title: Colo, rep1

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

description: The Genome-wide Analysis of Palindrome Formation (GAPF) procedure was performed as described previously with modifications (Tanaka et al., Nat Genet 37, 320-7, 2005). One ug of high molecular weight genomic DNA in 50 ul water with 100mM NaCl was boiled for 7 min and immediately transferred on ice (Snap-back). After snap-back treatment, 6 ul of S1 nuclease buffer, 4 ul of 3M NaCl and 100 units of S1 nuclease (Invitrogen) were added to the DNA and incubated at 37C for 1h. S1 nuclease was inactivated by adding 10 mM EDTA and phenol/chloroform extraction. DNA was precipitated with ethanol, dissolved in water and digested either with 40 units of MspI, TaqI or MseI (New England Biolab) for 16 h. DNA was precipitated, dissolved in 21 ul of water, and ligated to MspI-, TaqI- or MseI- specific linker by adding 5 ul of 20 mM linker, 3 ul of T4DNA ligase buffer and 400 units of T4 DNA ligase (New England Biolabs) at 16C for 16 hs. DNA was precipitated and dissolved in 200 ul TE, followed by application onto Microcon YM-50 spin column (Millipore) to remove excess linker. DNA was recovered in 20 ul H2O. Thus, for each Colo320DM and normal human foreskin fibroblast cell culture (HFF2), templates with three different linkers were prepared. For PCR, 2 ul of DNA, 0.5 ul of Faststart Taq DNA polymerase (Roche), 2.5 ul of 2 mM dNTP, 5 ul of 10xPCR buffer with MgCl2 (for Faststart Taq DNA polymerase, Roche), and 2 uM of a linker-specific primer were mixed with H2O for a total reaction volume of 50 ul. For MspI-linker ligated DNA, 5 ul of GC-rich solution (for Faststart Taq DNA polymerase, Roche) was also included in the reaction mixture. PCR was performed at 96C for 6 min followed by 25 cycles of 96C for 30 s, 55C for 30 s and 72C for 30 s on a GeneAmp PCR system 9700 (Perkin-Elmer). PCR reactions using the same template with three different linker-specific primers were concentrated using Microcon YM-50 spin column. DNA was recovered in 25 ul H2O, and fragmented using DNaseI (New England Biolab). After heat inactivation of DNaseI, DNA was labeled with biotin-11-dATP (Perkin Elmer) using terminal transferase (Roche). The procedure was performed in triplicate to produce three independent preparations of DNA for hybridization onto GeneChip Human Genome U133A arrays (Affymetrix).

hyb_protocol: standard Affymetrix hydridization procedures

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner

data_processing: The data were normalized by RMA using the Affy package of Bioconductor

source_name: Colo 320DM colon cancer cell line

extract_protocol: GAPF procedure from Hisashi Tanaka; Tanaka et al., Nat Genet 37, 320-7, 2005, PMID 15711546

tag: GAPF positives in Colo cells in culture


title: HFF, rep3

status: Public on Mar 01 2007

type: genomic

country: USA

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: HFF2 normal foreskin fibroblast cell line

label_protocol: DNA was labeled with biotin-11-dATP (Perkin Elmer) using terminal transferase (Roche).

tag: GAPF positives in HFF cells in culture


title: Colo, rep3


title: hy5 mutant vs wildtype expression, rep2

type: RNA

city: New Haven

first: Kun

last: He

state: CT

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

institute: Yale University

description: hy5 mutant vs. wildtype

hyb_protocol: 42C 50% formamide

scan_protocol: Axon GenePix 4000B

data_processing: LIMMA in bioconductor R package

molecule: total RNA

organism: Arabidopsis thaliana

source_name: wildtype reference

label_protocol: amino-allyl and monofunctional dye

growth_protocol: continuous white light for 4 days

extract_protocol: Trizol/RNeasy

tag: 4 days wildtype seedling

source_name: hy5 mutant

tag: 4 days hy5 mutant seedling


title: hy5 mutant vs wildtype expression, rep1

description: hy5 mutant vs. wildtype


title: Ecoli_UTI89_14d_gnotobiotic_mouse_cecum5

status: Public on Feb 02 2007

city: Saint Louis

first: Christopher

middle: Swanson

last: Reigstad

state: MO

address: 4444 Forest Park Blvd.

department: Center for Genome Sciences

institute: Washington University in St. Louis

description: Gene expression data from E. coli UTI89 harvested from gnotobiotic cecum 14d post-inoculation

hyb_protocol: Following fragmentation, 2-5 microg of cDNA were hybridized for 16 hr at 45C on GeneChip Antisense Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) after electronic masking; scaling = 500

organism: Escherichia coli

source_name: Ecoli UTI89 gnotobiotic cecum 14d post-inoculation

label_protocol: RNA isolated using RNeasy kit (Qiagen), reverse transcribed and labeled using BioArray Terminal Labeling Kit (Enzo).

extract_protocol: Extraction of total RNA (RNeasy kit; Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: RNA isolation using RNAprotect and RNeasy kit (Qiagen),

tag: Genotype


title: Ecoli_UTI89_14d_gnotobiotic_mouse_cecum4


title: MP G6 high 3 days vs. MP G4 control 3 days (ExpID 1995)

city: Chapel Hill

first: James

middle: Todd

last: Auman

state: NC

address: 3304 Kerr Hall, Campus Box 7360

department: Institute for Pharmacogenomics and Individualized Therapy

institute: University of North Carolina at Chapel Hill

description: Male Sprague-Dawley rats were treated with 3 daily doses of 100 mg/kg/day methapyrilene or water (vehicle).  24 hours after the last dose, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

data_processing: Five hundred nanograms (500 ng) of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer’s protocol.  For each two color comparison, 750 ng each of Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v. 7.1) using defaults for all parameters.

organism: Rattus norvegicus

source_name: MP G6 high 3 days (Cy3)

tag: MP G6 high 3 days

source_name: MP G4 control 3 days (Cy5)

tag: MP G4 control 3 days


title: Colo, rep2


title: Methapyrilene, Control 1day vs. Methapyrilene, High 1 day (ExpID 1467)

description: Male Sprague-Dawley rats were treated with a single dose of 100 mg/kg methapyrilene or water (vehicle).  24 hours after dosing, equal amounts of total RNA from 4 methapyrilene-treated rat kidneys was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat kidneys).  RNAs were isolated from kidneys with the RNeasy kit according to manufacturer’s protocols.

source_name: Methapyrilene, Control 1day (Cy3)

tag: Methapyrilene, Control 1day

source_name: Methapyrilene, High 1 day (Cy5)

tag: Methapyrilene, High 1 day


title: HFF, rep2


title: hy5 mutant vs wildtype expression, rep3

description: hy5 mutant vs. wildtype


title: MP G3 high 1 day vs. MP G1 control 1 day (ExpID 1994)

description: Male Sprague-Dawley rats were treated with a single dose of 100 mg/kg methapyrilene or water (vehicle).  24 hours after dosing, equal amounts of total RNA from 4 methapyrilene-treated rat livers was pooled and compared to vehicle RNA (pooled from equal amounts of total RNA from 4 vehicle-treated rat livers).  RNAs were isolated from livers with the RNeasy kit according to manufacturer’s protocols.

source_name: MP G3 high 1 day (Cy3)

tag: MP G3 high 1 day

source_name: MP G1 control 1 day (Cy5)

tag: MP G1 control 1 day


title: Ecoli_UTI89_14d_gnotobiotic_mouse_cecum2


title: hy5 mutant vs wildtype expression, rep4

description: hy5 mutant vs. wildtype


title: Ecoli_UTI89_14d_gnotobiotic_mouse_cecum3


title: Ecoli_MG1655_14d_gnotobiotic_mouse_cecum2

description: Gene expression data from E. coli MG1655 harvested from gnotobiotic cecum 14d post-inoculation

source_name: Ecoli MG1655 gnotobiotic cecum 14d post-inoculation


title: Ecoli_MG1655_14d_gnotobiotic_mouse_cecum3


title: Ecoli_MG1655_14d_gnotobiotic_mouse_cecum4


title: Ecoli_MG1655_14d_gnotobiotic_mouse_cecum5


title: HFF, rep1


title: Ecoli_UTI89_14d_gnotobiotic_mouse_cecum1


title: Ecoli_UTI89_6h_anaerobic1

description: Gene expression data from E. coli UTI89 grown anaerobically (6h) in Luria-Bertani medium.

source_name: Ecoli UTI89 anaerobic LB 6h


title: Ecoli_UTI89_3h30m_anaerobic2

description: Gene expression data from E. coli UTI89 grown anaerobically (3h30m) in Luria-Bertani medium.

source_name: Ecoli UTI89 anaerobic LB 3h30m

extract_protocol: Extraction of total RNA (Rneasy kit; Qiagen) was performed according to the manufacturer's instructions.


title: Ecoli_UTI89_4h_anaerobic1

description: Gene expression data from E. coli UTI89 grown anaerobically (4h) in Luria-Bertani medium.

source_name: Ecoli UTI89 anaerobic LB 4h


title: Ecoli_UTI89_6h_anaerobic2


title: Ecoli_UTI89_4h_anaerobic2


title: Ecoli_MG1655_14d_gnotobiotic_mouse_cecum1


title: Ecoli_UTI89_3h_anaerobic2

description: Gene expression data from E. coli UTI89 grown anaerobically (3h) in Luria-Bertani medium.

source_name: Ecoli UTI89 anaerobic LB 3h


title: Ecoli_UTI89_2h30m_anaerobic1

description: Gene expression data from E. coli UTI89 grown anaerobically (2h30m) in Luria-Bertani medium.

source_name: Ecoli UTI89 anaerobic LB 2h30m


title: Ecoli_UTI89_2h30m_anaerobic2


title: Ecoli_UTI89_3h_anaerobic1


title: Ecoli_MG1655_6h45m_anaerobic2

description: Gene expression data from E. coli MG1655 grown anaerobically (6h45m) in Luria-Bertani medium.

source_name: Ecoli MG1655 anaerobic LB 6h45m


title: Ecoli_MG1655_2h30m_anaerobic2

description: Gene expression data from E. coli MG1655 grown anaerobically (2h30m) in Luria-Bertani medium.

source_name: Ecoli MG1655 anaerobic LB 2h30m


title: Ecoli_UTI89_3h30m_anaerobic1


title: Ecoli_MG1655_4h30m_anaerobic1

description: Gene expression data from E. coli MG1655 grown anaerobically (4h30m) in Luria-Bertani medium.

source_name: Ecoli MG1655 anaerobic LB 4h30m


title: Ecoli_MG1655_6h45m_anaerobic1


title: Ecoli_MG1655_3h_anaerobic1

description: Gene expression data from E. coli MG1655 grown anaerobically (3h) in Luria-Bertani medium.

source_name: Ecoli MG1655 anaerobic LB 3h


title: Ecoli_MG1655_3h_anaerobic2


title: Ecoli_MG1655_4h30m_anaerobic2


title: Ecoli_UTI89_19h30m_aerobic1

description: Gene expression data from E. coli UTI89 grown aerobically (19h30m) in Luria-Bertani medium.

source_name: Ecoli UTI89 aerobic LB 19h30m


title: Ecoli_UTI89_26h_aerobic1

description: Gene expression data from E. coli UTI89 grown aerobically (26h) in Luria-Bertani medium.

source_name: Ecoli UTI89 aerobic LB 26h


title: Ecoli_UTI89_12h_aerobic2

description: Gene expression data from E. coli UTI89 grown aerobically (12h) in Luria-Bertani medium.

source_name: Ecoli UTI89 aerobic LB 12h


title: Ecoli_UTI89_26h_aerobic2


title: Ecoli_UTI89_19h30m_aerobic2


title: Ecoli_MG1655_3h45m_anaerobic1

description: Gene expression data from E. coli MG1655 grown anaerobically (3h45m) in Luria-Bertani medium.

source_name: Ecoli MG1655 anaerobic LB 3h45m


title: Ecoli_UTI89_8h_aerobic1

description: Gene expression data from E. coli UTI89 grown aerobically (8h) in Luria-Bertani medium.

source_name: Ecoli UTI89 aerobic LB 8h


title: Ecoli_MG1655_2h30m_anaerobic1


title: Ecoli_UTI89_2h30m_aerobic2

description: Gene expression data from E. coli UTI89 grown aerobically (2h30m) in Luria-Bertani medium.

source_name: Ecoli UTI89 aerobic LB 2h30m


title: Ecoli_UTI89_8h_aerobic2


title: Ecoli_UTI89_12h_aerobic1


title: Ecoli_UTI89_5h_aerobic1

description: Gene expression data from E. coli UTI89 grown aerobically (5h) in Luria-Bertani medium.

source_name: Ecoli UTI89 aerobic LB 5h


title: Ecoli_UTI89_2h30m_aerobic1


title: Ecoli_UTI89_5h_aerobic2


title: Ecoli_MG1655_26h_aerobic1

description: Gene expression data from E. coli MG1655 grown aerobically (26h) in Luria-Bertani medium.

source_name: Ecoli MG1655 aerobic LB 26h


title: Ecoli_MG1655_12h_aerobic1

description: Gene expression data from E. coli MG1655 grown aerobically (12h) in Luria-Bertani medium.

source_name: Ecoli MG1655 aerobic LB 12h


title: Ecoli_MG1655_18h_aerobic2

description: Gene expression data from E. coli MG1655 grown aerobically (18h) in Luria-Bertani medium.

source_name: Ecoli MG1655 aerobic LB 18h


title: Ecoli_MG1655_8h_aerobic2

description: Gene expression data from E. coli MG1655 grown aerobically (8h) in Luria-Bertani medium.

source_name: Ecoli MG1655 aerobic LB 8h


title: Ecoli_MG1655_3h45m_anaerobic2


title: Ecoli_MG1655_26h_aerobic2


title: Ecoli_MG1655_12h_aerobic2


title: Ecoli_MG1655_5h_aerobic1

description: Gene expression data from E. coli MG1655 grown aerobically (5h) in Luria-Bertani medium.

source_name: Ecoli MG1655 aerobic LB 5h


title: Ecoli_MG1655_5h_aerobic2


title: Ecoli_MG1655_18h_aerobic1


title: Ecoli_MG1655_8h_aerobic1


title: Ecoli_MG1655_2h30m_aerobic1

description: Gene expression data from E. coli MG1655 grown aerobically (2.5h) in Luria-Bertani medium.

source_name: Ecoli MG1655 aerobic LB 2h30m


title: Ecoli_MG1655_2h30m_aerobic2


title: UtrLaser3hr(3)-5_1

status: Public on Feb 01 2007

first: Kara

last: Powder

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

description: Laser-treated versus control, 3hr timepoint, biological replicate number 3

hyb_protocol: Labeled cDNA populations were precipitated and resuspended in 20ul hybridization buffer (50% formamide, 6x SSPE, 5x Denharts, 0.5% SDS. 10% dextran sulfate). Microarray slides were hybridized at 37 degrees C for 12h

scan_protocol: Microarray chips were scanned using a GMS 418 Scanner (Affymetrix, Santa Clara, CA)

data_processing: Microarray images were analyzed with the BioDiscovery Imagene software package to generate raw intensity data.

molecule: polyA RNA

organism: Gallus gallus

source_name: Utricle sensory epithelia

label_protocol: Purified run-off RNAs from each sample were used as templates in an oligo dT12-15 primed cDNA synthesis reaction that included amino-allyl dUTP (Sigma, 0.2mM). The cDNA was then either coupled to Cy3 or Cy5 mono ester dyes (Amersham Pharmacia) and purified as previously described (Hughes et al, 2001)

extract_protocol: Isolation of RNA, cDNA synthesis and amplification were carried out as described in Hawkins et al, 2003 (PMID: 12761041). Following the second round of amplification, cDNA was added to an in vitro transcription kit (Ambion) as per the manufacturers instructions

tag: Hair-cell lesions in the cultured sensory epithelia were created by laser microsurgery.  The sensory epithelia was then allowed to recover for 3hr

tag: time-matched control


title: UtrLaser3hr(3)-5_2


title: UtrLaser3hr(3)-5_3


title: UtrLaser3hr(1)-5_2

description: Laser-treated versus control, 3hr timepoint, biological replicate number 1


title: UtrLaser3hr(2)-5_1

description: Laser-treated versus control, 3hr timepoint, biological replicate number 2


title: UtrLaser3hr(1)-5_3


title: UtrLaser3hr(3)-3_3


title: UtrLaser3hr(1)-3_2


title: UtrLaser3hr(3)-3_1


title: UtrLaser3hr(2)-3_1


title: UtrLaser3hr(3)-3_2


title: UtrLaser3hr(1)-5_1


title: UtrLaser2hr(2)-5_2

description: Laser-treated versus control, 2hr timepoint, biological replicate number 2

tag: Hair-cell lesions in the cultured sensory epithelia were created by laser microsurgery.  The sensory epithelia was then allowed to recover for 2hr


title: UtrLaser3hr(1)-3_1


title: UtrLaser2hr(1)-5_1

description: Laser-treated versus control, 2hr timepoint, biological replicate number 1


title: UtrLaser2hr(2)-3_2


title: UtrLaser2hr(2)-5_1


title: UtrLaser2hr(1)-3_2


title: UtrLaser1hr(2)-5_1

description: Laser-treated versus control, 1hr timepoint, biological replicate number 2

tag: Hair-cell lesions in the cultured sensory epithelia were created by laser microsurgery.  The sensory epithelia was then allowed to recover for 1hr


title: UtrLaser2hr(1)-3_3


title: UtrLaser3hr(1)-3_3


title: UtrLaser1hr(1)-5_1

description: Laser-treated versus control, 1hr timepoint, biological replicate number 1


title: UtrLaser1hr(1)-3_2


title: UtrLaser30min(2)-5_1

description: Laser-treated versus control, 30min timepoint, biological replicate number 2

tag: Hair-cell lesions in the cultured sensory epithelia were created by laser microsurgery.  The sensory epithelia was then allowed to recover for 30min


title: UtrLaser1hr(1)-3_1


title: UtrLaser2hr(1)-3_1


title: UtrLaser30min(2)-3_1


title: UtrLaser1hr(1)-5_2


title: UtrLaser1hr(2)-3_1


title: UtrLaser30min(1)-3_2

description: Laser-treated versus control, 30min timepoint, biological replicate number 1


title: UtrLaser30min(1)-3_1


title: UtrLaser30min(1)-5_1


title: CochLaser3hr(2)-5_4

source_name: Cochleae sensory epithelia


title: CochLaser3hr(2)-5_1


title: UtrLaser2hr(2)-3_1


title: CochLaser3hr(2)-5_3


title: CochLaser3hr(1)-5_5


title: CochLaser3hr(2)-3_2


title: CochLaser3hr(1)-3_6


title: CochLaser3hr(1)-3_2


title: CochLaser3hr(1)-5_2


title: CochLaser3hr(1)-5_3


title: CochLaser3hr(1)-5_6


title: CochLaser3hr(1)-5_1


title: CochLaser3hr(2)-3_1


title: CochLaser3hr(1)-5_4


title: CochLaser3hr(2)-3_4


title: CochLaser3hr(2)-3_3


title: CochLaser2hr(2)-5_5


title: CochLaser2hr(2)-5_2


title: CochLaser3hr(1)-3_4


title: CochLaser3hr(2)-5_2


title: CochLaser2hr(2)-5_4


title: CochLaser2hr(1)-5_2


title: CochLaser3hr(1)-3_5


title: CochLaser2hr(1)-5_3


title: CochLaser3hr(1)-3_3


title: CochLaser2hr(2)-3_1


title: CochLaser2hr(2)-5_3


title: CochLaser2hr(2)-3_3


title: CochLaser2hr(1)-3_1


title: CochLaser3hr(1)-3_1


title: CochLaser2hr(1)-3_2


title: CochLaser2hr(1)-5_1


title: CochLaser2hr(1)-3_4


title: CochLaser1hr(1)-5_4


title: CochLaser1hr(2)-5_1


title: CochLaser1hr(2)-5_2


title: CochLaser2hr(1)-3_3


title: CochLaser1hr(2)-5_3


title: CochLaser1hr(2)-3_3


title: CochLaser1hr(2)-5_4


title: CochLaser1hr(1)-5_1


title: CochLaser1hr(1)-3_5


title: CochLaser1hr(2)-3_2


title: CochLaser1hr(2)-3_1


title: CochLaser1hr(1)-5_2


title: CochLaser1hr(1)-5_3


title: CochLaser1hr(1)-3_3


title: CochLaser1hr(2)-3_4


title: CochLaser2hr(2)-5_1


title: CochLaser30min(2)-5_3


title: CochLaser30min(2)-5_5


title: CochLaser1hr(1)-3_2


title: CochLaser1hr(1)-3_1


title: CochLaser30min(2)-5_4


title: CochLaser30min(2)-5_6


title: CochLaser30min(2)-5_1


title: CochLaser2hr(2)-3_2


title: CochLaser30min(2)-5_2


title: CochLaser30min(1)-5_7


title: CochLaser1hr(1)-3_4


title: CochLaser30min(1)-5_5


title: CochLaser30min(1)-5_4


title: CochLaser30min(1)-5_3


title: CochLaser30min(2)-3_6


title: CochLaser30min(1)-5_2


title: CochLaser30min(1)-5_6


title: CochLaser30min(1)-5_1


title: CochLaser30min(1)-3_6


title: CochLaser30min(2)-3_2


title: CochLaser30min(2)-3_3


title: CochLaser30min(1)-3_4


title: CochLaser30min(2)-3_1


title: CochLaser30min(2)-3_4


title: CochLaser30min(1)-3_5


title: CochNeo48hr(3)-5_2

description: Neo-treated versus control, 48hr timepoint, biological replicate number 3

tag: Isolated sensory epithelia were cultured in the presence of 1mM Neomycin for 24hrs and allowed to recover for 48hr in fresh media without neomycin


title: CochLaser30min(1)-3_2


title: CochNeo48hr(1)-5_4

description: Neo-treated versus control, 48hr timepoint, biological replicate number 1


title: CochNeo48hr(2)-5_2

description: Neo-treated versus control, 48hr timepoint, biological replicate number 2


title: CochNeo48hr(2)-5_3


title: CochNeo48hr(2)-5_1


title: CochLaser30min(1)-3_3


title: CochLaser30min(1)-3_1


title: CochLaser30min(2)-3_5


title: CochNeo48hr(3)-5_1


title: CochNeo48hr(1)-5_3


title: CochNeo48hr(1)-5_1


title: CochNeo48hr(1)-5_2


title: CochNeo48hr(2)-3_1


title: CochNeo48hr(2)-3_2


title: CochNeo48hr(2)-3_3


title: CochNeo48hr(1)-3_3


title: CochNeo48hr(1)-3_2


title: CochNeo48hr(1)-3_4


title: CochNeo48hr(1)-3_1


title: CochNeo24hr(3)-5_1

description: Neo-treated versus control, 24hr timepoint, biological replicate number 3

tag: Isolated sensory epithelia were cultured in the presence of 1mM Neomycin for 24hrs and allowed to recover for 24hr in fresh media without neomycin


title: CochNeo24hr(1)-5_5

description: Neo-treated versus control, 24hr timepoint, biological replicate number 1


title: CochNeo24hr(2)-3_2

description: Neo-treated versus control, 24hr timepoint, biological replicate number 2


title: CochNeo48hr(3)-3_2


title: CochNeo48hr(3)-3_1


title: CochNeo24hr(3)-5_2


title: CochNeo24hr(2)-5_2


title: CochNeo24hr(3)-3_2


title: CochNeo24hr(1)-5_2


title: CochNeo24hr(3)-3_1


title: CochNeo24hr(1)-5_4


title: CochNeo24hr(1)-5_1


title: CochNeo24hr(2)-3_1


title: CochNeo24hr(2)-5_1


title: CochNeo0hr(3)-5_1

description: Neo-treated versus control, 0hr timepoint, biological replicate number 3

tag: Isolated sensory epithelia were cultured in the presence of 1mM Neomycin for 24hrs and allowed to recover for 0hr in fresh media without neomycin


title: CochNeo0hr(3)-5_2


title: CochNeo24hr(1)-3_2


title: CochNeo0hr(3)-5_3


title: CochNeo24hr(1)-3_3


title: CochNeo0hr(2)-5_3

description: Neo-treated versus control, 0hr timepoint, biological replicate number 2


title: CochNeo24hr(1)-5_3


title: CochNeo0hr(2)-5_2


title: CochNeo24hr(1)-3_1


title: CochNeo0hr(1)-5_1

description: Neo-treated versus control, 0hr timepoint, biological replicate number 1


title: CochNeo0hr(1)-3_4


title: CochNeo0hr(2)-3_1


title: CochNeo0hr(2)-3_2


title: CochNeo0hr(1)-3_1


title: CochNeo0hr(2)-3_3


title: organotypic spheroid culture after 6 weeks from malignant glioma, patient 60

city: Amsterdam

first: Philip

middle: C

last: De Witt Hamer

address: PO Box 22660

department: Neurosurgery

country: Netherlands

institute: Academic Medical Center Amsterdam

description: DNA copy number information

scan_protocol: MicroArray Scanner G2505B (Agilent Technologies)

data_processing: Spot analysis and quality control was automated using BlueFuse version 3.2 (BlueGnome, Cambridge, UK). Spots were excluded with quality flag < 1 or confidence value < 0.85. Triplicates of the spot ratios (Cy3/Cy5 intensity signals) were fused within BlueFuse in a confidence weighted fashion. The resulting log2 transformed ratios were normalized to their mode value.

tag: male 45 yo, glioblastoma multiforme, prior surgical resection, whole brain irradiation and temozolomide chemotherapy

tag: 6-week organotypic spheroid culture

source_name: reference DNA

tag: Pooled DNA from the blood of 10 normal individuals


title: primary cell culture after 12 weeks from malignant glioma, patient 60

description: DNA copy number information

tag: 12-week primary cell culture, trypsinization passage 10


title: CochNeo0hr(3)-3_1


title: primary cell culture after 6 weeks from malignant glioma, patient 60

description: DNA copy number information

tag: 6-week primary cell culture, trypsinization passage 5


title: CochNeo0hr(2)-5_1


title: CochNeo0hr(1)-5_2


title: CochNeo0hr(1)-3_3


title: CochNeo0hr(1)-3_2


title: organotypic spheroid culture after 12 weeks from malignant glioma, patient 60

description: DNA copy number information

tag: 12-week organotypic spheroid culture


title: primary cell culture after 2 weeks from malignant glioma, patient 60

description: DNA copy number information

tag: 2-week primary cell culture, trypsinization passage 1


title: parental malignant glioma, patient 60

description: DNA copy number information

tag: parental tumor


title: organotypic spheroid culture after 12 weeks from malignant glioma, patient 58

description: DNA copy number information

tag: male 81 yo, glioblastoma multiforme, prior surgical resection and whole brain irradiation


title: primary cell culture after 12 weeks from malignant glioma, patient 58

description: DNA copy number information

tag: 12-week primary cell culture, trypsinization passage 11


title: primary cell culture after 6 weeks from malignant glioma, patient 58

description: DNA copy number information

tag: 6-week primary cell culture, trypsinization passage 2


title: primary cell culture after 6 weeks from malignant glioma, patient 55

description: DNA copy number information

tag: female 70 yo, glioblastoma multiforme, no prior treatment

tag: 6-week primary cell culture, trypsinization passage 4


title: primary cell culture after 12 weeks from malignant glioma, patient 55

description: DNA copy number information

tag: 12-week primary cell culture, trypsinization passage 8


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 55

description: DNA copy number information

tag: 2-week organotypic spheroid culture


title: parental malignant glioma, patient 55

description: DNA copy number information


title: primary cell culture after 2 weeks from malignant glioma, patient 55

description: DNA copy number information

tag: 2-week primary cell culture, trypsinization passage 0


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 160

description: DNA copy number information

tag: female 53 yo, glioblastoma multiforme, no prior treatment


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 58

description: DNA copy number information


title: parental malignant glioma, patient 3446

description: DNA copy number information

tag: male 34 yo, glioblastoma multiforme, no prior treatment


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 3446

description: DNA copy number information


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 60

description: DNA copy number information

tag: male 45 yo, glioblastoma multiforme, prior surgical resection, whole brain irradiation and temozolomide chemotherapy


title: parental malignant glioma, patient 58

description: DNA copy number information

tag: Pooled DNA from the blood of 10 normal individuals


title: organotypic spheroid culture after 12 weeks from malignant glioma, patient 55

description: DNA copy number information


title: primary cell culture after 2 weeks from malignant glioma, patient 58

description: DNA copy number information


title: organotypic spheroid culture after 6 weeks from malignant glioma, patient 58

description: DNA copy number information

tag: 6-week organotypic spheroid culture


title: organotypic spheroid culture after 6 weeks from malignant glioma, patient 55

description: DNA copy number information


title: primary cell culture after 2 weeks from malignant glioma, patient 3446

description: DNA copy number information

tag: 2-week primary cell culture, trypsinization passage 3


title: primary cell culture after 2 weeks from malignant glioma, patient 160

description: DNA copy number information


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 153

description: DNA copy number information

tag: male 66 yo, glioblastoma multiforme, no prior treatment


title: CochNeo0hr(1)-5_3

tag: Isolated sensory epithelia were cultured in the presence of 1mM Neomycin for 24hrs and allowed to recover for 0hr in fresh media without neomycin

tag: time-matched control


title: parental malignant glioma, patient 160

description: DNA copy number information

tag: parental tumor


title: primary cell culture after 2 weeks from malignant glioma, patient 153

description: DNA copy number information

tag: 2-week primary cell culture, trypsinization passage 1


title: DGCR8 homozygous knockout1 rep 2

status: Public on Jan 31 2007

type: other

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: RMB1018, 35 Medical Center Way

department: Urology

institute: UCSF

hyb_protocol: MicroRNA samples were hybridized with microarray using Ncode miRNA labeling system (Invitrogen).

scan_protocol: Microarrays were scanned on a GenePix 4000B scanner (Axon Instruments) and analyzed using GENEPIX PRO version 4.1.

data_processing: For microRNAs that give good signals in wild-type ES cell reference samples (> 2 times background signal and not labeled as bad signal by GENEPIX PRO software), ratios between samples and reference samples are calculated using median signal intensity (after subtracting background median). The ratios were normalized based on ratios of positive control RNAs.

molecule: other

organism: Mus musculus

source_name: microRNA from DGCR8 homozygous knockout ES cell

label_protocol: After addition of equal amount of positive control RNAs, PAGE purified miRNAs from 5-10 microgram total RNA were polyadenylated, ligated with capture sequences, and hybridized with microarray using Ncode miRNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen). 10-20 Microgram total RNA was then resolved in a 15% denaturing polyacrylamide gel. The gel portion corresponding to ~18-26 nt small RNAs was cut out. Small RNA was extracted in TEN buffer (10 mM Tris, pH 8.0, 1 mM EDTA, 300 mM NaCl) and precipitated by ethanol. Prior to PAGE separation, equal trace amount of 5’-32P-radiolabeled unrelated 18 nt small RNA was added to each total RNA sample. The 5’-radiolabeled small RNA serves as a control for monitoring extraction procedure, i.e., RNA degradation and extraction efficiency will be directly reflected by the integrity and amount of 5’-radiolabeled small RNA in the extracted RNA samples.

tag: Cell type

value: DGCR8 homozygous knockout embryonic stem cell

source_name: microRNA from wild-type ES cell

value: wild-type V6.5 embryonic stem cell


title: parental malignant glioma, patient 153

description: DNA copy number information


title: DGCR8 heterozygous knockout rep 1

value: V6.5 embryonic stem cell

source_name: microRNA from DGCR8 heterozygous knockout ES cell

value: DGCR8 heterozygous knockout embryonic stem cell (V6.5)


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 33

description: DNA copy number information

tag: male 38 yo, glioblastoma multiforme, no prior treatment


title: LNM35_1st_GF201

status: Public on Jan 20 2007

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

description: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the GeneFilters (Invitrogen) with slight modification.  The GeneFilters were prehybridized for 2 h at 51°C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51°C with the denatured radio-labeled probe.  Hybridization of the arrays was followed by two washings with a solution containing 2 M of urea, 0.1 % of SDS, 50 mM of Na phosphate buffer (pH 7.0), 150 mM of NaCl, 1 mM of MgCl2 and 0.2 % of AlkPhos DIRECT blocking reagent (Amersham Bioscience).  The arrays were then washed twice with a solution containing 2 mM of MgCl2, 50 mM of Tris and 100 mM of NaCl, and with a solution containing 2 mM of MgCl2, 50 mM of Tris and 15 mM of NaCl.  All procedures were carried out with the aid of custom-made AutoHybridizers (Fuji Photo Film, Tokyo, Japan).  The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified with ArrayGauge software (Fuji Photo Film).  After each hybridization, the arrays were stripped by boiling them in 0.5% SDS solution for 60 min and scanned for residual hybridization before the next round of hybridization with a newly labeled probe of the same sample to acquire their expression profiles in duplicate.

data_processing: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

source_name: highly metastatic subline

tag: Lung cancer cell line


title: DGCR8 homozygous knockout2 rep 2

source_name: microRNA from DGCR8 knockout ES cell

value: DGCR8 knockout embryonic stem cell (V6.5)

value: wild-type embryonic stem cell (V6.5)


title: DGCR8 heterozygous knockout rep 3


title: N15_1st_GF201

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51°C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51°C with the denatured radio-labeled probe.  Hybridization of the arrays was followed by two washings with a solution containing 2 M of urea, 0.1 % of SDS, 50 mM of Na phosphate buffer (pH 7.0), 150 mM of NaCl, 1 mM of MgCl2 and 0.2 % of AlkPhos DIRECT blocking reagent (Amersham Bioscience).  The arrays were then washed twice with a solution containing 2 mM of MgCl2, 50 mM of Tris and 100 mM of NaCl, and with a solution containing 2 mM of MgCl2, 50 mM of Tris and 15 mM of NaCl.  All procedures were carried out with the aid of custom-made AutoHybridizers (Fuji Photo Film, Tokyo, Japan).

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified with ArrayGauge software (Fuji Photo Film).

source_name: low metastatic subline

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the GeneFilters (Invitrogen) with slight modification.

extract_protocol: On average, 50 cryostat sections (7 mm-thick) were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist using every 10th section stained by May-Giemsa.  Careful attention was paid to the microdissection of only such tumor cell-rich areas, yielding an average of 75.4% tumor cell content.  RNAs were then isolated using RNAeasy (Quiagen, Valencia, CA) according to the manufacturer’s instruction, and their quality was checked with the RNA 6000 Nano Assay kit and the 2100 Bioanalyzer (Agilent, Palo Alto, CA).


title: LNM35_2nd_GF200


title: LNM35_1st_GF200


title: N15_2nd_Gf201


title: DGCR8 homozygous knockout1 rep1

source_name: microRNA from DGCR8 knockout ES cell 1


title: Mice embryonic fibroblast feeder rep 1

value: V6.5 wild-type embryonic stem cell

source_name: microRNA from mice embryonic fibroblast feeder cell

value: irradiated mice embryonic fibroblast feeder cell


title: LNM35_2nd_GF201


title: DGCR8 heterozygous knockout rep 2


title: primary cell culture after 2 weeks from malignant glioma, patient 33

description: DNA copy number information

tag: male 38 yo, recurrent anaplastic oligodendroglioma, prior surgical resection

tag: 2-week primary cell culture, trypsinization passage 2


title: Mice embryonic fibroblast feeder rep 2

value: wild-type V6.5 mice embryonic stem cell


title: parental malignant glioma, patient 33

description: DNA copy number information


title: N15_1st_GF200

source_name: low metastasis subline


title: DGCR8 homozygous knockout2 rep 1

tag: cell type


title: primary cell culture after 2 weeks from malignant glioma, patient 32

description: DNA copy number information DNA copy number information

tag: male 77 yo, glioblastoma multiforme, no prior treatment


title: N15_2nd_GF200


title: parental malignant glioma, patient 32

description: DNA copy number information


title: Gene expression changes during mouse mucosal mast cell in vitro differentiation, array1

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: The aim of the study was to find novel mucosal mast cell-specific genes.

hyb_protocol: 1-1 microgr labeled cRNA was hybridized at 60 C overnight. Slides were washed by the ozone-safe SSPE wash method and treated by Agilent Stabilizing and Drying Solution. All steps were carried out according to the manufacturer.

scan_protocol: Agilent Scanner, data were normalized by Feature Extraction 7.5 with default parameter settings for oligonucleotide 22K microarrays.

data_processing: Data were normalized by Feature Extraction 7.5 with default parameter settings for oligonucleotide 22K microarrays.

label_protocol: RNA was converted to labeled cRNA by Agilent Low-RNA Input Linear Amplification Kit.

extract_protocol: total RNA was isolated by the RNAEasy kit (Qiagen) and quality-checked by Agilent Bioanalyzer.

tag: Bone marrow cells were isolated from Balb/c 4-6 week-old mice and then cultured with IL-3+IL-9+SCF+TGF-betaI. Cells were magnetically sparated on day4 based on their c-kit expression.

tag: Bone marrow cells were isolated from Balb/c 4-6 week-old mice and then cultured with IL-3+IL-9+SCF+TGF-betaI. Cells were magnetically sparated on day20 based on their c-kit expression.


title: A549, let-7-a3, overexpression, Replicate 4

status: Public on Jan 15 2007

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

hyb_protocol: ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt’s solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

scan_protocol: arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)

data_processing: raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; after removal of bad quality clones, generalized log ratios from 26629 cDNA clones were given in the data table

source_name: P324 cell line A549

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.

growth_protocol: cells were cultivated in DMEM medium supplemented with 10% FCS

extract_protocol: total RNA was extracted using Qiagen RNeasy Midi Kit reagents; 2µg total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit)

treatment_protocol: non-treated

tag: cell line A549, control

source_name: P320 cell line A549

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column.

tag: cell line A549, let-7-a3, stable transfection


title: A549, let-7-a3, overexpression, Replicate 2

source_name: P322 cell line A549

source_name: P318 cell line A549


title: organotypic spheroid culture after 2 weeks from malignant glioma, patient 32

description: DNA copy number information

tag: 2-week organotypic spheroid culture

tag: Pooled DNA from the blood of 10 normal individuals


title: Gene expression changes during murine mucosal mast cell in vitro differentiation, array2

description: The aim of the study was to find novel mucosal mast cell-specific genes. This is a technical (dye-swap) and biological replicate to array1.

tag: Bone marrow cells were isolated from Balb/c 4-6 week-old mice and then cultured in IL-3+IL-9+SCF+TGF-beta1. Cells were magnetically isolated on the 20th day of culturing.

tag: Bone marrow cells were isolated from Balb/c 4-6 week-old mice and then cultured in IL-3+IL-9+SCF+TGF-beta1. Cells were magnetically isolated on the 4th day of culturing.


title: wgs4-49bot-rna1468Ecy5-174Jcy3

status: Public on Jan 10 2007

city: Cambridge

first: Adam

middle: M

last: Breier

state: MA

address: 77 Massachusetts Ave Bldg. 68-540D

department: Biology

institute: Massachsetts Institute of Technology

description: First of three replicates to analyze the effect of deleting spo0J on gene expression

hyb_protocol: As described in Auchtung, J.M., Lee, C.A., Monson, R.E., Lehman, A.P., and Grossman, A.D. (2005) Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci U S A 102: 12554-12559; Goranov, A.I., Katz, L., Breier, A.M., Burge, C.B., and Grossman, A.D. (2005) A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A 102: 12932-12937.

data_processing: Global median normalization was performed and considered only unflagged spots representing genes that had >90% of pixels 1 SD over background in at least one channel.

organism: Bacillus subtilis

source_name: B. subtilis strain AG1468 RNA prep E

label_protocol: Random priming with SSII RT to incorporate aminoallyl-dUTP, followed by NaOH hydrolysis of RNA and conjugation of cy5

extract_protocol: Qiagen RNeasy Mini

tag: Strain

tag: Media

value: S750 + glucose

source_name: B. subtilis strain AG174 RNA prep J

label_protocol: Random priming with SSII RT to incorporate aminoallyl-dUTP, followed by NaOH hydrolysis of RNA and conjugation of cy3


title: wgs4-50top-rna174Lcy5-1468Lcy3

scan_protocol: As described in Auchtung, J.M., Lee, C.A., Monson, R.E., Lehman, A.P., and Grossman, A.D. (2005) Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci U S A 102: 12554-12559; Goranov, A.I., Katz, L., Breier, A.M., Burge, C.B., and Grossman, A.D. (2005) A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A 102: 12932-12937.

source_name: B. subtilis strain AG174 RNA prep L

source_name: B. subtilis strain AG1468 RNA prep L


title: wgs4-49top-rna174Kcy5-1468Dcy3

source_name: B. subtilis strain AG174 RNA prep K

source_name: B. subtilis strain AG1468 RNA prep D


title: A549, let-7-a3, overexpression, Replicate 3

source_name: P319 cell line A549

source_name: P323 cell line A549


title: A549, let-7-a3, overexpression, Replicate 1

source_name: P317 cell line A549

source_name: P321 cell line A549


title: Primary human keratinocytes transduced to express Ras

status: Public on Jan 02 2007

city: Durham

first: Jennifer

middle: Yunyan

last: Zhang

address: 3 Genome Ct, rm4130

department: Dermatology

institute: Duke University

description: Gene expression data from primary human keratinocytes transduced to express Ras

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene U133A 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: keratinocytes isolated from foreskin

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

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

treatment_protocol: human keratinocytes isolated from fresh foreskin were seeded on triplicate 10-cm dishes, and transduced with retrovirus encoding Ras(v12). Cells were then mock transduced twice with 12 hour intervals.  At 48 hour post the last transduction, cells are used for total RNA isolation.

tag: retroviral transduced human keratinocytes


title: Primary human keratinocytes transduced to express MKK7 and Ras

description: Gene expression data from primary human keratinocytes transduced to express MKK7 and Ras

treatment_protocol: human keratinocytes isolated from fresh foreskin were seeded on triplicate 10-cm dishes, and transduced with retrovirus MKK7 followed by tretroviral transduction for expression of Ras (v12) and a mock transduction with 12 hour intervals. Cells were then used for  total RNA isolation at 48 hour post the last transduction. transduction.


title: Primary human keratinocytes transduced to express LacZ control

description: Gene expression data from primary human keratinocytes transduced to express LacZ control

treatment_protocol: human keratinocytes isolated from fresh foreskin were seeded on triplicate 10-cm dishes, and transduced with retrovirus encoding LacZ control. Cells were the mock transduced twice with 12 hour intervals.  At 48 hour post the last transduction, cells are used for total RNA isolation.


title: Primary human keratinocytes transduced to express MKK7, Ras and DNc-Jun

description: Gene expression data from primary human keratinocytes transduced to express MKK7, Ras and DNc-Jun

treatment_protocol: human keratinocytes isolated from fresh foreskin were seeded on triplicate 10-cm dishes, and transduced with retroviruses MKK7, Ras(V12) and DNc-Jun with 12 hour intervals between each transduction. Cells were then used for total RNA isolation at 48 hour post the last transducton.


title: Primary human keratinocytes transduced to express dominant negative c-Jun (DNc-Jun)

description: Gene expression data from primary human keratinocytes transduced to express dominant negative c-Jun (DNc-Jun)

treatment_protocol: human keratinocytes isolated from fresh foreskin were seeded on triplicate 10-cm dishes, and transduced with retrovirus encoding DNc-Jun, a dominant negative mutant of c-Jun. Cells were then mock transduced twice with 12 hour intervals.  At 48 hour post the last transduction, cells are used for total RNA isolation.


title: Primary human keratinocytes transduced to expressMKK7

description: Gene expression data from primary human keratinocytes transduced to expressMKK7

treatment_protocol: human keratinocytes isolated from fresh foreskin were seeded on triplicate 10-cm dishes, and transduced with retrovirus encoding constitutively active MKK7. Cells were mock transduced twice with 12 hour intervals.  At 48 hour post the last transduction, cells are used for total RNA isolation.


title: Mergen-MRP2-2

status: Public on Jan 01 2007

city: Boston

first: Winston

middle: Patrick

last: Kuo

address: 188 Longwood Avenue

institute: Harvard Medical School

description: MRP2 technical replicate 2

hyb_protocol: These probes were hybridized to the arrays overnight at 30°C with continuous agitation. The arrays were then washed, and hybridized probes were detected using a streptavidin/cyanine-3 fluorescent dye-conjugated antibody.

scan_protocol: Chips were imaged using a ScanArray scanner (PerkinElmer, Boston, MA).

data_processing: Signal intensities across microarrays were normalized using the quantile normalization (www.bioconductor.org).

source_name: Adult mouse retina pool 2

label_protocol: The ExpressChip MO3 DNA Microarray System (Mergen Ltd., San Leandro, CA) was used for this study. The assay was carried out according to the manufacturer's instructions. In brief, DNase-treated total RNA (20 µg) was reverse-transcribed using an oligo[(dT)24 T7 promoter]65 primer (consisting of the nucleotide binding sequence for the T7 RNA polymerase followed by 24 thymidine nucleotides) followed by second strand synthesis. ). The double-stranded cDNA was cleaned using the Qiaquick purification kit (Qiagen) all of which was used as a template for In Vitro Transcription (IVT) utilizing Ambion's T7 MEGA script reagents and Biotin-11-UTP (PerkinElmer/NEN).

extract_protocol: Retinas were dissected, collected and stored in Trizol (one pair of retinas per eppendorf tube) at -80°C prior to pooling.

tag: The adult mouse retina samples were obtained from pool 2 of C57/B6 mice (n = 350), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA). All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.


title: Mergen_MRP2_4

description: MRP2 technical replicate 4


title: Mergen_MRP2_3

description: MRP2 technical replicate 3


title: Layer Bone Marrow 60wk slide3783 dye555

city: Ames

first: Diane

last: Spurlock

state: IA

address: 243 Kildee Hall

department: Animal Science

institute: Iowa State University

description: Following euthanasia at 15 weeks of age, the right tibia was excised and cracked with a hammer.  Bone marrow was collected using a metal spatula from the entire length of the bone, frozen in liquid nitrogen and maintained in a -80 degree Celsius freezer pending RNA extraction.

hyb_protocol: The Fred Hutchinson Cancer Research Center (FHCRC) Chicken 13K array (Fred Hutchinson Cancer Research Center, Seattle, WA) was used to compare gene expression profiles from the layer and broiler lines.  Each array was pre-hybridized, hybridized, and washed per manufacturer’s recommended protocols (Burnside et al., BMC Genomics 6: 13, 2005), with the exception that wash 2 and 3 times were cut in half.  One layer and one broiler sample labeled with different dyes were hybridized to each array (6 arrays per time point) in 50 µl of hybridization buffer solution using Lifterslip (Erie Scientific Company, Portsmouth, NH) cover slips, and incubated in a 63°C water bath within individual hybridization chambers wrapped in foil to block out light to prevent dye bleaching from light exposure.

scan_protocol: Slides were scanned with array WoRxe Biochip Reader (Applied Precision, LLC, Issaquah, WA) and images analyzed with ImaGene (BioDiscovery Incorporated, El Segundo, CA) software.

data_processing: Three layer and three broiler samples were labeled with each dye to control for dye bias.  Features with an intensity level greater than two times its local background for at least one of the 12 channels (6 dual channel slides) in the dataset were retained.  Using the statistical software package R, these data were log transformed and normalized using lowess normalization and median centering across all hybridizations (Yang et al., Nucleic Acids Res. 30(4): e15, 2002).

label: Alexa Fluor 555

source_name: Bone marrow from 60wk old layer

label_protocol: Forty µg of bone marrow RNA was purified and concentrated using the RNase-Free DNase Set along with the RNeasy MinElute Cleanup Kit (QIAGEN Incorporated, Valencia, CA).  Twenty µg of total RNA was reverse transcribed into first-strand cDNA with oligo(dT)20 and random hexamer primers, then fluorescently labeled with either Alexa Fluor 555 or 647 dye using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen Corporation, Carlsbad, CA) with the exception that the PureLink PCR Purification Kit (Invitrogen Corporation, Carlsbad, CA) was used for the purification steps.

growth_protocol: Birds were obtained on day of hatch and fed a starter diet to 6 wks of age, a grower diet from 6 to 8 wks, a developer diet from 8 to 15 wks, a pre-lay diet from 15 to 18 wks, and a breeder diet from 18 wks until termination of the experiment.  Layers were provided feed and water ad libitum, however daily feed restriction beginning at 6 wks, based on average body weights collected at monthly intervals, was necessary to prevent obesity in the broilers.  All animal management procedures were approved by the Purdue University Animal Care and Use Committee.

extract_protocol: Total RNA was extracted from entire bone marrow samples with Trizol Reagent (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s recommended protocol.

tag: gender

value: female, age:60 weeks, strain:pedigree line Hy-Line White Leghorn layer, tissue:crude bone marrow sample


title: Mergen_MRP2_5

description: MRP2 technical replicate 5


title: Broiler Bone Marrow 60wk slide3783 dye647

label: Alexa Fluor 647

source_name: Bone marrow from 60wk old broiler

value: female, age:60 weeks, strain:commercial line Cobb-Cobb broiler, tissue:crude bone marrow sample


title: MPSS-MRP2-17bp

type: MPSS

data_processing: Supplied by LYNX (The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.)

tag: Total RNA (MRP2) was analyzed through Bioanalyzer and passed our quality control test. The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)

value: 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6):630-634). Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector. The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.


title: Mergen_MRP2_1

description: MRP2 technical replicate 1


title: MPSS-MRP1-17bp

source_name: Adult mouse retina pool 1

tag: Total RNA (MRP1) was analyzed through Bioanalyzer and passed our quality control test. The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Broiler Bone Marrow 60wk slide3782 dye647


title: T47D Nucleosome Sample

type: mixed

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

description: Raw and processed data

hyb_protocol: Performed by NimbleGen Systems Inc.

scan_protocol: Performed by NimbleGen Systems Inc.

data_processing: The Cy5/Cy3 ratios were denoised using wavelets and quantile normalized across different samples.

source_name: T47D Genomic Input

label_protocol: Random primer labeling

extract_protocol: Genomic DNA was isolated using the DNeasy Tissue Kit (Qiagen) and digested with hydroxyl radical-based cleavage in a sequence-independent manner

tag: Genomic Input DNA

source_name: T47D MNase digested and gel-extracted DNA

extract_protocol: DNA was treated with MNase, and the isolated DNA was run on a 1.5% agarose gel, and the band corresponding to mononucleosomes was gel-extracted using QiaQuick Gel Extraction Kit (Qiagen).

tag: MNase treated mononucleosomal DNA


title: Primary Melanocyte (PM) Nucleosome Sample

description: Raw and processed data

source_name: PM Genomic Input

source_name: PM MNase digested and gel-extracted DNA


title: MCF7 Nucleosome Sample

description: Raw and processed data

source_name: MCF7 Genomic Input

source_name: MCF7 MNase digested and gel-extracted DNA


title: A375 Nucleosome Sample1

description: Raw and processed data

source_name: A375 Genomic Input

tag: A375 Genomic Input DNA

source_name: A375 MNase digested and gel-extracted DNA

tag: A375 MNase treated mononucleosomal DNA


title: MALME Nucleosome Sample2

description: Raw and processed data

source_name: MALME Genomic Input

source_name: MALME MNase digested and gel-extracted DNA


title: IMR90 Nucleosome Sample1

description: Raw and processed data

source_name: IMR90 Genomic Input

source_name: IMR0 MNase digested and gel-extracted DNA


title: Mammary Epithelial Cells (MEC) Nucleosome Sample

description: Raw and processed data

source_name: MEC Genomic Input

source_name: MEC MNase digested and gel-extracted DNA


title: MALME Nucleosome Sample1

description: Raw and processed data


title: A375 Nucleosome Sample2

description: Raw and processed data


title: IMR90 Nucleosome Sample3

description: Raw and processed data


title: Layer Bone Marrow 60wk slide3778 dye647

source_name: Bone marrow from 60wk old layer


title: MALME Nucleosome Sample3

description: Raw and processed data


title: Layer Bone Marrow 60wk slide3775 dye555


title: IMR90 Nucleosome Sample2

description: Raw and processed data


title: Layer Bone Marrow 15wk slide3794 dye555

hyb_protocol: The Fred Hutchinson Cancer Research Center (FHCRC) Chicken 13K array (Fred Hutchinson Cancer Research Center, Seattle, WA) was used to compare gene expression profiles from the layer and broiler lines.  Each array was pre-hybridized, hybridized, and washed per manufacturer’s recommended protocols (Burnside et al., BMC Genomics 6:13, 2005), with the exception that wash 2 and 3 times were cut in half.  One layer and one broiler sample labeled with different dyes were hybridized to each array (6 arrays per time point) in 50 µl of hybridization buffer solution using Lifterslip (Erie Scientific Company, Portsmouth, NH) cover slips, and incubated in a 63°C water bath within individual hybridization chambers wrapped in foil to block out light to prevent dye bleaching from light exposure.

source_name: Bone marrow from 15wk old layer

growth_protocol: Birds were obtained on day of hatch and fed a starter diet to 6 wks of age, a grower diet from 6 to 8 wks, a developer diet from 8 to 15 wks.  Layers were provided feed and water ad libitum, however daily feed restriction beginning at 6 wks, based on average body weights collected at monthly intervals, was necessary to prevent obesity in the broilers.  All animal management procedures were approved by the Purdue University Animal Care and Use Committee.

value: female, age:15 weeks, strain:pedigree line Hy-Line White Leghorn layer, tissue:crude bone marrow sample


title: Broiler Bone Marrow 15wk slide3794 dye647

source_name: Bone marrow from 15wk old broiler

value: female, age:15 weeks, strain:commercial line Cobb-Cobb broiler, tissue:crude bone marrow sample


title: MM-160_3

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human multiple myeloma patient MM-160

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed..

source_name: Human multiple myeloma patient MM-160

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases

tag: Legend

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

tag: Sex

value: F; Age:75; Stage:II A; MC:Gl; BL:+

tag: TC


title: Broiler Bone Marrow 60wk slide3775 dye647

source_name: Bone marrow from 60wk old broiler


title: Layer Bone Marrow 60wk slide3777 dye647


title: Broiler Bone Marrow 60wk slide3778 dye555


title: Broiler Bone Marrow 60wk slide3779 dye555


title: Broiler Bone Marrow 15wk slide3784 dye647


title: Layer Bone Marrow 15wk slide3793 dye647


title: Layer Bone Marrow 15wk slide3784 dye555


title: Layer Bone Marrow 15wk slide3786 dye555


title: Broiler Bone Marrow 15wk slide3786 dye647

label: Alexa Fluor 647 dye


title: Layer Bone Marrow 60wk slide3782 dye555


title: Broiler Bone Marrow 15wk slide3792 dye555


title: Broiler Bone Marrow 15wk slide3796 dye555


title: Layer Bone Marrow 15wk slide3796 dye647


title: Broiler Bone Marrow 15wk slide3793 dye555


title: Broiler Bone Marrow 60wk slide3777 dye555


title: MM-161_3

description: Gene expression profiling data from human multiple myeloma patient MM-161

source_name: Human multiple myeloma patient MM-161

value: F; Age:74; Stage:I A; MC:Gl; BL:-


title: MM-159_3

description: Gene expression profiling data from human multiple myeloma patient MM-159

source_name: Human multiple myeloma patient MM-159

value: M; Age:56; Stage:IIA; MC:k; BL:+


title: Layer Bone Marrow 60wk slide3779 dye647


title: MM-167_3

description: Gene expression profiling data from human multiple myeloma patient MM-167

source_name: Human multiple myeloma patient MM-167

value: M; Age:75; Stage:II A; MC:Gl; BL:+


title: Layer Bone Marrow 15wk slide3792 dye647


title: Ec18n137 hfq- rpoE overexpression 20 min

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

description: Wild type (hfq+) vs hfq- RpoE (SigmaE) 20 min after overexpression

hyb_protocol: cDNA from 16 ug total RNA, 15 ug poly(dI-dC), 3xSSC, 25 mM Hepes (pH7), 0.225% SDS. Samples hybridized on array under a lifterslip for 12 hrs at 65 degrees C

scan_protocol: Slides scanned using GenePix 4000B scanner (Axon). TIFF images analyzed using GENEPIX 3.0 software (Axon).

data_processing: Data filtered for PCR success, >3x local background and spot quality (GenePix Flag). Normalized using Lowess smoothing from MA plot

source_name: hfq+ Wild type control (20 min)

label_protocol: Indirect labeling method as described in Khodursky et al (2003; Methods Mol Biol 224:61-78)

growth_protocol: M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm

extract_protocol: Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA).

treatment_protocol: At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction

tag: MG1655 rpoHp3::lacZ delta lacX74 hfq2::omega(Km;KpnI) (hfq+)/ptrc99A (control vector)

source_name: Hfq- RpoE overexpression (20 min)

tag: MG1655 rpoHp3::lacZ delta lacX74 hfq1::omega(Km;BclI) (hfq-)/pLC245 (vector carrying inducible Ptrc::rpoE)


title: EC18n140 hfq- rpoE overexpression 20 min


title: EC18n018 hfq+ rpoE overexpression 20 min

description: Wild type (hfq+) vs hfq+ RpoE (SigmaE) 20 min after overexpression

source_name: Wild type control (20 min)

source_name: RpoE induced (20 min)

tag: MG1655 rpoHp3::lacZ delta lacX74 hfq2::omega(Km;KpnI) (hfq+)/pLC245 (vector carrying inducible Ptrc::rpoE)


title: EC18n019 hfq- rpoE overexpression 20 min


title: MM-158_3

description: Gene expression profiling data from human multiple myeloma patient MM-158

source_name: Human multiple myeloma patient MM-158

value: M; Age:59; Stage:I A; MC:Gl; BL:-


title: EC18n136 hfq+ rpoE overexpression 20 min


title: MM-155_3

description: Gene expression profiling data from human multiple myeloma patient MM-155

source_name: Human multiple myeloma patient MM-155

value: F; Age:76; Stage:I A; MC:Gk; BL:-


title: EC18n035 delta rseA

description: Wild type vs delta rseA

source_name: Wild type control

treatment_protocol: Cells harvested at OD450 = 0.3

tag: MG1655 rpoHp3::lacZ delta lacX74

source_name: Delta rseA

tag: MG1655 rpoHp3::lacZ delta lacX74 nadB::Tn10 drseA


title: MM-153_3

description: Gene expression profiling data from human multiple myeloma patient MM-153

source_name: Human multiple myeloma patient MM-153

value: M; Age:65; Stage:II A; MC:Gk; BL:-


title: MM-146_3

description: Gene expression profiling data from human multiple myeloma patient MM-146

source_name: Human multiple myeloma patient MM-146

value: M; Age:68; Stage:II A; MC:Gl; BL:+


title: MM-149_3

description: Gene expression profiling data from human multiple myeloma patient MM-149

source_name: Human multiple myeloma patient MM-149

value: F; Age:52; Stage:I A; MC:Gl; BL:-


title: MM-150_3

description: Gene expression profiling data from human multiple myeloma patient MM-150

source_name: Human multiple myeloma patient MM-150

value: F; Age:68; Stage:II A; MC:Gl; BL:-


title: MM-148_3

description: Gene expression profiling data from human multiple myeloma patient MM-148

source_name: Human multiple myeloma patient MM-148

value: F; Age:55; Stage:I A; MC:Ak; BL:-


title: MM-151_3

description: Gene expression profiling data from human multiple myeloma patient MM-151

source_name: Human multiple myeloma patient MM-151

value: F; Age:71; Stage:I A; MC:Gl; BL:+


title: MM-143_3

description: Gene expression profiling data from human multiple myeloma patient MM-143

source_name: Human multiple myeloma patient MM-143

value: M; Age:56; Stage:II A; MC:Gk; BL:+


title: EC18n039 delta hfq

description: Wild type vs delta hfq

tag: MG1655 rpoHp3::lacZ delta lacX74 hfq2::omega(Km;KpnI) (hfq+)

source_name: delta hfq

tag: MG1655 rpoHp3::lacZ delta lacX74 hfq1::omega(Km;BclI) (hfq-)


title: MM-140_3

description: Gene expression profiling data from human multiple myeloma patient MM-140

source_name: Human multiple myeloma patient MM-140

value: M; Age:62; Stage:III B; MC:nd; BL:nd


title: MM-154_3

description: Gene expression profiling data from human multiple myeloma patient MM-154

source_name: Human multiple myeloma patient MM-154

value: F; Age:71; Stage:II A; MC:G; BL:-


title: EC18n139 hfq+ rpoE overexpression 20 min


title: EC18n040 delta hfq

description: Wild type vs delta hfq


title: EC18n037 delta hfq

description: Wild type vs delta hfq

source_name: Delta hfq


title: EC18n036 delta rseA

description: Wild type vs delta rseA


title: MM-139_3

description: Gene expression profiling data from human multiple myeloma patient MM-139

source_name: Human multiple myeloma patient MM-139

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: F; Age:57; Stage:II A; MC:Gl; BL:-


title: MM-133_3

description: Gene expression profiling data from human multiple myeloma patient MM-133

source_name: Human multiple myeloma patient MM-133

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: F; Age:64; Stage:II A; MC:Gk; BL:-


title: MM-131_3

description: Gene expression profiling data from human multiple myeloma patient MM-131

source_name: Human multiple myeloma patient MM-131

value: M; Age:69; Stage:I A; MC:Gk; BL:-


title: MM-152_3

description: Gene expression profiling data from human multiple myeloma patient MM-152

source_name: Human multiple myeloma patient MM-152

value: M; Age:67; Stage:I A; MC:Gk; BL:-


title: MM-128_3

description: Gene expression profiling data from human multiple myeloma patient MM-128

source_name: Human multiple myeloma patient MM-128

value: M; Age:54; Stage:II A; MC:k; BL:+


title: EC18n038 delta hfq

description: Wild type vs delta hfq

source_name: Wild type control


title: MM-126_3

description: Gene expression profiling data from human multiple myeloma patient MM-126

source_name: Human multiple myeloma patient MM-126

value: M; Age:62; Stage:II A; MC:Ak; BL:+


title: MM-123_3

description: Gene expression profiling data from human multiple myeloma patient MM-123

source_name: Human multiple myeloma patient MM-123

value: M; Age:56; Stage:III A; MC:Gk; BL:-


title: MM-121_3

description: Gene expression profiling data from human multiple myeloma patient MM-121

source_name: Human multiple myeloma patient MM-121


title: MM-119_3

description: Gene expression profiling data from human multiple myeloma patient MM-119

source_name: Human multiple myeloma patient MM-119

value: M; Age:50; Stage:II A; MC:l; BL:+


title: EC12n099 delta rseA

description: Wild type vs delta rseA

source_name: Delta rseA


title: AFFY_MRP2_3

description: MRP2 technical replicate 3

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

label: ENZO biotin labeled

source_name: Adult mouse retina pool 2

label_protocol: Approximately 10 micrograms of total RNA was processed to produce biotinylated cRNA targets.

tag: The adult mouse retina samples were obtained from pool 2 of C57/B6 mice (n = 350), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA). All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.


title: MM-116_3

description: Gene expression profiling data from human multiple myeloma patient MM-116

source_name: Human multiple myeloma patient MM-116

value: M; Age:73; Stage:II B; MC:nd; BL:nd


title: MM-117_3

description: Gene expression profiling data from human multiple myeloma patient MM-117

source_name: Human multiple myeloma patient MM-117

value: M; Age:49; Stage:III A; MC:Gl; BL:+


title: AFFY_MRP2_1

description: MRP2 technical replicate 1

tag: The adult mouse retina pool 2 samples were obtained from a pool of C57/B6 mice (n = 350), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA). All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.


title: MM-118_3

description: Gene expression profiling data from human multiple myeloma patient MM-118

source_name: Human multiple myeloma patient MM-118

value: M; Age:62; Stage:III B; MC:k; BL:+


title: AFFY_MRP2_2

description: MRP2 technical replicate 2


title: EC12n098 delta rseA

description: Wild type vs delta rseA


title: MM-111_3

description: Gene expression profiling data from human multiple myeloma patient MM-111

source_name: Human multiple myeloma patient MM-111

value: M; Age:64; Stage:I A; MC:Gl; BL:-


title: AFFY_MRP2_4

description: MRP2 technical replicate 4


title: MM-113_3

description: Gene expression profiling data from human multiple myeloma patient MM-113

source_name: Human multiple myeloma patient MM-113

value: F; Age:43; Stage:III A; MC:G; BL:+


title: MM-101_3

description: Gene expression profiling data from human multiple myeloma patient MM-101

source_name: Human multiple myeloma patient MM-101

value: M; Age:63; Stage:II A; MC:l; BL:+


title: MM-114_3

description: Gene expression profiling data from human multiple myeloma patient MM-114

source_name: Human multiple myeloma patient MM-114

value: F; Age:62; Stage:II A; MC:Ak; BL:-


title: EC12n097 delta rseA

description: Wild type vs delta rseA


title: MM-087_3

description: Gene expression profiling data from human multiple myeloma patient MM-087

source_name: Human multiple myeloma patient MM-087

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: F; Age:85; Stage:III A; MC:Gl; BL:+


title: AFFY_MRP2_5

description: MRP2 technical replicate 5


title: MM-092_3

description: Gene expression profiling data from human multiple myeloma patient MM-092

source_name: Human multiple myeloma patient MM-092

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: M; Age:65; Stage:I A; MC:Gl; BL:-


title: MM-106_3

description: Gene expression profiling data from human multiple myeloma patient MM-106

source_name: Human multiple myeloma patient MM-106

value: M; Age:83; Stage:I A; MC:Gk; BL:+


title: MM-107_3

description: Gene expression profiling data from human multiple myeloma patient MM-107

source_name: Human multiple myeloma patient MM-107

value: F; Age:67; Stage:II A; MC:Ak; BL:-


title: MM-104_3

description: Gene expression profiling data from human multiple myeloma patient MM-104

source_name: Human multiple myeloma patient MM-104

value: F; Age:63; Stage:III A; MC:Al; BL:+


title: MM-109_3

description: Gene expression profiling data from human multiple myeloma patient MM-109

source_name: Human multiple myeloma patient MM-109

value: M; Age:55; Stage:III B; MC:l; BL:+


title: MM-094_3

description: Gene expression profiling data from human multiple myeloma patient MM-094

source_name: Human multiple myeloma patient MM-094

value: M; Age:67; Stage:I A; MC:Al; BL:-


title: MM-083_3

description: Gene expression profiling data from human multiple myeloma patient MM-083

source_name: Human multiple myeloma patient MM-083

value: M; Age:70; Stage:I A; MC:Gl; BL:-


title: MM-103_3

description: Gene expression profiling data from human multiple myeloma patient MM-103

source_name: Human multiple myeloma patient MM-103

value: M; Age:56; Stage:III A; MC:Ak; BL:+


title: MM-129_3

description: Gene expression profiling data from human multiple myeloma patient MM-129

source_name: Human multiple myeloma patient MM-129

value: M; Age:62; Stage:II A; MC:G; BL:+


title: MM-115_3

description: Gene expression profiling data from human multiple myeloma patient MM-115

source_name: Human multiple myeloma patient MM-115

value: F; Age:53; Stage:III A; MC:k; BL:nd


title: MM-089_3

description: Gene expression profiling data from human multiple myeloma patient MM-089

source_name: Human multiple myeloma patient MM-089

value: F; Age:84; Stage:II A; MC:Ak; BL:-


title: MM-077_3

description: Gene expression profiling data from human multiple myeloma patient MM-077

source_name: Human multiple myeloma patient MM-077

value: M; Age:62; Stage:II A; MC:Gl; BL:+


title: MM-079_3

description: Gene expression profiling data from human multiple myeloma patient MM-079

source_name: Human multiple myeloma patient MM-079

value: F; Age:72; Stage:II A; MC:Gk + Gl; BL:+


title: MM-078_3

description: Gene expression profiling data from human multiple myeloma patient MM-078

source_name: Human multiple myeloma patient MM-078

value: F; Age:60; Stage:III A; MC:k; BL:+


title: MM-082_3

description: Gene expression profiling data from human multiple myeloma patient MM-082

source_name: Human multiple myeloma patient MM-082

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: M; Age:54; Stage:II A; MC:Ak; BL:+


title: MM-068_3

description: Gene expression profiling data from human multiple myeloma patient MM-068

source_name: Human multiple myeloma patient MM-068

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: M; Age:62; Stage:III A; MC:Ak; BL:-


title: MM-081_3

description: Gene expression profiling data from human multiple myeloma patient MM-081

source_name: Human multiple myeloma patient MM-081

value: M; Age:76; Stage:I A; MC:Ak; BL:-


title: MM-074_3

description: Gene expression profiling data from human multiple myeloma patient MM-074

source_name: Human multiple myeloma patient MM-074

value: M; Age:69; Stage:III A; MC:Ak; BL:+


title: MM-070_3

description: Gene expression profiling data from human multiple myeloma patient MM-070

source_name: Human multiple myeloma patient MM-070

value: F; Age:82; Stage:III B; MC:Dl; BL:+


title: MM-067_3

description: Gene expression profiling data from human multiple myeloma patient MM-067

source_name: Human multiple myeloma patient MM-067

value: F; Age:74; Stage:III A; MC:Gk; BL:+


title: MM-066_3

description: Gene expression profiling data from human multiple myeloma patient MM-066

source_name: Human multiple myeloma patient MM-066

value: F; Age:78; Stage:III A; MC:Ak; BL:-


title: MM-056_3

description: Gene expression profiling data from human multiple myeloma patient MM-056

source_name: Human multiple myeloma patient MM-056

value: M; Age:72; Stage:I A; MC:Gk; BL:+


title: MM-064_3

description: Gene expression profiling data from human multiple myeloma patient MM-064

source_name: Human multiple myeloma patient MM-064

value: F; Age:45; Stage:II A; MC:Gk; BL:-


title: MM-063_3

description: Gene expression profiling data from human multiple myeloma patient MM-063

source_name: Human multiple myeloma patient MM-063

value: F; Age:39; Stage:II A; MC:Gk; BL:-


title: MM-048_3

description: Gene expression profiling data from human multiple myeloma patient MM-048

source_name: Human multiple myeloma patient MM-048

value: M; Age:53; Stage:I A; MC:Gl; BL:+


title: MM-047_3

description: Gene expression profiling data from human multiple myeloma patient MM-047

source_name: Human multiple myeloma patient MM-047

value: F; Age:47; Stage:III A; MC:Gl; BL:+


title: MM-054_3

description: Gene expression profiling data from human multiple myeloma patient MM-054

source_name: Human multiple myeloma patient MM-054

value: M; Age:59; Stage:I A; MC:Gl; BL:+


title: MM-045_3

description: Gene expression profiling data from human multiple myeloma patient MM-045

source_name: Human multiple myeloma patient MM-045

value: M; Age:58; Stage:II A; MC:Gk; BL:+


title: MM-043_3

description: Gene expression profiling data from human multiple myeloma patient MM-043

source_name: Human multiple myeloma patient MM-043

value: F; Age:73; Stage:I A; MC:Gk + Gl; BL:+


title: MM-052_3

description: Gene expression profiling data from human multiple myeloma patient MM-052

source_name: Human multiple myeloma patient MM-052

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: F; Age:39; Stage:I A; MC:Gl + Al; BL:+


title: MM-040_3

description: Gene expression profiling data from human multiple myeloma patient MM-040

source_name: Human multiple myeloma patient MM-040

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: F; Age:77; Stage:III B; MC:Gl; BL:+


title: MM-072_3

description: Gene expression profiling data from human multiple myeloma patient MM-072

source_name: Human multiple myeloma patient MM-072

value: F; Age:75; Stage:I A; MC:Al; BL:-


title: MM-042_3

description: Gene expression profiling data from human multiple myeloma patient MM-042

source_name: Human multiple myeloma patient MM-042

value: M; Age:54; Stage:III A; MC:Al; BL:+


title: MM-037_3

description: Gene expression profiling data from human multiple myeloma patient MM-037

source_name: Human multiple myeloma patient MM-037

value: F; Age:51; Stage:II A; MC:Gk+Ak; BL:+


title: MM-069_3

description: Gene expression profiling data from human multiple myeloma patient MM-069

source_name: Human multiple myeloma patient MM-069

value: M; Age:66; Stage:II A; MC:Gk; BL:+


title: MM-050_3

description: Gene expression profiling data from human multiple myeloma patient MM-050

source_name: Human multiple myeloma patient MM-050

value: M; Age:71; Stage:I A; MC:Al; BL:-


title: MM-036_3

description: Gene expression profiling data from human multiple myeloma patient MM-036

source_name: Human multiple myeloma patient MM-036

value: M; Age:66; Stage:II A; MC:Gk; BL:-


title: MM-038_3

description: Gene expression profiling data from human multiple myeloma patient MM-038

source_name: Human multiple myeloma patient MM-038

value: F; Age:67; Stage:II A; MC:k; BL:+


title: MM-039_3

description: Gene expression profiling data from human multiple myeloma patient MM-039

source_name: Human multiple myeloma patient MM-039

value: M; Age:49; Stage:II A; MC:Gl; BL:+


title: Illumina-MRP1-1

description: MRP1 no echnical replicate

hyb_protocol: Employing materials and protocols by Illumina Inc.; hybridisation: 17h at 55 degC

scan_protocol: Using an Illumina scanner; gain factor: 2.5

data_processing: In BeadStudio 1.0 raw data were background subtracted and normalised using the "rank invariant" algorithm. Value = "null" denotes expression below background (p < 0.01).

source_name: Adult mouse retina pool 1

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions. Input amount: 300ng of total RNA; IVT: 6h

tag: The adult mouse retina samples were obtained from pool 1 of C57/B6 mice (n = 350), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA). All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.


title: MM-032_3

description: Gene expression profiling data from human multiple myeloma patient MM-032

source_name: Human multiple myeloma patient MM-032

value: M; Age:56; Stage:III B; MC:Gl; BL:-


title: Illumina-MRP2-1

description: MRP2 no echnical replicate

source_name: Adult mouse retina pool 2


title: MM-030_3

description: Gene expression profiling data from human multiple myeloma patient MM-030

source_name: Human multiple myeloma patient MM-030

value: M; Age:69; Stage:III A; MC:Gl; BL:-


title: MM-033_3

description: Gene expression profiling data from human multiple myeloma patient MM-033

source_name: Human multiple myeloma patient MM-033

value: F; Age:66; Stage:I A; MC:Gl; BL:-


title: MM-031_3

description: Gene expression profiling data from human multiple myeloma patient MM-031

source_name: Human multiple myeloma patient MM-031

value: M; Age:53; Stage:III A; MC:Ak; BL:+


title: MM-016_3

description: Gene expression profiling data from human multiple myeloma patient MM-016

source_name: Human multiple myeloma patient MM-016

value: M; Age:66; Stage:III B; MC:Gk; BL:+


title: MPSS-MRP2-20bp

tag: Total RNA (MRP2) was analyzed through Bioanalyzer and passed our quality control test. The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)

value: 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6):630-634). Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector. The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.


title: MM-034_3

description: Gene expression profiling data from human multiple myeloma patient MM-034

source_name: Human multiple myeloma patient MM-034

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: M; Age:72; Stage:I A; MC:Gk; BL:+


title: MM-138_3

description: Gene expression profiling data from human multiple myeloma patient MM-138

source_name: Human multiple myeloma patient MM-138

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: F; Age:62; Stage:I A; MC:G; BL:nd


title: MM-019_3

description: Gene expression profiling data from human multiple myeloma patient MM-019

source_name: Human multiple myeloma patient MM-019

value: M; Age:65; Stage:II A; MC:Gl; BL:+


title: MM-049_3

description: Gene expression profiling data from human multiple myeloma patient MM-049

source_name: Human multiple myeloma patient MM-049

value: M; Age:63; Stage:III B; MC:k; BL:+


title: MM-021_3

description: Gene expression profiling data from human multiple myeloma patient MM-021

source_name: Human multiple myeloma patient MM-021

value: M; Age:67; Stage:II A; MC:Gk; BL:-


title: MPSS-MRP1-20bp

tag: Total RNA (MRP1) was analyzed through Bioanalyzer and passed our quality control test. The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: MM-025_3

description: Gene expression profiling data from human multiple myeloma patient MM-025

source_name: Human multiple myeloma patient MM-025

value: F; Age:64; Stage:I A; MC:Gl; BL:-


title: MM-100_3

description: Gene expression profiling data from human multiple myeloma patient MM-100

source_name: Human multiple myeloma patient MM-100

value: M; Age:78; Stage:I A; MC:Ak; BL:+


title: MM-026_3

description: Gene expression profiling data from human multiple myeloma patient MM-026

source_name: Human multiple myeloma patient MM-026

value: F; Age:73; Stage:III B; MC:k; BL:+


title: Amersham-MRP2-5

description: MRP2 technical replicate 5

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

label: Biotin

label_protocol: CodeLink Expression Assay protocol


title: MM-014_3

description: Gene expression profiling data from human multiple myeloma patient MM-014

source_name: Human multiple myeloma patient MM-014

value: F; Age:59; Stage:II A; MC:Gk; BL:+


title: MM-015_3

description: Gene expression profiling data from human multiple myeloma patient MM-015

source_name: Human multiple myeloma patient MM-015

value: M; Age:70; Stage:II A; MC:Gk; BL:+


title: Amersham-MRP2-4

description: MRP2 technical replicate 4


title: MM-027_3

description: Gene expression profiling data from human multiple myeloma patient MM-027

source_name: Human multiple myeloma patient MM-027

value: M; Age:61; Stage:I A; MC:Gk; BL:-


title: MM-035_3

description: Gene expression profiling data from human multiple myeloma patient MM-035

source_name: Human multiple myeloma patient MM-035

value: M; Age:74; Stage:I A; MC:Gk; BL:-


title: Amersham-MRP2-3

description: MRP2 technical replicate 3

source_name: Adult mouse retina pool 2


title: Amersham-MRP2-2

description: MRP2 technical replicate 2


title: MM-004_3

description: Gene expression profiling data from human multiple myeloma patient MM-004

source_name: Human multiple myeloma patient MM-004

value: F; Age:54; Stage:I A; MC:Gk; BL:-


title: EC19n100 delta rseA

description: Wild type vs delta rseA

source_name: Wild type control

source_name: Delta rseA


title: ABI-MRP2-4

description: MRP2 technical replicate 4

hyb_protocol: Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.

label: DIG-UTP

label_protocol: 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.


title: ABI-MRP2-1

description: MRP2 technical replicate 1


title: Housekeeping gene analysis_SI12

status: Public on Dec 31 2006

first: Mark

last: Kidd

address: 333 Cedar Street

department: Surgery

institute: Yale University School of Medicine

source_name: Small intestine

extract_protocol: Total RNA was extracted from the sample using TRIzol (Invitrogen) followed by Qiagen RNeasy kit, and the RNA quality assessed using Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA.) to visually verify the absence of genomic DNA contamination, integrity and ratio of 28S and 18S bands.

tag: Small intestine


title: EC19n098 delta hfq

description: Wild type vs delta hfq

source_name: delta hfq


title: EC19n075 delta hfq

description: Wild type vs delta hfq


title: Housekeeping gene analysis_SI13


title: MM-055_3

description: Gene expression profiling data from human multiple myeloma patient MM-055

source_name: Human multiple myeloma patient MM-055

value: F; Age:69; Stage:III A; MC:Gk; BL:-


title: Housekeeping gene analysis_SI15


title: EC19n076 delta hfq

description: Wild type vs delta hfq


title: Housekeeping gene analysis_SI14


title: Housekeeping gene analysis_SI9


title: ABI-MRP2-5

description: MRP2 technical replicate 5


title: EC19n099 delta hfq

description: Wild type vs delta hfq


title: Housekeeping gene analysis_SI11


title: ABI-MRP2-2

description: MRP2 technical replicate 2


title: EC19n101 delta rseA

description: Wild type vs delta rseA


title: Housekeeping gene analysis_SI8


title: ABI-MRP2-3

description: MRP2 technical replicate 3


title: Amersham-MRP2-1

description: MRP2 technical replicate 1


title: Housekeeping gene analysis_SI6


title: Housekeeping gene analysis_SI7


title: Housekeeping gene analysis_SI5


title: Housekeeping gene analysis_SI10


title: Housekeeping gene analysis_SI4


title: Housekeeping gene analysis_L4

source_name: Liver

tag: Liver


title: Housekeeping gene analysis_L3


title: Housekeeping gene analysis_S16

source_name: Gastric mucosa

tag: Gastric mucosa


title: Housekeeping gene analysis_S7


title: Housekeeping gene analysis_S10


title: Housekeeping gene analysis_S9


title: Housekeeping gene analysis_S4


title: Housekeeping gene analysis_SI1


title: Housekeeping gene analysis_S11


title: Housekeeping gene analysis_S5


title: Housekeeping gene analysis_SI3


title: Housekeeping gene analysis_L1


title: Housekeeping gene analysis_SI2


title: Housekeeping gene analysis_L2


title: Housekeeping gene analysis_S3


title: Housekeeping gene analysis_S1


title: Housekeeping gene analysis_S2


title: Housekeeping gene analysis_S8


title: Housekeeping gene analysis_CO1

source_name: Colonic mucosa

tag: Colonic mucosa


title: Housekeeping gene analysis_S15


title: Housekeeping gene analysis_S6


title: Housekeeping gene analysis_S13


title: Housekeeping gene analysis_S14


title: elavGal4_adult_head_rep3

status: Public on Dec 30 2006

first: Yanmei

last: Huang

address: 136 Harrison Ave, A305B

department: Neuroscience

institute: Tufts University School of Medicine

description: The population contain a mixture of elav-gal4 male and elav-gal4/+ female.

hyb_protocol: Labeled RNAs were hybridized to the Drosophila genome array following standard protocol provided by Affymetrix. The array was washed and stained on a Affymetrix Fluidics Station 400 using standard protocols.

scan_protocol: An Agilent GeneArray Scanner was used to scan the array. Pixel size: 3 um, filter: 570nm, number of scan: 2

data_processing: Data generated by MAS5.0 with all default parameters and scaled to a target intensity of 100

organism: Drosophila melanogaster

source_name: Drosophila adult head with GAL4, ZT6

label_protocol: Affymetrix one cycle cDNA synthesis kit and and IVT labeling kit were used to label the RNAs following the standard protocols provided by Affymetrix.

growth_protocol: Fly cultures were grown in 25oC on standard media made from receipt provided by the Bloomington stock center. The culture were entrained to a 12 hour:12 hour light:dark cycle.

extract_protocol: Total RNAs were extracted from the head collections using the TriZol reagent from Invitrogen.

treatment_protocol: Female elav-gal4 flies were mated to male w1118 flies. Progenies from this cross were frozen at ZT6. Heads were collected from the frozen flies.

tag: Total RNA isolated from adult head of flies expressing GAL4 in their CNS neurons. Sample collected at ZT6.


title: Housekeeping gene analysis_S12