title: wild-type_Rap_rep#1

description: Gene expression data from yeast.


title: gcn4deletion_untreated_rep#1

status: Public on Mar 01 2010

type: RNA

city: Indianapolis

first: Ron

last: Wek

state: IN

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

country: USA

institute: Indiana University School of Medicine

description: Gene expression data from yeast.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS) using the MAS 5.0 algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: gcn4 deletion, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix, 2004).

growth_protocol: Cells were cultured in synthetic medium (SD) containing 2% dextrose and 0.5% ammonium sulfate and supplemented with all amino acids except histidine (SC).

extract_protocol: Total RNA was purified using the hot phenol method.

treatment_protocol: Microarray analysis was carried out using RNA prepared from cells treated for 1 hour with 10 mM 3-amino-1,2,4-triazole (3-AT), 200 nM rapamycin, or no stress, as indicated.

tag: treatment

value: untreated

tag: strain

tag: genotype

value: gcn4 deletion


title: gcn4deletion_3AT_rep#1

description: Gene expression data from yeast.

source_name: gcn4 deletion, 3AT


title: gcn2deletion_Rap_rep#1

description: Gene expression data from yeast.

source_name: gcn2 deletion, Rap

value: Rapamycin

value: gcn2 deletion


title: gcn2deletion_3AT_rep#1

description: Gene expression data from yeast.

source_name: gcn2 deletion, 3AT


title: wild-type_3AT_rep#1

description: Gene expression data from yeast.

source_name: wild-type, 3AT

value: wild-type


title: wild-type_untreated_rep#1

description: Gene expression data from yeast.

source_name: wild-type, untreated


title: Mutant Histone H2B K111A replicate 3

status: Public on Feb 28 2010

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Mutant yeast strain Histone H2B K111A

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GeneChip Operating Software v.1.4

source_name: Mutant yeast strain Histone H2B K111A

label_protocol: Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Cells were grown in YPD media until mid-log phase. Cells were harvested at OD600 of 0.35-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

value: WY317 (mutant Histone H2B K111A)


title: Kainate and neuroprotective peptide KN (KA+NAP)

city: Tel Aviv

first: Illana

last: Gozes

address: Einstein

country: Israel

institute: Tel Aviv University

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 7G scanner

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 250.

organism: Rattus norvegicus

source_name: Sprague-Dawley rats treated with KA and NAP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 2-cycle protocol from 500 ng total RNA (Expression Analysis Technical Manual v2, Affymetrix).

extract_protocol: Qiagen RNAeasy kit was used

treatment_protocol: Hippocampi were axtracted and quickly frozen. RNA extraction was done on all of the samples simultaneously.

tag: Brain tissue


title: Wild-type for H2B R102A and H2B K111A replicate 2

description: Wild-type yeast strain

source_name: Wild-type yeast strain

value: PY014 (wild-type Histone H2B)


title: Vehicle control PBS

source_name: Sprague-Dawley rats treated with PBS


title: Mutant Histone H2B R102A replicate 1

description: Mutant yeast strain Histone H2B R102A

source_name: Mutant yeast strain Histone H2B R102A

value: WY316 (mutant Histone H2B R102A)


title: Neuroprotective peptide NAP

source_name: Sprague-Dawley rats treated with NAP


title: Mutant Histone H2B K111A replicate 2

description: Mutant yeast strain Histone H2B K111A


title: Mutant Histone H2B R102A replicate 2

description: Mutant yeast strain Histone H2B R102A


title: Mutant Histone H2B R102A replicate 3

description: Mutant yeast strain Histone H2B R102A


title: Wild-type for H2B R102A and H2B K111A replicate 3

description: Wild-type yeast strain


title: Mutant Histone H2B K111A replicate 1

description: Mutant yeast strain Histone H2B K111A


title: Kainate KA

source_name: Sprague-Dawley rats treated with KA


status: Public on Feb 23 2010

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_wild type early stationary phase of growth rep 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7GPlus.

data_processing: The data were analyzed with GCOS 1.1 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Staphylococcus aureus strain MW2 (USA400) was selected based on clinical relevance and available genome sequence information (2;19-22). S. aureus were cultured and harvested as described (7;23).

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: To compare transcript levels of MW2 and saeR/S, bacteria were grown to mid-exponential (OD600 = 0.75) and early stationary phases of growth (OD600 = 2.0), and processed for microarray analysis as described (7). S. aureus cDNA was hybridized to custom Affymetrix GeneChips (RMLChip 3) containing 99.3% coverage of genes from MW2 (2613 probe sets of 2632 ORFs remaining 0.7% represented by identical probe sets from other staphylococci).


title: Wild-type for H2B R102A and H2B K111A replicate 1

description: Wild-type yeast strain


description: Gene expression data from_SAE mutant mid exponential phase of growth rep 3

value: MW2 isogenic deletion mutant of the saeR/S two-component gene regulatory system


description: Gene expression data from_wild type early stationary phase of growth rep 3


description: Gene expression data from_wild type mid exponential phase of growth rep 1


description: Gene expression data from_SAE mutant early stationary phase of growth rep 1


description: Gene expression data from_wild type mid exponential phase of growth rep 3


description: Gene expression data from_wild type early stationary phase of growth rep 2


description: Gene expression data from_wild type mid exponential phase of growth rep 2


description: Gene expression data from_SAE mutant early stationary phase of growth rep 2


description: Gene expression data from_SAE mutant early stationary phase of growth rep 3


description: Gene expression data from_SAE mutant mid exponential phase of growth rep 2


description: Gene expression data from_SAE mutant mid exponential phase of growth rep 1


title: 1257Q_EBBX airway fibroblasts rep3

status: Public on Feb 20 2010

city: Pittsburgh

first: Kazuhisa

last: Konishi

state: PA

address: 1212 Kaufmann Building  3471 Fifth Ave

department: Pulmonry, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

description: Fresh lung tissue specimens from airways were obtained through bronchoscopy, and primary fibroblasts were isolated and cultured.

hyb_protocol: Following fragmentation, 1.5 ug of cRNA were hybridized for 17 hr at 65C on Agilent 4x44k Whole Human Genome Array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Agilent Scanner protocol

data_processing: gProcessed values from the Agilent Feature Extraction software

organism: Homo sapiens

source_name: airway fibroblasts rep3

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol from 500ng total RNA.

extract_protocol: RNA was isolated from lung tissue using Trizol (Invitrogen) and purified using the RNeasy Mini kit (Qiagen).

tag: cell type

value: Primary airway fibroblasts


title: 0349Q_EBBX airway fibroblasts rep1

source_name: airway fibroblasts rep1


title: Adjacent normal tissue from patient 224635-1

status: Public on Feb 11 2010

city: beijing

first: wu

last: jp

address: 18 Life Science Parkway

country: China

institute: National Engineering Research Center

description: the microRNA expression in the tissue

hyb_protocol: Hybridization was performed at 42oC under LifterSlipTM (Erie, Portsmouth, NH) in a hybridization chamber which was placed in a 3D-tilting agitator BioMixerTM  II (CapitalBio) to provide continuous mixing of the hybridization buffer that results in more uniform hybridization across the entire slide surface, preventing edge effects and giving improved signal intensity, the efficiency of which has been demonstrated with our genome-wide mRNA expression profiling (Patterson et al., Nat Biotechnol. 2006, 24:1140-1150).The array was then washed with two consecutive washing solutions of 0.2% SDS, 2¡ÁSSC at 42¡ãC for 5 min, and 0.2% SSC for 5 min at room temperature

scan_protocol: Arrays were scanned with a LuxScanTM 10K-A laser confocal scanner and the images obtained were then analyzed using LuxScan 3.0TM software (both from CapitalBio, Beijing, China)

data_processing: After average values of the replicate spots of each miRNA were background subtracted, faint spots were filtered out when expression signal were lower than 800 in all samples.

source_name: human

label_protocol: 4 ug of low-molecular-weight RNA was labeled with 500 ng of 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon, Lafayette, CO) with 2 units T4 RNA ligase (New England Biolabs, Ipswich, MA).  The labeling reaction was performed at 4oC for 2 h.  Labeled RNA was precipitated with 0.3 M sodium acetate and 2.5 volumes ethanol and after washing with ethanol and drying was resuspended in 15 ¦Ìl of hybridization buffer containing 3¡ÁSSC, 0.2% SDS and 15% formamide.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen, Carlsbad, CA) and the low-molecular-weight RNA was isolated by using the Ambion miRNA Isolation Kit

tag: tissue


title: Adjacent normal tissue from patient 224581-1

description: the microRNA expression in the tissue


title: 0944E_TBBX distal lung fibroblasts rep2

description: Fresh lung tissue specimens from distal lungs were obtained through bronchoscopy, and primary fibroblasts were isolated and cultured.

source_name: distal lung fibroblasts rep2

value: Primary distal lung fibroblasts


title: 0349Q_TBBX distal lung fibroblasts rep1

source_name: distal lung fibroblasts rep1


title: Adjacent normal tissue from patient 224635-2

description: the microRNA expression in the tissue


title: 1257Q_TBBX distal lung fibroblasts rep3

source_name: distal lung fibroblasts rep3


title: Adjacent normal tissue from patient 225727-1

description: the microRNA expression in the tissue


title: 0944E_EBBX airway fibroblasts rep2

source_name: airway fibroblasts rep2


title: Cancer tissue from patient 224435-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 224435-1


title: Cancer tissue from patient 224581-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 224581-1


title: Adjacent normal tissue from patient 224435-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 224429-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 224429-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 224429-1


title: Cancer tissue from patient 224257-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 224257-1


title: Cancer tissue from patient 224069-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 224069-1


title: Adjacent normal tissue from patient 224257-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 224157-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 224157-1


title: Adjacent normal tissue from patient 224157-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 223941-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223941-1


title: Adjacent normal tissue from patient 224069-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 223938-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223938-1


title: Adjacent normal tissue from patient 223938-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 223941-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 223936-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223936-1


title: Adjacent normal tissue from patient 223936-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 223888-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223888-1


title: Adjacent normal tissue from patient 223858-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 223888-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 223433-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223433-1


title: Cancer tissue from patient 223858-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223858-1


title: Cancer tissue from patient 223430-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223430-1


title: Adjacent normal tissue from patient 223433-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 223171-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 223430-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 223168-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 223168-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 223168-1


title: Adjacent normal tissue from patient 223171-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 222986-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 222986-1


title: Adjacent normal tissue from patient 222986-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 221840-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 222617-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 221840-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221840-1


title: Cancer tissue from patient 221810-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221810-1


title: Cancer tissue from patient 221756-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221756-1


title: Cancer tissue from patient 222617-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 222617-1


title: Adjacent normal tissue from patient 221492-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 221810-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 221492-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221492-1


title: Adjacent normal tissue from patient 221756-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 221334-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221334-1


title: Adjacent normal tissue from patient 221550-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 221334-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 221150-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221150-1


title: Adjacent normal tissue from patient 221145-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 219796-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 219796-1


title: Adjacent normal tissue from patient 220699-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 221087-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 220749-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 221145-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221145-1


title: Cancer tissue from patient 220749-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 220749-1


title: Cancer tissue from patient 220432-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 220432-1


title: Cancer tissue from patient 221087-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 221087-1


title: Adjacent normal tissue from patient 220432-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 219796-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 219710-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 219773-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 219773-1


title: Adjacent normal tissue from patient 219773-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 219710-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 219710-1


title: Cancer tissue from patient 220699-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 220699-1


title: Adjacent normal tissue from patient 219706-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 218589-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 218589-1


title: Adjacent normal tissue from patient 218589-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 218585-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 218585-1


title: Adjacent normal tissue from patient 218585-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 218502-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 218502-1


title: Cancer tissue from patient 218499-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 218499-1


title: Adjacent normal tissue from patient 218502-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 219706-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 219706-1


title: Cancer tissue from patient 217332-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 217332-1


title: Adjacent normal tissue from patient 217332-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 216989-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 216989-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 216989-1


title: Adjacent normal tissue from patient 218047-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 215828-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 215828-1


title: Cancer tissue from patient 218172-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 218172-1


title: Adjacent normal tissue from patient 218172-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 218046-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 218046-1


title: Adjacent normal tissue from patient 215828-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 218047-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 218047-1


title: Adjacent normal tissue from patient 218046-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 218499-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 215824-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 215824-1


title: Adjacent normal tissue from patient 215823-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 215459-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 215459-1


title: Cancer tissue from patient 215167-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 215167-1


title: Adjacent normal tissue from patient 215824-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 215274-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 215823-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 215823-1


title: Adjacent normal tissue from patient 215167-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 215274-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 215274-1


title: Adjacent normal tissue from patient 214634-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 215459-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 214633-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 214633-1


title: Cancer tissue from patient 214634-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 214634-1


title: Adjacent normal tissue from patient 215165-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 215165-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 214633-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 214580-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 214580-1


title: Adjacent normal tissue from patient 214578-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 214131-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 214518-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 214518-1


title: Adjacent normal tissue from patient 214580-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 214519-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 214295-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 214519-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 214519-1


title: Adjacent normal tissue from patient 214578-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 214518-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 214295-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 214295-1


title: Cancer tissue from patient 214131-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 214131-1


title: Cancer tissue from patient 213382-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 213382-1


title: Adjacent normal tissue from patient 213721-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 213721-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 213721-1


title: Adjacent normal tissue from patient 212197-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 212196-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 212196-1


title: Cancer tissue from patient 212197-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 212197-1


title: Adjacent normal tissue from patient 212196-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 212437-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 212437-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 212437-1


title: Adjacent normal tissue from patient 213382-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 211961-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211961-1


title: Cancer tissue from patient 212075-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 212075-1


title: Adjacent normal tissue from patient 212075-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 211961-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 211486-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211486-2


title: Cancer tissue from patient 211486-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211486-1


title: Adjacent normal tissue from patient 211043-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 211486-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 211043-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211043-2


title: Adjacent normal tissue from patient 211257-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 211043-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211043-1


title: Adjacent normal tissue from patient 211043-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 211486-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 211038-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211038-1


title: Cancer tissue from patient 211038-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211038-2


title: Adjacent normal tissue from patient 211038-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 211038-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 210971-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210971-2


title: Adjacent normal tissue from patient 211257-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 210971-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 210971-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 210971-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210971-1


title: Cancer tissue from patient 210644-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210644-1


title: Adjacent normal tissue from patient 210644-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 210644-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210644-2


title: Cancer tissue from patient 210618-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210618-2


title: Adjacent normal tissue from patient 210644-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 211257-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211257-1


title: Cancer tissue from patient 211257-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 211257-2


title: Cancer tissue from patient 210618-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210618-1


title: Adjacent normal tissue from patient 210618-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 210618-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 210429-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210429-2


title: Adjacent normal tissue from patient 210429-2

description: the microRNA expression in the tissue


title: Lung tissue from normal person 210423-2

description: the microRNA expression in the tissue

value: Lung tissue from normal person 210423-2


title: Cancer tissue from patient 210416-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210416-1


title: Lung tissue from normal person 210416-2

description: the microRNA expression in the tissue

value: Lung tissue from normal person 210416-2


title: Lung tissue from normal person 210416-1

description: the microRNA expression in the tissue

value: Lung tissue from normal person 210416-1


title: Cancer tissue from patient 210423-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210423-1


title: Lung tissue from normal person 210423-1

description: the microRNA expression in the tissue

value: Lung tissue from normal person 210423-1


title: Cancer tissue from patient 210423-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210423-2


title: Adjacent normal tissue from patient 210429-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 209772-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 209772-2


title: Adjacent normal tissue from patient 209772-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 210017-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 210416-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210416-2


title: Cancer tissue from patient 209762-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 209762-2


title: Cancer tissue from patient 210429-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210429-1


title: Adjacent normal tissue from patient 209772-1

description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 209762-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 209762-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 209762-1


title: Adjacent normal tissue from patient 210017-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 210017-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210017-2


title: Cancer tissue from patient 210017-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 210017-1


title: Adjacent normal tissue from patient 209727-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 209727-3

description: the microRNA expression in the tissue


title: Cancer tissue from patient 209727-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 209727-2


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 209673-2


title: Adjacent normal tissue from patient 209727-1

description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 209673-1


title: Lung tissue from normal person 209673-2

description: the microRNA expression in the tissue

value: Lung tissue from normal person 209673-2


title: Lung tissue from normal person 209673-1

description: the microRNA expression in the tissue

value: Lung tissue from normal person 209673-1


title: Cancer tissue from patient 209727-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 209727-1


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description: the microRNA expression in the tissue

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description: the microRNA expression in the tissue

value: Cancer tissue from patient 209118-1


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title: Adjacent normal tissue from patient 208944-2

description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue

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description: the microRNA expression in the tissue

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title: Adjacent normal tissue from patient 207359-2

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description: the microRNA expression in the tissue

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title: Adjacent normal tissue from patient 206843-1

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description: the microRNA expression in the tissue

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title: Cancer tissue from patient 206084-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 206084-1


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 206090-2


title: Adjacent normal tissue from patient 206169-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 206090-1

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description: the microRNA expression in the tissue

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description: the microRNA expression in the tissue

value: Cancer tissue from patient 206084-2


title: Cancer tissue from patient 205882-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205882-1


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title: Adjacent normal tissue from patient 205876-2

description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue

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description: the microRNA expression in the tissue

value: Cancer tissue from patient 205649-2


title: Adjacent normal tissue from patient 205876-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205649-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205649-2

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title: Cancer tissue from patient 205477-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205477-1


title: Cancer tissue from patient 205477-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205477-2


title: Adjacent normal tissue from patient 205477-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205353-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 205876-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205876-1


title: Cancer tissue from patient 205381-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205381-1


title: Cancer tissue from patient 204950-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 204950-1


title: Cancer tissue from patient 205381-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205381-2


title: Lung tissue from normal person 205381-2

description: the microRNA expression in the tissue

value: Lung tissue from normal person 205381-2


title: Adjacent normal tissue from patient 205477-1

description: the microRNA expression in the tissue


title: Lung tissue from normal person 205381-1

description: the microRNA expression in the tissue

value: Lung tissue from normal person 205381-1


title: Cancer tissue from patient 205353-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205353-1


title: Cancer tissue from patient 205353-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 205353-2


title: Adjacent normal tissue from patient 205353-1

description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 204950-2


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description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 204932-2


title: Adjacent normal tissue from patient 204932-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 204703-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 204703-2


title: Adjacent normal tissue from patient 204932-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 204932-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 204932-1


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 204703-1


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description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 204703-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 204691-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 204691-1


title: Cancer tissue from patient 204691-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 204691-2


title: Adjacent normal tissue from patient 204691-2

description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 204435-2


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description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 204435-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 204435-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 204435-1


title: Cancer tissue from patient 203903-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203903-1


title: Adjacent normal tissue from patient 203903-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 203903-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 203903-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203903-2


title: Adjacent normal tissue from patient 204435-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 203892-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203892-1


title: Adjacent normal tissue from patient 203892-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 203892-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203892-2


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 203707-2


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 203707-1


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 203327-1


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description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue

value: Cancer tissue from patient 203327-2


title: Adjacent normal tissue from patient 203707-2

description: the microRNA expression in the tissue


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description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 203327-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 203299-3

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203299-3


title: Cancer tissue from patient 203299-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203299-2


title: Cancer tissue from patient 203299-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203299-1


title: Cancer tissue from patient 203170-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203170-1


title: Cancer tissue from patient 203170-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 203170-2


title: Adjacent normal tissue from patient 203299-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 203299-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 203170-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 202687-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202687-2


title: Adjacent normal tissue from patient 202687-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 202687-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202687-1


title: Adjacent normal tissue from patient 203170-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 202687-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 202684-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202684-2


title: Cancer tissue from patient 202684-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202684-1


title: Adjacent normal tissue from patient 202684-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 202684-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 202578-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202578-2


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description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 202578-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 202578-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202578-1


title: Cancer tissue from patient 202292-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202292-2


title: Cancer tissue from patient 202292-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202292-1


title: Adjacent normal tissue from patient 202292-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 201983-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 201983-2


title: Cancer tissue from patient 201983-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 201983-1


title: Adjacent normal tissue from patient 201983-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 202292-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 201983-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 202192-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202192-2


title: Adjacent normal tissue from patient 200771-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 202192-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 202192-1


title: Adjacent normal tissue from patient 202192-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 202192-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 200771-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 200771-1


title: Adjacent normal tissue from patient 200771-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 200771-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 200771-2


title: Cancer tissue from patient 200746-2

description: the microRNA expression in the tissue

value: Cancer tissue from patient 200746-2


title: Cancer tissue from patient 200746-3

description: the microRNA expression in the tissue

value: Cancer tissue from patient 200746-3


title: Cancer tissue from patient 200746-1

description: the microRNA expression in the tissue

value: Cancer tissue from patient 200746-1


title: Adjacent normal tissue from patient 200746-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 200746-2

description: the microRNA expression in the tissue


title: Melanoma cell line A375+miRNA211_R_1

status: Public on Dec 31 2009

city: Savannah

first: ranjan

middle: joseph

last: perera

state: GA

address: 4700 Waters Ave

department: DLOR

institute: Anderson Cancer Center

description: Gene Expression data

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

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

data_processing: The data was analyzed with GeneSpring 10x using Plier16 as the normalization method and is log2 transformed.

label: Biotin

source_name: Melanoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: Melanoma and melanocytes were grown in standard ATCC growth media

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

treatment_protocol: Overexpression of miR-211 in both WM1552C and A375 cells

tag: cell line

value: Melanoma cell line A375

tag: protocol

value: miR-211 overexpression


title: Melanoma cell line A375_R_3

description: Gene Expression data

value: control


title: Melanocytes_R_3

description: Gene Expression data

source_name: Melanocytes

value: Melanocyte


title: Melanoma cell line WM1552C+miRNA211_R_3

description: Gene Expression data

value: Melanoma cell line WM1552C


title: Melanoma cell line A375+miRNA211_R_2

description: Gene Expression data


title: Melanoma cell line A375+miRNA211_R_3

description: Gene Expression data


title: Melanoma cell line A375_R_1

description: Gene Expression data


title: Melanoma cell line WM1552C_R_1

description: Gene Expression data


title: Melanoma cell line A375_R_2

description: Gene Expression data


title: Melanoma cell line WM1552C_R_2

description: Gene Expression data


title: Melanoma cell line WM1552C+miRNA211_R_2

description: Gene Expression data


title: Melanocytes_R_2

description: Gene Expression data


title: Melanoma cell line WM1552C_R_3

description: Gene Expression data


title: Melanoma cell line WM1552C+miRNA211_R_1

description: Gene Expression data


title: Melanocytes_R_1

description: Gene Expression data


title: P.NP rat - region hipp - animal 6

city: Westfield

first: Mark

middle: William

last: Kimpel

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

description: Gene expression data from brain Nucleus Accumbens from P rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on rat 230.2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

data_processing: The data were analyzed with RMA

source_name: Nucleus Accumbens from P rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 2-cycle protocol from 25 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: RNA was extracted using Trizol followed by Qiagen RNeasy mini kit.

value: P

value: Nucleus Accumbens


title: P.NP rat - region hipp - animal 4


title: P.NP rat - region hipp - animal 9


title: P.NP rat - region hipp - animal 7


title: P.NP rat - region hipp - animal 8


title: P.NP rat - region hipp - animal 2


title: P rat - region hipp - animal 8

description: Gene expression data from brain Nucleus Accumbens from P.NP rat

source_name: Nucleus Accumbens from P.NP rat


title: P.NP rat - region hipp - animal 5


title: P.NP rat - region hipp - animal 3


title: P rat - region hipp - animal 9


title: P rat - region hipp - animal 5


title: P rat - region hipp - animal 7


title: P rat - region fctx - animal 16

description: Gene expression data from brain Hippocampus from P.NP rat

source_name: Hippocampus from P.NP rat

value: Hippocampus


title: P rat - region hipp - animal 4


title: P rat - region fctx - animal 12


title: P rat - region fctx - animal 14


title: P rat - region fctx - animal 10


title: P rat - region fctx - animal 15


title: P rat - region hipp - animal 2


title: P rat - region fctx - animal 11


title: P rat - region fctx - animal 13


title: P rat - region hipp - animal 3


title: P rat - region hipp - animal 6


title: P.NP rat - region fctx - animal 8

description: Gene expression data from brain Hippocampus from P rat

source_name: Hippocampus from P rat


title: P rat - region fctx - animal 9


title: P.NP rat - region fctx - animal 7


title: P.NP rat - region fctx - animal 6


title: P.NP rat - region fctx - animal 3


title: P.NP rat - region fctx - animal 1


title: P rat - region cp - animal 16

description: Gene expression data from brain Frontal Cortex from P rat

source_name: Frontal Cortex from P rat

value: Frontal Cortex


title: P.NP rat - region fctx - animal 5


title: P rat - region cp - animal 14


title: P rat - region cp - animal 15


title: P rat - region cp - animal 12


title: P.NP rat - region fctx - animal 2


title: P.NP rat - region fctx - animal 4


title: P rat - region cp - animal 11


title: P rat - region cp - animal 9


title: P rat - region cp - animal 13


title: P.NP rat - region cp - animal 7

description: Gene expression data from brain Frontal Cortex from P.NP rat

source_name: Frontal Cortex from P.NP rat


title: P.NP rat - region cp - animal 6


title: P.NP rat - region cp - animal 5


title: P.NP rat - region cp - animal 3


title: P.NP rat - region cp - animal 1


title: P.NP rat - region cp - animal 8


title: P.NP rat - region cp - animal 2


title: P rat - region cp - animal 10


title: P rat - region amyg - animal 13

description: Gene expression data from brain Caudate-Putamen from P rat

source_name: Caudate-Putamen from P rat

value: Caudate-Putamen


title: P rat - region amyg - animal 14


title: P.NP rat - region cp - animal 4


title: P rat - region amyg - animal 16


title: P rat - region amyg - animal 12


title: P rat - region amyg - animal 10


title: P.NP rat - region amyg - animal 1

description: Gene expression data from brain Caudate-Putamen from P.NP rat

source_name: Caudate-Putamen from P.NP rat


title: P rat - region amyg - animal 9


title: P.NP rat - region amyg - animal 7


title: P.NP rat - region amyg - animal 8


title: P rat - region amyg - animal 11


title: P.NP rat - region amyg - animal 5


title: P.NP rat - region amyg - animal 4


title: P.NP rat - region amyg - animal 6


title: P.NP rat - region amyg - animal 2


title: P rat - region acb - animal 9

description: Gene expression data from brain Amygdala from P rat

source_name: Amygdala from P rat

value: Amygdala


title: P.NP rat - region acb - animal 7

description: Gene expression data from brain Amygdala from P.NP rat

source_name: Amygdala from P.NP rat


title: P rat - region acb - animal 10


title: P rat - region acb - animal 11


title: P rat - region acb - animal 12


title: P.NP rat - region acb - animal 8


title: P.NP rat - region acb - animal 5


title: P.NP rat - region acb - animal 6


title: P rat - region acb - animal 14


title: P.NP rat - region amyg - animal 3


title: P rat - region acb - animal 15


title: P rat - region acb - animal 16


title: P rat - region acb - animal 13


title: P.NP rat - region acb - animal 4


title: P.NP rat - region acb - animal 2


title: P.NP rat - region acb - animal 3


title: P.NP rat - region acb - animal 1


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, water-27

description:
no ethanol
time from last drinking episode (hrs):6
Gene expression data from brain nucleus accumbens shell

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RGU34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

value: P rat

value: Nucleus Accumbens Shell


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, water-25


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, water-26


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, water-24

description:
no ethanol
time from last drinking episode (hrs):1
Gene expression data from brain nucleus accumbens shell


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, water-22


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, water-33

description:
no ethanol
time from last drinking episode (hrs):24
Gene expression data from brain nucleus accumbens shell


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, water-32


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, water-28


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, water-20


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-60

description:
exposed to limited access ethanol
time from last drinking episode (hrs):24
Gene expression data from brain nucleus accumbens shell


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, water-19


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, water-34


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-62


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, water-30


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, water-21


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, water-29


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, water-31


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, water-18


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-58


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, water-23


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-61


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-59


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-53


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-54


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-55


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-57


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-51

description:
exposed to limited access ethanol
time from last drinking episode (hrs):6
Gene expression data from brain nucleus accumbens shell


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-50


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-49


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-56


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-40

description:
exposed to limited access ethanol
time from last drinking episode (hrs):1
Gene expression data from brain nucleus accumbens shell


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-42


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-43


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-38


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-37


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):24, ethanol-52


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-39


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-41


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-46


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-45


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-35


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-36


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-47


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-48


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-34


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):6, ethanol-44


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-33


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, water-13

description:
no ethanol
time from last drinking episode (hrs):6
Gene expression data from brain central nucleus of the amygdala

value: Central Nucleus of Amygdala


title: Nucleus Accumbens Shell, time from last drinking episode (hrs):1, ethanol-32


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, water-17


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, water-12

description:
no ethanol
time from last drinking episode (hrs):1
Gene expression data from brain central nucleus of the amygdala


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, water-4


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, water-10


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, water-3

description:
no ethanol
time from last drinking episode (hrs):24
Gene expression data from brain central nucleus of the amygdala


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, water-16


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, water-7


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, water-15


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, water-11


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, water-9


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, water-8


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, water-14


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, water-2


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-30

description:
exposed to limited access ethanol
time from last drinking episode (hrs):6
Gene expression data from brain central nucleus of the amygdala


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, water-5


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-29


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, water-6


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-31

description:
exposed to limited access ethanol
time from last drinking episode (hrs):24
Gene expression data from brain central nucleus of the amygdala


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-27

description:
exposed to limited access ethanol
time from last drinking episode (hrs):1
Gene expression data from brain central nucleus of the amygdala


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, water-1


title: Etiolation and nitrate treatment on rice (Flip dye replicate)

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

hyb_protocol: Agilent’s In situ Hybridzation kit 5184-3568 was used for hybridization as per the directions of the manufacturer

scan_protocol: Scanning was performed with AGILENT DNA Microarray scanner SureScan High-Resolution Technology with GeneSpring software and image analyses were performed using the same.

data_processing: The normalization was done using GeneSpring GX as per the recommended Per Spot and Per Chip protocol. Ratio of intensities values above 1.5 were considered significant for upregulated genes while ratio less than 0.66 was considered for down regulated genes.

organism: Oryza sativa

source_name: Oryza sativa indica

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA using Agilent's Low input RNA linear amplification Kit Cat # 5184-3523. Protocol was followed as per manufacturers directions.cRNA was purified using Qiagen’s RNeasy minikit Cat#74104

growth_protocol: Rice seedlings were germinated on cotton in plastic trays and grown for 8-10 days in the absence of light and nutrients on distilled water prior to treatment.

extract_protocol: Hot-Phenol method for total RNA isolation was used for the current experiment.

treatment_protocol: 8-10 day old etiolated rice plantlets  were treated with 120mM nitrate for 2 hours. Total RNA was isolated from the tissue and used for labeling.

tag: Oryza sativa indica var. Panvel Age

value: 8-10 days Growth Conditions:25 °C with 80-90% humidity


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-20


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-26


title: Etiolation and nitrate treatment on rice

description: The normalization was done using GeneSpring GX as per the recommended Per Spot and Per Chip protocol.


title: Light and nitrate treatment on rice (Flipdye)

hyb_protocol: Agilent’s In situ Hybridzation kit 5184-3568 was used for hybridization as per the directions of the manufacturer.

growth_protocol: Rice seedlings were germinated on cotton in plastic trays and grown for 8-10 days in the absence of nutrients on distilled water prior to treatment.12-hour diurnals were maintained throughout.

treatment_protocol: 8-10 day old rice plantlets grown in light and 12-hour diurnals were treated with 120mM nitrate for 2 hours. Total RNA was isolated from the tissue and used for labeling.


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-24


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-18


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-21


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-22


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-16


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-28


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-19


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-17


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-15


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-23


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-25


title: Light and nitrate treatment on rice plants

value: 8-10 days Growth Conditions: 25 °C with 80-90% humidity


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-14


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-10


title: CN_AML Patient 61: Wildtype CEBPA

city: Munich

first: Klaus

middle: H

last: Metzeler

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University of Munich

description: CN_AML Patient 61

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the variance stabilizing normalization algorithm. Custom chip definition files based on the  GeneAnnot database were used for probe-set summarization, and probe set expression values were calculated by the median polish method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set  summarization.

source_name: bone marrow mononuclear cells: AML, normal karyotype

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from bone marrow (BM) or peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow or peripheral blood mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML) with a normal karyotype

value: bone-marrow mononuclear cells from CN-AML patient

value: Wildtype CEBPA


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-11


title: CN_AML Patient 60: Wildtype CEBPA

description: CN_AML Patient 60


title: CN_AML Patient 59: Monoallelic CEBPA mutation

description: CN_AML Patient 59

value: Monoallelic CEBPA mutation


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-13


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-12


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-9


title: CN_AML Patient 58: Biallelic CEBPA mutation

description: CN_AML Patient 58

value: Biallelic CEBPA mutation


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-8


title: CN_AML Patient 56: Wildtype CEBPA

description: CN_AML Patient 56


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-6


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-7


title: CN_AML Patient 57: Wildtype CEBPA

description: CN_AML Patient 57


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-5


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):6, ethanol-3


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):24, ethanol-4


title: CN_AML Patient 53: Wildtype CEBPA

description: CN_AML Patient 53


title: CN_AML Patient 54: Wildtype CEBPA

description: CN_AML Patient 54


title: CN_AML Patient 55: Biallelic CEBPA mutation

description: CN_AML Patient 55


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-2


title: Central Nucleus of Amygdala, time from last drinking episode (hrs):1, ethanol-1


title: CN_AML Patient 52: Wildtype CEBPA

description: CN_AML Patient 52


title: CN_AML Patient 50: Wildtype CEBPA

description: CN_AML Patient 50


title: CN_AML Patient 49: Biallelic CEBPA mutation

description: CN_AML Patient 49


title: CN_AML Patient 51: Monoallelic CEBPA mutation

description: CN_AML Patient 51


title: CN_AML Patient 48: Monoallelic CEBPA mutation

description: CN_AML Patient 48


title: CN_AML Patient 42: Monoallelic CEBPA mutation

description: CN_AML Patient 42


title: CN_AML Patient 45: Wildtype CEBPA

description: CN_AML Patient 45


title: CN_AML Patient 40: Monoallelic CEBPA mutation

description: CN_AML Patient 40


title: CN_AML Patient 43: Monoallelic CEBPA mutation

description: CN_AML Patient 43


title: CN_AML Patient 39: Wildtype CEBPA

description: CN_AML Patient 39


title: CN_AML Patient 46: Wildtype CEBPA

description: CN_AML Patient 46


title: CN_AML Patient 41: Monoallelic CEBPA mutation

description: CN_AML Patient 41


title: CN_AML Patient 36: Wildtype CEBPA

description: CN_AML Patient 36


title: CN_AML Patient 34: Biallelic CEBPA mutation

description: CN_AML Patient 34


title: CN_AML Patient 37: Wildtype CEBPA

description: CN_AML Patient 37


title: CN_AML Patient 35: Wildtype CEBPA

description: CN_AML Patient 35


title: CN_AML Patient 32: Wildtype CEBPA

description: CN_AML Patient 32


title: CN_AML Patient 33: Wildtype CEBPA

description: CN_AML Patient 33


title: CN_AML Patient 31: Wildtype CEBPA

description: CN_AML Patient 31


title: CN_AML Patient 27: Biallelic CEBPA mutation

description: CN_AML Patient 27


title: CN_AML Patient 28: Wildtype CEBPA

description: CN_AML Patient 28


title: CN_AML Patient 29: Wildtype CEBPA

description: CN_AML Patient 29


title: CN_AML Patient 30: Wildtype CEBPA

description: CN_AML Patient 30


title: CN_AML Patient 38: Wildtype CEBPA

description: CN_AML Patient 38


title: CN_AML Patient 26: Wildtype CEBPA

description: CN_AML Patient 26


title: CN_AML Patient 25: Wildtype CEBPA

description: CN_AML Patient 25


title: CN_AML Patient 24: Wildtype CEBPA

description: CN_AML Patient 24


title: CN_AML Patient 22: Wildtype CEBPA

description: CN_AML Patient 22


title: CN_AML Patient 21: Wildtype CEBPA

description: CN_AML Patient 21


title: CN_AML Patient 20: Wildtype CEBPA

description: CN_AML Patient 20


title: CN_AML Patient 23: Wildtype CEBPA

description: CN_AML Patient 23


title: CN_AML Patient 18: Wildtype CEBPA

description: CN_AML Patient 18


title: CN_AML Patient 19: Wildtype CEBPA

description: CN_AML Patient 19


title: CN_AML Patient 17: Wildtype CEBPA

description: CN_AML Patient 17


title: CN_AML Patient 15: Wildtype CEBPA

description: CN_AML Patient 15


title: CN_AML Patient 12: Wildtype CEBPA

description: CN_AML Patient 12


title: CN_AML Patient 16: Wildtype CEBPA

description: CN_AML Patient 16


title: CN_AML Patient 14: Wildtype CEBPA

description: CN_AML Patient 14


title: CN_AML Patient 5: Wildtype CEBPA

description: CN_AML Patient 5


title: CN_AML Patient 10: Wildtype CEBPA

description: CN_AML Patient 10


title: CN_AML Patient 11: Wildtype CEBPA

description: CN_AML Patient 11


title: CN_AML Patient 44: Wildtype CEBPA

description: CN_AML Patient 44


title: CN_AML Patient 4: Wildtype CEBPA

description: CN_AML Patient 4


title: CN_AML Patient 9: Wildtype CEBPA

description: CN_AML Patient 9


title: CN_AML Patient 6: Wildtype CEBPA

description: CN_AML Patient 6


title: CN_AML Patient 8: Wildtype CEBPA

description: CN_AML Patient 8


title: GLY 3

status: Public on Dec 01 2009

city: Ithaca

first: James

middle: M

last: Gossett

state: NY

address: 220 Hollister Hall

department: Civil and Environmental Engineering

institute: Cornell University

description: Glycolate 2007_10_19_rep2b

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data were normalized with a robust multichip analysis (RMA) scheme with per-chip and per-gene median polishing.  A threshold of 100 for the baseline raw signal intensity was required in at least one replicate transcript to reduce noise due to low expression.

organism: Polaromonas sp. JS666

source_name: Glycolate-grown JS666

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: JS666 was grown on minimal-salts medium as described by Coleman et al.  Appl. Environ. Microbiol. 68(6):2726.  Cells were harvested for RNA extraction during mid-exponential growth phase.

extract_protocol: Total RNA was extracted from frozen cell pellets using a hot phenol/chloroform extraction method similar to that described by Cury and Koo Anal. Biochem. 365(2):208.  Extracted RNA was further purified with an ethanol precipitation and Rneasy Mini Clean-up Kit (Qiagen).  The purity and quantity of the RNA was assessed using a NanoDrop ND-1000 spectrophotometer.  The quality of the RNA was verified using a FlashGel System (Cambrex).  cDNA was synthesized following NimbleGen's protocol.

tag: growth protocol

value: 10 mM glycolate growth substrate


title: CN_AML Patient 7: Wildtype CEBPA

description: CN_AML Patient 7


title: GLY 1

description: Glycolate 2007_08_10


title: CN_AML Patient 3: Wildtype CEBPA

description: CN_AML Patient 3


title: CN_AML Patient 1: Biallelic CEBPA mutation

description: CN_AML Patient 1


title: CN_AML Patient 2: Wildtype CEBPA

description: CN_AML Patient 2


title: GLY 2

description: Glycolate 2007_10_19_rep2a


title: DCE 2

description: DCE 2007_10_19_rep1a

source_name: cDCE-grown JS666

value: 0.52 mM (nominal) cDCE growth substrate


title: DCE 3

description: DCE 2007_10_19_rep1b


title: FVB Kidney 8wk

status: Public on Dec 25 2009

city: Seattle

first: Neal

middle: A

last: Paragas

address: 850 Republican St

institute: University of Washington

description: FVB 8week kidneys

hyb_protocol: Following fragmentation, 15ug biotinylated cDNA were hybridized in duplicate to Mouse Genome 430 2.0 Genechip arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The results of the Affymetrix chip experiments where normalized using GCRMA (Matlab R2008a, The Mathworks Inc., Bioinformatics Toolbox).

organism: Mus musculus

source_name: Whole Kidney from FVB mice

label_protocol: For microarray analysis double-stranded cDNA was synthesized from total RNA (7µg) extracted from whole kidneys, and in vitro transcription biotin labeled cRNA was generated for GeneChip hybridization (GeneChip One-Cycle Target Labeling Kit, Affymetrix). Fragmented biotin labeled cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 GeneChips.

extract_protocol: RNA isolated with the mirVANA RNA extraction kit (Ambion) and quantified by NanoDrop and gel electrophoresis.

tag: FVB, 8 weeks, Kidney


title: TgFVB Kidney 6wk

description: TgFVB 6week kidneys

data_processing: The data were analyzed with robust multichip analysis (RMA) using the Affymetrix microarray *.cel image file and GeneTraffic(R) (Silicon Genetics) software

source_name: Whole Kidney from TgFVB mice

tag: TgN(pNL43d14)26Lom 26 (TgFVB)


title: TgFVB Kidney 8wk

description: TgFVB 8week kidneys


title: FVB Kidney 6wk

description: FVB 6week kidneys

tag: FVB, 6 weeks, Kidney


title: DCE 1

description: DCE 2007_08_10


title: HL60-Trrap-ChIP-rep13

status: Public on Nov 24 2009

type: genomic

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: 13441088-_cy3_TRRAP-exp14_TRRAP-14_IgG-690-640_0635

hyb_protocol: The mixed DNA was resuspended in 5 μL of H2O and mixed with 85 μL hybridization mix (100 μL of DIG Easy Hyb solution (Roche 603 558), 5 μL of 10 mg/mL calf thymus DNA (Sigma D8661), 5 μL of 10 mg/mL yeast tRNA (Invitrogen 15401-029)). The resulting solution was incubated at 65 °C for 2 minutes, then cooled to room temperature and applied to a CpG island array slide (UHN Microarray Centre HCGI12K) and incubated overnight at 42 °C in a hybridization chamber. After hybridization, the microarray slide was washed once with washing buffer 1 (1x SSC, 0.1% SDS) at 50°C for 5 minutes. This was followed by a wash with washing buffer 1 (room temperature for 5 minutes) and 2 washes with washing buffer 2 (0.2x SSC for 5 minutes) and one final wash with washing buffer 3 (0.1x SSC for 5 minutes at room temperature). The slide was then dried by spinning at 700 rpm for 15 minutes. To preserve the Cy5 dye from ozone-dependent degradation, which was observed during the summertime when the hybridization occurred, the slides were then dipped in DyeSaver 2 (Genisphere Q500600) and allowed to air dry.

scan_protocol: The microarray slides were scanned using a Gene Pix 4000B scanner (Axon Instruments) at multiple PMT voltages. Array images were first manually examined for image artifacts, and then quantitated using GenePix Pro (v6.0.1.27). A scan that maximized the dynamic range without saturating high-intensity signals was selected and carried forward for analysis. This scan was quantified using the “circular” segmentation algorithm.

data_processing: All data were pre-processed using the variance-stabilizing normalization algorithm as implemented in the vsn package (v3.8.0) for the BioConductor open-source library for the R statistical environment (v2.8.1). Print-tip groups were used as strata and default parameterization was employed.

molecule: genomic DNA

source_name: Growing HL60 Cells, Trrap ChIP

label_protocol: A total of 3 μg of amplified DNA from the antibody sample, no antibody, or IgG sample were vacuum desiccated and resuspended in 2.5 μL of H2O (Sigma W4502). 4.5 μL of 0.1 M NaHCO3 at pH 9 was added. The DNA was resuspended by vortexing several times. 2 μL of Cy3 or Cy5 dye (Amersham, PA23001 and PA25001 respectively) were added to the sample. The mix was incubated for 1.5 hours at room temperature in the dark. After incubation, 35 μL of 100 mM Na-Acetate pH5.2 was added and topped with H2O (Sigma W4502) to a total volume of 100 μL for each sample. The fluorescent labeled probes were purified using QIAquick PCR Purification kit (Qiagen 28106). The DNA was eluted with 50 μL of EB buffer from the kit, heated to 65°C. The 100 μL combined ChIP and no antibody samples were vacuum desiccated using a SpeedVac for 60 minutes at maximum heat.

extract_protocol: Exponentially growing HL60 cells were cross-linked with 1% formaldehyde for 10 minutes at 37 °C. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphatebuffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4 °C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then sonicated using 8 pulses (12-13 Watts, setting 10, 10 seconds per pulse, 45 seconds on ice between pulses) from a Model 60 Sonic Dismembrator (Fisher Scientific 15-338-53) to generate fragments between 600 bp and 1000 bp. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) and precleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmonsperm DNA at a final concentration of 50 μg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 10^6 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours with each of the following antibodies: no-antibody control, 0.7 μg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), Trrap antibody. 50 μL of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 μL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Crosslinks were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 μL of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 μL of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 μL of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was extracted from each sample using phenol:chloroform:isoamyl alcohol (25:24:1), then precipitated with 1/10th volume of 3 M sodium acetate (pH 5.3), 5 μg of glycogen, and 2 volumes of ethanol at -20 °C overnight. Pellets were collected by microcentrifugation and resuspended in 60 μL of H2O.

tag: antibody

value: Trrap

tag: sample type

value: ChIP

source_name: Growing HL60 Cells, IgG ChIP

value: IgG


title: HL60-Trrap-ChIP-rep8


title: HL60-Trrap-ChIP-rep12

description: 13441087-_cy5_TRRAP-exp13_TRRAP-13_IgG-640-600_0635


title: HL60-Trrap-ChIP-rep11


title: HL60-Trrap-ChIP-rep7


title: HL60-Trrap-ChIP-rep9


title: HL60-Trrap-ChIP-rep10


title: HL60-Trrap-ChIP-rep4


title: HL60-Trrap-ChIP-rep2


title: HL60-Trrap-ChIP-rep5


title: HL60-Trrap-ChIP-rep1


title: HL60-Trrap-ChIP-rep3


title: HL60-Mnt-ChIP-rep6

source_name: Growing HL60 Cells, Mnt ChIP

extract_protocol: Exponentially growing HL60 cells were cross-linked with 1% formaldehyde for 10 minutes at 37 °C. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphatebuffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4 °C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then sonicated using 8 pulses (12-13 Watts, setting 10, 10 seconds per pulse, 45 seconds on ice between pulses) from a Model 60 Sonic Dismembrator (Fisher Scientific 15-338-53) to generate fragments between 600 bp and 1000 bp. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) and precleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmonsperm DNA at a final concentration of 50 μg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 10^6 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours with each of the following antibodies: no-antibody control, 0.7 μg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), Mnt antibody. 50 μL of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 μL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Crosslinks were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 μL of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 μL of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 μL of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was extracted from each sample using phenol:chloroform:isoamyl alcohol (25:24:1), then precipitated with 1/10th volume of 3 M sodium acetate (pH 5.3), 5 μg of glycogen, and 2 volumes of ethanol at -20 °C overnight. Pellets were collected by microcentrifugation and resuspended in 60 μL of H2O.

value: Mnt


title: HL60-Mnt-ChIP-rep9

description: 13440764_Cy3Mnt_Igg12_Mnt12_710_620_0635


title: HL60-Trrap-ChIP-rep6


title: HL60-Mnt-ChIP-rep8

description: 13440753_Cy3Mnt_IgG14_Mnt14_720_600_0635


title: HL60-Mnt-ChIP-rep2

description: 13435982_Cy5Mnt _4Mnt_4IgG_710_570_0635