title: Head Short Day Cy3 Rep3

status: Public on Nov 28 2006

city: Le Rheu

first: Denis

last: TAGU

department: UMR 1099 BiO3P

country: France

institute: INRA Rennes

hyb_protocol: Hybridizations were performed in a Discovery XT System hybridization robot using the ChipMap 80 kit (Ventana Medical Systems, Tucson, AZ, USA) at the OUEST-Genopole and Agenae transcriptomic facilities (INRA Sribe, Rennes, France). Prehybridization was performed at 42ºC for 1 h in 2 ml of ChipSpread buffer containing 4xSSC and 0.2% SDS. Target cDNAs were mixed before hybridizations at 42ºC for 6 h (protocol N°2, ALC-D60/10-H48/8, Ventana). Washes were performed manually at room temperature in 1xSSC.

scan_protocol: Fluorescent images of the microarrays were generated with a Genepix 4000B scanner and Genepix Pro analysis software v5.0 (Axon Instruments, Molecular Devices Co., Sunnyvale, CA, USA).

data_processing: Raw data were normalized by the MADSCAN software. After subtraction of the fluorescence background, a rank-invariant method and a spatial normalisation were performed before a scaling of the variance within each slide and between all the slides at the same rank. The normalized values were log-transformed and used to perform statistical analysis by GeneANOVA. The contribution of each experimental factor (Gene, Photoperiod, Biological replicate, Dye, Technical replicate) and the interaction between them was evaluated by a global ANOVA. Differentially expressed genes where selected by imposing stringent cut-offs on the local ANOVA graphic of the interaction “Gene-Photoperiod”

organism: Acyrthosiphon pisum

source_name: Head of pea aphid reared under 12h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“short-day” or SD) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at SD photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood (wingless adults or WA) and produced offspring (G1) that were transferred onto new plants and kept under SD conditions. A batch of 50 L3-G1 aphids was collected in the middle of the photophase (15:00) and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in SD.

extract_protocol: RNAs were extracted from heads using either the RNeasy Mini kit (Qiagen, Germantown, MD, USA). RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 2 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).

treatment_protocol: Short Day reared pea aphids

tag: Strain

value: YR2 (red holocyclic clone)

tag: Parthenogenetic female

tag: 10 days of 12h photoperiod

tag: Instar stage L3

tag: Parthenogenetic female producing sexual individuals

source_name: Head of pea aphid reared under 16h photoperiod: reference channel

label_protocol: 5 µg of aRNA were labelled and purified using the CyScribe Post-labelling (anchored oligo-dT primed) and the CyScribe GFX Purification kits (Amersham Biosciences-GE, Fairfield, CT, USA).

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“long-day” or LD) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under LD photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood (wingless adults or WA) and produced offspring (G1) that were transferred onto new plants and kept under LD conditions. A batch of 50 L3-G1 aphids was collected in the middle of the photophase (15:00) and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in LD.

extract_protocol: RNAs were extracted from heads using either the RNeasy Mini kit (Qiagen, Germantown, MD, USA). This Channel 2 sample corresponds to a mixture of total RNAs taken from the three replicated samples reared under Long Day photoperiod. RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 2 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).

treatment_protocol: Long Day reared pea aphids

tag: 10 days of 16h photoperiod

tag: Female producing parthenogenetic females


title: Head Short Day Cy5 Rep3

type: RNA

molecule: total RNA

label_protocol: 5 µg of aRNA were labelled and purified using the CyScribe Post-labelling (anchored oligo-dT primed) and the CyScribe GFX Purification kits (Amersham Biosciences-GE, Fairfield, CT, USA)

extract_protocol: RNAs were extracted from heads using either the RNeasy Mini kit (Qiagen, Germantown, MD, USA). This Channel 1 sample corresponds to a mixture of total RNAs taken from the three replicated samples reared under Long Day photoperiod. RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 2 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).


title: Head Short Day Cy5 Rep1


title: Head Short Day Cy3 Rep2


title: 48h bufalin vs. 48h DMSO in HL60

status: Public on Nov 29 2006

city: Beijing

first: Chen

middle: Ai

last: Liang

address: Haidian District

department: Medical  School

country: China

institute: Tsinghua University

description: the genomic influence of bufalin on HL60 after treatment 48h

hyb_protocol: Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and mixed into 30 μl hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s solution). DNA in hybridization solution was denatured at 95℃ for 3 min before loading onto a microarray. The array was hybridized at 42℃ overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Express fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

data_processing:
A space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency (both above 1.5-fold) in both microarray were selected as differentially expressed genes
Raw data files for the dye-swap hybridizations are linked below as supplementary files:
GSM146701.txt [bufalin_Cy3 vs. 48h_DMSO_Cy5]
GSM146701_dyeswap.txt [bufalin_Cy5 vs. 48h_DMSO_Cy3]

organism: Homo sapiens

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.

treatment_protocol: treatment with bufalin for 48h

label_protocol: Sample_label_protocol_ch1 = Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

treatment_protocol: treatment with DMSO for 48h


title: Head Short Day Cy3 Rep1


title: RNA Polymerase II ChIP-chip on GM06990 cells using polyclonal antibody (N-20) Sample 3

status: Public on Nov 30 2006

type: genomic

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

country: USA

institute: Yale Med

description: RNA polymerase II ChIP-chip in ENCODE region in GM06990 cells using anti-Pol II (N-20) rabbit polyclonal antibody

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: value = log_2(Signal for Cy5 / Signal for Cy3)

molecule: genomic DNA

source_name: RNA Polymerase II ChIP in GM06990 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from Pol II-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: GM06990 cells were grown in RPMI medium supplemented with 15% FBS and antibiotics (kanamycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-Pol II (N-20) rabbit polyclonal antibody (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: Polyclonal antibody for Pol II (N-20)

source_name: IgG control ChIP in GM06990 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: GM06990 cells were grown in RPMI medium supplemented with 15% FBS and antibiotics (kanamycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with normal rabbit IgG (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: IgG reference


title: 1412082023B_Parent1

city: Los Angeles

first: Yelena

last: Bykhovskaya

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description: Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Raw data for each sample was output using the Illumina BeadStudio

label: Biotin-Labeled cRNA

source_name: EBV-transformed cell line of lymphoblasts extrated from peripheral blood

label_protocol: Illlumina® TotalPrep RNA amplification kit, manufactured by Ambion, Inc (Austin, TX) according to the manufacturer’s protocol

growth_protocol: RPMI-1640 medium (Invitrogen, Inc., Carlsbad, CA), containing 2 mmol/L L-glutamine, 100 ug/ml streptomycin, and 10% fetal calf serum

extract_protocol: Trizol reagent (Invitrogen, Inc.)

treatment_protocol: No treatment

tag: Immortalized lymphoblastoid cell line


title: Head Long Day Cy5 Rep3

source_name: Head of pea aphid reared under 16h photoperiod


title: Head Long Day Cy5 Rep2


title: Head Long Day Cy5 Rep1


title: RNA Polymerase II ChIP-chip on HeLaS3 cells using monoclonal antibody (8WG16) Sample 2

description: RNA polymerase II ChIP-chip in ENCODE region in HeLaS3 cells using monoclonal anti-Pol II (8WG16) antibody

source_name: RNA Polymerase II ChIP in HeLaS3 Cells

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-Pol II monoclonal antibody (Covance MMS-126R). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: Monoclonal antibody for Pol II (8WG16)

source_name: IgG control ChIP in HeLaS3 Cells

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with normal rabbit IgG (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.


title: 1412082072F_Control8_2

scan_protocol: Refer to the Illumina Gene Expression System Manual


title: Head Long Day Cy3 Rep3

extract_protocol: RNAs were extracted from heads using either the RNeasy Mini kit (Qiagen, Germantown, MD, USA). This Channel 2 sample corresponds to a mixture of total RNAs taken from the three replicated samples reared under Long Day photoperiod. RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 2 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).Channel 2 label


title: Head Long Day Cy3 Rep2


title: Tetra-acetylated Histone H4 ChIP-chip on HeLaS3 cells Sample 1

description: Tetra-acetylated Histone H4 ChIP-chip in ENCODE region in HeLaS3 cells

source_name: Tetra-acetylated Histone H4 ChIP in HeLaS3 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from acetylated Histone H4-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-acetyl-Histone H4 rabbit polyclonal antiserum (Upstate 06-866). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: Tetra-acetylated Histone H4 antibody


title: Head Long Day Cy3 Rep1


title: RNA Polymerase II ChIP-chip on HeLaS3 cells using polyclonal antibody (N-20) Sample 3

description: RNA polymerase II ChIP-chip in ENCODE region in HeLaS3 cells using anti-Pol II (N-20) rabbit polyclonal antibody

source_name: RNA polymerase II ChIP in HeLaS3 Cells

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-Pol II (N-20) rabbit polyclonal antibody (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.


title: Saccharomyces cerevisiae cells exposed to 100 Gy Gamma Radiation replicate 3

city: Madison

first: Michael

middle: G

last: Benton

state: WI

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

description: wt S. cerevisiae cells from W303 background

data_processing: After background correction and removal of outliers (two standard deviations from the mean intensity for that spot), average (of 15 PM/MM pairs for each gene) intensity values for perfect match, mismatch, and perfect match-mismatch were calculated

organism: Saccharomyces cerevisiae


title: RNA Polymerase II ChIP-chip on HeLaS3 cells using polyclonal antibody (N-20) Sample 1


title: Saccharomyces cerevisiae cells exposed to 0 Gy Gamma Radiation replicate 3

source_name: wt S. cerevisiae cells from W303 background


title: Saccharomyces cerevisiae cells exposed to 1 Gy Gamma Radiation replicate 3

tag: wt S. cerevisiae cells from W303 background


title: RNA Polymerase II ChIP-chip on HeLaS3 cells using monoclonal antibody (8WG16) Sample 3


title: Saccharomyces cerevisiae cells exposed to 10 Gy Gamma Radiation replicate 2


title: RNA Polymerase II ChIP-chip on GM06990 cells using polyclonal antibody (N-20) Sample 1


title: Saccharomyces cerevisiae cells exposed to 100 Gy Gamma Radiation replicate 2


title: Saccharomyces cerevisiae cells exposed to 0 Gy Gamma Radiation replicate 2


title: RNA Polymerase II ChIP-chip on HeLaS3 cells using monoclonal antibody (8WG16) Sample 1


title: Saccharomyces cerevisiae cells exposed to 1 Gy Gamma Radiation replicate 2


title: Saccharomyces cerevisiae cells exposed to 10 Gy Gamma Radiation replicate 1


title: Saccharomyces cerevisiae cells exposed to 100 Gy Gamma Radiation replicate 1


title: Saccharomyces cerevisiae cells exposed to 10 Gy Gamma Radiation replicate 3


title: Saccharomyces cerevisiae cells exposed to 0 Gy Gamma Radiation replicate 1


title: Saccharomyces cerevisiae cells exposed to 0% (v/v) MMS replicate 3


title: Saccharomyces cerevisiae cells exposed to 1 Gy Gamma Radiation replicate 1


title: Saccharomyces cerevisiae cells exposed to 0.001% (v/v) MMS replicate 3


title: Head Short Day Cy5 Rep2


title: Saccharomyces cerevisiae cells exposed to 0.01% (v/v) MMS replicate 3


title: Tetra-acetylated Histone H4 ChIP-chip on HeLaS3 cells Sample 2


title: Saccharomyces cerevisiae cells exposed to 0.1% (v/v) MMS replicate 3


title: Saccharomyces cerevisiae cells exposed to 0.01% (v/v) MMS replicate 2


title: Saccharomyces cerevisiae cells exposed to 0.1% (v/v) MMS replicate 2


title: 13503280

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

country: Canada

institute: Université de Montréal - Faculté de Médecine Vétérinaire

description: Competitive hybridization of cDNA generated from A. pleuropneumoniae sero 1 strain s4074 RNA extracted in BHI broth or iron-restricted BHI broth (EDDHA) complemented with FeCl3

scan_protocol: Scanning using a Perkins Elmer ScanArray Laser intensity : 92% (Cy3), 85% (Cy5) PMF : 92% (Cy3), 85% (Cy5)

data_processing: Image processing software: SpotFinder v.3.1.1. Net median intensities were normalized using Lowess algorithm (MIDAS) and log2 ratios were generated

organism: Actinobacillus pleuropneumoniae

label_protocol:
RNA was reverse-transcribed to cDNA, using Invitrogen's SuperScript II and  amino-allyl dUTP.  Samples were then indirectly labelled with Cy3 ou Cy5 esters.  Complete protocol is described in :
Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.

extract_protocol: Total RNA was extracted at an A600 of 0.300 using the QIAGEN RNeasy protocol with the on-column DNAse treatment.  The RNA was then treated with Ambion Turbo DNAse, as prescribed by the manufacturer, to remove residual DNA.

tag: serotype 1, strain s4074

tag: BHI broth

tag: BHI broth + 50 ug/ml EDDHA + 50 ug/ml FeCl3


title: 13503895

hyb_protocol: Complete protocol is described in : Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.

scan_protocol: Scanning using a Perkins Elmer ScanArray Laser intensity : 90% (Cy3), 82% (Cy5) PMF : 90% (Cy3), 85% (Cy5)


title: Saccharomyces cerevisiae cells exposed to 0.1% (v/v) MMS replicate 1


title: 13503894

scan_protocol: Scanning using a Perkins Elmer ScanArray Laser intensity : 85% (Cy3), 85% (Cy5) PMF : 90% (Cy3), 85% (Cy5)


title: Tetra-acetylated Histone H4 ChIP-chip on HeLaS3 cells Sample 3


title: 13503278

scan_protocol: Scanning using a Perkins Elmer ScanArray Laser intensity : 92% (Cy3), 90% (Cy5) PMF : 92% (Cy3), 85% (Cy5)


title: Saccharomyces cerevisiae cells exposed to 0% (v/v) MMS replicate 2


title: RNA Polymerase II ChIP-chip on HeLaS3 cells using polyclonal antibody (N-20) Sample 2


title: Saccharomyces cerevisiae cells exposed to 0.01% (v/v) MMS replicate 1


title: Saccharomyces cerevisiae cells exposed to 0.001% (v/v) MMS replicate 1


title: Yeast gcr1 null mutant in glucose rep4

status: Public on Nov 27 2006

city: Hattiesburg

first: Kellie

last: Barbara

state: MS

address: 118 College Dr. #5018

department: Biological Sciences

institute: Univ. of Southern MS

description: labeling done with Agilent's Low RNA Input Linear Amp kit; hyb and slide processing done according to Agilent's instructions

data_processing: log2 ratio after ratio-based and LOWESS normalization in Acuity 4.0

source_name: yeast, 2% glucose

tag: wild type strain, S288C background, grown to early/mid log in YEP containing indicated carbon source

tag: gcr1 null mutant, S288C background, grown to early/mid log in YEP containing indicated carbon source


title: Saccharomyces cerevisiae cells exposed to 0.001% (v/v) MMS replicate 2


title: Saccharomyces cerevisiae cells exposed to 0% (v/v) MMS replicate 1


title: Yeast gcr1 null mutant in glucose rep2


title: Yeast gcr1 null mutant in glucose rep3

tag: gcr1 nul mutant, S288C background, grown to early/mid log in YEP containing indicated carbon source


title: Yeast gcr1 null mutant in glucose rep1


title: Yeast gcr1 null mutant in raffinose rep4

source_name: yeast 3% raffinose

source_name: yeast, 3% raffinose


title: Yeast gcr1 null mutant in galactose rep4

source_name: yeast, 3% galactose


title: Yeast gcr1 null mutant in galactose rep1


title: Yeast gcr1 null mutant in galactose rep3


title: Yeast gcr1 null mutant in galactose rep2


title: Yeast_null mutant 20min glucose

description: labeling done with Agilent's low RNA input linear amp kit; hyb and slide processing done according to Agilent's instructions

source_name: Yeast, 20min glucose

tag: gcr1 null mutant, S288C background, grown to early/mid log in YEP containing pyruvate; sample taken 20min after glucose upshift

tag: wild type, S288C background, grown to early/mid log in YEP containing pyruvate; sample taken 20min after glucose upshift


title: Yeast gcr1 null mutant in raffinose rep3


title: Yeast gcr1 null mutant in raffinose rep2


title: Yeast gcr1 null mutant in raffinose rep1


title: Yeast_null mutant 60min glucose

source_name: Yeast, 60min glucose

tag: gcr1 null mutant, S288C background, grown to early/mid log in YEP containing pyruvate; sample taken 60min after glucose upshift

tag: wild type, S288C background, grown to early/mid log in YEP containing pyruvate; sample taken 60min after glucose upshift


title: Yeast_null mutant 0min glucose

source_name: yeast, 3% pyruvate

tag: gcr1 null mutant, S288C background, grown to early/mid log in YEP containing indicated carbon source, prior to glucose addition

tag: wild type, S288C background, grown to early/mid log in YEP containing indicated carbon source, prior to glucose addition


title: Brain of P10 Gja9 (+/-) C57Bl/6j mouse, replica H3

status: Public on Nov 25 2006

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Compare the brain transcriptomes of Gja9 (-/-) and Gja9 (+/-) mice with that of wildtype mice to detect transcriptomic alterationss induced by total or partial ablation of Gja9

hyb_protocol: 60 ug Trizol extracted RNA from each of the brains (or our mouse reference in the case of neonates) was reverse transcribed in the presence of fluorescent Cy3 and Cy5 dUTPs to obtain labeled cDNAs. Hybridization was done overnight at 50C. After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned at 750V (635nm) and 670V (532nm). Hybridization design ("multiple yellow" strategy) described in Iacobas DA, Fan C, Iacobas S et al., Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38

scan_protocol: Slides were scanned with GenePix 4100A scanner (Axon Instruments, CA) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in house developed algorithms described in Iacobas DA, Iacobas S, Li WEI, et al. Physiol Genomics 20: 211-223, 2005. PMID: 15585606.

organism: Mus musculus

label_protocol: 60 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Cy5 fluorescent dye (Amersham Biosciences, NJ)

extract_protocol: RNA samples were extracted in Trizol (Invitrogen, CA)

treatment_protocol: The mouse was decapitated under aseptic conditions and brain was removed and immediately stored into -80 ºC freezer for later total RNA extraction.


title: Brain of P10 Gja9 (+/-) C57Bl/6j mouse, replica H4

label_protocol: 60 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Cy3 fluorescent dye (Amersham Biosciences, NJ)


title: Bic/4AP/MK801

first: Guangxin

last: Xiang

address: Tsinghua University

institute: Medical Systems Biology Research Center

description: The genomic influcence of the combination of three reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP), which were significantly affected by the addition of the NMDA receptor antagonist 10 μM MK801.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a confocal LuxScanTM scanner (CapitalBio) and image intensity data were extracted and analyzed with SpotData software (CapitalBio).

data_processing: A space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Genes with signal intensity (Cy3 or Cy5) ≥ 800 were regarded as the expressed genes. Besides, those genes whose alteration tendency kept consistent in both arrays and mean expression ratios averaged above 2-fold, were selected as differentially expressed genes.

organism: Rattus norvegicus

source_name: Cultured cortical neurons

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. The amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Neurons were plated with a density of 1500 cells/mm2 and maintained in a combination medium (MEM+/NB), which consisted of 50% MEM+ medium (modified Eagle’s medium supplemented with 10% fetal bovine serum) and 50% NB medium (NeurobasalTM with B27 supplement plus 0.5 mM glutamine).

treatment_protocol: treatment with 50 μM bicuculline (Bic), 5 μM 4-aminopyridine (4AP) and 10 μM MK801 for 8 h

tag: Cortical neurons were harvested from embryonic day 18 (E18) Sprague-Dawley rats and cultured in vitro for 9-11 days

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents

treatment_protocol: treatment with the solvent DMSO (Ctrl) for 8 h


title: Brain of P10 Gja9 (-/-) C57Bl/6j mouse, replica K4


title: Bic/4AP 2h pulse

description: The genomic consequences of bursts of action potential firing induced (2 h pulse) by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 μM) and the potassium channel blocker 4-aminopyridine (4AP, 5 μM).

treatment_protocol: treatment with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP) for 2 h and maintain for 6 h after the removal of Bic/4AP

treatment_protocol: treatment with the solvent DMSO (Ctrl) for 2 h and maintain for 6 h after the removal of DMSO


title: Brain of P10 Gja9 (-/-) C57Bl/6j mouse, replica K3


title: Bic/4AP/MK801/Nif

description: The genomic influcence of the combination of four reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP), which were significantly affected by the addition of 10 μM MK801 and 5 μM nifedipine (Nif).

treatment_protocol: treatment with 50 μM bicuculline (Bic), 5 μM 4-aminopyridine (4AP), 10 μM MK801 and 5 μM nifedipine (Nif) for 8 h


title: Brain of P10 Gja9 (+/-) C57Bl/6j mouse, replica H2


title: Bic/4AP 2h

description: The genomic consequences of bursts of action potential firing induced by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 μM) and the potassium channel blocker 4-aminopyridine (4AP, 5 μM).

treatment_protocol: treatment with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP) for 2 h

treatment_protocol: treatment with the solvent DMSO (Ctrl) for 2 h


title: Brain of P10 Gja9 (+/-) C57Bl/6j mouse, replica H1


title: Brain of P10 Gja9 (-/-) C57Bl/6j mouse, replica K2


title: Bic/4AP/Nif

description: The genomic influcence of the combination of three reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP), which were significantly affected by the addition of the L-type VGCC antagonist 5 μM nifedipine (Nif).

treatment_protocol: treatment with 50 μM bicuculline (Bic), 5 μM 4-aminopyridine (4AP) and 5 μM nifedipine (Nif) for 8 h


title: Bic/4AP(2)

treatment_protocol: treatment with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP) for 8 h


title: Brain of P10 Gja9 (-/-) C57Bl/6j mouse, replica K1


title: Brain of P10 wildtype C57Bl/6j mouse, replica W3


title: Bic/4AP/TTX

description: The genomic influcence of the combination of three reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP), which were abolished by the addition of the sodium channel blocker TTX (1 μM).

treatment_protocol: treatment with 50 μM bicuculline (Bic), 5 μM 4-aminopyridine (4AP) and 1 μM tetrodotoxin (TTX) for 8 h


title: Bic

description: The genomic consequences of bursts of action potential firing induced by the treatment of cultured cortical neurons (9-11 DIV) with the GABAA receptor antagonist bicuculline (Bic, 50 μM).

treatment_protocol: treated with 50 μM bicuculline (Bic) for 8 h

tag: Cortical neurons were harvested from embryonic day 18 (E18) Sprague-Dawley rats and cultured in vitro for 9-11 days.


title: Brain of P10 wildtype C57Bl/6j mouse, replica W4


title: Bic/4AP/EGTA

description: The genomic influcence of the combination of three reagents on cultured cortical neurons (9-11 DIV). Bursts of action potential firing were induced by the treatment of cultured cortical neurons with 50 μM bicuculline (Bic) and 5 μM 4-aminopyridine (4AP), which were abolished by the addition of the Ca2+ chelator EGTA (4 mM).

treatment_protocol: treatment with 50 μM bicuculline (Bic), 5 μM 4-aminopyridine (4AP) and 4 mM EGTA for 8 h


title: Brain of P10 wildtype C57Bl/6j mouse, replica W2


title: Brain of P10 wildtype C57Bl/6j mouse, replica W1

hyb_protocol: 60 ug Trizol extracted RNA from each of the brains (or our mouse reference in the case of neonates) was reverse transcribed in the presence of fluorescent Cy3 and Cy5 dUTPs to obtain labeled cDNAs. Hybridization was done overnight at 50C. After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned at 750V (635nm) and 670V (532nm). Hybridization design ("multiple yellow" strategy) described in Iacobas DA, Fan C, Iacobas S, et al., Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38

source_name: Brain of P10 wildtype C57Bl/6j mouse (W1)

extract_protocol: RNA samples were extracted in Trizol (Invitrogen, CA) from the brain


title: Mpool2 vs IRF4 KO - unstimulated - repeat 3 - mAdbID:63644

status: Public on Nov 24 2006

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 63644

hyb_protocol: Lymphochip Hybridization Protocol Wash procedure: 1-2xssc 0.1%SDS 2-1xssc 1-0.5xssc 1-0.25xssc spin dry Qty. of labeled target: 50ug total RNA Time: 16-20hrs Volume: 40ul final volume Temperature: 65C Other: see Nature. 2000 Feb 3;403(6769):503-11. AND Immunity. 2000 Aug;13(2):199-212.

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 660;; 720 ScanPower: 100;; 100 LaserPower: 1.2;; 1.7 Temperature: 34.92

data_processing:
mAdb Standard Data Processing Protocol
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Mouse Lymphochip RNA Ref Pool 2

label_protocol:
Lymphochip Labeling-cy3
Label amount: 4ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: Cell line

tag: Cell type

value: B-cell, T-cell, monocyte cell

tag: Other

value: Mixture of total RNAs from 21 cell lines:6312 (proB); 18-81, 220-8, PD31, ED2 (preB); 70Z/3 (immature B); BCL1, M1.2.4.1 (mature B); S107, APBC4 (plasmacytoma); 2017(preT); 3DO (mature T); B6206-3 (follicular lymphoma); NFS201 (centroblastic lymphoma); NFS204 (marginal zone lymphoma); NFS205 (diffuse large B cell lymphoma), NFS210 (T cell lymphoma); BSJ003-2 (Burkitt-like lymphoma); MAPS-1 (T cell lymphoma); JZ74A1 (macrophage).

source_name: mouse IRF4 KO - Untreated

label_protocol:
Lymphochip Labeling-cy5
Label amount: 4ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.

growth_protocol:
mouse B cells in vitro Growth Protocol
Media: RPMI+10%FBS
Max. temp.: 37C
Min. time: 24-96hrs
Other: see Sciammas, et al Immunity. 2006 Aug;25(2):225-36.

tag: Strain

value: Balb-c

tag: Tissue

value: spleen

tag: Developmental stage

value: adult

value: mouse splenic B cells

tag: genotype/variation gene knock out

tag: genotype/variation

value: IRF4 homozygous (-/-)


title: Bic/4AP(1)


title: Mpool2 vs IRF4 KO - LPS treated 48 hrs - repeat 2 - mAdbID:63647

description: mAdb experiment ID: 63647

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 620;; 730 ScanPower: 100;; 100 LaserPower: 1.22;; 1.71 Temperature: 35.36

source_name: mouse IRF4 KO - 48 hours

treatment_protocol:
Treatment type: compound
Agent: LPS
Treatment dose: 20-25 mg/ml
Treatment time: 48 hours
Treatment temperature: 37C


title: Bic/4AP(3)


title: Mpool2 vs IRF4 KO - LPS treated 24 hrs - repeat 3 - mAdbID:63646

description: mAdb experiment ID: 63646

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 650;; 720 ScanPower: 100;; 100 LaserPower: 1.09;; 1.71 Temperature: 35.16

source_name: mouse IRF4 Het - 24 hours

treatment_protocol:
Treatment type: compound
Agent: LPS
Treatment dose: 20-25 mg/ml
Treatment time: 24 hours
Treatment temperature: 37C

value: IRF4 heterozygous (-/+)


title: Mpool2 vs IRF4 KO - LPS treated 96 hrs - repeat 3 - mAdbID:63649

description: mAdb experiment ID: 63649

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 690;; 740 ScanPower: 100;; 100 LaserPower: 1.13;; 1.71 Temperature: 35.7

source_name: mouse IRF4 KO - 96 hours

treatment_protocol:
Treatment type: compound
Agent: LPS
Treatment dose: 20-25 mg/ml
Treatment time: 96 hours
Treatment temperature: 37C


title: Mpool2 vs IRF4 HET - unstimulated - repeat 3 - mAdbID:63639

description: mAdb experiment ID: 63639

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 720;; 700 ScanPower: 100;; 100 LaserPower: 1.08;; 1.79 Temperature: 33.42

source_name: mouse IRF4 Het - Untreated


title: Mpool2 vs IRF4 KO - LPS treated 48 hrs - repeat 3 - mAdbID:63648

description: mAdb experiment ID: 63648

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 670;; 740 ScanPower: 100;; 100 LaserPower: 1.12;; 1.71 Temperature: 35.51

source_name: mouse IRF4 Het - 48 hours


title: Mpool2 vs IRF4 KO - LPS treated 24 hrs - repeat 1 - mAdbID:58833

description: mAdb experiment ID: 58833

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 900;; 670 ScanPower: 100;; 100 LaserPower: 3.21;; 5.7 Temperature: 38.63

source_name: mouse IRF4 KO - 24 hours


title: Mpool2 vs IRF4 HET - LPS treated 24 hrs - repeat 1 - mAdbID:58831

description: mAdb experiment ID: 58831

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 700;; 670 ScanPower: 100;; 100 LaserPower: 3.07;; 5.62 Temperature: 38.17


title: Mpool2 vs IRF4 KO - unstimulated - repeat 1 - mAdbID:58916

description: mAdb experiment ID: 58916

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 790;; 710 ScanPower: 100;; 100 LaserPower: 3.1;; 5.8 Temperature: 39.6


title: Mpool2 vs IRF4 HET - unstimulated - repeat 1 - mAdbID:58830

description: mAdb experiment ID: 58830

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 700;; 670 ScanPower: 100;; 100 LaserPower: 3.06;; 5.61 Temperature: 38.05


title: Mpool2 vs IRF4 HET - LPS treated 24 hrs - repeat 2 - mAdbID:60817

description: mAdb experiment ID: 60817

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 700 ScanPower: 100;; 100 LaserPower: 3.09;; 5.94 Temperature: 39.69


title: Mpool2 vs IRF4 HET - LPS treated 48 hrs - repeat 1 - mAdbID:60819

description: mAdb experiment ID: 60819

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 750;; 730 ScanPower: 100;; 100 LaserPower: 3.03;; 5.96 Temperature: 39.88


title: Mpool2 vs IRF4 HET - LPS treated 48hrs - repeat 2 - mAdbID:63386

description: mAdb experiment ID: 63386

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 660;; 690 ScanPower: 100;; 100 LaserPower: 1.21;; 1.82 Temperature: 34.36


title: Mpool2 vs IRF4 KO - LPS treated 48 hrs - repeat 1 - mAdbID:60822

description: mAdb experiment ID: 60822

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 760;; 730 ScanPower: 100;; 100 LaserPower: 2.91;; 5.96 Temperature: 40.3


title: Mpool2 vs IRF4 KO - LPS treated 96 hrs - repeat 2 - mAdbID:63377

description: mAdb experiment ID: 63377

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 630;; 650 ScanPower: 100;; 100 LaserPower: 1.21;; 1.81 Temperature: 34.14


title: Mpool2 vs IRF4 HET - LPS treated 96 hrs - repeat 2 - mAdbID:63177

description: mAdb experiment ID: 63177

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 820;; 600 ScanPower: 100;; 100 LaserPower: 3.17;; 6.03 Temperature: 45.52

source_name: mouse IRF4 Het - 96 hours


title: Mpool2 vs IRF4 HET - LPS treated 96 hrs - repeat 4 - mAdbID:63363

description: mAdb experiment ID: 63363

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 640;; 650 ScanPower: 100;; 100 LaserPower: 1.13;; 1.77 Temperature: 33.8


title: Mpool2 vs IRF4 HET - LPS treated 96 hrs - repeat 3 - mAdbID:63358

description: mAdb experiment ID: 63358

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 620;; 650 ScanPower: 100;; 100 LaserPower: 1.24;; 1.78 Temperature: 33.56


title: Mpool2 vs IRF4 KO - LPS treated 96 hrs - repeat 1 - mAdbID:63370

description: mAdb experiment ID: 63370

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 670;; 650 ScanPower: 100;; 100 LaserPower: 1.24;; 1.79 Temperature: 33.97


title: Mpool2 vs IRF4 HET - unstimulated - repeat 2 - mAdbID:58832

description: mAdb experiment ID: 58832

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 700;; 670 ScanPower: 100;; 100 LaserPower: 3.05;; 5.65 Temperature: 38.26


title: Mpool2 vs IRF4 KO - LPS treated 24 hrs - repeat 2 - mAdbID:60821

description: mAdb experiment ID: 60821

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 720;; 710 ScanPower: 100;; 100 LaserPower: 2.93;; 5.96 Temperature: 40.12


title: Mpool2 vs IRF4 KO - unstimulated - repeat 2 - mAdbID:60612

description: mAdb experiment ID: 60612

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 700;; 640 ScanPower: 100;; 100 LaserPower: 3.14;; 5.95 Temperature: 38.87


title: Spleen Day 0

city: Toronto

first: Fiona

middle: E

last: Lovegrove

state: ON

address: 1 King's College Circle, MSB Rm 7318

department: Institute of Medical Science

institute: University of Toronto

description: Baseline samples (prior to P. berghei infection)

data_processing: VSN, Loess, Median subtraction

molecule: polyA RNA

source_name: Spleen Day0

tag: Male Balb/c, 6-8 weeks

tag: Male C57BL/6, 6-8 weeks


title: Spleen Day 6

description: Day6 post P. berghei infection

organism:
Plasmodium berghei
Mus musculus

source_name: Spleen Day6

tag: Male BALB/c, 6-8 weeks, Infected IP with 1x10^6 P. berghei ANKA

tag: Male C57BL/6, 6-8 weeks, Infected IP with 1x10^6 P. berghei ANKA


title: Lung Day 0

source_name: Lung Day0

tag: Male BALB/c, 6-8 weeks


title: Lung Day 6

description: Day 6 post P. berghei infection

source_name: Lung Day6

tag: Male Balb/c, 6-8 weeks, Infected IP with 1x10^6 P. berghei ANKA


title: Liver Day 6

description:
Day 6 post P. berghei infection
Note:  In the original GPR, the Cy5 channel is actually BALB/c Liver Day 0 due to a sample swap.  For ease of analysis here, we have given the Liver Day 6 ratios based on the intensities, normalized across all arrays.  See also GSM132735.

source_name: Liver Day6

tag: Male Balb/c, 6-8 weeks, infected IP with 1x10^6 P. berghei ANKA

tag: Male C57BL/6, 6-8 weeks, infected IP with 1x10^6 P. berghei ANKA


title: Brain(uninfected) Blood(infected)

description: Test Hybridization

data_processing: VSN, Loess

source_name: Infected Peripheral Blood

tag: Male C57BL/6, 6-8 weeks, Infected IP with 1x10^6 P. berghei ANKA parasites

source_name: Uninfected Brain


title: Ocily7 puro vs IRF4 - day 3 - repeat 2 - mAdbID:60615

description: mAdb experiment ID: 60615

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 780;; 640 ScanPower: 100;; 100 LaserPower: 3.14;; 5.98 Temperature: 39.3

source_name: Ocily7 Vxypuro empty vector - Control

tag: Cell line

value: human GCB-like DLBCL cell line with empty expression vector Vxy

tag: Disease state

value: DLBCL

source_name: Ocily7 Vxy-IRF4 - 3 days

growth_protocol:
OCILY7 Growth Protocol - 3 days
Media: IMEM+10% FBS
Max. temp.: 37C
Min. time: 3 days
Other: see Sciammas, et al. Immunity. 2006 Aug;25(2):225-36

value: human GCB-like DLBCL cell line expressing human IRF4 from the Vxy vector


title: Ocily7 puro vs IRF4 - day 2 - mAdbID:60617

description: mAdb experiment ID: 60617

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 650 ScanPower: 100;; 100 LaserPower: 3.17;; 5.96 Temperature: 39.02

tag: Cell type

source_name: Ocily7 Vxy-IRF4 - 2 days

growth_protocol:
OCILY7 Growth Protocol - 2 days
Media: IMEM+10% FBS
Max. temp.: 37C
Min. time: 2 days
Other: see Sciammas, et al. Immunity. 2006 Aug;25(2):225-36


title: Spleen Day 3

description: Day 3 post P. berghei infection

source_name: Spleen Day3


title: Brain Day 6

description: Day 6 post PbA infection

source_name: Brain Day 6

source_name: Brain Day6


title: Lung Day 3

description: Day 3 post P. berghei infection

source_name: Lung Day3


title: Haltere sample 51681 Block2

status: Public on Nov 23 2006

city: Clemson

first: Brad

last: Hersh

state: SC

address: 132 Long Hall

institute: Clemson University

description: Raw signal data

hyb_protocol: As described in Nuwaysir et al., 2002. Genome Research 12: 1749-1755

data_processing: Non-normalized signal data

label: Biotin

organism: Drosophila melanogaster

source_name: Third instar haltere imaginal discs from Drosophila melanogaster yw strain

label_protocol: Labeling was performed using the Enzo BioArray High Yield RNA transcript labeling kit following the manufacturer's instructions

extract_protocol: Total RNA isolated with Qiagen RNeasy columns following the manufacturer's instructions

tag: Strain

value: yw

tag: Age

value: Third-instar larva

value: haltere imaginal disc


title: Ocily7 puro vs IRF4 - day 3 - repeat 1 - mAdbID:59713

description: mAdb experiment ID: 59713

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 790;; 750 ScanPower: 100;; 100 LaserPower: 2.98;; 5.91 Temperature: 39.63

tag: Developmental stage


title: Haltere sample 51681 Block3

description: Raw signal data

scan_protocol: As described in Nuwaysir et al., 2002. Genome Research 12: 1749-1755

tag: Tissue


title: Liver Day 0

description:
Baseline samples (prior to PbA infection)
Note:  In the original GPR, the Cy5 channel is actually BALB/c Liver Day 6 due to a sample swap.  For ease of analysis here, we have given the Liver Day 0 ratios based on the intensities, normalized across all arrays.  See also GSM132739.

source_name: Liver Day 0

tag: Male Balb/c mice, 6-8 weeks

tag: Male C57BL/6 mice, 6-8 weeks old


title: Haltere sample 51681 Block1

description: Raw signal data


title: Haltere sample 51603 Block4

description: Raw signal data


title: Ocily7 puro vs IRF4 - day 5 - mAdbID:59714

description: mAdb experiment ID: 59714

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 770;; 620 ScanPower: 100;; 100 LaserPower: 2.97;; 5.92 Temperature: 39.75

source_name: Ocily7 Vxy-IRF4 - 5 days

growth_protocol:
OCILY7 Growth Protocol - 5 days
Media: IMEM+10% FBS
Max. temp.: 37C
Min. time: 5 days
Other: see Sciammas, et al. Immunity. 2006 Aug;25(2):225-36


title: Haltere sample 51681 Block4

description: Raw signal data


title: Haltere sample 51599 Block2

description: Raw signal data


title: Haltere sample 51603 Block2

description: Raw signal data


title: Cardia vs posteriorfemale midgut 3

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: 2-dye hybridization assay

hyb_protocol: agilent

scan_protocol: genepix

data_processing: genepix

organism: Anopheles gambiae

source_name: Cardia part 4 day old female unfed midgut 3b

label_protocol: agilent

extract_protocol: qiagen

source_name: 4 day old posterior female unfed midgut 3b


title: Haltere sample 51603 Block1

description: Raw signal data


title: Liver Day 3

description: Day 3 post P. berghei infection

source_name: Liver Day3


title: Haltere sample 51603 Block3

description: Raw signal data


title: posterior-posterior vs 4 day unfed female midgut 3

description: 2-dye hybridization assay

source_name: posterior-posterior part of 4 day unfed female midgut 3

source_name: 4 day old female unfed midgut 3d

tag: 4 day old female unfed midgut 3d


title: 4 day old male midgut vs 4 day unfed female midgut 2

description: 2-dye hybridization assay

source_name: 4 day old male midgut 2

tag: 4 day old male midgut 2

source_name: 4 day unfed female midgut 2e

tag: 4 day unfed female midgut 2e


title: 4 day old male midgut vs 4 day unfed female midgut 3

description: 2-dye hybridization assay

source_name: 4 day old male midgut 3

tag: 4 day old male midgut 3

source_name: 4 day unfed female midgut 3

tag: 4 day unfed female midgut 3


title: posterior-posterior vs 4 day unfed female midgut 2

description: 2-dye hybridization assay

source_name: posterior-posterior part of 4 day unfed female midgut 2

source_name: 4 day old female unfed midgut 2d

tag: 4 day old female unfed midgut 2d


title: Haltere sample 51599 Block3

description: Raw signal data


title: posterior-posterior vs 4 day unfed female midgut 1

description: 2-dye hybridization assay

source_name: posterior-posterior part of 4 day unfed female midgut 1

source_name: 4 day old female unfed midgut 1d

tag: 4 day old female unfed midgut 1d


title: Vg Sample 51549 Block3

description: Raw signal data

source_name: Third instar wing imaginal discs from Drosophila melanogaster vg strain

value: wing imaginal disc


title: Haltere sample 51599 Block1

description: Raw signal data

source_name: Third instar haltere imaginal discs from Drosophila melanogaster yw strain


title: 4 day old male midgut vs 4 day unfed female midgut 1

description: 2-dye hybridization assay

source_name: 4 day old male midgut 1

tag: 4 day old male midgut 1

source_name: 4 day unfed female midgut 1e

tag: 4 day unfed female midgut 1e


title: Vg Sample 51549 Block1

description: Raw signal data


title: Vg Sample 51549 Block2

description: Raw signal data


title: Cardia vs posteriorfemale midgut 2

description: 2-dye hybridization assay

source_name: Cardia part 4 day old female unfed midgut 2b

source_name: 4 day old posterior female unfed midgut 2b


title: Cardia vs posterior female midgut 1

description: 2-dye hybridization assay

source_name: Cardia part 4 day old female unfed midgut 1b

source_name: 4 day old posterior female unfed midgut 1b


title: Vg Sample 51549 Block4

description: Raw signal data


title: Brain Day 3

description: Day 3 post PbA infection

source_name: Brain Day3

tag: Male Balb/c, 6-8 weeks, Infected IP with 1x10^6 P.berghei ANKA

source_name: Brain Day 3

tag: Male C57BL/6, 6-8 weeks, Infected IP with 1x10^6 P.berghei ANKA


title: Cardia vs whole female midgut 3

description: 2-dye hybridization assay

source_name: Cardia part 4 day old female unfed midgut 3

source_name: 4 day old female unfed midgut 3c

tag: 4 day old female unfed midgut 3c


title: Vg Sample 51530 Block3

description: Raw signal data

tag: Strain

tag: Age


title: Brain Day 0

description: Baseline Samples (Prior to PbA infection)

source_name: Brain Day0

tag: Male BALB/c, 6-8weeks

tag: Male C57BL/6, 6-8weeks


title: Mpool2 vs IRF4 HET - LPS treated 96 hrs - repeat 1 - mAdbID:63176

description: mAdb experiment ID: 63176

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 820;; 600 ScanPower: 100;; 100 LaserPower: 3.2;; 6 Temperature: 45.25

source_name: Mouse Lymphochip RNA Ref Pool 2

tag: Cell line

tag: Cell type

tag: Other

source_name: mouse IRF4 Het - 96 hours

tag: Tissue

tag: Developmental stage

tag: genotype/variation


title: Vg Sample 51530 Block1

description: Raw signal data


title: Cardia vs whole female midgut 1

description: 2-dye hybridization assay

source_name: Cardia part 4 day old female unfed midgut 1

source_name: 4 day old female unfed midgut 1c

tag: 4 day old female unfed midgut 1c


title: Vg Sample 51518 Block4

description: Raw signal data

source_name: Third instar wing imaginal discs from Drosophila melanogaster vg strain


title: Vg Sample 51518 Block2

description: Raw signal data


title: Anterior-posterior vs whole female midgut 2

description: standard 2 dye hybridization

source_name: Anterior-posterior part 4 day old female unfed midgut 2

source_name: 4 day old female unfed midgut 2b

tag: 4 day old female unfed midgut 2b


title: Cbx Sample 51511 Block4

description: Raw signal data

source_name: Third instar wing imaginal discs from Drosophila melanogaster Cbx strain


title: Cbx sample 50326

description: Raw signal data


title: Vg Sample 51530 Block2

description: Raw signal data


title: Anterior vs whole female midgut 3

description: standard 2 dye hybridization

source_name: Anterior 4 day old female unfed midgut 3

source_name: 4 day old female unfed midgut 3

tag: 4 day old female unfed midgut 3


title: Cbx Sample 51511 Block3

description: Raw signal data


title: Cbx sample 50358

description: Raw signal data


title: Haltere sample 51599 Block4

description: Raw signal data

source_name: Third instar haltere imaginal discs from Drosophila melanogaster yw strain


title: Vg Sample 51518 Block3

description: Raw signal data


title: Cbx sample 50279

description: Raw signal data


title: Cbx Sample 51511 Block1

description: Raw signal data


title: Vg Sample 51518 Block1

description: Raw signal data


title: Cbx Sample 51510 Block4

description: Raw signal data


title: Cbx sample 50283

description: Raw signal data


title: Anterior vs whole female midgut 2

description: standard 2 dye hybridization

hyb_protocol: AGILENT

scan_protocol: GENEPIX

data_processing: GENEPIX

source_name: Anterior 4 day old female unfed midgut

label_protocol: AGILENT

extract_protocol: QUAGEN

tag: Anterior 4 day old female unfed midgut

source_name: 4 day old female unfed midgut

extract_protocol: QIAGEN

tag: 4 day old female unfed midgut


title: Vg sample 3329

description: Raw signal data


title: Stage 2, PT#12, Normal (HG-U133B)

city: Jacksonville

first: John

middle: A

last: Copland

state: FL

address: 4500 San Pablo Road

department: Biochemistry & Molecular Biology

institute: Mayo Clinic College of Medicine

description: Normal HRE

hyb_protocol: Follow fragmentation, 10ug of cRNA were hybridized for 16 hrs at 45C on HG U133A and HG U133B 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 GCOS 1.2 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500

label: biotin

source_name: Human Renal Epithelium

label_protocol: Biotinylated cRNA were prepared accordiing to the standard Affymetrix protocol from 8.4 ug of total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

tag: Normal, PT#12, STG2


title: Vg sample 3306

description: Raw signal data


title: Cbx sample 50344

description: Raw signal data


title: Stage 2, PT#12, Tumor (HG-U133B)

description: Tumor HRE

tag: Tumor, PT#12, STG2


title: Anterior vs whole female midgut 1

description: 2-dye hybridization

scan_protocol: AXON GENEPIX

source_name: Anterior female midgut

tag: anterior midgut of 4 day old sugarfed female mosquito

source_name: whole female midgut


title: Cbx Sample 51510 Block2

description: Raw signal data

tag: Strain

tag: Age


title: Anterior-posterior vs whole female midgut 1

description: standard 2 dye hybridization

source_name: Anterior-posterior part 4 day old female unfed midgut 1

source_name: 4 day old female unfed midgut 1b

tag: 4 day old female unfed midgut 1b


title: Stage 2, PT#11, Tumor (HG-U133B)

description: Tumor HRE

tag: Tumor, PT#11, STG2


title: Cbx sample 50286

description: Raw signal data


title: Vg sample 3322

description: Raw signal data


title: Cbx Sample 51510 Block3

description: Raw signal data


title: Stage 2, PT#12, Tumor (HG-U133A)

description: Tumor HRE


title: Cbx Sample 51511 Block2

description: Raw signal data


title: Stage 2, PT#11, Normal (HG-U133B)

description: Normal HRE

tag: Normal, PT#11, STG2


title: Stage 2, PT#11, Normal (HG-U133A)

description: Normal HRE


title: Stage 2, PT#11, Tumor (HG-U133A)

description: Tumor HRE


title: Vg sample 3253

description: Raw signal data


title: Wing sample 3330

description: Raw signal data

source_name: Third instar wing imaginal discs from Drosophila melanogaster yw strain


title: Stage 2, PT#10, Tumor (HG-U133A)

description: Tumor HRE

tag: Tumor, PT#10, STG2


title: Stage 2, PT#10, Normal (HG-U133B)

description: Normal HRE

tag: Normal, PT#10, STG2


title: Stage 2, PT#9, Tumor (HG-U133A)

description: Tumor HRE

tag: Tumor, PT#9, STG2


title: Cbx Sample 51501 Block3

description: Raw signal data

value: third-instar larva

tag: Tissue


title: Vg sample 3300

description: Raw signal data


title: Cbx Sample 51510 Block1

description: Raw signal data


title: Stage 2, PT#9, Normal (HG-U133A)

description: Normal HRE

tag: Normal, PT#9, STG2


title: Cbx Sample 51501 Block4

description: Raw signal data


title: Stage 2, PT#10, Normal (HG-U133A)

description: Normal HRE


title: Stage 2, PT#10, Tumor (HG-U133B)

description: Tumor HRE


title: Stage 2, PT#9, Tumor (HG-U133B)

description: Tumor HRE


title: Stage 2, PT#8, Normal (HG-U133A)

description: Normal HRE

tag: Normal, PT#8, STG2


title: Vg sample 3337

description: Raw signal data


title: Cbx Sample 51501 Block2

description: Raw signal data


title: Stage 2, PT#9, Normal (HG-U133B)

description: Normal HRE


title: Wing sample 3313

description: Raw signal data


title: Stage 2, PT#8, Tumor (HG-U133A)

description: Tumor HRE

tag: Tumor, PT#8, STG2


title: Stage 2, PT#8, Tumor (HG-U133B)

description: Tumor HRE


title: Cbx Sample 51501 Block1

description: Raw signal data


title: Stage 2, PT#8, Normal (HG-U133B)

description: Normal HRE


title: Stage 1, PT#6,Tumor (HG-U133B)

description: Tumor HRE

tag: Tumor, PT#6, STG1


title: Wing Sample 51499 Block4

description: Raw signal data


title: Stage 1, PT#6,Tumor (HG-U133A)

description: Tumor HRE


title: Wing sample 3278

description: Raw signal data


title: Stage 1, PT#6, Normal (HG-U133A)

description: Normal HRE

tag: Normal, PT#6, STG1


title: Wing Sample 51499 Block3

description: Raw signal data


title: Wing sample 3325

description: Raw signal data


title: Wing Sample 51497 Block3

description: Raw signal data


title: Stage 1, PT#6, Normal (HG-U133B)

description: Normal HRE


title: Stage 1, PT#3, Tumor (HG-U133B)

description: Tumor HRE

tag: Tumor, PT#3, STG1


title: Wing Sample 51499 Block2

description: Raw signal data


title: Stage 2, PT#12, Normal (HG-U133A)

description: Normal HRE

tag: Normal, PT#12, STG2


title: Wing Sample 51499 Block1

description: Raw signal data


title: Wing sample 3231

description: Raw signal data


title: TNF alpha treated, starved vs control (Smpl 2)

city: Ljubljana

first: Drago

last: Kuzman

address: Verovskova 57

country: Slovenia

institute: Lek pharmaceuticals d.d.

description: No extra notes.

hyb_protocol: Tha labeled total RNA was hybridized on Agilent cDNA arrays (G4104A) according to manufactures instructions. Individual sampls fromTNF alpha treated and starved animal was hybridized versus the pooled control sample.

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately by TECAN LS200 scanner (Tecan Group Ltd.). The image data were analyzed using ArrayPro4.5 software (Media Cybernetics).

data_processing: Features where Cy3 and Cy5 signal was not 2.6 times higher than the local background were filtered out. Remaining data were loess normalized (span 20%).

source_name: TNF alpha treated, starved (Smpl 2)

tag: Total RNA from individual TNF alpha treated mouse.

source_name: Control sample

label_protocol: 10 µg of total RNA was labeled using Agilent Direct Labelling Kit with Cy5 (starved and TNF-α treated) and Cy3 (control) fluorescent dyes (Amersham).

extract_protocol: Total RNA was extracted using TRI-reagent (Sigma) according to the manufacturer’s instructions and subjected to RNeasy Cleanup (Qiagen). RNA concentration and quality was determined by RNA 6000 Nano Assay with Agilent 2100 Bioanalyzer (Agilent Technologies). RNA from three animals was pooled in equal proportions.

tag: RNA pool of three control mice.


title: Stage 1, PT#5, Tumor (HG-U133A)

description: Tumor HRE

tag: Tumor, PT#5, STG1


title: Stage 1, PT#5, Tumor (HG-U133B)

description: Tumor HRE


title: Stage 1, PT#4,Tumor (HG-U133B)

description: Tumor HRE

tag: Tumor, PT#4, STG1


title: Wing Sample 51497 Block4

description: Raw signal data

tag: Age


title: Stage 1, PT#4,Tumor (HG-U133A)

description: Tumor HRE


title: Stage 1, PT#4, Normal (HG-U133B)

description: Normal HRE

tag: Normal, PT#4, STG1


title: Stage 1, PT#4, Normal (HG-U133A)

description: Normal HRE


title: Wing sample 3262

description: Raw signal data

tag: Strain


title: Stage 1, PT#3, Normal (HG-U133B)

description: Normal HRE

tag: Normal, PT#3, STG1


title: Wing Sample 51497 Block2

description: Raw signal data


title: Stage 1, PT#2, Normal (HG-U133A)

description: Tumor HRE

data_processing: The data were analyzed with GCOS 1.2 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Normal, PT#2, STG1


title: Wing Sample 51489 Block2

description: Raw signal data

value: third instar larva

tag: Tissue


title: Wing Sample 51489 Block1

description: Raw signal data


title: Wing Sample 51489 Block3

description: Raw signal data


title: Stage 1, PT#3, Tumor (HG-U133A)

description: Tumor HRE


title: Wing Sample 51497 Block1

description: Raw signal data


title: TNF alpha treated, starved vs control  (Smpl 1)

description: No extra notes.

hyb_protocol: Tha labeled total RNA was hybridized on Agilent cDNA arrays (G4104A) according to manufactures instructions. Individual sampels from TNF alpha treated and starved animals was hybridized versus the pooled control sample.

source_name: TNF alpha treated, starved (Smpl 1)

label_protocol: 10 µg of total RNA was labeled using Agilent Direct Labelling Kit with Cy5 (starved and TNF-α treated) and Cy3 (control) fluorescent dyes (Amersham)

extract_protocol: Total RNA was extracted using TRI-reagent (Sigma) according to the manufacturer’s instructions and subjected to RNeasy Cleanup (Qiagen). RNA concentration and quality was determined by RNA 6000 Nano Assay with Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: Total RNA from individual TNF alpha treated and starved mouse.


title: Stage 1, PT#2, Normal (HG-U133B)

description: Tumor HRE


title: Wing Sample 51489 Block4

description: Raw signal data


title: Stage 1, PT#3, Normal (HG-U133A)

description: Normal HRE


title: Starvation vs control (Smpl2)

description: No extra notes.

hyb_protocol: Tha labeled total RNA was hybridized on Agilent cDNA arrays (G4104A) according to manufactures instructions. Individual sampls from starved animal was hybridized versus the pooled control sample.

source_name: Starvation (Smpl2)

tag: Total RNA from individual starved mouse.


title: Vg Sample 51530 Block4

description: Raw signal data

source_name: Third instar wing imaginal discs from Drosophila melanogaster vg strain


title: Stage 1, PT#2, Tumor (HG-U133B)

description: Tumor HRE

tag: Tumor, PT#2, STG1


title: Stage 1, PT#2, Tumor (HG-U133A)

description: Tumor HRE


title: Starvation vs control (Smpl1)

description: No extra notes.

source_name: Starvation (Smpl1)


title: mRNA isolated from rat hippocampus

status: Public on Nov 22 2006

city: San Francisco

first: Kimberly

middle: Frances

last: Raab-Graham

department: Physiology

institute: UCSF

description: The goal of this experiment was to compare mRNA isolated from synaptosomes (pre and post synaptic nerve endings) to total hippocampal mRNA in order to identify putative mRNAs that are enriched at the synapse.

hyb_protocol: Hybridization was carried out by Affymetrix.

scan_protocol: The microarray scan was carried out by Affymetrix.

source_name: rat hippocampus

label_protocol: cDNA was generated using the SMART cDNA synthesis kit (Clontech) with a modified oligo dT primer that included the T7 bacterial phage sequence. Biotin-labeled cRNA was generated by in vitro transcription using the T7 Ampliscribe kit in the presence of biotin-CTP and biotin-UTP.

extract_protocol: Total RNA was extracted using RNeasy columns (Qiagen).

value: Sprague Dawley

value: postnatal day 70

value: Brain (hippocampus)


title: mRNA isolated from hippocampal synaptosomes

source_name: synaptosomes from rat hippocampi

extract_protocol: Synaptosomes were biochemically isolated according to the protocol outlined in Raab-Graham and Vandenberg (1998) J. Biol. Chem. 273, 19699. Total RNA was extracted using RNeasy columns (Qiagen).


title: A3_3

city: Torino

first: Roberto

last: Piva

address: Via Santena 7

department: Department of Pathology and CeRMS

country: Italy

institute: University of Torino

description: Gene expression data from ALCL TS cell line treated with ALK inhibitor A3

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

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

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 200.

source_name: Human ALK positive Anaplastic Large Cell Lymphoma (ALCL) TS cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human ALK positive ALCL cells were grown in RPMI 1640 medium with 10% FCS.

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

treatment_protocol: Pellets from cell culture were washed with PBS and frozen at -80?C.

tag: TS cell line treated with ALK inhibitor A3 at 6 hr - replicate 3


title: A2_1

description: Gene expression data from ALCL TS cell line treated with ALK inhibitor A2

tag: TS cell line treated with ALK inhibitor A2 at 6 hr - replicate 1


title: A1_2

description: Gene expression data from ALCL TS cell line treated with ALK inhibitor A1

tag: TS cell line treated with ALK inhibitor A1 at 6 hr - replicate 2


title: DHL A5 72h_3 DOX-

description: Gene expression data from ALCL Su-DHL1 cell line treated with ALK shRNA

source_name: Human ALK positive Anaplastic Large Cell Lymphoma (ALCL) Su-DHL1 cell line

tag: TS cell line without shRNA induction at 72 hr - replicate 3


title: A3_1

tag: TS cell line treated with ALK inhibitor A3 at 6 hr - replicate 1


title: U_2

description: Gene expression data from untreated ALCL cell line TS

tag: TS cell line untreated 6 hr - replicate 2


title: A3_2

tag: TS cell line treated with ALK inhibitor A3 at 6 hr - replicate 2


title: A1_3

tag: TS cell line treated with ALK inhibitor A1 at 6 hr - replicate 3


title: U_1

tag: TS cell line untreated 6 hr - replicate 1


title: DHL A5 72h_2 DOX+

tag: Su-DHL1 cell line with shRNA induction at 72 hr - replicate 2


title: U_3

tag: TS cell line untreated 6 hr - replicate 3


title: A2_3

tag: TS cell line treated with ALK inhibitor A2 at 6 hr - replicate 3


title: DHL A5 72h_1 DOX-

tag: TS cell line without shRNA induction at 72 hr - replicate 1


title: A1_1

tag: TS cell line treated with ALK inhibitor A1 at 6 hr - replicate 1


title: DHL A5 72h_3 DOX+

tag: Su-DHL1 cell line with shRNA induction at 72 hr - replicate 3


title: DHL A5 72h_2 DOX-

tag: TS cell line without shRNA induction at 72 hr - replicate 2


title: TS A5 72h_3 DOX-

description: Gene expression data from ALCL TS cell line treated with ALK shRNA


title: TS A5 72h_2 DOX+

tag: TS cell line with shRNA induction at 72 hr - replicate 2


title: TS A5 72h_3 DOX+

tag: TS cell line with shRNA induction at 72 hr - replicate 3


title: TS A5 72h_2 DOX-


title: TS A5 72h_1 DOX-


title: TS A5M 84h_3 DOX+

description: Gene expression data from ALCL TS cell line treated with mutated ALK shRNA

tag: TS cell line with mutated shRNA induction at 84 hr - replicate 3


title: TS A5 72h_1 DOX+

tag: TS cell line with shRNA induction at 72 hr - replicate 1


title: TS A5M 84h_1 DOX+

tag: TS cell line with mutated shRNA induction at 84 hr - replicate 1


title: TS A5M 84h_2 DOX+

tag: TS cell line with mutated shRNA induction at 84 hr - replicate 2


title: TS A5 84h_2 DOX-

tag: TS cell line without shRNA induction at 84 hr - replicate 2


title: TS A5 84h_1 DOX-

tag: TS cell line without shRNA induction at 84 hr - replicate 1


title: TS A5 84h_2 DOX+

tag: TS cell line with shRNA induction at 84 hr - replicate 2


title: TS A5 84h_3 DOX-

tag: TS cell line without shRNA induction at 84 hr - replicate 3


title: TS A5 84h_1 DOX+

tag: TS cell line with shRNA induction at 84 hr - replicate 1


title: A2_2

tag: TS cell line treated with ALK inhibitor A2 at 6 hr - replicate 2


title: DHL A5 72h_1 DOX+

tag: Su-DHL1 cell line with shRNA induction at 72 hr - replicate 1


title: TS A5 84h_3 DOX+

tag: TS cell line with shRNA induction at 84 hr - replicate 3


title: A/J (2)

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description: replicate

data_processing: normalization: qspline

tag: sex

value: male

tag: tissue

value: tail


title: Poloxamer P-407 treated vs non treated mice (day 96) Smpl3

description: All treated biologicaly replicated samples were hybridized with the same non tretaed (reference) sample.

hyb_protocol: Agilent oligonucleotide microarray in situ Hybridization Plus kit

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately by TECAN LS200 scanner (Tecan Group Ltd., Maennedorf, Switzerland). The image data were analyzed using ArrayPro4.5 software (Media Cybernetics).

data_processing: adjustment local background subtraction and global background Normalization method : Linear&Lowess method. only features with a Signal-to-Noise Ratio (SNR) in at least one channel ≥ 2.6 were used for further analysis

source_name: Poloxamer P-407 treated treated mice (day 96)

label_protocol: 10 ug of total RNA was used for labelling. Synthesis of Cyanine 3- and Cyanine 5-labeled cDNA was performed by Fluorescent Direct label Kit Protocol (Agilent Technologies, CA, USA) according to the manufacturer's instructions.

extract_protocol: Liver samples were homogenized in TRI reagent (Sigma, Taufkirchen, Germany) and total RNA was isolated according to the manufacturer’s instructions. Total RNA was subjected to RNeasy Cleanup (Qiagen, Valencia, CA). RNA concentration and quality was determined by RNA 6000 Nano Assay with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: 7-week-old female mice (C57BL/6, Harlan, Italy) were fed the standard, low-fat chow diet (4,4% fat, diet 3430, Provimi Kliba AG, Kaiseraugst, Switzerland). They  were administered 0.5 g/kg poloxamer P-407 by intraperitoneal (i.p.) injection 96 days every third day.  Livers were collected, weighted, frozen in liquid nitrogen and stored in RNAlater

tag: A pool of 4 poloxamer treated mouse liver samples

source_name: Non treated mice (day 96)

treatment_protocol: 7-week-old female mice (C57BL/6, Harlan, Italy) were fed the standard, low-fat chow diet (4,4% fat, diet 3430, Provimi Kliba AG, Kaiseraugst, Switzerland). They  were injected 96 days every third day with normal saline. Livers were collected, weighted, frozen in liquid nitrogen and stored in RNAlater

tag: A pool of 4 non treated mouse liver samples


title: Poloxamer P-407 treated vs non treated mice (day 96) Smpl1

source_name: Poloxamer P-407 treated mice  (day 96)

tag: Pooled liver samples of 4 poloxamer P-407 treated mice C57BL/6.

source_name: Non treated mice  (day 96)

tag: Pooled liver samples of 4 non treated mice C57BL/6.


title: Poloxamer P-407 treated vs non treated mice (day 96) oligo Smpl3

data_processing: Adjustment local background subtraction and global background Normalization method : Linear&Lowess method. only features with a Signal-to-Noise Ratio (SNR) in at least one channel ≥ 2.6 were used for further analysis.

source_name: Poloxamer P-407 treated mice (day 96)

label_protocol: 0.5 ug of total RNA was used for labelling. Synthesis of Cyanine 3- and Cyanine 5-labeled cDNA was performed by Low RNA input fluorescence linear amplification kit (Agilent Technologies, CA, USA) according to the manufacturer's instructions.

treatment_protocol: 7-week-old female mice (C57BL/6, Harlan, Italy) were fed the standard, low-fat chow diet (4,4% fat, diet 3430, Provimi Kliba AG, Kaiseraugst, Switzerland). They were administered 0.5 g/kg poloxamer P-407 by intraperitoneal (i.p.) injection 96 days every third day. Livers were collected, weighted, frozen in liquid nitrogen and stored in RNAlater

treatment_protocol: 7-week-old female mice (C57BL/6, Harlan, Italy) were fed the standard, low-fat chow diet (4,4% fat, diet 3430, Provimi Kliba AG, Kaiseraugst, Switzerland). They were injected 96 days every third day with normal saline. Livers were collected, weighted, frozen in liquid nitrogen and stored in RNAlater


title: NOD/LtJ (S)

description: replicate

value: spleen

source_name: NOD/LtJ (S)


title: Poloxamer P-407 treated vs non treated mice (day 96) Smpl2


title: BALB/cByJ

description: replicate

source_name: BALB/cByJ


title: Poloxamer P-407 treated vs non treated mice (day 96) oligo Smpl1


title: 129S1/SvImJ (S)

description: replicate

source_name: 129S1/SvImJ (S)


title: CAST/EiJ (2)

description: replicate

source_name: CAST/EiJ (2)


title: A/J (3)

description: replicate


title: A/J

description: replicate

source_name: A/J


title: MOLF/EiJ (2)

description: replicate

source_name: MOLF/EiJ (2)


title: large airways, smoker 049, MAS5

status: Public on Nov 21 2006

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: large airways, smoker 049, MAS5

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: F

tag: Ethnic group

value: black

tag: Smoking Status

value: smoker, 23 pack-years


title: Poloxamer P-407 treated vs non treated mice (day 96) oligo Smpl2


title: MOLF/EiJ

description: replicate

source_name: MOLF/EiJ


title: SM/J

description: replicate

source_name: SM/J


title: large airways, smoker 003, MAS5

description: large airways, smoker 003, MAS5

value: smoker, 25 pack-years


title: 129X1/SvJ (2)

description: replicate


title: large airways, smoker 025, MAS5

description: large airways, smoker 025, MAS5

value: white

value: smoker, 30 pack-years


title: C57BL/6J

description: replicate


title: large airways, smoker 023, MAS5

description: large airways, smoker 023, MAS5

value: M

value: smoker, 20 pack-years


title: large airways, non-smoker 030, MAS5

description: large airways, non-smoker 030, MAS5

value: non-smoker


title: large airways, smoker 002, MAS5

description: large airways, smoker 002, MAS5

value: smoker, 21 pack-years


title: AKR/J

description: replicate

source_name: AKR/J


title: large airways, non-smoker 008, MAS5

description: large airways, non-smoker 008, MAS5


title: C58/J

description: replicate


title: CAST/EiJ

description: replicate

source_name: CAST/EiJ


title: SJL/J

description: replicate

source_name: SJL/J


title: LG/J

description: replicate

source_name: LG/J


title: large airways, non-smoker 004, MAS5

description: large airways, non-smoker 004, MAS5


title: small airways, early-COPD 001, MAS5

description: small airways, early-COPD 001, MAS5

value: early-COPD, 23 pack-years


title: M_U133Plus_121_nAcc

city: Ann Arbor

first: Fan

last: Meng

state: MI

address: 205 Zina Pitcher Place

department: Psychiatry

institute: U of Michigan

description: Gene expression data from postmorten brain regions

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133Plus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with the GCRMA method using custom CDF file Hs133A_Hs_UG_3.

source_name: Postmorten human brain: Nucleus Accumbens

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

value: Nucleus Accumbens

tag: Redo

value: Yes

tag: Cohort

value: Outlier


title: FVB/NJ

description: replicate

value: male

source_name: FVB/NJ


title: M_U133Plus_120_nAcc


title: M_U133Plus_125_nAcc


title: M_U133Plus_124_nAcc


title: M_U133Plus_119_nAcc


title: M_U133Plus_122_nAcc


title: M_U133Plus_123_nAcc


title: PL/J

description: replicate

value: tail

source_name: PL/J


title: M_U133A_118_nAcc

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

value: No


title: C3H/HeJ

description: replicate


title: M_U133A_117_nAcc


title: SWR/J

description: replicate

source_name: SWR/J


title: 129S1/SvImJ

description: replicate


title: AKR/J (2)

description: replicate

source_name: AKR/J (2)


title: M_U133Plus_117_nAcc


title: M_U133Plus_126_nAcc


title: NZB/B1NJ

description: replicate


title: M_U133Plus_114_nAcc


title: M_U133Plus_112_nAcc


title: C57L/J

description: replicate


title: 129S1/SvImJ (2)

description: replicate


title: M_U133A_112_nAcc


title: M_U133Plus_113_nAcc


title: M_U133Plus_111_nAcc


title: M_U133A_114_nAcc


title: M_U133A_111_nAcc


title: NOD/LtJ

description: replicate

source_name: NOD/LtJ


title: M_U133A_109_nAcc


title: M_U133Plus_105_nAcc


title: M_U133Plus_116_nAcc


title: M_U133Plus_115_nAcc


title: M_U133A_107_nAcc


title: M_U133Plus_110_nAcc


title: M_U133Plus_109_nAcc


title: M_U133Plus_107_nAcc


title: M_U133A_105_nAcc


title: M_U133Plus_108_nAcc


title: M_U133Plus_104_nAcc


title: M_U133Plus_106_nAcc


title: DBA/2J

description: replicate


title: large airways, non-smoker 005, MAS5

description: large airways, non-smoker 005, MAS5


title: M_U133A_106_nAcc


title: M_U133Plus_101_nAcc


title: M_U133Plus_97_nAcc


title: M_U133A_102_nAcc


title: SWR/J (2)

description: replicate

source_name: SWR/J (2)


title: M_U133Plus_118_nAcc


title: M_U133A_104_nAcc


title: M_U133A_98_nAcc


title: M_U133Plus_99_nAcc


title: M_U133A_99_nAcc


title: M_U133A_97_nAcc


title: M_U133A_89_nAcc


title: M_U133A_96_nAcc


title: M_U133A_88_nAcc


title: M_U133A_92_nAcc


title: M_U133Plus_89_nAcc


title: M_U133A_91_nAcc


title: M_U133A_93_nAcc


title: M_U133Plus_87_nAcc


title: M_U133A_83_nAcc


title: M_U133Plus_92_nAcc


title: M_U133A_87_nAcc


title: M_U133Plus_93_nAcc


title: M_U133Plus_84_nAcc


title: M_U133Plus_83_nAcc


title: M_U133Plus_88_nAcc


title: M_U133Plus_94_nAcc


title: M_U133A_84_nAcc


title: C57BL/6Tac

description: replicate


title: M_U133A_101_nAcc


title: M_U133A_74_nAcc


title: M_U133A_76_nAcc


title: M_U133A_63_nAcc


title: M_U133A_54_nAcc


title: M_U133Plus_61_nAcc


title: M_U133Plus_73_nAcc


title: M_U133A_61_nAcc


title: M_U133A_51_nAcc


title: M_U133A_75_nAcc


title: M_U133A_50_nAcc


title: M_U133A_52_nAcc


title: M_U133A_62_nAcc


title: M_U133Plus_78_nAcc


title: M_U133Plus_56_nAcc


title: M_U133A_60_nAcc


title: M_U133A_49_nAcc


title: M_U133Plus_70_nAcc


title: M_U133A_68_nAcc


title: M_U133A_48_nAcc


title: M_U133Plus_59_nAcc


title: M_U133A_80_nAcc


title: M_U133A_71_nAcc


title: M_U133A_77_nAcc


title: M_U133Plus_55_nAcc


title: M_U133A_37_nAcc


title: M_U133Plus_38_nAcc


title: M_U133Plus_36_nAcc


title: M_U133A_55_nAcc


title: M_U133A_42_nAcc


title: M_U133Plus_46_nAcc


title: M_U133A_41_nAcc


title: M_U133A_34_nAcc


title: M_U133A_28_nAcc


title: M_U133A_66_nAcc


title: M_U133Plus_77_nAcc


title: M_U133A_33_nAcc


title: M_U133A_31_nAcc


title: M_U133A_44_nAcc


title: M_U133A_27_nAcc


title: M_U133A_35_nAcc


title: M_U133A_26_nAcc


title: M_U133A_23_nAcc


title: M_U133A_29_nAcc


title: M_U133A_70_nAcc


title: M_U133A_46_nAcc


title: M_U133A_78_nAcc


title: M_U133A_56_nAcc


title: M_U133A_20_nAcc


title: M_U133A_30_nAcc


title: M_U133A_32_nAcc


title: M_U133A_19_nAcc


title: M_U133A_21_nAcc


title: M_U133A_18_nAcc


title: M_U133A_22_nAcc


title: M_U133A_15_nAcc


title: M_U133A_14_nAcc


title: M_U133A_12_nAcc


title: M_U133Plus_16_nAcc


title: M_U133A_11_nAcc


title: M_U133A_13_nAcc


title: M_U133A_17_nAcc


title: M_U133A_7_nAcc


title: M_U133A_6_nAcc


title: M_U133A_1_nAcc


title: D_U133Plus_122_nAcc

value: D


title: D_U133Plus_119_nAcc


title: M_U133A_2_nAcc


title: M_U133A_10_nAcc


title: D_U133Plus_118_nAcc


title: D_U133Plus_123_nAcc


title: M_U133A_9_nAcc


title: D_U133Plus_124_nAcc


title: D_U133Plus_114_nAcc


title: M_U133A_3_nAcc


title: D_U133Plus_120_nAcc


title: D_U133Plus_117_nAcc


title: D_U133Plus_115_nAcc


title: D_U133Plus_125_nAcc


title: M_U133A_5_nAcc


title: D_U133Plus_121_nAcc


title: D_U133Plus_116_nAcc


title: D_U133Plus_113_nAcc


title: D_U133Plus_112_nAcc


title: D_U133Plus_110_nAcc


title: D_U133Plus_126_nAcc


title: D_U133Plus_111_nAcc


title: D_U133Plus_108_nAcc


title: D_U133Plus_106_nAcc


title: D_U133Plus_105_nAcc


title: D_U133Plus_109_nAcc


title: D_U133Plus_107_nAcc


title: D_U133Plus_104_nAcc


title: D_U133Plus_101_nAcc


title: D_U133Plus_97_nAcc


title: D_U133Plus_89_nAcc


title: D_U133A_102_nAcc


title: D_U133Plus_94_nAcc


title: D_U133Plus_77_nAcc


title: D_U133Plus_84_nAcc


title: D_U133A_80_nAcc


title: D_U133A_96_nAcc


title: D_U133A_71_nAcc


title: D_U133Plus_93_nAcc


title: D_U133Plus_92_nAcc


title: D_U133Plus_78_nAcc


title: D_U133Plus_99_nAcc


title: D_U133Plus_83_nAcc


title: D_U133Plus_87_nAcc


title: D_U133Plus_88_nAcc


title: D_U133A_91_nAcc


title: D_U133Plus_70_nAcc


title: D_U133A_98_nAcc


title: D_U133A_74_nAcc


title: D_U133A_63_nAcc


title: D_U133Plus_73_nAcc


title: D_U133A_75_nAcc


title: D_U133Plus_61_nAcc


title: D_U133A_62_nAcc


title: D_U133A_66_nAcc


title: D_U133A_76_nAcc


title: D_U133A_54_nAcc


title: D_U133A_68_nAcc


title: D_U133Plus_59_nAcc


title: D_U133Plus_56_nAcc


title: D_U133A_50_nAcc


title: D_U133A_34_nAcc


title: D_U133Plus_36_nAcc


title: D_U133A_52_nAcc


title: D_U133A_41_nAcc


title: D_U133A_42_nAcc


title: D_U133A_35_nAcc


title: D_U133A_51_nAcc


title: D_U133Plus_38_nAcc


title: D_U133Plus_46_nAcc


title: D_U133Plus_55_nAcc


title: D_U133A_49_nAcc


title: D_U133A_60_nAcc


title: D_U133A_29_nAcc


title: D_U133A_30_nAcc


title: D_U133A_48_nAcc


title: D_U133A_28_nAcc


title: D_U133A_33_nAcc


title: D_U133A_22_nAcc


title: D_U133A_44_nAcc


title: D_U133A_26_nAcc


title: D_U133A_23_nAcc


title: D_U133A_32_nAcc


title: D_U133A_20_nAcc


title: D_U133A_37_nAcc


title: D_U133A_31_nAcc


title: D_U133A_19_nAcc


title: D_U133A_15_nAcc


title: D_U133A_21_nAcc


title: D_U133A_14_nAcc


title: D_U133Plus_16_nAcc


title: D_U133A_10_nAcc


title: D_U133A_18_nAcc


title: D_U133A_1_nAcc


title: M_U133Plus_122_HC

source_name: Postmorten human brain: Hippocampus

value: Hippocampus


title: D_U133A_5_nAcc


title: M_U133Plus_125_HC


title: M_U133Plus_126_HC


title: M_U133Plus_121_HC


title: D_U133A_11_nAcc


title: M_U133Plus_118_HC


title: D_U133A_2_nAcc


title: D_U133A_12_nAcc


title: D_U133A_17_nAcc


title: D_U133A_13_nAcc


title: M_U133Plus_115_HC


title: M_U133Plus_123_HC


title: D_U133A_3_nAcc


title: M_U133Plus_117_HC


title: D_U133A_9_nAcc


title: M_U133Plus_116_HC


title: M_U133Plus_113_HC


title: M_U133Plus_119_HC


title: M_U133Plus_114_HC


title: M_U133Plus_110_HC


title: M_U133Plus_111_HC


title: M_U133Plus_108_HC


title: M_U133Plus_112_HC


title: D_U133A_6_nAcc


title: M_U133Plus_107_HC


title: M_U133Plus_106_HC


title: M_U133Plus_104_HC


title: M_U133Plus_105_HC


title: M_U133A_102_HC


title: M_U133Plus_97_HC


title: M_U133A_96_HC


title: M_U133Plus_101_HC


title: M_U133A_98_HC


title: M_U133Plus_89_HC


title: M_U133Plus_87_HC


title: M_U133Plus_99_HC


title: M_U133Plus_94_HC


title: M_U133Plus_88_HC


title: M_U133Plus_93_HC


title: M_U133A_91_HC


title: M_U133Plus_83_HC


title: M_U133A_80_HC


title: M_U133Plus_92_HC


title: M_U133Plus_73_HC


title: M_U133Plus_84_HC


title: M_U133A_71_HC


title: M_U133Plus_77_HC


title: M_U133A_75_HC


title: M_U133A_76_HC


title: M_U133Plus_78_HC


title: M_U133Plus_70_HC


title: M_U133A_66_HC


title: M_U133A_63_HC


title: M_U133A_68_HC


title: M_U133A_74_HC


title: M_U133Plus_59_HC


title: M_U133A_60_HC


title: M_U133Plus_56_HC


title: M_U133Plus_61_HC


title: M_U133Plus_55_HC


title: M_U133A_51_HC


title: M_U133A_37_HC


title: M_U133A_52_HC


title: M_U133A_48_HC


title: M_U133A_35_HC


title: M_U133A_41_HC


title: M_U133A_49_HC


title: M_U133A_62_HC


title: M_U133A_54_HC


title: M_U133A_50_HC


title: M_U133A_44_HC


title: M_U133Plus_36_HC


title: M_U133A_42_HC


title: M_U133A_31_HC


title: M_U133A_32_HC


title: M_U133A_33_HC


title: M_U133Plus_38_HC


title: M_U133Plus_46_HC


title: M_U133A_47_HC


title: M_U133A_27_HC


title: M_U133A_26_HC


title: M_U133A_29_HC


title: M_U133A_22_HC


title: M_U133A_30_HC


title: M_U133A_34_HC


title: M_U133A_28_HC


title: M_U133A_23_HC


title: M_U133A_21_HC


title: M_U133A_20_HC


title: M_U133A_19_HC


title: M_U133A_18_HC


title: M_U133A_11_HC


title: M_U133A_14_HC


title: M_U133A_17_HC


title: M_U133A_6_HC


title: M_U133A_13_HC


title: M_U133A_12_HC


title: M_U133A_9_HC


title: M_U133A_5_HC


title: D_U133Plus_121_HC


title: M_U133A_15_HC


title: M_U133A_1_HC


title: M_U133A_3_HC


title: D_U133Plus_123_HC


title: M_U133Plus_16_HC


title: M_U133A_2_HC


title: D_U133Plus_125_HC


title: D_U133Plus_126_HC


title: D_U133Plus_118_HC


title: D_U133Plus_122_HC


title: D_U133Plus_114_HC


title: D_U133Plus_113_HC


title: D_U133Plus_119_HC


title: D_U133Plus_116_HC


title: M_U133A_10_HC


title: D_U133Plus_111_HC


title: D_U133Plus_117_HC


title: D_U133Plus_112_HC


title: D_U133Plus_115_HC


title: D_U133Plus_107_HC


title: D_U133Plus_110_HC


title: D_U133Plus_105_HC


title: D_U133Plus_104_HC


title: D_U133Plus_106_HC


title: D_U133A_98_HC


title: D_U133A_102_HC


title: D_U133Plus_99_HC


title: D_U133A_96_HC


title: D_U133Plus_97_HC


title: D_U133Plus_101_HC


title: D_U133A_91_HC


title: D_U133Plus_94_HC


title: D_U133Plus_88_HC


title: D_U133Plus_89_HC


title: D_U133A_80_HC


title: D_U133Plus_92_HC


title: D_U133Plus_84_HC


title: D_U133Plus_77_HC


title: D_U133Plus_83_HC


title: D_U133Plus_93_HC


title: D_U133Plus_87_HC


title: D_U133A_71_HC


title: D_U133Plus_78_HC


title: D_U133Plus_73_HC


title: D_U133Plus_70_HC


title: D_U133A_74_HC


title: D_U133A_75_HC


title: D_U133A_76_HC


title: D_U133A_63_HC


title: D_U133A_66_HC


title: D_U133A_47_HC


title: D_U133Plus_61_HC


title: D_U133A_51_HC


title: D_U133Plus_55_HC


title: D_U133A_54_HC


title: D_U133A_62_HC


title: D_U133A_41_HC


title: D_U133A_68_HC


title: D_U133A_37_HC


title: D_U133Plus_36_HC


title: D_U133A_48_HC


title: D_U133Plus_46_HC


title: D_U133Plus_38_HC


title: D_U133Plus_59_HC


title: D_U133A_44_HC


title: D_U133A_35_HC


title: D_U133A_34_HC


title: D_U133A_32_HC


title: D_U133A_50_HC


title: D_U133Plus_56_HC


title: D_U133A_60_HC


title: D_U133A_42_HC


title: D_U133A_52_HC


title: D_U133A_33_HC


title: D_U133A_30_HC


title: D_U133A_31_HC


title: D_U133A_49_HC


title: D_U133A_29_HC


title: D_U133Plus_108_HC


title: D_U133A_27_HC


title: D_U133A_26_HC


title: D_U133A_23_HC


title: D_U133A_28_HC


title: D_U133Plus_16_HC


title: D_U133A_19_HC


title: D_U133A_20_HC


title: D_U133A_17_HC


title: D_U133A_10_HC


title: D_U133A_2_HC


title: D_U133A_15_HC


title: D_U133A_14_HC


title: D_U133A_12_HC


title: D_U133A_22_HC


title: D_U133A_3_HC


title: D_U133A_11_HC


title: D_U133A_21_HC


title: D_U133A_6_HC


title: D_U133A_1_HC


title: M_U133Plus_124_DLPFC

source_name: Postmorten human brain: Dorsal Lateral Prefrontal Cortex

value: Dorsal Lateral Prefrontal Cortex


title: D_U133A_18_HC


title: D_U133A_13_HC


title: M_U133Plus_126_DLPFC


title: D_U133A_9_HC


title: M_U133Plus_125_DLPFC


title: D_U133A_5_HC


title: M_U133Plus_123_DLPFC


title: M_U133Plus_121_DLPFC


title: M_U133Plus_122_DLPFC


title: M_U133Plus_120_DLPFC


title: M_U133A_118_DLPFC


title: M_U133Plus_116_DLPFC


title: M_U133A_114_DLPFC


title: M_U133Plus_115_DLPFC


title: M_U133A_111_DLPFC


title: M_U133A_102_DLPFC


title: M_U133A_112_DLPFC


title: M_U133A_103_DLPFC


title: M_U133A_104_DLPFC


title: M_U133A_105_DLPFC


title: M_U133Plus_113_DLPFC


title: M_U133A_95_DLPFC


title: M_U133A_107_DLPFC_R


title: M_U133A_97_DLPFC


title: M_U133Plus_108_DLPFC


title: M_U133A_96_DLPFC


title: M_U133A_117_DLPFC


title: M_U133A_98_DLPFC


title: M_U133A_109_DLPFC


title: M_U133A_101_DLPFC_R


title: M_U133A_106_DLPFC


title: M_U133A_92_DLPFC


title: M_U133A_99_DLPFC


title: M_U133A_100_DLPFC


title: M_U133A_93_DLPFC


title: M_U133Plus_94_DLPFC


title: M_U133A_101_DLPFC


title: M_U133A_107_DLPFC


title: M_U133A_91_DLPFC


title: M_U133A_89_DLPFC


title: M_U133A_88_DLPFC


title: M_U133A_86_DLPFC


title: M_U133Plus_119_DLPFC


title: M_U133A_84_DLPFC


title: M_U133A_87_DLPFC


title: M_U133A_82_DLPFC


title: M_U133A_83_DLPFC


title: M_U133A_75_DLPFC


title: M_U133A_80_DLPFC


title: M_U133Plus_73_DLPFC


title: M_U133A_61_DLPFC


title: M_U133A_60_DLPFC


title: M_U133A_70_DLPFC


title: M_U133A_81_DLPFC


title: M_U133A_62_DLPFC


title: M_U133A_74_DLPFC


title: M_U133A_71_DLPFC


title: M_U133A_79_DLPFC


title: M_U133A_78_DLPFC


title: M_U133A_67_DLPFC


title: M_U133Plus_59_DLPFC


title: M_U133A_50_DLPFC


title: M_U133A_54_DLPFC


title: M_U133A_66_DLPFC


title: M_U133A_68_DLPFC


title: M_U133A_77_DLPFC


title: M_U133A_76_DLPFC


title: M_U133A_56_DLPFC


title: M_U133A_52_DLPFC


title: M_U133A_63_DLPFC


title: M_U133A_49_DLPFC


title: M_U133A_55_DLPFC


title: M_U133A_48_DLPFC


title: M_U133A_48_DLPFC_R