title: Chip 12719802 Non-transgenic 6hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 6 hours after excision from a non-transgenic donor plant.


title: Day 7 Chick Breast Muscle- Replicate #1

status: Public on Mar 27 2009

type: RNA

city: Beltsville

first: Mark

middle: P

last: Richards

state: MD

address: 10300 Baltimore Avenue

department: ANRI

country: USA

institute: USDA, ARS

description: Gene expression data for breast muscle from 7 day-old broiler chicken.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 42C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 using the EukGE-WS2v5_450 script.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner using factory set PMT settings.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to the default value of 500.

label: biotin

molecule: total RNA

organism: Gallus gallus

source_name: 7 day-old Chick

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Broiler chicken eggs were hatched and chicks were sampled immediately after emergence from the egg (day 0) and at 7 days post-hatch.

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

treatment_protocol: Samples of liver, duodenum, breast muscle and whole brain were collected on days 0 and 7 post-hatch, snap frozen in liquid nitrogen and stored at -80C prior to isolation of total RNA.

tag: tissue

value: Breast Muscle

tag: genotype

value: Ross broiler chicken

tag: gender

value: male

tag: age

value: 7 day-old


title: Chip 12715202 Non-transgenic 0hr

city: Gainesville

first: Christopher

last: Dervinis

state: FL

address: 2033 Mowry Road, rm 320

department: SFRC

institute: University of Florida

description: Populus tremula x Populus alba INRA-clone No. 717-1-B4 plants expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ΔDDKPtRR13)were generated via an Agrobacterium-mediated protocol developed by Han et al. (2000). Non-transgenic and ΔDDKPtRR13 line were grown to a height of 60 cm. A 14 cm tall apical cuttings were collected from the mother plants. Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation. Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting).

hyb_protocol: 1.5ug labeled ds-cDNA was denatured at 95C for 5min and hybridized to custom in situ synthesized oligonucleotide microarrays (produced by NimbleGen, Madison, WI) at 42C overnight (16-20h). Hybridization and wash buffers are described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf)

scan_protocol: As described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf).

data_processing: Raw intensity data was background corrected (Irizarry et al. 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264) and normalized using the Quantile normalization method (Bolstad et al. 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193).

organism: Populus tremula x Populus alba

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 0 hours after excision from a non-transgenic donor plant.

label_protocol: RNA extracted from each progeny was converted to double-stranded (ds-) cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturerÆs protocol, except that synthesis of first and second strands were extended to 16h. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37C

growth_protocol: Experiments were conducted in a greenhouse at ambient temperature between the months of September and December in Gainesville, Florida. Populus balsamifera ssp. trichocarpa (Torr. and Gray) genotype Nisqually-1 and Populus tremula x Populus alba INRA-clone No. 717-1-B4 plants were given 12-14 hours of natural light, supplemented in the winter with artificial illumination to maintain indeterminate growth. Plants were grown in 11.4 liter pots on flood benches subirrigated once daily with a nutrient solution containing Peters Professional Blend 20-10-20 fertilizer solution (adjusted to 4 mM nitrogen). When plants reached 60-80 cm tall, single cuttings per plant were collected, planted in 25 cm2 pots containing Fafard #4 mix and placed under mist until harvested.

extract_protocol: Total RNA was isolated using a cetyltrimethylammonium bromide (CTAB) method (Chang S, J. Puryear, J. Cairney 1993, A simple and efficent method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116). RNA samples were subjected to DNase treatment with RQ1 RNase-free DNase (Promega, Madison, WI, USA) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA)

treatment_protocol: For these analyses, 14 cm tall apical cuttings were collected from 60cm tall mother plants (from non-transgenic and ΔDDKPtRR13). Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation. Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting).

tag: isolate

value: INRA-clone No. 717-1-B4


title: Day 0 Chick Breast Muscle- Replicate #2

description: Gene expression data for breast muscle from newly hatched broiler chicken.

source_name: Newly Hatched Chick

value: 0 day-old


title: iPS cells from episomal vectors (Defined Factor) DF19_10 (set of 16)

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an AFX GC3000 G7 scanner

scan_protocol: AFX GC3000 G7 scanner

data_processing: RMA

organism: Homo sapiens

label_protocol: Approximately 3 µg of RNA from each sample was labeled using the MessageAmp™ Biotin II-Enhanced IVT kit (Ambion) following manufacturer’s instructions.

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion or Tri-Reagent (Sigma).

treatment_protocol: IPS cells treated with episomal vectors

tag: cell type


title: Day 0 Chick Breast Muscle- Replicate #3


title: Chip 13103802 transgenic ΔDDKPtRR13-line16 24hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 24 hours after excision from a ΔDDKPtRR13-line16 transgenic donor plant.


title: Day 7 Chick Breast Muscle- Replicate #3


title: Day 0 Chick Breast Muscle- Replicate #1


title: iPS cells from episomal vectors (Defined Factor) DF19_6 (set of 16)


title: Chip 12715002 Non-transgenic 6hr


title: Chip 12712602 Non-transgenic 24hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 24 hours after excision from a non-transgenic donor plant.


title: Day 7 Chick Duodenum- Replicate #3

description: Gene expression data for duodenum from 7 day-old broiler chicken.

value: Duodenum


title: Chip 12712502 Non-transgenic 48hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 48 hours after excision from a non-transgenic donor plant.


title: iPS cells from episomal vectors (Defined Factor) DF19_5 (set of 16)


title: iPS cells from episomal vectors (Defined Factor) DF19_7 (set of 16)


title: Chip 12706202 Non-transgenic 6hr


title: Day 7 Chick Duodenum- Replicate #2


title: Chip 12714902 Non-transgenic 48hr


title: Chip 12706002 Non-transgenic 24hr


title: Day 0 Chick Duodenum- Replicate #2

description: Gene expression data for duodenum from newly hatched broiler chicken.


title: Chip 12706302 transgenic ΔDDKPtRR13-line16 24hr


title: Chip 12228702 transgenic ΔDDKPtRR13-line16 6hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 6 hours after excision from a ΔDDKPtRR13-line16 transgenic donor plant.


title: Day 0 Chick Duodenum- Replicate #3


title: iPS cells from episomal vectors (Defined Factor) DF19_4 (set of 16)


title: Chip 12228602 transgenic ΔDDKPtRR13-line16 6hr


title: Day 7 Chick Duodenum- Replicate #1


title: Chip 12712302 transgenic ΔDDKPtRR13-line16 0hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 0 hours after excision from a ΔDDKPtRR13-line16 transgenic donor plant.


title: iPS cells from episomal vectors (Defined Factor) DF19_2 (set of 16)


title: Chip 12228502 transgenic ΔDDKPtRR13-line16 48hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 48 hours after excision from a ΔDDKPtRR13-line16 transgenic donor plant.


title: iPS cells from episomal vectors (Defined Factor) DF19_1 (set of 16)


title: LPS1-60

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

description: LPS 60 minutes

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

organism: Mus musculus

source_name: Mouse bone-marrow macrophages - LPS 60 minutes

label_protocol: GeneChip® One-Cycle Target Labeling Kit

growth_protocol: BMDM were grown for 7days in DMEM suppplemented with 50µg/mL rh-MCSF

extract_protocol: essentially as described in PMID: 16688188

treatment_protocol: LPS 10ng/ml for 60 min

tag: strain

value: female

value: Femur Bone Marrow-Derived Macrophages


title: Chip 12227702 Non-transgenic 0hr


title: Chip 12227602 Non-transgenic 24hr


title: Chip 12227502 Non-transgenic 24hr


title: Chip 12227402 transgenic ΔDDKPtRR13-line16 0hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 0 hours after excision from a ΔDDKPtRR13-line16 transgenic donor plant


title: Chip 11476902 Non-transgenic 48hr


title: Day 7 Chick Whole Brain- Replicate #3

description: Gene expression data for whole brain from 7 day-old broiler chicken.

value: Whole Brain


title: Day 0 Chick Whole Brain- Replicate #3

description: Gene expression data for whole brain from newly hatched broiler chicken.


title: Day 0 Chick Duodenum- Replicate #1


title: Day 7 Chick Whole Brain- Replicate #2


title: Day 7 Chick Whole Brain- Replicate #1


title: Chip 11476702 transgenic ΔDDKPtRR13-line16 24hr


title: Chip 11476802 transgenic ΔDDKPtRR13-line16 24hr


title: Chip 11477002 Non-transgenic 48hr


title: Day 0 Chick Whole Brain- Replicate #2


title: Day 0 Chick Whole Brain- Replicate #1


title: Chip 10577902 Non-transgenic 48hr


title: Chip 10843202 transgenic ΔDDKPtRR13-line16 24hr


title: Chip 10577802 transgenic ΔDDKPtRR13-line16 48hr


title: Chip 10577602 transgenic ΔDDKPtRR13-line16 48hr


title: H1L ESC (set of 12)

description: Human Embryonic Stem Cell line

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an AFX GC3000 G7 scanner.

source_name: Human Embryonic Stem Cells

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).

treatment_protocol: Lentiviral transduction of fibroblast cells was performed as previously described.

value: H1 passage 42 Human Embryonic Stem Cells


title: Day 7 Chick Liver- Replicate #3

description: Gene expression data for liver from 7 day-old broiler chicken.

value: Liver


title: Chip 10305902 transgenic ΔDDKPtRR13-line16 6hr


title: Chip 10305802 transgenic ΔDDKPtRR13-line16 48 hr


title: Day 7 Chick Liver- Replicate #2


title: Chip 12228402 Non-transgenic 6hr


title: H14A ESC (set of 16)

description: Human Embryonic Stem Cell line

value: H14B passage 61 Human Embryonic Stem Cells


title: Day 7 Chick Liver- Replicate #1


title: Chip 12712402 Non-transgenic 24hr


title: H13B ESC (set of 16)

description: Human Embryonic Stem Cell line

value: H13B passage 43 Human Embryonic Stem Cells


title: Day 0 Chick Liver- Replicate #2

description: Gene expression data for liver from newly hatched broiler chicken.


title: Chip 10272802 Non-transgenic 0hr

treatment_protocol: For these analyses, 14 cm tall apical cuttings were collected from 60cm tall mother plants (from non-transgenic and ΔDDKPtRR13). Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation.  Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting).


title: Chip 10273002 transgenic ΔDDKPtRR13-line 16 0hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 0 hours after excision from a ΔDDKPtRR13-line 16 -transgenic donor plant.


title: Chip 10305602 Non-transgenic 0hr


title: Chip 10305702 transgenic ΔDDKPtRR13-line 16 48 hr

source_name: 5 mm basal stem section from a 14 cm apical cutting taken 48 hours after excision from a ΔDDKPtRR13-line 16 transgenic donor plant.


title: Chip 10272702 transgenic ΔDDKPtRR13-line16 6hr


title: Day 0 Chick Liver- Replicate #3


title: 360_LPS_NRS_BMM_G2_T1_20071105

type: genomic

description: LPS stimulated

hyb_protocol: ChIP DNA was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

data_processing: Analysis of the ChIP-on-chip data was performed using Model-based Analysis of Tiling-arrays.

molecule: genomic DNA

source_name: Mouse bone-marrow macrophages stimulated with LPS for 6hr

label_protocol: TdT labeling essentially as described in Affymetrix protocol

extract_protocol: Essentially as described in PMID: 16688168

treatment_protocol: On day 7, the BMDM were stimulated with 10 ng/mL LPS (List Biological Laboratories, Inc. # 434) for 6 hours and then fixed with 1% formaldehyde (FisherBiotech) for 5 minutes at room temperature.

value: C57BL/6, Gender:female, Tissue:Femur Bone Marrow-Derived Macrophages, Antibody:C/EBPdelta, Stimulus:LPS, Time:360 minutes


title: Chip 10272602 Non-transgenic 6hr

description: Populus tremula x Populus alba INRA-clone No. 717-1-B4 plants  expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ΔDDKPtRR13)were generated via an Agrobacterium-mediated protocol developed by Han et al. (2000). Non-transgenic and  ΔDDKPtRR13 line were grown to a height of 60 cm.  A 14 cm tall apical cuttings were collected from the mother plants. Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation.  Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting).


title: H9 ESC (set of 16)

description: Human Embryonic Stem Cell line

value: H9 passage 50 Human Embryonic Stem Cells


title: 360_LPS_C-EBPdelta_BMM_G2_T1_20071105

description: LPS stimulated


title: 0_NoStim_C-EBPdelta_BMM_C_T1_20070315

description: Unstimulated

source_name: Mouse bone-marrow macrophages

value: C57BL/6, Gender:female, Tissue:Femur Bone Marrow-Derived Macrophages, Antibody:C/EBPdelta


title: 360_LPS_C-EBPdelta_BMM_G1_20071105

description: LPS stimulated


title: 0_NoStim_C-EBPdelta_BMM_A_T1_20070315

description: Unstimulated


title: Day 0 Chick Liver- Replicate #1


title: 0_NoStim_C-EBPdelta_BMM_G2_T1_20071105

description: Unstimulated


title: H7 ESC (set of 16)

description: Human Embryonic Stem Cell line

value: H7 passage 73 Human Embryonic Stem Cells


title: human prostate cancer specimen Gleason score 8 (sample J)

city: Toronto

first: Ken

last: Kron

address: 60 Murray Street

country: Canada

institute: Mount Sinai Hospital

description: 2 ug of amplicon DNA was hybridized to arrays for both tumour sample and reference lymphocyte sample.

hyb_protocol: Hybridization was carried out using Agilent aCGH Hybridization Kit accoring to protocol. All protocols are available from www.agilent.com.

scan_protocol: Scanning was performed using the G2565BA DNA scanner according to the protocol provided for dual channel arrays at www.agilent.com.

data_processing: Data was obtained using Agilent's Feature Extraction software version 9.5. Detailed information for spot finding and flagging of outliers is available from www.agilent.com. QC report results were obtained and the metrics were based on those used for CHIP-chip experiments. All metrics were deterimined to be in range.

source_name: Gleason score 8 prostate cancer

extract_protocol: Tumour was snap frozen in liquid nitrogen and crushed prior to DNA extraction. Qiagen QIAamp DNA Mini Kit was used for genomic DNA isolation according to manufacturer's protocol with RNAase digestion step. DNA was then processed according to the differential methylation hybridization (DMH) protocol developed by Yan et al. (Methods, 2002).

value: fresh frozen Gleason score 8 prostate tumour removed by radical prostatectomy.

source_name: Pooled lymphocyte DNA

label_protocol: Sample was labeled using the Agilent Genomic DNA labeling Kit according to the protocol provided at www.agilent.com.

extract_protocol: Qiagen QIAamp DNA Mini Kit was used for genomic DNA isolation according to manufacturer's protocol with RNAase digestion step. DNA was then processed according to the differential methylation hybridization protocol developed by Yan et al. (Methods, 2002).

tag: reference sample

value: pooled DMH amplicons from six age-matched, healthy men.


title: Polysomal Profile of poliovirus-infected HUVECs

city: Salt Lake City

first: Douglas

middle: I.

last: Schmid

state: UT

department: HMBG

institute: University of Utah

hyb_protocol: Biotin- labeled cRNA samples (15 µg) were fragmented and combined with Affymetrix hybridization reagents (50 pM Control Oligonucleotide B2, Eukaryotic hybridization controls, 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml BSA, 1X Hybridization Buffer, 10% DMSO).  The hybridization mixture was injected into a GeneChip cartridge and hybridizations were performed in an Affymetrix GeneChip Hybridization Oven 450, set to 45ºC.  GeneChip cartridges were rotated within the hybridization oven at 60 rpm for approximately 16 hours.  Following hybridization, the mixture was removed from the GeneChip cartridge and replaced with Non-Stringent Wash Buffer (6X SSPE, 0.01% Tween-20).  Wash and Stain steps on the hybridized microarray were accomplished by loading the GeneChip into an Affymetrix Fluidics Station 450 and running the EukGE-WS2v5_450 fluidics script.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  The scanner is capable of simultaneously detecting Cyanine-3 and Cyanine-5 signal on the hybridized slide.  An extended dynamic range scan of the microarray slide is accomplished by performing a primary scan at 100% laser power and a secondary scan at 10% power, thus generating two separate TIF images from the scans.  Pixel intensities for non-saturating features are calculated from the primary scan.  In contrast, saturating features in the primary scan make use of the secondary scan for defining pixel intensities.  In this scenario, average pixel intensities of these features are multiplied by the magnitude of decrease in laser power to calculate an equivalent signal representative of 100% power.

data_processing:
TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 9.5.1.  The software automatically positions a grid and finds the centroid positions of each feature on the microarray.  This information is used to perform calculations that include feature intensities, background measurements and statistical analyses.  Data generated by the software is recorded as a tab-delimited text file.
Each Cy3 or Cy5 signal was normalized by total Cy3 or Cy5 signal on the slide respectively.  The ratios of normalized Cy5 to Cy3 were then calculated.

molecule: polyA RNA

source_name: Polysomal RNA from mock-infected HUVECs

label_protocol: The polyadenylated fraction of the RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.  Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

extract_protocol: Polysome RNA were isolated from mock-infected HUVECs using Trizol LS (Invitrogen, Carlsbad, CA) acording to manufacture's directions.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

source_name: Polysomal RNA from poliovirus-infected HUVECs

extract_protocol: Polysomal RNA were isolated from mock-infected HUVECs using Trizol LS (Invitrogen, Carlsbad, CA) acording to manufacture's directions.


title: human prostate cancer specimen Gleason score 8 (sample I)

label_protocol: Sample was labeled using the Agilent Genomic DNA labeling Kit according to the protocol provided at www.agilent.com


title: human prostate cancer specimen Gleason score 8 (sample C)


title: human prostate cancer specimen Gleason score 6 (sample 9)

source_name: Gleason score 6 prostate cancer

value: fresh frozen Gleason score 6 prostate tumour removed by radical prostatectomy.


title: human prostate cancer specimen Gleason score 6 (sample 10)


title: human prostate cancer specimen Gleason score 8 (sample G)


title: human prostate cancer specimen Gleason score 8 (sample F)


title: human prostate cancer specimen Gleason score 8 (sample H)


title: Valine addition

status: Public on Mar 26 2009

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Valine

hyb_protocol: Samples were loaded onto cDNA microarrays and hybridized at 65 C for 5-7 hours. according to Khodursky et al (PMID 12710666)

scan_protocol: Scanned on GenePix4000B scanner.

data_processing:
Images were quantified using GenePix Pro software
Median of intensity data was extracted, LOESS normalized and an ANOVA model was fit using the MAANOVA package in R. The Log (Cy5/Cy3) values were extracted from the VG matrix of the model fit.

label: Cy3, Cy5

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli cells 0 min before perturbation

label_protocol: 10 µg of total RNA were primed with 1 µl of Random hexamers at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U SuperScript II RTase (Invitrogen), according to Khodursky et al (PMID 12710666)

growth_protocol: E. coli cells grown to mid-exponential phase after 6-8 generations after stationary phase in M9 minimal medium + 0.4 % glucose.

extract_protocol: Total RNA extracted using Qiagen RNEASY kit according to directions

treatment_protocol: Amino acid or nucleotide added to final concentration of 1 mM not exceeding 1/100th volume of culture. After 10 mins, samples were spun down and snap frozen in liquid nitrogen and stored at -80 C

tag: stress

value: control (before perturbation)

source_name: E. coli cells 10 min after specific perturbation

value: Valine addition


title: Uridine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Uridine

value: Uridine addition


title: human prostate cancer specimen Gleason score 6 (sample 6)


title: human prostate cancer specimen Gleason score 8 (sample A)


title: human prostate cancer specimen Gleason score 8 (sample E)


title: Transcriptional Profile of poliovirus-infected HUVECs

source_name: Mock-infected HUVECs

extract_protocol: Total RNA were isolated from mock-infected HUVECs using Trizol LS (Invitrogen, Carlsbad, CA) acording to manufacture's directions.

source_name: Poliovirus-infected HUVECs


title: Tryptophan addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Tryptophan

value: Tryptophan addition


title: Threonine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Threonine

value: Threonine addition


title: Proline addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Proline

value: Proline addition


title: Phenylalanine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Phenylalanine

value: Phenylalanine addition


title: Thymidine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Thymidine

value: Thymidine addition


title: human prostate cancer specimen Gleason score 6 (sample 1)


title: Serine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Serine

value: Serine addition


title: human prostate cancer specimen Gleason score 6 (sample 4)


title: Lysine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Lysine

value: Lysine addition


title: Methionine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Methionine

value: Methionine addition


title: Guanosine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Guanosine

value: Guanosine addition


title: Histidine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Histidine

value: Histidine addition


title: human prostate cancer specimen Gleason score 6 (sample 5)


title: Isoleucine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Isoleucine

value: Isoleucine addition


title: human prostate cancer specimen Gleason score 8 (sample D)

value: fresh frozen Gleason score 8 prostate tumour removed by radical prostatectomy.

value: pooled DMH amplicons from six age-matched, healthy men.


title: human prostate cancer specimen Gleason score 6 (sample 8)

value: fresh frozen Gleason score 6 prostate tumour removed by radical prostatectomy.


title: human prostate cancer specimen Gleason score 8 (sample B)


title: Glycine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Glycine

value: control (before perturbation)

value: Glycine addition


title: human prostate cancer specimen Gleason score 6 (sample 2)


title: human prostate cancer specimen Gleason score 6 (sample 7)


title: Glutamine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Glutamine

value: Glutamine addition


title: human prostate cancer specimen Gleason score 6 (sample 3)


title: Cytidine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Cytidine

value: Cytidine addition


title: Alanine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Alanine

value: Alanine addition


title: Arginine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Arginine

value: Arginine addition


title: Aspartate addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Aspartate

value: Aspartate addition


title: Adenosine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Adenosine

value: Adenosine addition


title: Glutamate addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Glutamate

value: Glutamate addition


title: F2 female CNS-4

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

country: India

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: F2 female CNS-4

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides. The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

organism: Drosophila melanogaster

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche) and purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 generation which were kept in normal food for 7 days and again shifted to normal food for next 7 days, were allowed to mate with female flies(never treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected, males and females were separated, and after 3-4 days were kept for crossing in normal food vials and removed after 2 days. F2 progeny thus emerged was collected and used for experiments after 3-4 days.

extract_protocol: Total RNA was isolated from head using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: Female flies from F2 generation (controls) were allowed to grow on normal media till 3-4 days old, and then heads collected and stored at –70ºC.

tag: generation

value: Oregon R

tag: sex

value: female

value: head

source_name: Drosophila melanogaster, females, unmated (F0 were PTZ-treated)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche) and purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 generation which were kept in PTZ food for 7 days and again shifted to normal food for next 7 days, were allowed to mate with female flies(never treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected, males and females were separated, and after 3-4 days were kept for crossing in normal food vials and removed after 2 days. F2 progeny thus emerged was collected and used for experiments after 3-4 days.

treatment_protocol: Female flies from F2 generation (treatment) were allowed to grow on normal media till 3-4 days old, and then heads collected and stored at –70ºC.


title: F1 male head II-2

description: F1 male head II-2

source_name: Drosophila melanogaster, males, unmated (F0 were PTZ-treated)

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 progeny which were treated with PTZ for 7 days and kept on normal food for next 7 days, were allowed to mate with female flies of F0 progeny(not treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Male flies were thereafter maintained for another 3-4 days on NF.

treatment_protocol: Flies of F1 progeny were not treated with any drug

value: male

source_name: Drosophila melanogaster, males, unmated

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 progeny which were kept in normal food for 7 days and again shifted to normal food for next 7 days, were allowed to mate with female flies of F0 progeny(not treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Male flies were thereafter maintained for another 3-4 days on NF.


title: F1 male head II-3

description: F1 male head II-3


title: F2 male CNS-4

description: F2 male CNS-4

treatment_protocol: Male flies from F2 generation (controls) were allowed to grow on normal media till 3-4 days old, and then heads collected and stored at –70ºC.

treatment_protocol: Male flies from F2 generation (treatment) were allowed to grow on normal media till 3-4 days old, and then heads collected and stored at –70ºC.


title: F2 male CNS-2

description: F2 male CNS-2


title: F1 male head II-1

description: F1 male head II-1


title: F2 male CNS-1

description: F2 male CNS-1

treatment_protocol: Male flies from F2 generation (control) were allowed to grow on normal media till 3-4 days old, and then heads collected and stored at –70ºC.


title: F2 male CNS-3

description: F2 male CNS-3


title: F2 female CNS-2

description: F2 female CNS-2

source_name: Drosophila melanogaster, females, unmated


title: Cysteine addition

description: 2-3 biological replicates. Comparison of total RNA abundance 10 min after and before addition of Cysteine

value: Cysteine addition


title: F2 female CNS-3

description: F2 female CNS-3


title: F1 males head-3

description: F1 males head-3


title: F1 males head-4

description: F1 males head-4


title: F1 male head II-4

description: F1 male head II-4


title: F0-testis-3

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides. The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

source_name: Drosophila melanogaster, males, unmated, treated

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle, and flies from identical cultures were first allowed to lay eggs in bottles containing NF. Flies were transferred to fresh bottle every 12 hr. After discarding first 4 batches of bottles, only those flies that emerged in subsequent bottles were used.Flies were collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Male flies were thereafter maintained for another 3-4 days on NF.

extract_protocol: Total RNA was isolated from testes using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) mixed in normal fly food at a concentration of 8 mg/ml ,for 7days.On the final day of treatment, i.e. 7th day, testes were collected, snap frozen in liquid nitrogen and stored at –70ºC.

value: Male

value: testis

source_name: Drosophila melanogaster, males, unmated, untreated

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days. On 7th day, testes were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: F1 males head-1

description: F1 males head-1


title: F1 males head-2

description: F1 males head-2


title: F1 females head-4

description: F1 females head-4

source_name: Drosophila melanogaster, females, virgin (F0 were PTZ-treated)

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 progeny which were treated with PTZ for 7 days and kept on normal food for next 7 days, were allowed to mate with female flies of F0 progeny(not treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Female flies were thereafter maintained for another 3-4 days on NF.

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 progeny which were kept in normal food for 7 days and again shifted to normal food for next 7 days, were allowed to mate with female flies of F0 progeny(not treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Female flies were thereafter maintained for another 3-4 days on NF.


title: F2 female CNS-1

description: F2 female CNS-1


title: F1-testis-1

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 progeny which were treated with PTZ for 7 days and kept on normal food for next 7 days,  were allowed to mate with female flies of F0 progeny(not treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Male flies were thereafter maintained for another 3-4 days on NF.

growth_protocol: D. melanogaster Oregon-R wild type male flies of F0 progeny which were kept in normal food for 7 days and again shifted to normal food for next 7 days,  were allowed to mate with female flies of F0 progeny(not treated with drug). After 2 days parents were removed and eggs were allowed to grow on standard fly medium.F1 progeny was collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Male flies were thereafter maintained for another 3-4 days on NF.


title: F1-testis-2


title: sa6-fosf-1-40min

city: Ljubljana

first: Drago

last: Kuzman

address: Verovskova 57

country: Slovenia

institute: Lek pharmaceuticals d.d.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were analyzed with Expression Console version 1.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Staphylococcus aureus

source_name: fosformycin 1ug 40min

label_protocol: Standard Affymetrix procedures

growth_protocol: Staphylococcus aureus, strain ATTC 29213 was used in the experiments. Overnight culture was set in a small volume of cation-adjusted Mueller–Hinton broth medium (Sigma-Aldrich) and grown in Erlenmeyer flask on gyratory shaker (200 rpm) at 37°C. The overnight culture was diluted 100-fold in 300 ml of medium and grown under same conditions in 1-L Erlenmeyer flasks until OD600 (measured by Beckman DU640 spectrophotometer) reached 0.3, which corresponded to the early exponential stage of the growth curve.

extract_protocol: RNA was isolated from an aliquot of 7ml of the culture using enzyme cell wall lysis (30) followed by RNeasy Mini Kit (Qiagen) purification.

treatment_protocol: Bacterial cultures were treated with 0, 1 and 4 µg/ml, respectively, of fosfomycin. Bacterial cells were harvested at the start of the experiment (t0) and at 3 time points (10, 20 and 40 minutes) after treatment. The experiment was repeated at least three times.


title: F0-testis-4


title: F1-testis-4


title: F1 females head-3

description: F1 females head-3

source_name: Drosophila melanogaster, females, virgin


title: sa6-fosf-1-10min

description: sa6-fosf-1-10min 0028-6744.cel

source_name: fosformycin 1ug 10min


title: sa6-fosf-4-20min

description: sa6-fosf-4-20min 0028-6748.cel

source_name: fosformycin 4ug 20min


title: F1 females head-2

description: F1 females head-2


title: sa6-fosf-1-20min

description: sa6-fosf-1-20min 0028-6747.cel

source_name: fosformycin 1ug 20min


title: F1 females head-1

description: F1 females head-1


title: F1-testis-3


title: sa6-control-0min

description: sa6-control-0min 0028-6742.cel

source_name: fosformycin 0ug 0min


title: F0-testis-2


title: F0-testis-1


title: sa5-fosf-4-40min

description: sa5-fosf-4-40min 0028-6741.cel

source_name: fosformycin 4ug 40min


title: sa6-control-10min

description: sa6-control-10min 0028-6743.cel

source_name: fosformycin 0ug 10min


title: sa6-control-20min

description: sa6-control-20min 0028-6746.cel

source_name: fosformycin 0ug 20min


title: sa5-fosf-4-20min

description: sa5-fosf-4-20min 0028-6738.cel


title: sa6-control-40min

description: sa6-control-40min 0028-6749.cel

source_name: fosformycin 0ug 40min


title: sa5-fosf-1-20min

description: sa5-fosf-1-20min 0028-6737.cel


title: sa5-fosf-4-10min

description: sa5-fosf-4-10min 0028-6735.cel

source_name: fosformycin 4ug 10min


title: sa5-fosf-1-40min

description: sa5-fosf-1-40min 0028-6740.cel


title: sa4-fosf-1-40min

description: sa4-fosf-1-40min 0027-2322.cel


title: sa4-fosf-4-20min

description: sa4-fosf-4-20min 0027-2320.cel


title: sa4-fosf-4-10min

description: sa4-fosf-4-10min 0027-2317.cel


title: sa4-fosf-4-40min-23

description: sa4-fosf-4-40min 0027-2323.cel


title: sa5-control-10min

description: sa5-control-10min 0028-6733.cel


title: sa5-control-40min

description: sa5-control-40min 0028-6739.cel


title: sa4-fosf-1-10min

description: sa4-fosf-1-10min 0027-2316.cel


title: sa5-fosf-1-10min

description: sa5-fosf-1-10min 0028-6734.cel


title: sa4-fosf-4-40min-32

description: sa4-fosf-4-40min 0028-6732.cel


title: sa4-fosf-1-20min

description: sa4-fosf-1-20min 0027-2319.cel


title: sa5-control-20min

description: sa5-control-20min 0028-6736.cel


title: sa4-control-10min

description: sa4-control-10min 0027-2315.cel


title: sa4-control-40min

description: sa4-control-40min 0027-2321.cel


title: sa4-control-20min

description: sa4-control-20min 0027-2318.cel


title: Deep-sowing 10d treatment TIBA, biological rep2

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

country: China

institute: Chinese Academy of Agricultural Sciences

description: Gene expression data from maize mesocotyl

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

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

data_processing: The data were analyzed with GCOS software (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 500.

organism: Zea mays

source_name: Mesocotyl, TIBA

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

extract_protocol: The total RNA was extracted by the TRIzol method (Invitrogen, USA). Mesocotyls were ground in liquid nitrogen, and 50-100 mg of frozen tissue was transferred into a tube with 1 ml TRIzol. Next, RNA was isolated, dried and dissolved in 50 µl DEPC-H2O. RNA quality and concentration were determined by 1.0% agarose gel electrophoresis and spectrophotometry.

value: Maize inbred line 3681-4

value: 10d after sowing

value: mesocotyls


title: sa3-control-0min

description: sa3-control-0min 0027-2312.cel


title: sa4-control-0min

description: sa4-control-0min 0027-2314.cel


title: sa3-fosf-4-10min

description: sa3-fosf-4-10min 0027-2313.cel


title: Deep-sowing 10d treatment IAA, biological rep2

source_name: Mesocotyl, IAA


title: sa1-fosf-4-40min

description: sa1-fosf-4-40min 0027-2309.cel


title: sa1-fosf-1-40min

description: sa1-fosf-1-40min 0027-2308.cel


title: Deep-sowing 10d treatment TIBA, biological rep1


title: Sporophytic Tissue Replicate 2

city: Parkville

first: Chui

middle: E

last: WONG

state: Victoria

address: University of Melbourne

department: Land and Food

country: Australia

institute: University of Melbourne

description: GeneChip Soybean Genome array (Affymetrix, Inc.) containing 37,500 unique transcript (probe) was used in this study.Two independent biological replicates were collected for the sporophytic tissues.

hyb_protocol: abelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)

data_processing:
AffylmGUI that is a graphical user interface for analysis of Affymetrix microarray data, was used for data analysis (http://www.r-project.org). Data normalization (Quantile normalization method) and expression measures were done using RMA (Robust Multiarray Averaging) algorithm (R package) [69, 70], differential expression and contrast analysis was performed using sporophytic (non-meristematic) tissues hybridized chips as the baseline. We chose the p value cutoff of P Ã¢â€°Â¤0.001( from t-test) and empirical bayes log odds of differential expression (B) to zero.
Hybridization quality was tested by checking the soybean control genes including 18S rRNA, Actin, GSTa, cytochrome P450, SBP, Ubiquitin, and GAPDH (spotted by the manufacturer). The expression ratios [P (-)/P (+)] of the control genes were consistently in the range of 0.16-2.84.

organism: Glycine max

source_name: Sporophytic tissues from soybean

growth_protocol: Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown in a greenhouse located at the University of Melbourne, Victoria, Australia. Plant tissues were harvested form 10-day-old seedlings.

extract_protocol: Total RNA from various tissues was isolated using QIAGEN RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocols and eluted with ultra pure nuclease-free water.

tag: Sporophytic tissues consisting of primary stem, primary roots and mature leaves


title: sa2-control-10min

description: sa2-control-10min 0027-2310.cel


title: Deep-sowing 10d treatment IAA, biological rep1


title: Spleen_ Haemophilus Parasuis infection_control 3_7days_rep1

city: Wuhan

first: Shuhong

last: Zhao

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

description: Comparison of piglets that were challenged with the Haemophilus parasuis (HPS) pathogen versus a control group to investigate global expression changes in the spleen.

hyb_protocol: 1.Mix the following components together(Hybridization solution).    Fragmented cRNA: 5 μg;    Control Oligonucleotide B2(3nM): 1.7 μL;    20× Eukaryotic Hybridization Controls(bioB, bioC, bioD, cre): 5 μL;   Herring Sperm DNA(10mg/mL): 1 μL;    Acetylated BSA(50mg/mL): 1 μL;    2× Hybridization Buffer: 50 μL;    DMSO: 10μL;    H2O: 31.3μL; 2. Equilibrate probe array to room temperature immediately before use. 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block. 4. Meanwhile, wet the array by filling it through one of the septa with appropriate volume of 1X Hybridization Buffer using a micropipettor and appropriate tips. 5. Incubate the probe array filled with 1X Hybridization Buffer at 45°C for 10 minutes with rotation. 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 7. Spin hybridization cocktail(s) at maximum speed in a microcentrifuge for 5 minutes to remove any insoluble material from the hybridization mixture. 8. Remove the buffer solution from the probe array cartridge and fill with appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. 9. Place probe array into the Hybridization Oven, set to 45°C. Avoid stress to the motor; load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 10. Hybridize at 45℃ for 16 h with constant rotation at 60rpm. 11. After 16 hours of hybridization, remove the hybridization cocktail from the probe array and fill the probe array completely with the appropriate volume of the following Non-Stringent Wash Buffer(Wash Buffer A:6X SSPE, 0.01% Tween-20). Post Hyb Wash #1: 10 cycles of 2 mixes/cycle with Wash Buffer A at 25°C. 12. Preparing the Staining Reagents. 12.1 SAPE Stain Solution(Mix well and divide into two aliquots of 600 μL each to be used for stains 1 and 3):     2X Stain Buffer  600.0 μL;     50 mg/mL BSA 48.0 μL;      1 mg/mL Streptavidin Phycoerythrin (SAPE) 12.0 μL;      DI H20 540.0 μL; 12.2 Antibody Solution:       2X Stain Buffer 300.0 μL;       50 mg/mL BSA 24.0 μL;       10 mg/mL Goat IgG Stock 6.0 μL;       0.5 mg/mL biotinylated antibody 3.6 μL;       DI H20 266.4 μL; 13. Post Hyb Wash #2: 4 cycles of 15 mixes/cycle with Wash Buffer B(100 mM MES, 0.1M [Na+], 0.01% Tween-20) at 50°C. 14. Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C. 15. Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C. 16. 2nd Stain: Stain the probe array for 10 minutes in antibody solution at 25°C. 17. 3rd Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C. 18. Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C. Annotation: Chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The probe arrays were scanned using the Affymetrix® GeneChip® Scanner 3000. Apply the spots just before scanning: 1. On the back of the probe array cartridge, clean excess fluid from around septa. 2. Carefully apply one Tough-Spots to each of the two septa. Press to ensure that the spots remain flat. If the Tough-Spots do not apply smoothly, that is, if you observe bumps, bubbles, tears, or curled edges, do not attempt to smooth out the spot. Remove the spot and apply a new spot. 3. Insert the cartridge into the scanner and test the autofocus to ensure that the Tough-Spots do not interfere with the focus. Scanning the Probe Array: 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. ⇒ The Scanner dialog box appears with a drop-down list of experiments that have not been run. 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list. 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required. 4. Once the experiment has been selected, click the Start button. ⇒ A dialog box prompts you to load an array into the scanner. 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam. ■ Pixel value = 3 μm ■ Wavelength = 570 nm If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed. 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. 7. Click OK in the Start Scanner dialog box. ⇒ The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.

data_processing: There are 11 paired perfect match (PM) and mismatch (MM) 25-mer probes in the Affymetrix GeneChip porcine genome array for each probeset representing a gene. The signals from these probe pairs are used to determine whether a given gene is expressed and to measure the gene expression level. The probe-pair (PM-MM) data were used to detect the expression level of genes on the array (present call, marginal call, and absent call) by MAS 5.0 (Wilcoxon signed rank test). Raw data from .CEL files were converted to gene signal files by MAS 5.0 (Ver.2.3.1). Natural logarithms were then taken on quantile normalization（GeneSpring 7.31. Identification of DE genes was conducted using SAS (Ver.8.1, T-test). The p value cutoff for DE genes was set at 0.05.

label: Biotin

organism: Sus scrofa

source_name: Porcine spleen,Haemophilus Parasuis infection_control,7days

label_protocol:
GeneChip® IVT Labeling Kit (Affymetrix) protocol:
1.Transfer the needed amount of template cDNA (12 μL) to RNase-free  microfuge tubes and add Rnase-free Water(8 μL), 10× IVT Labeling Buffer (4 μL), IVT Labeling NTP Mix(12 μL), IVT Labeling Enzyme Mix(4 μL) in the order.
2. Carefully mix the reagents and collect the mixture at the bottom of the tube by brief (5 second) microcentrifugation.
3. Incubate at 37°C for 16 hours. To prevent condensation that may result from water bath-style incubators,incubations are best performed in oven incubators for even temperature distribution, or in a thermal cycler.
4.Store labeled cRNA at -20°C, or -70°C if not purifying immediately.

extract_protocol: Spleens from both the treatment group and the control group were snap frozen in liquid nitrogen after collection and stored at –80℃ until RNA extraction. TRIzol (Invitrogen) and RNeasy Mini Kit (QIAGEN) were used for RNA extractions and purifications respectively followed by manufacturer’s instructions. RNA quality and concentration were checked by Agilent Bioanalyser 2100.

tag: Pig age:30 days; Pig tissue:spleen; Bacteria:Haemophilus Parasuis, strain 0165 (serotype 5); Infection_control time

value: for 7 days;


title: Spleen_ Haemophilus Parasuis infection_control 1_7days_rep1


title: sa1-fosf-1-20min-07

description: sa1-fosf-1-20min 0027-2307.cel


title: Sporophytic Tissue Replicate 1

scan_protocol: abelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)


title: EZH1 bioChIP in Ezh2-/- cells on F chip

status: Public on Mar 25 2009

city: Boston

first: Xiaohua

last: Shen

state: MA

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: ChIP-chip

hyb_protocol: About 2-4 ug of labeled DNA were hybridized for 16 hr at 45C on tiling arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Model-based Analysis of Tiling-arrays for ChIP-chip (MAT) developed by the Liu lab and processed based on MM8 annotation. MATScore, p value (in form of -10log10_Pvalue), fold-change, FDR, peak position and length were reported for each peak identified by MAT program (results provided as supplementary text files).

source_name: EZH1 bioChIP in Ezh2-/- cells (3 replicates)

label_protocol: Fragmented DNA was labeled with biotin-N6-ddATP by terminal deoxynucleiotidyl transferase.

growth_protocol: standard culture conditions were used to culture ES cells.

extract_protocol: pulled down chromatin was reversely crosslinked and DNA was precipitated by isopropanol.

treatment_protocol: wild-type (WT) and Ezh2-/- mutant ES cells were fixed with 0.8% formaldehyde for 10 min at room temperature. Cell lydates were ChIP'ed by antibody recognizing H3K27me3 mark (Upstate) or by using streptavidin-Dyna beads (Invitrogen). DNA fragments were isolated and amplified by LM-PCR. Amplified DNA was fragmented and biotin labeled before hybridiztion.

value: embryonic stem

tag: antibody

tag: cell line

source_name: INPUT CONTROL

tag: input 1

value: genomic DNA from J1 cells expressing bfEZH1

tag: input 2

value: genomic DNA from CJ7 cells

tag: input 3

value: genomic DNA from Ezh2-/- cells


title: EZH1 bioChIP in Ezh2-/- cells on G chip

description: ChIP-chip

tag: genotype


title: Spleen_ Haemophilus Parasuis infection_control 2_7days_rep1


title: EZH1 bioChIP in CJ7 cells on F chip

description: ChIP-chip

source_name: EZH1 bioChIP in CJ7 cells (3 replicates)

value: wild-type


title: sa1-fosf-1-20min-06

description: sa1-fosf-1-20min 0027-2306.cel


title: H3K27me3 ChIP in Ezh2-/- cells on F chip

description: ChIP-chip

source_name: H3K27me3 ChIP in Ezh2-/- cells (3 replicates)


title: H3K27me3 ChIP in Ezh2-/- cells on G chip

description: ChIP-chip


title: sa1-control-20min

description: sa1-control-20min 0027-2305.cel


title: Mature Soybean (Glycine max) pollen grains Replicate 3

description: GeneChip Soybean Genome array (Affymetrix, Inc.) containing 37,500 unique transcript (probe) was used in this study. Three biological replicates for pollen and two biological replicates for sporophytic tissues were used

hyb_protocol: Labelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)

data_processing:
AffylmGUI that is a graphical user interface for analysis of Affymetrix microarray data, was used for data analysis (http://www.r-project.org). Data normalization (Quantile normalization method) and expression measures were done using RMA (Robust Multiarray Averaging) algorithm (R package) [69, 70], differential expression and contrast analysis was performed using sporophytic (non-meristematic) tissues hybridized chips as the baseline [71]. We chose the p value cutoff of P â‰¤0.001( from t-test) and empirical bayes log odds of differential expression (B) to zero.
Hybridization quality was tested by checking the soybean control genes including 18S rRNA, Actin, GSTa, cytochrome P450, SBP, Ubiquitin, and GAPDH (spotted by the manufacturer). The expression ratios [P (-)/P (+)] of the control genes were consistently in the range of 0.16-2.84.

source_name: Mature pollen grains from soybean

growth_protocol: The plants used for pollen collection were grown in a temperature controlled glasshouse with a 16 hour light / 8 hour dark photoperiod at 30 degrees C.  They were grown in vermiculite with the addition of a slow release fertilizer (osmocote).   When the plants had matured and developed significant biomass, flowering was induced by changing the photoperiod to 12 hours.  Pollen was collected on cover slips by rubbing isolated anthers together, and non-pollen tissue was removed from cover slip prior to freezing at -80 degrees.

tag: Mature pollen grains


title: Spleen_ Haemophilus Parasuis infected 3_7days_rep1

source_name: Porcine spleen,Haemophilus Parasuis infected,7days

tag: Pig age:30 days; Pig tissue:spleen; Bacteria:Haemophilus Parasuis, strain 0165 (serotype 5); Infection time


title: H3K27me3 ChIP in CJ7 cells on G chip

description: ChIP-chip

source_name: H3K27me3 ChIP in CJ7 cells (3 replicates)


title: Mature Soybean (Glycine max) pollen grains Replicate 2

scan_protocol: Labelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)

tag: Mature Pollen Grains


title: EZH1 bioChIP in CJ7 cells on G chip

description: ChIP-chip

tag: cell type


title: Spleen_ Haemophilus Parasuis infected 2_7days_rep1


title: Mature Soybean (Glycine max) pollen grains replicate 1

description: GeneChip Soybean Genome array (Affymetrix, Inc.) containing 37,500 unique transcript (probe) was used in this study. Three biological replicates for pollen and two biological replicates for sporophytic tissues were used.

data_processing:
AffylmGUI that is a graphical user interface for analysis of Affymetrix microarray data, was used for data analysis (http://www.r-project.org). Data normalization (Quantile normalization method) and expression measures were done using RMA (Robust Multiarray Averaging) algorithm (R package) [69, 70], differential expression and contrast analysis was performed using sporophytic (non-meristematic) tissues hybridized chips as the baseline [71]. We chose the p value cutoff of P ≤0.001( from t-test) and empirical bayes log odds of differential expression (B) to zero.
Hybridization quality was tested by checking the soybean control genes including 18S rRNA, Actin, GSTa, cytochrome P450, SBP, Ubiquitin, and GAPDH (spotted by the manufacturer). The expression ratios [P (-)/P (+)] of the control genes were consistently in the range of 0.16-2.84.

label_protocol: Labelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)

growth_protocol: All plants were grown in a temperature controlled glasshouse with a 16 hour light / 8 hour dark photoperiod at 30 degrees C.

treatment_protocol: The plants used for pollen collection were grown in a temperature controlled glasshouse with a 16 hour light / 8 hour dark photoperiod at 30 degrees C.  They were grown in vermiculite with the addition of a slow release fertilizer (osmocote).   When the plants had matured and developed significant biomass, flowering was induced by changing the photoperiod to 12 hours.


title: H3K27me3 ChIP in CJ7 cells on F chip

description: ChIP-chip


title: Spleen_ Haemophilus Parasuis infected 1_7days_rep1

extract_protocol: Spleens from both the treatment group and the control group were snap frozen in liquid nitrogen after collection and stored at –80℃ until RNA extraction. TRIzol (Invitrogen) and RNeasy Mini Kit (QIAGEN) were used for RNA extractions and purifications respectively followed by manufacturer’s instructions. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity(close to  2.0).Integrity of total RNA samples were also checked by Agilent Bioanalyser 2100.

tag: Pig age:30 days;

tag: Pig tissue:spleen;

tag: Bacteria:Haemophilus Parasuis, strain 0165 (serotype 5);

tag: Infection time


title: EZH1 bioChIP in Ezh2-/- cells on D chip

description: ChIP-chip


title: EZH1 bioChIP in CJ7 cells on D chip

description: ChIP-chip


title: H3K27me3 ChIP in Ezh2-/- cells on D chip

description: ChIP-chip


title: H3K27me3 ChIP in CJ7 cells on D chip

description: ChIP-chip


title: EZH1 bioChIP in Ezh2-/- cells on E chip

description: ChIP-chip


title: EZH1 bioChIP in CJ7 cells on E chip

description: ChIP-chip


title: H3K27me3 ChIP in CJ7 cells on E chip

description: ChIP-chip


title: H3K27me3 ChIP in Ezh2-/- cells on E chip

description: ChIP-chip


title: Patient 18R2_Gain50

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description: For more details, please see Gillet J-P, J. Pathol. in submission

hyb_protocol: Hybridization, quantification and data analysis were performed as described by de Longueville et al. Toxicol Sci 2003; 75:378-392 and Biochem Pharmacol 2002; 64:137-149. and provided in the DualChip microarray protocol of direct labelling.(http://www.eppendorf.com/int/index.php?l=l&action=support&sitemap=4.1&catalognode=27780).

scan_protocol: Briefly, after hybridization, the detection was performed using a Cy3-conjugated anti-biotin IgG antibody (Jackson Immuno Research Laboratories, USA). The arrays were scanned with the ScanArray 4000 XL laser confocal scanner (Applied Biosystems, USA) at a resolution of 10 µm. To maximize the dynamic range of microarrays, the same arrays were scanned using different photomultiplier settings (PMT). The use of different intensities (termed gains) allows the quantification of genes that are expressed at both high and low copy numbers.

data_processing: After image acquisition, the scanned 16-bit image was used to quantify the signal intensities with ImaGene 5.5 software (BioDiscovery, USA) and the file was imported into the DualChip software provided by Eppendorf (Hamburg, Germany).  The signal intensities were normalized by housekeeping genes and internal standards.

source_name: Spleen

label_protocol: After performing a total RNA concentration curve, a concentration of 25 µg was chosen for preparation of labeled cDNA, for more details please see de Longueville F et al. Biochem Pharmacol 2002;64:137– 49.

growth_protocol: Cell lines were seeded in RPMI 1640 (Invitrogen, UK) supplemented with 10% FCS (GibcoBRL, USA).

extract_protocol: Total RNA was extracted by the Trizol method (GibcoBRL, USA) from 6 frozen 50 µm sections of each biopsy.

tag: SMZL


title: Patient 16_Gain50

source_name: Lymph node

tag: Follicular lymphoma


title: Patient 21_Gain50

tag: MCL


title: Patient 17_Gain50


title: Patient 18R1_Gain50


title: Patient 20_Gain50


title: Patient 19R1_Gain50


title: Patient 15_Gain50


title: Patient 14R2_Gain50

tag: B-CLL


title: Patient 14R1_Gain50


title: Patient 13R1_Gain50


title: Patient 12R2_Gain50


title: Patient 13R2_Gain50


title: Patient 19R2_Gain50


title: Patient 12R1_Gain50


title: Patient 11R2_Gain50


title: Patient 12R3_Gain50


title: Patient 10R2_Gain50


title: Patient 9R1_Gain50


title: Patient 9R2_Gain50


title: Patient 9R3_Gain50


title: Patient 7R2_Gain50


title: Patient 8R2_Gain50


title: Patient 7R1_Gain50


title: Patient 8R3_Gain50


title: Patient 8R1_Gain50


title: Patient 10R1_Gain50


title: Patient 6R2_Gain50


title: Patient 6R1_Gain50


title: Patient 11R1_Gain50


title: Patient 6R3_Gain50


title: Patient 5R3_Gain50


title: Patient 4R3_Gain50


title: Patient 5R1_Gain50


title: Patient 4R2_Gain50


title: Patient 4R1_Gain50


title: Patient 3R2_Gain50


title: Patient 2R2_Gain50


title: Patient 2R1_Gain50


title: Patient 11R3_Gain50


title: Patient 1R2_Gain50


title: Patient 1R1_Gain50


title: Validation 8R2_Gain70


title: Validation 7R2_Gain70


title: Validation 6R1_Gain70


title: Validation 5_Gain70


title: Patient 3R1_Gain50


title: Validation 9_Gain70


title: Validation 6R2_Gain70


title: Validation 4_Gain70


title: Validation 7R1_Gain70


title: Validation 3_Gain70


title: Patient 2R3_Gain50


title: Patient 40R2_Gain70


title: Patient 40R1_Gain70


title: Validation 2R2_Gain70


title: Validation 1_Gain70


title: Validation 2R1_Gain70


title: Patient 39R3_Gain70


title: Patient 38R3_Gain70


title: Patient 39R2_Gain70


title: Patient 39R1_Gain70


title: Patient 38R2_Gain70


title: Patient 36_Gain70


title: Patient 37_Gain70


title: Patient 38R1_Gain70


title: Patient 35_Gain70


title: Patient 33_Gain70


title: Patient 32R2_Gain70


title: Patient 31R2_Gain70


title: Patient 30_Gain70


title: Patient 29R2_Gain70


title: Patient 31R1_Gain70


title: Patient 34_Gain70


title: Patient 31R3_Gain70


title: Patient 32R1_Gain70


title: Patient 28_Gain70


title: Patient 5R2_Gain50


title: Patient 27R1_Gain70


title: Patient 26_Gain70


title: Patient 27R3_Gain70


title: Patient 27R2_Gain70


title: Patient 29R1_Gain70


title: Patient 25R2_Gain70


title: Patient 23R2_Gain70


title: Validation 8R1_Gain70


title: Patient 24R1_Gain70


title: Patient 23R1_Gain70


title: Patient 22R2_Gain70


title: Patient 22R1_Gain70


title: Patient 19R1_Gain70


title: Patient 17_Gain70


title: Patient 18R2_Gain70


title: Patient 19R2_Gain70


title: Patient 20_Gain70


title: Patient 18R1_Gain70


title: Patient 16_Gain70


title: Patient 21_Gain70


title: Patient 13R2_Gain70


title: Patient 14R1_Gain70


title: Patient 14R2_Gain70


title: Patient 12R3_Gain70


title: Patient 12R2_Gain70


title: Patient 12R1_Gain70


title: Patient 11R3_Gain70


title: Patient 15_Gain70


title: Patient 8R3_Gain70


title: Patient 10R2_Gain70


title: Patient 11R1_Gain70


title: Patient 10R1_Gain70


title: Patient 9R2_Gain70


title: Patient 8R1_Gain70


title: Patient 9R1_Gain70


title: Patient 7R1_Gain70


title: Patient 7R2_Gain70


title: Patient 9R3_Gain70


title: Patient 6R3_Gain70


title: Patient 8R2_Gain70


title: Patient 6R2_Gain70


title: Patient 11R2_Gain70


title: Patient 6R1_Gain70


title: Patient 5R3_Gain70


title: Patient 5R2_Gain70


title: Patient 5R1_Gain70


title: Patient 3R2_Gain70


title: Patient 4R3_Gain70


title: Patient 4R1_Gain70


title: Patient 3R1_Gain70


title: Patient 4R2_Gain70


title: Patient 2R3_Gain70


title: Patient 25R1_Gain70


title: Patient 1R2_Gain70


title: Validation 9_Gain100


title: Validation 8R2_Gain100


title: Patient 2R2_Gain70


title: Validation 8R1_Gain100


title: Validation 7R2_Gain100


title: Patient 2R1_Gain70


title: Validation 6R2_Gain100


title: Validation 5_Gain100


title: Validation 6R1_Gain100


title: Validation 3_Gain100


title: Validation 4_Gain100


title: Patient 13R1_Gain70


title: Validation 2R1_Gain100


title: Validation 1_Gain100


title: Patient 1R1_Gain70


title: Patient 40R2_Gain100


title: Patient 40R1_Gain100


title: Validation 7R1_Gain100


title: Patient 39R3_Gain100


title: Patient 39R2_Gain100


title: Patient 39R1_Gain100


title: Patient 38R1_Gain100


title: Patient 38R3_Gain100


title: Patient 35_Gain100


title: Patient 36_Gain100


title: Patient 37_Gain100


title: Patient 32R2_Gain100


title: Patient 32R1_Gain100


title: Patient 33_Gain100


title: Patient 31R3_Gain100


title: Patient 31R1_Gain100


title: Patient 29R1_Gain100


title: Patient 34_Gain100


title: Patient 31R2_Gain100


title: Patient 30_Gain100


title: Patient 29R2_Gain100


title: Patient 38R2_Gain100


title: Patient 27R3_Gain100


title: Patient 27R2_Gain100


title: Patient 27R1_Gain100


title: Patient 26_Gain100


title: Patient 25R2_Gain100


title: Patient 22R2_Gain100


title: Patient 24R1_Gain100


title: Patient 25R1_Gain100


title: Patient 24R2_Gain100


title: Patient 23R1_Gain100


title: Patient 22R1_Gain100


title: Patient 23R2_Gain100


title: Patient 21_Gain100


title: Patient 20_Gain100


title: Patient 19R2_Gain100


title: Patient 19R1_Gain100


title: Patient 18R2_Gain100


title: Patient 17_Gain100


title: Patient 18R1_Gain100


title: Patient 16_Gain100


title: Patient 15_Gain100


title: Validation 2R2_Gain100


title: Patient 14R2_Gain100


title: Patient 12R3_Gain100


title: Patient 13R1_Gain100


title: Patient 12R1_Gain100


title: Patient 14R1_Gain100


title: Patient 13R2_Gain100


title: Patient 11R2_Gain100


title: Patient 12R2_Gain100


title: Patient 10R2_Gain100


title: Patient 11R1_Gain100


title: Patient 9R1_Gain100


title: Patient 9R2_Gain100


title: Patient 9R3_Gain100


title: Patient 10R1_Gain100


title: Patient 8R3_Gain100


title: Patient 8R2_Gain100


title: Patient 8R1_Gain100


title: Patient 7R2_Gain100


title: Patient 11R3_Gain100


title: Patient 7R1_Gain100


title: Patient 6R2_Gain100


title: Patient 6R1_Gain100


title: Patient 5R2_Gain100


title: Patient 6R3_Gain100


title: Patient 5R3_Gain100


title: Patient 5R1_Gain100


title: Patient 4R3_Gain100


title: Patient 4R1_Gain100


title: Patient 3R2_Gain100


title: Patient 4R2_Gain100


title: Patient 2R3_Gain100


title: Patient 3R1_Gain100


title: Patient 1R2_Gain100


title: Patient 28_Gain100


title: Patient 1R1_Gain100


title: Validation 7R2_Gain50


title: Validation 8R2_Gain50


title: Validation 7R1_Gain50


title: Validation 9_Gain50


title: Validation 8R1_Gain50


title: Validation 6R2_Gain50


title: Validation 4_Gain50


title: Patient 2R1_Gain100


title: Validation 6R1_Gain50


title: Validation 2R2_Gain50


title: Validation 5_Gain50


title: Validation 3_Gain50


title: Patient 40R1_Gain50


title: Patient 40R2_Gain50


title: Validation 1_Gain50


title: Validation 2R1_Gain50


title: Patient 39R2_Gain50


title: Patient 39R3_Gain50


title: Patient 37_Gain50


title: Patient 36_Gain50


title: Patient 39R1_Gain50


title: Patient 32R2_Gain50


title: Patient 38R2_Gain50


title: Patient 35_Gain50


title: Patient 31R3_Gain50


title: Patient 38R1_Gain50


title: Patient 31R1_Gain50


title: Patient 34_Gain50


title: Patient 38R3_Gain50


title: Patient 33_Gain50


title: Patient 29R2_Gain50


title: parental RK3E, biological rep1

city: Chicago

first: Joon Won

last: Yoon

state: IL

address: 2430 N Halsted

institute: Children's Memorial Reseach Center

description: Gene expression data from RK3E cells.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr on Rat 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Rattus norvegicus

source_name: RK3E cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: RK3E cells were maintained in DMEM supplemented with 10%FBS

extract_protocol:
400,000 RK3E cells in 60mm dish was transfected with 4 ug of GLI1 expression construct and 12 ul Lipofectamine 2000.
transformed cells form foci.  The individual focus was isolated and was maintained.
total RNA was purified according to the manufacturer's instructions (Qiagen).

tag: kidney cell


title: parental RK3E, biological rep2

description: Gene expression data from RK3E cells.


title: Patient 29R1_Gain50


title: transformed by GLI1 clone II, biological rep2

description: Gene expression data from RK3E cells transformed by GLI1.

source_name: transformed cells by GLI1


title: Patient 28_Gain50


title: Patient 2R2_Gain100


title: Patient 27R3_Gain50


title: Patient 30_Gain50


title: Patient 27R2_Gain50


title: transformed by GLI1 clone II, biological rep1


title: Patient 27R1_Gain50


title: Patient 26_Gain50


title: transformed by GLI1, biological rep1


title: transformed by GLI1 clone I, biological rep2


title: Patient 25R2_Gain50


title: Patient 24R2_Gain50


title: Patient 24R1_Gain50


title: Patient 31R2_Gain50


title: Patient 23R2_Gain50


title: Patient 25R1_Gain50


title: Patient 32R1_Gain50


title: Patient 22R2_Gain50


title: PA-TU-8988T_STY

city: Charlestown

first: Patricia

last: Greninger

department: Center for Molecular Therapeutics

institute: Massachusetts General Hospital Cancer Center

description: Hybridized to 250K_Sty

hyb_protocol: Labeling and hybridization was performed as described by the 500k assay manual (P/N 701930 Rev. 2)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the Dynamic Model Mapping algorithm) were processed by Bioconductor/PLASQ. PLASQ copy number and segmented copy number are included in Sample table. SNP genotype calls are provided as supplementary text files. Call data in the TXT files corresponding to the raw CEL files were generated using GTYPE ver. 4.0 with the Dynamic Model Mapping Algorithm. The threshold for Allele A, Allele B and Allele AB was 0.33.

source_name: Pancreas cell line PA-TU-8988T

extract_protocol: Genomic DNA was extracted Qiagen Blood Amp (P/N 51161).

tag: tissue

value: Pancreas

tag: cell line


title: SW 1573_STY

description: Hybridized to 250K_Sty

source_name: Lung:NSCLC cell line SW 1573

label_protocol: Labeling and hybridization was performed as described by the 500k assay manual (P/N 701930 Rev. 2)

value: Lung


title: SK-LU-1_STY

description: Hybridized to 250K_Sty

source_name: Lung:NSCLC cell line SK-LU-1


title: EZH1 bioChIP in Ezh2-/- cells on A chip

description: ChIP-chip

tag: antibody

tag: input 1

tag: input 2

tag: input 3


title: Patient 22R1_Gain50


title: Patient 23R1_Gain50


title: NCI-H358_STY

description: Hybridized to 250K_Sty

source_name: Lung:NSCLC cell line NCI-H358


title: NCI-H727_STY

description: Hybridized to 250K_Sty

source_name: Lung cell line NCI-H727


title: H3K27me3 ChIP in CJ7 cells on A chip

description: ChIP-chip

tag: genotype


title: NCI-H23_STY

description: Hybridized to 250K_Sty

source_name: Lung:NSCLC cell line NCI-H23


title: NCI-H441_STY

description: Hybridized to 250K_Sty

source_name: Lung:NSCLC cell line NCI-H441


title: NCI-H460_STY

description: Hybridized to 250K_Sty

source_name: Lung:NSCLC cell line NCI-H460


title: H3K27me3 ChIP in Ezh2-/- cells on A chip

description: ChIP-chip

tag: cell type

source_name: INPUT CONTROL


title: EZH1 bioChIP in Ezh2-/- cells on C chip

description: ChIP-chip

source_name: EZH1 bioChIP in Ezh2-/- cells (3 replicates)


title: Infected_kernel_28C_rep2

city: Raleigh

first: Carrie

middle: A.

last: Smith

state: NC

address: 2510 Gardner Hall

department: Department of Plant Pathology

institute: NC State University

hyb_protocol: Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip® and to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

scan_protocol: Standard Affymetrix protocols were followed  to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

data_processing: Only the A. flavus specific probes were used in this study.To extract perfect match values without mismatch probe data, dChip software was used (Li and Wong 2001).  The raw intensity values were imported into JMP Genomics (SAS, Cary, NC) and log2 transformed.  To determine if the expression of any NATs was affected by the change in temperature, the 352 NATs were analyzed separately.  The NAT log2 values were normalized across the six arrays using Loess normalization procedures (Colantuoni et al. 2002).  Analysis of variance (ANOVA) was performed and a false discovery rate of (0.05) was applied (Benjamini and Hochberg 1995) using normalized log2 values. Temperature was the class variable, fixed effect, and LSmeans effect.  To determine if expression of the sense transcripts corresponding to the NATs was affected by the temperature shift, the sense transcripts were analyzed separately using the same methods.  To determine the global effect of the temperature change on transcription, the 13,548 A. flavus elements were analyzed using the same methods.  The false discovery rate determines a p-value cut off for significant genes specific to each test: for the whole genome analysis a p-value cut off of 0.01 was used, for the antisense-only analysis a p-value cut off of 0.003343 was used, and for the sense-only analysis a p-value cut off of 0.012298 was used.

organism:
Zea mays
Aspergillus flavus

source_name: 8 inoculated kernels, 37C 4 days, 28C 1 day

growth_protocol: Maize inbred line B73 was grown in the field at Clayton, NC.  Ears containing kernels at the late milk to early dough stage of development (Ritchie et al. 1997) were harvested, placed on ice, and taken to the laboratory. Once in the laboratory, intact kernels were plucked from each ear.  Only sound, intact kernels with no visible injury were chosen.  Kernels were surface disinfested using the following protocol: kernels were dipped in 95% ethanol, transferred to a 10% bleach solution containing 0.1% Tween 20 and soaked for 4 minutes, transferred to autoclaved diH2O and soaked for 4 minutes, and transferred again to autoclaved diH2O and soaked for 4 minutes.  The kernels were then placed on sterile paper towels in a laminar flow hood and allowed to dry for 10-15 minutes.  Conidia from the wild-type A. flavus strain NRRL 3357, obtained from the National Center for Agricultural Utilization Research in Peoria, IL, were collected with 0.05% Triton-X100 from PDA plates incubated at 28ºC for 10 days.  Conidia were counted using a hemacytometer and a diluted conidial suspension of 1x106/ml was created using 0.05% Triton X-100.  A sterilized stainless steel pin was dipped into the conidial suspension and inserted once through the top of each kernel to a depth of approximately 5 mm.  Eight inoculated kernels from a single ear were placed in a glass scintillation vial.  Each maize ear served as a biological replicate in this study and  a fresh conidial suspension was used for each replicate.  The lids of each vial were tightened and then loosened by rotating the cap lid 360º.  This procedure provided uniform air exchange in the vials.

extract_protocol: The eight kernels from each vial were ground into a fine powder using a pestle in a mortar containing liquid nitrogen and glass beads (Sigma, St. Louis, MO). A 0.1g sample was set aside for AF analysis and the rest was used for RNA extraction.  The ground kernel/mycelia tissue was immediately transferred to an Oak Ridge centrifuge tube containing 5 ml phenol.  The tube was vortexed, 5 ml of 2M Tris buffer solution pH 7 (Acros Organics, Geel, Belgium) was added, and the tube was vortexed again.  The tubes were spun in a centrifuge at 10K rpm for 10 minutes at 4°C.  The supernatant was transferred to another Oak Ridge centrifuge tube containing 5 ml of 5:1 Phenol: Chloroform at pH 4.5 (Ambion, Foster City, CA).  The tubes were vortexed and spun in the centrifuge at 10K rpm for 10 minutes at 4°C.  The supernatants were transferred to an additional Oak Ridge centrifuge tube and the Phenol: Chloroform extraction was repeated.  The supernatant was transferred to another Oak Ridge centrifuge tube and two volumes of ice cold 95% ethanol were added.  The tubes were incubated at -20ºC for 1 hour and then spun at 10K rpm for 30 minutes at 4°C.  The liquid was decanted and the pellets were dried.  450 μl of buffer RLT was added as per the RNeasy RNA isolation kit instructions (Qiagen, Valencia, CA) and the rest of the protocol was performed, including DNase treatment.

treatment_protocol: The vials were incubated at 37ºC in the dark for 4 days.  Each day, the vials were briefly shaken to prevent moisture from collecting on the bottom of the vials.  After 4 days, half of the vials were moved to a 28ºC incubator.  The vials were incubated for one additional day (24 hours) at the respective temperatures.  After 5 days of incubation, the kernels were flash frozen in liquid nitrogen and stored at -80ºC until RNA extraction.

tag: Maize inbred line B73, A. flavus strain 3357


title: EZH1 bioChIP in CJ7 cells on C chip

description: ChIP-chip

source_name: EZH1 bioChIP in CJ7 cells (3 replicates)


title: Infected_kernel_28C_rep3


title: HPAF-II_STY

description: Hybridized to 250K_Sty

source_name: Pancreas cell line HPAF-II

value: HPAF-II


title: NCI-H2009_STY

description: Hybridized to 250K_Sty

source_name: Lung:NSCLC cell line NCI-H2009


title: EZH1 bioChIP in CJ7 cells on B chip

description: ChIP-chip


title: Infected_kernel_37C_rep3

source_name: 8 inoculated kernels, 37C 5 days


title: Infected_kernel_37C_rep2


title: Infected_kernel_28C_rep1


title: H3K27me3 ChIP in CJ7 cells on B chip

description: ChIP-chip

source_name: H3K27me3 ChIP in CJ7 cells (3 replicates)


title: H3K27me3 ChIP in Ezh2-/- cells on B chip

description: ChIP-chip

source_name: H3K27me3 ChIP in Ezh2-/- cells (3 replicates)


title: H3K27me3 ChIP in Ezh2-/- cells on C chip

description: ChIP-chip


title: H3K27me3 ChIP in CJ7 cells on C chip

description: ChIP-chip


title: EZH1 bioChIP in CJ7 cells on A chip

description: ChIP-chip


title: EZH1 bioChIP in Ezh2-/- cells on B chip

description: ChIP-chip


title: Infected_kernel_37C_rep1


title: Disc tissue 15

status: Public on Mar 24 2009

city: Charlotte

first: Helen

last: Gruber

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

description: CHTN specimen

hyb_protocol: Fragmented cRNA was hybridized to the  X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned once via the Affymetrix 3000G scanner.

data_processing: The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used.

source_name: Disc Tissue

label_protocol: Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.

extract_protocol: Cells were collected via laser capture mircodissection (LCM) and total RNA was isolated according to the Paradise reagent system.

value: Disc Tissue

tag: site

tag: grade

value: III


title: Disc tissue 14

description: Surgical specimen

value: IV


title: Disc tissue 10

description: CHTN specimen

value: II


title: Disc tissue 12

description: Surgical specimen


title: Disc tissue 5

description: Surgical specimen


title: Disc tissue 9

description: CHTN specimen


title: Disc tissue 11

description: CHTN specimen


title: Disc tissue 2

description: Surgical specimen


title: Disc tissue 8

description: CHTN specimen


title: Disc tissue 7

description: CHTN specimen


title: Disc tissue 3

description: Surgical specimen


title: Disc tissue 13

description: CHTN specimen

value: Lumbar


title: Disc tissue 6

description: Surgical specimen


title: Disc tissue 4

description: Surgical specimen


title: RL95-2 (Hind240)

first: Rameen

last: Beroukhim

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

scan_protocol: Standard Affymetrix protocol

data_processing: Genotyping was performed using Affymetrix Genotyping Tools Version 2.0.  dChip was used to normalize probe-level signal intensities to a baseline array with median intensity using invariant set normalization and obtain SNP-level signal intensities using a model-based (PM/MM) method,

source_name: endometrial cancer cell line

label_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

extract_protocol: biotin

treatment_protocol: Genomic DNA was isolated from tissue or cell pellets using SDS/proteinase K followed by phenol/chloroform and isopropanol precipitation, and quantified using Picogreen.


title: MFE319 (Hind240)


title: MFE296 (Hind240)


title: KLE (Hind240)

value: KLE


title: EFE184 (Hind240)


title: 75T (Hind240)

source_name: endometrial cancer

tag: gender

value: F

tag: histologic type

value: endometrioid

tag: metastatic phenotype

value: FIGO III/IV or recurrence


title: AN-3CA (Hind240)


title: Disc tissue 1

description: CHTN specimen


title: 95T (Hind240)

value: non-endometrioid

value: FIGO I/II and no recurrence


title: 83T (Hind240)


title: 6T (Hind240)


title: Ischikawaa (Hind240)

value: Ischikawaa


title: 87T (Hind240)


title: 8T (Hind240)


title: 78T (Hind240)


title: 67T (Hind240)


title: 63T (Hind240)


title: 4T (Hind240)


title: 51T (Hind240)


title: 45T (Hind240)


title: 46T (Hind240)


title: 441T (Hind240)


title: 439T (Hind240)


title: 430T (Hind240)


title: 456T (Hind240)


title: 436T (Hind240)


title: 445T (Hind240)


title: 435T (Hind240)


title: 48T (Hind240)


title: 443T (Hind240)


title: D08-864 Hodgkin cell line HDLM2 SNP 6.0 array

city: Kiel

first: Inga

last: Vater

address: Arnold-Heller-Strasse 3, Haus 10

department: Institute of Human Genetics

country: Germany

institute: Univeesity hospital Schleswig-Holstein

description: hybridized to 6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Cel files were processed using the Genotyping Console software version 3.0, algorithm-name: birdseed-v2, version 2.4

CN5 data provided as a supplementary file

source_name: Hodgkin cell line HDLM2

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using the Gentra Puregene DNA Isolation Kit (Qiagen, Hilden, Germany).

value: Hodgkin lymphoma HDLM2


title: 431T (Hind240)


title: D08-62 Hodgkin cell line L1236 SNP 6.0 array

description: hybridized to 6.0 array

source_name: Hodgkin cell line L1236

value: Hodgkin lymphoma L1236


title: D08-1255 Hodgkin cell line U-HO1 SNP 6.0 array

description: hybridized to 6.0 array

source_name: Hodgkin cell line U-HO1

value: Hodgkin lymphoma U-HO1


title: 426T (Hind240)


title: 405T (Hind240)


title: 41T (Hind240)


title: 37T (Hind240)


title: 32T (Hind240)


title: 367T (Hind240)


title: 336T (Hind240)


title: 334T (Hind240)


title: 31T (Hind240)


title: 38T (Hind240)


title: 30T (Hind240)


title: 394T (Hind240)


title: 325T (Hind240)


title: 328T (Hind240)


title: 324T (Hind240)


title: 306T (Hind240)


title: 290T (Hind240)


title: 288T1 (Hind240)


title: 293T (Hind240)


title: 213T (Hind240)


title: 235T (Hind240)


title: 225T (Hind240)


title: 214T (Hind240)


title: 256T (Hind240)


title: 234T (Hind240)


title: 279T (Hind240)


title: 262T (Hind240)


title: 206T (Hind240)


title: 247T (Hind240)


title: 272T (Hind240)


title: 244T (Hind240)


title: 202T (Hind240)


title: 201T (Hind240)


title: 185T (Hind240)


title: 168T (Hind240)


title: 162T (Hind240)


title: 14T (Hind240)


title: 177T (Hind240)


title: 172T (Hind240)


title: 129T (Hind240)


title: 161T (Hind240)


title: 108T (Hind240)


title: 10T2 (Hind240)


title: 110T (Hind240)


title: 128T (Hind240)


title: 141T (Hind240)


title: 113T (Hind240)


title: 111T (Hind240)


title: 159T (Hind240)


title: 192T (Hind240)


title: KLE (Xba240)


title: gln3deletion_3AT_rep#2

status: Public on Mar 01 2010

city: Indianapolis

first: Ron

last: Wek

state: IN

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description: Gene expression data from yeast.

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

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

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

organism: Saccharomyces cerevisiae

source_name: gln3 deletion, 3AT

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

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

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

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

tag: treatment

tag: strain

value: gln3 deletion


title: MFE-280 (Xba240)


title: MFE319 (Xba240)


title: 83T (Xba240)


title: 75T (Xba240)


title: EFE-184 (Xba240)


title: Ischikawaa (Xba240)


title: gcn4deletion_3AT_rep#4

description: Gene expression data from yeast.

source_name: gcn4 deletion, 3AT

value: gcn4 deletion


title: 104T (Hind240)


title: 78T (Xba240)


title: MFE-296 (Xba240)


title: RL95-2 (Xba240)


title: 95T (Xba240)


title: 101T (Hind240)


title: 8T (Xba240)


title: 6T (Xba240)


title: AN3-CA (Xba240)


title: 87T (Xba240)


title: 4T (Xba240)


title: 67T (Xba240)


title: 456T (Xba240)


title: 8T (expression)

hyb_protocol: Per manufacturer's instructions

scan_protocol: Agilent Microarray Scanner Bundle

data_processing: Signal intensities were determined using J-express, filtered to remove genes with low signal intensity, batch corrected, and mean-centered across the tumor set.

label_protocol: Per manufacturer's instructions

extract_protocol: RNA was isolated from tissue or cell pellets using Rneasy kit (Qiagen).

source_name: Stratagene Universal RNA


title: 45T (Xba240)


title: 5T (Xba240)


title: 443T (Xba240)


title: 48T (Xba240)


title: 445T (Xba240)


title: 354T (expression)


title: 63T (Xba240)


title: 51T (Xba240)


title: 46T (Xba240)


title: 456T (expression)


title: 441T (Xba240)


title: 445T (expression)


title: 342T (expression)


title: 439T (Xba240)


title: 436T (Xba240)


title: 441T (expression)


title: 430T (expression)


title: 443T (expression)


title: 394T (Xba240)


title: 405T (Xba240)


title: 431T (expression)


title: 436T (expression)


title: 435T (expression)


title: 435T (Xba240)


title: 431T (Xba240)


title: 41T (Xba240)


title: 430T (Xba240)


title: 426T (expression)


title: 38T (Xba240)


title: 405T (expression)


title: 116T (expression)


title: 37T (Xba240)


title: 426T (Xba240)


title: 40T (expression)


title: 95T (expression)


title: 367T (expression)


title: 38T (expression)


title: 367T (Xba240)


title: 336T (Xba240)


title: 394T (expression)


title: 334T (Xba240)


title: 83T (expression)


title: MCF7 treated with DZNep rep 1

city: Los Angeles

first: Tina

last: Miranda

state: CA

address: 1441 Eastlake Ave

institute: USC

description: MCF7 treated with DZNep

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The data was processed using Illumina Beadstudio which averaged the two raw data files. There is no normalization.

source_name: MCF7 cells were treated with DZNep and harvested after 72 h

label_protocol: According to Illumina protocol

extract_protocol: Qiagen RNAEasy Kit

value: MCF7 cells


title: 32T (Xba240)


title: 334T (expression)


title: 78T (expression)


title: 87T (expression)


title: 336T (expression)


title: 328 (Xba240)


title: MCF7 treated with DZNep rep 2

description: MCF7 treated with DZNep


title: MCF7 treated with 5-AzaCdR rep 2

description: MCF7 treated with 5-AzaCdR

source_name: MCF7 Cells treated with 1 uM 5-Aza-CdR and harvested after 72 h


title: 328 (expression)


title: gcn4deletion_Rap_rep#3

description: Gene expression data from yeast.

source_name: gcn4 deletion, Rap

value: Rapamycin


title: 6T (expression)


title: Untreated MCF7 rep 1

description: Untreated MCF7

source_name: Untreated MCF7 cells


title: 75T (expression)


title: 325T (expression)


title: MCF7 treated with 5-AzaCdR rep 1

description: MCF7 treated with 5-AzaCdR


title: Untreated MCF7 rep 2

description: Untreated MCF7


title: 325T (Xba240)


title: 30T (Xba240)


title: 324T (Xba240)


title: 67T (expression)