title: GRO2-C-F15

description: In vivo labeled total RNA of SJY6 yeast strain. Control time before adding doxycycline. Hybridization on filter 15. Replicate 2.

source_name: SJY6 yeast strain, exponential growth in YPD.


title: V5R2-L1-5 NA YPD

status: Public on Aug 24 2009

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Mock IP, negative control. Replicate 1. Filter V5R2-L1-5.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2X SSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

data_processing: Raw image quantization background subtracted.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BQS252. Exponential growth in YPD.

label_protocol: Ligation Mediated PCR (Ren B. et al. 2000) was used for DNA amplification. Briefly,the DNA was blunted by T4 phage DNA polymerase. The reaction was allowed to proceed for 20 minutes at 12°C. After phenol/chloroform/isoamylic alcohol extraction, DNA was ethanol-precipitated and ligated in a final volume of 50 μl with annealed linkers oJW102 and oJW103 (1.5 μM of each primer). The reaction was carried out overnight at 16°C and ligated DNA was precipitated and resuspended in 25 μl milliQ water. The ligated DNA was amplified by PCR. The PCR  program was 2 minutes at 95°C and 33 cycles of 30 s at 95°C, 30 s at 55°C and 2 minutes at 72°C. The DNA was precipitated overnight and resuspended in 50 μl of milliQ water. The LMPCR product was used as a template for the radioactive labeling reaction. The reaction mixture contained 5-15 μL of amplified DNA in 50 μl (1× DNApol buffer, 2 mM MgCl2, 0.2 mM dATP, dTTP and dGTP, 25 μM dCTP, 1 μM oJW102, 0.8 μCi α-33P-dCTP and 5 U DNApol). The mix was denatured for 5 minutes at 95°C, annealed 5 minutes at 50°C and was amplified during 30 minutes at 72°C. The reaction product was purified through a ProbeQuant G-50 column to remove unincorporated 33P-dCTP and oligonucleotides.

growth_protocol: Exponential growth in YPD.

tag: biomaterial


title: genomic F16

description: Filter 16 hybridization with labeled yeast genomic DNA.

source_name: Yeast (Sc288c background)

label_protocol: Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [α-33P] dCTP (2500 Ci/mmol).The mixture was incubated at 37ºC for 1-2 h. In order to eliminate non-incorporated components, Probe Quant G-50 columns (Amersham Biosciences) were used.

growth_protocol: Yeast strain (Sc288c background)exponentially growing in YPD

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267-272

value: In vitro genomic DNA labelling with 33P in a yeast strain exponentially growing in YPD


title: V5R2-L1-20 IP Spt16

description: IP of Spt16-Myc. Replicate 1. Filter V5R2-L1-20.

source_name: Saccharomyces cerevisiae SJY25 (Spt16-Myc). Exponential growth in YPD

growth_protocol: Exponential growth in YPD

extract_protocol: 50 mL of cells were cross-linked by adding formaldehyde to a final concentration of 1% for 15 minutes at room temperature, and the cross-link was quenched by adding glycine to a final concentration of 125 mM. Cell were washed 4 times with 30 mL ice-cold TBS buffer (20mM Tris-HCl, 140 mM NaCl, pH 7.5) and frozen. Cells were thawed on ice and resuspended in 300 μl lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF (Phenylmethylsulfonyl fluoride), 1 mM benzamidine and 1 pill of protease inhibitor cocktail (Roche Diagnostics, Mannheim, Germany) dissolved in every 50 ml of buffer). The equivalent of 0.3 ml of frozen glass beads (425-600 mm; Sigma-Aldrich, St Louis, MO, USA) was added to the cellular suspension and cells were lysed at 4°C for 12 minutes of vortexing at maximum power. Lysis buffer (300 μl) was added and the extract was transferred to a new tube. Sonication of DNA was performed to obtain DNA fragments between 200 and 500 bp, with an average size of 350 bp. Chromatin was sonicated on ice-cold water, with 5 pulses of 30 s at High output (200W) in a Bioruptor (Diagenode SA, Liège, Belgium). Cell debris was removed by centrifugation at 12,000 rpm at 4°C for 5 minutes. An aliquot of 10 μl of this whole cell extract (WCE) was kept as positive control.


title: V5R2-L1-22 WCE 14.5hGal 2

description: Whole Cell Extract. Exponential growth. 14.5h after the change to YPGal medium. Replicate 3. Filter V5R2-l1-22.

source_name: Saccharomyces cerevisiae BQS252. Exponential growth 14.5 h after the change to YPGal medium.


title: GRO2-5h-F16

type: RNA

description: In vivo labeled total RNA of SJY6 yeast strain. 5h after adding doxycycline. Hybridization on filter 16. Replicate 2.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

molecule: total RNA

source_name: SJY6 yeast strain,5 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.

label_protocol: In vivo labeling by run-on (GRO) using 33P-UTP.Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 Ci/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York


title: GRO1-5h-F15

description: In vivo labeled total RNA of SJY6 yeast strain. 5h after adding doxycycline. Hybridization on filter 15. Replicate 1.

growth_protocol: SJY6 yeast strain,5 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: GRO3-C-F16

description: In vivo labeled total RNA of SJY6 yeast strain. Control time before adding doxycycline. Hybridization on filter 16. Replicate 3.

growth_protocol: SJY6 yeast strain, exponential growth in YPD.


title: genomic F14

description: Filter 14 hybridization with labeled yeast genomic DNA.


title: genomic F15

description: Filter 15 hybridization with labeled yeast genomic DNA.


title: GRO1-C-F14

description: In vivo labeled total RNA of SJY6 yeast strain. Control time before adding doxycycline. Hybridization on filter 14. Replicate 1.

value: SJY6 yeast strain, exponential growth in YPD.


title: V5R2-L1-21 WCE 14.5hGal

description: Whole Cell Extract. Exponential growth. 14.5h after the change to YPGal medium. Replicate 1. Filter V5R2-l1-21.

value: Saccharomyces cerevisiae BQS252. Exponential growth 14.5 h after the change to YPGal medium.


title: V5R2-L1-21 IP 14.5hGal

description: IP of RNApol II CTD using 8WG16 Ab (Covance). Exponential growth. 14.5h after the change to YPGal medium. Replicate 1. Filter V5R2-l1-21.

growth_protocol: Exponential growth 14.5 h after the change to YPGal medium.


title: V5R2-L1-22 IP 14.5hGal 2

description: IP of RNApol II CTD using 8WG16 Ab (Covance). Exponential growth. 14.5h after the change to YPGal medium. Replicate 3. Filter V5R2-l1-22.


title: cDNA3-5h-F14

description: Total RNA from SJY6 yeast strain. 5h after adding doxycycline. Hybridization on filter 14. Replicate 3.

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 ÂµL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL  dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

value: SJY6 yeast strain,5 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: V5R2-L1-21 WCE 2hGal

description: Whole Cell Extract. 2h after the change to YPGal medium. Replicate 2. Filter V5R2-l1-21.

source_name: Saccharomyces cerevisiae BQS252. 2h after the change to YPGal medium.

growth_protocol: 2h after the change to YPGal medium.


title: cDNA3-7h-F15

description: Total RNA from SJY6 yeast strain. 7h after adding doxycycline. Hybridization on filter 15. Replicate 3.

source_name: SJY6 yeast strain,7 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: V5R2-L1-22 WCE 2hGal

description: Whole Cell Extract. 2h after the change to YPGal medium. Replicate 3. Filter V5R2-l1-22.

value: Saccharomyces cerevisiae BQS252. 2h after the change to YPGal medium.


title: V5R2-L1-22 IP 14.5hGal 1

description: IP of RNApol II CTD using 8WG16 Ab (Covance). Exponential growth. 14.5h after the change to YPGal medium. Replicate 2. Filter V5R2-l1-22.


title: cDNA1-7h-F16

description: Total RNA from SJY6 yeast strain. 7h after adding doxycycline. Hybridization on filter 16. Replicate 1.

growth_protocol: SJY6 yeast strain,7 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: V5R2-L1-5 WCE YPD

description: Whole Cell Extract. Replicate 1. Filter V5R2-l1-5.

value: Saccharomyces cerevisiae BQS252. Exponential growth in YPD.


title: cDNA2-7h-F14

description: Total RNA from SJY6 yeast strain. 7h after adding doxycycline. Hybridization on filter 14. Replicate 2.

value: SJY6 yeast strain,7 h after adding doxycycline to exponential growing cells in YPD in order to deplete Spt16p.


title: cDNA1-5h-F15

description: Total RNA from SJY6 yeast strain. 5h after adding doxycycline. Hybridization on filter 15. Replicate 1.


title: cDNA2-5h-F16

description: Total RNA from SJY6 yeast strain. 5h after adding doxycycline. Hybridization on filter 16. Replicate 2.


title: V5R2-L1-20 WCE 2hGal

description: Whole Cell Extract. 2h after the change to YPGal medium.  Replicate 1. Filter V5R2-l1-20.


title: cDNA3-C-F16

description: Total RNA from SJY6 yeast strain. Control time before adding doxycycline. Hybridization on filter 16. Replicate 3.


title: V5R2-L1-21 IP 2hGal

description: IP of RNApol II CTD using 8WG16 Ab (Covance). 2h after the change to YPGal medium. Replicate 2. Filter V5R2-l1-21.


title: V5R2-L1-22 IP 2hGal

description: IP of RNApol II CTD using 8WG16 Ab (Covance). 2h after the change to YPGal medium. Replicate 3. Filter V5R2-l1-22.


title: V5R2-L1-20 IP 2hGal

description: IP of RNApol II CTD using 8WG16 Ab (Covance). 2h after the change to YPGal medium. Replicate 1. Filter V5R2-l1-20.

growth_protocol: 2h after the change to YPGal medium


title: V5R2-L1-22 WCE 14.5hGal 1

description: Whole Cell Extract. Exponential growth. 14.5h after the change to YPGal medium. Replicate 2. Filter V5R2-l1-22.


title: cDNA1-C-F14

description: Total RNA from SJY6 yeast strain. Control time before adding doxycycline. Hybridization on filter 14. Replicate 1.


title: V5R2-L1-6 WCE YPD

description: Whole Cell Extract. Replicate 2. Filter V5R2-l1-6.


title: cDNA2-C-F15

description: Total RNA from SJY6 yeast strain. Control time before adding doxycycline. Hybridization on filter 15. Replicate 2.


title: V8-L1-8 gDNA

description: Filter V8-L1-8 hybridization with labeled yeast genomic DNA.

hyb_protocol: Hybridization Solution was: 1mM EDTA and 7% SDS . The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65C. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 16h. Washing conditions were: 20 min at 65C in 1X SSC, 0.5% SDS, and twice at 65C for 10 min in 0.5X SSC, 0.1% SDS.

source_name: In vitro genomic DNA labelling with 33P-dCTP in a yeast strain exponentially growing in YPD

growth_protocol: Exponentian growth in YPD

value: In vitro genomic DNA labeled with 33P in a yeast strain exponentially growing in YPD


title: V5R2-L1-7 WCE YPD

description: Whole Cell Extract. Replicate 3. Filter V5R2-l1-7.


title: V8-L1-7 gDNA

description: Filter V8-L1-7 hybridization with labeled yeast genomic DNA.


title: V5R2-l1-7 IP 8GW16

description: IP of RNApol II CTD using 8WG16 Ab (Covance). Replicate 3. Filter V5R2-l1-7.


title: V8-L1-9 WCE tpk1

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a tpk1 mutant strain. Replicate 2. Filter V8-L1-9.

source_name: Saccharomyces cerevisiae Y01261 (Euroscarf) tpk1 mutant. Exponential growth in YPD

extract_protocol: 50 mL of cells were cross-linked by adding formaldehyde to a final concentration of 1% for 15 minutes at room temperature, and the cross-link was quenched by adding glycine to a final concentration of 125 mM. Cell were washed 4 times with 30 mL ice-cold TBS buffer (20mM Tris-HCl, 140 mM NaCl, pH 7.5) and frozen. Cells were thawed on ice and resuspended in 300 μl lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF (Phenylmethylsulfonyl fluoride), 1 mM benzamidine and 1 pill of protease inhibitor cocktail (Roche Diagnostics, Mannheim, Germany) dissolved in every 50 ml of buffer). The equivalent of 0.3 ml of frozen glass beads (425-600 mm; Sigma-Aldrich, St Louis, MO, USA) was added to the cellular suspension and cells were lysed at 4°C for 12 minutes of vortexing at maximum power. Lysis buffer (300 μl) was added and the extract was transferred to a new tube. Sonication of DNA was performed to obtain DNA fragments between 200 and 500 bp, with an average size of 350 bp. Chromatin was sonicated on ice-cold water, with 5 pulses of 30 s at High output (200W) in a Bioruptor (Diagenode SA, Liège, Belgium). Cell debris was removed by centrifugation at 12,000 rpm at 4°C for 5 minutes. An aliquot of 10 μl of this whole cell extract (WCE) was kept as positive control. Or IP of RNApol II CTD using 8WG16 Ab (Covance).

tag: fraction

value: WCE of RNApol II CTD


title: V8-L1-8 WCE tpk1

description: WCE of RNApol II CTD using 8WG16 Ab (Covance) in a tpk1 mutant strain. Replicate 1. Filter V8-L1-8.

value: Saccharomyces cerevisiae Y01261 (Euroscarf) tpk1 mutant. Exponential growth in YPD


title: V5R2-l1-6 IP 8WG16

description: IP of RNApol II CTD using 8WG16 Ab (Covance). Replicate 2. Filter V5R2-l1-6.


title: V8-L1-8 GRO tpk1

description: In vivo labeled total RNA of tpk1 mutant strain. Replicate 2. Filter V8-L1-8.

value: In vivo labeled total RNA of Saccharomyces cerevisiae Y01261 (Euroscarf) tpk1 mutant. Exponential growth in YPD


title: V5R2-l1-5 IP 8GW16

description: IP of RNApol II CTD using 8WG16 Ab (Covance). Replicate 1. Filter V5R2-l1-5.


title: V8-L1-9 IP tpk1

value: IP of RNApol II CTD

tag: antibody

value: 8WG16 Ab


title: V5R2-L1-5 IP RPB1

description: IP of Rpb1-Myc S. cerevisiae (ARG1 Strain). Replicate 1. Filter V5R2-L1-5.

value: Saccharomyces cerevisiae ARG1 (Rpb1-Myc). Exponential growth in YPD


title: V8-L1-8 IP tpk1

description: IP of RNApol II CTD using 8WG16 Ab (Covance) in a tpk1 mutant strain. Replicate 1. Filter V8-L1-8.


title: Patient 4260341, renal graft bx Z18, diagnosis non-rejecting

status: Public on Aug 22 2009

city: Kontiolahti

first: Andreas

last: Scherer

address: Pajutie 3A

country: Finland

institute: Spheromics

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of no rejection

hyb_protocol: Hybridization of arrays was carried out at 45°C for about18 h, then arrays were stained on a GeneChip Fluidics Workstation 450 according to the manufacturer’s technical manual (Affymetrix).

scan_protocol: GeneChips were scanned on a GeneArray Scanner 3000 according to the manufacturer’s technical manual (Affymetrix).

data_processing: The data were analyzed using global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

organism: Homo sapiens

source_name: Biopsy from non-rejecting human transplanted kidney

label_protocol: Labeled probes were prepared either according to the Affymetrix 2-cycle cDNA amplification protocol (Affymetrix, Santa Clara, CA) from 50 ng total RNA of all biopsy samples, or from 5 microg of total RNA of all control kidney samples according to the standard Affymetrix protocol. The cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray high-yield T7 DNA transcription kit; ENZO Life Sciences, Inc.). The biotinylated cRNA was purified on an affinity resin (RNeasy; Qiagen), quantified, and fragmented into strands of 50–200 nucleotides in length.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen, Hilden, Germany).

tag: patient identifier

tag: sex

value: male

tag: age of patient

tag: serum creatinine

value: 108 microMol/L

tag: renal graft bx

value: non-rejecting


title: V8-L1-7 GRO tpk1

description: In vivo labeled total RNA of tpk1 mutant strain. Replicate 1. Filter V8-L1-7.


title: V5R2-L1-7 IP RPB1

description: IP of Rpb1-Myc S. cerevisiae (ARG1 Strain). Replicate 3. Filter V5R2-L1-7.

source_name: Saccharomyces cerevisiae ARG1 (Rpb1-Myc)


title: V5R2-L1-6 IP RPB1

description: IP of Rpb1-Myc S. cerevisiae (ARG1 Strain). Replicate 2. Filter V5R2-L1-6.


title: Patient 6836879, renal graft bx Z21, diagnosis non-rejecting

value: female

value: 94 microMol/L


title: Patient 525928, renal graft bx Z07, diagnosis AR IB, IIA

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of acute rejection IB, IIA

source_name: Acute rejection biopsy grade Ib, IIA from human transplanted kidney

value: 163 microMol/L

value: AR IB, IIA


title: Patient 525928, renal graft bx Z06, diagnosis non-rejecting

value: 167 microMol/L


title: Patient 718181, renal graft bx Z10, diagnosis non-rejecting

value: 95 microMol/L


title: Patient 718181, renal graft bx Z11, diagnosis non-rejecting

value: 106 microMol/L


title: Patient 2727137, renal graft bx Z16, diagnosis non-rejecting

value: 117 microMol/L


title: Patient 7974116, renal graft bx Z15, diagnosis non-rejecting

value: 114 microMol/L


title: Patient 7409460, renal graft bx Z20, diagnosis non-rejecting

value: n.d. microMol/L


title: Patient 7974116, renal graft bx Z14, diagnosis non-rejecting

value: 115 microMol/L


title: Patient 4260341, renal graft bx Z17, diagnosis non-rejecting

value: 152 microMol/L


title: Patient 4138406, renal graft bx Z19, diagnosis AR IIA

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of acute rejection IIA

source_name: Acute rejection biopsy grade IIB from human transplanted kidney

value: 144 microMol/L

value: AR IIA


title: Patient 7358285, renal graft bx Z13, diagnosis non-rejecting

value: male

value: 159 microMol/L


title: Patient 7409460, renal graft bx Z02, diagnosis non-rejecting

value: n.d. Renal graft bx:Z02

value: non-rejecting


title: Patient 7668988, renal graft bx Z05, diagnosis borderline changes

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of borderline changes

source_name: Biopsy with borderline rejection / suspicious changes from human kidney allograft

value: 94 microMol/L

value: borderline changes


title: Eyediscs_selectedlines_rep4

city: College Park

first: Gerald

middle: S

last: Wilkinson

state: MD

address: Bldg 144, 4094 Campus Dr

department: Biology

country: USA

institute: University of Maryland

description: To identify genes that influence the length of eyestalks we compared gene expression between lines of flies that have been under artificial sexual selection to increase or decrease male eye span for 65 generations.  We compared gene expression between male flies from the high (H2) and low (L2) lines that had deviated furthest from the average control lines.  At the time of these experiments the eyespan of H2 male flies was 9.36 ± 0.07 mm and the eyespan of L2 male flies was 7.39 ± 0.07 mm, which represents a difference of 5.7 s.d. between these two lines.

hyb_protocol: Hybridization followed Agilent protocols and used an Agilent rotator rack and oven.

scan_protocol: Arrays were scanned with a GenePix 4200A with pixel size set to 5 microns.  Temperatute was 23.63.

data_processing: A custom-fitted grid was aligned to the array, and then median signal intensity was calculated for circular features.  Data were removed if median intensity/background < 2 or pixel saturation exceeded 70%.  Dye bias was corrected using the ratio of medians from all features.  Background subtraction was set to Local Feature.  Lowess normalization was then applied.

organism: Teleopsis dalmanni

label_protocol: We used the Ovation amino allyl RNA amplification kit (NuGen) to amplify messenger RNA prior to labeling.  This procedure uses reverse transcription to make single-stranded cDNA and then DNA polymerization to make double-stranded (ds) cDNA.  The ds cDNA was then amplified using a linear amplification procedure. Samples were labeled using an amino allyl cDNA labeling kit (Ambion)

growth_protocol: Larvae were reared at low density in pureed corn media at constant temperature (25 degrees C).

extract_protocol: Imaginal disc and brain tissue were dissected from wandering male larvae just after gut purge. Male larvae were identified by genital disc morphology and their eye discs, optic lobes and brains were removed and submerged in RNAlater solution (Ambion) and stored at -20o. Total RNA was subsequently extracted from disc and brain tissue using an RNA isolation kit (Promega).  Each biological sample consisted of twenty-five sets of eye discs which were homogenized by grinding with plastic pestles in 175 µl lysis buffer. After treating with DNase I enzyme, RNA was concentrated by lyophilization and the quality of each sample was checked with an Agilent 2100 bioanalyzer.

treatment_protocol: Flies had been under selection for 65 generations to decrease eyespan/body length.

tag: selected line

value: low eyespan/bodylength, gen 65

tag: tissue

value: eye antennal imaginal discs

tag: developmental stage

value: late instar wandering larvae

treatment_protocol: Flies had been under selection for 65 generations to increase eyespan/body length.

value: high eyespan/bodylength, gen 65


title: Eyediscs_selectedlines_rep8


title: MCF-7-anti-MTA3

status: Public on Aug 21 2009

city: Beijing

first: Yongfeng

last: Shang

address: 38 Xue Yuan Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University

description: whole genome target analysis for MTA3

hyb_protocol: standard AVIVA Methods

scan_protocol: CapitalBio manual

data_processing: After background correction and removal of bad spots, expression ratio was linear normalized using 50 percentile rank

source_name: enriched DNA using anti-MTA3

label_protocol: primer labeled with fluorescence molecules

extract_protocol: common cell lysate

tag: Breast cancer cell line

source_name: Input DNA


title: Patient 4285557, renal graft bx Z01, diagnosis non-rejecting

value: female

value: 107 microMol/L


title: MCF-7-anti-MTA2

description: whole genome target analysis for MTA2

source_name: enriched DNA using anti-MTA2


title: Eyediscs_selectedlines_rep3


title: Eyediscs_selectedlines_rep7


title: Eyediscs_selectedlines_rep1


title: Eyediscs_selectedlines_rep5


title: MCF-7-anti-MTA1

description: whole genome target analysis for MTA1

source_name: enriched DNA using anti-MTA1


title: MCF-7-anti-LSD1

description: whole genome target analysis for LSD1

source_name: enriched DNA using anti-LSD1


title: MCF-7-anti-ZIP

description: whole genome target analysis for ZIP transcription repressor

source_name: enriched DNA using antibody

tag: Breast cancer cell line MCF-7


title: MCF-7-control IgG(2)

description: whole genome target analysis for LSD1, MTA1, MTA2, and MTA3

source_name: enriched DNA using normal IgG


title: AGMPED_Blood_1 1990016

city: Pittsburgh

first: Anna

middle: J

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

description: Illumina_project_number: 2008-036

hyb_protocol: Illumina Beadstation, standard Illumina protocol

data_processing: Raw signal was background corrected in BeadStudio. VST transformation and RSN normalization was performed using Lumi package.

organism: Chlorocebus sabaeus

source_name: blood

label_protocol: cDNA was synthesized and in vitro transcribed into biotinylated cRNA using the Illumina Totalprep RNA amplification kit, following the manufacturer’s instructions (Ambion)

extract_protocol: Total RNA was extracted from brain tissues with PefectPure RNA Cell and Tissue Kit (5 Prime) and from peripheral blood collected to PaxGene RNA blood tubes using PAXgene Blood RNA Kit (PreAnalyticX).

tag: ucla animal id


title: MCF-7-control IgG


title: AGMPED_Blood_1 2002026

description: Illumina_project_number: 2008-036

scan_protocol: Illumina Beadstation, standard Illumina protocol


title: AGMPED_Blood_1 2002078

description: Illumina_project_number: 2008-036


title: Eyediscs_selectedlines_rep2


title: AGMPED_Blood_1 2003023

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1996053

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004038

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004067

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1996033

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005077

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1992042

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1996096

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005071

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2002059

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005086

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004044

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1996097

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1988081

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005088

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1992090

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999033

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005078

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1991090

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2003045

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2001050

description: Illumina_project_number: 2008-036


title: V5R2-L1-6 NA YPD

description: Mock IP, negative control. Replicate 2. Filter V5R2-L1-6.

source_name: Saccharomyces cerevisiae BQS252. Exponential growth in YPD.


title: AGMPED_Blood_1 2001055

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2001097

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2003012

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005083

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999100

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2003036

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005085

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2000087

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2002100

description: Illumina_project_number: 2008-036


title: Eyediscs_selectedlines_rep6


title: AGMPED_Blood_1 2001074

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1989004

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1998020

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1984011

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999017

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1995029

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1992013

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1984014

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004066

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005076

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005084

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1996019

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005062

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005064

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2004042

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005081

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005060

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005069

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005080

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005058

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005045

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005052

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005040

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005056

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005053

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005025

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005036

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005024

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005038

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 1993066

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1996058

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2000074

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1995046

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005079

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2000065

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1988006

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004077

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999067

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2001081

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999109

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004069

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005067

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005010

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2005087

description: Illumina_project_number: 2008-065


title: AGMPED_Blood_1 2005065

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005016

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2005014

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2004005

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2004021

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2004006

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2003090

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2003047

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2004019

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2003052

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2003042

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1990025

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2003054

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002090

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2003038

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2003069

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2003018

description: Illumina_project_number: 2008-064


title: RA patient 29 peripheral blood cells

status: Public on Aug 21 2010

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

country: Japan

institute: Wakayama Medical University

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 42ﾟC. Slides were washed in 2xSSC+0.1% SDS, 2xSSC, 1xSSC, and 0.1xSSC before air pressure drying and scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: Log2 ratios of Cy3 to Cy5 were calculated and normalized by the method of global ratio median normalization.

source_name: peripheral blood cells from RA patient 29

label_protocol: Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3/Cy5.

extract_protocol: Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA Kit with the optimal on-column DNase digestion according to the manufacturer`s instructions.

tag: gender

tag: age

tag: disease

value: rheumatoid arthritis

value: peripheral blood

source_name: Total RNA from pooled whole blood of 45 healthy individuals

tag: sample type

value: pooled control


title: AGMPED_Blood_1 2003009

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002076

description: Illumina_project_number: 2008-064


title: RA patient 31 peripheral blood cells

source_name: peripheral blood cells from RA patient 31


title: AGMPED_Blood_1 2002064

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002036

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002099

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002057

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002053

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002082

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002045

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002085

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002051

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002001

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002025

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002024

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001058

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002033

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002012

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001028

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001054

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002010

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001031

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001069

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001047

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001016

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000095

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000052

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000117

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000054

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001024

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000088

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999086

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000063

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999070

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999099

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000029

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999072

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000022

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000069

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2000018

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999026

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999034

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999054

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999025

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999007

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1999057

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1995097

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1998042

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1994095

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1997012

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1995120

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1995103

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1994093

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1994072

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1994069

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1996076

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1996098

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1998036

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1995067

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1995049

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1996088

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1995052

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1995061

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1994014

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002062

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1992029

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1992015

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1994003

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1991006

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1993065

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1992087

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1993078

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2001040

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1991003

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1993018

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1994010

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1993090

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1992098

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1994008

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1989096

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1991095

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2002079

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1987004

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1988086

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1991010

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1991097

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1984084

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2004075

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 1986079

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 2004086

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004095

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004056

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004048

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004055

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004050

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004047

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004074

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004045

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004033

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004049

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004046

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004053

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004030

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004029

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004028

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004026

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2001007

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1995040

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004084

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1991028

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1998015

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999053

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2001107

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1991022

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005082

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2001101

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1996040

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2002028

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2002096

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005070

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999059

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005001

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005013

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1993038

description: Illumina_project_number: 2008-064


title: AGMPED_Blood_1 1993041

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1999028

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004016

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1995079

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 1989024

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2004032

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 1996027

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003081

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005023

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003079

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2001109

description: Illumina_project_number: 2008-036


title: AGMPED_Blood_1 2005008

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1989017

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1997018

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005057

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004064

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1992041

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999048

description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1988014

description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005044

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999064

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999010

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2001039

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005054

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2000001

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2000012

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005027

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005026

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005034

description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2000037

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1992046

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003051

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002084

description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1992051

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1998011

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1985092

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1998070

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004041

description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004054

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1994094

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2001015

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005019

description: Illumina_project_number: 2008-020


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description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999112

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005022

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1987082

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1996087

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002106

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002049

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002060

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002080

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004039

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002086

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002102

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002073

description: Illumina_project_number: 2008-020


title: D. melanogaster male adult replicate 2

status: Public on Aug 03 2010

city: Hamilton

first: Rama

middle: S.

last: Singh

state: Ontario

address: 1280 Main Street West

department: Biology Department

country: Canada

institute: McMaster University

description: All information is provided above.

hyb_protocol: 80 μL of hybridization buffer (75 μl of DIG Easy Hyb [Roche], 4 μl of 10 mg/ml yeast tRNA [Invitrogen], and 4 μl of 10 mg/ml salmon sperm DNA [Sigma]) was added to each resuspended probe, followed by incubation at 65°C for 10 min. Both sample and reference probes were placed on the array, which was then placed in a sealed chamber in a 37°C water bath for 16-18 hours. The array was then washed for 3 × 15 min in pre-warmed 1 × SSC, 0.1% SDS. The array was then washed with room temperature 1 × SSC for ≤1min, followed by room temperature 0.1 × SSC for ≤ 15 sec.

scan_protocol: Array was scanned using a ScanArray 4000 XL (GSI Lumonics/Packard Biochips); images were preprocessed and quantified using QuantArray v3.0 (PerkinElmer).

data_processing:
While the CH1_SIG_MEAN, CH1_BKD_MEAN, CH2_SIG_MEAN, and CH2_BKD_MEAN columns are derived from the raw data, the VALUE column was derived as follows:
Data from the scanned microarrays were uploaded into GeneTraffic™ DUO version 3.0 (Iobion Informatics) and replicate spots were filtered such that any element showing greater than 200% covariance or a 2-fold greater difference among the highest and lowest measured replicate spot (including all elements within an array or between replicate arrays) was flagged. All elements flagged according to these criteria as well as those flagged by the internal quality control standards of the software were then manually inspected for the presence of unacceptable spots (e.g., incorrectly printed, contained visible surface scratches or matter interfering with the scanning, etc.). Such spots were removed, and if less than 6 usable replicates (i.e., 2 replicate spots per array) remained, the entire element was discarded. Furthermore, an element was discarded if a subset of the within-array replicate spots showed consistently different hybridization intensities; these spots likely represent clones that were incorrectly annotated as belonging to the same element in the CDMC’s Drosophila 12kv2 microarray annotation file (http://142.150.8.217/GT_annot.zip). The filtered raw data was then downloaded from GeneTraffic™ DUO version 3.0 and subjected to a second round of quality control, where spots were removed if they did not show an expression intensity of at least 100, as well as a two-fold expression intensity above either the local or global average background. All genes that did not have usable data from both replicate spots on all three microarrays in all four stages within a species were then removed from further analysis. The CDMC’s Drosophila 12kv2 microarray annotation file was then manually inspected in order to identify all spots for which a single Flybase gene number (FBgn) (FB2008_10 Dmel Release 5.13; http://flybase.org/) could unambiguously be identified. All control spots as well ambiguous clone spots were removed from further analysis, leaving only genes that were detectably expressed in all 4 stages in at least one of the 3 species or the hybrid.
	The data remaining after quality control were normalized using the ‘rlowess’ procedure (spatial-intensity joint loess) as implemented in the ‘maanova’ package in the R statistical software (http://research.jax.org/faculty/churchill/software/Rmaanova/index.html), using default values and a ‘TwoColor’ array type. The output for each spot on each array from maanova was then transformed into its log2(sample/reference) ratio, which is reported in the 'VALUE' column.

organism: Drosophila melanogaster

source_name: D. melanogaster male whole-body adult 2x amplified mRNA

label_protocol:
RNase-free water was added to 5 μg of total RNA from each sample to bring the final volume to 14.5 μl. 4 μl of random primer was added followed by incubation at 70°C for 10 min, then 42°C for 5 min. 19.5 μl of modified Indirect RT master mix was added to each tube, along with 2.0 μl of Superscript II RT and the reaction was incubated at 42°C for 3 hours.
The cDNA product was cleaned and precipitated by adding 8 μl of 1N NaOH to each reaction with mixing by pipetting followed by a quick spin and immediate incubation at 65°C for 10 min. 8 μl of 1N HCl was then added, followed by 4 μL of 1M Tris (pH 7.5), mixing by pipetting after each addition. 38 μl of water was added to bring the total volume to 100 μl, and the amino allyl-cDNA was purified using either the Qiagen PCR clean up or Invitrogen Purelink purification kit (using 80% EtOH for the wash buffer and eluting with 2 × 50 μl of water). After purification, 10 μl of 3M NaOAc, 1 μl of glycogen (20 μg/μl) and 120 μl of ice-cold isopropanol were added, and the cDNA was allowed to precipitate at –20°C for at least 75 min or overnight. The precipitated cDNA was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, followed by another spin at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.
Samples were then dye conjugated by addition of 3 μl of 0.3 M NaHCO3 to the resuspended amino allyl-cDNA, followed by 2 μl of reactive dye and subsequent incubation at room temperature in the dark for 1 hour. 90 μl of ddH2O was added to each sample, followed by purification using either the Qiagen PCR clean up or Invitrogen Purelink purification kit, washing with 80% EtOH 3 × and eluting with 3 × 50 μl of water. 15 μl of 3M NaOAc, 1.5 μl of glycogen (20 μg/μl) and 170 μl of ice-cold isopropanol were added to the labeled probe, and the DNA was allowed to precipitate at –20°C for at least 30 min. The precipitated probe was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, and spun at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.

extract_protocol: mRNA was extracted from a pool of 25 males using the RNeasy Mini kit (Qiagen). Samples were then amplified twice using the MessageAmp II aRNA kit (Ambion).

treatment_protocol: Flies were grown on standard cornmeal-molasses medium on 10 cm culture plates, painted with a small amount of water-diluted yeast. No more than 30 individuals were on a single  plate to prevent growth-dependent density effects. When flies reached the appropriate stage, they were collected in RNAlater (Ambion) on ice and placed immediately at -80 degrees centigrade.

tag: strain

value: Male

tag: stage

value: 1.5h post pupal eclosion

source_name: D. melanogaster male mixed-stage whole-body mRNA reference

label_protocol:
RNase-free water was added to 60 μg of total RNA from each sample, to bring the final volume to 19 μl. 21 μl of Indirect RT master mix was added into each tube and the reaction was incubated at 65°C for 5 min, then 42°C for 5 min. 2 μl of Superscript II RT was added to the sample, followed by incubation at 42°C for 3 hours.
The cDNA product was cleaned and precipitated by adding 8 μl of 1N NaOH to each reaction with mixing by pipetting followed by a quick spin and immediate incubation at 65°C for 10 min. 8 μl of 1N HCl was then added, followed by 4 μL of 1M Tris (pH 7.5), mixing by pipetting after each addition. 38 μl of water was added to bring the total volume to 100 μl, and the amino allyl-cDNA was purified using either the Qiagen PCR clean up or Invitrogen Purelink purification kit (using 80% EtOH for the wash buffer and eluting with 2 × 50 μl of water). After purification, 10 μl of 3M NaOAc, 1 μl of glycogen (20 μg/μl) and 120 μl of ice-cold isopropanol were added, and the cDNA was allowed to precipitate at –20°C for at least 75 min or overnight. The precipitated cDNA was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, followed by another spin at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.
	Samples were then dye conjugated by addition of 3 μl of 0.3 M NaHCO3 to the resuspended amino allyl-cDNA, followed by 2 μl of reactive dye and subsequent incubation at room temperature in the dark for 1 hour. 90 μl of ddH2O was added to each sample, followed by purification using either the Qiagen PCR clean up or Invitrogen Purelink purification kit, washing with 80% EtOH 3 × and eluting with 3 × 50 μl of water. 15 μl of 3M NaOAc, 1.5 μl of glycogen (20 μg/μl) and 170 μl of ice-cold isopropanol were added to the labeled probe, and the DNA was allowed to precipitate at –20°C for at least 30 min. The precipitated probe was then spun at >12,000 g for 30 min and the pellet was washed with 200 μl of 75% EtOH, and spun at >12,000 g for 5 min. All EtOH was carefully pipetted from the tube and the probe pellet was allowed to dry for ≤ 1 min before resuspension in 5 μl of water.

extract_protocol: mRNA was extracted from pools of 25 males at each stage listed above individually  using the RNeasy Mini kit (Qiagen). A large number of extracts were performed for each stage. Within-stage extracts were pooled, quantified, and the four stages were mixed together in equal concentration in order to produce the reference sample.

treatment_protocol: Flies were grown on standard cornmeal-molasses medium on 10 cm culture plates, painted with a small amount of water-diluted yeast. No more than 30 individuals were on a single  plate to prevent growth-dependent density effects. When flies reached the appropriate stage (synchronized to a 2h window), they were collected in RNAlater (Ambion) on ice and placed immediately at -80 degrees centigrade.

value: Equal concentration mix of 96h post larval emergence, 4h post puparium formation, 72h post puparium formation, and 1.5h post eclosion individuals.


title: AGMPED_Blood_1 2002011

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003044

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002019

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999090

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1996055

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004040

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005031

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999073

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002018

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2000083

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003017

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1994005

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1991035

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1995030

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1995025

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005061

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1987012

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002068

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999103

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1998028

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1999060

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003076

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005041

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2002040

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1992024

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003039

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1996016

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004015

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1991030

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2005018

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2003104

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1996068

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1995116

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2002063

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2004082

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2000034

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 1992093

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 1988082

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2004036

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2004088

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2004087

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2003063

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2003022

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 1996093

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2003058

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 1995087

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 1993035

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2001129

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2002056

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2001113

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2001111

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2005049

description: Illumina_project_number: 2008-020


title: AGMPED_Blood_1 2001057

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 1986009

description: Illumina_project_number: 2008-012


title: AGMBR_Blood_biological replicate I  2003038

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 2004008

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2000035

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2000010

description: Illumina_project_number: 2008-012


title: AGMPED_Blood_1 2003087

description: Illumina_project_number: 2008-012


title: AGMBR_Blood_biological replicate II  2003036

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2002090

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2003038

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2003036

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2002073

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2002056

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2002056

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2002073

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2002049

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2002049

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2002090

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2002012

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2002012

description: Illumina_project_number: 2008-063


title: AGMPED_Blood_1 1994050

description: Illumina_project_number: 2008-020


title: AGMBR_Blood_biological replicate II  2001111

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2000088

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2001047

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2001113

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2001016

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2001031

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2001113

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2001111

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2001031

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2001129

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2000117

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2001047

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2000088

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2001016

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2000117

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2000018

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2000018

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2000035

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2000035

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate II  2000010

description: Illumina_project_number: 2008-063


title: AGMBR_Blood_biological replicate I  2000010

description: Illumina_project_number: 2008-063


title: D. melanogaster male larval replicate 1

description: All information is provided above.

source_name: D. melanogaster male whole-body larval 2x amplified mRNA

value: 96h post larval emergence


title: AGMBB_blood 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_Pulvinar 200483

description: Illumina_project_number: 2008-063


title: AGMBB_blood 2004083

description: Illumina_project_number: 2008-063


title: AGMBB_Hippocampus 2004090

description: Illumina_project_number: 2008-063


title: AGMBB_Occipital Pole 200483

description: Illumina_project_number: 2008-063

source_name: postmortem_Occipital Pole


title: AGMBB_blood 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_Cereballar vermis 2004027

description: Illumina_project_number: 2008-063

source_name: postmortem_Cereballar vermis


title: AGMBB_Occipital Pole 2004072

description: Illumina_project_number: 2008-063


title: AGMBB_Occipital Pole 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_Occipital Pole 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_Orbital Frotal Cortex 2004072

description: Illumina_project_number: 2008-063

source_name: postmortem_Orbital Frotal Cortex


title: AGMBB_Orbital Frotal Cortex 200483

description: Illumina_project_number: 2008-063


title: AGMBB_Orbital Frotal Cortex 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_DLPFC 200483

description: Illumina_project_number: 2008-063


title: AGMBB_Pulvinar 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_Pulvinar 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_DLPFC 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_DLPFC 2004072

description: Illumina_project_number: 2008-063


title: AGMBB_Frontal Pole 2004072

description: Illumina_project_number: 2008-063

source_name: postmortem_Frontal Pole


title: AGMBB_DLPFC 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_hippocampus 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_Frontal Pole 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_hippocampus 2004072

description: Illumina_project_number: 2008-063


title: AGMBB_Cereballar vermis 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_Cereballar vermis 200483

description: Illumina_project_number: 2008-063


title: AGMBB_hippocampus 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_hippocampus 200483

description: Illumina_project_number: 2008-063


title: AGMBB_Head of caudate 200483

description: Illumina_project_number: 2008-063

source_name: postmortem_Head of caudate


title: AGMBB_Frontal Pole 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_Head of caudate 2004072

description: Illumina_project_number: 2008-063


title: AGMBB_Occipital Pole 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004072

description: Illumina_project_number: 2008-063


title: AGMBB_Occipital Pole 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Occipital Pole 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_Head of caudate 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_Occipital Pole 2004027

description: Illumina_project_number: 2008-048


title: AGMBR_Blood_biological replicate II  2001129

description: Illumina_project_number: 2008-063


title: AGMBB_Occipital Pole 2004090

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Occipital Pole 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004027

description: Illumina_project_number: 2008-048


title: AGMBB_Occipital Pole 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004090

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004090

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Pulvinar 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004027

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004027

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_DLPFC 2004090

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004027

description: Illumina_project_number: 2008-048


title: AGMBB_Hippocampus 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004090

description: Illumina_project_number: 2008-048


title: AGMBB_Hippocampus 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Frontal Pole 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_Hippocampus 2004027

description: Illumina_project_number: 2008-048


title: AGMBB_Hippocampus 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Hippocampus 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_Hippocampus 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Orbital Frotal Cortex 2004014

description: Illumina_project_number: 2008-063


title: AGMBB_Hippocampus 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004081

description: Illumina_project_number: 2008-063


title: AGMBB_Cereballar vermis 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004027

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004070

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004090

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004025

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004090

description: Illumina_project_number: 2008-048


title: AGMBB_Cereballar vermis 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Head of caudate 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004058

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004034

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004076

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004072

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004061

description: Illumina_project_number: 2008-048


title: AGMBB_Blood 2004090

description: Illumina_project_number: 2008-048


title: CCD33Lu

city: Boston

first: Ben

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: CCD33Lu fibroblast cell line

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: fibroblasts were cultured in DMEM supplemented with 10% fetal calf serum, L-glutamine, penicillin, and streptomycin

extract_protocol: QIAGEN RNeasy protocol and reagents for extraction of total RNA

value: M

tag: race

value: cau

value: Lung


title: CCD11Lu

description: CCD11Lu fibroblast cell line

tag: sex

value: asn


title: AGMBB_Frontal Pole 200483

description: Illumina_project_number: 2008-063


title: CRL2054

description: CRL2054 fibroblast cell line

value: F

value: Skin


title: LL86

description: LL86 fibroblast cell line


title: AG14446

description: AG14446 fibroblast cell line

value: black


title: AG13066

description: AG13066 fibroblast cell line


title: CCD29Lu

description: CCD29Lu fibroblast cell line


title: AGMBB_Occipital Pole 2004076

description: Illumina_project_number: 2008-048


title: CCD25Lu

description: CCD25Lu fibroblast cell line


title: CCD16Lu

description: CCD16Lu fibroblast cell line


title: CCD1108SK

description: CCD1108SK fibroblast cell line


title: CCD13Lu

description: CCD13Lu fibroblast cell line


title: CCD19Lu

description: CCD19Lu fibroblast cell line


title: CCD8Lu

description: CCD8Lu fibroblast cell line


title: AG11726

description: AG11726 fibroblast cell line


title: LL47

description: LL47 fibroblast cell line


title: AG11696

description: AG11696 fibroblast cell line


title: AG06237

description: AG06237 fibroblast cell line


title: AG07307

description: AG07307 fibroblast cell line


title: AG09877

description: AG09877 fibroblast cell line


title: AG04351

description: AG04351 fibroblast cell line


title: 7-8 wk In Vivo, Mmu23

status: Public on Jul 12 2010

city: Urbana

first: Rebecca

last: Krisher

state: IL

address: 1207 West Gregory Drive

institute: University of Illinois

description: Gene expression data of developmentally incompetent or immature oocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 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. The trimmed mean target intensity of each array was arbitrarily set to 100.

molecule: polyA RNA

organism: Mus musculus

source_name: In vivo matured MII oocytes derived from 7-8 wk old B6D2F1 female mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol following two-cycle amplification

growth_protocol: Germinal vesicle (GV) oocytes were isolated from mouse ovaries 48 hrs post-PMSG injection.  GV oocytes were matured in vitro for 16 hours in Gmat medium.  For collection of in vivo matured oocytes, mice were stimulated with hCG 48 hours post-PMSG.  Oocyte

extract_protocol: Poly A+ RNA extraction was performed using the DynaBeads mRNA Direct Kit from Invitrogen

treatment_protocol: GV, in vivo matured, and in vitro matured oocytes were exposed to 1% v/v (80-160 U/mL) hyaluronidase to remove the cumulus cells.

tag: Age

tag: Maturation

value: In vivo matured MII


title: AG08046

description: AG08046 fibroblast cell line


title: AG07139

description: AG07139 fibroblast cell line


title: AG13145

description: AG13145 fibroblast cell line


title: AG08904

description: AG08904 fibroblast cell line


title: AG04655

description: AG04655 fibroblast cell line


title: CLL patient 20, thalidomide treated

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

description: Gene expression data from CLL patient 20 following 7 days of thalidomide treament

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133plus2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with the GCOS software and BRB Array Tools

source_name: peripheral blood derived sample of CLL patient 20 past thalidomide therapy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA using the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix; manufacturer’s recommendations)

extract_protocol: RNA was isolated from peripheral blood samples enriched for leukemic cells by Ficoll-density gradient centrifugation (percentage of leukemic cells > 90%) using Trizol according to the manufacturer’s recommendations

treatment_protocol: CLL patients received thalidomide (100mg p.o./day) for 7 days

tag: treatment response

value: no response (NR)

tag: wbc change

tag: treg fold change

tag: flare reaction

value: no

tag: deletion 17p13

tag: deletion 11q22-q23

value: yes


title: AG05416

description: AG05416 fibroblast cell line


title: CLL patient 18, thalidomide treated

description: Gene expression data from CLL patient 18 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 18 past thalidomide therapy

value: complete response (CR)


title: AG08048

description: AG08048 fibroblast cell line


title: CLL patient 19, thalidomide treated

description: Gene expression data from CLL patient 19 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 19 past thalidomide therapy

value: partial response (PR)


title: CLL patient 16, thalidomide treated

description: Gene expression data from CLL patient 16 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 16 past thalidomide therapy


title: CLL patient 17, thalidomide treated

description: Gene expression data from CLL patient 17 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 17past thalidomide therapy


title: AG10049

description: AG10049 fibroblast cell line


title: CLL patient 08, thalidomide treated

description: Gene expression data from CLL patient 08 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 08 past thalidomide therapy


title: CLL patient 10, thalidomide treated

description: Gene expression data from CLL patient 10 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 10 past thalidomide therapy


title: CLL patient 09, thalidomide treated

description: Gene expression data from CLL patient 09 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 09 past thalidomide therapy


title: CLL patient 07, thalidomide treated

description: Gene expression data from CLL patient 07 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 07 past thalidomide therapy


title: CLL patient 13, thalidomide treated

description: Gene expression data from CLL patient 13 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 13past thalidomide therapy


title: CLL patient 06, thalidomide treated

description: Gene expression data from CLL patient 06 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 06 past thalidomide therapy


title: CLL patient 14, thalidomide treated

description: Gene expression data from CLL patient 14 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 14 past thalidomide therapy


title: CLL patient 05, thalidomide treated

description: Gene expression data from CLL patient 05 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 05 past thalidomide therapy


title: CLL patient 15, thalidomide treated

description: Gene expression data from CLL patient 15 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 15 past thalidomide therapy


title: CLL patient 11, thalidomide treated

description: Gene expression data from CLL patient 11 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 11 past thalidomide therapy


title: CLL patient 04, thalidomide treated

description: Gene expression data from CLL patient 04 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 04 past thalidomide therapy


title: CLL patient 12, thalidomide treated

description: Gene expression data from CLL patient 12 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 12 past thalidomide therapy


title: CLL patient 03, thalidomide treated

description: Gene expression data from CLL patient 03 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 03 past thalidomide therapy


title: CLL patient 02, thalidomide treated

description: Gene expression data from CLL patient 02 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 02 past thalidomide therapy


title: CLL patient 01, thalidomide treated

description: Gene expression data from CLL patient 01 following 7 days of thalidomide treament

source_name: peripheral blood derived sample of CLL patient 01 past thalidomide therapy


title: AGMBB_Blood 2004027

description: Illumina_project_number: 2008-048

tag: ucla animal id


title: CLL patient 19, untreated

description: Gene expression data from CLL patient 19 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 19 prior to therapy


title: CLL patient 18, untreated

description: Gene expression data from CLL patient 18 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 18 prior to therapy


title: CLL patient 16, untreated

description: Gene expression data from CLL patient 16 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 16 prior to therapy


title: CLL patient 15, untreated

description: Gene expression data from CLL patient 15 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 15 prior to therapy


title: CLL patient 17, untreated

description: Gene expression data from CLL patient 17 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 17prior to therapy


title: CLL patient 11, untreated

description: Gene expression data from CLL patient 11 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 11 prior to therapy


title: CLL patient 20, untreated

description: Gene expression data from CLL patient 20 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 20 prior to therapy


title: CLL patient 13, untreated

description: Gene expression data from CLL patient 13 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 13prior to therapy


title: CLL patient 07, untreated

description: Gene expression data from CLL patient 07 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 07 prior to therapy


title: CLL patient 09, untreated

description: Gene expression data from CLL patient 09 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 09 prior to therapy


title: CLL patient 12, untreated

description: Gene expression data from CLL patient 12 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 12 prior to therapy


title: CLL patient 14, untreated

description: Gene expression data from CLL patient 14 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 14 prior to therapy


title: CLL patient 06, untreated

description: Gene expression data from CLL patient 06 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 06 prior to therapy


title: CLL patient 08, untreated

description: Gene expression data from CLL patient 08 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 08 prior to therapy


title: CLL patient 10, untreated

description: Gene expression data from CLL patient 10 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 10 prior to therapy


title: CLL patient 05, untreated

description: Gene expression data from CLL patient 05 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 05 prior to therapy


title: CLL patient 02, untreated

description: Gene expression data from CLL patient 02 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 02 prior to therapy


title: Foxa3-/-_OVA_rep3

city: San Francisco

first: Andrea

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description: 11 arrays were hybridized and represent 3 lung samples for groups WT saline, WT OVA and KO OVA. There are 2 samples for the KO saline group.

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 , and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome custom arrays (platform acc# GPL7202). Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent). The dataset was normalized using the quantile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.

source_name: Lung tissue from Foxa3 KO challenged with OVA

label_protocol: 400ng of RNA was amplified and labeled using the One-Color Agilent Low RNA  Input Linear Amplification Kit

extract_protocol: Total RNA was extracted using  Qiagen RNEasy columns. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer


title: Clone BT/HerR0.2J rep1

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Gene expression data from Herceptin-resistant BT/HerR0.2J clone

hyb_protocol: The GeneChip arrays were hybridized with 20 ug of fragmented cRNA for 16 h at 45 °C and were then washed and stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix Fluidics Station 450 according to Affymetrix specification.

scan_protocol: Affymetrix GeneChip images were scanned at 11 um resolution using a high resolution GeneChip Scanner 3000 (Hewlett-Packard).

data_processing: Quality assessment and statistical analysis of gene expression data were performed using the R/Bioconductor packages.  To ensure the quality of the microarray assay, a set of quality assessment steps implemented in Bioconductor package “AffyExpress” were applied to the data.  Raw intensity measurements of all probe sets were converted into expression measurements using the “RMA” method.

source_name: Herceptin-resistant clone BT/HerR0.2J

label_protocol: Biotinylated cRNA was generated according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Cells were maintained in DMEM with 10% FBS and 1% penicillin/streptomycin in 5% CO2.

extract_protocol: Total RNA was purified using the RNeasy kit purchased from Qiagen (Valencia, CA).

tag: cell type

value: Herceptin-resistant clone BT/HerR0.2J


title: CLL patient 03, untreated

description: Gene expression data from CLL patient 03 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 03 prior to therapy


title: Clone BT/HerR0.2J rep2


title: Foxa3-/-_OVA_rep1


title: CLL patient 01, untreated

description: Gene expression data from CLL patient 01 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 01 prior to therapy


title: CLL patient 04, untreated

description: Gene expression data from CLL patient 04 before thalidomide treament

source_name: peripheral blood derived sample of CLL patient 04 prior to therapy


title: Foxa3-/-_OVA_rep2


title: Clone BT/HerR1.0E rep2

description: Gene expression data from Herceptin-resistant BT/HerR1.0E clone

source_name: Herceptin-resistant clone BT/HerR1.0E

value: Herceptin-resistant clone BT/HerR1.0E


title: Foxa3-/-_Saline_rep2

source_name: Lung tissue from Foxa3 KO challenged with saline


title: Clone BT/HerR0.2D rep2

description: Gene expression data from Herceptin-resistant BT/HerR0.2D clone

source_name: Herceptin-resistant clone BT/HerR0.2D

value: Herceptin-resistant clone BT/HerR0.2D


title: WT_OVA_rep3

source_name: Lung tissues from littermate control mice challenged with OVA


title: WT_OVA_rep1


title: WT_OVA_rep2


title: Clone BT/HerR0.2D rep1


title: AG09699

description: AG09699 fibroblast cell line

tag: age


title: Akt1-/-  LPS

city: Heraklion

first: Christos

last: Tsatsanis

state: Crete

address: Voutes

country: Greece

institute: University of Crete

description:
samples were processed using a Taq-man array for miRNA at DANA Farber Genome Facility, Boston, MA
LPS-stimulated Macrophages

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
samples were processed using the miRNA detection kit purchased by Ambion
samples were allowed to run for 40 PCR cycles and Ct values were obtained

label: TaqMan primers

source_name: macrophages -primary

label_protocol: not applicable

growth_protocol: Thioglycollate-elicited macrophages grown in culture in the presence of 10% FBS

extract_protocol: RNA was extracted using the standard TRIZOL protocol

treatment_protocol: cells were stimulated with LPS (1ug/ml) for 3 hours

tag: genotype

tag: agent

value: LPS


title: AG11364

description: AG11364 fibroblast cell line

value: M


title: Akt1+/+

description:
samples were processed using a Taq-man array for miRNA at DANA Farber Genome Facility, Boston, MA
unstimulated macrophages


title: Akt1+/+  LPS


title: Akt1-/-


title: Foxa3-/-_Saline_rep1