title: 220604 C2

description: No further description available.


title: 220604 K2

status: Public on Mar 25 2008

type: RNA

city: Giessen

first: Alexander

middle: Claus

last: Langheinrich

state: Hessen

address: Klinikstrasse 36

department: Radiology

country: Germany

institute: University of Giessen

description: No further description available.

hyb_protocol: The activity was measured with a liquid scintillization counter (Hidex). cDNA with 8–14x10E6 cpm was used for hybridization at 68°C overnight on nylon filters. Hybridization was carried out in Atlas ExpressHyp buffer supplied with the kit. The filters were then washed according to the kit protocol.

scan_protocol: For scanning, filters were wrapped in plastic foil and exposed for 4–7 days to imaging plates (Fuji Photo Film) in a lead sheathing. The films were read out with a phosphoimager system (FUJIX BAS 1000). The scanned images were analyzed using the AtlasImage 2.0 software.

data_processing:
Spot intensities were adjusted by a global normalization using the sum method
provided by the software. The mean global background was subtracted from the spot intensities. Spots were considered present when the spot intensity was at least twice the background intensity.

molecule: total RNA

organism: Homo sapiens

source_name: hCASMC

label_protocol:
RNA was reverse transcribed and labeled following the protocol given in the Altlas cDNA Expression Arrays User Manual (PT3140-1) using the reagents supplied by the Atlas Human Array Kit.
Briefly, 2-5 μg total RNA per sample were primed with 1.2 μl CDS primer (5’ 70°C; RT 10’) and reverse transcribed and radioactively labeled using
the master mix supplied with the kit following the kit protocol. The reverse transcriptase of the kit was substituted by 100U MMLV-RT obtained from Promega. Radioactively labeled cDNAs were purified using the purification columns provided with the kit and eluted in 100 μl elution buffer.

growth_protocol:
hCASMC were grown in supplemented growth medium containing 5%
FCS (SmGM-2; Clonetics, Verviers, Belgium). Following 24h of serum starvation (synchronization) in basal medium lacking growth factors and FSC in the presence of c³Ado (50µM), cells were incubated in SmGM-2 for additional 24h in the presence of c³Ado (50µM). Finally, c3Ado-treated cells were harvested for further microarray analysis.

extract_protocol: total RNA was extracted using the QIAgen RNA Micro Kit following the kit protocol including DNAse treatment.

tag: Treated

tag: Cell cultures grown in 5% FCS in the presence of c³Ado


title: 290404 K2

description: No further description available.


title: TG hippocampus 3 (Illumina)

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: illumina default hyb kit

scan_protocol: illumina default scan kit

data_processing: no background correction, VSN trasformation and normalization

label: biotin

organism: Mus musculus

source_name: Hippocampus DLCK transgenic mice

label_protocol: Ambion's amplification and labelling kit for Illumina

extract_protocol: Trizol

tag: Male C57/BL6j


title: 210504 K1

description: No further description available.


title: 210504 K2

description: No further description available.


title: Cancer tissue from patient 773276-2

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: the microRNA expression in the tissue

hyb_protocol: Hybridization was performed at 42C 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, 2X SSC at 42C 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.  Signal was normalized using the median center tool for genes in the Cluster 3.0 software before performing the unsupervised clustering with complete linkage and uncentered Pearson correlation to underlying the structure of the miRNA expression (Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns (Proc Natl Acad Sci U S A 1998;95:14863-8).

source_name: Cancer tissue from patient 773276-2

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 4C 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 ul of hybridization buffer containing 3X SSC, 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: Cancer tissue from patient 773276-2


title: 220604 C1

description: No further description available.

growth_protocol:
hCASMC were grown in supplemented growth medium containing 5%
FCS (SmGM-2; Clonetics, Verviers, Belgium). Following 24h of serum starvation (synchronization) in basal medium lacking growth factors and FSC, cells were incubated in SmGM-2 for additional 24h. Finally, cells were harvested for further microarray analysis.

tag: Control

tag: Cell cultures grown in 5% FCS in the absence of c³Ado


title: WT hippocampus 4 (Illumina)

source_name: Hippocampus WT mice


title: Cancer tissue from patient 773276-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 773276-1

tag: Cancer tissue from patient 773276-1


title: Adjacent normal tissue from patient 773276-1

description: the microRNA expression in the tissue


title: WT hippocampus 2 (Illumina)


title: Cancer tissue from patient 773073-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 773073-2

tag: Cancer tissue from patient 773073-2


title: 210504 C2

description: No further description available.


title: TG hippocampus 5 (Illumina)


title: TG hippocampus 4 (Illumina)


title: TG hippocampus 2 (Illumina)


title: WT hippocampus 6 (Illumina)


title: Adjacent normal tissue from patient 773276-2

description: the microRNA expression in the tissue


title: TG hippocampus 1 (Illumina)


title: WT hippocampus 3 (Illumina)


title: WT hippocampus 1 (Illumina)


title: Cancer tissue from patient 773073-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 773073-1

tag: Cancer tissue from patient 773073-1


title: Adjacent normal tissue from patient 773073-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 773073-1

description: the microRNA expression in the tissue


title: Ath_infection_rep9

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000

hyb_protocol: Hybridization and washing was done as recommended on the supplier’s web page (http://www.ag.arizona.edu/microarray/)

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: 'Automic Imageprocessing for Microarrays' (for detailsUniversität Bielefeld Applied Computer Science webpage)

data_processing:
- dye swap design
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- variance homogenisation by division of each value with the standard deviation of the normalized log2-ratios
- as statistical software we use 'R'

organism: Arabidopsis thaliana

source_name: rosettes of A. thaliana col-0

label_protocol: The Amino Allyl MessageAmpTM II aRNA Amplifcation Kit (Ambion, Darmstadt, Germany) was used for Cy3/Cy5-labeling of the 5-(3-aminoallyl)-UTP-containing aRNAs with the following modifications: Purification and concentration of double-stranded cDNA was done using the DNAclearTM Kit (Ambion, Darmstadt, Germany), and the large scale transcription reaction was purified with the MEGAclaerTM Kit (Ambion, Darmstadt, Germany)

tag: mock treated

source_name: rosettes of A. thalina col-0

extract_protocol: - Trizol (Invitrogen) isolation according to the manufactures standard protocol

tag: V. longisporum treated


title: 210504 C1

description: No further description available.


title: P24_R2

city: Sao Paulo

first: Glauber

middle: Costa

last: Brito

state: Sao paulo

address: Av. Prof. Lineu Prestes, 748 - sala 1.200

department: Instituto de Quimica - Dep Bioquimica

country: Brazil

institute: Universidade de Sao Paulo

description: Hybridization included external mRNA spikes for quality control of the experiment (Lucidea Microarray ScoreCard). Raw images were analyzed using the ArrayVision software (Version 8.0, Imaging Research Inc.). An array template (or grid) was first automatically aligned to locate the position of each spot in the array, and subsequently manually adjusted to obtain the best possible alignment.

hyb_protocol: Labeled targets were ressuspended in 250 (l of 1 x hybridization buffer (25% formamide, 12.5% of proprietary Microarray Hybridization Buffer Version 2 from Amersham Biosciences cat. RPK0325) denatured for 2 min at 92 ºC and centrifuged at 13,000 rpm for 5 min. All slide processing steps (blocking, hybridization, washing) were carried out on an automated slide processor (ASP) from Amersham Biosciences. The slides were incubated for 16h at 42ºC and subsequently washed at room temperature in 1xSSC/0.2%SDS for 5min, 0.1xSSC/0.2%SDS for 5 min and in 0.1XSSC for 3 min. After the washing steps, slides were flushed with isopropanol and dried with an air flush at 42ºC.

scan_protocol: Images were obtained from each channel by laser scanning using GenePix 4000B microarray scanner (Axon Instruments). Slides were scanned with the following parameters: scanning resolution: 10 -(m pixel;  excitation wave length: 633 nm (Cy5-labeled targets);  emission filter: 675 nm (Cy5-labeled targets); PMT voltage: 600 volts (Cy5-labeled targets).

data_processing: We employed in our analyses the Artifact-Removed density value (ARM) calculated for each spot by ArrayVision. The ARM value represents the average of all the pixels remaining in the spot, after first removing pixels with density values that exceed four median absolute deviations (MADs) from the median. The ARM density for each spot was subtracted by the median background surrounding the spot (distance of 2 pixels with 3 widths of pixels).The raw data of each spot was compared to the value of hibridization background using the Lucidea Microarray Scorecard to determine which spots have a signal above or below the detection limit of each hybridization, where the background was given by the signal measured on a negative control (plant cDNA). If their signal were at least 3 standard deviations above the average signal of the negative control, spots were considered expressed in tissues. We decided to use the mean intensity signal (40% trimmed) of each dataset for normalization between experiments.

source_name: Renal tumor tissue from patient 24

label_protocol: For each patient, aliquots containing 20 ug of total RNA from tumor or adjacent non-tumor tissue were labeled in parallel with either Cy3- or Cy5-derivatized deoxyribonucleotides (CyScribe first-strand cDNA labeling kit; GE Healthcare) using a mixture of oligo-dT and 9-mer random oligonucleotides as primers.

extract_protocol: Total RNA was isolated from tissue samples (approximately 200 mg) with Trizol reagent (Invitrogen), quantified by UV spectrophotometry (Nanodrop ND1000) and analysed for integrity by inspection of 18S/28S ribosomal RNA ratios following separation by gel electrophoresis.

tag: Renal tumor tissue from patient 24; Histological pattern

value: clear cell

source_name: Adjacent non-tumor renal tissue from patient 24


title: Cancer tissue from patient 772733-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772733-2

tag: Cancer tissue from patient 772733-2


title: Cancer tissue from patient 772733-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772733-1

tag: Cancer tissue from patient 772733-1


title: P23_L2

source_name: Renal tumor tissue from patient 23

tag: Renal tumor tissue from patient 23; Histological pattern

value: sarcomatoid

source_name: Adjacent non-tumor renal tissue from patient 23


title: Cancer tissue from patient 772698-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772698-1

tag: Cancer tissue from patient 772698-1


title: P23_R2

tag: Adjacent non-tumor renal tissue from patient 23


title: Ath_infection_rep8

extract_protocol: - Trizol (Invitrogen) isolation according to the manufactures standard


title: P24_L2

tag: Adjacent non-tumor renal tissue from patient 24


title: Ath_infection_rep7


title: P16_R2

source_name: Renal tumor tissue from patient 16

tag: Renal tumor tissue from patient 16; Histological pattern

value: papillary

source_name: Adjacent non-tumor renal tissue from patient 16


title: P19_R2

source_name: Renal tumor tissue from patient 19

tag: Renal tumor tissue from patient 19; Histological pattern

source_name: Adjacent non-tumor renal tissue from patient 19


title: Cancer tissue from patient 772698-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772698-2

tag: Cancer tissue from patient 772698-2


title: Ath_infection_rep4


title: Ath_infection_rep5


title: P22_R2

source_name: Renal tumor tissue from patient 22

tag: Renal tumor tissue from patient 22; Histological pattern

value: chromophilic

source_name: Adjacent non-tumor renal tissue from patient 22


title: Ath_infection_rep6


title: Ath_infection_rep2


title: Adjacent normal tissue from patient 772698-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 772698-2

description: the microRNA expression in the tissue


title: P16_L2

tag: Adjacent non-tumor renal tissue from patient 16


title: Ath_infection_rep1


title: Cancer tissue from patient 772603-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772603-2

tag: Cancer tissue from patient 772603-2


title: P15_R2

source_name: Renal tumor tissue from patient 15

tag: Renal tumor tissue from patient 15; Histological pattern

source_name: Adjacent non-tumor renal tissue from patient 15


title: Ath_infection_rep3

source_name: rosettes of A. thalina col-0

source_name: rosettes of A. thaliana col-0


title: P22_L2

tag: Adjacent non-tumor renal tissue from patient 22


title: P15_L2

tag: Adjacent non-tumor renal tissue from patient 15


title: P9_L2

source_name: Renal tumor tissue from patient 9

tag: Renal tumor tissue from patient 9; Histological pattern

source_name: Adjacent non-tumor renal tissue from patient 9


title: P14_R2

source_name: Renal tumor tissue from patient 14

tag: Renal tumor tissue from patient 14; Histological pattern

value: solid pattern

source_name: Adjacent non-tumor renal tissue from patient 14


title: P14_L2

tag: Adjacent non-tumor renal tissue from patient 14


title: P9_R2

tag: Renal tumor tissue from patient 9


title: P19_L2

tag: Adjacent non-tumor renal tissue from patient 19


title: P12_L2

source_name: Renal tumor tissue from patient 12

tag: Renal tumor tissue from patient 12; Histological pattern

source_name: Adjacent non-tumor renal tissue from patient 12


title: Adjacent normal tissue from patient 772603-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 772542-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772542-2

tag: Cancer tissue from patient 772542-2


title: P5_L2

source_name: Renal tumor tissue from patient 5

tag: Renal tumor tissue from patient 5; Histological pattern

source_name: Adjacent non-tumor renal tissue from patient 5


title: P4_R2

source_name: Renal tumor tissue from patient 4

tag: Renal tumor tissue from patient 4; Histological pattern

source_name: Adjacent non-tumor renal tissue from patient 4


title: P5_R2

tag: Adjacent non-tumor renal tissue from patient 5


title: P23_R1

source_name: Adjacent non-tumor renal tissue from patient 23

source_name: Renal tumor tissue from patient 23

tag: Renal tumor tissue from patient 23; Histological pattern


title: P12_R2

tag: Adjacent non-tumor renal tissue from patient 12


title: P4_L2

tag: Adjacent non-tumor renal tissue from patient 4


title: Cancer tissue from patient 772387-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772387-2

tag: Cancer tissue from patient 772387-2


title: Adjacent normal tissue from patient 772542-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 772603-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772603-1

tag: Cancer tissue from patient 772603-1


title: P23_L1

tag: Adjacent non-tumor renal tissue from patient 23


title: Adjacent normal tissue from patient 772603-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 772345-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772345-2

tag: Cancer tissue from patient 772345-2


title: Adjacent normal tissue from patient 772345-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 772542-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772542-1

tag: Cancer tissue from patient 772542-1


title: Cancer tissue from patient 772345-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772345-1

tag: Cancer tissue from patient 772345-1


title: Adjacent normal tissue from patient 772345-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 772143-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772143-2

tag: Cancer tissue from patient 772143-2


title: Adjacent normal tissue from patient 772143-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 772542-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 772387-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 772387-1

tag: Cancer tissue from patient 772387-1


title: P4_R1

source_name: Tumor renal tissue from patient 4


title: P22_R1

source_name: Adjacent non-tumor renal tissue from patient 22

source_name: Renal tumor tissue from patient 22

tag: Renal tumor tissue from patient 22; Histological pattern


title: P12_R1

source_name: Adjacent non-tumor renal tissue from patient 12

source_name: Renal tumor tissue from patient 12

tag: Renal tumor tissue from patient 12; Histological pattern


title: P16_R1

source_name: Adjacent non-tumor renal tissue from patient 16

source_name: Renal tumor tissue from patient 16

tag: Renal tumor tissue from patient 16; Histological pattern


title: P14_R1

source_name: Adjacent non-tumor renal tissue from patient 14

source_name: Renal tumor tissue from patient 14

tag: Renal tumor tissue from patient 14; Histological pattern


title: Adjacent normal tissue from patient 772387-2

description: the microRNA expression in the tissue


title: P5_R1

source_name: Adjacent non-tumor renal tissue from patient 5

source_name: Tumor renal tissue from patient 5

tag: Renal tumor tissue from patient 5; Histological pattern


title: P15_L1

source_name: Adjacent non-tumor renal tissue from patient 15

source_name: Renal tumor tissue from patient 15

tag: Renal tumor tissue from patient 15; Histological pattern


title: P19_R1

source_name: Adjacent non-tumor renal tissue from patient 19

source_name: Renal tumor tissue from patient 19

tag: Renal tumor tissue from patient 19; Histological pattern


title: P14_L1

tag: Adjacent non-tumor renal tissue from patient 14


title: P9_L1

source_name: Adjacent non-tumor renal tissue from patient 9

source_name: Tumor renal tissue from patient 9

tag: Renal tumor tissue from patient 9; Histological pattern


title: P24_L1

source_name: Adjacent non-tumor renal tissue from patient 24

source_name: Renal tumor tissue from patient 24

tag: Renal tumor tissue from patient 24; Histological pattern


title: P19_L1

tag: Adjacent non-tumor renal tissue from patient 19


title: P5_L1

tag: Adjacent non-tumor renal tissue from patient 5


title: P3_L2

source_name: Tumor renal tissue from patient 3

tag: Renal tumor tissue from patient 3; Histological pattern

source_name: Adjacent non-tumor renal tissue from patient 3


title: Cancer tissue from patient 771916-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 771916-2

tag: Cancer tissue from patient 771916-2


title: P3_R1

tag: Adjacent non-tumor renal tissue from patient 3

source_name: Renal tumor tissue from patient 3


title: Cancer tissue from patient 771916-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 771916-1

tag: Cancer tissue from patient 771916-1


title: P3_R2


title: P16_L1

source_name: Adjacent non-tumor renal tissue from patient 16

source_name: Renal tumor tissue from patient 16


title: P12_L1

source_name: Adjacent non-tumor renal tissue from patient 12

source_name: Renal tumor tissue from patient 12


title: P22_L1

source_name: Adjacent non-tumor renal tissue from patient 22

source_name: Renal tumor tissue from patient 22


title: P4_L1

source_name: Adjacent non-tumor renal tissue from patient 4

source_name: Tumor renal tissue from patient 4

tag: Renal tumor tissue from patient 4; Histological pattern


title: Adjacent normal tissue from patient 771916-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 771621-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 771521-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 771521-2

tag: Cancer tissue from patient 771521-2


title: Cancer tissue from patient 771621-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 771621-1

tag: Cancer tissue from patient 771621-1


title: Cancer tissue from patient 771521-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 771521-1

tag: Cancer tissue from patient 771521-1


title: P24_R1

source_name: Adjacent non-tumor renal tissue from patient 24

source_name: Renal tumor tissue from patient 24


title: P15_R1

source_name: Adjacent non-tumor renal tissue from patient 15

source_name: Renal tumor tissue from patient 15


title: P9_R1

source_name: Adjacent non-tumor renal tissue from patient 9

source_name: Tumor renal tissue from patient 9


title: Adjacent normal tissue from patient 771521-2

description: the microRNA expression in the tissue


title: P3_L1

source_name: Adjacent non-tumor renal tissue from patient 3

source_name: Renal tumor tissue from patient 3


title: 3T3L1_adipocyte_TetOff_3

status: Public on Mar 24 2008

city: College Station

first: Arul

last: Jayaraman

state: TX

address: 3122 TAMU

department: Artie McFerrin Department of Chemical Engineering

country: USA

institute: Texas A&M University

description: RNA quality was assessed using the Agilent 2100 Bioanalyzer.

hyb_protocol: Codelink Expression assay protocol.

scan_protocol: Codelink Expression assay protocol.

data_processing: CodeLink Expression Analysis 4.1.0.29054

source_name: RNA was collected from 3T3L1 adipocytes expression only Tet-off plasmid.

label_protocol: Codelink Expression assay protocol.

growth_protocol:
3T3-L1 preadipocytes were grown until confluence and differentiated
adipocytes using a standard adipogenic cocktail.

extract_protocol: Adipocytes (10 days after differentiation) were used for extracting total RNA using the Nucleospin II RNA isolation kit (Clontech).

tag: 3T3-L1 adipocytes with control plasmid. 3T3-L1 adipocytes expressing uncoupling protein 1 (UCP1)


title: 3T3L1_adipocyte_UCP1

source_name: RNA was collected from 3T3L1 adipocytes expressing Uncoupling protein 1.


title: 3T3L1_adipocyte_UCP3

source_name: RNA was collected from 3T3L1 adipocytes expressing Uncoupling Protein 1.

tag: 3T3-L1 adipocytes with control plasmid.

tag: 3T3-L1 adipocytes expressing uncoupling protein 1 (UCP1)


title: 3T3L1_adipocyte_TetOff_2

growth_protocol: 3T3-L1 preadipocytes were grown until confluence and differentiated into adipocytes using a standard adipogenic cocktail.

tag: 3T3L1 adipocytes with control plasmid.

tag: 3T3L1 adipocytes expressing Uncoupling protein 1 (UCP1).


title: 3T3L1_adipocyte_TetOff_1


title: 3T3L1_adipocyte_UCP2


title: F1-Vinclozolin embryonic testis day E16, replica 2

status: Public on Mar 22 2008

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data for E16-day embryos testis from F1 vinclozolin generation

hyb_protocol: standard Affymetrix procedure

scan_protocol: chips were scanned using Agilent GeneArray Scanner G2500A

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software using default normalization method. Target signal was set to 125. MAS preprocessing was used.

organism: Rattus norvegicus

source_name: E16-day rat testis

label_protocol: standard Affymetrix procedures

extract_protocol: About 10 testis with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).

treatment_protocol: Pregnant rats were given intraperitoneal injections of vinclozolin (100 mg/kg/day) from pregnancy day 8 to 14. 16 days pregnant female rat  were euthanized and rat testis from E16 male embryos (F1 generation) were removed according to IACUC-approved animal use protocols.

tag: testis were dissected from E16-day old embryos of F1-Vinclozolin Sprague-Dawley rats


title: F3-Vinclozolin embryonic testis day E16, replica 2

description: Gene expression data for E16-day embryos testis from F3 vinclozolin generation

scan_protocol: chips were scanned using Agilent Gene Chip Scanner 3000

treatment_protocol: Pregnant rats were given intraperitoneal injections of  vinclozolin (100 mg/kg/day) from pregnancy day 8 to 14. F1-generation male and female from different control lines were mated to produce F2 generation animals which were mated again. F2-generation 16 days pregnant female rat  were euthanized and rat testis from E16 male embryos (F3 generation) were removed according to IACUC-approved animal use protocols.

tag: testis were dissected from E16-day old embryos of F3-Vinclozolin Sprague-Dawley rats


title: F3-Control embryonic testis day E16, replica 1

description: Gene expression data for E16-day embryos testis from F3 control generation

treatment_protocol: Pregnant rats were given intraperitoneal injections of vehicle suspense (sesame oil and DMSO) from pregnancy day 8 to 14. F1-generation male and female from different control lines were mated to produce F2 generation animals which were mated again. F2-generation 16 days pregnant female rat  were euthanized and rat testis from E16 male embryos (F3 generation) were removed according to IACUC-approved animal use protocols.

tag: testis were dissected from E16-day old embryos of F3-control Sprague-Dawley rats


title: F2-Vinclozolin embryonic testis day E16, replica 1

description: Gene expression data for E16-day embryos testis from F2 vinclozolin generation

treatment_protocol: Pregnant rats were given intraperitoneal injections of vinclozolin (100 mg/kg/day) from pregnancy day 8 to 14. F1-generation male and female from different control lines were mated, 16 days pregnant female rat  were euthanized and rat testis from E16 male embryos (F2 generation) were removed according to IACUC-approved animal use protocols.

tag: testis were dissected from E16-day old embryos of F2-Vinclozolin Sprague-Dawley rats


title: Infected_Chardonnay_pool_5

status: Public on Mar 21 2008

city: Ljubljana

first: Kristina

last: Gruden

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: Infected_Chardonnay_pool was prepared from 3 samples (shoots), which had similar expression levels of three marker genes: Alcohol dehydrogenase I, Sucrose synthase and Heat shock protein 70

hyb_protocol: Immediately prior to hybridization, 60 ul of cRNA mixture, 60 ul of 4X hybridization buffer (Amersham) and 120 ul of deionized formamide were combined and vortexed, denatured for 5 min at 95°C and cooled for 3 min on ice. Microarrays were placed into the Amersham Lucidea hybridization station chambers, hybridization mixtures containing 20 ug of labeled cRNA were injected and hybridized for 16 hours at 37°C. Microarray slides were washed in three successive steps: i) 20 min with 1X SSC and 0.2% SDS, ii) twice 10 min with 0.1X SSC, 0.2% SDS, iii) 10 min with 0.1X SSC. All washing solutions were filtered through 0.2 um filters and heated to 37°C. Microarray slides were final washed with isopropanol andair-dryed .

scan_protocol: Microarrays were scanned with Axon Genepix 4000B (Axon Instruments) on the same day, as described in Terrier et al. (2005). Images were processed with GenePix Pro 3.0: all microarrays were visually inspected and all spots with bad morphology were flagged to be left out from further analysis.

data_processing: Raw signal data were background corrected using method half (all negative values after background correction were reset to an arbitrary value 50) and then normalized using method vsn. All pre-processing was performed in statistical environment R 2.6.2 (package limma).

organism: Vitis vinifera

source_name: Leaf midribs of infected plants/shoots (a pool of individual samples 3, 4, 30)

label_protocol: Total RNA was cleaned up using High Pure RNA Tissue Kit (Roche) according to the manufactures’ instructions and spectrofotometrically quantified. Antisense RNA amplification and simultaneous Cy3- and Cy5-labeling were performed as described in Terrier et al. (2005) except that hybridization mixtures were prepared by combining 10 ug of Cy-5 labeled sample cRNA and 10 ug of Cy-3 labeled common reference cRNA.

growth_protocol: plants were grown in a private vineyard in uncontrolled conditions

extract_protocol: Samples were ground with a pestle and mortar in liquid nitrogen. RNeasy Plant Mini Kit (Qiagen) with a modified protocol was used for total RNA extraction. 1 mL of RLC buffer (heated to 56°C), containing 10 ul mL-1 b-mercapto-ethanol (Sigma) and 10 mg mL-1 PVP Mw 40.000 (Sigma), was added to 100 to 150 mg of ground frozen plant material, vortexed vigorously, incubated three min at 56°C and centrifuged 30 s at 10000 g. Using only the supernatant, the subsequent steps were performed according to the manufacturer’s instructions.

tag: cultivar

value: Chardonnay

tag: age

tag: disease status

value: bois noir infected

tag: tissue

value: leaf midrib with 1-2 mm of lamina

source_name: Common reference RNA: total RNA  pooled from 123 samples of field collected Vitis vinifera samples

tag: cultivars

value: Chardonnay, Barbera, Prosecco

value: healthy, bois noir infected, flavescence doree infected, recovered plants


title: F2-Control embryonic testis day E16, replica 2

description: Gene expression data for E16-day embryos testis from F2 control generation

treatment_protocol: Pregnant rats were given intraperitoneal injections of vehicle suspense (sesame oil and DMSO) from pregnancy day 8 to 14. F1-generation male and female from different control lines were mated, 16 days pregnant female rat  were euthanized and rat testis from E16 male embryos (F2 generation) were removed according to IACUC-approved animal use protocols.

tag: testis were dissected from E16-day old embryos of F2-control Sprague-Dawley rats


title: F3-Control embryonic testis day E16, replica 2


title: F3-Vinclozolin embryonic testis day E16, replica 1


title: Infected_Chardonnay_pool_2

source_name: Leaf midribs of infected plants/shoots (a pool of individual samples 41, 56, 59)


title: F1-Control embryonic testis day E16, replica 2

description: Gene expression data for E16-day embryos testis from F1 control generation

treatment_protocol: Pregnant rats were given intraperitoneal injections of vehicle suspense (sesame oil and DMSO) from pregnancy day 8 to 14. 16 days pregnant female rat  were euthanized and rat testis from E16 male embryos (F1 generation) were removed according to IACUC-approved animal use protocols.

tag: testis were dissected from E16-day old embryos of F1-control Sprague-Dawley rats


title: Yellow leaves in F9Y RILs from parents lines

city: Taichung

first: Angeline

last: Su

address: Kuo Kuang road

country: Taiwan

institute: NCHU

description: yellow leaf tip in the vegetative stage

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

organism: Oryza sativa

source_name: Oryza sativa leaf from recombinant inbreed line , mutant, vegetative stage

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

extract_protocol: Total RNA was prepared with the RNeasy plant Mini Kit (Qiagen).

tag: yellow  leaf tip in the vegetative stage


title: F2-Control embryonic testis day E16, replica 1


title: F2-Vinclozolin embryonic testis day E16, replica 2


title: Infected_Chardonnay_pool_4

source_name: Leaf midribs of infected plants/shoots (a pool of individual samples 46, 53, 54)


title: F1-Control embryonic testis day E16, replica 1


title: Infected_Chardonnay_pool_1

source_name: Leaf midribs of infected plants/shoots (a pool of individual samples 39, 43, 45)


title: F1-Vinclozolin embryonic testis day E16, replica 1


title: Green leaves in F9G RILs from parents lines

description: green  leaf tip in the vegetative stage

source_name: Oryza sativa leaf from recombinant inbreed line, normal green

tag: green leaf in the vegetative stage


title: Healthy_Chardonnay_pool_2

description: Healthy_Chardonnay_pool was prepared from 3 samples (shoots), which had similar expression levels of three marker genes: Alcohol dehydrogenase I, Sucrose synthase and Heat shock protein 70

source_name: Leaf midribs of healthy plants/shoots (a pool of individual samples: 1, 17, 28)

value: healthy


title: 1519138033_C_10GyIR_BRCAX-LCS

city: Brisbane

first: Nic

last: Waddell

address: Herston Road

country: Australia

institute: QIMR

description: classifications for mutations are described at www.kconfab.org/progress/classification.shtml

hyb_protocol: Standard Illumina protocols were followed for hybridisation, washing and staining of Human-6 Bead chips.

scan_protocol: Slides were scanned with an Illumina Beadarray reader at a factor of 2

data_processing: Data was processed using Beadstudio II (Illumina) with no normalisation and then exported Genesping v7.3 (Agilent) where normailsation was performed per chip: to the 50th percentile and per gene: normalized to median)

source_name: Lymphoblastoid Cell Line, 30 min post 10 Gy IR

label_protocol: 450 ng of RNA was amplified with the Illumina Totalprep RNA amplification kit (Applied Biosystems)

growth_protocol: lymphoblastoid cell lines were removed from liquid nitrogen and grown for a minimum of 2 weeks prior to treatment with IR. LCLs were cultered in RPMI 1640 media with 15% fetal bovine serum, 1% penicillin-streptomycin and 1% glutamine

extract_protocol: RNA was extracted 30 minutes after IR treatment using an RNeasy mini kit (Qiagen)

treatment_protocol: 24 hrs prior to treatment cells were counted and put at 500000 cells/ml. 10 ml Cells were treated with 10 Gy gamma irradation

tag: BRCAX-LCS

tag: Gender

value: Female

tag: AGE


title: Healthy_Chardonnay_pool_3

source_name: Leaf midribs of healthy plants/shoots (a pool of individual samples 6, 16, 58)


title: Healthy_Chardonnay_pool_4

description: Healthy_Chardonnay_pool was prepared from 4 samples (shoots), which had similar expression levels of three marker genes: Alcohol dehydrogenase I, Sucrose synthase and Heat shock protein 70

source_name: Leaf midribs of healthy plants/shoots (a pool of individual samples 14, 23, 26, 27)


title: 1519138005_F_10GyIR_BRCA2 P missense

tag: BRCA2  missense


title: Healthy_Chardonnay_pool_5

source_name: Leaf midribs of healthy plants/shoots (a pool of individual samples 7, 19, 29)


title: 1519138005_E_10GyIR_BRCA2 P missense


title: 1519138033_F_10GyIR_BRCAX-LCS


title: 1519138005_B_10GyIR_BRCA1 P missense

tag: BRCA1  missense


title: 1519138005_D_10GyIR_BRCA1 P


title: 1519138005_A_10GyIR_BRCA1 P missense


title: 1519138033_A_10GyIR_BRCA1 P


title: 1488802107_E_10GyIR_BRCAx

tag: BRCAx


title: 1488802107_B_10GyIR_BRCAx


title: 1519138005_C_10GyIR_BRCA1 P


title: 1488802107_D_10GyIR_BRCAx


title: 1488802107_F_10GyIR_BRCAx


title: 1488802107_C_10GyIR_BRCAx


title: 1488802093_B_10GyIR_BRCAx


title: 1488802093_C_10GyIR_BRCAx


title: 1488802092_B_10GyIR_BRCA2 P


title: 1488802093_A_10GyIR_BRCAx


title: 1488802093_E_10GyIR_BRCAx


title: 1488802092_A_10GyIR_BRCA1 P missense


title: 1488802092_C_10GyIR_BRCA2 P


title: 1488802089_E_10GyIR_BRCAX-LCS


title: 1488802087_F_10GyIR_BRCAx


title: 1488802089_D_10GyIR_BRCA2 P


title: 1488802093_D_10GyIR_BRCA1 P


title: 1488802087_E_10GyIR_BRCAx


title: 1488802086_D_10GyIR_BRCA1 P


title: 1488802087_D_10GyIR_BRCAx


title: 1488802087_B_10GyIR_BRCA2 P


title: 1412091150_E_10GyIR_BRCA1 P


title: 1488802087_C_10GyIR_BRCAx


title: 1488802086_C_10GyIR_BRCAx


title: 1412091150_F_10GyIR_BRCA1 P


title: 1412091150_A_10GyIR_BRCA1 P


title: 1488802087_A_10GyIR_BRCA1 P


title: 1412091139_B_10GyIR_BRCA1 P missense


title: 1488802086_A_10GyIR_BRCAx


title: 1412091150_C_10GyIR_BRCA2 P


title: 1412091139_C_10GyIR_BRCA2 P


title: 1412091137_C_10GyIR_BRCA2 P


title: 1412091139_D_10GyIR_BRCA2 P


title: 1412091137_D_10GyIR_BRCA2 P


title: 1412091150_D_10GyIR_BRCA2 P


title: 1412091139_A_10GyIR_BRCA1 P


title: 1412091122_F_10GyIR_BRCA2 P


title: C3H10T1/2_dex_90min_rep2

city: san francisco

first: Alex

middle: Steven (Yick-Lun)

last: So

state: CA

department: cellular and molecular pharmacology

institute: university of california san francisco

description: 3 replicates

hyb_protocol: 2 days at 63 °C

scan_protocol: Scanned on Axon 4000B

data_processing: SpotReader to extract intensities; limma to normalize (normalizeWithinArrays function)

label_protocol: Couple Cy3 NHS ester to amino allyl dU in cDNA

growth_protocol: DMEM with 10% FBS, pyruvate, penicillin, streptomycin, 5% CO2

extract_protocol: Qiagen RNeasy

treatment_protocol: Treat with 1uM dexamethasone for 90 minutes.

tag: c3h10t1/2 cells

treatment_protocol: Pool of RNA from DMSO, dexamethasone, and myostatin treated C3H10T1/2 cells


title: C3H10T1/2_dex_90min_rep1

description: 3 replicates

tag: c3h1t0t1.2 cells


title: 1488802086_B_10GyIR_BRCAx


title: C3H10T1/2_vehicle_90min_rep2

description: replicate 2 of 3

treatment_protocol: Treat with DMSO.

tag: C3H10T1/2 cells


title: 1412091137_B_10GyIR_BRCA1 P missense


title: C3H10T1/2_vehicle_90min_rep1

description: replicate 1 of 3


title: 1412091122_A_10GyIR_BRCA1 P


title: C3H10T1/2_vehicle_90min_rep3

description: replicate 3 of 3


title: 1412091122_C_10GyIR_BRCA1 P


title: 1412091121_D_10GyIR_BRCA1 P missense


title: 1412091121_C_10GyIR_BRCA2 P


title: 1412091122_E_10GyIR_BRCA2 P


title: 1412091122_D_10GyIR_BRCA2 P


title: C3H10T1/2_dex_90min_rep3

description: 3 replicates


title: 1412091121_E_10GyIR_BRCA2 P


title: 1412091121_B_10GyIR_BRCA1 P


title: 1412091121_F_10GyIR_BRCAX-LCS


title: 1412091122_B_10GyIR_BRCA1 P


title: 1412091121_A_10GyIR_BRCA1 P


title: 1401771228_E_10GyIR_BRCA2 P missense


title: Male HNF4alpha knockout/Female HNF4alpha knockout comparison/Replicate #3

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The genetic expression profile for a single male HNF4alpha knockout liver pool and a single female HNF4alpha knockout liver pool is given as a normalized ratio. The purpose of this comparison is to study the impact of HNF4alpha deletion on sex-specific liver gene expression.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA.  Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm.  After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 micrometer scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation.  TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: Rosetta Resolver pipeline

label: Alexa 555

source_name: frozen adult Male mouse liver tissue prepared using Trizol

label_protocol: amino-allyl reverse transcription

extract_protocol: Trizol extraction

tag: Strain

value: 129/SV x C57B6 x FVB

tag: Genotype

value: HNF4alpha knockout

tag: Sex

value: male

tag: Tissue

value: liver

tag: Age

value: 7 weeks

label: Alexa 647

source_name: frozen adult female mouse liver tissue prepared using Trizol

value: female


title: Male wild type/Female wild type comparison/Replicate #4

description: The genetic expression profile for a single male liver pool and a single female liver pool is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in mouse liver gene expression.

source_name: frozen adult male mouse liver tissue prepared using Trizol

value: wild type


title: 1401771228_F_10GyIR_BRCA1 P


title: 1401771217_C_10GyIR_BRCA2 P


title: Male HNF4alpha knockout/Female HNF4alpha knockout comparison/Replicate #4


title: 1401771227_E_10GyIR_BRCAX

tag: BRCAX


title: Male wild type/Male HNF4alpha knockout comparison/Replicate #3

description: The genetic expression profile for a single male wild type liver pool and a single male HNF4alpha knockout liver pool is given as a normalized ratio. The purpose of this comparison is to study the impact of HNF4alpha deletion on male liver gene expression.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation.  TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).


title: Female wild type/Female HNF4alpha knockout comparison/Replicate #4

description: The genetic expression profile for a single female wild type liver pool and a single female HNF4alpha knockout liver pool is given as a normalized ratio. The purpose of this comparison is to study the impact of HNF4alpha deletion on female liver gene expression.


title: 1401771217_F_10GyIR_BRCAx


title: 1401771217_E_10GyIR_BRCAx


title: Female wild type/Female HNF4alpha knockout comparison/Replicate #2


title: Male wild type/Male HNF4alpha knockout comparison/Replicate #4


title: Female wild type/Female HNF4alpha knockout comparison/Replicate #3


title: Male wild type/Male HNF4alpha knockout comparison/Replicate #2


title: 1401771217_A_10GyIR_BRCAX-LCS


title: 1401771227_F_10GyIR_BRCAX-LCS


title: 1401771217_B_10GyIR_BRCA1 P missense


title: 1401771190_E_10GyIR_BRCAX-LCS


title: Male HNF4alpha knockout/Female HNF4alpha knockout comparison/Replicate #2


title: 1401771190_D_10GyIR_BRCA1 P


title: 1401771190_B_10GyIR_BRCA2 P


title: 1401771190_F_10GyIR_BRCAX-LCS


title: 1401771190_C_10GyIR_BRCA2 P


title: 1398241080_C_10GyIR_BRCA2 P


title: 1398241080_D_10GyIR_BRCAX-LCS


title: Female wild type/Female HNF4alpha knockout comparison/Replicate #1


title: Male wild type/Female wild type comparison/Replicate #2


title: 1401771190_A_10GyIR_BRCA2 P


title: Male HNF4alpha knockout/Female HNF4alpha knockout comparison/Replicate #1


title: 1398241080_B_10GyIR_BRCA2 P


title: 1398241080_F_10GyIR_BRCA1 P


title: BW25113 wild type LB 24h biofilm cells

status: Public on Mar 19 2008

first: Xiaole

last: Yang

address: Chemical Engineering Department

institute: Texas A & M University

description: RNA extracted from biofilm cells of E. coli K12 BW25113 wild type after 24 hours of growth in LB with glass wool

hyb_protocol: Affymetrix Genechip Expression Analysis Technical Manual

data_processing: MAS 5.0 Expression Analysis Default Setting

label: Biotin

organism: Escherichia coli

source_name: BW25113 wild type; 24 hours; LB

label_protocol: Enzo BioArray Terminal Labeling Kit

extract_protocol: Qiagen RNeasy Mini Kit


title: BW25113 with R1drd19 LB 7h biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 BW25113 with R1drd19 after 7 hours of growth in LB with glass wool

scan_protocol: Affymetrix Genechip Expression Analysis Technical Manual

source_name: BW25113 with R1drd19; 7 hours; LB


title: BW25113 with R1drd19 LB 24h biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 BW25113 with R1drd19 after 24 hours of growth in LB with glass wool

source_name: BW25113 with R1drd19; 24 hours; LB


title: MG1655 wild type M9C glu 24hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 MG1655 wild type  after 24 hours of growth in M9C glu with glass wool

source_name: MG1655 wild type; 24 hours of growth; M9C glu


title: BW25113 with R1drd19 LB 15h biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 BW25113 with R1drd19 after 15 hours of growth in LB with glass wool

source_name: BW25113 with R1drd19; 15 hours; LB


title: ATCC25404 wild type with R1drd19 LB 24hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 ATCC25404 wild type with R1drd19 after 24 hours of growth in LB with glass wool

source_name: ATCC25404 wild type with R1drd19; 24 hours; LB


title: BW25113 wild type LB 15h biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 BW25113 wild type after 15 hours of growth in LB with glass wool

source_name: BW25113 wild type; 15 hours; LB


title: ATCC25404 wild type LB 24hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 ATCC25404 wild type after 24 hours of growth in LB with glass wool

source_name: ATCC25404 wild type; 24 hours; LB


title: MG1655 wild type with R1drd19 M9C glu 24hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 MG1655 wild type with R1drd19 after 24 hours of growth in M9C glu with glass wool

source_name: MG1655 wild type with R1drd19; 24 hours; M9C glu


title: NCR7

city: Riverside

first: Stephen

middle: R.

last: Spindler

department: Biochemistry

institute: University of California, Riverside

description:
Normal female Ames mouse (+/+ or +/df)  with ad libitum access to water and fed 30% less of the standard pelleted diet with respect to the amount consumed by normal female ad libitum fed +/+ and +/df mice (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops.  Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted).
Keywords = Ames dwarf
Keywords = mouse
Keywords = Affymetrix
Keywords = caloric restriction

source_name: Phenotypically normal mouse (+/+ or +/df) fed 30% less of standard pelleted diet with respect to the amount consumed by normal female ad libitum fed +/+ and +/df mice


title: NCR8


title: BW25113 wild type LB 7h biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 BW25113 wild type after 7 hours of growth in LB with glass wool

source_name: BW25113 wild type; 7 hours; LB


title: 1398241080_A_10GyIR_BRCA1 P

description: classifications for mutations are described at www.kconfab.org/progress/classification.shtml

source_name: Lymphoblastoid Cell Line, 30 min post 10 Gy IR


title: Male wild type/Male HNF4alpha knockout comparison/Replicate #1


title: NCR6


title: Male wild type/Female wild type comparison/Replicate #1


title: NCR5


title: NCR4


title: NCR3


title: NCR2


title: Male wild type/Female wild type comparison/Replicate #3


title: NCR1


title: Azucena root tip_Before the wax layer_Rep2

city: Aberdeen

first: Gareth

last: Norton

address: St Machar drive

department: Plant and Soil Science

country: United Kingdom

institute: University of Aberdeen

description: Gene expression data from rice root tips (variety Azucena) which were above the 60% wax layer, rep2

hyb_protocol: Hybridisation, washing and staining procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.

scan_protocol: Scanning procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.

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

source_name: Azucena root tip_Before the wax layer

label_protocol: RNA was processed for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. Briefly, 5 ug of total RNA was used in the one-cycle cDNA synthesis reaction. After the generation of double stranded cDNA an in vitro transcription reaction was performed to generate biotinylated cRNA. (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Plants were grown in a controlled environment room with a 12 hour day and night, with a day temperature of 30oC and a night temperature of 24oC with 300 µmol m-2 s-1 PAR.

extract_protocol: A total of 100 mg of root tips (last 5 mm of the root) was harvested and RNA extracted using the TRIzol method (Invitrogen) followed by further purification and DNase treatment using the RNeasy clean up kit (Qiagen).

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. RNA was harvested from root tips which were 5-10 mm above the wax layer. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep2.


title: Azucena root tip_Buckled at the wax layer_rep3

description: Gene expression data from rice root tips (variety Azucena) which had buckled at a 60% wax layer, rep3

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. RNA was harvested from root tips whixh had buckled at the wax layer. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep3.


title: Azucena root tip_Before the wax layer_rep1

description: Gene expression data from rice root tips (variety Azucena) which were above the 60% wax layer, rep1

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. RNA was harvested from root tips which were 5-10 mm above the wax layer. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep1.


title: Bala root tip_At the wax layer_rep1

description: Gene expression data from rice root tips (variety Bala) in contact with a 60% wax layer, rep1

source_name: Bala root tip_At the wax layer

tag: Rice variety Bala, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep1.


title: Azucena root tip_Before the wax layer_Rep3

description: Gene expression data from rice root tips (variety Azucena) which were above the 60% wax layer, rep3

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. RNA was harvested from root tips which were 5-10 mm above the wax layer. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep3.


title: Bala root tip_At the wax layer_rep3

description: Gene expression data from rice root tips (variety Bala) in contact with a 60% wax layer, rep3

tag: Rice variety Bala 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep3.


title: Azucena root tip Buckled at the wax layer_rep2

description: Gene expression data from rice root tips (variety Azucena) which had buckled at a 60% wax layer, rep2

source_name: Azucena root tip Buclked at the wax layer

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. RNA was harvested from root tips whixh had buckled at the wax layer. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep2.


title: Azucena root tip_Buckled at the wax layer_rep1

description: Gene expression data from rice root tips (variety Azucena) in which had buckled at a 60% wax layer, rep1

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of root tips which had buckled after contact with the wax layer. Rep1.


title: Azucena root tip_At the wax layer_rep3

description: Gene expression data from rice root tips (variety Azucena) in contact with a 60% wax layer, rep3

source_name: Azucena root tip_At the wax layer

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep3.


title: Bala root tip_At the wax layer_rep2

description: Gene expression data from rice root tips (variety Bala) in contact with a 60% wax layer, rep2

tag: Rice variety Bala, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep2.


title: Azucena root tip_At the wax layer_rep1

description: Gene expression data from rice root tips (variety Azucena) in contact with a 60% wax layer, rep1

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep1.


title: Bovine adult versus prepubertal cumulus cells, Replicate 9

status: Public on Mar 18 2008

city: East Lansing

first: George

middle: W

last: Smith

state: MI

address: 1230 Anthony Hall

institute: Michigan State University

hyb_protocol: 100 ul of pre-warmed (70°C) hybridization buffer (Slidehybe 3, Ambion) was added to probe mixtures and final probe solutions applied to pre-warmed microarray slides. Hybridizations were conducted for 18 hours using step down temperatures from 65°C to 42°C in sealed chambers of a Gene Tac hybridization chamber (Genomic Solutions, Inc., Ann Arbor, MI, USA). Following hybridization, slides were washed 2X with medium stringency buffer, 1X with high stringency buffer (Genomic Solutions), rinsed briefly at room temperature in 2X saline sodium citrate and then water, and dried by centrifugation at 1000 RPM in a cushioned 50-ml conical centrifuge tube.

scan_protocol: Dried microarrays were scanned immediately using a GeneTac LS IV microarray scanner (Genomic Solutions). GeneTac Integrator 4.0 software was then used to process array images, align spots, integrate robot-spotting files with the microarray image, and to export reports of spot intensity data.

data_processing: For microarray experiments, estimates of FDR and differentially expressed genes (FDR = 5%) were identified using the significance analysis of microarrays program [34].  Differences in ratios of Cy3/Cy5 < 0.7 (P < 0.05; FDR = 5%) or Cy3/Cy5>1.3 (P < 0.05; FDR = 5%) were considered significant.  Initial annotation and gene symbols for features on the array were obtained using the Gene Links toolkit (http://cafg.msu.edu) and Unigene search function (http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene). Identification of biological themes (overrepresented genes) within lists of genes showing greater mRNA abundance in cumulus cells of prepubertal and adult oocytes was performed using expression analysis systematic explorer (EASE) [35] with a FDR of 10%.

organism: Bos taurus

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 9

label_protocol: A total of 15 µg amplified RNA from cumulus samples were used for cDNA synthesis and labeling [Patel et al., Vet Immunol Immunopathol 2005; 105: 331-342]. Amplified RNAs were used for cDNA synthesis and labeling using the Clontech PowerScript Fluorescent Labeling System (BD Biosciences, Alameda, CA, USA) with oligo (dT)18 as primer. Synthesis of cDNA in this system incorporates an amino-modified dUTP into the cDNA. Following first strand synthesis, cDNAs were labeled using n-hydroxysuccinate (NHS-) derivitized Cy3 and Cy5 dyes (Amersham Biosciences Corp., Little Chalfont, England). Labeled cDNAs were purified to remove unincorporated dyes, combined and concentrated to approximately 10 μl using Microcon 30 spin concentrators (Millipore Corp., Bedford, MA, USA).

growth_protocol: The cumulus-oocyte-complexes (COCs) were aspirated from all visible 3-7 mm follicles, selected (those with more than four compact layers of cumulus cells and homogenous cytoplasm), washed three to four times in Hepes-buffered hamster embryo culture (HH) medium and cumulus cells were completely separated by hyaluronidase (0.1%) digestion and repeated pipetting. The separated cumulus cells (four pools of cumulus cells from 18-20 oocytes each from adult and prepubertal animals) were snap frozen in 100 µl of lysis solution (RNAqueous Micro Kit, Ambion Inc., Austin, TX) and stored at -80 C until RNA isolation and subsequent microarray analysis.

extract_protocol:
Total RNA was extracted from each of the cumulus cell samples using the RNAqueous micro kit (Ambion) according to manufacturer’s instructions. RNA was eluted twice using 10 µl volume of prewarmed (75 C) elution solution according to manufacturer’s instructions. Residual genomic DNA in all extracted samples was removed by DNAse I digestion (Ambion). The RNA from each pool of cumulus samples was divided into two 10 µl aliquots.  One aliquot of extracted total RNA was used for cDNA microarray analysis.
Total RNA (10 µl) from pools of cumulus cells (n = 4) was amplified using the RiboAmp Kit (Arcturus, Mountain View, CA) using previously validated procedures [Patel et al., Vet Immunol Immunopathol 2005; 105: 331-342]. The quality and quantity of the amplified RNA generated were estimated using a u.v. spectrophotometer (Beckman Instruments, Fullerton, CA) and the Bioanalyzer 2100 RNA 6000 nanochip (Agilent Technologies, Walbronn, Germany).  Only those amplification reactions yielding amplified RNA of consistent size range and quality across samples were utilized in subsequent microarray experiments.

tag: Cumulus cells surrounding prepubertal oocytes

source_name: Bovine cumulus cells surrounding adult oocytes, 9

tag: Cumulus cells surrounding adult oocytes


title: Bovine adult versus prepubertal cumulus cells, Replicate 7

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 7

source_name: Bovine cumulus cells surrounding adult oocytes, 7


title: Bovine adult versus prepubertal cumulus cells, Replicate 4

source_name: Bovine cumulus cells surrounding adult oocytes, 4

label_protocol: A total of 15 µg amplified RNA from cumulus samples were used for cDNA synthesis and labeling [Patel et al., Vet Immunol Immunopathol 2005; 105: 331-342]. Amplified RNAs were used for cDNA synthesis and labeling using the Clontech PowerScript Fluorescent Labeling System (BD Biosciences, Alameda, CA, USA) with oligo (dT)18 as primer. Synthesis of cDNA in this system incorporates an amino-modified dUTP into the cDNA. Following first strand synthesis, cDNAs were labeled using n-hydroxysuccinate (NHS-) derivitized Cy3 and Cy5 dyes (Amersham Biosciences Corp., Little Chalfont, England). Labeled cDNAs were purified to remove unincorporated dyes, combined and concentrated to approximately 10 μl using Microcon 30 spin concentrators (Millipore Corp., Bedford,  MA, USA).

extract_protocol:
Total RNA was extracted from each of the cumulus cell samples using the RNAqueous micro kit (Ambion) according to manufacturer’s instructions.  RNA was eluted twice using 10 µl volume of prewarmed (75 C) elution solution according to manufacturer’s instructions.  Residual genomic DNA in all extracted samples was removed by DNAse I digestion (Ambion).  The RNA from each pool of cumulus samples was divided into two 10 µl aliquots.  One aliquot of extracted total RNA was used for cDNA microarray analysis.
Total RNA (10 µl) from pools of cumulus cells (n = 4) was amplified using the RiboAmp Kit (Arcturus, Mountain View, CA) using previously validated procedures [Patel et al.,  Vet Immunol Immunopathol 2005; 105: 331-342].  The quality and quantity of the amplified RNA generated were estimated using a u.v. spectrophotometer (Beckman Instruments, Fullerton, CA) and the Bioanalyzer 2100 RNA 6000 nanochip (Agilent Technologies, Walbronn, Germany).  Only those amplification reactions yielding amplified RNA of consistent size range and quality across samples were utilized in subsequent microarray experiments.

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 4


title: Bovine adult versus prepubertal cumulus cells, Replicate 6

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 6

source_name: Bovine cumulus cells surrounding adult oocytes, 6


title: IGF_2

city: London

first: Pedro

last: Echave

address: Gower Street

department: MRC LMCB

institute: University College London

description: IGF

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix CEL files were processed using RMA

source_name: Primary Rat Schwann cells

label_protocol: Standard Affymetrix protocol

extract_protocol: QIagen RNeasy plus

value: sciatic nerve


title: Azucena root tip_At the wax layer_rep2

description: Gene expression data from rice root tips (variety Azucena) in contact with a 60% wax layer, rep2

tag: Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep2.


title: NRG_3

description: NRG

tag: Tissue


title: IGF_3

description: IGF


title: Bovine adult versus prepubertal cumulus cells, Replicate 8

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 8

source_name: Bovine cumulus cells surrounding adult oocytes, 8


title: Bovine adult versus prepubertal cumulus cells, Replicate 1

source_name: Bovine cumulus cells surrounding adult oocytes, 1

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 1


title: NRG_2

description: NRG


title: IGF_1

description: IGF


title: Control_1

description: Control


title: NRG_1

description: NRG


title: Bovine adult versus prepubertal cumulus cells, Replicate 2

source_name: Bovine cumulus cells surrounding adult oocytes, 2

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 2


title: Control_2

description: Control


title: NRG+IGF_1

description: NRG+IGF


title: NRG+IGF_2

description: NRG+IGF


title: Bovine adult versus prepubertal cumulus cells, Replicate 3

source_name: Bovine cumulus cells surrounding adult oocytes, 3

source_name: Bovine cumulus cells surrounding prepubertal oocytes, 3


title: Control_3

description: Control


title: Amniocytes_euploid_1569

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

institute: National Taiwan University

hyb_protocol: Cy-labeled cRNA (2 ug) was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA was then pooled and hybridized to a Human 1A (version 2) oligo microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying under a nitrogen gun blowing, the microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. The scanned images were analyzed by Feature Extraction software (Agilent Technologies, USA), image analysis and normalization software was used to quantify the signal and background intensities for each feature.

data_processing: The data were substantially normalized by the rank-consistency-filtering LOWESS method. Finally, the data were presented as log2.

source_name: amniocytes, euploid, 1569

label_protocol: Total RNA (0.5 ug) was amplified by a low RNA input fluor linear amp kit (Agilent Technologies, USA) and labeled at Cy5 (CyDye, PerkinElmer, USA) during in vitro transcription.

growth_protocol: Primary cultures of amniocytes were collected from fetuses between 16-22 weeks of pregnancy, following routine diagnostic cytogenetic analysis of singleton pregnancies. The cells were grown in a commercial medium optimized for amniocyte culture at 37˚C in 5% CO2. Only culture flasks showing normal cell morphology were used for RNA extraction. Informed consent was given by the parents and the study design was approved by the research and ethics committee of the hospital.

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), followed by use of an RNeasy Mini Kit (Qiagen, Germany). The purified RNA was quantified by OD260nm using by a ND-1000 spectrophotometer (Nanodrop Technology, USA) and its quality was assessed by a Bioanalyzer 2100 (Agilent Technology, USA).

source_name: Human reference RNA pooled from 10 cell lines

label_protocol: To serve as reference for microarray comparison, a human reference RNA pooled from 10 cell lines (Stratagene, USA) was used. Total RNA (0.5 ug) was amplified by a low RNA input fluor linear amp kit (Agilent Technologies, USA) and labeled at Cy3 (CyDye, PerkinElmer, USA) during in vitro transcription.

tag: Stratagene® QPCR Human Reference Total RNA Cell Line Derivations

tag: Adenocarcinoma, mammary gland

tag: Hepatoblastoma, liver

tag: Adenocarcinoma, cervix

tag: Embryonal carcinoma, testis

tag: Glioblastoma, brain

tag: Melanoma, skin

tag: Liposarcoma

tag: Histiocytic lymphoma; macrophage; histocyte

tag: Lymphoblastic leukemia, T lymphoblast

tag: Plasmacytoma; myeloma; B lymphocyte


title: Amniocytes_euploid_1567

source_name: Amniocytes, euploid, 1567


title: Amniocytes_euploid_1565

source_name: amniocytes, euploid, 1565


title: NRG+IGF_3

description: NRG+IGF


title: Amniocytes_trisomy 21_1575

description: Amniocytes_trisomy 21_1575

source_name: Amniocytes, trisomy 21, 1575


title: Amniocytes_euploid_1563

source_name: Amniocytes, euploid, 1563


title: Amniocytes_euploid_1561

source_name: Amniocytes, euploid, 1561


title: Amniocytes_trisomy 21_1573

description: Amniocytes_trisomy 21_1573

source_name: Amniocytes, trisomy 21, 1573


title: Amniocytes_Euploid_1559

source_name: Amniocytes, euploid, 1559


title: Amniocytes_trisomy 21_1551

description: Amniocytes_trisomy 21_1551

source_name: Amniocytes, trisomy 21, 1551


title: Snf2 IP after heat shock vs Input DNA set5

status: Public on Mar 17 2008

type: genomic

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: Genome-wide targets of Snf2 after heat shock

hyb_protocol: The Cy3 and Cy5 labeled DNA were combined,5 ?g of tRNA, 10 ?g of polyA were added, 20x SSC was added to a final concentration of 3.5x and SDS was added to a final concentration of 0.25%. The mixture was denatured at 100°C for 2 min, cooled down to room temperature and hybridized onto microarrays for 6 hrs to over night at 65°C. Arrays were washed once each in wash solution I (0.57x SSC, 0.028% SDS) and wash solution II (0.057X SSC), dried by centrifuging at 600 rpm for 5 min at room temperature in a table top centrifuge.

scan_protocol: The arrays were scanned with the Axon 4000B scanner (Axon Instruments) and quantitated using GenePix Pro 5.1 software. The data was uploaded into Acuity microarray informatics software 4.037 (Axon Laboratory), and filtered to remove spots with bad signal intensity and passed though other quality control thresholds.

data_processing: normalized log2 ratio

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Snf-Myc IP using anti Myc tag antibody

label_protocol: Cy5 fluorophores were incorporated according to published protocol (Iyer 2003 In DNA microarrays: a molecular cloning manual (ed. D.B.a.J. Sambrook), pp. 453–463. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.)

extract_protocol: Cells are cross-linked in vivo using 1% formaldehyde and chromatin is sheared to less than 1 kb fragments using a sonicator. Specific protein-dna complexes are pulled down using a specific antibody. After adequate washing, the protein-dna complexes are eluted, reverse cross-linked and the DNA purified by phenol-chloroform extraction.

tag: mid-log growth, heat shock at 39 degree C for 15 min

source_name: Input DNA from Myc tagged Snf2 cells

label_protocol: Cy3 fluorophores were incorporated according to published protocol (Iyer 2003 In DNA microarrays: a molecular cloning manual (ed. D.B.a.J. Sambrook), pp. 453–463. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.)

extract_protocol: Genomic DNA was extracted by lysis of cells, phenol extraction, precipitation of DNA and sonication to less than 1 kb using a sonicator


title: Snf2 IP 30 degree C vs Input DNA set3

description: Genome-wide targets of Snf2 at 30 degree C

tag: mid-log growth

tag: mid-log growth at 30 degree C


title: Snf2 IP 30 degree C vs Input DNA set1


title: Amniocytes_trisomy 21_1549

description: Amniocytes_trisomy 21_1549

source_name: Amniocytes, trisomy 21, 1549


title: Snf2 IP 30 degree C vs Input DNA set2


title: Snf2 IP after heat shock vs Input DNA set3


title: Snf2 IP after heat shock vs Input DNA set1


title: Snf2 IP after heat shock vs Input DNA set2


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T900 vs Genomic DNA set3

description: Time course analysis of Acetyl H4 occupancy change after heat shock

source_name: Acetyl H4 IP from snf2 deletion cells at T900

source_name: Genomic DNA from snf2 deletion unstressed cells


title: Snf2 IP after heat shock vs Input DNA set4


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T300 vs Genomic DNA set3

source_name: Acetyl H4 IP from snf2 deletion cells at T300


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T30 vs Genomic DNA set3

source_name: Acetyl H4 IP from snf2 deletion cells at T30


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T60 vs Genomic DNA set3

source_name: Acetyl H4 IP from snf2 deletion cells at T60


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T5 vs Genomic DNA set3

source_name: Acetyl H4 IP from snf2 deletion cells at T5


title: Time course analysis Acetyl H4 occupancy WT cells T900 vs Genomic DNA set3

source_name: Acetyl H4 IP from WT cells at T900

source_name: Genomic DNA from WT unstressed cells


title: Time course analysis Acetyl H4 occupancy WT cells T5 vs Genomic DNA set3

source_name: Acetyl H4 IP from WT cells at T5


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T15 vs Genomic DNA set3

source_name: Acetyl H4 IP from snf2 deletion cells at T15


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T900 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy WT cells T0 vs Genomic DNA set3

source_name: Acetyl H4 IP from WT cells at T0


title: Time course analysis Acetyl H4 occupancy WT cells T15 vs Genomic DNA set3

source_name: Acetyl H4 IP from WT cells at T15


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T15 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy WT cells T60 vs Genomic DNA set3

source_name: Acetyl H4 IP from WT cells at T60


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T0 vs Genomic DNA set3

source_name: Acetyl H4 IP from snf2 deletion cells at T0


title: Time course analysis Acetyl H4 occupancy WT cells T300 vs Genomic DNA set3

source_name: Acetyl H4 IP from WT cells at T300


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T300 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy WT cells T30 vs Genomic DNA set3

source_name: Acetyl H4 IP from WT cells at T30


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T60 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T5 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T0 vs Genomic DNA set2


title: 1412091137_A_10GyIR_BRCA1 P

source_name: Lymphoblastoid Cell Line, 30 min post 10 Gy IR

tag: Gender

tag: AGE


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T30 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy WT cells T60 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T60 vs Genomic DNA set1


title: Time course analysis Acetyl H4 occupancy WT cells T30 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy WT cells T15 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy WT cells T5 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy WT cells T300 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T5 vs Genomic DNA set1


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T300 vs Genomic DNA set1


title: Time course analysis Acetyl H4 occupancy WT cells T900 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T30 vs Genomic DNA set1


title: Time course analysis Acetyl H4 occupancy WT cells T0 vs Genomic DNA set2


title: Time course analysis Acetyl H4 occupancy snf2 deletion cells T15 vs Genomic DNA set1


title: Time course analysis Acetyl H4 occupancy WT cells T900 vs Genomic DNA set1


title: Time course analysis total H4 occupancy snf2 deletion cells T300 vs Genomic DNA set3

description: Time course analysis of H4 occupancy change after heat shock

source_name: Total H4 IP from snf2 deletion cells at T300


title: Time course analysis Acetyl H4 occupancy WT cells T300 vs Genomic DNA set1


title: Time course analysis Acetyl H4 occupancy WT cells T15 vs Genomic DNA set1


title: Time course analysis total H4 occupancy snf2 deletion cells T60 vs Genomic DNA set3

source_name: Total H4 IP from snf2 deletion cells at T60


title: Time course analysis total H4 occupancy snf2 deletion cells T30 vs Genomic DNA set3

source_name: Total H4 IP from snf2 deletion cells at T30


title: Time course analysis Acetyl H4 occupancy WT cells T30 vs Genomic DNA set1


title: Time course analysis total H4 occupancy WT cells T30 vs Genomic DNA set3

source_name: Total H4 IP from WT cells at T30

tag: mid-log growth, heat shock at 39 degree C


title: Time course analysis total H4 occupancy snf2 deletion cells T0 vs Genomic DNA set3

source_name: Total H4 IP from snf2 deletion cells at T0


title: Time course analysis total H4 occupancy snf2 deletion cells T5 vs Genomic DNA set3

source_name: Total H4 IP from snf2 deletion cells at T5


title: BL30 vs BL30 (B95-8) – RNA pair 2 (Dye Swap)

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description: No additional description

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray  processing protocol using the Agilent Gene Expression Hybridization Kit  (Agilent  Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA  were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome  Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated  0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing  step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using  Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the  microarray image files. The software determines feature intensities and ratios (including  background subtraction and normalization), rejects outliers and calculates statistical  confidences (p-values). For determination of differential gene expression FES derived output  data files were further analyzed using the Rosetta Resolver  gene expression data analysis  system (Rosetta Biosoftware).

source_name: Epstein Barr virus infected Burkitt’s lymphoma cell line, BL30 (B95-8)

label_protocol: Standard Agilent labeling protocol

extract_protocol: Qiagen total RNA purification kit – Standard conditions

tag: BL30 (B95-8) RNA prep 2

source_name: Epstein Barr virus negative Burkitt's lymphoma cell line, BL30

tag: BL30 – RNA prep 2


title: BL30 vs BL30 (B95-8) – RNA pair 1 (Dye Swap)

description: No additional description

tag: BL30 (B95-8) RNA prep 1

tag: BL30 – RNA prep 1


title: Time course analysis Acetyl H4 occupancy WT cells T60 vs Genomic DNA set1

source_name: Genomic DNA from WT unstressed cells


title: Time course analysis total H4 occupancy WT cells T900 vs Genomic DNA set3

source_name: Total H4 IP from WT cells at T900


title: Time course analysis total H4 occupancy snf2 deletion cells T15 vs Genomic DNA set3

source_name: Total H4 IP from snf2 deletion cells at T15


title: BL30 vs BL30 (B95-8) – RNA pair 2 – Repeat (Dye Swap)

description: No additional description


title: Akata miR-155 vs Akata cntl Infection pair 1

description: No additional description

source_name: Epstein Barr virus positive Burkitt’s Lymphoma cell line transduced with control retrovirus, pEhyg

tag: Akata – pEhyg A1 – Infection 1

source_name: Epstein Barr virus positive Burkitt’s Lymphoma cell line transduced with miR-155 retrovirus, pEhyg-miR-155

tag: Akata – pEhyg-miR-155 A1 – Infection 1


title: Time course analysis total H4 occupancy WT cells T5 vs Genomic DNA set3

source_name: Total H4 IP from WT cells at T5


title: Time course analysis total H4 occupancy WT cells T300 vs Genomic DNA set3

source_name: Total H4 IP from WT cells at T300


title: BL30 (B95-8) vs BL30 – RNA pair 1

description: No additional description


title: Time course analysis Acetyl H4 occupancy WT cells T5 vs Genomic DNA set1

source_name: Acetyl H4 IP from WT cells at T5


title: Time course analysis total H4 occupancy WT cells T15 vs Genomic DNA set3

source_name: Total H4 IP from WT cells at T15


title: BL30 vs BL30 (B95-8) – RNA pair 1 – Repeat (Dye Swap)

description: No additional description


title: Time course analysis total H4 occupancy snf2 deletion cells T300 vs Genomic DNA set2

source_name: Total H4 IP from snf2 deletion cells at T300


title: Akata miR-155 vs Akata cntl Infection pair 2

description: No additional description

tag: Akata – pEhyg A1 – Infection 2

tag: Akata – pEhyg-miR-155 A1 – Infection 2


title: Time course analysis total H4 occupancy snf2 deletion cells T900 vs Genomic DNA set2-b

source_name: Total H4 IP from snf2 deletion cells at T900


title: Time course analysis total H4 occupancy snf2 deletion cells T60 vs Genomic DNA set2

source_name: Total H4 IP from snf2 deletion cells at T60


title: Time course analysis total H4 occupancy WT cells T0 vs Genomic DNA  set3

source_name: Total H4 IP from WT cells at T0


title: Time course analysis total H4 occupancy WT cells T60 vs Genomic DNA set2

source_name: Total H4 IP from WT cells at T60


title: Time course analysis total H4 occupancy WT cells T300 vs Genomic DNA set2


title: Time course analysis total H4 occupancy WT cells T900 vs Genomic DNA set2


title: Time course analysis total H4 occupancy snf2 deletion cells T30 vs Genomic DNA set2

source_name: Total H4 IP from snf2 deletion cells at T30


title: Time course analysis total H4 occupancy snf2 deletion cells T0 vs Genomic DNA set2

source_name: Total H4 IP from snf2 deletion cells at T0


title: Time course analysis total H4 occupancy snf2 deletion cells T15 vs Genomic DNA set2


title: Time course analysis total H4 occupancy WT cells T30 vs Genomic DNA set2

source_name: Total H4 IP from WT cells at T30


title: BL30 (B95-8) vs BL30 – RNA pair 2

description: No additional description

source_name: Epstein Barr virus negative Burkitt's lymphoma cell line, BL30

source_name: Epstein Barr virus infected Burkitt’s lymphoma cell line, BL30(B95-8)


title: Time course analysis total H4 occupancy snf2 deletion cells T5 vs Genomic DNA set2

source_name: Total H4 IP from snf2 deletion cells at T5

source_name: Genomic DNA from WT unstressed cells


title: Time course analysis total H4 occupancy WT cells T60 vs Genomic DNA set3


title: Akata cntl vs miR-155 Infection pair 1 (Dye Swap)

description: No additional description

source_name: Epstein Barr virus positive Burkitt’s Lymphoma cell line transduced with miR-155 retrovirus, pEhyg-miR-155

source_name: Epstein Barr virus positive Burkitt’s Lymphoma cell line transduced with control retrovirus, pEhyg


title: Time course analysis total H4 occupancy WT cells T5 vs Genomic DNA set2

source_name: Total H4 IP from WT cells at T5


title: Time course analysis total H4 occupancy snf2 deletion cells T900 vs Genomic DNA set1


title: Time course analysis total H4 occupancy WT cells T15 vs Genomic DNA set2


title: Time course analysis total H4 occupancy WT cells T60 vs Genomic DNA set1


title: Time course analysis total H4 occupancy WT cells T300 vs Genomic DNA set1

source_name: Total H4 IP from WT cells at T300


title: Time course analysis total H4 occupancy WT cells T0 vs Genomic DNA set2


title: Time course analysis total H4 occupancy snf2 deletion cells T900 vs Genomic DNA set3


title: Time course analysis total H4 occupancy WT cells T900 vs Genomic DNA set1

source_name: Total H4 IP from WT cells at T900


title: BL30 (B95-8) vs BL30 – RNA pair 1 – Repeat

description: No additional description

tag: BL30 – RNA prep 1 - Repeat

source_name: Epstein Barr virus infected Burkitt’s lymphoma cell line, BL30 (B95-8)

tag: BL30 (B95-8) RNA prep 1 - Repeat


title: Time course analysis total H4 occupancy snf2 deletion cells T5 vs Genomic DNA set1


title: Time course analysis total H4 occupancy WT cells T15 vs Genomic DNA set1

source_name: Total H4 IP from WT cells at T15


title: Time course analysis total H4 occupancy snf2 deletion cells T15 vs Genomic DNA set1

source_name: Total H4 IP from snf2 deletion cells at T15


title: Time course expression snf2 deletion T30 vs control

description: Time course expression profile after heat shock

molecule: polyA RNA

source_name: Poly A RNA purified from snf2 deletion cells 30s after heat shock

extract_protocol: Cells from a 50 ml culture were re-suspended in 8 ml of AE buffer (50mM Sodium Acetate pH5.2, 10mM EDTA, 1.7% SDS) and total RNA was extracted using acid phenol lysis protocol described previously (Spellman et al. 1998). Poly (A) RNA was purified by allowing the mRNA to bind to oligo-dT cellulose for 90 min in the presence of 500mM NaCl. The oligo-dT cellulose was washed three times with 10mM Tris-Cl pH 7.5, 500mM NaCl, two times with 10mM Tris-Cl pH 7.5, 250mM NaCl and eluted in 10mM Tris-Cl pH7.5 pre-warmed to 65oC.

source_name: Control RNA from WT unstressed cells


title: Time course analysis total H4 occupancy WT cells T30 vs Genomic DNA set1


title: Time course analysis total H4 occupancy snf2 deletion cells T30 vs Genomic DNA set1

source_name: Total H4 IP from snf2 deletion cells at T30


title: Time course expression snf2 deletion T0 vs control set2

source_name: Poly A RNA purified from snf2 deletion cells before heat shock


title: Time course expression snf2 deletion T0 vs control set1


title: Time course analysis total H4 occupancy WT cells T5 vs Genomic DNA set1


title: Time course expression WT T900 vs control set2

source_name: Poly A RNA purified from WT cells 900s after heat shock


title: Time course expression snf2 deletion T900 vs control

source_name: Poly A RNA purified from snf2 deletion cells 900s after heat shock


title: Time course expression snf2 deletion T300 vs control

source_name: Poly A RNA purified from snf2 deletion cells 300s after heat shock


title: Time course analysis total H4 occupancy snf2 deletion cells T300 vs Genomic DNA set1

source_name: Total H4 IP from snf2 deletion cells at T300


title: Time course expression snf2 deletion T60 vs control

source_name: Poly A RNA purified from snf2 deletion cells 60s after heat shock


title: Time course expression WT T300 vs control

source_name: Poly A RNA purified from WT cells 300s after heat shock


title: Time course expression WT T60 vs control

source_name: Poly A RNA purified from WT cells 60s after heat shock


title: Time course expression WT T0 vs control set1

source_name: Poly A RNA purified from WT cells before heat shock


title: Akata cntl vs miR-155 Infection pair 2 (Dye Swap)

description: No additional description

source_name: Epstein Barr virus positive Burkitt’s Lymphoma cell line transduced with miR-155 retrovirus, pEhyg-miR-155

source_name: Epstein Barr virus positive Burkitt’s Lymphoma cell line transduced with control retrovirus, pEhyg


title: Time course expression WT T0 vs control set2


title: YBR245C deletion 39 degree C vs 30 degree C

description: YBR245C deletion cell expression profile at 39 degree C

source_name: Total RNA extracted from YBR245C deletion cells after heat shock at 39 degree C

extract_protocol: Cells from a 50 ml culture were re-suspended in 8 ml of AE buffer (50mM Sodium Acetate pH5.2, 10mM EDTA, 1.7% SDS) and total RNA was extracted using acid phenol lysis protocol described previously (Spellman et al. 1998).

source_name: Total RNA extracted from YBR245C deletion cells grown to mid-log phase at 30 degree C


title: YBR245C deletion 39 degree C

description: YBR245C deletion strain expression profile at 39 degree C

source_name: Total RNA extracted from YBR245C deletion after heat shock at 39 degree C

source_name: Total RNA extracted from WT after heat shock at 39 degree C


title: YER164W deletion 39 degree C vs 30 degree C

description: YER164W deletion cell expression profile at 39 degree C

source_name: Total RNA extracted from YER164W deletion cells after heat shock at 39 degree C

source_name: Total RNA extracted from YER164W deletion cells grown to mid-log phase at 30 degree C


title: BL30 (B95-8) vs BL30 – RNA pair 2 – Repeat

description: No additional description

source_name: Epstein Barr virus negative Burkitt's lymphoma cell line, BL30

tag: BL30 – RNA prep 2 - Repeat

source_name: Epstein Barr virus infected Burkitt’s lymphoma cell line, BL30 (B95-8)

tag: BL30 (B95-8) RNA prep 2 - Repeat


title: YOR304W deletion 39 degree C vs 30 degree C

description: YOR304W deletion cell expression profile at 39 degree C

source_name: Total RNA extracted from YOR304W deletion cells after heat shock at 39 degree C

source_name: Total RNA extracted from YOR304W deletion cells grown to mid-log phase at 30 degree C


title: YOR290C deletion 39 degree C vs 30 degree C

description: YOR290C deletion cell expression profile at 39 degree C

source_name: Total RNA extracted from YOR290C deletion cells after heat shock at 39 degree C

source_name: Total RNA extracted from YOR290C deletion cells grown to mid-log phase at 30 degree C


title: Time course expression WT T900 vs control set1

source_name: Poly A RNA purified from WT cells 900s after heat shock

source_name: Control RNA from WT unstressed cells


title: YOR304W deletion 39 degree C

description: YOR304W deletion strain expression profile at 39 degree C

source_name: Total RNA extracted from YOR304W deletion after heat shock at 39 degree C


title: Time course expression WT T30 vs control

source_name: Poly A RNA purified from WT cells 30s after heat shock


title: YOR290C deletion

description: YOR290C deletion strain expression profile at 30 degree C

source_name: Total RNA extracted from YOR290C deletion mid-log growth

source_name: Total RNA extracted from WT mid-log growth


title: YOR304W deletion

description: YOR304W deletion strain expression profile at 30 degree C

source_name: Total RNA extracted from YOR304W deletion mid-log growth


title: YOR290C deletion 39 degree C

description: YOR290C deletion strain expression profile at 39 degree C

source_name: Total RNA extracted from YOR290C deletion after heat shock at 39 degree C


title: YBR245C deletion

description: YBR245C deletion strain expression profile at 30 degree C

source_name: Total RNA extracted from YBR245C deletion mid-log growth


title: YER164W deletion 39 degree C

description: YER164W deletion strain expression profile at 39 degree C

source_name: Total RNA extracted from YER164W deletion after heat shock at 39 degree C

source_name: Total RNA extracted from WT after heat shock at 39 degree C


title: YER164W deletion

description: YER164W deletion strain expression profile at 30 degree C

source_name: Total RNA extracted from YER164W deletion mid-log growth


title: Expression Stationary vs log cells set3

description: expression profile of cells after stationary phase stress

source_name: Total RNA extracted from stationary phase cells

tag: grown to stationary phase at 30 degree C

source_name: Total RNA extracted from log phase cells


title: WT 39 degree C vs 30 degree C

description: WT cell expression profile at 39 degree C

source_name: Total RNA extracted from WT grown to mid-log phase at 30 degree C

tag: mid-log growth at 30 degree C


title: Acetyl H4 IP Stationary phase cells vs Acetyl H4 IP Log phase cells set3

description: Immnoprecipitation of Acetyl H4 using anti Myc tag antibody

source_name: Acetyl H4 IP from Stationary phase cells

tag: grown to OD 5.0 at 30 degree C

source_name: Acetyl H4 IP from Log phase cells


title: Expression Stationary vs log cells set2


title: Total H4 IP Stationary phase cells vs Total H4 IP Log phase cells set2

description: Immnoprecipitation of Total H4 using anti Myc tag antibody

source_name: Total H4 IP from Stationary phase cells

source_name: Total H4 IP from Log phase cells


title: Total H4 IP Stationary phase cells vs Total H4 IP Log phase cells set1


title: Acetyl H4 IP Stationary phase vs Total H4 IP Stationary phase set2

description: Immnoprecipitation of Acetyl H4 using anti Acetyl H4 antibody


title: Acetyl H4 IP Stationary phase cells vs Acetyl H4 IP Log phase cells set1


title: Total H4 IP Stationary phase cells vs Total H4 IP Log phase cells set3


title: Expression Stationary vs log cells set1


title: Acetyl H4 IP Log phase vs Total H4 IP Log phase set2


title: Acetyl H4 IP Stationary phase vs Genomic set2

data_processing: normalized Log2 ratio

tag: Growth to Stationary phase at 30C

source_name: Sonicated Genomic DNA

tag: Sonicated genomic DNA


title: Acetyl H4 IP Stationary phase vs Genomic set1


title: Acetyl H4 IP Stationary phase vs Total H4 IP Stationary phase set1


title: Acetyl H4 IP Log phase vs Total H4 IP Log phase set3


title: Acetyl H4 IP log phase vs Genomic set3

source_name: Acetyl H4 IP from log phase cells

tag: mid-log growth at 30C


title: Acetyl H4 IP log phase vs Genomic set2


title: Total H4 IP Stationary phase vs Genomic set2


title: Acetyl H4 IP Stationary phase cells vs Acetyl H4 IP Log phase cells set2


title: Acetyl H4 IP Stationary phase vs Genomic set3


title: Total H4 IP Stationary phase vs Genomic set1


title: Acetyl H4 IP Stationary phase vs Total H4 IP Stationary phase set3


title: Total H4 IP log phase vs Genomic set1

source_name: Total H4 IP from log phase cells

tag: mid-log growth at log phase


title: Acetyl H4 IP log phase vs Genomic set1


title: Total H4 IP log phase vs Genomic set2


title: Total H4 IP Stationary phase vs Genomic set3


title: Expression heat shock vs unsressed cells set3

description: expression profile of cells after heat shock stress

source_name: Total RNA extracted from heat shocked cells

tag: mid-log growth at 30 degree C, heat shock at 39C for 15 min

source_name: Total RNA extracted from unstressed cells


title: Expression heat shock vs unsressed cells set2


title: Expression heat shock vs unsressed cells set1


title: Acetyl H4 IP Log phase vs Total H4 IP Log phase set1


title: Total H4 IP log phase vs Genomic set3


title: Time course analysis total H4 occupancy snf2 deletion cells T900 vs Genomic DNA set2-a

description: Time course analysis of H4 occupancy change after heat shock

source_name: Total H4 IP from snf2 deletion cells at T900

tag: mid-log growth

source_name: Genomic DNA from WT unstressed cells


title: Acetyl H4 IP 30C vs Total H4 IP 30C set2

source_name: Acetyl H4 IP from unstressed cells

source_name: Total H4 IP from unstressed cells


title: Acetyl H4 IP 30C vs Genomic set3


title: Total H4 IP 30C vs Genomic set1


title: Acetyl H4 IP 30C vs Total H4 IP 30C set1


title: Acetyl H4 IP 39C vs Genomic set3

source_name: Acetyl H4 IP from Heat shocked cells


title: Acetyl H4 IP 30C vs Genomic set1


title: Total H4 IP 30C vs Genomic set2


title: Acetyl H4 IP 39C vs Total H4 IP 39C set3

source_name: Acetyl H4 IP from heat shocked cells

source_name: Total H4 IP from heat shocked cells

tag: mid-log growth at 30 degree C followed by heat shock for 15 min at 39C


title: Total H4 IP 39C vs Genomic set2

tag: mid-log growth, heat shock for 15 min at 39 degree C


title: Acetyl H4 IP 39C vs Total H4 IP 39C set1


title: Acetyl H4 IP 39C vs Total H4 IP 39C set2


title: Total H4 IP 30C vs Genomic set3


title: Total H4 IP 39C vs Genomic set3


title: Acetyl H4 IP 30C vs Genomic set2


title: H4 IP 39 vs 30 set3

description: Immnoprecipitation of H4-Myc using anti Myc antibody

source_name: H4 IP from heat shock cells

source_name: H4 IP from unstressed cells


title: Acetyl H4 IP 39C vs Genomic set1


title: Acetyl H4 IP 39 vs 30 set1

source_name: Acetyl H4 IP from heat shock cells


title: Acetyl H4 IP 39C vs Genomic set2


title: H4 IP 39 vs 30 set1


title: Acetyl H4 IP 30C vs Total H4 IP 30C set3


title: Acetyl H4 IP 39 vs 30 set3


title: Total H4 IP 39C vs Genomic set1


title: H4 IP 39 vs 30 set2