title: breast cancer patient 258

status: Public on Dec 10 2007

first: Marc

middle: E.

last: Lenburg

address: 715 Albany Street, E613B

department: Genetics and Genomics

description: breast cancer histologically normal breast epithlieum patient 258

hyb_protocol: For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases.  15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm.  Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).

scan_protocol: The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: MAS5.0, target intensity = 500

source_name: breast epithelium adjacent to tumor

label_protocol: A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion.  In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY).  The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).

extract_protocol: Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.

tag: disease-state

value: breast cancer

tag: tissue-type

value: breast epithlieum

tag: patient-id

tag: age-at-biopsy-years


title: breast cancer patient 232

type: RNA

city: Boston

state: MA

country: USA

institute: Boston University School of Medicine

description: breast cancer histologically normal breast epithlieum patient 232

label: biotin

molecule: total RNA

organism: Homo sapiens


title: breast cancer patient 274

description: breast cancer histologically normal breast epithlieum patient 274


title: breast cancer patient 316

description: breast cancer histologically normal breast epithlieum patient 316


title: breast cancer patient 226

description: breast cancer histologically normal breast epithlieum patient 226


title: breast cancer patient 237

description: breast cancer histologically normal breast epithlieum patient 237


title: breast cancer patient 304B

description: breast cancer histologically normal breast epithlieum patient 304B


title: breast cancer patient 297B

description: breast cancer histologically normal breast epithlieum patient 297B


title: breast cancer patient 248

description: breast cancer histologically normal breast epithlieum patient 248


title: breast cancer patient 351

description: breast cancer histologically normal breast epithlieum patient 351


title: reduction mammoplasty patient 368

description: reduction mammoplasty histologically normal breast epithlieum patient 368

source_name: breast epithelium from reduction mammoplasty

value: normal (reduction mammoplasty)


title: breast cancer patient 318

description: breast cancer histologically normal breast epithlieum patient 318


title: breast cancer patient 359

description: breast cancer histologically normal breast epithlieum patient 359


title: reduction mammoplasty patient 340

description: reduction mammoplasty histologically normal breast epithlieum patient 340


title: breast cancer patient 251

description: breast cancer histologically normal breast epithlieum patient 251


title: breast cancer patient 320

description: breast cancer histologically normal breast epithlieum patient 320


title: reduction mammoplasty patient 328

description: reduction mammoplasty histologically normal breast epithlieum patient 328


title: reduction mammoplasty patient 347

description: reduction mammoplasty histologically normal breast epithlieum patient 347


title: reduction mammoplasty patient 360

description: reduction mammoplasty histologically normal breast epithlieum patient 360


title: reduction mammoplasty patient 352

description: reduction mammoplasty histologically normal breast epithlieum patient 352


title: reduction mammoplasty patient 350

description: reduction mammoplasty histologically normal breast epithlieum patient 350


title: reduction mammoplasty patient 361

description: reduction mammoplasty histologically normal breast epithlieum patient 361


title: reduction mammoplasty patient 357

description: reduction mammoplasty histologically normal breast epithlieum patient 357


title: reduction mammoplasty patient 334

description: reduction mammoplasty histologically normal breast epithlieum patient 334


title: reduction mammoplasty patient 314

description: reduction mammoplasty histologically normal breast epithlieum patient 314


title: reduction mammoplasty patient 278

description: reduction mammoplasty histologically normal breast epithlieum patient 278


title: reduction mammoplasty patient 288

description: reduction mammoplasty histologically normal breast epithlieum patient 288


title: reduction mammoplasty patient 310

description: reduction mammoplasty histologically normal breast epithlieum patient 310


title: reduction mammoplasty patient 309

description: reduction mammoplasty histologically normal breast epithlieum patient 309


title: polecell_st4_1G

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

description: To screen transcripts enriched in pole cells, primordial germ cells of Drosophila, during early embryogenesis, we compared the transcriptome between pole cells and whole body at the same developmental stage.

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/5-screw Hyb Chamber). See manufacturer's manual (#G4140-90010).

scan_protocol: Scanned using Agilent microarray scanner (G2565BA).

data_processing: Scanned data extracted with Agilent Feature Extraction Software were imported into GeneSpring software. Lowess normalization was applied.

organism: Drosophila melanogaster

source_name: Pole cells of fly embryos (stage 4)

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol. 100ng of total RNA was used.

extract_protocol: We used FACS to isolate pole cells from transgenic Drosophila embryos harboring the germ-line marker EGFP-Vas.

tag: Pole cells isolated from 4 (AEL

value: 1h20m-2h20m) fly embryos. Collected by FACS.

source_name: Whole body of fly embryos (stage 4)

extract_protocol: Stage 4 (AEL: 1h20m-2h20m) fly embryos were homogenized.

tag: Whole body of stage 4 (AEL

value: 1h20m-2h20m) fly embryos.


title: Whole Daphnia_20microg/LCadmium_48hr_rep1

status: Public on Dec 07 2007

city: Bloomington

first: Joseph

middle: R

last: Shaw

state: IN

address: 1315 E. Tenth Street

department: The School of Public and Environmental Affairs

institute: Indiana University

hyb_protocol: Hybridization followed recommendations given by The Institute for Genome Research (TIGR; Hedge et al. 2000). Samples were dried and resuspended in hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 20 microg SSDNA and 20 microg of poly(A)-DNA). The hybridization solution was placed on microarray and hybridization was accomplished overnight at 42 degrees C. Following hybridization, the glass slides were washed successively in a low stringency solution (0.1X SSC, 0.2% SDS) at room temperature for 4 minutes, twice in 0.1X SSC for 2.5 minutes, dipped in water, dried and immediately scanned.

scan_protocol: Images were quantified using GenePix Professional 3000 with GenePix Pro software (version 5.1).

data_processing: Signal intensities determined by GenePix Pro software version 5.1 (Axon Instruments, Union City, CA).

label: Alexa Fluor 647

organism: Daphnia pulex

source_name: Whole body, 20microg/L cadmium exposure, 48 hr

label_protocol: cDNA was labeled using amino-allyl labeling methods as given by The Institute for Genome Research (TIGR; Hedge et al. 2000).

growth_protocol: Genetically homogeneous Daphnia pulex were cultured in modified COMBO (Kilham et al. 1998) and kept at 20 degree C in an environmental chamber with a 16-h light/ 8-h dark cycle.  The D. pulex were fed daily Ankistrodesmus falcatus at a rate of 75,000 cells/mL. Stock culture medium were renewed and neonates seperated from adults three times weekly.

extract_protocol: Total RNA was extracted using Qiashredder columns (QIAGEN) and RNeasy Kit (QIAGEN) according to manufacturers recommendations followed by Dnase digestion (Ambion).

treatment_protocol: 48-h exposure to 20 microg/L cadmium as cadmium chloride

tag: Daphnia pulex, strain

tag: Age

value: 15 days

label: Alexa Fluor 555

source_name: Whole body, unexposed

treatment_protocol: 48-hr Unexposed


title: polecell_st4_1R

tag: Pole cells isolated from stage 4 (AEL


title: HEK293_untreated_rep2

status: Public on Dec 08 2007

city: Berkeley

first: Jonathan

middle: L

last: Bingham

state: CA

address: 733 Allston Way

institute: Jivan Biologics, Inc

description: HEK293 cell line untreated

hyb_protocol: NimbleGen expression protocol

scan_protocol: NimbleGen expression protocol

data_processing: Quantile-normalized raw data

source_name: HEK293 cell line untreated

label_protocol: Cy3-labeled cDNA were prepared from total RNA using NimbleGen protocol

extract_protocol: NimbleGen expression protocol

tag: tissue

value: kidney


title: Whole Daphnia_20microg/LCadmium_48hr_rep2


title: MCF7_untreated_rep1

description: MCF7 cell line untreated

source_name: MCF7 cell line untreated

value: breast


title: Whole Daphnia_20microg/LCadmium_48hr_rep3


title: MCF7_untreated_rep2

description: MCF7 cell line untreated


title: Capan1_untreated_rep1

description: Capan1 cell line untreated

source_name: Capan1 cell line untreated

value: pancreas


title: CoCa1_untreated_rep2

description: CoCa1 cell line untreated

source_name: CoCa1 cell line untreated

value: colon


title: MBG treated 9 hr (M_1.2 9)

city: Toledo

first: Khew-Voon

last: Chin

state: OH

address: 3000 Arlington Avenue

department: Medicine

institute: The University of Toledo College of Medicine

description: Duplicate

hyb_protocol: The HumanOneArray was hybridized using 2X Gex Hybridization Buffer (Agilent) for 17 h at 65oC; then washed in Gene Expression Wash Buffer 1 and 2 (Agilent) per manufacturer's instruction.

scan_protocol: The arrays were scanned with GenePix 4000B array scanner, images of the hybridized arrays were processed BioDiscovery's ImaGene and signal intensities quantified.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: Human Dermal Fibroblast

label_protocol: cDNA were synthesized from the isolated total RNA by reverse transcription followed by second strand synthesis using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion, Austin, TX) with oligo(dT) primer that contain a T7 RNA polymerase promoter sequence, according to the manufacturer’s specification.  In vitro transcription was then performed with the purified cDNA and amino allyl UTP was incorporated during transcription to produce amino allyl modified aRNA that was subsequently coupled to cy5 dye label.

growth_protocol: Human skin fibroblasts, obtained from Cambrex, were cultured at 37oC in 5% CO2.

extract_protocol: Total RNA was isolated using Qiagen's Rneasy column according to manufacturer's specification.

treatment_protocol: Cell were treated with 10 nM of marinobufagenin (MBG) for the indicated times follows by RNA isolation.

tag: Cell line


title: MBG treated 6 hr (M_1.2 6)

description: Duplicate


title: MBG treated 12 hr (M_1.2 12)

description: Duplicate


title: MBG treated 0.75 hr (M_1.2 0.75)

description: Duplicate


title: MBG treated 3 hr (M_1.2 3)

description: Duplicate


title: MBG treated 1 hr (M_1.2 1)

description: Duplicate


title: MBG treated 0.25 hr (M_1.2 0.25)

description: Duplicate


title: MBG treated 15 hr (M_1.2 15)

description: Duplicate


title: Saccharomyces cerevisiae oligo microarray_rep2_dictamnine

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in  hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.hybridization solution was denatured at 95  for 3 min prior to loading onto a microarray.then,hybridizing at a rotation speed of 8 rpm and a temperature of 42  overnight and washed with two consecutive solutions.

scan_protocol: LuxScanTM 3.0 software

data_processing: A space- and intensity-dependent normalization based on a LOWESS program,For further statistical analyses, The Significance Analysis of Microarrays (SAM ) add-in to Microsoft Excel was used to  compare the replicate arrays experiments.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae_dictamnine

label_protocol: cDNA products subjected to transcription reactions .Klenow enzyme labeling strategy was adopted after reverse transcription.

growth_protocol: S. cerevisiae strain L1190 was incubated in a rotary shaker. Subsequently, dictamnine stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the culture. Then, the yeast cells were further incubated for a certain time.

extract_protocol: Totole RNA was extracted by a hot acidic phenol method. Collart,M.A. & Oliviero, S. (1995). Preparation of yeast RNA.In Short Protocols in Molecular Biology, 3rd edn, (Ausubel F., Brent R., Kingston, R. T., Moode, D. D, Seidman, J. G., Smith, J. A. et al., Eds), pp. 13-46-13-47. John Wiley and Sons, Inc., New York, NY.

treatment_protocol: plant medcine  dictamnine

tag: strain L1190 refer to the previous study done by liang zhang et al 2002 JAC

source_name: Saccharomyces cerevisiae_DMSO

growth_protocol: S. cerevisiae strain L1190 was incubated in a rotary shaker. Subsequently,DMSO was added to the culture. Then, the yeast cells  were further incubated for a certain time.

treatment_protocol: DMSO


title: MBG treated 24 hr (M_1.2 24)

description: Duplicate


title: MBG treated 2 hr (M_1.2 2)

description: Duplicate


title: MBG treated 0 hr (M_1.2 0)

description: Duplicate


title: Saccharomyces cerevisiae oligo microarray_rep1_dictamnine

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in  hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.Hybridization solution was denatured at 95  for 3 min prior to loading onto a microarray.then,hybridizing at a rotation speed of 8 rpm and a temperature of 42  overnight and washed with two consecutive solutions.


title: CoCa1_untreated_rep1

description: CoCa1 cell line untreated


title: HEK293_untreated_rep4

description: HEK293 cell line untreated


title: HEK293_untreated_rep3

description: HEK293 cell line untreated


title: Saccharomyces cerevisiae oligo microarray_rep3_dictamnine


title: Capan1_untreated_rep2

description: Capan1 cell line untreated


title: HEK293_untreated_rep1

description: HEK293 cell line untreated


title: MBG treated 24 hr (M_1.1 24)


title: MBG treated 0.5 hr (M_1.2 0.5)

description: Duplicate


title: MBG treated 3 hr (M_1.1 3)


title: MBG treated 12 hr (M_1.1 12)


title: Untreated Control at 6 hr (C_1.2 6)

description: Duplicate


title: MBG treated 9 hr (M_1.1 9)


title: Untreated Control at 24 hr (C_1.2 24)

description: Duplicate


title: MBG treated 0.75 hr (M_1.1 0.75)


title: MBG treated 2 hr (M_1.1 2)


title: MBG treated 6 hr (M_1.1 6)


title: MBG treated 0.25 hr (M_1.1 0.25)


title: Untreated Control at 0 hr (C_1.2 0)

description: Duplicate


title: Untreated Control at 15 hr (C_1.2 15)

description: Duplicate


title: MBG treated 1 hr (M_1.1 1)


title: Untreated Control at 1 hr (C_1.2 1)

description: Duplicate


title: Untreated Control at 24 hr (C_1.1 24)


title: Untreated Control at 0.75 hr (C_1.2 0.75)

description: Duplicate


title: Untreated Control at 0.25 hr (C_1.2.25)

description: Duplicate


title: Untreated Control at 0.5 hr (C_1.2 0.5)

description: Duplicate


title: Untreated Control at 2 hr (C_1.2 2)

description: Duplicate


title: MBG treated 0.5 hr (M_1.1 0.5)


title: Untreated Control at 12 hr (C_1.2 12)

description: Duplicate


title: Untreated Control at 3 hr (C_1.2 3)

description: Duplicate


title: Untreated Control at 15 hr (C_1.1 15)


title: MBG treated 0 hr (M_1.1 0)


title: Untreated Control at 6 hr (C_1.1 6)


title: Untreated Control at 12 hr (C_1.1 12)


title: Untreated Control at 9 hr (C_1.2 9)

description: Duplicate


title: Untreated Control at 9 hr (C_1.1 9)


title: Untreated Control at 3 hr (C_1.1 3)


title: Untreated Control at 2 hr (C_1.1 2)


title: Untreated Control at 1 hr (C_1.1 1)


title: MycER tumor 120 (low Myc)

status: Public on Dec 05 2007

city: Baltimore

first: Tsung-Cheng

last: Chang

state: MD

address: 733 N. Broadway

institute: Johns Hopkins University School of Medicine

hyb_protocol: 1.  Pipet 35µL of the prehyb solution into one hyb portal of the hyb cap. Prehyb Solution: (prepare immediately before use) Amount appropriate for one array 22.5µL 20X SSC 1.5µL 10% SDS 15µL 10X (2%) BSA 111µL DEPC H2O Make sure there are no bubbles in the hyb chamber.  Also take care that none of the prehyb solution comes out of the hyb portal on the other side hyb chamber.	 Securely tape the hyb portals with Scotch Tape.  Place the hyb clamp assembly into a hyb tube fitted with a large kimwipe in such a way that the clamp assembly does not move.  Place the hyb tube into a hybridization oven, and allow to rotate for a minimum of 1 hour at 37°C. 2.  Prepare hybridization buffer: (amounts are per sample) 17.5µL 2X Hyb Solution (7.5mL 1M Na2HPO4, 150mg BSA, 0.938g Ultrapure SDS, 1.88ml DEPC Water) 4.2µL DI Formamide 7.3µL DEPC Water Add labeled RNA to 29µL of hybridization buffer. 3.  Heat sample for 3 minutes at 95°C. 4.  Remove prehyb solution from the hyb portals.  Add 35µL of sample-hyb mix directly to hyb portals Make sure there are no bubble in the hyb chamber.  Also take care that none of the hyb solution comes out of the hyb portal on the other side hyb chamber. 5.  Securely tape the hyb portals with Scotch Tape.  Place the hyb clamp assembly into a hyb tube fitted with a large kimwipe in such a way that the clamp assembly does not move.  Place the hyb tube into a hybridization oven, and allow to rotate overnight at 37°C. 6.  Remove hyb solution from the hyb portals.  Quickly rinse the chambers with Wash #1 (2X SSC, 0.025% SDS).  Remove Wash, and refill chambers with 35µL Wash #1.  Incubate at room temp for 3 minutes. 7.  Remove Wash #1, and quickly rinse chambers with 35µL Wash #2 (1.6X SSC). Remove Wash, and refill chambers with 35µL Wash #2.  Incubate at room temp for 3 minutes.  Repeat 2 more times. 8.  Remove Wash #2, and quickly rinse chambers with 35µL of ice cold Wash #3 (0.8X SSC) in a cold room. Remove Wash, and refill chambers with 35µL Wash #3.  Incubate at 4°C room temp for 3 minutes.  Repeat 2 more times.  Remove all wash solution. 9.  Remove array from hyb clamp, and remove hyb cap. 10.  Add 1 or 2 drops of Imaging Solution (from Combimatrix) to array. 11.  Carefully clean hyb cover slips with 70% EtOH. 12.  Using forceps, place cover slip over semiconductor portion of array, with the white (rough) strips down, making sure no bubbles are trapped.  Blot excess solution from edges of cover slip. 13.  Keep in the dark until ready to scan.

scan_protocol: Scan with GenePix 4000B microarray scanner.

data_processing: Hybridization signals extracted using Combimatrix Microarray Imager software. VALUE column represents median-normalized, background-subtracted hybridization signals.

organism: Mus musculus

source_name: MycER tumor following estradiol withdrawal (low Myc)

label_protocol:
1. Assemble RNA Labeling Reaction:
 (amounts are per sample to be tested)
1.2µL 10X Iglori Buffer
1.2mL 100% DMSO
1µL .105µM Bio B Primer
1µL .35µM Bio C Primer
2µL Cy-3 (250ng/µL)
1µL 20U/µL T4 RNA Ligase
Add 7.4µL Labeling Solution to 5µL of 10µg Total RNA
	Incubate on ice for 2 hours.
2.  After 2 hours of labeling, add 46µL of RNA precipitation solution:
(prepare immediately before use)
40µL DEPC Water
5µL 3M Sodium Acetate (pH5.2)
1µL Glycogen
Add 150µL of 100% ethanol and finger vortex.  Place on ice for 10 minutes.  Centrifuge for 10 minutes, max speed @ 4°C.  Remove supernatant.  Add 150µL of 70% ethanol.  Finger vortex.  Spin 5 minutes, max speed @ 4°C.  Remove ethanol.  Briefly spin again at max speed.  Remove remaining ethanol with a p20 pipet.  Let pellet air dry for 2-3 minutes. Resuspend pellet with 6µL DEPC water.

extract_protocol: Trizol according to manufacturer's instructions


title: MycER tumor 119 (high Myc)

source_name: MycER tumor treated with estradiol (high Myc)


title: MycER tumor 121 (low Myc)

tag: MycER tumor following estradiol withdrawal (low Myc)


title: Untreated Control at 0.75 hr (C_1.1 0.75)


title: P493 +tet (low Myc)

source_name: P493 cells treated with tetracycline for 72 hours

label_protocol:
1. Assemble RNA Labeling Reaction:
 (amounts are per sample to be tested)
1.2µL 10X Iglori Buffer
1.2mL 100% DMSO
1µL .105µM Bio B Primer
1µL .35µM Bio C Primer
2µL Cy-3 (250ng/µL)
1µL 20U/µL T4 RNA Ligase
Add 7.4µL Labeling Solution to 5µL of 10µg Total RNA
	Incubate on ice for 2 hours.
2.  After 2 hours of labeling, add 46µL of RNA precipitation solution:
(prepare immediately before use)
40µL DEPC Water
5µL 3M Sodium Acetate (pH5.2)
1µL Glycogen
Add 150µL of 100% ethanol and finger vortex.  Place on ice for 10 minutes.  Centrifuge for 10 minutes, max speed @ 4°C.  Remove supernatant.  Add 150µL of 70% ethanol.  Finger vortex.  Spin 5 minutes, max speed @ 4°C.  Remove ethanol.  Briefly spin again at max speed.  Remove remaining ethanol with a p20 pipet.  Let pellet air dry for 2-3 minutes.  Remove supernatant. Resuspend pellet with 6µL DEPC water.


title: MycER tumor 118 (high Myc)

tag: MycER tumor treated with estradiol (high Myc)


title: P493 -tet (high Myc)

source_name: P493 cells

tag: P493 cells


title: Untreated Control at 0.25 hr (C_1.1 0.25)


title: e.coli_1%tannin_#5

status: Public on Dec 06 2007

city: Waukesha

first: Alexandra

middle: H

last: Smith

state: WI

address: W227 N752 Westmound Dr

department: Ruminant Research

institute: Agtech Products

description: Microarray Core Facility University Of Illinois Urbana-Champaign

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix Microarray Suite 5.0

label: Biotin

organism: Escherichia coli

source_name: Escherichia coli continuous culture with 1% tannins

label_protocol: Standard Affymetrix protocol

growth_protocol:
Dilution rate = 0.14/h
Incubation temperature = 37C
pH = 5.3

extract_protocol:
Qiagen Rneasy mini kit
Promega RNase-free DNase

tag: Escherichia coli BW13711 grown anaerobically in continuous culture in MOPS medium plus 0.4% glucose with 1% Acacia mearnsii condensed tannins.


title: E.coli_1%tannin_#3

source_name: Escherichia coli with 1% tannins


title: E.coli_0%tannin_#2

source_name: Escherichia coli continous culture without tannins

growth_protocol:
Dilution rate = 0.14/h
Incubation temperature = 37C
pH = 5.7

tag: Escherichia coli BW13711 grown anaerobically in continuous culture in MOPS medium plus 0.4% glucose without Acacia mearnsii condensed tannins.


title: Untreated Control at 0.5 hr (C_1.1 0.5)


title: E.coli_0%tannin_#8


title: Col-0 vs rot3-1

type: genomic

city: Kitashirakawa, Sakyoku

first: Ikuko

last: Hara-Nishimura

state: Kyoto

address: Oiwakecho

department: Depertment of Botany

institute: Kyoto University

description: The full-output file from Feature Extraction Software was attached as a Supplementary file.

hyb_protocol: Hybridization was performed with an Oligo aCGH/ChIP-on-Chip Hybridization Kit (Agilent Technology) according to the standard protocol, except that Cot-1 DNA was not added to the hybridization solution. After 24-h, the microarray was washed in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technology) for 5 min at room temperature, in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technology) for 1 min at 37 ˚C and in acetonitrile for 1 min at room temperature.

scan_protocol: Immediately after washing the microarray slide was scanned by a DNA microarray scanner (Agilent Technologies).

data_processing: The signals were quantified and normalized of signals were performed with Feature Extraction Software ver. 9.1 (Agilent Technologies) with default parameters.

molecule: genomic DNA

organism: Arabidopsis thaliana

label_protocol: One half of the genomic DNA was digested with RsaI/AluI and the half was digested with DraI. The DNA digested by two sets of restriction enzymes was mixed and used for labeling reaction. Genomic DNA (0.6 micro g) was used for labeling reaction with a Genomic DNA Labeling Kit (Agilent technology) according to direct labeling protocol.

extract_protocol: Genomic DNA was extracted with a DNeasy Plant Mini Kit (Qiagen, Valencia, CA). Double-stranded DNA was quantified with a Quant-iT dsDNA Broad-Range Assay Kit (Invitrogen, Carlsbad, CA). Quality of genomic DNA prepared was checked by agarose gel electrophoresis.

tag: Arabidopsis thaliana Col-0.

tag: Arabidopsis thaliana mutant rot3-1 reported in Kim et al.,(1998) Gene Dev.. 12, 2381-91.


title: Untreated Control at 0 hr (C_1.1 0)


title: Col-0 vs zig-2

tag: Arabidopsis thaliana mutant zig-2 reported in Kato et al.,(2002) Plant Cell. 14, 33-46.


title: DRG_sema3A_12h_rep2

status: Public on Dec 04 2007

city: Princeton

first: Moriah

last: Szpara

state: NJ

address: 301 Schultz

department: Molecular Biology

institute: Princeton University

hyb_protocol: All SCG samples were hybridized to Affymetrix MG-U74v2 A and B arrays, and DRG samples were hybridized to MOE430A arrays. All hybridizations were performed via Affymetrix protocols at the Stanford Protein and Nucleic Acid Biotechnology Facility.

scan_protocol: All scans were performed via Affymetrix protocols at the Stanford Protein and Nucleic Acid Biotechnology Facility.

data_processing: Since SCG and DRG samples used two different series of Affymetrix arrays, the data for each was extracted separately.  gcrma (version 1.1) was used to extract data.  To balance the median array intensity between array platforms, a constant value of 1.83 was added to the logged intensity values for the SCG (MG-U74v2) arrays.  Based on Affymetrix probeset descriptions and the disproportionate number of low-intensity probesets in these categories, probesets annotated as incomplete (i), rules dropped (r), or cross-hybridizing (x) were excluded.  Data for each group of arrays was baselined to the appropriate (SCG or DRG) acutely-dissected reference pool.  This facilitated comparison between Affymetrix platforms as well as to spotted microarray data.  The Affymetrix same-species best-match comparison spreadsheet was used to match probe sets between platforms used for SCG and DRG hybridizations.  Due to redundancies in the older array design, multiple probe sets on the U74v2 arrays have the same best match in the 430A design.  For these cases, the Affymetrix probe descriptions were used to determine a single best match, by selecting if possible the probeset match without any annotation qualifier, followed in decreasing preference those with g, f, or s annotations.  The final dataset included 11,268 probesets matched across platforms; these were used for all further analysis.

source_name: DRG explant cultured for 12 hours in vitro, in the presence of Sema3A

label_protocol: For each microarray sample, 50-500 ng of total RNA was amplified using a modified Eberwine procedure.  200 ng of T7-oligo dT primer was added to each (AAATTAATACGACTCACTATAGGGAGACCACA(T)21)).  A 20 µl reverse transcription reaction was carried out for each sample using Superscript III (SSIII; Invitrogen) as per manufacturer’s protocol, with reaction time extended to 16 hours.  Second strand cDNA synthesis utilized DNA ligase, DNA polymerase I holoenzyme (both New England Biolabs, Ipswich, MA), dNTPs, and second strand buffer (Invitrogen) for 2-6 hours at 16 degrees C.  cDNA was isolated by phenol chloroform extraction and precipitated.   cRNA was produced from cDNA with an Ambion T7 Megascript kit, and collected via Qiagen RNeasy column.  RNA was quantitated by spectrophotometer and gel electrophoresis.  Second round amplification followed the Affymetrix Small-Sample Target Labeling Assay Version II from step 6 onward.  Biotin-labeled cRNA was made using the BioArray High Yield RNA Transcript Labeling kit (Enzo Diagnostics, Farmingdale, NY) and eluted by RNeasy column.  cRNA was fragmented according to Affymetrix protocol.

growth_protocol: For each culture, embryonic explants were dissected from two litters of outbred CD1 mice of either embryonic day 13 (E13) for SCG or E12 for DRG.  Culture medium for SCG consisted of D-MEM/F-12 medium with 100 U/ml penicillin/streptomycin (P/S), 2 mM L-Glutamine (all Invitrogen, Carlsbad, CA), 1 mg/ml bovine albumin, and 25 ng/ml of NGF-7S (both Sigma, St. Louis, MO).  Culture medium for DRG consisted of 1:1 F-12 and Opti-MEM I, 0.5% heat-inactivated horse serum, 2 mM GlutaMAX, 100 U/ml P/S, 40 mM glucose, and 25 ng/ml NGF.

extract_protocol: RNA was isolated as per Invitrogen protocol, treated with RNase-free DNase (Promega, Madison, WI), cleaned via Zymo-RNA column (ZYMO Research, Orange, CA), and quantitated by Ribogreen assay (Molecular Probes/Invitrogen).  For DRG samples, all five time points of each replicate were collected consecutively from one culture setup, making them continuous replicates.  SCG sample tissue was more limited, and therefore the microarray replicates are discontinuous, composed of intermingled time points from multiple culture setups. Two biological replicates for each tissue type were collected for hybridization to Affymetrix arrays.

treatment_protocol: After dissection, two to four explants were embedded in a collagen sandwich with an aggregate of Cos7 cells. The Cos7 cells were either mock-transfected or transiently transfected with 5µg Sema3A plasmid, using Lipofectamine 2000 (Invitrogen) as per manufacturer’s instructions.  Cultured DRG or SCG were harvested into Trizol at 2, 5, 12, 24, 40, and 65 hours (final time point for SCG only).  A reference pool for microarray comparisons was created by dissecting explants as above, and transferring tissues to Trizol RNA isolation reagent (Invitrogen) without culturing.

tag: strain

tag: age

value: embryonic day 12

value: dorsal root ganglia (DRG)

tag: treatment

value: exposed to Sema3A (cos cells Sema3A-transfected)


title: DRG_sema3A_2h_rep2

source_name: DRG explant cultured for 2 hours in vitro, in the presence of Sema3A


title: DRG_sema3A_5h_rep2

source_name: DRG explant cultured for 5 hours in vitro, in the presence of Sema3A


title: DRG_control_40h_rep2

source_name: DRG explant cultured for 48 hours in vitro

value: control (cos cells mock-transfected)


title: DRG_control_24h_rep2

source_name: DRG explant cultured for 24 hours in vitro


title: DRG_control_5h_rep2

source_name: DRG explant cultured for 5 hours in vitro


title: DRG_sema3A_40h_rep1

source_name: DRG explant cultured for 48 hours in vitro, in the presence of Sema3A


title: DRG_control_2h_rep2

source_name: DRG explant cultured for 2 hours in vitro


title: DRG_reference_pool

source_name: DRG acutely dissected from embryos

value: none (acutely dissected)


title: SCG_reference_pool

source_name: SCG acutely dissected from embryos

value: embryonic day 13

value: superior cervical ganglia (SCG)


title: DRG_control_12h_rep2

source_name: DRG explant cultured for 12 hours in vitro


title: DRG_sema3A_24h_rep1

source_name: DRG explant cultured for 24 hours in vitro, in the presence of Sema3A


title: DRG_sema3A_5h_rep1


title: DRG_sema3A_12h_rep1


title: DRG_sema3A_40h_rep2


title: MBG treated 15 hr (M_1.1 15)

source_name: Human Dermal Fibroblast


title: DRG_sema3A_24h_rep2


title: DRG_sema3A_2h_rep1


title: DRG_control_24h_rep1


title: DRG_control_12h_rep1


title: DRG_control_40h_rep1


title: DRG_control_5h_rep1


title: DRG_control_2h_rep1


title: Exp C_4, 10mg/kg CPF

city: WPAFB

first: Victor

last: Chan

address: 2729 R St. Area B Bldg. 837

department: Applied Biotechnology Branch

institute: Air Force Research Laboratory

description:
Exp C, Animal #4, 10mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours

hyb_protocol: After fragmentation 15ug of cRNA was hybridized for 16 hours @ 45C on GeneChip Rat Expression Array 230A.  GeneChips were washed and stained in an Affymetrix Fluidics Station 400.

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

data_processing: Data was analyzed with Data Mining Tool version 3.0 (DMT 3.0) using the following parameters:  Alpha1=0.05; Alpha2=0.06; Tau=0.015; Gamma1H=0.005; Gamma1L=0.005; Gamma2H=0.006; Gamma2L=0.006; Perturbation=1.35; Scaling (All Probe Sets) Target Intensity=500

organism: Rattus norvegicus

source_name: Brain tissue from Fisher 344 male rat treated with 10mg/kg CPF

label_protocol: Biotinylated cRNA was prepared according to the RNA transcript labeling procedures of Enzo from 15ug of total RNA

extract_protocol: Qiagen MiniRNeasy total RNA extraction was performed according to the manufacturer's instructions

treatment_protocol: F344 male rats were treated with a single dose (0, 0.5, 1.0, 5.0, 10, 30, or 50mg/kg) of CPF (Sigma) in three separate experiments and sacrificed after 96 hours of exposure to CPF.

tag: Sex

value: male

value: adult (11-12 weeks)


title: Exp C_3, 10mg/kg CPF, 1st repeat

description:
Exp C, Animal #3, 10mg/kg CPF, 1st repeat
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours

tag: Age


title: Exp C_3, 5mg/kg CPF

description:
Exp C, Animal #3, 5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours

source_name: Brain tissue from Fisher 344 male rat treated with 5mg/kg CPF


title: Exp C_1, 30mg/kg CPF

description:
Exp C, Animal #1, 30mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours

source_name: Brain tissue from Fisher 344 male rat treated with 30mg/kg CPF


title: Exp C_2, 30mg/kg CPF

description:
Exp C, Animal #2, 30mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours


title: Exp C_1, 10mg/kg CPF

description:
Exp C, Animal #1, 10mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours


title: Exp C_2, 5mg/kg CPF

description:
Exp C, Animal #2, 5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours


title: Exp C_4, 5mg/kg CPF

description:
Exp C, Animal #4, 5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours


title: Exp C_1, 5mg/kg CPF

description:
Exp C, Animal #1, 5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours


title: Exp C_3, 1mg/kg CPF

description:
Exp C, Animal #3, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours

source_name: Brain tissue from Fisher 344 male rat treated with 1mg/kg CPF


title: Exp C_2, 10mg/kg CPF, 1st repeat

description:
Exp C, Animal #2, 10mg/kg CPF, 1st repeat
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours


title: Exp C_4, 1mg/kg CPF

description:
Exp C, Animal #4, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Exp C_2, control (0mg/kg) CPF

description:
Exp C, Animal #2, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours

source_name: Brain tissue from Fisher 344 male rat treated with vehicle (control 0mg/kg)


title: Exp C_1, control (0mg/kg) CPF, 1st repeat

description:
Exp C, Animal #1, control (0mg/kg) CPF, 1st repeat
Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours


title: Exp C_3, control (0mg/kg) CPF

description:
Exp C, Animal #3, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours


title: Exp B_4, 30mg/kg CPF

description:
Exp B, Animal #4, 30mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours


title: Exp B_2, 0.5mg/kg CPF

description:
Exp B, Animal #2, 0.5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 0.5mg/kg of CPF for 96 hours

source_name: Brain tissue from Fisher 344 male rat treated with 0.5mg/kg CPF


title: Exp C_1, 1mg/kg CPF

description:
Exp C, Animal #1, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Exp B_1, 0.5mg/kg CPF

description:
Exp B, Animal #1, 0.5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 0.5mg/kg of CPF for 96 hours


title: MeDIP set 2 methyl C

city: Davis

first: Dag

last: Yasui

address: 1 Shields Avenue

department: Medical Microbiology and Immunology

institute: University of California at Davis

description: Analysis of human gene promoter CpG methylation by MeDIP analysis in SHSY-5Y neurons

hyb_protocol: Samples were hybridized and washed according to Nimblegen protocol.

scan_protocol: Microarrays were scanned on a GenePix 4000B scanner (Axon) according to Nimblegen protocol.

data_processing: data processing was minimal

source_name: anti methyl C Cy5

label_protocol: Samples were labeled according to Nimblegen protocol.

growth_protocol: SHSY-5Y cells were grown in MEM media containing 15% Fetal Bovine sera, antibiotics and L-glutamine at 37°C in 5% CO2 at a density of approximately 500,000 cells ml.

extract_protocol: Genomic DNA was purified from SHSY-5Y cells using a Puregene kit, treated with proteinase K and extracted with phenol/chloroform. Genomic DNA was fragmented by sonication to an average size of 200-300 base pairs. Immunoprecipitation was performed with an anti-methyl cytidine antibody (Eurogentec) according to Weber et al (2005) Nat Genet 37, 853-62.

treatment_protocol: SHSY-5Y cells were differentiated in media containing 16 nanomolar phorbol 12-myristate 13-acetate for 48 hours then fixed by addition of 1% formaldehyde for 10 minutes at room temperature. Glycine was added to a final concentration of 125 mM to inactivate formaldehyde.

tag: SHSY-5Y neurons

source_name: total genomic Cy3


title: Exp B_4, control (0mg/kg) CPF

description:
Exp B, Animal #4, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Exp B_3, 30mg/kg CPF

description:
Exp B, Animal #3, 30mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours


title: Exp B_2, 30mg/kg CPF

description:
Exp B, Animal #2, 30mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 30mg/kg of CPF for 96 hours


title: Exp B_2, control (0mg/kg) CPF

description:
Exp B, Animal #2, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Exp B_1, control (0mg/kg) CPF

description:
Exp B, Animal #1, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Pol2 ChIP-chip C

description: Analysis of MeCP2 binding, to selected genomic regions plus promoters assayed for CpG methylation in SHSY-5Y cells

source_name: anti Pol2 ChIP DNA Cy5

extract_protocol: SHSY-5Y cells were washed twice with ice cold 1xPBS and nuclei were released by dounce homogenization with pestle B. Nuclei were lysed by resuspension in a hypotonic lysis buffer then chromatin was sonicated with 3, 15 second pulses on a Fisher Sonicator set to setting 3 to a size between 200 to 400 base pairs in length. Sheared chromatin was incubated with either a custom anti MeCP2 antibody or Pol2 antibody (MMS-126R, Covance). Immune complexes were pulled down with either goat anti chicken agarose beads (Aves Labs) or protein A/G beads (Pierce). Chromatin-immune complexes were washed with buffer containing 1% NP-40, 1% deoxycholic acid and 1% SDS. DNA fragments were purified using a PCR cleanup kit (Qiagen).

source_name: total reference DNA Cy3


title: Exp A_3, 50mg/kg CPF

description:
Exp A, Animal #3, 50mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours

source_name: Brain tissue from Fisher 344 male rat treated with 50mg/kg CPF


title: Exp C_2, 1mg/kg CPF

description:
Exp C, Animal #2, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Exp B_3, control (0mg/kg) CPF

description:
Exp B, Animal #3, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: MeCP2 ChIP-chip B

source_name: anti MeCP2 ChIP DNA Cy5


title: Exp A_1, 50mg/kg CPF

description:
Exp A, Animal #1, 50mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours


title: MeCP2 ChIP-chip A


title: Pol2 ChIP set 2

description: Analysis of MeCP2 binding to 24,275 promoters SHSY-5Y cells

source_name: anti Pol2 ChIP DNA

source_name: total reference DNA


title: MeCP2 ChIP set 1

source_name: anti MeCP2 ChIP DNA


title: Exp A_4, 10mg/kg CPF

description:
Exp A, Animal #4, 10mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours


title: Pol2 ChIP-chip B


title: Exp A_3, 10mg/kg CPF

description:
Exp A, Animal #3, 10mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours


title: Exp A_3, 1mg/kg CPF

description:
Exp A, Animal #3, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Exp A_1, 10mg/kg CPF

description:
Exp A, Animal #1, 10mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours


title: Exp B_1, 5mg/kg CPF

description:
Exp B, Animal #1, 5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 5mg/kg of CPF for 96 hours


title: Exp A_2, 50mg/kg CPF

description:
Exp A, Animal #2, 50mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours


title: Exp B_4, 0.5mg/kg CPF

description:
Exp B, Animal #4, 0.5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 0.5mg/kg of CPF for 96 hours


title: Exp A_4, 50mg/kg CPF

description:
Exp A, Animal #4, 50mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 50mg/kg of CPF for 96 hours


title: Exp A_3, control (0mg/kg) CPF

description:
Exp A, Animal #3, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours


title: Pol2 ChIP-chip A


title: Exp A_4, 1mg/kg CPF

description:
Exp A, Animal #4, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: MeCP2 ChIP-chip C


title: Exp B_3, 0.5mg/kg CPF

description:
Exp B, Animal #3, 0.5mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 0.5mg/kg of CPF for 96 hours


title: DRG_reference_pool

description: DRG acutely dissected from embryos

source_name: DRG acutely dissected from embryos

tag: tissue


title: MeCP2 ChIP set 2


title: Exp A_2, control (0mg/kg) CPF

description:
Exp A, Animal #2, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours


title: Exp A_1, 1mg/kg CPF

description:
Exp A, Animal #1, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: Pol2 ChIP set 1


title: Exp A_4, control (0mg/kg) CPF

description:
Exp A, Animal #4, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours


title: Exp A_1, control (0mg/kg) CPF

description:
Exp A, Animal #1, control (0mg/kg) CPF
Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours


title: Exp A_2, 10mg/kg CPF

description:
Exp A, Animal #2, 10mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours


title: SCG_sema3A_65h_rep2

description: SCG explant cultured for 65 hours in vitro, in the presence of Sema3A

source_name: SCG explant, 65 hours in vitro, with Sema3A


title: SCG_sema3A_40h_rep2

description: SCG explant cultured for 48 hours in vitro, in the presence of Sema3A

source_name: SCG explant, 48 hours in vitro, with Sema3A


title: Exp A_2, 1mg/kg CPF

description:
Exp A, Animal #2, 1mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 1mg/kg of CPF for 96 hours


title: SCG_reference_pool

description: SCG acutely dissected from embryos

source_name: SCG acutely dissected from embryos


title: SCG_sema3A_5h_rep2

description: SCG explant cultured for 5 hours in vitro, in the presence of Sema3A

source_name: SCG explant, 5 hours in vitro, with Sema3A


title: SCG_sema3A_12h_rep2

description: SCG explant cultured for 12 hours in vitro, in the presence of Sema3A

source_name: SCG explant, 12 hours in vitro, with Sema3A


title: SCG_sema3A_2h_rep2

description: SCG explant cultured for 2 hours in vitro, in the presence of Sema3A

source_name: SCG explant, 2 hours in vitro, with Sema3A


title: SCG_sema3A_24h_rep2

description: SCG explant cultured for 24 hours in vitro, in the presence of Sema3A

source_name: SCG explant, 24 hours in vitro, with Sema3A


title: SCG_control_2h_rep2

description: SCG explant cultured for 2 hours in vitro

source_name: SCG explant, 2 hours in vitro


title: SCG_control_40h_rep2

description: SCG explant cultured for 48 hours in vitro

source_name: SCG explant, 48 hours in vitro


title: MeDIP set 1 methyl C

description: Analysis of human gene promoter CpG methylation by MeDIP analysis in SHSY-5Y neurons

source_name: anti methyl C Cy5

source_name: total genomic Cy3


title: SCG_control_65h_rep2

description: SCG explant cultured for 65 hours in vitro

source_name: SCG explant, 65 hours in vitro


title: SCG_control_24h_rep2

description: SCG explant cultured for 24 hours in vitro

source_name: SCG explant, 24 hours in vitro


title: SCG_control_12h_rep2

description: SCG explant cultured for 12 hours in vitro

source_name: SCG explant, 12 hours in vitro


title: SCG_control_5h_rep2

description: SCG explant cultured for 5 hours in vitro

source_name: SCG explant, 5 hours in vitro


title: SCG_sema3A_24h_rep1


title: SCG_sema3A_12h_rep1


title: SCG_control_24h_rep1


title: SCG_control_5h_rep1


title: SCG_sema3A_5h_rep1


title: SCG_control_65h_rep1


title: SCG_sema3A_2h_rep1


title: SCG_control_12h_rep1


title: DRG_reference_pool

description: DRG acutely dissected from embryos


title: SCG_sema3A_12h_rep2


title: SCG_sema3A_24h_rep2


title: SCG_reference_pool

description: SCG acutely dissected from embryos


title: SCG_sema3A_2h_rep2


title: SCG_sema3A_5h_rep2


title: SCG_sema3A_40h_rep1


title: SCG_sema3A_65h_rep2


title: SCG_sema3A_40h_rep2


title: SCG_control_65h_rep2


title: SCG_sema3A_65h_rep1


title: SCG_control_40h_rep1


title: SCG_control_12h_rep2


title: SCG_control_5h_rep2


title: SCG_control_40h_rep2


title: SCG_control_24h_rep2


title: SCG_control_2h_rep2


title: SCG_control_2h_rep1


title: SCG_sema3A_24h_rep1


title: SCG_sema3A_12h_rep1


title: mcf520c-3

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description: MCF7 cells were infected with miR-520c

hyb_protocol: Basic Illumina Hyb

scan_protocol: Illumina Setting with PMTFactor=2

data_processing:
Illumina BeadStudio data on
1. The raw data of the spot density was extracted from Illumina BeadStudio software.
2. Check samples outlier.
3. The raw data filtering by the p-value 0.05 of each spot. If no one below p-value 0.05, the spot would be filtered out.
4. Quantile normalization for the filtering data.
5. Apply one-way ANOVA on the quantile normalization data to find out the significant gene data.

label: Illumina Label

source_name: Human CELL LINE: MCF7 cells infected with miR-520c

label_protocol: Illumina Label Protocol

extract_protocol: total RNA

tag: Human RNA


title: SCG_control_65h_rep1


title: SCG_sema3A_5h_rep1


title: SCG_sema3A_2h_rep1


title: SCG_control_24h_rep1


title: SCG_control_12h_rep1


title: mcf520c-1

description: MCF7 cells were infected with miR-520c


title: mcf520c-2

description: MCF7 cells were infected with miR-520c

hyb_protocol: Illumina Illumina Hyb


title: mcf7-1

description: MCF7 cells were not infected with miR-373 or miR-520c

source_name: Human CELL LINE: MCF7 cells not infected with miR-373 or miR-520c


title: mcf373-3

description: MCF7 cells were infected with miR-373

source_name: Human CELL LINE: MCF7 cells infected with miR-373


title: mcf7-2


title: mcf373-1

description: MCF7 cells were infected with miR-373


title: mcf7-3


title: SCG_control_5h_rep1


title: mcf373-2

description: MCF7 cells were infected with miR-373


title: Control C2C12 Rep1

city: suwon

first: Eun Kyung

last: Lee

state: Gyeonggi-do

address: 300 Cheoncheon-dong, Jangan-gu

department: pharmacy

country: South Korea

institute: Sungkyunkwan university

description: C2C12 cells were treated with DMSO for 4 days. Microarrays were performed in duplicated, C1 and C2

hyb_protocol: Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imageing, auto gridding and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1. 0. 3.

data_processing: Signal intensities across microarrays were normalized using the quantile-quantile method (www.bioconductor.org).

label: DIG-UTP

source_name: mouse myoblast

label_protocol: 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT kit V2.0.

growth_protocol: The C2C12 cell line, which is mouse myoblast, was cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: Total RNA was isolated using easy-Blue reagent (iNtRON Biotechnology, Sungnam, Gyeonggi, Korea). RNA was stored at -70C in Rnase free H20 supplemented with the Rnase inhibitor. Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturer procedures(Agilent Technologies, Palo Alto, CA)

treatment_protocol: C2C12 cells were treated with DMSO (control) or 5uM reversine.

tag: DMSO-treated C2C12 cells


title: Reversine treated C2C12 Rep2

description: C2C12 cells were treated with 5mM reversine. Microarrays were performed in duplicated, R1 and R2

tag: reversine-treated C2C13 cells


title: Reversine treated C2C12 Rep1

description: C2C12 cells were treated with 5mM reversine. for 4 days.Microarrays were performed in duplicated, R1 and R2

tag: reversine-treated C2C12 cells


title: F2, chip MOE430B

status: Public on Dec 01 2007

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=235#SAMPLE_364

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

source_name: fertilized blastocyst

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

growth_protocol: Growth medium:				KSOM

extract_protocol:
RNA prep method:				Brady/Iscove
Amplification method:			Brady/Iscove
Contaminating cell type:			none
Method for estimating purity:		Visual inspection

treatment_protocol: Assays to confirm viability:		Development to blastocyst

tag: Strain:					(C57Bl6 x DBA2) F1 x (C57Bl6 x DBA2) F1

tag: Gender:					Unknown


title: F3, chip MOE430A


title: F3, chip MOE430B


title: Exp A_5, 10mg/kg CPF

description:
Exp A, Animal #5, 10mg/kg CPF
Gene expression data from male F344 rats treated with a single dose of 10mg/kg of CPF for 96 hours

source_name: Brain tissue from Fisher 344 male rat treated with 10mg/kg CPF


title: Control C2C12 Rep2

description: C2C12 cells were treated with DMSO for 4 days.Microarrays were performed in duplicated, C1 and C2

tag: DMSO-treated C2C13 cells


title: F1, chip MOE430A


title: A3, chip MOE430B

description: SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=235#SAMPLE_362

source_name: androgenetic blastocyst


title: A2, chip MOE430B


title: G2, chip MOE430A

description: SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=235#SAMPLE_363

source_name: gynogenetic blastocyst


title: F1, chip MOE430B


title: A1, chip MOE430B


title: A3, chip MOE430A


title: G3, chip MOE430A


title: F2, chip MOE430A


title: G3, chip MOE430B


title: G1, chip MOE430A


title: G2, chip MOE430B


title: G1, chip MOE430B


title: HUVEC isolate A, confluent

city: Amsterdam

first: Oscar

middle: Leonard

last: Volger

state: Noor Holland

address: Meibergdreef 15

department: Cardiology

country: Netherlands

institute: Academic Medical Center

description: See the methods section of the linked publication for additional information

hyb_protocol: Each cRNA sample (1 micrograms; Cy5-labeled) was hybridized in duplicate against a common reference cRNA sample (1 micrograms; Cy3-labeled), for 16 hours at 40 degrees Celsius.

scan_protocol: Agilent scanner: resolution: 10 micrometer, scan area: 60 x 21.6 mm, PMT: 50%, Laser power: 50%

data_processing: After print-tip Loess-normalization (Loess span: 0.3; limma package, Bioconductor, available online: http://www.bioconductor.org), and background subtraction, the microarray intensity data imported in the Rosetta Resolver database.

molecule: polyA RNA

source_name: common reference RNA

label_protocol: Within these cRNAs the molar ratio of incorporated aminoallyl-rUTP (A5660, Sigma, St. Louis, MO) to rUTP was 1:1. Cy3 mono reactive dyes (PA23001, Amersham Biosciences, Piscataway, NJ) were coupled according to the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy purification kit (Qiagen GmbH, Hilden, Germany).

extract_protocol: Total RNA of each one of the three reference components was isolated by Trizol, and treated with DNAse-I. Thereafter, mRNA of each component was linearly amplified for one round (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.

tag: The common reference cRNA sample comprised equal quantities of the following three components

value: (1) human umbilical cord endothelial cells (HUVEC), stimulated with TNF-alpha (50 microgram/ml, 6 hrs); (2) THP-1 cell line stimulated for 24 hours with phorbyl myristate (PMA, 100 microgram /ml), and subsequently for 6 hours with lipopolysaccharide (LPS, 1 microgram /ml), and (3) a mix of whole mount human aorta and iliac artery.

source_name: HUVEC isolate A, confluent

label_protocol: Within these cRNAs the molar ratio of incorporated aminoallyl-rUTP (A5660, Sigma, St. Louis, MO) to rUTP was 1:1. Cy5 mono reactive dyes (PA25001, Amersham Biosciences, Piscataway, NJ) were coupled according to the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy purification kit (Qiagen GmbH, Hilden, Germany).

growth_protocol: HUVEC, grown to confluency in T80 plates.

extract_protocol: Total RNA molecules were isolated from HUVEC by Trizol, and treated with DNAse-I, and then purified by using RNeasy spin columns (Qiagen). Thereafter, mRNA of each component was linearly amplified for one round (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.

tag: HUVEC grown to confluency


title: HUVEC isolate B, confluent

source_name: HUVEC isolate B, confluent


title: HUVEC isolate B1, subconfluent

source_name: human umbilical vein endothelial cells cultured to subconfluency

growth_protocol: HUVEC, grown to sub-confluency in T80 plates.


title: HUVEC isolate C, confluent

source_name: HUVEC isolate C, confluent


title: A2, chip MOE430A


title: HUVEC isolate C7, subconfluent

tag: HUVEC, grown to sub-confluency in T80 plates.


title: A1, chip MOE430A


title: HUVEC isolate A1, subconfluent

source_name: Title: HUVEC isolate A1, subconfluent


title: Untreated MMR deficient Ku86+/- HCT116 cell line: KU_3

city: San Francisco

first: Antoine

last: Snijders

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

hyb_protocol: We combined and precipitated 50 ml Cy3 labeled test DNA, 50 ml Cy5 labeled reference DNA and 100 mg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2 volumes of ice-cold ethanol. We collected the precipitate by centrifugation and dissolved the pellet in a final hybridization mixture containing 50% formamide, 2xSSC and 4% SDS. We denatured the hybridization mixture at 75°C for 10-15 min and then incubated the samples at 37°C for 1 hour to block repetitive DNA sequences. We applied a ring of rubber cement closely around the array to form a well, into which we added 50 ml of a pre-incubation solution containing 250 mg salmon sperm DNA, 50% formamide, 2xSSC and 4% SDS.  After a 30 min incubation at room temperature, we removed ~30 ml of the pre-incubation solution and added the denatured and re-annealed hybridization mixture.  We placed a silicone gasket around each hybridization area, placed a microscope slide on top of the gasket, which was thick enough to prevent the microscope slide from contacting the hybridization solution and clamped the whole unit together using binder clips to create an air tight environment.  We carried out the hybridization to the arrays for ~48 hrs on a slowly rocking table at 37°C.  After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min.  Subsequently, we removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system We used “UCSF SPOT” software to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the August, 2001 freeze of the draft human genome sequence (http://genome.ucsc.edu).

data_processing: SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.  We edited the data files to remove ratios on clones for which only one of the triplicates remained after SPROC analysis and/or the standard deviation of the log2ratios of the triplicates was > 0.2.

source_name: Genomic DNA from MMR deficient Ku86+/- HCT116 cell line labeled with Cyanine-3

label_protocol: We labeled genomic DNA by random priming in a 50 ml reaction by combining 300 ng genomic DNA, 1x random primers solution (BioPrime DNA Labeling System, Gibco BRL), 1x dNTP solution (0.2 mM each of dATP, dTTP, dGTP, 0.05 mM dCTP, 1 mM Tris base (pH 7.6), 0.1 mM EDTA), 40 mM Cy3 or Cy5-dCTP (Amersham) and 40 U Klenow fragment (BioPrime DNA Labeling System, Gibco BRL).  We incubated the DNA and the random primers in a volume of 42 ml at 100°C for 10-15 min, placed the reaction on ice and added the dNTP solution, labeled nucleotides and Klenow fragment. We incubated the random priming reaction overnight at 37°C. We removed unincorporated nucleotides using a Sephadex spin-column.

extract_protocol: We incubated cells from a T75 flask overnight at 55°C in a 3 ml solution containing 0.01 M Tris, pH 7.5, 0.001 M EDTA, pH 8, 0.5% SDS and 0.1 mg/ml proteinase K. We precipitated the DNA with ethanol, recovered it by spooling and then dissolved it in ~300 ml H2O.

tag: cell line DNA

tag: KU

tag: parent

source_name: Genomic DNA isolated from blood

tag: reference DNA


title: Untreated MMR deficient Ku86+/- HCT116 cell line: KU_4


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X9A

tag: child


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X8A


title: Untreated MMR deficient Ku86+/- HCT116 cell line: KU_2


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X1A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X7A


title: Untreated MMR deficient Ku86+/- HCT116 cell line: KU_1


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X10A


title: Hypertensive Study Hypertensive Animal 4 Time Point 105

type: mixed

city: Phildelphia

first: Rishi

last: Khan

address: 1020 Locust Street Room 381

department: Pathology

institute: Thomas Jefferson University

description: See other fields

hyb_protocol: Microarrays were prehybridized in 1% bovine serum albumin, 5x SSC, 0.1% SDS for 45 min at 42°C, washed in H2O and dried by centrifugation. Cy3-vDNA and Cy5- cDNA samples were mixed with 50 µl of DIG Easy Hybridization buffer (Roche, Indianapolis, IN) containing 25 µg each of yeast tRNA and calf thymus DNA and applied to the microarrays for hybridization at 37°C for 16 hours in a hybridization chamber (Corning, Corning, NY) in the dark with gentle agitation. Slides were washed for 10 minutes at 50°C in 1x SSC and 0.1% SDS in shaking incubator, followed by a 1 minute wash in 1x SSC, three 1 minute washes in 0.1x SSC, and one rinse in H2O, at room temperature. Slides were dried by centrifugation.

scan_protocol: Slides were scanned with the ScanArray 5000XL (PerkinElmer, Wellesley, MA).

data_processing: Spots were identified with ScanArray Express 2.0 and segmented using Adaptive Threshold method.

molecule: other

organism: unidentified

source_name: Reference RNA

label_protocol: vRNA was reverse transcribed (detailed further below) with dNTPs, amino allyl-dUTP and random nanomers and coupled with the monoreactive succinimide ester derivative of a Cy3 or Cy5 dye to create labeled vector derived cDNA (vcDNA).

extract_protocol: The EST clones used to manufacture the cDNA arrays described herein all used the pT7T3D-Pac vector (generously provided by the BMAP group at University of Iowa). Therefore, they all contained the same sequence between the viral promoters (T3 and T7) and the multicloning site between the NotI and EcoRI. PCR of an empty vector using GF200 primers (5-CTGCAAGGCGATTAAGTTGGGTAAC-3 and 5-G-T-G-A-G-C-G-G-A-T-A-A-C-A-A-T-T-T-C-A-C-A-C-A-G-G-A-A-A-C-A-G-C-3) yields a template for T7 based RNA amplification (MessageAmpTM T7 Linear Amplification Kit, Ambion, Austin, TX) to produce “vector RNA” (vRNA).

tag: PCR of vector of empty clone. Hybridizes to all spots evenly.

source_name: Hypertensive 105-4

label_protocol: aRNA (1.125 µg) was reverse transcribed (Superscript II, Invitrogen) using random primers to generate single stranded amino-allyl derivatized cDNA, which was coupled with Cy dyes (Cy3 or Cy5) to produce fluorescently labeled cDNA.

extract_protocol: Total RNA (70-400 ng) was amplified using two rounds of the antisense RNA (aRNA) technique, yielding on average 180 µg aRNA (MessageAmp, Ambion, Austin, TX).

tag: Strain:Sprague-Dawley', 'Gender:Male', 'Tissue:Nucleus Tractus Solitarius', 'Condition:phenylephrine injection


title: Hypertensive Study Hypertensive Animal 4 Time Point 120

description: See other fields

source_name: Hypertensive 120-4


title: Hypertensive Study Hypertensive Animal 2 Time Point 120

description: See other fields

source_name: Hypertensive 120-2


title: Untreated MMR deficient Ku86+/- HCT116 cell line: KU_5


title: Hypertensive Study Hypertensive Animal 3 Time Point 120

description: See other fields

source_name: Hypertensive 120-3


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X6A


title: Hypertensive Study Hypertensive Animal 1 Time Point 120

description: See other fields

source_name: Hypertensive 120-1


title: Hypertensive Study Hypertensive Animal 3 Time Point 105

description: See other fields

source_name: Hypertensive 105-3


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X5A


title: Hypertensive Study Hypertensive Animal 2 Time Point 105

description: See other fields

source_name: Hypertensive 105-2


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X3A


title: Hypertensive Study Hypertensive Animal 1 Time Point 105

description: See other fields

source_name: Hypertensive 105-1


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X4A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X2A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_X11A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W11A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W8A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W7A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W9A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W5A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W4A


title: Hypertensive Study Hypertensive Animal 4 Time Point 90

description: See other fields

source_name: Hypertensive 90-4


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W12A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W6A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W3A


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W10A


title: Hypertensive Study Hypertensive Animal 2 Time Point 90

description: See other fields

source_name: Hypertensive 90-2


title: Hypertensive Study Hypertensive Animal 3 Time Point 90

description: See other fields

source_name: Hypertensive 90-3


title: Hypertensive Study Hypertensive Animal 2 Time Point 75

description: See other fields

source_name: Hypertensive 75-2


title: Methotrexate treated MMR deficient Ku86+/- HCT116 cell line: KU_W2A


title: Untreated MMR deficient BLM deficient HCT116 cell line: Blmko_1

source_name: Genomic DNA from MMR deficient BLM deficient HCT116 cell line labeled with Cyanine-3

tag: BLM KO


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B7


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B6


title: Untreated MMR deficient BLM deficient HCT116 cell line: Blmko_2


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B23


title: Hypertensive Study Hypertensive Animal 3 Time Point 75

description: See other fields

source_name: Hypertensive 75-3


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B24


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B20


title: Hypertensive Study Hypertensive Animal 1 Time Point 75

description: See other fields

source_name: Hypertensive 75-1


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B13

source_name: Genomic DNA isolated from blood


title: Hypertensive Study Hypertensive Animal 4 Time Point 75

description: See other fields

source_name: Reference RNA

source_name: Hypertensive 75-4


title: Hypertensive Study Hypertensive Animal 4 Time Point 60

description: See other fields

source_name: Hypertensive 60-4


title: Spike-in sample technical replicate 1

city: Stanford

first: David

middle: Scott

last: Johnson

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description: For each replicate array, we labeled 1µg of spike-in sample and 1µg of control sample.  The Bioprime Plus Array CGH labeling Module (Invitrogen Catolog number 18095-014) was used.  The spike-in was labeled with the red channel dye (Alexa Fluor-647) and the control was labeled with the green channel dye (Alexa Fluor-555) in two of the replicates.  A dye swap was performed for the third replicate.  These samples were then competitively hybridized to three replicate 244k arrays from Agilent, (AMADID 25150451).  We hybridized the samples to the arrays using the Agilent Array CGH protocol, with some modifications.  Briefly, labeled DNA was combined with Cot-1 DNA, blocking reagent, and hybridization buffer.  The hybridizations were carried out at 60°C.  The arrays were scanned using an Agilent dual laser scanner, and the images were processed using Agilent Feature Extraction Software.

scan_protocol: The arrays were scanned using an Agilent dual laser scanner.

data_processing: Agilent Feature Extraction Software

label: Alexa 647

source_name: Roche gDNA + spike

label_protocol: standard Agilent protocol

extract_protocol: not applicable

tag: spike-in

label: Alexa 555

source_name: Roche gDNA

tag: control


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B22


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B2


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B16


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B15


title: Hypertensive Study Hypertensive Animal 3 Time Point 60

description: See other fields

source_name: Hypertensive 60-3


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B1


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B8


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B14


title: Hypertensive Study Control 4 Time Point 120

description: See other fields

source_name: Control 120-4

tag: Strain:Sprague-Dawley', 'Gender:Male', 'Tissue:Nucleus Tractus Solitarius', 'Condition:saline injection


title: Hypertensive Study Control 3 Time Point 120

description: See other fields

source_name: Control 120-3


title: Hypertensive Study Hypertensive Animal 1 Time Point 60

description: See other fields

source_name: Hypertensive 60-1


title: Hypertensive Study Control 4 Time Point 105

description: See other fields

source_name: Control 105-4


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B21


title: Hypertensive Study Hypertensive Animal 1 Time Point 90

description: See other fields

source_name: Hypertensive 90-1


title: Hypertensive Study Control 1 Time Point 120

description: See other fields

source_name: Control 120-1


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B9


title: Hypertensive Study Hypertensive Animal 2 Time Point 60

description: See other fields

source_name: Hypertensive 60-2


title: Spike-in sample technical replicate 2

hyb_protocol: Agilent Array CGH protocol, with some modifications. Briefly, labeled DNA was combined with Cot-1 DNA, blocking reagent, and hybridization buffer.  The hybridizations were carried out at 60°C.


title: Spike-in sample technical replicate 3, dye swap


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B19

source_name: Genomic DNA from MMR deficient BLM deficient HCT116 cell line labeled with Cyanine-3


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B5


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B11


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B18


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B17


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B4


title: Untreated MMR deficient BLM wt HCT116 cell line: Blmwt_2

source_name: Genomic DNA from MMR deficient BLM wt HCT116 cell line labeled with Cyanine-3

tag: BLM WT


title: Untreated MMR deficient BLM wt HCT116 cell line: Blmwt_1


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B3


title: Hypertensive Study Control 2 Time Point 120

description: See other fields

source_name: Control 120-2


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A9

source_name: Genomic DNA isolated from blood


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B12


title: Hypertensive Study Control 3 Time Point 105

description: See other fields

source_name: Reference RNA

source_name: Control 105-3


title: Methotrexate treated MMR deficient BLM deficient HCT116 cell line: Blmko_B10


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A6


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A12


title: Hypertensive Study Control 2 Time Point 105

description: See other fields

source_name: Control 105-2


title: Hypertensive Study Control 1 Time Point 105

description: See other fields

source_name: Control 105-1


title: Hypertensive Study Control 4 Time Point 90

description: See other fields

source_name: Control 90-4


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A5


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A4


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A3


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A2


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A1


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A8


title: Hypertensive Study Control 3 Time Point 90

description: See other fields

source_name: Control 90-3


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A10


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A7


title: Hypertensive Study Control 1 Time Point 90

description: See other fields

source_name: Control 90-1


title: Hypertensive Study Control 2 Time Point 90

description: See other fields

source_name: Control 90-2


title: Hypertensive Study Control 4 Time Point 75

description: See other fields

source_name: Control 75-4


title: Hypertensive Study Control 3 Time Point 75

description: See other fields

source_name: Control 75-3


title: Methotrexate treated MMR deficient BLM wt HCT116 cell line: Blmwt_A11


title: Hypertensive Study Control 4 Time Point 60

description: See other fields

source_name: Control 60-4


title: Hypertensive Study Control 3 Time Point 60

description: See other fields

source_name: Control 60-3


title: Hypertensive Study Control 1 Time Point 75

description: See other fields

source_name: Control 75-1


title: Kidney_P15_2

first: Gregory

middle: G

last: Germino

address: 720 Rutland Ave., room 958

department: Medicine, Division of Nephrology

institute: Johns Hopkins School of Medicine

description: The primary Illumina data is returned from the scanner in the form of an .idat file which contains single intensity data values/gene following the computation of a trimmed mean average for each probe type represented by a variable number of bead probes/gene on the array.

hyb_protocol: 0.85 ugs of biotin-labeled cRNA was hybridized (16 hours) to Illuminas Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA 92121-1975, cat.no. BD-26-201).

scan_protocol: The hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using Illuminas BeadStation 500GX Genetic Analysis Systems scanner.

data_processing:
The column VALUE in the table refers to the raw intensity value as returned from the scanner (see "Description").
The NORMALIZED VALUE column was used for all the analysis and was obtained by:
log2 of expression values followed by quantile normalization as described by Bolstad, B. M., Irizarry R. A., Astrand, M., and Speed, T. P. (2003), A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193. Using the limma package in Bioconductor (R), the function used was: nz=normalizeBetweenArrays(log2(Expression values),method="quantile").

source_name: Mouse kidney, post-natal day 15, animal 2

label_protocol: RNA samples were labeled according to the chip manufacturers recommended protocols.  In brief, for Illumina, 0.5 µg of total RNA from each sample was labeled by using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX 78744-1832, cat. no. IL1791) in a process of cDNA synthesis and in vitro transcription.  Single stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnosics GmbH, Mannheim, Germany, cat. no. 11388908910).

extract_protocol: RNA extraction: QIAGEN Rneasy, according to manufacturer

tag: Mouse kidneys from uninduced Pkd1cond/cond; tamoxifen-Cre- and -Cre+; Rosa26+

tag: Mouse strain

value: C57/Bl6 Pkd1cond mice were crossed to 5th generation C57/Bl6 tamoxifen-Cre (B6.Cg-Tg(cre/Esr1)5Amc/J mice (Jackson Laboratories) and C57/Bl6 congenic B6.129S4-Gt(ROSA)26Sortm1Sor/J (Jackson Laboratories).


title: Hypertensive Study Control 2 Time Point 75

description: See other fields

source_name: Control 75-2


title: Kidney_P15_1

source_name: Mouse kidney, post-natal day 15, animal 1


title: Kidney_P15_2_replicate

source_name: Mouse kidney, post-natal day 15, technical replicate of P15_2


title: Hypertensive Study Control 2 Time Point 60

description: See other fields

source_name: Reference RNA

source_name: Control 60-2


title: Kidney_P15_4

source_name: Mouse kidney, post-natal day 15, animal 4


title: Data set Y

city: Birmingham

first: Hong

last: Lin

address: Vincent Drive

department: Anatomy

country: United Kingdom

institute: Institute of Biomedical

description: Scanned image were automatically aligned using GenePix (version 6.0) software and then “cherry-picked” manually to eliminate abnormal spots. Microarray data (GPR file) were then extracted by Genepix (version 6.0)

hyb_protocol: The labelled samples were purified again and equal amounts (80~120pmol each) of Cy3- and Cy5-labelled cDNAs were combined and precipitated to a final vol. of 21.1ul. A hybridization reaction that contains Formamide (20ul), labelled probes (21.1ul), 10%SDS (0.8ul), 20xSSC (20ul), Cot1	(10ug) and Poly dA (8ug) are denatured at 95C for 2min and applied to arrays followed by overnight incubation at 42C.

scan_protocol: Slides were scanned using a GenePix 4000B scanner. PMT settings were set so as to balance overall signal in the Cy3 and Cy5 channels.

data_processing: The data in GPR file were normalised by Gepas software with global loess approach.

source_name: Female ICM

label_protocol: 200ng aliquots of cDNA were labelled with Cy5 fluorophore (Amersham) using Invitrogen Bioprime random primer labelling kits. Briefly, the cDNA was annealed with 20μl 2.5x random primers at 95C for 2 minutes. 1.2mM each of dATP, dGTP, dTTP and 0.6mMdCTP, 1ul of Cy5 dye and 1ul of Klenow fragment were then added to the reaction and incubated overnight at 37C.

growth_protocol: Cryopreserved two-cell Balb/c mouse embryos (Embryotech) were thawed and cultured in M16 media (Specialty Media) to the expanded blastocyst stage. Isolation of the inner cell mass (ICM) was achieved by immunosurgery using the method developed by Solter and Knowles35, with minor alterations. Briefly, cultured blastocysts from which the zona pellucida had been removed with 0.5% Pronase (Sigma) were exposed to 1:100 dilution of rabbit anti-mouse serum (Sigma). Blastocysts were washed with PBS and transferred to guinea-pig complement solution (Sigma). Lysed trophectoderm cells were removed and each ICM transferred into a single droplet of trypsin-EDTA solution in order to disaggregate the cells.

extract_protocol: For ICM, the RNA were prepared and treated with DNAse I using RNAqueous-Micro Kit (Ambion) according to manufacture’s procedure. Total amount of RNA were then subjected to two round of amplification using MessageAmpTM II aRNA Amplification Kit (Ambion) according to manufacture’s procedure. Briefly, the RNA prepared from the single ICM were used to synthesis first strand cDNA primed with T7 Oligo(dT) primer. The single stranded cDNA were converted to double stranded cDNA with DNA polymerase. After RNase H degradation of  RNA, the purified double stranded cDNA were then subjected to 14 hours in vitro transcription to generate multiple copies of aRNA. The purified and concentrated aRNA from first round of amplification were then subject to a second round amplification with a similar procedure.

treatment_protocol: Cells extracted from ICM of female blastocysts

tag: Female ICM

source_name: Male ICM

label_protocol: 200ng aliquots of cDNA were labelled with Cy3 fluorophore (Amersham) using Invitrogen Bioprime random primer labelling kits. Briefly, the cDNA was annealed with 20μl 2.5x random primers at 95C for 2 minutes. 1.2mM each of dATP, dGTP, dTTP and 0.6mMdCTP, 1ul of Cy3 dye and 1ul of Klenow fragment were then added to the reaction and incubated overnight at 37C.

treatment_protocol: Cells extracted from ICM of male blastocysts

tag: Male ICM


title: Data set V

source_name: Female Lymphocytes

growth_protocol: The mouse embryonic stem (ES) cell lines PGK12.1 (Norris et al. 1994), CCE/R (O'Neill et al. 2003) and 3F1 (Lee and Lu, 1999) were cultured as previously described (O'Neill et al. 2003). Differentiation was induced by replating on non-adherent plastic dishes in the absence of LIF. Adult control cells were thymic lymphocytes from 4 week old Balb/c mice.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen), according to the manufacturer’s protocol and treated with DNaseI (Qiagen). First strand cDNAs were reverse transcribed from 3μg total RNA in a reaction containing 4μl 5x first-strand buffer, 1 μl 0.1M DTT, 1μl oligo dT primer (50 μM), 200unit RT-Superscript III transcriptase (RT-SSIII, Invitrogen), 40unit RNAase inhibitor (Boehringer Mannheim) made up to 20μl. The cDNA was purified with a Qiagen PCR purification kit.

treatment_protocol: Cells extracted from female mouse thymus

tag: Female Lymphocytes

source_name: Male Lymphocytes

treatment_protocol: Cells extracted from male mouse thymus

tag: Male Lymphocytes


title: Kidney_P15_3

source_name: Mouse kidney, post-natal day 15, animal 3


title: Data Set U

source_name: Female Lymphocyte

tag: Female lymphocyte

tag: Male lymphocytes


title: Kidney_P15_1_replicate

source_name: Mouse kidney, post-natal day 15, technical replicate of P15_1


title: Hypertensive Study Control 1 Time Point 60

description: See other fields

source_name: Control 60-1


title: Data set X

source_name: female ICM


title: Kidney_P14_4

source_name: Mouse kidney, post-natal day 14, animal 4


title: Kidney_P14_3

source_name: Mouse kidney, post-natal day 14, animal 3


title: Kidney_P14_2

source_name: Mouse kidney, post-natal day 14, animal 2


title: Data set Q

source_name: D21 Female

treatment_protocol: Cells after 21 days of differentiation

tag: D21 Female ES cells

source_name: D21 Male

treatment_protocol: cells after 21 days of differentiation

tag: D21 Male ES cells


title: Kidney_P14_1_replicate

source_name: Mouse kidney, post-natal day 14, technical replicate of P14_1


title: Kidney_P14_1

source_name: Mouse kidney, post-natal day 14, animal 1


title: Data Set T

tag: D21 female Es cell

tag: D21 male ES cells


title: Data Set R


title: Kidney_P12_2_replicate

source_name: Mouse kidney, post-natal day 12, technical replicate of P12_2


title: Kidney_P12_4

source_name: Mouse kidney, post-natal day 12, animal 4


title: Kidney_P14_2_replicate

source_name: Mouse kidney, post-natal day 14, technical replicate of P14_2


title: Data set L

source_name: D12 female

treatment_protocol: Cells after 12 days of differentiation

tag: D12 female ES cells

source_name: D12 male

treatment_protocol: cells after 12 days of differentiation

tag: D12 male ES cells


title: Data set N

source_name: D15 Male

treatment_protocol: Cells after 15 days of differentiation

tag: D15 male ES cells

source_name: D15 Female

treatment_protocol: cells after 15 days of differentiation

tag: D15 female ES cells


title: Data Set K

source_name: D12 Female

tag: D12 Female Es cells

source_name: D12 males

tag: D12 Male ES cells


title: Data Set I

source_name: D7 Female

treatment_protocol: Cells after 7 days of differentiation

tag: D7 female ES cells

source_name: D7 male

treatment_protocol: cells after 7 days of differentiation

tag: D7 male ES cells


title: Data Set F

source_name: D2 Female

treatment_protocol: Cells after 2 days of differentiation

tag: D2 female ES cells

source_name: D2 Male

treatment_protocol: cells after 2 days of differentiation

tag: D2 male ES cells


title: Kidney_P12_3

source_name: Mouse kidney, post-natal day 12, animal 3

tag: Mouse kidneys from uninduced Pkd1cond/cond; tamoxifen-Cre- and -Cre+; Rosa26+

tag: Mouse strain


title: Kidney_P12_1r

source_name: Mouse kidney, post-natal day 12, technical replicate of P12_1


title: Data set J

description: Microarray data (GPR file) was extracted by Genepix (version 6.0).

scan_protocol: Slides were scanned using a GenePix 4000B scanner. PMT settings were set so as to balance overall signal in the Cy3 and Cy5 channels. Scans were automatically aligned using GenePix (version 6.0) software and then “cherry-picked” manually to eliminate abnormal spots.

data_processing: GPR file was normalised by Gepas software with global loess approach.

source_name: D7 Male

growth_protocol: The mouse embryonic stem (ES) cell lines PGK12.1 (Norris et al. 1994), CCE/R (O'Neill et al. 2003) and 3F1 (Lee and Lu, 1999) were cultured as previously described (O'Neill et al. 2003). Differentiation was induced by replating on non-adherent plastic dishes in the absence of LIF.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen), according to the manufacturer’s protocol and treated with DNaseI (Qiagen).

tag: D7 Male ES cells


title: Kidney_P11_2_replicate

source_name: Mouse kidney, post-natal day 11, technical replicate of P11_2


title: Kidney_P12_2

source_name: Mouse kidney, post-natal day 12, animal 2


title: Kidney_P12_1

source_name: Mouse kidney, post-natal day 12, animal 1


title: Data set C

source_name: D0 Male

treatment_protocol: Cells before differentiation

tag: D0 male ES cells

source_name: D0 Female

tag: D0 Female ES cells


title: Data set H

source_name: D4 male

treatment_protocol: Cells after 4 days of differentiation

tag: D4 male ES cells

source_name: D4 Female

tag: D4 female ES cells


title: Kidney_P11_4

source_name: Mouse kidney, post-natal day 11, animal 4


title: Data set G

treatment_protocol: cells after 4 days of differentiation


title: Data set E


title: Dataset P

source_name: D21 Female

tag: D21 female ES cells

source_name: D21 Male

tag: D21 male ES cells


title: Kidney_P11_1_replicate

source_name: Mouse kidney, post-natal day 11, technical replicate of P11_1


title: Data Set D

treatment_protocol: D0 cell before differentiation

tag: D0 male ES cell


title: Kidney_P11_2

source_name: Mouse kidney, post-natal day 11, animal 2


title: Data Set O

source_name: D15 Female

tag: D15 Female ES cell

source_name: D15 Male

tag: D15 Male ES cell


title: Data set B

source_name: D0 male

tag: D0 female ES cells


title: Kidney_P11

source_name: Mouse kidney, post-natal day 11


title: Kidney_P11_3

source_name: Mouse kidney, post-natal day 11, animal 3


title: Mononucleosome_rpb1-1_Permissive_replicate3

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

description: Biological replicate 3 of 3 for mononucleosome DNA hybridization for the rpb1-1 strain at permissive temperature.

hyb_protocol: An aliquot of 250 ng of labeled DNA for each sample (channel) was used. Eight experiments were prepared for simultaneous hybridization to each array on the 8 pack slide using the 8 pack gasket coverslip. Hybridizations and washes were performed according to manufacturer's recommended procedures (Agilent Technologies).

scan_protocol: Slides were scanned using an Agilent Technologies Scanner G2505B.

data_processing: Data was extracted from the scanned images using Agilent Feature Extraction software version 8.5.1.1. The 22K 8 pack array format requires a minimum list of 50 pre-identified probes to use as median normalization controls. A list of 312 probes representing genomic loci previously reported as having low RSC occupancy was used as the normalization list in this experiment. Ratios between ChIP and Input channels were determined for probes that were not saturated or below background in either channel. Data from probes that had multiple genomic targets as determined by BLAST analysis were not included.

source_name: Genomic DNA derived from YBC2465

label_protocol: The template DNA was diluted in 25 ul volume containing 1.2X New England Biolab Buffer 2 and 1 ug of random primers (Invitrogen). The DNA was denatured by incubating at 94 C for 2 minutes and rapid cooled to 8 C. To the reaction 1 nM dATP, 1 nM dTTP, 1 nM dGTP, 0.5 nM dCTP, 1 nM labeled-dCTP, and 5 units of Exo-Klenow (New England Biolabs) was added for a final volume of 30 ul. The reaction was incubated at 37 C for 3 hours. The labeled products were purified using Qiagen PCR cleanup columns (not recommended) with an additional 35% guanidine HCl wash. DNA was eluted in 30 ul Elution Buffer. Incorporation and yield was checked using a Nano-Drop spectrophotometer.

growth_protocol: Cells were grown in liquid YP containing 1% raffinose and 1% galactose at 23 C. An aliquot of cells were removed and crosslinked in 1% formaldehyde for 5 minutes.

extract_protocol: Cells were spheroplasted in spheroplastiing solution (1 M sorbitol, 10 mM Tris-HCl pH 7.4, 10 mM 2-Mercaptoethanol) using zymolyase at 37 C. Spheroplasting was stopped when the OD600 absorbance of an aliquot of cells in 1% SDS dropped to < 10% of the starting value. The cell suspension was adjusted to 0.5% SDS and 5 mM EDTA. Proteinase K was added to 50 ug/ml concentration and the suspension incubated at 65 C for overnight. The suspension was adjusted to 1.2 M potassium acetate and incubated in water/ice bath to precipitate proteins/SDS/salts. The samples were centrifuged at 20K x g for 10 minutes and the pellet discarded. Nucleic acids were then ethanol precipitated from the supernatant. The nucleic acids were resuspended in TE, RNase added, and incubated at 37 C for 10 minutes. The samples were then extracted once with phenol/chloroform, once with chloroform, and ethanol precipitated again. The yield of genomic DNA was measured by OD260. An aliquot of genomic DNA was then fragmented by three rounds of sonication for 25 seconds at 90% duty cycle at power setting 4. An aliquot of 2 ug of fragmented genomic DNA was used as template in the labeling reaction.

tag: Yeast strain

tag: relevant genotype

source_name: Mononucleosomal DNA from YBC2465 biological replicate 3 at permissive temperature.

label_protocol: refer to Sample_label_protocol_ch1.

growth_protocol: Cells were grown in liquid YP containing 1% raffinose and 1% galactose at 23 C until OD600 of 0.4Ð0.6. An aliquot of cells were removed and crosslinked in 1% formaldehyde for 5 minutes.

extract_protocol: Cell pellets were resuspended in 1 ml of spheroplasting solution (1 M sorbitol, 10 mM Tris-HCl pH 7.4, 10 mM 2-Mercaptoethanol). The density of cell suspension was measured by absorbance at OD600 and an aliquot equal in cell amount to the other replicates (20-30 OD600 units) was taken. The aliquot of cells were pelleted and resuspended in 1 ml of fresh spheroplasting solution. Zymolyase was added to the samples and incubated at 37 C. Spheroplasting was stopped when the OD600 absorbance of an aliquot of cells in 1% SDS dropped to < 10% of the starting value. Spheroplasts were pelleted and resuspended in 500 ul MNase Digestion Buffer (1 M sorbitol, 50 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40). To the suspension 3.75 units of Micrococcal Nuclease (USB) was added, followed by incubation at 37 C for 25 minutes. The digestion was stopped by adjusting to 0.5% SDS and 5 mM EDTA. Proteinase K was added to 50 ug/ml concentration and incubated at 65 C overnight. The suspension was adjusted to 1.2 M potassium acetate and incubated in water/ice bath to precipitate proteins/SDS/salts. The samples were centrifuged at 20K x g for 10 minutes and the pellet discarded. Nucleic acids were then ethanol precipitated from the supernatant. The nucleic acids were resuspended in TE, RNase added, and incubated at 37 C for 10 minutes. Samples were loaded on a 1.2% agarose gel and DNA fragments separated by electrophoresis. Mononucleosome DNA was excised from the gel and purified using the Qiagen Gel Extraction Kit. DNA yield was measured by OD260. An aliquot of 0.5-1.0 ug DNA was used as template in the labeling reaction.


title: Mononucleosome_rpb1-1_NonPermissive_replicate1

description: Biological replicate 1 of 3 for mononucleosome DNA hybridization for the rpb1-1 strain at non-permissive temperature.

source_name: Mononucleosomal DNA from YBC2465 biological replicate 1 at non-permissive temperature.

growth_protocol: Cells were grown in liquid YP containing 1% raffinose and 1% galactose at 23 C until OD600 of 0.4Ð0.6. The 'permissive' aliquot was removed from the culture. The culture was then placed at 37 C for 120 minutes. An aliquot of cells were removed and crosslinked in 1% formaldehyde for 5 minutes.


title: Mononucleosome_rpb1-1_NonPermissive_replicate2

description: Biological replicate 2 of 3 for mononucleosome DNA hybridization for the rpb1-1 strain at non-permissive temperature.

source_name: Mononucleosomal DNA from YBC2465 biological replicate 2 at non-permissive temperature.


title: Mononucleosome_rpb1-1_NonPermissive_replicate3

description: Biological replicate 3 of 3 for mononucleosome DNA hybridization for the rpb1-1 strain at non-permissive temperature.

source_name: Mononucleosomal DNA from YBC2465 biological replicate 3 at non-permissive temperature.


title: Mononucleosome_Control_Before_replicate2

description: Biological replicate 2 of 3 for mononucleosome DNA hybridization for the control strain before Sth1 degradation.

source_name: Genomic DNA derived from YBC2192

growth_protocol: Cells were grown in liquid YP containing 2% raffinose and/or 2% galactose and 0.05 mM Cu(II)SO4.

value: Sth1td ubr1(delta)

source_name: Mononucleosomal DNA from YBC2192 biological replicate 2 before Sth1 degradation.

growth_protocol: Cells were grown in liquid YP containing 2% raffinose and 0.05 mM Cu(II)SO4 at 27 C until OD600 of 0.4Ð0.6. An aliquot of cells were removed and crosslinked in 1% formaldehyde for 5 minutes.


title: Mononucleosome_Control_After_replicate1

description: Biological replicate 1 of 3 for mononucleosome DNA hybridization for the control strain after Sth1 degradation.

source_name: Mononucleosomal DNA from YBC2192 biological replicate 1 after Sth1 degradation.

growth_protocol: Cells were grown in liquid YP containing 2% raffinose and 0.05 mM Cu(II)SO4 at 27 C until OD600 of 0.4Ð0.6. The 'before' aliquot was removed from the culture and galactose was added to the remaining culture to 2% final and incubated for 60 minutes. The culture was then placed at 37 C for 120 minutes. An aliquot of cells were removed and crosslinked in 1% formaldehyde for 5 minutes.


title: Mononucleosome_Control_After_replicate3

description: Biological replicate 3 of 3 for mononucleosome DNA hybridization for the control strain after Sth1 degradation.

source_name: Mononucleosomal DNA from YBC2192 biological replicate 3 after Sth1 degradation.


title: Mononucleosome_Control_Before_replicate3

description: Biological replicate 3 of 3 for mononucleosome DNA hybridization for the control strain before Sth1 degradation.

source_name: Mononucleosomal DNA from YBC2192 biological replicate 3 before Sth1 degradation.


title: Mononucleosome_rpb1-1_Permissive_replicate2

description: Biological replicate 2 of 3 for mononucleosome DNA hybridization for the rpb1-1 strain at permissive temperature.

source_name: Mononucleosomal DNA from YBC2465 biological replicate 2 at permissive temperature.


title: Mononucleosome_rpb1-1_Permissive_replicate1

description: Biological replicate 1 of 3 for mononucleosome DNA hybridization for the rpb1-1 strain at permissive temperature.

source_name: Mononucleosomal DNA from YBC2465 biological replicate 1 at permissive temperature.