title: HBP ALL day 3 1uM MRK-003

description: T-ALL cell line

source_name: HBP ALL day 3 DMSO

source_name: HBP ALL day 3 1uM MRK-003


title: Exposed to Diamide 5 mM H37Rv (wild type)

status: Public on Aug 04 2007

type: RNA

city: Stanford

first: SMD

last: Staff

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description: Biological replicate 1 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. H37Rv (wild type)

hyb_protocol: The quality of cDNA labeling was monitored by quantitatively measuring the intensities of Cy3- and Cy5-labeled samples hybridized to the MTB genomic positive control spots.

scan_protocol: Microarrays were scanned using a GenePix 4000 A (Axon Instruments). The intensities of the two dyes at each spot were quantified using SCANALYZE (M. Eisen; http://rana.lbl.gov/EisenSoftware.htm).

data_processing: The overall reproducibility of the microarray experiments was evaluated using the Signifi-cance Analysis of Microarrays (SAM) program.  The SAM algorithm was set for two-class unpaired analysis with 500 permutations and K-nearest imputer for missing data. Significantly regulated genes were selected by adjusting the delta value to give a false discovery rate below 1%. In each data set, all genes regulated 1.5-fold and greater were determined to be significant with a false discovery rate of less than 1%, indicating a high degree of reproducibility.

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Cell culture untreated

label_protocol: All steps in the MTB DNA microarray gene expression analysis were performed as described. Controls for array quality were printed onto each slide and included a dilution series of MTB genomic DNA (positive control) and salmon sperm DNA (negative control). Additionally, DNA prelabeled with the cyanine dyes Cy3 or Cy5 were printed to ascertain whether spot-to-spot carryover contamination had occurred during the printing step.

growth_protocol: All the experiments were performed with M. tuberculosis H37Rv and its derivatives obtained during this study. Bacteria were grown in either Middlebrook 7H9 (liquid medium) or 7H10 (solid medium; Difco) both supplemented with ADN, 0.2% glycerol and 0.05% Tween 80. Liquid cultures were grown in roller bottles at 37 C. Plates were incubated at 37 C in sealed plastic bags. Escherichia coli strain JM109 was grown in Luria broth (LB; Difco) at 37 C in shaking cultures. When required, antibiotics were added at the following concentrations: kanamycin, 20 ug/ml for M. tuberculosis or 50 ug/ml for E. coli; hygromycin, 150 ug/ml for M. tuberculosis or 50 ug/ml for E. coli; ampicillin, 100 ug/ml; streptomycin, 20 ug/ml. Sucrose selection was performed on 7H10 plates with 8% sucrose.

extract_protocol:
RNA extraction for RTÐPCR experiments was performed as described previously. Briefly, bacteria were thawed on ice, broken with zirconia beads
(Biospec Products), extracted twice with phenolÐchloroformÐ isoamyl alcohol (25:24:1) and then precipitated in ethanol. To remove the chromosomal DNA, samples were treated twice with TRI reagent (Molecular Research Center) according to the manufacturerÕs instructions. RNA extraction for microarray experiments was performed using the following protocol: the frozen cell pellets were suspended in 1ml of Trizol reagent (Gibco BRL) and transferred to 2ml screw cap tubes containing 0.5 ml of 0.1-mm-diameter zirconia/silica beads (BioSpec Products). Cells were disrupted by two 30 s pulses in a BioSpec Products bead beater. After a 5 min incubation at room temperature, samples were centrifuged at maximum speed for 45 s, and the supernatants were transferred to 2ml Heavy Phase Lock Gel I tubes (Eppendorf) containing 300 ul of chloroformÐisoamyl alcohol (24:1), inverted rapidly for 15 s and incubated 2 min. The samples were centrifuged for 5 min, and the aqueous phase was added to 270 ul of isopropanol. After the addition of 270 ul of 0.8M Na citrate-1.2M NaCl, samples were incubated overnight at 4 C and centrifuged for 10 min at 4 C. The RNA pellets were washed with 1ml of 75% ethanol, centrifuged for 5 min and air dried. After suspension of the RNA pellets in 90 ul of water, 10 ul of DNase I 10x  buffer and 4 units of DNase I (Ambion) were added, and the samples were incubated for 30 min. Final purification of RNA used an RNeasy column (Qiagen).

treatment_protocol: Frozen cell pellets were suspended in 1 ml of Trizol reagent (GIBCOy BRL) and transferred to 2-ml screw-cap tubes containing 0.4-ml of 0.1-mm diameter zirconiaysilica beads (BioSpec Products, Bartlesville, OK).

tag: H37Rv (wild type)


title: Exposed to Diamide 5 mM H37Rv (wild type) rep1

description: Biological replicate 2 of 6. Cell culture exposed to Diamide 5 mM for 60 minutes. H37Rv (wild type)


title: koptk1 day 3 1uM MRK-003

status: Public on Aug 06 2007

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: T-ALL cell line

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

organism: Homo sapiens

source_name: koptk1 day 3 DMSO

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

growth_protocol: T-ALL cell lines were plated at a density of 5e4-1.5e5 cells per ml (depending on doubling time) and were treated with 1uM MRK-003 for 3 days.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: T-ALL cell line

source_name: koptk1 day 3 1uM MRK-003


title: Exposed to 0.05% SDS sigE mutant rep3

status: Public on Aug 03 2007

description: Biological replicate 4 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. sigE mutant

scan_protocol: Microarrays were scanned using a GenePix 4000 A (Axon Instruments). The intensities of the two dyes at each spot were quantified using SCANALYZE (M. Eisen)

extract_protocol: RNA extraction for RTÐPCR experiments was performed as described previously. Briefly, bacteria were thawed on ice, broken with zirconia beads(Biospec Products), extracted twice with phenolÐchloroformÐ isoamyl alcohol (25:24:1) and then precipitated in ethanol. To remove the chromosomal DNA, samples were treated twice with TRI reagent (Molecular Research Center) according to the manufacturerÕs instructions. RNA extraction for microarray experiments was performed using the following protocol: the frozen cell pellets were suspended in 1ml of Trizol reagent (Gibco BRL) and transferred to 2ml screw cap tubes containing 0.5 ml of 0.1-mm-diameter zirconia/silica beads (BioSpec Products). Cells were disrupted by two 30 s pulses in a BioSpec Products bead beater. After a 5 min incubation at room temperature, samples were centrifuged at maximum speed for 45 s, and the supernatants were transferred to 2ml Heavy Phase Lock Gel I tubes (Eppendorf) containing 300 ul of chloroformÐisoamyl alcohol (24:1), inverted rapidly for 15 s and incubated 2 min. The samples were centrifuged for 5 min, and the aqueous phase was added to 270 ul of isopropanol. After the addition of 270 ul of 0.8M Na citrate-1.2M NaCl, samples were incubated overnight at 4 C and centrifuged for 10 min at 4 C. The RNA pellets were washed with 1ml of 75% ethanol, centrifuged for 5 min and air dried. After suspension of the RNA pellets in 90 ul of water, 10 ul of DNase I 10x  buffer and 4 units of DNase I (Ambion) were added, and the samples were incubated for 30 min. Final purification of RNA used an RNeasy column (Qiagen).

tag: sigE mutant (H37Rv sigE::hyg)


title: Exposed to 0.05% SDS H37Rv (wild type) rep5

description: Biological replicate 6 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. H37Rv (wild type)


title: Exposed to 0.05% SDS sigE mutant

description: Biological replicate 1 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. sigE mutant


title: Exposed to 0.05% SDS sigE mutant rep4

description: Biological replicate 5 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. sigE mutant


title: Exposed to 0.05% SDS H37Rv (wild type) rep4

description: Biological replicate 5 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. H37Rv (wild type)


title: Exposed to 0.05% SDS sigE mutant rep2

description: Biological replicate 3 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. sigE mutant


title: Exposed to 0.05% SDS sigE mutant rep5

description: Biological replicate 6 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. sigE mutant


title: Comparison between H37Rv (wild type) and sigE mutant rep2

description: Biological replicate 3 of 3. Comparison between H37Rv (wild type) and sigE mutant. Cell culture untreated.


title: Exposed to 0.05% SDS H37Rv (wild type) rep2

description: Biological replicate 3 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. H37Rv (wild type)


title: Exposed to 0.05% SDS sigE mutant rep1

description: Biological replicate 2 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. sigE mutant


title: Exposed to 0.05% SDS H37Rv (wild type) rep3

description: Biological replicate 4 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. H37Rv (wild type)


title: Comparison between H37Rv (wild type) and sigE mutant rep1

description: Biological replicate 2 of 3. Comparison between H37Rv (wild type) and sigE mutant. Cell culture untreated.


title: Exposed to 0.05% SDS H37Rv (wild type) rep1

description: Biological replicate 2 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. H37Rv (wild type)


description: Biological replicate 1 of 3. Comparison between H37Rv (wild type) and sigE mutant. Cell culture untreated.


title: SHBL6_S24

city: Cardiff

first: Fiona

middle: Catherine

last: Mansergh

state: Wales

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

description: Arrays were repeated 12 times with fluor switching, in order to counteract any issues of dye bias that may have arisen from direct labelling. 6 biological repeats were carried out (6 ES cell RNA samples for each ES cell line) Scanned images were stored and filtered, then analysed using the program ImaGene™ 5.5 (BioDiscovery). Analysis  and other methods were carried out similarly to another published experiment, please see below and Mansergh et al. 2004 PMID: 15303089 for more details.

hyb_protocol: Array slides were incubated in prehybe for 1 hour at 42oC (50% formamide, 5XSSC, 0.1% SDS, 1% BSA). Targets were dried down via vacuum centrifugation then resuspended in 50l hybe solution (49.9% de-ionised formamide, 49.9% 20xSSC, 0.2% SDS) with added 1l Cot1 DNA and 1l poly A oligo as blocking agents, heated to 95oC for 5 minutes and then added to the face of one slide. The printed face of the second slide of the pair was then placed face to face with the first, using the same probe. Slide pairs were then placed on a level plastic cover above some 1xSSC moistened tissue in a slide box. The slide box was sealed with Nescofilm (Karlan Research Products Corporation, Santa Rosa, CA, USA), placed floating in a waterbath and  hybridized for 24-48 hours at 42oC.  Following hybridization, slides were washed once in Wash solution 1 (1X SSC, 2% SDS, filtered autoclaved ddH2O) for 20 minutes, then twice in Wash solution 2 (0.1X SSC, 0.2% SDS, filtered autoclaved distilled deionised H2O (ddH2O) for 20 minutes each. Slides were dipped in nuclease free filtered water, then spray dried, finally, the backs of the slides were cleaned with filtered autoclaved ddH2O, then wiped with 100% EtOH, then wiped dry and scanned.

scan_protocol: Scans were carried out at 12.5 micrometers, using the averaging setting (GeneTac LSIV scanner, (Genomic Solutions, Cambridgeshire, UK)). It is possible to carry out quick draft scans using this scanner, gain and black settings, which affect image intensity and background were varied slightly in order to optimize the signal/noise ratio for each channel and each slide before proper scans were initiated

data_processing:
Output files from ImaGene were saved in MS Excel spreadsheet format. MS Excel was used for all further data manipulation. We normalised each channel via total array methods, via calculation of the mean intensity value. Normalised intensities were then analysed using two different methods. Firstly, we transferred normalised intensity values for each experimental repetition into a separate Excel file, ensuring a standard order of samples. These data were then formatted for Significance Analysis of Microarrays (SAM; http://www-stat.stanford.edu/~tibs/SAM ). SAM analysis was carried out and genes that showed a fold change of 2 or above and that appeared in a SAM analysis as statistically significant above a delta value of 0.5 (which denotes an error rate of 5%) were selected for further appraisal. We supplemented SAM analysis with a second analysis method as follows: We subtracted the background median from the signal median, removing values of less than zero using the following equation :IF(k2>0,k2,0.0001), where k2 is the row and column number of the background subtracted data column. This equation replaced any negative values with 0.0001. The data column was then normalised by division by the mean, resulting in values >1 being above average intensity and vice versa.  The mean background + 2 standard deviations of the background were calculated from the median background column, and divided by the normalisation factor calculated above. Fold changes were calculated for control and experimental data, furthermore, datapoints that were below background + 2sd were rejected.
Meaningful data (above background + 2SD values, fold change of > 2) were retained, combined with similar data from other replicates and sorted via accession number. Genes that appeared above background + 2SD values with a fold change of > 2, in at least 9 out of 12 replicates were retained for further analysis. Finally, accession numbers obtained from this method and from SAM were compared. Genes appearing as differentially regulated using BOTH methods were deemed significant by us. In other words, significant ESTs are changed in expression by at least two fold, are above background + 2SD in at least one channel and have a delta value of 0.5 using SAM.  These ESTs were subjected to bioinformatic analysis and were ALL assessed via RT PCR in order to confirm array results.

molecule: cytoplasmic RNA

organism: Mus musculus

source_name: Undifferentiated mouse ES cell line SHBL6

label_protocol: Different RNA samples were used for labelling array repetitions. 10ug of total RNA was labelled with either Cy3 or Cy5 dyes using the CyScribe labelling system (GE Healthcare, Chalfont St.Giles, Bucks, UK), according to the manufacturer’s protocol. 1ul of labelled cDNA was combined with 2ul 50% glycerol, run on a ‘John gel’ (a microscope slide sized, 1.5% agarose gel) and scanned using a GeneTac LS IV scanner (Genomic Solutions, Huntingdon, Cambs. UK) in order to assess successful incorporation of label. Control and experimental samples were then combined and prepared for hybridization.

growth_protocol: ES cells were maintained in their undifferentiated state in the medium MEM-Alpha (GibcoTM, Invitrogen Ltd, Paisley, Renfrewshire, UK) supplemented with 10-4M -Mercaptoethanol (Merck KGaA, 64293 Darmstadt, Germany), 2mM glutamine and 10-3 U/ml murine LIF (ESGROTM, Invitrogen, Ltd, Paisley, Renfrewshire, UK), 10% FBS and 10% NBS (selected batches, PAA Laboratories GmbH, Linz, A-4020 Austria). The cells were maintained at 37oC in a humidified atmosphere with 5% CO2 on 0.1% gelatin (Stem Cell Technologies) coated tissue culture grade plastic ware (NUNCTM, Fisher Scientific, Loughborough, Leics, UK).

extract_protocol: ES cells were washed twice with DPBS-A and treated with trypsin-EDTA (Invitrogen Ltd., Paisley, UK). The cells were counted in a haemocytometer and appropriate cell numbers were pelleted by centrifugation at 200g. The QIAgen RNeasyTM Midi Kit (Qiagen Ltd., Crawley, Sussex, UK) was used according to the manufacturer’s protocol for RNA extraction. These RNA samples were quantified and checked for degradation via OD 260/280 spectrophotometry (Camspec, Cambridge, UK) and gel electrophoresis using dissociating conditions (NorthernMax™ buffers; Ambion, Huntingdon, UK), used according to the manufacturer’s protocol.

treatment_protocol: See growth protocol. These ES cell lines were maintained normally, as the purpose of this experiment was to detect differences between different ES cell lines under normal tissue culture conditions. All cell lines were at passage 23 when sampled.

source_name: Pooled control, pool of HM1, IMT11 and SHBl6.3 undifferentiated mouse ES cell lines, p23

tag: Pooled control consisting of equal amounts of RNA from 3 undifferentiated mouse ES cell lines, HM1, IMT11 and SHBl6.3, all at passage 23


title: Exposed to 0.05% SDS H37Rv (wild type)

description: Biological replicate 1 of 6. Cell culture exposed to 0.05% SDS for 90 minutes. H37Rv (wild type)


title: SHBL6_S2

tag: Undifferentiated mouse ES cell line SHBL6


title: IOBA3

city: Singapore

first: Louis

last: Tong

address: 11, Third Hospital Avenue

country: Singapore

institute: Singapore National Eye Center

description: Affymetrix protocol

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Genespring GX 7.3

label: Biotin

source_name: IOBA cells sample 3

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

tag: total RNA after cell lysis


title: NA12847 growth 1

status: Public on Aug 08 2007

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Probeset expression data from NA12847 growth 1

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix Power Tools package using Affymetrix default analysis settings and sketch quantile as normalization method.

label: biotin

source_name: CEU NA12847 Biological growth 1

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).

growth_protocol: Cells were grown at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin

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

treatment_protocol: Cells were harvested at a density of 0.8-1.1 x 10e6 cells/mL. Cells were then resuspended and lysed in TRIzol reagent

tag: Gender

value: male, Cell-type:lymphoblasts

tag: Coriell cell line repository identifier:GM12847


title: SHBL6_S4


title: SHBL6_S22


title: SHBL6_S12


title: SHBL6_S21


title: SHBL6_S9

scan_protocol: Scans were carried out at 12.5 micrometers, using the averaging setting (GeneTac LSIV scanner, (Genomic Solutions, Cambridgeshire, UK)). It is possible to carry out quick draft scans using this scanner, gain and black settings, which affect image intensity and background were varied slightly in order to optimize the signal/noise ratio for each channel and each slide before proper scans were initiated.


title: IOBA4

description: Affymetrix protocol

source_name: IOBA cells sample 4


title: PrimaryConj2

description: Affymetrix protocol

source_name: Primary conjunctival epithelial cells sample 2


title: SHBL6_S3


title: SHBL6_S10


title: SHBL6_S11


title: SHBL6_S1


title: IOBA5

description: Affymetrix protocol

source_name: IOBA cells sample 5


title: IMT11_S35

source_name: Undifferentiated mouse ES cell line IMT11


title: PrimaryConj3

description: Affymetrix protocol

source_name: Primary conjunctival epithelial cells sample 3


title: IMT11_S36

tag: Undifferentiated mouse ES cell line IMT11


title: IMT11_S32


title: IMT11_S8


title: PrimaryConj1

description: Affymetrix protocol

source_name: Primary conjunctival epithelial cells sample 1


title: IOBA1

description: Affymetrix protocol

source_name: IOBA cell sample 1

tag: Total RNA after cell lysis


title: SHBL6_S23


title: IMT11_S31


title: IOBA2

description: Affymetrix protocol

source_name: IOBA cells sample 2


title: IMT11_S7


title: IMT11_S34


title: IMT11_S33


title: Conjtissue4

description: Affymetrix protocol

source_name: Cpnjunctival tissue sample 4

tag: Total RNA after tissue homogenisation


title: Conjtissue3

description: Affymetrix protocol

source_name: Conjunctival tissue sample 3


title: Conjtissue2

description: Affymetrix protocol

source_name: Conjunctival tissue sample 2


title: IMT11_S19


title: ChWK3

description: Affymetrix protocol

source_name: Chang Conjunctival cells sample 3


title: HM1_S6

source_name: Undifferentiated mouse ES cell line HM1

tag: Undifferentiated mouse ES cell line HM1


title: IMT11_S20


title: ChWK4

description: Affymetrix protocol

source_name: Chang conjunctival cell sample 4


title: ChWK2

description: Affymetrix protocol

source_name: Chang conjunctival cells sample 2


title: IMT11_S17

source_name: Pooled control, pool of HM1, IMT11 and SHBl6.3 undifferentiated mouse ES cell lines, p23


title: Conjtissue1

description: Affymetrix protocol

source_name: Conjunctival tissue sample 1


title: HM1_S28


title: Spike-in at 0.25pmol with 18 replicates

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis Street

department: Stem Cell and Developmental Biology

institute: GIS

description: In this study, total mRNA was extracted from mouse hybridoma CRL1606 cells and divided equally into two samples. These two samples are essentially the same, but will be referred to as ‘Sample R’ and ‘Sample G’ for the sake of explanation. From self-hybridization results, 200 random genes were selected ensuring uniform representation of the whole intensity range to avoid expression intensity-biased spikes. mRNA that correspond to these 200 genes were obtained from in-vitro transcription, as described above.  RNA gel electrophoresis was performed on selected samples and quantified by a spectrometer (Genequant Pro RNA/DNA calculator, Amersham Biosciences). Due to inefficiency in in-vitro transcription, 31 of 200 genes were dropped. A total of 169 genes were used eventually. To create artificial differential expression, one group with 78 transcripts was mixed with Sample G and labelled with Cy3 whilst the other group with 91 transcripts was mixed with sample R and labelled with Cy5.  Since mRNA from Sample R and Sample G are the same, the only ‘truly’ differentially expressed genes should be those that were spiked in. The in vitro transcripts were spiked-in with 18 array replicates with a concentration of 0.25 pmol.

hyb_protocol: Standard hybridization protocol. Microarray slides were pre-hybridized at 45C for 1 hr, washed in ultra-pure water and dried by centrifugation. Labelled probes were added to hybridization buffer containing poly(dA) DNA, 10 nmol of NotINIAF primer, SalINIAT7 primer, Mouse Cot 1 DNA, Yeast tRNA, Cy3 landing light, and Cy5 landing light. SalINIAT7 and NotINIAF primers were added to block these sites on the cDNA and on the reporters.

scan_protocol: Standard scan protocol

data_processing: The intensities of all spots were background subtracted.  If the intensity after subtracting the background is smaller than twice the standard deviation of the overall background, the intensity is assigned to twice this standard deviation (Thomas et al, 2003). Normalization was performed with the Cross-correlation method (Chua et al, 2006). No dye bias was found for these sets of microarray data.

molecule: polyA RNA

source_name: mRNA spike-in

label_protocol: Cy3 labelled with standard protocol

extract_protocol: Trizol reagent (Life technologies). {Standard Extract protocol}

tag: mRNA spike-in

label_protocol: Cy5 labelled with standard protocol


title: HM1_S29


title: HM1_S5


title: IMT11_S18


title: HM1_s26


title: ChWk

description: Affymetrix protocol

source_name: Chang conjunctival cells

tag: Total RNA from cell lysate


title: HM1_S30


title: HM1_S27


title: Gene expression in wild type zebrafish larvae at 56 hours postfertilization

city: Norman

first: Han

last: Wang

state: OK

address: 101 David L. Boren Boulevard

department: Zoology/Stephenson Research and Technology Center

institute: University of Oklahoma

hyb_protocol: The labeled cDNA was added to ChipHybeTM hybridization buffer (Ventana Medical Systems, Tucson) containing Cot-1 DNA (0.5 mg/ml), yeast tRNA (0.2 mg/ml), and poly(dA)40-60 (0.4 mg/ml). Hybridization was performed on a Ventana Discovery system for 9 hr at 58 0C

scan_protocol: Agilent DNA Microarray Scanner Model G2505B with fluorescent intensity was measured by Imagene™ software

data_processing: ’associative analysis' method of Dozmorov & Centola, Bioinformatics 19:204-211, 2003. PubMed ID (PMID): 12538240

organism: Danio rerio

source_name: Wild type zebrafish larvae at 56 hours postfertilization

label_protocol: Direct labeling incorporating Cy3-dUTP in cDNA from 2 micrograms total RNA with anchored oligo-dT priming and Omniscript reverse transcriptase

growth_protocol: Embryos were growed at 28.5 0C according to a standard procedure (Westerfield. 2000. The zebrafish book)

extract_protocol: Trizol

treatment_protocol: Total RNA was obtained from approximately 50 larvae post-fertilization

tag: RNA obtained from wild-type zebrafish larvae at 56 hours postfertilization


title: Gene expression in mutant zebrafish larvae at 72 hours postfertilization

source_name: Mutant zebrafish larvae at 72 hours postfertilization

tag: RNA obtained from mutant zebrafish larvae at 72 hours postfertilization


title: Gene expression in mutant zebrafish larvae at 96 hours postfertilization

source_name: Mutant zebrafish larvae at 96 hours postfertilization

tag: RNA obtained from mutant zebrafish larvae at 96 hours postfertilization


title: HM1_S25


title: Gene expression in wild type zebrafish larvae at 96 hours postfertilization

source_name: Wild type zebrafish larvae at 96 hours postfertilization

tag: RNA obtained from wild-type zebrafish larvae at 96 hours postfertilization


title: Gene expression in mutant zebrafish larvae at 84 hours postfertilization

source_name: Mutant zebrafish larvae at 84 hours postfertilization

tag: RNA obtained from mutant zebrafish larvae at 84 hours postfertilization


title: HM1_S16


title: Gene expression in mutant zebrafish larvae at 56 hours postfertilization

source_name: Mutant zebrafish larvae at 56 hours postfertilization

tag: RNA obtained from mutant zebrafish larvae at 56 hours postfertilization


title: Gene expression in wild type zebrafish larvae at 84 hours postfertilization

source_name: Wild type zebrafish larvae at 84 hours postfertilization

tag: RNA obtained from wild-type zebrafish larvae at 84 hours postfertilization


title: HM1_S15

source_name: Pooled control

tag: Pooled control, pool of HM1, IMT11 and SHBl6.3 undifferentiated mouse ES cell lines, p23


title: Control fibroblast 7

status: Public on Aug 02 2007

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

description: average value computed from duplicate spots and technical replicates

hyb_protocol: Prehybridization was performed using 2x Hybridization Buffer (Genisphere, Hatfield, PA) according to the manufacturer protocol.

scan_protocol: The hybridized slides were scanned with GenePix 4200A scanner (Axon Instrument, Union City, CA) with PMT gains adjusted to obtain highest intensity unsaturated images. Gene PixPro software (Axon Instruments) was used for image analysis the of TIFF files, as generated by the scanner.

data_processing: Data from individual arrays were background corrected (using normexp method),  log transformed and normalized using Loess and G-quantile functions.The correlation between 3 duplicate spots per gene in each array were used to increase the robustness. Linear model was fitted for each gene given a series of arrays using lmFit function. Normalization was performed in R statistic environment using Limma package.

source_name: Total RNA from control fibroblast labeled with Cyanine-5 (red)

label_protocol: Total RNA (5μg) was reverse transcribed and labeled by Array 900 Expression Detection Kit (Genisphere, Hatfield, PA) according to the manufacturer protocol.

growth_protocol: Skin fibroblasts were cultured in the Dulbecco’s modified Eagle’s medium supplemented by 10 % fetal calf serum, 20mM HEPES pH 7.5, 0.2 % NaHCO3 and gentamycin 0.02 mg/ml at 37°C and 5 % CO2 in air

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: For experiments, confluent cell were harvested using 0.05 % trypsine and 0.02 % EDTA

tag: fibroblast

source_name: Total RNA from reference HeLa cell lines labeled with Cyanine-3 (green)

tag: HeLa


title: Control fibroblast 6


title: Control fibroblast 9


title: Control fibroblast 5


title: HM1 ES cell, slide 13

source_name: HM1 ES cell,

tag: Undifferentiated mouse ES cell line HM1, p23

tag: Pooled control consisting of equal amounts of RNA from 3 undifferentiated mouse ES cell lines, HM1, IMT11 and SHBl6.3, all at passage 23


title: Gene expression in wild type zebrafish larvae at 72 hours postfertilization

source_name: Wild type zebrafish larvae at 72hours postfertilization

tag: RNA obtained from wild-type zebrafish larvae at 72 hours postfertilization


title: Control fibroblast 4


title: Control fibroblast 1


title: Control fibroblast 2


title: Control fibroblast 3


title: Patient fibroblast 8

source_name: Total RNA from patient fibroblast labeled with Cyanine-5 (red)


title: Patient fibroblast 13


title: Patient fibroblast 9


title: Patient fibroblast 12


title: Patient fibroblast 10


title: Patient fibroblast 2


title: Patient fibroblast 6


title: Patient fibroblast 5


title: Patient fibroblast 3


title: Patient fibroblast 11


title: Patient fibroblast 1


title: Control fibroblast 8


title: HM1_Slide 14

source_name: Undifferentiated mouse ES cell line HM1

source_name: Pooled control, pool of HM1, IMT11 and SHBl6.3 undifferentiated mouse ES cell lines, p23


title: Patient fibroblast 7


title: Patient fibroblast 4


title: RNAPII_Gal+AlphaFactor_rep2

type: genomic

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

institute: Institut de recherches cliniques de Montréal (IRCM)

description: RNAPII occupancy measured by the IP/Input ratio in alpha-factor arrested-cells induced in galactose for 1 hour.

hyb_protocol: Resuspend Cy5 labeled IP in 4ul of water and combine with corresponding Cy3 labeled sample. Prepare the hybing solution planning to use 450ul for each slide (45ul 0.5M Mes NaOH (pH 6.9), 135ul Formamide, 58.5ul 5M NaCl, 45ul 5% N-Lauroylsarcosine (FLUKA), 1ul 250 ug/ml Salmon Sperm DNA, 10ul 8 mg/ml yeast tRNA, 5.4ul 0.5 M EDTA, 150.1ul mQH2O). Boil samples for 3 minutes in 100ºC heat block. Transfer to 40ºC heat block for another 10 minutes. Follow standard Agilent chamber hybridization protocols. Incubate overnight at 40C in hybridization oven. Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.

scan_protocol: Axon GenePix 4000B scanner and the GenePix Pro extraction software were used. Scan at 100% laser power for both channels. Set the "Pixel Size" to 5um / pixel. Set the "Lines to average" to 1. Set the "Focus Position" to 0um. Adjust PMTs so that approximately 1-2% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 when looking at intensity values greater than or equal to 3000 on the Intensity / Frequence histogram.

data_processing:
The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)).
The supplementary file contains the raw GPR and TIFF files.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol:
Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.
Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.
Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness. Phosphate Wash Buffer (100mL): 0.5mL 1M KPO4, pH 8.5 15.25mL ddH2O 84.25mL 95% EtOH Solution will be cloudy upon mixing. Phosphate Elution Buffer (10mL): 0.04mL 1M KPO4, pH 8.5 9.96mL ddH2O 1M KPO4, pH 8.5 (10mL): 9.5mL 1M K2HPO4 0.5mL 1M KH2PO4 1M Sodium Carbonate Buffer, pH 9.0 (100mL): 10.8g Na2CO3 80mL ddH2O pH to 9.0 with concentrated HCl Adjust volume to 100mL with ddH2O DILUTE 1:10 WHEN USING! Solution will change composition over time. Use only if less than a month old. Reference: Drouin S., Robert F. Methods (in press).

growth_protocol:
20 to 40 mL of YEP+2% Glucose were inoculated with 0.4 ml of over-night culture and incubated at 30ºC to OD600 0.8-1.0. The cells were then washed twice with water, transferred in 140 ml of YEP+2% Raffinose and incubated 10 to 12 hours until they reached OD600 of 0.5.
To arrest the cells in G1, alpha-Factor was added at a final concentration of 500ng/ml and the cells were incubated for 2 to 3 hours at 30ºC.
For the induction of new histone H3, Galactose 2% was added directly into the media for 1 hour.
The cells were crosslinked at the indicated time by adding the formaldehyde to a final concentration of 1 %.

extract_protocol:
Crosslinked cells are washed twice with 50mL ice cold TBS and quickly frozen by immersion in liquid nitrogen. Subsequently, they are thawed on ice, resuspended in 250uL breaking buffer and 500uL of acid-washed glass beads are added to the mixture. Then, cells are lysed using bead-beater (2x30 sec, with 5min breaks on ice). The whole cell extract is mixed with 500ul of FA-lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL Pepstatin) and centrifuged at 14000rpm for 1 minute. Then, the pellet is resuspended in 1 ml of FA-lysis buffer. This step is repeated. The resulting extract is sonicated (10X30sec) using Diagenode sonicator and subsequently centrifuged at 14000rpm for 30 minutes. The supernatant containing the sonicated chromatin is transferred to a new tube.
For the immunoprecipitation, 100ul of chromatin were added to 900 ul of FA-lysis buffer. After adding the antibody at the below indicated concentration, the mixture is incubated overnight at 4 ºC on wheel. Subsequently 12.5 ul of protein G sepharose beads are added and the incubation is continued for 4-6 hours. The beads are then washed twice with 1mL ice cold FA-lysis Buffer, twice with 1mL ice cold FA-lysis Buffer (500mM NaCl), twice with ice cold ChIP wash buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA) and once with ice cold TE. The bound proteins are eluted by incubating the beads at 65ºC for 20 minutes in 100ul of TE-SDS1%. To reverse the crosslinks the eluted material is incubated overnight at 65ºC.
To clean-up the DNA, the protein are digested by adding 100ul of TE, 1ul of glycogen (20mg/ml) and 7.5ul Proteinase K (20mg/ml) and incubated for 1 hour at 65ºC. The samples are then extracted with 350uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA is then precipitated with 1 ml of 100% ethanol and 12.5uL of 5M NaCl. After an overnight incubated at -20ºC, the samples are centrifuged at maximum velocity for 1 hour at 4ºC. The supernatant is discarded and the pellet is resuspended in 100ul of water.

tag: Strain

tag: antibody

value: 8WG16 anti-CTD of Rpb1 (Covance)


title: 1st MPSS library produced from activated CD4+ T cell clone 29

type: MPSS

city: Oxford

first: Edward

middle: J

last: Evans

state: Oxfordshire

address: HIU, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Nuffield Dept. Clinical Medicine

institute: University of Oxford

description: 1st MPSS library produced from a single sample of RNA from an activated CD4+ T-cell clone.

data_processing: Data file includes simply the tags identified and their counts in the library.  The supplementary data file contains the equivalent data after fewer cycles of the sequencing process (i.e. 17 base and 14 base MPSS tags) as provided by Lynx therpeutics.

source_name: human CD4+ T cell clone 29

growth_protocol: The clone was established in culture with IL-7 and the HIV-1 gag peptides KRWIILGLNKVIRMY and GEIYKRWIILGLNKI (but later shown to be specific for the former)

extract_protocol:
Total RNA was extracted from T cells using Trizol according to standard
methods and sent to Lynx therpeutics for the generation and sequencing of an MPSS library.

treatment_protocol:
T cells were activated with beads coated in monoclonal antibodies
specific for CD3 and CD28.

tag: CD4+ T cell clone 29 derived from PBMC from subject

tag: Immunogen

value: MVA virus containing HIV-1 gag gene

tag: Peptide Specificity

value: KRWIILGLNKVIRMY

tag: TCR usage


title: Asf1-dependence_rep2

description: Asf1 dependence measured by the Flag-H3 (WT/asf1D) ratio in alpha-factor arrested cells induced in galactose for 1 hour.

data_processing:
The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)).
The supplementary file contains GPR and TIFF files.

value: anti-Flag M2 "R" (Sigma)


title: RNAPII_Gal+AlphaFactor_rep1


title: Asf1-dependence_rep1


title: Asf1-dependence_rep3


title: H3-exchange_WT_rep1

description:
Histone H3 exchange measured by the Flag-H3/Myc-H3 ratio in alpha-factor arrested cells.
Flag-H3 is expressed in G1 using the GAL1 inducible promoter.
Myc-H3 is expressed from its endogenous promoter.

value: 9E10 anti-c-Myc (Babco)


title: Top1 distribution in HU(SUP fraction)

status: Public on Aug 01 2007

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: WCE fraction used for normalization of GSM205925.

hyb_protocol: Hybridization, blocking and washing steps were carried out as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). Each sample was hybridized to the array in 150ul containing 6XSSPE, 0.005% TritonX-100, 15ug fragmented denatured salmon sperm DNA (Gibco-BRL), and 1nmole of a 3’-biotin control oligonucleotide (oligo B2 probes) that hybridized to the border features on the array. Samples were heated to 100°C for 10 min., and then cooled on ice. Samples were hybridized for 16h at 42°C in a hybridization oven (GeneChip hybri oven 320, Affymetrix, CA). Washing and staining protocol (Mini_euk1 ver2) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix, CA).

scan_protocol: Each array was scanned by HP GeneArray Scanner (Affymetrix, CA) at an emission wavelength of 560nm at 7.5uM resolution. Grids were aligned to the scanned images using the know feature of the array. Primary data analyses were carried out using the Affymetrix Microarray Suite Ver.5.0 software to obtain hybridization intensity, fold change value, change p-value, and detection p-value for each locus.

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

source_name: Whole cell extract

label_protocol: DNA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998)

extract_protocol: 1.5X10^8 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (http://inside.wi.mit.edu/young/pub/locationanalysis.html). Purified DNA was random primed and amplified by the protocol of Brown’s lab (http://www.microarrays.org). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).

tag: Top1 with 10XFLAG tag was ChIPped from yeast cells arrested by HU.


title: Resting CD8 +Tcells_chipB

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description: To minimize biases in RNA amplification only one round amplification was performed and using similar incubations times and 200 ng of total RNA of good quality as template for the reverse transcription reaction.The quality and quantity of aRNA was monitored on agarose gel electrophoresis and by spectrophotometer. Typically, 10-20 ug of aRNA was generated from 200 ng of total RNA by one round of amplification and 10 ug of aRNA were employed for hybridization.

hyb_protocol: Labeled aRNA from CD8T cells and the lymphoid standard was combined in 6 ul of deionized water prior to the addition of poly (dA), human cot-1 DNA and yeast t-RNA at a final concentration of 10 ug each in a total volume of 45 ul containing 4.4 x SSC, 4.1 x Denharts and 50% formamide. Hybridisation and washing was described in following ref [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]

scan_protocol: Arrays were scanned using an Axon 4000 scanner at 10 um resolution and images were analyzed using Genepix 5.0 software (Axon Instruments, Union City, CA).

data_processing: The fluorescent intensity levels corresponding to each hybridized DNA spot was analyzed with Genepix 5.0 software (Axon Instruments, Union City, CA), and hybridized spots having signal-to-noise ratios below 1.25 and spots with blemishes were flagged and removed prior to further analysis. Local background was subtracted from the individual spots and intensities for each channel were normalized with respect to median intensity from each channel for the entire array. The raw expression data from all the time series were uploaded in BRB-ArrayTools software (Biometric Research Branch-NCI, MA) and global normalization was used to median center the log-ratios on each array in order to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes on different arrays. We excluded genes from the analysis showing minimal variation across time series experiments, and genes whose expression differed by at least 1.25 fold from the median in at least 20% of the arrays were retained. Adjusted data were further filtered to remove genes with opposite ratio values and genes differing more than 3 fold in duplicate analysis of the same  sample

label_protocol: aRNA was chemically labeled with a platinum-linked cyanine dye using the MicroMax ASAP RNA labeling kit (PerkinElmer, Boston, MA) as per the manufactures instruction. Briefly, 10 ug of aRNA was incubated at 85°C for 15 minutes with labeling buffer and either Cy5 or Cy3 in a total volume of 20 ul prior to termination of the reaction by cooling on ice and addition of 5 ul of stop buffer. Labeled aRNA was purified on MicroCon 50 columns before the final volume was reduced to 3 ul by vacuum centrifuge (Savant, Farmingdale, NY). aRNA from NK cells was labeled with Cy5

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA. For each time point, equal amounts of RNA from at least 3 different healthy donors were pooled prior to one round of RNA amplification using MessageAMPTm aRNA kit (Ambion, Austin, TX) according to the manufacturer’s instruction.

tag: RNA was extracted from CD8 positive cells of healthy individuals

source_name: Lymphoid RNA reference standard

label_protocol: same as channel1

extract_protocol: same as channel1

tag: amplified lymphoid RNA reference standard, consisting of RNA from tonsil, thymus, spleen, and cell lines derived from malignant pre-B cells, plasma cells and NK cells


title: BrdU incorporation at 60min. after HU treatment on Chr3,4,5.

description: BrdU incorporated regions after 1h in HU.

source_name: Chromatin-immunoprecipitated DNA by BrdU antibody

extract_protocol: BrdU immunoprecipitation in HU arrested cells were performed as previously described (Katou et al., Nature, 2003,424:1078-1083).

tag: Cells that can incorporate BrdU by expressing TK was used. Cells were arrested in HU for 60 min.


title: Tonsil_RNA_ChipB

hyb_protocol: Labeled aRNA from tonsillar cells and the lymphoid standard was combined in 6 ul of deionized water prior to the addition of poly (dA), human cot-1 DNA and yeast t-RNA at a final concentration of 10 ug each in a total volume of 45 ul containing 4.4 x SSC, 4.1 x Denharts and 50% formamide. Hybridisation and washing was described in following ref [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]

source_name: Tonsils from healthy individuals

tag: RNA was extracted from tonsils of several healthy donors


title: Top1 distribution in HU(ChIP fraction)

description: Top1 distribution in HU.

source_name: Chromatin-immunoprecipitated DNA by Top1

tag: Strain with 10XFLAG tagged Top1 was arrested by HU.


title: Top2 distribution in HU (SUP)

description: WCE fraction used for normalization of GSM205927.

source_name: WCE fraction used for normalization of Top2 in HU

tag: Strain expressing Top2 with 10XFLAG tagged was used. Cells were arrested by HU.


title: Patient 5

city: Belfast

first: Ken

last: Mills

address: 97 Lisburn Road

department: CCRCB

institute: Queens University Belfast

description: Patient 5 had t(11;17) and was RARA-PLZF negative, but very poor RNA quality which was associated with poor QC for cDNA and chip status.

hyb_protocol: Standard Affymetrix hybridisation protocol

scan_protocol: Scanned using Affymetrix scanner

source_name: AML Patient 5

label_protocol: Standard Affymetrix labeling protocol for IVT

extract_protocol: RNeasy extraction method from Qiagen

treatment_protocol: Diagnostic sample

tag: Bone marrow


title: NK_timepoint8hr_chipB_replicate

hyb_protocol: Labeled aRNA from NK cells and the lymphoid standard was combined in 6 ul of deionized water prior to the addition of poly (dA), human cot-1 DNA and yeast t-RNA at a final concentration of 10 ug each in a total volume of 45 ul containing 4.4 x SSC, 4.1 x Denharts and 50% formamide. Hybridisation and washing was described in following ref [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]

source_name: NK cells isolated from healthy individuals

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 8 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.


title: NK_timepoint 24hr_chipB_repeat

description: To minimize biases in RNA amplification only one round amplification was performed and using similar incubations times and 200 ng of total RNA of good quality as template for the reverse transcription reaction.The quality and quantity of aRNA was monitored on agarose gel electrophoresis and by spectrophotometer. Typically, 10-20 ug of aRNA was generated from 200 ng of total RNA by one round of amplification and 10 ug of aRNA were employed for hybridization

data_processing: The fluorescent intensity levels corresponding to each hybridized DNA spot was analyzed with Genepix 5.0 software (Axon Instruments, Union City, CA), and hybridized spots having signal-to-noise ratios below 1.25 and spots with blemishes were flagged and removed prior to further analysis. Local background was subtracted from the individual spots and intensities for each channel were normalized with respect to median intensity from each channel for the entire array. The raw expression data from all the time series were uploaded in BRB-ArrayTools software (Biometric Research Branch-NCI, MA) and global normalization was used to median center the log-ratios on each array in order to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes on different arrays. We excluded genes from the analysis showing minimal variation across time series experiments, and genes whose expression differed by at least 1.25 fold from the median in at least 20% of the arrays were retained. Adjusted data were further filtered to remove genes with opposite ratio values and genes differing more than 3 fold in duplicate analysis of the same sample.

label_protocol: aRNA was chemically labeled with a platinum-linked cyanine dye using the MicroMax ASAP RNA labeling kit (PerkinElmer, Boston, MA) as per the manufactures instruction. Briefly, 10 ug of aRNA was incubated at 85°C for 15 minutes with labeling buffer and either Cy5 or Cy3 in a total volume of 20 ul prior to termination of the reaction by cooling on ice and addition of 5 ul of stop buffer. Labeled aRNA was purified on MicroCon 50 columns before the final volume was reduced to 3 ul by vacuum centrifuge (Savant, Farmingdale, NY). aRNA from NK cells was labeled with

label_protocol: same as for channe1 extract

extract_protocol: same as for channe1 extract

tag: Amplified lymphoid RNA reference standard, consisting of RNA from tonsil, thymus, spleen, and cell lines derived from malignant pre-B cells, plasma cells and NK cells

tag: Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan

value: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.


title: Patient 4

description: Patient 4 has t(7;17) and was RARA-PLZF negative

source_name: AML patient 4

tag: Bone Marrow


title: H3-exchange_WT_rep2

tag: Strain

tag: antibody


title: H3-exchange_asf1D_rep1

description: H3 exchange in the asf1D mutant measured by the Flag-H3/Myc-H3 ratio in alpha-factor arrested cells induced in galactose for 1 hour.


title: Patient 3

description: Patient 3 had an insertion and was RARA-PLZF negative

source_name: AML patient 3


title: H3K56ac_rep1

description: H3K56ac measured by the H3K56ac/H3 ratio in alpha-factor arrested cells induced in galactose for 1 hour.

value: anti-H3K56ac (Upstate)

value: anti-H3 C-terminal  (Abcam)


title: BrdU incorporation at 60min. after HU treatment (WCE).

description: WCE fraction for normalization of BrdU distribution Analayses (GSM205929).

source_name: WCE fraction used for normalization of BrdU in HU

extract_protocol: BrdU immunoprecipitation in HU arrested cells were performed as previously described (Katou et al., Nature. 2003, 424:1078-1083).

tag: Cells that can incorporate BrdU by expressing TK was arrested by HU fro 60 min. and then used.


title: Patient 1

description: Patient 1 had t(11;17) translocation and was RARA-PLZF positive

source_name: AML patient 1


title: Patient 2

description: Patient 2 had t(11;17) translocation and was RARA-PLZF positive

source_name: AML Patient 2


title: H3K56ac_rep2

value: anti-H3 C-terminal (Abcam)


title: Top2 distribution in HU(ChIP fraction)

description: Top2 binding profile in HU.

source_name: Chromatin-immunoprecipitated DNA by Top2

tag: Strain expressing 10XFLAG tagged Top2 was used. Cells were arrested by HU.


title: Tonsil_ChipB_repeat

hyb_protocol: Labeled aRNA from tonsils and the lymphoid standard was combined in 6 ul of deionized water prior to the addition of poly (dA), human cot-1 DNA and yeast t-RNA at a final concentration of 10 ug each in a total volume of 45 ul containing 4.4 x SSC, 4.1 x Denharts and 50% formamide. Hybridisation and washing was described in following ref [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]

tag: RNA was extracted from tonsil.


title: CD4_T-cell_clone_activated_LongSAGE

type: SAGE

anchor: NlaIII

description: Standard Long SAGE library from a single CD4+ T-cell clone activated with anti-CD3 and anti-CD28 monoclonal antibodies.

data_processing: SAGE tags were extracted from the sequencing files using the Perl scripts of A G McArthur, with a cutoff at a Phred score of 10 for a reliable base call.  VALUE field contains raw counts for each tag sequence in the library of 503,431 tags.

source_name: human CD4+ T Cell clone 29

growth_protocol: The clone was established in culture with IL-7 and the HIV-1 gag peptides KRWIILGLNKVIRMY and GEIYKRWIILGLNKI (but later shown to be specific for the former).

extract_protocol: Total RNA was extracted from T cells using Trizol according to standard methods, and the I-SAGE Long kit (Invitrogen, Paisley, UK) was used to produce polyA RNA and derive a Long SAGE library with anchoring enzyme Nla III and tagging enzyme Mme I.  Concatamers of SAGE ditags were sequenced by standard dideoxy sequencing, and quality scores were assigned using Phred - raw sequence and quality scores are attached in the supplemental file.

treatment_protocol: T cells were activated with beads coated in monoclonal antibodies specific for CD3 and CD28.

tag: CD4+ T cell clone 29 derived from PBMC from subject

tag: Immunogen

tag: Peptide Specificity

tag: TCR usage


title: NK_timepoint24hr_chipB

tag: amplified lymphoid RNA reference standard, consisting of RNA from tonsil, thymus, spleen, and cell lines derived from malignant pre-B cells, plasma cells and NK cells


title: Resting NK0_chipB_replicate

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were immediately stored  in Trizol at -80°C till RNA isolation


title: H3-exchange_MNase_WT_rep1

description: H3 exchange from mononuclease digestion measured by the Flag-H3/Myc-H3 ratio in alpha-factor arrested cells induced in galactose for 1 hour.

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)).

extract_protocol:
The protocol for Mnase-ChIP assays is generally similar to the standard ChIP procedure. The following modifications were introduced. Cross-linked cells were washed twice with cold water, once with MNase buffer (15 mM Tris-HCl pH 8.0 , 50 mM NaCl, 1.4 mM CaCl2, 0.2 mM EGTA, and 0.2 mM EDTA) and resuspended in 400 ul of MNase buffer. The cell were lysed using bead-beater (2x30 sec, with 5min breaks on ice). The whole-cell-extract was then treated with different MNase concentrations. The concentration that digested chromatin to mononucleosomes (200 units/ml) was chosen and the reaction was stopped by adding 1/10 of the volume of the reaction mixture of 0.5M EGTA and of 10% SDS.  The cell lysate was centrifuged and the supernatant was diluted 1:2 with 2X FA lysis-buffer.
For the immunoprecipitation, 100ul of chromatin were added to 900 ul of FA-lysis buffer. After adding the antibody at the below indicated concentration, the mixture is incubated overnight at 4 ºC on wheel. Subsequently 12.5 ul of protein G sepharose beads are added and the incubation is continued for 4-6 hours. The beads are then washed twice with 1mL ice cold FA-lysis Buffer, twice with 1mL ice cold FA-lysis Buffer (500mM NaCl), twice with ice cold ChIP wash buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA) and once with ice cold TE. The bound proteins are eluted by incubating the beads at 65ºC for 20 minutes in 100ul of TE-SDS1%. To reverse the crosslinks the eluted material is incubated overnight at 65ºC.
To clean-up the DNA, the protein are digested by adding 100ul of TE, 1ul of glycogen (20mg/ml) and 7.5ul Proteinase K (20mg/ml) and incubated for 1 hour at 65ºC. The samples are then extracted with 350uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA is then precipitated with 1 ml of 100% ethanol and 12.5uL of 5M NaCl. After an overnight incubated at -20ºC, the samples are centrifuged at maximum velocity for 1 hour at 4ºC. The supernatant is discarded and the pellet is resuspended in 100ul of water.

tag: strain


title: NK_timepoint2_ChipB

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 2 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.


title: H3-exchange_asf1D_rep2


title: NK_timepoint8hr_chipB

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 8 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.


title: 16 year old male with classic medulloblastoma of Mstage 0, sandwich protocol (M16)

city: Heidelberg

first: Stefan

middle: M

last: Pfister

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

description: Comparison of tumor DNA (Cy3-labeled) vs. normal DNA (Cy5-labeled). Whole-genome screening of DNA copy-number aberrations using array-CGH

hyb_protocol: Ten micrograms each of tumor and reference DNA were combined with 300µg of human Cot-1 DNA (Roche Diagnostics, Mannheim, Germany) and suspended in 125µl of UltrahybTM hybridization buffer (Ambion, Bad Soden, Germany). Denaturation of combined DNA was performed at 75°C for 10 min, followed by preannealing at 37°C for 30 min. Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 37°C. Slides were washed with 2× SSC/0.05% Tween-20 at 37°C for 1 cycle, 2× SSC/0.05% Tween-20 at 44°C for 2 cycles, 50% formamide/2× SSC/0.1% Tween-20 at 44°C for 3 cycles, 2× SSC/0.05% Tween-20 at 44°C for 2 cycles, and finally 1× PBS/0.05% Tween-20 at 25°C for 2 cycles. Slides were dried by centrifugation at 54 g for 1 min, followed by centrifugation at 216 g for 1 min in a clinical centrifuge.

scan_protocol: Arrays were scanned at a 5µm resolution with an Axon 4000B scanner (Axon Instruments, Burlingame, USA) and images analyzed using GenePix Pro 6.0 software (Axon Instruments). Results files containing all relevant raw data were processed by use of ChipYard microarray analysis platform software (developed in-house), the statistical programming language R, and packages of the Bioconductor project; Ihaka and Gentleman, 1996).

data_processing: Fluorescence intensities of all spots were filtered consistently (intensity/local background >3; mean/median intensity <1.3; standard deviation of clone log2 ratios <0.2) and globally normalized using the printtip-loess algorithm (Smyth and Speed, 2003).

source_name: tumor DNA

label_protocol: Genomic DNA (300-500 ng) was labeled with Cy3-labeled dCTP (tumor) or Cy5-conjugated dCTP (control) by use of a BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany). Unincorporated nucleotides, random primers, and dyes were removed by use of MicroCon YM30 Spin Columns (Millipore, Schwalbach, Germany). Incorporation of dyes into the labeled DNA was determined by UV spectrophotometry.

extract_protocol: Genomic DNA from tumor tissue was isolated using the Blood and Cell Culture Kit (Qiagen,Hilden, Germany) following the instructions of the suppliers.  Genomic DNA from peripheral blood mononuclear cells of healthy donors was isolated by use of the Quiagen DNA Blood Midi-Kit (Hilden, Germany).

tag: tissue

value: 16 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with sandwich protocol

source_name: Pooled lymphocyte DNA from 10 healthy individuals (age 25-40 years)

value: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 11 year old female with classic medulloblastoma of Mstage 0, sandwich protocol (M15)

value: 11 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with sandwich protocol


title: 11 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1015)

value: 11 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Resting_NK0_A_ChipB

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were directly stored  in Trizol at -80°C till RNA isolation.


title: 4 year old male with classic medulloblastoma of Mstage 0, sandwich protocol (M10)

value: 4 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with sandwich protocol


title: Near term replicate 7

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

country: Norway

institute: Universitetet i Tromsø

description: Biological replicate 7 of 17. Placenta from labouring women vs. placenta from non-labouring women

hyb_protocol: Hybridizations were carried out with a TECAN HS4800 instrument using the formamide-based hybridization buffer from Genisphere containing 5% dextran sulphate and 0.5 micrograms COT1 DNA/?g RNA at 37°C for 23 hours. 3DNA dendrimer hybridizations were carried out in formamide-based hybridization buffer alone. Post-hybridization washes were carried out at room temperature with 2xSSC for 1 min, 0.2% SDS/2xSSC for 1 min and finally with0.2xSSC for 30 sec.

scan_protocol: Scanned on an AXON 4000B scanner Images were quantified using GenePix pro 6.0 software

data_processing: Images were quantified using GenePix pro 6.0 software. The background estimates were calculated using the morphological opening method. Spots that displayed a signal-to-noise ratio of less than 3 or that were significantly saturated (more than 20 % saturation among foreground pixels) were filtered out. The median was used as the averaging measure of the foreground pixels.  After quality control, genes that were present in less than 50 % of the arrays were filtered out. Normalization was carried out using lowess normalization Sample labelling was balanced across the groups, presumably attenuating any dye-effect. For the purpose of finding differentially expressed genes empirical Bayes analysis, using the LIMMA package was applied. The data were analysed using a two-component linear model. The prior guess of the number of D.E genes was set to 0.01. Multiple testing was accounted for by estimating the false discovery rate. We applied the Benjamini-Hochberg procedure, as well as Storeys less conservative Q-value procedure was applied. In none of the cases were any genes significant at a reasonable (15-20% FDR) level. In summary, a 2.5-fold change in expression of any gene that was present on ? 8 arrays was considered significant, if the difference in fluorescence intensity between two matched samples reached a p-value of < 0.01.

source_name: total RNA from placenta tissue

label_protocol: 1.55 micrograms of total RNA was reverse transcribed and labeled with Cy5-attached dendrimer using the Genisphere 3DNA HS kit (Genisphere) as described in the manufacturer’s protocol

extract_protocol: MagNa Pure Compact RNA Isolation Kit (Roche Applied Science)

tag: Placenta tissue from non-labouring women

label_protocol: 1.55 micrograms of total RNA was reverse transcribed and labeled with Cy3-attached dendrimer using the Genisphere 3DNA HS kit (Genisphere) as described in the manufacturer’s protocol

tag: Placenta tissue from labouring women


title: NK_timepoint2_ChipB_replicate

source_name: Lymphoid RNA reference standard

tag: Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan


title: Near term replicate 16

description: Biological replicate 16 of 17. Placenta from labouring women vs. placenta from non-labouring women

extract_protocol: Pure Compact RNA Isolation Kit (Roche Applied Science)


title: Near term replicate 11

description: Biological replicate 11 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: 8 year old female with large cell/anaplastic medulloblastoma of Mstage 3, sandwich protocol (1014)

value: 8 years old female patient with  large cell/anaplastic medulloblastoma of Mstage 3 ,treated postoperatively with sandwich protocol


title: Near term replicate 12

description: Biological replicate 12 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 6

description: Biological replicate 6 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 3

description: Biological replicate 3 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: 13 year old female with classic medulloblastoma of Mstage 0, Philadelphia protocol (1017)

value: 13 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 15 year old male with classic medulloblastoma of Mstage 3, sandwich protocol (879)

value: 15 years old male patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with sandwich protocol


title: Near term replicate 5

description: Biological replicate 5 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: 5 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1000)

value: 5 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 2 year old female with classic medulloblastoma of Mstage 0, infant protocol (772)

value: 2 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with infant protocol


title: Near term replicate 8

description: Biological replicate 8 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 9

description: Biological replicate 9 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 15

description: Biological replicate 15 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 17

description: Biological replicate 17 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 13

description: Biological replicate 13 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: 7 year old male with classic medulloblastoma of Mstage 2, Philadelphia protocol (704)

value: 7 years old male patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with Philadelphia protocol


title: Near term replicate 1

description: Biological replicate 1 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 4

description: Biological replicate 4 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: 1 year old female with nodular/desmoplastic medulloblastoma of Mstage 2, sandwich protocol (964)

value: 1 years old female patient with nodular/desmoplastic medulloblastoma of Mstage 2 ,treated postoperatively with sandwich protocol


title: 3 year old female with classic medulloblastoma of Mstage 0, sandwich protocol (738)

value: 3 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with sandwich protocol


title: Near term replicate 10

description: Biological replicate 10 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: Near term replicate 2

description: Biological replicate 2 of 17. Placenta from labouring women vs. placenta from non-labouring women


title: 5 year old female with  large cell/anaplastic medulloblastoma of Mstage 2, sandwich protocol (666)

description: Comparison of tumor DNA (Cy3-labeled) vs. normal DNA (Cy5-labeled). Whole-genome screening of DNA copy-number aberrations using array-CGH

value: 5 years old female patient with large cell/anaplastic medulloblastoma of Mstage 2 ,treated postoperatively with sandwich protocol


title: 3 year old male with classic medulloblastoma of Mstage 3, sandwich protocol (702)

value: 3 years old male patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with sandwich protocol


title: 6 year old male with classic medulloblastoma of Mstage 0, sandwich protocol (665)

value: 6 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with sandwich protocol


title: 6 year old male with classic medulloblastoma of Mstage 2, sandwich protocol (645)

value: 6 years old male patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with sandwich protocol


title: 8 year old male with classic medulloblastoma of Mstage 0, sandwich protocol (599)

value: 8 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with sandwich protocol


title: 2 year old female with classic medulloblastoma of Mstage 3, infant protocol (626)

value: 2 years old female patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with infant protocol

value: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 4 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (751)

value: 4 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 9 year old male with classic medulloblastoma of Mstage 2, sandwich protocol (639)

value: 9 years old male patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with sandwich protocol


title: 1 year old female with nodular/desmoplastic medulloblastoma of Mstage 0, infant protocol (528)

value: 1 years old female patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with infant protocol


title: 4 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (564)


title: 3 year old female with classic medulloblastoma of Mstage 2, sandwich protocol (557)

value: 3 years old female patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with sandwich protocol


title: 3 year old male with classic medulloblastoma of Mstage 1, sandwich protocol (501)

value: 3 years old male patient with classic medulloblastoma of Mstage 1 ,treated postoperatively with sandwich protocol


title: 5 year old male with classic medulloblastoma of Mstage 0, sandwich protocol (612)

value: 5 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with sandwich protocol


title: 1 year old male with nodular/desmoplastic medulloblastoma of Mstage 0, infant protocol (625)

value: 1 years old male patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with infant protocol


title: 13 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (518)

value: 13 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 2 year old male with nodular/desmoplastic medulloblastoma of Mstage 0, infant protocol (490)

value: 2 years old male patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with infant protocol


title: 7 year old male with classic medulloblastoma of Mstage 3, Philadelphia protocol (441)

value: 7 years old male patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: 3 year old male with classic medulloblastoma of Mstage 2, sandwich protocol (246)

value: 3 years old male patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with sandwich protocol


title: 3 year old male with nodular/desmoplastic medulloblastoma of Mstage 0, Philadelphia protocol (2M20)

value: 3 years old male patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 2 year old female with classic medulloblastoma of Mstage 2, infant protocol (242)

value: 2 years old female patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with infant protocol


title: 13 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M19)


title: 11 year old female with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M22)

value: 11 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 7 year old female with classic medulloblastoma of Mstage 2, Philadelphia protocol (2M21)

value: 7 years old female patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with Philadelphia protocol


title: 5 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (601)

value: 5 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 8 year old female with classic medulloblastoma of Mstage 0, Philadelphia protocol (575)

value: 8 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol

value: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 14 year old male with classic medulloblastoma of Mstage 3, Philadelphia protocol (2M18)

value: 14 years old male patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: 46 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M17)

value: 46 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 9 year old female with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M16)

value: 9 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 3 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M13)

value: 3 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 16 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M12)

value: 16 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 47 year old male with nodular/desmoplastic medulloblastoma of Mstage 0, Philadelphia protocol (2M11)

value: 47 years old male patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 3 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M10)


title: Stomach

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description: Using a quantitative alternative splicing (AS) microarray platform, we have identified a large number of widely-expressed mouse genes containing single or coordinated-pairs of alternative exons that are spliced in a tissue-regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural-specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS-tissues, relative to the other profiled tissues.

hyb_protocol: Mixed labeled cDNAs were added to hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate (MES), pH 6.5, 33% formamide and 40 μg herring sperm DNA (Invitrogen, Carlsbad, USA). Hybridizations were carried out in a final volume of 0.5 ml injecting into an Agilent hybridization chamber at 42°C on a rotating platform in a hybridization oven (Robbins Scientific Corporation, Sunnyvale, USA) for 16–24 h. Slides were then washed (rocking for approximately 30 seconds in 6 × SSPE, 0.005% sarcosine, then rocking for approximately 30 seconds in 0.06 × SSPE) and scanned with a 4000A microarray scanner (Axon Instruments, Union City, USA). Hybridizations were performed in duplicate with fluor reversal: that is, each mRNA sample was examined in duplicate, once in the Cy3 channel and once in the Cy5 channel, on separate arrays. Each array was hybridized with two samples simultaneously, each from an individual tissue.

scan_protocol: Slides were scanned with a 4000A microarray scanner (Axon Instruments, Union City, USA).

data_processing: TIFF images were quantitated with GenePix 3.0 (Axon Instruments). Individual channels were spatially denoised (i.e., overall correlations between spot intensity and position on the slide removed) by using spatial trend removal (STR) with 10% outliers. We applied variance stabilizing normalization (VSN) by using 25% of the genes to normalize all single channels to each other. Finally, we manually identified and removed data from residual artifacts apparent on microarray images and measurements that showed high inconsistency between dye-swaps.

label: Cy3 or Cy5

source_name: Pooled mouse CD1 strain stomach

label_protocol: The mRNA (1–2 μg) was reverse-transcribed with random nonamer primers (1 μg per reaction) and T18VN (0.25 μg per reaction) to synthesize cDNA. The reaction contained a 1:1 mixture of 5-(3-aminoallyl) thymidine 5'-triphosphate (Sigma, St. Louis, USA) and thymidine triphosphate (TTP) in place of TTP alone. The cDNA products were bound to QIAquick PCR Purification columns (Qiagen, Hilden, Germany) following the manufacturer's instructions, washed three times with 80% ethanol, and eluted with water. Purified cDNA was reacted with N-hydroxy succinimide esters of Cy3 or Cy5 (Amersham Pharmacia Biotech, Piscataway, USA) following the manufacturer's instructions.

extract_protocol: RNA was extracted using homogenization and Trizol reagent (Invitrogen, Carlsbad, USA) following the instructions from the manufacturer.

tag: Pooled mouse CD1 strain stomach


title: Striatum

source_name: Pooled mouse CD1 strain striatum

tag: Pooled mouse CD1 strain striatum


title: Spleen

source_name: Pooled mouse CD1 strain spleen

tag: Pooled mouse CD1 strain spleen


title: Teeth

source_name: Pooled mouse CD1 strain teeth

tag: Pooled mouse CD1 strain teeth


title: Liver

source_name: Pooled mouse CD1 strain liver

tag: Pooled mouse CD1 strain liver


title: Spinal Cord

source_name: Pooled mouse CD1 strain spinal cord

tag: Pooled mouse CD1 strain spinal cord


title: Cortex

source_name: Pooled mouse CD1 strain cortex

tag: Pooled mouse CD1 strain cortex


title: Midbrain

source_name: Pooled mouse CD1 strain midbrain

tag: Pooled mouse CD1 strain midbrain


title: Tongue

source_name: Pooled mouse CD1 strain tongue

tag: Pooled mouse CD1 strain tongue


title: Ovary

source_name: Pooled mouse CD1 strain ovary

tag: Pooled mouse CD1 strain ovary


title: Muscle

source_name: Pooled mouse CD1 strain muscle

tag: Pooled mouse CD1 strain muscle


title: Heart

source_name: Pooled mouse CD1 strain heart

tag: Pooled mouse CD1 strain heart


title: 5 year old male with nodular/desmoplastic medulloblastoma of Mstage 0, Philadelphia protocol (2M9)

tag: tissue

value: 5 years old male patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Kidney

source_name: Pooled mouse CD1 strain kidney

tag: Pooled mouse CD1 strain kidney


title: Eye

source_name: Pooled mouse CD1 strain eye

tag: Pooled mouse CD1 strain eye


title: Lung

source_name: Pooled mouse CD1 strain lung

tag: Pooled mouse CD1 strain lung


title: Hindbrain

source_name: Pooled mouse CD1 strain hindbrain

tag: Pooled mouse CD1 strain hindbrain


title: Testes

source_name: Pooled mouse CD1 strain testes

tag: Pooled mouse CD1 strain testes


title: Salivary

source_name: Pooled mouse CD1 strain salivary

tag: Pooled mouse CD1 strain salivary


title: 7 year old female with classic medulloblastoma of Mstage 1, Philadelphia protocol (2M15)

source_name: tumor DNA

value: 7 years old female patient with classic medulloblastoma of Mstage 1 ,treated postoperatively with Philadelphia protocol

source_name: Pooled lymphocyte DNA from 10 healthy individuals (age 25-40 years)


title: 35 year old female with nodular/desmoplastic medulloblastoma of Mstage 0, Philadelphia protocol (2M8)

value: 35 years old female patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Cerebellum

source_name: Pooled mouse CD1 strain cerebellum

tag: Pooled mouse CD1 strain cerebellum


title: Mammary

source_name: Pooled mouse CD1 strain mammary

tag: Pooled mouse CD1 strain mammary


title: Near term replicate 14

description: Biological replicate 14 of 17. Placenta from labouring women vs. placenta from non-labouring women

source_name: total RNA from placenta tissue

tag: Placenta tissue from labouring women

tag: Placenta tissue from non-labouring women


title: 19 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M6)

value: 19 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 4 year old male with classic medulloblastoma of Mstage 1, Philadelphia protocol (2M7)

value: 4 years old male patient with classic medulloblastoma of Mstage 1 ,treated postoperatively with Philadelphia protocol


title: Bladder

source_name: Pooled mouse CD1 strain bladder

tag: Pooled mouse CD1 strain bladder


title: E9

source_name: Pooled mouse CD1 strain E9

tag: Pooled mouse CD1 strain E9


title: E15

source_name: Pooled mouse CD1 strain E15

tag: Pooled mouse CD1 strain E15


title: Intestine

source_name: Pooled mouse CD1 strain intestine

tag: Pooled mouse CD1 strain intestine


title: 10 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M2)

value: 10 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Top2 distribution in G2(ChIP fraction)

description: Top2 Binding Profile in G2 phase

source_name: Chromatin-immunoprecipitated DNA by Top2

tag: Strain expressing 10XFLAG Top2 was arrested by Nocodazole.


title: 32 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M3)

value: 32 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 5 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M5)


title: Top2 distribution in G2 (SUP fraction)

description: This file is used for normalization of GSM206241.

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors.

source_name: SUP fraction after ChIP (equal to Whole cell extract DNA)


title: ES

source_name: Pooled mouse CD1 strain ES

tag: Pooled mouse CD1 strain ES


title: Top1 distribution in HU (SUP)

description: This file was used for the normalization of GSM206227.

source_name: Sup fraction after ChIP (equal to Whole cell extract DNA)

extract_protocol:
1.5X10^8 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (http://inside.wi.mit.edu/young/pub/locationanalysis.html). Purified DNA was random primed and amplified by the protocol of Brown’s lab (http://www.microarrays.org). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).
For the analysis of BrdU incorporated regions, total DNA from 3X10^8 cells was purified by Qiagen Genomic-tip system (P/N10223, QIAGEN, Germany). DNA was sheared to 300bp by sonication, denatured, and mixed with 2ug of anti-mouse IgG1 dynabeads (P/N110.12, Dynal AS, Norway) bound anti-BrdU monoclonal antibody (2B1D5F5H4E2, MBL, Japan). Immunoprecipitation and purification of antibody bound DNA fraction was carried out following the protocol of Cimbora et al. (Mol. Cel. Biol. 20, 5581-5591, 2000). Purified DNA was random primed and amplified by the Brown’s lab protocol. 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling.

tag: Strain expressing 10XFLAG Top1 was used.


title: 10 year old male with classic medulloblastoma of Mstage 3, Philadelphia protocol (2M4)

tag: tissue

value: 10 years old male patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: 8 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M32)

value: 8 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 18 year old female with classic medulloblastoma of Mstage 0, Philadelphia protocol (2M1)

value: 18 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 31 year old male with large cell/anaplastic medulloblastoma of Mstage 3, Philadelphia protocol (1M26)

value: 31 years old male patient with large cell/anaplastic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol

value: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 28 year old female with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M29)

value: 28 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 6 year old female with large cell/anaplastic medulloblastoma of Mstage 2, Philadelphia protocol (1M28)

value: 6 years old female patient with large cell/anaplastic medulloblastoma of Mstage 2 ,treated postoperatively with Philadelphia protocol


title: 7 year old male with large cell/anaplastic medulloblastoma of Mstage 3, Philadelphia protocol (1M24)

value: 7 years old male patient with large cell/anaplastic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: Brain

source_name: Pooled mouse CD1 strain brain

tag: Pooled mouse CD1 strain brain


title: Top2 distribution in HU(ChIP fraction), in HU for 2h

description: Top2 binding profile in HU after 2h.

tag: Cells expressing 10XFLAG Top2 were arrested by HU for 2hrs and then used.


title: 5 year old male with classic medulloblastoma of Mstage 3, Philadelphia protocol (1M25)

value: 5 years old male patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: 24 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M23)

value: 24 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Dpb3 distribution in HU after 1h.

description:
DPB3 distribution after 1h in HU.
For nomalization of this sample GSM206234 was used.

source_name: Chromatin-immunoprecipitated DNA by Dpb3

tag: Cells expressing 3XHA tagged DPB3 were used.


title: Dpb3 distribution in HU after 2h.

description:
Dpb3 binding profile after 2h in HU.
For nomalization of this sample GSM206234 was used.

label_protocol: NA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998)

tag: Cells expressing 3XHA tagged DPB3 were arrested by HU for 2hrs and then used.

tag: GSM206232 was used for normalization.


title: 12 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M22)

value: 12 years old male patient with cliassic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Top1 distribution in G2(SUP fraction)

description: SUP fraction used for the normalization of GSM206239.

tag: Strain expressing 10XFLAG Top1 was arrested by Nocodazole.


title: Top2 distribution in HU(SUP fraction),  after 2h treatment by HU

description: SUP fraction used for the normalization of GSM206235

tag: Strain expressing 10XFLAG tagged Top2 was used. Cells were arrested by HU for 2hrs.