title: 32-9 Cr(III) treated

status: Public on Jul 15 2005

city: Ocean Springs

first: Jonathan

last: Roling

state: MS

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

description: liver from adult male Fundulus heteroclitus

hyb_protocol: Probes are heated to 100C for 10 minutes, and then chilled on ice.  Arrays are prehybridized with 5 mL of ExpressHyb Hybridization Solution (Clontech, Palo Alto, CA) and 1 mg sheared salmon sperm (denatured at 95C for 10 minutes then chilled on ice) at 68C for greater than 4 hours.  Arrays were hybridized overnight at 68C.  The blots were washed four times for 15 minutes at 64C using 2x SSC/0.5% SDS, then four times for 15 minutes at 64C using 0.5x SSC/0.5% SDS.

scan_protocol: Blots are wrapped in plastic wrap and exposed to a phosphoscreen at room temperature, visualized on BioRad FX Imager (Hercules, CA), and quantified with Invitrogen ResGen Pathways software (Carlsbad, CA).

data_processing: Data normalized to immediate background using ResGen Pathways software.

label: radioactive phosphorus 33 - [33P] dATP

organism: Fundulus heteroclitus

source_name: Fundulus heteroclitus adult male liver

label_protocol: 2 ug RNA is diluted into 10 uL of DEPC water. 10 uL of 0.5 uM poly T primers are added and incubated at 65C for 5 minutes and cooled to room temperature for two minutes.  Radiolabelled cDNA is made by adding 30 uL of a mix containing 10 uL 5x reverse transcription buffer, 6 uL 10 mM dNTPs (without dATP), 10 uCi [33P]dATP, and 200 units MMLV-RT and incubating for 2 hours at 37C.  Probes are cleaned of short nucleotide sequences through ProbeQuant G-50 Micro Columns (Amersham Biosciences, Piscataway, NJ) and counted on scintillation counter.

extract_protocol: RNA isolation performed by TriReagent according to manufacture’s protocols, followed by DNAse treatment.

treatment_protocol: Laboratory acclimated fish were exposed in individual tanks to chromium chloride hexahydrate at 32 mg/L Cr(III) (0.62mM) for 7 days with water exchanges every other day.  Fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand.  Fish were fed daily Tetramin flake fish food.  At the conclusion of the exposure, livers were excised and frozen at -80C.

tag: Adult (>4cm in length) male liver excised immediately upon euthanasia


title: 32-10 Cr(III) treated

type: RNA

country: USA

molecule: total RNA


title: ab003 D

status: Public on Jul 25 2005

city: SG

first: Amit

last: Aggarwal

department: Cellular and Molecular Research

country: Singapore

institute: National Cancer Centre of Singapore

description: Biopsy; Laurens::DIFFUSED

organism: Homo sapiens

source_name: mRNA from Gastric tissue

source_name: mRNA from pooled cell lines


title: ab001 I

description: Biopsy; Laurens::INTESTINAL


title: 32-3 Cr(III) treated


title: NCC33

description: Gastric cancer; biopsy

source_name: mRNA from Gastric Cancer


title: 32-8 Cr(III) treated


title: NCC20

description: Gastric cancer; biopsy


title: ab002 CG

description: Biopsy; Chronic Gastritis


title: WI38_7812

status: Public on Jul 03 2005

type: genomic

city: Basel

first: Michael

last: Weber

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

description: Methylated DNA prepared by MeDIP (Cy3) is co-hybridized with total genomic DNA (Cy5). The ratio between Cy3 and Cy5 signal is calculated for all high quality features. Ratios were normalized and log2 transformed using Genepix standard settings.

molecule: genomic DNA

source_name: Cy5, total input DNA

source_name: Cy3, methylated DNA


title: SW48_7745


title: SW48_7724


title: Papillary RCC_Sample18

status: Public on Jul 01 2005

city: Grand Rapids

first: Min-Han

last: Tan

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

data_processing: RMA

label: streptavidin-phycoerythrin

source_name: Papillary RCC

tag: 'Age

value: 71 years', 'Gender:F', 'Histo:2B', 'Class:2'


title: Colon_7551


title: Colon_7529


title: Papillary RCC_Sample30

value: 63 years', 'Gender:M', 'Histo:2A', 'Class:2'


title: Papillary RCC_Sample23

value: 54 years', 'Gender:M', 'Histo:2B', 'Class:2'


title: Colon_7794


title: Papillary RCC_Sample33


title: Papillary RCC_Sample29

value: 43 years', 'Gender:M', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample27

value: 74 years', 'Gender:M', 'Histo:Type 1 and 2A', 'Class:1'


title: Papillary RCC_Sample28

value: 37 years', 'Gender:M', 'Histo:1 and 2A', 'Class:1'


title: Papillary RCC_Sample24

value: 50 years', 'Gender:M', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample26

value: 75 years', 'Gender:M', 'Histo:2A', 'Class:1'


title: WI38_7728


title: Papillary RCC_Sample16

value: 72 years', 'Gender:M', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample20

value: 71 years', 'Gender:M', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample22

value: 53 years', 'Gender:M', 'Histo:1 and 2A', 'Class:1'


title: Papillary RCC_Sample17

value: 55 years', 'Gender:M', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample31

value: 62 years', 'Gender:M', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample25

value: 44 years', 'Gender:M', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample19

value: 76 years', 'Gender:M', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample32

value: 56 years', 'Gender:M', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample15

value: 76 years', 'Gender:M', 'Histo:1 and 2A', 'Class:1'


title: Papillary RCC_Sample34

value: 49 years', 'Gender:F', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample21

value: 80 years', 'Gender:F', 'Histo:2A', 'Class:1'


title: Papillary RCC_Sample14

value: 44 years', 'Gender:M', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample13

value: 64 years', 'Gender:M', 'Histo:1', 'Class:1'


title: HFL-1

city: Vancouver

first: Jon

last: Davies

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer Research Centre

description:
Male primary lung fibroblast DNA enriched via a monoclonal antibody against 5-methylcytidine co-hybridized against the original input DNA
Keywords = Normal male methylation profile

source_name: Sonicated DNA input material for MeDIP

source_name: DNA Methylation-dependent immunoprecipitated (MeDIP) probes


title: SW48_2

description:
Colon cancer cell line DNA enriched via a monoclonal antibody against 5-methylcytidine co-hybridized against the original input DNA
Keywords = Colon cancer methylation profile


title: Papillary RCC_Sample10

value: 56 years', 'Gender:F', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample03

value: 68 years', 'Gender:M', 'Histo:1', 'Class:1'


title: 12.5dpc Gli3Xt/Xt Vs wild type hindlimb

city: St Lucia

first: Sean

middle: M

last: Grimmond

state: QLD

address: IMB, Uni of Qld

country: Australia

institute: Institute of Molecular Bioscience

description: Dual colour hybridisation of the RNA from the anterior region of 12.5dpc hindlimbs of Gli3 extra toes mutants (Gli3Xt/Xt) Vs wildtype.

organism: Mus musculus

source_name: 12.5dpc Gli3Xt/Xt hindlimb

label_protocol: Ambion Messamp

extract_protocol: RNeasy mini

tag: Pool of:

tag: Strain

tag: Genotype

value: Gli3 Xta/Xta

tag: Gender

value: mixed

source_name: 12.5dpc wildtype hindlimb

value: Wildtype


title: Papillary RCC_Sample11

value: 56 years', 'Gender:M', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample09

value: 84 years', 'Gender:F', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample02

value: 59 years', 'Gender:M', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample06

value: 70 years', 'Gender:M', 'Histo:1', 'Class:1'


title: Papillary RCC_Sample04

value: 32 years', 'Gender:M', 'Histo:2A', 'Class:1'


title: 12.5dpc Gli3Xt/Xt Vs wild type forelimb

description: Dual colour hybridisation of the RNA from the anterior region of 12.5dpc forelimbs of Gli3 extra toes mutants (Gli3Xt/Xt) Vs wildtype.

data_processing: Imagene5.0, Genespring5.0

source_name: 12.5dpc Gli3Xt/Xt forelimb

tag: Age

source_name: 12.5dpc wildtype forelimb

value: wildtype


title: 12.5dpc Gli3Xt/Xt Vs wild type forelimb b

source_name: 12.5dpc wild type forelimb


title: 11.5dpc Gli3Xt/Xt Vs wild type forelimb b

description: Dual colour hybridisation of the RNA from the anterior region of 11.5dpc forelimbs of Gli3 extra toes mutants (Gli3Xt/Xt) Vs wildtype.

data_processing: Imagene5, Genespring5.0

source_name: 11.5dpc Gli3Xt/Xt forelimb

value: Glie Xta/Xta

source_name: 11.5dpc wildtype forelimb


title: Papillary RCC_Sample08

value: 73 years', 'Gender:F', 'Histo:1', 'Class:1'


title: 12.5dpc Gli3Xt/Xt Vs wild type hindlimb b


title: 11.5dpc Gli3Xt/Xt Vs wild type hindlimb b

description: Dual colour hybridisation of the RNA from the anterior region of 11.5dpc hindlimbs of Gli3 extra toes mutants (Gli3Xt/Xt) Vs wildtype.

source_name: 11.5dpc Gli3Xt/Xt hindlimb

source_name: 11.5dpc wildtype hindlimb


title: Papillary RCC_Sample01

value: 46 years', 'Gender:F', 'Histo:2B', 'Class:2'


title: Papillary RCC_Sample07

value: 72 years', 'Gender:F', 'Histo:1', 'Class:1'


title: 11.5dpc Gli3Xt/Xt Vs wild type hindlimb


title: 11.5dpc Gli3Xt/Xt Vs wild type forelimb

source_name: 11.5dpc Gli3-/- forelimb

source_name: 11.5dpc wild type forelimb


title: Papillary RCC_Sample05

value: 71 years', 'Gender:M', 'Histo:1 and 2A', 'Class:1'


title: WI-38

description:
Female primary lung fibroblast DNA enriched via a monoclonal antibody against 5-methylcytidine co-hybridized against the original input DNA
Keywords = Normal female methylation profile


title: Papillary RCC_Sample12

value: 80 years', 'Gender:F', 'Histo:1', 'Class:1'


title: SW48_1


title: 12.5dpc Gli3Xt/Xt Vs wild type forelimb NIA B

source_name: 12.5dpc Gli3Xt/Xt Forelimb

label_protocol: MessageAmp

extract_protocol: RNeasy Mini


title: 12.5dpc Gli3Xt/Xt Vs wild type forelimb NIA


title: 11.5dpc Gli3Xt/Xt Vs wild type hindlimb NIA B

label_protocol: Message Amp


title: 12.5dpc Gli3Xt/Xt Vs wild type hindlimb NIA

description: Dual colour hybridisation of the RNA from the anterior region of 12.5dpc Forelimbs of Gli3 extra toes mutants (Gli3Xt/Xt) Vs wildtype


title: 11.5dpc Gli3Xt/Xt Vs wild type hindlimb NIA

description: Dual colour hybridisation of the RNA from the anterior region of 11.5dpc hindlimbs of Gli3 extra toes mutants (Gli3Xt/Xt) Vs wildtype


title: 12.5dpc Gli3Xt/Xt Vs wild type hindlimb B


title: 11.5dpc Gli3Xt/Xt Vs wild type forelimb NIA

description: Dual colour hybridisation of the RNA from the anterior region of 11.5dpc forelimbs of Gli3 extra toes mutants (Gli3Xt/Xt) Vs wildtype

value: Gli3 Wildtype


title: 11.5dpc Gli3Xt/Xt Vs wild type forelimb NIA B


title: genome scan: TAF1-IMR90 set 4 of 38

status: Public on Jun 29 2005

city: San Diego

first: Chunxu

last: Qu

state: CA

department: Gene Regulation

institute: Ludwig Institute for Cancer Research

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 4.

source_name: Chromatin immunoprecipitated DNA using TAF1 antibody

source_name: input DNA


title: Condense array: TAF1-IMR90 Rep2

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy5 channel.


title: genome scan: TAF1-IMR90 set 2 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 2.


title: Condense array: acH3-IMR90 Rep2

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of acetylated Histone3 binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy3 channel.

source_name: Chromatin immunoprecipitated DNA using acetylated Histone3 antibody


title: Condense array: MeH3K4-IMR90 Rep1

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of K4 methylated Histone3 binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy3 channel.

source_name: Chromatin immunoprecipitated DNA using K4 methylated Histone3 antibody


title: genome scan: TAF1-IMR90 set 32 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 32.


title: genome scan: TAF1-IMR90 set 31 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 31.


title: Condense array: MeH3K4-IMR90 Rep2

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of K4 methylated Histone3 binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy5 channel.


title: genome scan: TAF1-IMR90 set 19 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 19.


title: Condense array: TAF1-IMR90 Rep1

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy3 channel.


title: genome scan: TAF1-IMR90 set 37 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 37.


title: genome scan: TAF1-IMR90 set 35 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 35.


title: genome scan: TAF1-IMR90 set 1 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 1.


title: Condense array: acH3-IMR90 Rep1

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of acetylated Histone3 binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy5 channel.


title: genome scan: TAF1-IMR90 set 25 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 25.


title: genome scan: TAF1-IMR90 set 33 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 33.


title: genome scan: TAF1-IMR90 set 20 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 20.


title: genome scan: TAF1-IMR90 set 29 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 29.


title: genome scan: TAF1-IMR90 set 21 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 21.


title: genome scan: TAF1-IMR90 set 18 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 18.


title: genome scan: TAF1-IMR90 set 34 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 34.


title: genome scan: TAF1-IMR90 set 23 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 23.


title: genome scan: TAF1-IMR90 set 24 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 24.


title: genome scan: TAF1-IMR90 set 28 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 28.


title: genome scan: TAF1-IMR90 set 38 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 38.


title: genome scan: TAF1-IMR90 set 3 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 3.


title: genome scan: TAF1-IMR90 set 36 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 36.


title: genome scan: TAF1-IMR90 set 30 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 30.


title: Condense array: Pol II-IMR90 Rep2

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of RNA polymerase II binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy5 channel.

source_name: Chromatin immunoprecipitated DNA using RNA polymerase II antibody


title: Condense array: Pol II-IMR90 Rep1

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of RNA polymerase II binding using the condensed array which includes 9966 putative TAF1 binding sequences plus 29 control genomic loci, selected from the ENCODE regions. This is one of the two dye-swapped replicates with target hydridized on cy3 channel.


title: genome scan: TAF1-IMR90 set 16 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 16.


title: gene express in IMR90 cells, biological replicate 1 of 2

description:
In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is one of the two independent IMR90 samples.
Keywords = human
Keywords = IMR90
Keywords = RNA
Keywords = GWLA
Keywords = promoter
Keywords = LICR renlab

source_name: total RNA from IMR90 cells


title: genome scan: TAF1-IMR90 set 5 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 5.


title: CSR3

status: Public on Jun 24 2005

city: Oxford

first: Natalie

last: Schweitzer

state: OH

institute: Miami University

description: Expression report for pooled samples CSR3

organism: Rattus norvegicus

source_name: Rat Heart - Left Ventricle


title: CSS1

description: Expression report for pooled samples CSS1


title: CSS2

description: Expression report for pooled samples CSS2


title: CSA3

description: Expression report for pooled samples CSA3


title: CSS4

description: Expression report for pooled samples CSS4


title: CSR1

description: Expression report for pooled samples CSR1


title: CSR2

description: Expression report for pooled samples CSR2


title: CSS3

description: Expression report for pooled samples CSS3


title: genome scan: TAF1-IMR90 set 22 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 22.


title: gene express in IMR90 cells, biological replicate 2 of 2


title: CSA4

description: Expression report for pooled samples CSA4


title: genome scan: TAF1-IMR90 set 7 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 7.


title: genome scan: TAF1-IMR90 set 14 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 14.


title: CSA1

description: Expression report for pooled samples CSA1


title: CSA2

description: Expression report for pooled samples CSA2


title: genome scan: TAF1-IMR90 set 11 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 11.


title: CSR4

description: Expression report for pooled samples CSR4


title: genome scan: TAF1-IMR90 set 15 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 15.


title: Giessen_dOxyR_7C

status: Public on Jun 22 2005

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

description: hydrogen peroxide stress in delta-oxyR mutant; 7 min after H2O2 addition

data_processing: MAS 5.0 (CEL files for alternative processing are available)

organism: Cereibacter sphaeroides

source_name: Rhodobacter sphaeroides

growth_protocol: The cells were cultivated at 32 °C in malate minimal salt medium under semiaerobic conditions (approx. 0.85 mg l-1 dissolved oxygen) with continuous shaking at 140 rpm.

extract_protocol: Cells (at OD600~0.5) were collected by centrifugation. Total RNA was isolated by the hot phenol method, quantified by spectrophotometric analysis (A260).

treatment_protocol: 1 mM H2O2 (final concentration) for 7 min


title: Giessen_dOxyR_7B


title: genome scan: TAF1-IMR90 set 8 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 8.


title: genome scan: TAF1-IMR90 set 12 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 12.


title: genome scan: TAF1-IMR90 set 9 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 9.


title: Giessen_dOxyR_7A


title: Giessen_dOxyR_B

description: control for dOxyR strain (no stress)


title: Giessen_dOxyR_C

description: control for dOxyR strain (no stress)


title: Giessen-WT_7B

description: 7 min of hydrogen peroxide stress


title: Giessen_WT_30B

description: 30 min of hydrogen peroxide stress

treatment_protocol: 1 mM H2O2 (final concentration) for 30 min


title: Giessen_WT_7C

description: 7 min of hydrogen peroxide stress


title: Giessen_doxyR_A

description: control for dOxyR strain (no stress)


title: genome scan: TAF1-IMR90 set 17 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 17.


title: Giessen_WT_30C

description: 30 min of hydrogen peroxide stress


title: genome scan: TAF1-IMR90 set 10 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 10.


title: mRNA expression in IMR90 cells using the putative promoter tiling array

status: Public on Jun 23 2005

description: To verify the putative promoters drive transcription, the mRNA expression was measured using the tiling array covering these regions.

source_name: IMR90 cells

tag: IMR90 cells, putative promoter


title: Giessen_WT_30A

description: 30 min of hydrogen peroxide stress


title: Giessen-WT_A

description: control culture for oxidative stress experiments


title: Giessen-WT_7A

description: 7 min of hydrogen peroxide stress


title: Giessen-WT_C


title: Giessen-WT_B


title: Seguin_IDR_BrownNorway_Liver_treated6

status: Public on Jun 21 2005

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: D-PA sample #6

label: Affymetrix

source_name: Brown Norway DPA-Treated Liver

growth_protocol: Male Brown Norway (BN) rats weighing 150-170 g were purchased from Charles River (Montreal, QC). All animals were housed in plastic cages (two/cage) with wooden chips as bedding in a 12:12 h light:dark cycle at 22 °C. Rats were given access to standard rat chow (Agribrands, Purina Canada, Strathroy, ON) and ad libitum access to tap water for 1 week (acclimatization period) before starting experiments.

extract_protocol: Total RNA was isolated from frozen liver tissues of individual rats using Qiagen RNeasy mini kits as described by the manufacturer. RNA concentrations and purity were determined spectrophotometrically. RNA quality was further assessed by capillary electrophoresis using the Agilent Bioanalyzer. We used 10 micrograms of total RNA from each individual animal for microarray analysis.

treatment_protocol: Rats were given water (vehicle, n = 4) or 1 mL of D-penicillamine dissolved in tap water in a single dose of 150 mg/kg by oral gavage (n = 8).  Animals were sacrificed 6 hours after initial dosing.

tag: Organism

value: Rattus norvegicus

value: Brown Norway

tag: Weight

tag: Tissue

value: liver

value: male

tag: Sacrifice Time

value: 6 hours

tag: Treatment

value: D-penicillamine 150 mg/kg by oral gavage


title: Seguin_IDR_BrownNorway_Liver_treated5

description: D-PA sample #5


title: Seguin_IDR_BrownNorway_Liver_treated4

description: D-PA sample #4


title: Btk KO primary splenic B-cells (sample1)

city: Huddinge

first: Jessica

last: Lindvall

address: Hälsovägen 7

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: primary whole splenic B-lymphocytes from Btk KO mice

data_processing: Scaling factor 100

label: Biotin Streptavidin-phycoerythrin

source_name: whole splenic B-cells from adult Btk KO mice

value: Btk KO/CBA were created by back-crossing Btk KO/SW129 mice on CBA background strain for 9 generations


title: Seguin_IDR_BrownNorway_Liver_treated2

description: D-PA sample #2

growth_protocol:
Male Brown Norway (BN) rats weighing 150-
170 g were purchased from Charles River (Montreal, QC). All
animals were housed in plastic cages (two/cage) with wooden
chips as bedding in a 12:12 h light:dark cycle at 22 °C. Rats
were given access to standard rat chow (Agribrands, Purina
Canada, Strathroy, ON) and ad libitum access to tap water for
1 week (acclimatization period) before starting experiments.

extract_protocol:
Total RNA was isolated from frozen liver
tissues of individual rats using Qiagen RNeasy mini kits as
described by the manufacturer. RNA concentrations and purity
were determined spectrophotometrically. RNA quality was
further assessed by capillary electrophoresis using the Agilent
Bioanalyzer. We used 10 micrograms of total RNA from each individual
animal for microarray analysis.

treatment_protocol:
Rats were given water (vehicle, n = 4) or 1 mL of D-penicillamine
dissolved in tap water in a single dose of 150 mg/kg by oral
gavage (n = 8).  Animals were sacrificed 6 hours after initial dosing.


title: Seguin_IDR_BrownNorway_Liver_treated7

description: D-PA sample #7


title: Seguin_IDR_BrownNorway_Liver_treated3

description: D-PA sample #3


title: genome scan: TAF1-IMR90 set 27 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 27.


title: Xid primary splenic B-cells (sample2)

description: primary whole splenic B-lymphocytes from Xid mice

source_name: whole splenic B-cells from adult Xid mice

value: CBA/N (mutation R28C)


title: genome scan: TAF1-IMR90 set 6 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 6.


title: Seguin_IDR_BrownNorway_Liver_treated8

description: D-PA sample #8


title: Seguin_IDR_BrownNorway_Liver_control1

description: Control sample #1

source_name: Brown Norway Control Liver

extract_protocol:
Total RNA was isolated from frozen liver
tissues of individual rats using Qiagen RNeasy mini kits as
described by the manufacturer. RNA concentrations and purity
were determined spectrophotometrically. RNA quality was
further assessed by capillary electrophoresis using the Agilent
Bioanalyzer. We used 10 íg of total RNA from each individual
animal for microarray analysis

treatment_protocol:
Rats were given water (vehicle, n = 4) or 1 mL of D-penicillamine
dissolved in tap water in a single dose of 150 mg/kg by oral
gavage (n = 8).


title: Seguin_IDR_BrownNorway_Liver_control2

description: Control sample #2

extract_protocol:
Total RNA was isolated from frozen liver
tissues of individual rats using Qiagen RNeasy mini kits as
described by the manufacturer. RNA concentrations and purity
were determined spectrophotometrically. RNA quality was
further assessed by capillary electrophoresis using the Agilent
Bioanalyzer. We used 10 micrograms of total RNA from each individual
animal for microarray analysis

tag: Characteristics:


title: wild type CBA (sample2)

description: primary whole splenic B-lymphocytes from wild type CBA adult mice

source_name: whole splenic B-cells from adult CBA mice

tag: strain

value: CBA


title: Seguin_IDR_BrownNorway_Liver_treated1

description: D-PA sample #1


title: genome scan: TAF1-IMR90 set 13 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 13.


title: THYM2

status: Public on Jun 20 2005

city: La Jolla

first: Jennifer

middle: A

last: Hammond

address: 10550 N. Torrey Pines Rd.

institute: The Scripps Research Institute

description: full description of sample found in Elena M. Comelli, Steven R. Head, Tim Gilmartin, Thomas Whisenant, Stuart M. Haslam, Simon J. North, Nyet-Kui Wong, Takashi Kudo, Hisashi Narimatsu, Jeffrey D. Esko, Kurt Drickamer, Anne Dell, and James C. Paulson. (2005) A Focused Microarray Approach to Functional Glycomics: Transcriptional Regulation of the Glycome.

data_processing: dCHIPv1.3, PM-only algorithm

label: biotin

source_name: Thymus tissue from WT C57BL/6 male mice

value: 6-8 weeks

value: thymus

value: wild-type


title: THYM1


title: TEST3

source_name: Testis tissue from WT C57BL/6 male mice

value: testis


title: Seguin_IDR_BrownNorway_Liver_control4

description: Control sample #4


title: TEST2


title: Seguin_IDR_BrownNorway_Liver_control3

description: Control sample #3


title: SPLN3

source_name: Spleen tissue from WT C57BL/6 male mice

value: spleen


title: TEST1


title: Xid primary splenic B-cells (sample1)


title: wild type CBA (sample1)


title: SPLN2


title: THYM3


title: LNG3

source_name: Lung tissue from WT C57BL/6 male mice

value: lung


title: LN2

source_name: Lymph node tissue from WT C57BL/6 male mice

value: lymph node


title: SPLN1


title: LN1


title: LIV1

source_name: Liver tissue from WT C57BL/6 male mice


title: LN3


title: LIV3


title: LIV2


title: LNG2


title: LNG1


title: KID3

source_name: Kidney tissue from WT C57BL/6 male mice

value: kidney


title: Btk KO primary splenic B-cells (sample2)


title: KID2


title: KID1


title: BRN3

source_name: Brain tissue from WT C57BL/6 male mice

value: brain


title: BM2

source_name: Bone marrow tissue from WT C57BL/6 male mice

value: bone marrow


title: Brain versus common control derived from a mixture of Placenta, Testis, Thymus and Brain

status: Public on Jun 19 2005

city: Rehovot

first: Omer

last: Barad

address: Plaut 10, Science Park

country: Israel

institute: Rosetta Genomics Ltd.

description: Determining the expression of known and computationally predicted microRNAs as described in Bentwich et al., submitted to Nature genetics, 2005

data_processing: Median intensity

molecule: other

source_name: Brain

tag: Small RNAs

source_name: A mixture of Placenta, Testis, Thymus and Brain


title: BRN2


title: Prostate

source_name: Prostate


title: BM3


title: BRN1


title: Placenta versus common control derived from a mixture of Placenta, Testis, Thymus and Brain

source_name: Placenta


title: Testis versus common control derived from a mixture of Placenta, Testis, Thymus and Brain

source_name: Testis


title: BM1


title: Thymus versus common control derived from a mixture of Placenta, Testis, Thymus and Brain

source_name: Thymus


title: KIV-1-GAS-24E08-1-RML

status: Public on Jun 17 2005

city: Hamilton

first: Steve

middle: F

last: Porcella

state: MT

address: 903 SOUTH 4TH Street

department: Rocky Mountain Laboratories

institute: NIAID

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24E08 column.

label: unknown

organism:
Streptococcus pyogenes
Macaca fascicularis

source_name: Throat Swab

extract_protocol: Total RNA was extracted from monkey tonsillar throat swabs with the  FastPrep FP 120 kit (Qbiogene, Carlsbad, CA) by immersing the swab tips directly  into the FastPrep Blue tubes containing 300 ul 5 mM ammonium  aurintricarboxylate, 500 ul CRSR-Blue(Qbiogene), and acid phenol:chloroform  (5:1, pH 4.5; Ambion, Austin, TX).   The mixture was homogenized (80 sec at speed  #5), heated at 65 oC for 20 min, and centrifuged at 16,000xg for 15 min.  The aqueous phase was collected, 250 ug glycogen (Roche Applied Science, Indianapolis, IN) and 0.8 ug MS2 carrier RNA (Roche Applied Science, Indianapolis, IN) was added, and the mixture was concentrated to 100 ul with a vacuum concentrator  (Eppendorf, Germany).  The concentrate was purified using the Qiagen RNeasy 96 kit following the manufacturer's protocol (Qiagen, Valencia, CA).

tag: Day

value: 4 Gender:Male GAS CFU:200


title: KIV-1-GAS-24E09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24E09 column.

value: 1 Gender:Male GAS CFU:0


title: KIV-1-GAS-24F08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24F08 column.

value: 7 Gender:Male GAS CFU:90


title: KIV-1-GAS-24F07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24F07 column.

value: 16 Gender:Male GAS CFU:1000


title: KIV-1-GAS-24F05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24F05 column.

value: 32 Gender:Male GAS CFU:1000


title: KIV-1-GAS-24E05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24E05 column.

value: 23 Gender:Male GAS CFU:0


title: KIV-1-GAS-24F04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24F04 column.

value: 58 Gender:Male GAS CFU:0


title: KIV-1-GAS-24E07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24E07 column.

value: 9 Gender:Male GAS CFU:20


title: KIV-1-GAS-24F03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24F03 column.

value: 86 Gender:Male GAS CFU:0


title: KIV-1-GAS-24E03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24E03 column.

value: 72 Gender:Male GAS CFU:0


title: KIV-1-GAS-24E04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24E04 column.

value: 45 Gender:Male GAS CFU:10


title: KIV-1-GAS-24C09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24C09 column.

value: 86 Gender:Female GAS CFU:0


title: KIV-1-GAS-24C04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24C04 column.

value: 7 Gender:Female GAS CFU:4100


title: KIV-1-GAS-24C07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24C07 column.

value: 32 Gender:Female GAS CFU:1


title: KIV-1-GAS-24C08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24C08 column.

value: 58 Gender:Female GAS CFU:0


title: KIV-1-GAS-24E06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24E06 column.

value: 0 Gender:Male GAS CFU:0


title: KIV-1-GAS-24C03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24C03 column.

value: 2 Gender:Female GAS CFU:1


title: KIV-1-GAS-24C05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24C05 column.

value: 16 Gender:Female GAS CFU:1


title: KIV-1-GAS-24B09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24B09 column.

value: 72 Gender:Female GAS CFU:0


title: KIV-1-GAS-24B08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24B08 column.

value: 45 Gender:Female GAS CFU:1


title: KIV-1-GAS-24B06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24B06 column.

value: 0 Gender:Female GAS CFU:0


title: KIV-1-GAS-24B07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24B07 column.

value: 23 Gender:Female GAS CFU:3000


title: KIV-1-GAS-24B03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24B03 column.

value: 1 Gender:Female GAS CFU:1000


title: KIV-1-GAS-24B04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24B04 column.

value: 4 Gender:Female GAS CFU:500


title: KIV-1-GAS-23F07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23F07 column.

value: 16 Gender:Female GAS CFU:1010


title: KIV-1-GAS-23F09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23F09 column.

value: 2 Gender:Female GAS CFU:90


title: KIV-1-GAS-23F05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23F05 column.

value: 32 Gender:Female GAS CFU:2600


title: KIV-1-GAS-23F08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23F08 column.

value: 7 Gender:Female GAS CFU:1100


title: KIV-1-GAS-23F04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23F04 column.


title: KIV-1-GAS-23C09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23C09 column.

value: 86 Gender:Male GAS CFU:0


title: KIV-1-GAS-24B05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 24B05 column.

value: 9 Gender:Female GAS CFU:600


title: KIV-1-GAS-23E08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23E08 column.

value: 4 Gender:Female GAS CFU:160


title: KIV-1-GAS-23E03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23E03 column.


title: KIV-1-GAS-23C03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23C03 column.

value: 2 Gender:Male GAS CFU:800


title: KIV-1-GAS-23E07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23E07 column.

value: 9 Gender:Female GAS CFU:12400


title: KIV-1-GAS-23E04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23E04 column.


title: KIV-1-GAS-23E09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23E09 column.

value: 1 Gender:Female GAS CFU:0


title: KIV-1-GAS-23E06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23E06 column.


title: KIV-1-GAS-23C07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23C07 column.

value: 32 Gender:Male GAS CFU:0


title: KIV-1-GAS-23C08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23C08 column.

value: 58 Gender:Male GAS CFU:0


title: KIV-1-GAS-23F03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23F03 column.

value: 86 Gender:Female GAS CFU:40


title: KIV-1-GAS-23C04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23C04 column.

value: 7 Gender:Male GAS CFU:1200


title: KIV-1-GAS-23B09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23B09 column.

value: 72 Gender:Male GAS CFU:0


title: KIV-1-GAS-23B08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23B08 column.

value: 45 Gender:Male GAS CFU:1000


title: KIV-1-GAS-23B07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23B07 column.

value: 23 Gender:Male GAS CFU:5000


title: KIV-1-GAS-23C05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23C05 column.

value: 16 Gender:Male GAS CFU:9000


title: KIV-1-GAS-23E05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23E05 column.

value: 23 Gender:Female GAS CFU:20


title: KIV-1-GAS-23B06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23B06 column.

value: 0 Gender:Male GAS CFU:0


title: KIV-1-GAS-22E09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22E09 column.

value: 1 Gender:Male GAS CFU:1


title: KIV-1-GAS-23B03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23B03 column.


title: KIV-1-GAS-23B04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23B04 column.

value: 4 Gender:Male GAS CFU:3000


title: KIV-1-GAS-22E08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22E08 column.

value: 4 Gender:Male GAS CFU:6100


title: KIV-1-GAS-22E03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22E03 column.

value: 72 Gender:Male GAS CFU:300


title: KIV-1-GAS-22F09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22F09 column.

value: 2 Gender:Male GAS CFU:33000


title: KIV-1-GAS-22F05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22F05 column.

value: 32 Gender:Male GAS CFU:111000


title: KIV-1-GAS-22F07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22F07 column.

value: 16 Gender:Male GAS CFU:36000


title: KIV-1-GAS-22C05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22C05 column.

value: 16 Gender:Female GAS CFU:61000


title: KIV-1-GAS-22F04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22F04 column.

value: 58 Gender:Male GAS CFU:5700


title: KIV-1-GAS-22E04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22E04 column.

value: 45 Gender:Male GAS CFU:57000


title: KIV-1-GAS-23B05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 23B05 column.

value: 9 Gender:Male GAS CFU:1


title: KIV-1-GAS-22B09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22B09 column.

value: 72 Gender:Female GAS CFU:0


title: KIV-1-GAS-22E07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22E07 column.

value: 9 Gender:Male GAS CFU:19000


title: KIV-1-GAS-22C08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22C08 column.

value: 58 Gender:Female GAS CFU:0


title: KIV-1-GAS-22C07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22C07 column.

value: 32 Gender:Female GAS CFU:1


title: KIV-1-GAS-22C03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22C03 column.

value: 2 Gender:Female GAS CFU:0


title: KIV-1-GAS-22F03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22F03 column.

value: 86 Gender:Male GAS CFU:0


title: KIV-1-GAS-22F08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22F08 column.

value: 7 Gender:Male GAS CFU:300


title: KIV-1-GAS-22E05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22E05 column.

value: 23 Gender:Male GAS CFU:25000


title: KIV-1-GAS-22E06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22E06 column.

value: 0 Gender:Male GAS CFU:0


title: KIV-1-GAS-22B07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22B07 column.

value: 23 Gender:Female GAS CFU:14000


title: KIV-1-GAS-22B06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22B06 column.

value: 0 Gender:Female GAS CFU:0


title: KIV-1-GAS-22C04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22C04 column.

value: 7 Gender:Female GAS CFU:10


title: KIV-1-GAS-21F08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21F08 column.

value: 7 Gender:Female GAS CFU:85000


title: KIV-1-GAS-22B03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22B03 column.

value: 1 Gender:Female GAS CFU:0


title: KIV-1-GAS-21F07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21F07 column.

value: 16 Gender:Female GAS CFU:18000


title: KIV-1-GAS-22B04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22B04 column.

value: 4 Gender:Female GAS CFU:0


title: KIV-1-GAS-22B05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22B05 column.

value: 9 Gender:Female GAS CFU:0


title: KIV-1-GAS-21F09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21F09 column.

value: 2 Gender:Female GAS CFU:6000


title: KIV-1-GAS-22B08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22B08 column.

value: 45 Gender:Female GAS CFU:1


title: KIV-1-GAS-22C09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 22C09 column.

value: 86 Gender:Female GAS CFU:0


title: KIV-1-GAS-21C05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21C05 column.

value: 16 Gender:Male GAS CFU:109000


title: KIV-1-GAS-21E07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21E07 column.

value: 9 Gender:Female GAS CFU:56000


title: KIV-1-GAS-21C08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21C08 column.

value: 58 Gender:Male GAS CFU:200


title: KIV-1-GAS-21E06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21E06 column.


title: KIV-1-GAS-21C07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21C07 column.

value: 32 Gender:Male GAS CFU:18000


title: KIV-1-GAS-21E08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21E08 column.

value: 4 Gender:Female GAS CFU:92000


title: KIV-1-GAS-21E09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21E09 column.

value: 1 Gender:Female GAS CFU:21000


title: KIV-1-GAS-21F03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21F03 column.

value: 86 Gender:Female GAS CFU:100


title: KIV-1-GAS-21C04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21C04 column.

value: 7 Gender:Male GAS CFU:3500


title: KIV-1-GAS-21C03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21C03 column.

value: 2 Gender:Male GAS CFU:1800


title: KIV-1-GAS-21B08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21B08 column.

value: 45 Gender:Male GAS CFU:2000


title: KIV-1-GAS-21E05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21E05 column.

value: 23 Gender:Female GAS CFU:21000


title: KIV-1-GAS-21F04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21F04 column.

value: 58 Gender:Female GAS CFU:90


title: KIV-1-GAS-21C09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21C09 column.

value: 86 Gender:Male GAS CFU:0


title: KIV-1-GAS-21B06-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21B06 column.

value: 0 Gender:Male GAS CFU:0


title: KIV-1-GAS-21B07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21B07 column.

value: 23 Gender:Male GAS CFU:2900


title: KIV-1-GAS-21E03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21E03 column.

value: 72 Gender:Female GAS CFU:1400


title: KIV-1-GAS-21B05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21B05 column.

value: 9 Gender:Male GAS CFU:1800


title: KIV-1-GAS-21B09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21B09 column.

value: 72 Gender:Male GAS CFU:300


title: KIV-1-GAS-21B04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21B04 column.

value: 4 Gender:Male GAS CFU:1500


title: KIV-1-GAS-21F05-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21F05 column.

value: 32 Gender:Female GAS CFU:12000


title: KIV-1-GAS-20F09-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 20F09 column.

value: 2 Gender:Male GAS CFU:200


title: KIV-1-GAS-21B03-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 21B03 column.

value: 1 Gender:Male GAS CFU:2300


title: KIV-1-GAS-20F04-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 20F04 column.

value: 58 Gender:Male GAS CFU:800


title: KIV-1-GAS-20F08-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 20F08 column.

value: 7 Gender:Male GAS CFU:7400


title: KIV-1-GAS-20F07-1-RML

description: Data can be found for this sample in CEL, EXP, and PPA files included as an attachment to this submission. The filename for the CEL and EXP files is the same as the Sample_title field. The column in the PPA file corresponding to this sample is the 20F07 column.

value: 16 Gender:Male GAS CFU:700


title: genome scan: TAF1-IMR90 set 26 of 38

description: In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex (PIC) throught the non-repeat sequences of the human genome using IMR90 cells and nimblegen platform.  The resulting map defines 10571 active promoters corresponding to 6763 known genes and at least 1199 unannotated transcriptional units.  Tha map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  The examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. This is the genome-wide location analysis of TAF1 binding using genome scan array 26.

source_name: Chromatin immunoprecipitated DNA using TAF1 antibody

source_name: input DNA