206


title: Airway epithelial cells, uninfected rep1, 1.5 h

description: Biological samples from two independent infection experiments were used in two independent microarray experiments as outlined below. Total RNA was isolated from epithelial cells using an RNeasy Kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed using DNA-free (Ambion) and confirmed by PCR to be free of DNA, prior to cDNA synthesis. Isolated RNA was used in the preparation of fragmented cRNA for microarray hybridization according to the manufacturer’s protocol (Affymetrix). Briefly, 8.5µg of RNA was converted to double stranded cDNA by reverse transcription, using a Superscript cDNA synthesis kit (Invitrogen), with an oligo dT primer containing a T7 RNA polymerase site added 3’ of the poly (T) (Affymetrix). After second strand synthesis, cDNA was converted to biotin-labelled cRNA by in vitro transcription (Enzo). The labelled cRNA was purified using Genechip clean up module (Qiagen). Total cRNA quality and yield was measured using a GeneQuant spectrophotometer and 20 µg of cRNA was fragmented at 94ºC for 35 mins in fragmentation buffer (40 mM tris acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate). Full length and fragmented cRNA sample integrity was assessed by electrophoresis on a 1% agarose-TBE gel visualized by staining with SyBr green. Fragmented cRNA was sent to MRC geneservice (Cambridge, UK) for assessment of RNA quality using a Bioanalyzer (Agilent) before hybridization to Human Genome U133A array (Affymetrix). The arrays were washed and stained in a fluidics station and scanned according to the manufacturer’s protocols (Affymetrix).


title: Airway epithelial cells, uninfected rep2, 1.5 h


title: MAQC_ILM_3_C5

status: Public on Sep 08 2006

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

hyb_protocol: Illumina Human-6 whole genome microarrays (Illumina; catalog # BD-25-101) were hybridized to 1.5 micrograms of labeled, amplified material, and then washed, stained, and scanned according to the protocol described in the Illumina Whole Genome Gene Expression for BeadStation Manual, Revision D.

scan_protocol: Scanning software was BeadScan 2.3.0.10.

data_processing: Data was processed using Illumina BeadStudio version 1.5.0.34 software using background subtraction and cubic spline normalization.

source_name: MAQC sample C, i.e., MAQC samples A and B mixed at 75%:25% ratio (A:B).

label_protocol: 200 ng of total RNA provided by the MAQC were amplified and labeled using the Illumina(R) TotalPrep(TM) RNA Amplification kit (Ambion; catalog #IL1791).


title: MAQC_ILM_3_D1

source_name: MAQC sample D, i.e., MAQC samples A and B mixed at 25%:75% ratio (A:B).


title: MAQC_ILM_3_D2


title: AM217


title: AM214


title: AM218


title: AM213


title: MAQC_ILM_3_C2


title: MAQC_ILM_3_C1


title: MAQC_ILM_3_B5

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)


title: AM210


title: AM204


title: MAQC_ILM_3_B2


title: MAQC_ILM_3_B4


title: MAQC_ILM_3_B3


title: AM209


title: PAO1_PCP_26hr_B

city: Blacksburg

first: Nancy

middle: G.

last: Love

state: VA

address: 418 Durham Hall

department: Civil and Environmental Engineering

institute: Virginia Tech

description: Fourth of four timepoints in experiment, pentachlorophenol concentration 35 mg/L, replicate 2 of 2

hyb_protocol: As described by Affymetrix

scan_protocol: As described by Affymetrix

data_processing: GCOS 1.1.1, using default parameters and scaled to 100 average intensity over entire genechip

organism: Pseudomonas aeruginosa

source_name: whole cells

label_protocol: As described by Affymetrix

growth_protocol: Cells were grown in a chemostat at a 12 hour generation time in a minimal medium that contained acetate as the sole carbon source.

extract_protocol: RNeasy Mini Kit from Qiagen, with on-column DNase-digestion as described by the manufacturer.

treatment_protocol: Treated with RNA Bacterial Protect Reagent (Qiagen, Valencia, CA)

tag: strain PAO1


title: MAQC_ILM_3_D3


title: PAO1_PCP_13hr_B

description: Third of four timepoints in experiment, pentachlorophenol concentration 25 mg/L, replicate 2 of 2


title: MAQC_ILM_3_D5


title: MAQC_ILM_2_D7


title: MAQC_ILM_3_B1


title: MAQC_ILM_3_A1

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)


title: PAO1_PCP_6.5hr_B

description: Second of four timepoints in experiment, pentachlorophenol concentration 15 mg/L, replicate 2 of 2


title: MAQC_ILM_3_C3


title: PAO1_PCP_0hr_B

description: First of four timepoints in experiment, pre-pentachlorophenol exposure, replicate 2 of 2


title: MAQC_ILM_3_D4


title: MAQC_ILM_2_D4


title: PAO1_PCP_26hr

description: Fourth of four timepoints in experiment, pentachlorophenol concentration 35 mg/L, replicate 1 of 2


title: PAO1_PCP_13hr

description: Third of four timepoints in experiment, pentachlorophenol concentration 25 mg/L, replicate 1 of 2

source_name: Whole cells

tag: Strain PAO1


title: PAO1_PCP_6.5hr

description: Second of four timepoints in experiment, pentachlorophenol concentration 15 mg/L, replicate 1 of 2


title: MAQC_ILM_2_D2


title: PAO1RpoS-_PCP_26hr

description: Fourth of four timepoints in experiment, Pentachlorophenol concentration approximately 35 mg/L

tag: Strain PAO1 RpoS-


title: PAO1_PCP_0hr

description: First of four timepoints in experiment, Pre-pentachlorophenol exposure, replicate 1 of 2

source_name: Whole cells, pre-PCP exposure


title: MAQC_ILM_2_D1


title: MAQC_ILM_3_A5


title: MAQC_ILM_2_C5


title: PAO1RpoS-_PCP_13hr

description: Thrid of four timepoints in experiment, Pentachlorophenol concentration approximately 25 mg/L


title: MAQC_ILM_3_A2


title: MAQC_ILM_3_C4


title: MAQC_ILM_3_A3


title: MAQC_ILM_3_A4


title: MAQC_ILM_2_C3


title: MAQC_ILM_2_C4


title: PAO1RpoS-_PCP_6.5hr

description: Second of four timepoints in experiment, Pentachlorophenol concentration approximately 15 mg/L


title: PAO1RpoS-_PCP_0hr

description: First of four timepoints in experiment


title: MAQC_ILM_2_D6


title: MAQC_ILM_2_C1


title: MAQC_ILM_2_B4


title: MAQC_ILM_2_B5


title: MAQC_ILM_2_A5


title: MAQC_ILM_2_B1


title: MAQC_ILM_2_A3


title: MAQC_ILM_2_B2


title: MAQC_ILM_2_A4


title: MAQC_ILM_2_B3


title: MAQC_ILM_2_C2


title: MAQC_ILM_2_A1


title: MAQC_ILM_2_A2


title: MAQC_ILM_1_D5


title: MAQC_ILM_1_D2


title: MAQC_ILM_1_D3


title: MAQC_ILM_1_C4


title: MAQC_ILM_1_C2


title: MAQC_ILM_1_B3


title: MAQC_ILM_1_B2


title: MAQC_ILM_1_B5


title: MAQC_ILM_1_B1


title: MAQC_ILM_1_A5


title: MAQC_ILM_1_C5


title: MAQC_ILM_1_A4


title: MAQC_AGL_3_C5

description: AGL sample-pair convention: A (A/A, Cy3/Cy5), B (B/B, Cy3/Cy5), C (A/B, Cy3/Cy5), and D (B/A, Cy3/Cy5).  Only MAQC samples A and B were used in AGL two-color experiments.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 8.5 (P/N G2567AA).

data_processing: Data were extracted using Agilent's Feature Extraction software, version 8 (P/N G2567AA), Cy3 corresponding to the gProcessedSignal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file.

label_protocol: Labeled cRNAs were generated from 500 ng of total RNA for each of AG1 and AGL using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).  The two-color protocol was modified such that 1.5 µg of labeled cRNA was hybridized per dye channel per microarray.

tag: MAQC sample


title: MAQC_ILM_1_A1


title: MAQC_AGL_3_D4


title: MAQC_ILM_1_A2


title: MAQC_ILM_1_A3


title: MAQC_AGL_3_D1


title: MAQC_ILM_1_B4


title: MAQC_ILM_1_D1


title: MAQC_AGL_3_D2


title: MAQC_ILM_1_C1


title: MAQC_ILM_1_D4


title: MAQC_AGL_3_D3


title: MAQC_AGL_3_D5


title: MAQC_AGL_3_C2


title: MAQC_AGL_3_C3


title: MAQC_AGL_3_C1


title: MAQC_AGL_3_B5


title: MAQC_AGL_3_B4


title: MAQC_AGL_3_B3


title: MAQC_AGL_3_B2


title: MAQC_AGL_3_C4


title: MAQC_AGL_3_B1


title: MAQC_AGL_3_A4


title: MAQC_AGL_3_A2


title: MAQC_AGL_2_D5


title: MAQC_AGL_3_A5


title: MAQC_AGL_2_D3


title: MAQC_AGL_3_A3


title: MAQC_AGL_3_A1


title: MAQC_AGL_2_D2


title: MAQC_AGL_2_D1


title: MAQC_AGL_2_D4


title: MAQC_AGL_2_C5


title: MAQC_AGL_2_B5


title: MAQC_AGL_2_B4


title: MAQC_AGL_2_C1


title: MAQC_AGL_2_C3


title: MAQC_AGL_2_A2


title: MAQC_AGL_2_A1


title: MAQC_AGL_2_B2


title: MAQC_AGL_2_B3


title: MAQC_AGL_2_C4


title: MAQC_AGL_2_A3


title: MAQC_AGL_1_D5


title: MAQC_AGL_2_B1


title: MAQC_AGL_2_C2


title: MAQC_AGL_2_A5


title: MAQC_AGL_2_A4


title: MAQC_AGL_1_D4


title: MAQC_AGL_1_D2


title: MAQC_AGL_1_C5


title: MAQC_ABI_3_D2

hyb_protocol: Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

scan_protocol: Chemiluminescent Detection Kit (P/N 4339627, http://docs.appliedbiosystems.com/pebiodocs/04339627.pdf) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).

data_processing: The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation.  The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values.  The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values.  The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise.  In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.

label: Chemiluminescence - Digoxigenin

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each MAQC sample (A, B, C, D) using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol.


title: MAQC_AGL_1_C3


title: MAQC_ABI_3_D1


title: MAQC_AGL_1_D3


title: MAQC_AGL_1_C1


title: MAQC_ABI_3_D3


title: MAQC_ABI_3_D4


title: MAQC_ABI_3_D5


title: MAQC_AGL_1_C4


title: MAQC_AGL_1_C2


title: MAQC_ABI_3_C5


title: MAQC_ABI_3_C4


title: MAQC_AGL_1_B4


title: MAQC_ABI_3_C3


title: MAQC_AGL_1_B5


title: MAQC_ABI_3_C2


title: MAQC_AGL_1_B2


title: MAQC_ABI_3_B4


title: MAQC_ABI_3_B5


title: MAQC_ABI_3_C1


title: MAQC_AGL_1_B3


title: MAQC_ABI_3_B2


title: MAQC_ABI_3_B3


title: MAQC_ABI_3_B1


title: MAQC_AGL_1_B1


title: MAQC_AGL_1_A5


title: MAQC_ABI_3_A5


title: MAQC_ABI_3_A4


title: MAQC_ABI_3_A2


title: MAQC_AGL_1_A4


title: MAQC_AGL_1_A3


title: MAQC_ABI_2_D4


title: MAQC_ABI_2_D5


title: MAQC_ABI_3_A1


title: MAQC_ABI_2_D3


title: MAQC_AGL_1_A2


title: MAQC_ABI_3_A3


title: MAQC_ABI_2_D2


title: MAQC_AGL_1_A1


title: MAQC_ABI_2_D1


title: MAQC_ABI_2_C2


title: MAQC_ABI_2_C3


title: MAQC_ABI_2_C5


title: MAQC_ABI_2_C1


title: MAQC_ABI_2_B5


title: MAQC_ABI_2_B3


title: MAQC_ABI_2_C4


title: MAQC_ABI_2_A5


title: MAQC_ABI_2_B2


title: MAQC_ABI_2_A4


title: MAQC_ABI_2_B4


title: MAQC_ABI_2_B1


title: MAQC_ABI_2_A3


title: MAQC_ABI_1_D4


title: MAQC_ABI_2_A2


title: MAQC_ABI_1_D5


title: MAQC_ABI_2_A1


title: MAQC_ABI_1_C5


title: MAQC_ABI_1_C4


title: MAQC_ABI_1_D1


title: MAQC_ABI_1_D2


title: MAQC_ABI_1_C2


title: MAQC_ABI_1_C1


title: MAQC_ABI_1_B5


title: MAQC_ABI_1_C3


title: MAQC_ABI_1_B4


title: MAQC_ABI_1_D3


title: MAQC_ABI_1_B3


title: MAQC_ABI_1_B2


title: MAQC_ABI_1_A3


title: MAQC_ABI_1_A4


title: MAQC_ABI_1_B1


title: MAQC_ABI_1_A2


title: MAQC_ABI_1_A5


title: MAQC_GEH_3_D2

scan_protocol: All arrays were scanned on the GenePix 4000B scanner using manufacturer recommended settings of 600 PMT, 100% laser power, and 5 micron resolution.

data_processing: The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics.  These quality metrics are applied to each spot and are displayed both numerically and as a qualitative assignment.  In the MAQC study, for all microarray platforms, genes which were not detected (i.e., 'absent') were excluded from subsequent analyses.   The spots which are below noise on the GE Healthcare platform are flagged by the software package as 'L' and represent cases where the spot mean intensity is less than local background median plus 1.5 standard deviations of local background.   Details on the CodeLink(TM) detection algorithms can be found at the www.codelinkbioarrays.com (http://www1.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AImproved+method%28275651129-B500%29?OpenDocument&hometitle=WebDocs).

label_protocol: MAQC total RNA samples were processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol (Please refer to CodeLink(TM) iExpress Expression Assay Regent Kit Technical Manual for details at www.codelinkbioarrays.com) and hybridized to CodeLink(TM) Human Whole Genome bioarrays (catalog #300026).


title: MAQC_GEH_3_D3


title: MAQC_GEH_3_D4


title: MAQC_GEH_3_C5


title: MAQC_ABI_1_A1


title: MAQC_GEH_3_D5


title: MAQC_GEH_3_D1


title: MAQC_GEH_3_C3


title: MAQC_GEH_3_C2


title: MAQC_GEH_3_C4


title: MAQC_GEH_3_B5


title: MAQC_GEH_3_C1


title: MAQC_GEH_3_A5


title: MAQC_GEH_3_B2


title: MAQC_GEH_3_B4


title: MAQC_AGL_1_D1


title: MAQC_GEH_3_B3


title: MAQC_GEH_3_A2


title: MAQC_GEH_3_A4


title: MAQC_GEH_3_A3


title: MAQC_GEH_3_A1


title: MAQC_GEH_3_B1


title: MAQC_GEH_2_D5


title: MAQC_GEH_2_D4


title: MAQC_GEH_2_D3


title: MAQC_GEH_2_C5


title: MAQC_GEH_2_D1


title: MAQC_GEH_2_D2


title: MAQC_GEH_2_B5


title: MAQC_GEH_2_B2


title: MAQC_GEH_2_C2


title: MAQC_GEH_2_C3


title: MAQC_GEH_2_C1


title: MAQC_GEH_2_B4


title: MAQC_GEH_2_C4


title: MAQC_GEH_2_A3


title: MAQC_GEH_2_A4


title: MAQC_GEH_2_B1


title: MAQC_GEH_2_B3


title: MAQC_GEH_2_A5


title: MAQC_GEH_2_A2


title: MAQC_GEH_2_A1


title: MAQC_GEH_1_D4


title: MAQC_GEH_1_D3


title: MAQC_GEH_1_D5


title: MAQC_GEH_1_C5


title: MAQC_GEH_1_C1


title: MAQC_GEH_1_C4


title: MAQC_GEH_1_C2


title: MAQC_GEH_1_D2


title: MAQC_GEH_1_D1


title: MAQC_GEH_1_C3


title: MAQC_GEH_1_B5


title: MAQC_GEH_1_B3


title: MAQC_GEH_1_B4


title: MAQC_GEH_1_B2


title: MAQC_GEH_1_B1


title: MAQC_GEH_1_A5


title: MAQC_GEH_1_A3


title: plusDRB_mouse_COC_cultured_25min_(with_transcriptional_inhibitor)

status: Public on Sep 01 2006

type: SAGE

anchor: NlaIII

city: Raleigh

first: Charlotte

middle: E.

last: Farin

address: 231B Polk Hall

department: Department of Animal Science

institute: North Carolina State University

description:
plusDRB (treatment) SAGE library used to compare with minusDRB (control) SAGE library.  See following reference:
Rodriguez et al., 2006. Identification of candidate mRNAs associated with gonadotropin-induced maturation of murine cumulus oocyte complexes using serial analysis of gene expression. Physiological Genomics (in press).

source_name: Mouse COC harvested from PMSG-primed females

treatment_protocol:
Murine COC cultured 25 min in Waymouth medium in atmosphere of 5% CO2 in air in the presence of 120 uM DRB, a transcriptional inhibitor.  For protocol reference see:
Rodriguez et al., 2006. Identification of candidate mRNAs associated with gonadotropin-induced maturation of murine cumulus oocyte complexes using serial analysis of gene expression. Physiological Genomics (in press).

tag: Mouse strain

value: Swiss-albino; age:20-23 days old; pretreatment:PMSG 48 h before ovary harvest and COC collection.  COC released from ovaries into DRB-containing medium.  DRB is a transcriptional inhibitor.


title: MAQC_GEH_1_A4


title: MAQC_GEH_1_A2


title: minusDRB_mouse_COC_cultured_25min_(no transcriptional_inhibitor)

description:
minusDRB SAGE library used to compare with plusDRB SAGE library.  See following reference:
Rodriguez et al., 2006. Identification of candidate mRNAs associated with gonadotropin-induced maturation of murine cumulus oocyte complexes using serial analysis of gene expression. Physiological Genomics (in press).

source_name: Mouse COC from PMSG-primed females

extract_protocol:
Protocol reference:
Rodriguez et al., 2006. Identification of candidate mRNAs associated with gonadotropin-induced maturation of murine cumulus oocyte complexes using serial analysis of gene expression. Physiological Genomics (in press).

treatment_protocol:
Murine COC cultured 25 min in Waymouth medium in atmosphere of 5% CO2 in air.  Protocol reference see:
Rodriguez et al., 2006. Identification of candidate mRNAs associated with gonadotropin-induced maturation of murine cumulus oocyte complexes using serial analysis of gene expression. Physiological Genomics (in press).

value: Swiss-albino; age:20-23 days; pretreatment:PMSG, 48 h before ovary harvest and COC collection


title: Dicer knockdown clone #2b2 replicate 2 6 days induced

city: Basel

first: Daniela

last: Schmitter

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institut

description: 293 cells expressing the tet-repressor protein_ date of analysis_04032005

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix and Expressionist

source_name: T-REx-293 cells

label_protocol: 15 micrograms of biotinylated fragmented cRNA was hybridized to each chip.

extract_protocol: RNA was extracted from cells in a confluent 6-well dish using Absolutely RNA Miniprep Kit (Stratagene)

tag: embryonic kidney cells

tag: 293 cells stably expressing the tet-repressor and the hairpin 2b2 against Dicer, female, 2days induced with 1ug/ml Doycyclin


title: MAQC_GEH_1_A1


title: empty vector ctrl replicate 2 6 days induced

tag: 293 cells stably expressing the tet-repressor and pTER plasmid with no hairpin inserted, female, 2days induced with 1ug/ml Doycyclin


title: Dicer knockdown clone #2-2 replicate 1 6 days induced

tag: 293 cells stably expressing the tet-repressor and the hairpin 2-2 against Dicer, female, 2days induced with 1ug/ml Doycyclin


title: Dicer knockdown clone #2b2 replicate 1 2 days induced


title: Dicer knockdown clone #2-2 replicate 2 6 days induced


title: empty vector ctrl replicate 1 6 days induced


title: Dicer knockdown clone #2b2 replicate 1 6 days induced


title: Dicer knockdown clone #2b2 replicate 2 2 days induced


title: empty vector ctrl replicate 2 2 days induced


title: Dicer knockdown clone #2-2 replicate 1 2 days induced


title: Dicer knockdown clone #2-2 replicate 2 2 days induced


title: empty vector ctrl replicate 1 2 days induced


title: Dicer knockdown clone #2-2 replicate 1

tag: 293 cells stably expressing the tet-repressor and the hairpin 2-2 against Dicer, female, not induced


title: Dicer knockdown clone #2-2 replicate 2


title: T-REx ctrl replicate 2 exp2

description: 293 cells expressing the tet-repressor protein_ date of analysis_01122005

tag: 293 cells stably expressing the tet-repressor, female, induced for 48 hrs with 10ug/ml of Tetracycline


title: shRNA ctrl replicate 2 exp2

tag: 293 cells stably expressing the tet-repressor and a scrambled hairpin after induction, female, induced for 48 hrs with 10ug/ml of Tetracycline


title: shRNA ctrl replicate 1 exp2


title: Ago4 knock down clone #2 replicate 1

tag: 293 cells stably expressing the tet-repressor and a hairpin against Ago4 after induction, female, induced for 48 hrs with 10ug/ml of Tetracycline


title: empty vector ctrl replicate 1

tag: 293 cells stably expressing the tet-repressor and pTER plasmid with no hairpin inserted, female, not induced


title: T-REx ctrl replicate 1 exp2


title: Dicer knockdown clone #2b2 replicate 2

tag: 293 cells stably expressing the tet-repressor and the hairpin 2b2 against Dicer, female, not induced


title: Ago4 knock down clone #1 replicate 2


title: Ago4 knock down clone #1 replicate 1


title: Ago1 knock down clone #2 replicate 2

tag: 293 cells stably expressing the tet-repressor and a hairpin against Ago1 after induction, female, induced for 48 hrs with 10ug/ml of Tetracycline


title: Ago1 knock down clone #2 replicate 1


title: Ago3 knock down replicate 2

description: 293 cells expressing the tet-repressor protein_ date of analysis_01062005

tag: 293 cells stably expressing the tet-repressor and a hairpin against Ago3 after induction, female, induced for 48 hrs with 10ug/ml of Tetracycline


title: Ago1 knock down clone #1 replicate 2


title: Dicer knockdown clone #2b2 replicate 1


title: Ago3 knock down replicate 1


title: shRNA ctrl replicate 2


title: T-REx ctrl replicate 2


title: empty vector ctrl replicate 2


title: T-REx ctrl replicate 1


title: Ago1 knock down clone #1 replicate 1


title: Ago4 knock down clone #2 replicate 2