title: stp_30899

status: Public on Mar 31 2011

type: genomic

city: Seattle

first: Tom

last: Nicholas

state: WA

address: Foege Building S-250, Box 355065 3720 15th Ave NE

country: USA

institute: University of Washington

hyb_protocol: Standard NimbleGen protocols

scan_protocol: Standard NimbleGen protocols

data_processing: Standard NimbleGen protocols using NimbleScan software.

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Standard Poodle

label_protocol: Standard NimbleGen protocols

extract_protocol: Standard NimbleGen protocols

tag: breed

value: Standard Poodle

source_name: Boxer

value: Boxer


title: shp_29244

source_name: Shar Pei

value: Shar Pei


title: shp_29244self


title: shp_29267


title: stp_47


title: stp_30719


title: shp_25024


title: lbr_31489

source_name: Labrador Retriever

value: Labrador Retriever


title: lbr_30554


title: lbr_30299


title: stp_30963


title: lbr_34


title: shp_25017


title: lbr_30966


title: stp_31183


title: lbr_30307


title: jrt_31180

source_name: Jack Russell Terrier

value: Jack Russell Terrier


title: shp_24995


title: stp_30680


title: jrt_31170


title: jrt_31070


title: gsh_31232

source_name: German Shepherd

value: German Shepherd


title: jrt_31069


title: gsh_30456


title: gsh_164


title: gry_30843

source_name: Greyhound

value: Greyhound


title: gry_31474self


title: gry_30822r


title: gry_31474


title: dsh_21710

source_name: Dachshund

value: Dachshund


title: jrt_31162


title: gry_30829


title: dsh_21759


title: gsh_30434


title: gry_30769


title: dsh_30032


title: dsh_21690


title: PAO1ut pellicle #2

type: RNA

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

country: Japan

institute: The University of Tokyo

description: GeneChip Hybridization Oven 640 and Fluidics Station 450 were used for target hybridization and staining under the control of the Affymetrix GeneChip Operating Software.

hyb_protocol: Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix.

scan_protocol: Affymetrix GeneChip Scanner 3000 was used.

data_processing: The Affymetrix GeneChip Operating Software was used for data acquisition and processing.

label: biotin

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: strain PAO1ut, 24-hours old pellicle cells #2

label_protocol: Enzo BioArray terminal labeling kit

growth_protocol: P. aeruginosa cells were cultivated aerobically in LB medium in Erlenmeyer flasks under static conditions. Total RNA was extracted at 24 hours after the inoculation.

extract_protocol: Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).

treatment_protocol: The pellicle cells were suspended in RNAprotect Bacterial Reagent (Qiagen) before RNA purification.

tag: growth phase

value: 24-hours old pellicle #2

tag: genotype

value: wild type


title: bxr_37645


title: bxr_179self


title: dsh_21682r


title: brt_25027

source_name: Brittany

value: Brittany


title: brt_27100


title: bxr_37644


title: gsh_31175


title: PAO1ut pellicle #1

source_name: strain PAO1ut, 24-hours old pellicle cells #1

value: 24-hours old pellicle #1


title: brt_30805


title: brt_30624


title: bxr_tasha


title: bxr_37641r


title: breast normal 6

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

description: Gene expression profiling of laser-microdissected stroma.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA, using the “affy” package from Bioconductor.

organism: Homo sapiens

source_name: Normal breast stroma

label_protocol: Biotin-labeled nucleotides were incorporated to obtain biotin-labeled aRNA required for Affymetrix microarray hybridization.

extract_protocol: Total RNA was extracted immediately following microdissection using the PicoPure RNA isolation kit (Arcturus, Mountain View, CA, USA) according to the manufacturer’s instructions.

tag: tissue

value: breast

tag: normal/tumor

value: normal


title: breast tumor 6

source_name: Stroma associated to breast invasive tumor

value: tumor


title: bgl_30556

source_name: Beagle

value: Beagle


title: breast tumor 5


title: bgl_30393


title: bgl_30271


title: bgl_30406


title: breast normal 5


title: self


title: brt_30293


title: breast tumor 4


title: rottweiler

source_name: Rottweiler

value: Rottweiler


title: poodle

value: Standard Poodle


title: breast normal 3


title: breast normal 4


title: breast tumor 3


title: breast tumor 2


title: bcc_26458

source_name: Border Collie

value: Border Collie

value: Boxer


title: bcc_27201


title: pug

source_name: Pug

value: Pug


title: bcc_27199


title: bcc_26371


title: basenji

source_name: Basenji

value: Basenji


title: doberman

source_name: Doberman Pinscher

value: Doberman Pinscher

source_name: Boxer


title: wolf

organism: Canis lupus

source_name: Gray Wolf

value: Gray Wolf


title: bgl_30228


title: breast normal 2


title: shusky

source_name: Siberian Husky

value: Siberian Husky


title: bcc_24948


title: prostate normal 6

source_name: Normal prostate stroma

value: prostate


title: breast tumor 1


title: breast normal 1


title: prostate tumor 6

source_name: Stroma associated to prostate invasive tumor


title: akm_1005r

source_name: Alaskan Malamute

value: Alaskan Malamute


title: pooled root tips from genotype Cvi, biological replicate 3

city: Madison

first: Laura

last: Vaughn

state: WI

address: 425-G Henry Mall

department: Genetics

institute: University of Wisconsin

description: Gene expression data from the root tips of ~600 pooled 5-day-old Cvi seedlings grown on tilted, hard agar plates.

hyb_protocol: For each sample, the labeled cDNA was hybridized overnight on an ATH1 GeneChip (Affymetrix, Santa Clara, CA) in an AFX HybOven 480 (Affymetrix).  Post processing was done on an automated Fluidics 450 Station (Affymetrix).

scan_protocol: Chips were scanned with the GC 3000 G7 scanner (Affymetrix).

data_processing: Quality of microarray hybridization was determined using the Affymetrix MAS5 algorithm.  Expression differences were analyzed using ArrayStar 3 (DNAStar, Madison, WI).  The data were preprocessed using RMA and a quantile normalization method.  For statistical comparisons of expression levels, the student’s t-test option was employed with a FDR (Benjamini-Hochberg correction) multiple testing correction algorithm.

organism: Arabidopsis thaliana

source_name: root tips from seedlings grown on hard agar plates for 5 days, plated tilted for the last 3

label_protocol: Biotin-labeled cDNA was generated using the MessageAmp II kit (Ambion, Austin, TX) according to manufacturer instructions.

growth_protocol: Sterilized seeds of 170G-55-16, Cvi and Ler were placed on 1/2 LSPS + 1.5% agar E plates, stratified for 8 days at 4° C, and then placed in a 22° C growth chamber on a 16 h day/8 h night cycle.  Each replicate consisted of two rows of 60 seeds per row over five plates for a total of ~600 seedlings per replicate.  The plates were positioned vertically for 2 days, and then tilted back 30° for the final 3 days of growth.

extract_protocol: RNA extraction of the ground root tissue was carried out with the RNAeasy kit (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: On the fifth day, approximately 7 mm of root tip was harvested for each seedling and pooled for each replicate.  The order of sample collection was randomized.  The root tips were flash frozen in liquid nitrogen then stored at -80° C until the time of RNA extraction.

value: Natural Accession Cape Verde Islands (Cvi-1)

tag: age

value: 5 day old seedlings

value: ~600 pooled 7 mm root tips


title: akm_1007


title: pooled root tips from genotype Ler-2, biological replicate 1

description: Gene expression data from the root tips of ~600 pooled 5-day-old Ler-2 seedlings grown on tilted, hard agar plates.

value: Natural Accession Landsberg erecta (Ler-2)


title: pooled root tips from genotype Ler-2, biological replicate 3


title: prostate tumor 5

value: tumor


title: shetland

source_name: Shetland Sheepdog

value: Shetland Sheepdog


title: prostate normal 5

value: normal


title: prostate tumor 3


title: gshepherd

source_name: German Shepherd

value: German Shepherd


title: prostate tumor 4


title: prostate normal 4


title: pooled root tips from genotype Ler-2, biological replicate 2


title: lab

source_name: Labrador Retriever

value: Labrador Retriever


title: bxr_37643

value: Boxer


title: pooled root tips from genotype Cvi, biological replicate 2


title: prostate normal 3


title: prostate normal 2


title: pooled root tips from genotype Cvi, biological replicate 1


title: prostate tumor 1


title: prostate normal 1


title: prostate tumor 2


title: pooled root tips from genotype 170G-55-16, biological replicate 2

description: Gene expression data from the root tips of ~600 pooled 5-day-old 170G-55-16 seedlings grown on tilted, hard agar plates.

value: Near Isogenic Line 170G-55-16 a.k.a. HGI2.1


title: pooled root tips from genotype 170G-55-16, biological replicate 3


title: K562 un-treated for 12hr, biological rep3

city: Hsin-Chu

first: Sophia

last: Chan

address: 75 Bo-Ai Street

department: Institute of Bioniformatics and Systems Biology

country: Taiwan

institute: National Chiao Tung University

description: Gene expression data from leukemia cell (K562) untreated drug

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip® Operating Software vers. 1.3 (Affymetrix) on a PC-compatible workstation. And the expression values of the remaining probe sets were normalized and analyzed using dChip2010 software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human leukemia K562 cells were maintained in RPMI 1640 medium supplemented with 10% FCS, 2 mM glutamine, and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin) at 37 °C in a humidified atmosphere of 5% CO2.

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

tag: cell line

value: leukemia cell (K562)

tag: agent


city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
chip_id: 18764802
DNA methylation in the paternal allele along central chr7

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Mus musculus

source_name: methylated-CpG island recovery assay (MIRA) DNA from  PatDup.dist7 MEFs

label_protocol: According to standard NimbleGen Protocol

growth_protocol: Standard

extract_protocol: MEFs were grown in 25 ml of culture medium (Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 10–4 M β-mercaptoethanol, nonessential amino acids, L-glutamine, and antibiotics at standard concentrations). Confluent 15-cm plates provided about 15 to 35 million cells. Formaldehyde (1% final concentration) was added directly into the medium, and the dishes were incubated at room temperature for exactly 2 min (for native ChIP [N-ChIP] assay) or 10 min (for cross-linking and ChIP [X-ChIP]) on an orbiting platform. Cross-linking was stopped with a 0.125 M final concentration of glycine solution. Cells were washed twice with 20 ml of ice-cold phosphate-buffered saline and scraped off the plate with a rubber policeman; cells were then pelleted by centrifugation for 3 min at 250 x g and resuspended in 750 µl of ChIP lysis buffer (1% sodium dodecyl sulfate, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) containing protease inhibitors (Complete protease inhibitor cocktail tablets, catalog number 1697498; Roche Applied Science). Sonication was carried out on ice in 1.7-ml Eppendorff tubes using a Branson Sonifer with a micro tip three or four times (N-ChIP or X-ChIP, respectively) for 10 s at 40% output. The sheared chromatin was centrifuged at 13,000 rpm for 15 min at 4°C. The supernatant was transferred to a fresh tube. An aliquot of the chromatin preparation was reverse cross-linked, proteinase K digested, phenol-chloroform extracted, precipitated, and resuspended in Tris-EDTA buffer. DNA concentration was determined using a UV spectrophotometer. One microgram of DNA was resolved on a 1.5% agarose gel to check sonication efficiency. Fragment sizes ranged from 0.2 to 1.5 kb, with a peak at 0.8 kb. Chromatin preparations were diluted to 0.4 µg/µl with ChIP lysis buffer containing protease inhibitors and were snap-frozen in liquid nitrogen in small aliquots and stored at –80 °C. 10 µl (4 µg) of chromatin and 4 µg of specific antibody was used for each immunoprecipitation. The immunoprecipitated chromatin was eluted from 40 µl of protein A/G agarose beads and reverse cross-linked, and DNA was isolated with a QIAquick kit, (Qiagen, Germany) and eluted in 100 µl of Elution Buffer.

treatment_protocol: No treatment

tag: parental duplication of  distal chr7

tag: epigenetic feature

value: DNA methylation

tag: cell type

value: MEF

source_name: Input DNA from Patdup.dist7 MEFs

value: none, input DNA


description:
chip_id: 18765502
H3K9me3 in the paternal allele along central chr7

source_name: H3K9me3 ChIP DNA from  PatDup.dist7 MEFs


title: K562 treated 0.15mM calactin for 12hr, biological rep1

description: Gene expression data from leukemia cell (K562) treatment 0.15mM calactin for 12hr

treatment_protocol: Human leukemia K562 (2 x 105/ml) cells were treated with 0.15mM of calactin and harvested at 12hr

value: 0.15mM calactin


title: K562 un-treated for 12hr, biological rep2


description:
chip_id: 18765002
H3K9me3 in the maternal allele along central chr7

source_name: H3K9me3 ChIP DNA from  MatDup.dist7 MEFs

source_name: Input DNA from Matdup.dist7 MEFs


description:
chip_id: 18763802
DNA methylation in the maternal allele along central chr7

source_name: methylated-CpG island recovery assay (MIRA) DNA from  MatDup.dist7 MEFs


title: K562 treated 0.15mM calactin for 12hr, biological rep3


title: K562 un-treated for 12hr, biological rep1


title: pooled root tips from genotype 170G-55-16, biological replicate 1


title: Sample13791-USC-G3

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v3 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

source_name: Fresh frozen tissue

label_protocol: Initially, 250ng total RNA was converted to cDNA, followed by an in vitro transcription step to generate labeled cRNA using the Ambion Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX) as per manufacturer’s instructions.

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy midi kits (Qiagen, Valencia, CA) following manufacturer’s instructions. After elution, RNA samples were concentrated by EtOH precipitation at –20oC overnight, and resuspended in nuclease-free water.  Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop Wilmington, DE) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were required to have a RIN >6.5, an OD 260:280 of 1.9-2.1, an OD 260/230 >1.5 and >1.5 28S:18S ratio of the ribosomal bands for gene expression array analysis.

value: USC

tag: Stage

value: early

tag: grade


title: Sample8616-EAC-G3

value: EAC


title: K562 treated 0.15mM calactin for 12hr, biological rep2


title: Sample11572-EAC-G1


title: Sample16674-USC-G3


title: At-hh pRNAi 12K-01

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

institute: JT Biohistory Research Hall

hyb_protocol: cRNA probes were hybridized to a microarray in Hybridization buffer (5x SSC, 0.1% SDS, 10% formamide) at 42˚C for 16-20 h.

scan_protocol: Microarray slides were scanned using a GenePix 4000B Scanner (Molecular Devices).

data_processing: Obtained images were analyzed using an Array-Pro Analyzer Ver. 4.5 (Media Cybernetics, Inc.). The quantitative data were subjected to Loess normalization.

organism: Parasteatoda tepidariorum

source_name: At-hh pRNAi embryos

label_protocol: cRNA labeled with Cy3 was prepared from 2 µg of total RNA using RNA Transcript SureLABEL Core Kit (Takara).

extract_protocol: Total RNA was extracted from approximately 250 embryos of the same stage using MagExtractor (Toyobo). RNA integrity was examined with an Agilent Bioanalyzer 2100.

treatment_protocol: A mated female was injected with approximately 1.5µl of At-hh dsRNA solution (2µg/µl) four times at 2-3 days intervals. Embryos derived from an egg sac produced by this female 20 days after the first injection of At-hh dsRNA were used for RNA extraction.

value: whole embryo

tag: developmental stage

value: late stage 5

tag: treatment

value: At-hh pRNAi

source_name: Normal embryos

label_protocol: cRNA labeled with Cy5 was prepared from 2 µg of total RNA using RNA Transcript SureLABEL Core Kit (Takara).

treatment_protocol: Embryos derived from a different egg sac produced by the same female one day before the first injection of At-hh dsRNA were used for RNA extraction.


title: Sample15255-EAC-G1


title: Sample16516-EAC-G3


title: Sample17276-EAC-G3


title: Sample14409-USC-G3


title: Sample15367-EAC-G1


description:
chip_id: 330797
CTCF in the paternal allele along central chr7

source_name: transcription factor CTCF ChIP DNA from PatDup.dist7 MEFs

value: CTCF binding


title: Sample17518-2P-EAC-G1


description:
chip_id: 18768402
H3K4me3 in the paternal allele along central chr7

source_name: H3K4me3 ChIP DNA from  PatDup.dist7 MEFs


description:
chip_id: 18765702
H3K9ac in the maternal allele along central chr7

source_name: H3K9ac ChIP DNA from  MatDup.dist7 MEFs


title: Sample15973-EAC-G3


description:
chip_id: 18769102
H3K9ac in the paternal allele along central chr7

source_name: H3K9ac ChIP DNA from  PatDup.dist7 MEFs


title: Sample15793-EAC-G3


description:
chip_id: 18765602
H3K4me3 in the maternal allele along central chr7

source_name: H3K4me3 ChIP DNA from  MatDup.dist7 MEFs


title: Sample10890-EAC-G3


title: Sample16706-EAC-G1


description:
chip_id: 330868
CTCF in the maternal allele along central chr7

source_name: transcription factor CTCF ChIP DNA from MatDup.dist7 MEFs


title: Sample15965-EAC-G3


title: Sample17680-USC-G3


title: Reference Design timecourse c_t8.2

city: Ikoma

first: Naotake

last: Ogasawara

state: Nara

institute: Nara Institute of Science and Technology

description: RNA was isolated from W3110 cells, grown in LB media.

hyb_protocol: Prehybridization of the array slides was performed for 4h in filtered prehybridization solution [25% formamide, 5x SSC, 10mg l-1 BSA (fraction V), 0.1% SDS] at 42℃. Slides were briefly washed in ethanol and dried by centrifugation at 1000g for 5 min. Hybridization of the probe was performed using hybridization solution (25% formamide, 5x SSC, 0.1% SDS, 0.1µg poly(A) ml-1, 1x Denhardt's solution and 80pmol Cy3 and Cy5 combined probe). The hybridization solution containing the Cy-Dye-labelled cDNA was heated to 95℃ for 3 min, Hybridization is performed by dvalytix hybridaization macine.

scan_protocol: After hybridization, slides were washed in wash buffer I (2x SSC/0.1% SDS) for 2min at 42℃, in wash buffer II (0.2x SSC) for 2min at room temperature and then twice in wash buffer III (0.05x SSC) for 2min at room temperature. All washes were done with vigorous shaking of the microarray slides. The slides were dried by centrifugation at 1000g for 5min, and then analysed using an Fuji FLA-8000 scanner and Array gauge ver.2.0 software (Fuji film)

data_processing: Normalization is performed by TREBAX, using MA-plots. MA-plots can reveal the spot artifacts globally and show the intensity-dependent logarithmic ratio of raw microarray data. In MA-plots, we calculate two parameters, average of logarithmic transferred intensity As=(log(Ts)+log(Rs))/2 and logarithmic ratio of intensity Ms=log(Ts/Rs) Here, Ts and Rs are the intensity of target and control experiments for sth spot, respectively.By plotting values of As on the abscissa and Ms on the ordinate of a coordinate system, it is possible to evaluate the bias error with respects to the average logarithmic intensities. Normalized log ratio M’’s is estimated as the difference between Ms and baseline M’s. Here, using a relation between Ms and As, (Ms=f(As)+es, es is the difference between Ms and f(As) for gene s) by MA plot; the baseline for sth spot is estimated by M’=f(A). The genes whose signal intensity is regarded as zero are eliminated in the present analysis. With this methodology, it is assumed that there is no large error due to expression intensity in the majority of the spots and that expression change does not occur on the majority of the spots.

organism: Escherichia coli

source_name: common reference (OD600=0.5)

label_protocol: Cyscribe Kit

growth_protocol: LB

extract_protocol: Qiagen RNeasy mini Kit

tag: Strain

tag: OD


title: Reference Design timecourse c_t6.2


title: Sample16444-USC-G3


title: Sample15605-EAC-G1


title: Sample16022-EAC-G3


title: Reference Design timecourse c_t9.2


title: Sample14367-EAC-G1


title: Reference Design timecourse c_t10.2


title: akm_1003

source_name: Alaskan Malamute

tag: breed

value: Alaskan Malamute

source_name: Boxer


title: Reference Design timecourse c_t7.2


title: Sample14017-EAC-G1


title: Sample12878-EAC-G1


title: Reference Design timecourse c_t5.2


title: Sample13661-EAC-G3


title: Sample14124-EAC-G1


title: Sample13377-USC-G3


title: Sample16302-USC-G3


title: Sample10963-USC-G3


title: Reference Design timecourse c_t3.2


title: Reference Design timecourse c_t4.2


title: Reference Design timecourse c_t2.2


title: Sample17344-USC-G3


title: Sample14052-USC-G3


title: Reference Design timecourse c_t1.2


title: Sample16936-USC-G3


title: Reference Design timecourse c_t9.1


title: Reference Design timecourse c_t11.1


title: Reference Design timecourse c_t10.1


title: Immortalized conjunctival epithelial cells DHT Treated Biological Replicate 1

city: Boston

first: David

middle: A

last: Sullivan

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: Biological Replicate 1

hyb_protocol: Standard Illumina hybridization protocol was used. Briefly, cRNA/hybridization buffer mixtures were incubated at 65°C for 5 minutes, followed by brief centrifugation to collect.  The mixtures were added to BeadChips and then BeadChips inserted into hybridization chambers, and hybridization was carried out at 58°C for 16-18 hours at rocking speed set to 5.

scan_protocol: Standard Illumina scanning protocol was followed using an Illumina BeadArray Reader.  Scanner settings were set at a default, Factor 1 setting, and scanned images were visually examined for the presence of anomalies and to ensure that average P95 values for each array is greater than 500.  .

data_processing: Illumina BeadScan software was used to produce .idat, .xml, and .tif files for each array on a slide and .sdf files for each barcode on a slide of 12 arrays.  Raw data were extracted using Illumina BeadStudio software v 3.   Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction in an Excel report containing the project description (sample key), gene identifiers and corresponding probe IDs, table of detection p-values, tables of normalized data with and without background subtraction, array quality control metrics, and array quality control metric cut-offs and definitions.  The following array quality control  metrics were met: hybridization control graphs must have increasing signal intensities, negative graph must show an average background of less than 200, and the average biotin signal must be around 6000 or higher.

label: Biotin

source_name: Conjunctiva

label_protocol: Samples for mRNA profiling studies were processed by Asuragen, Inc., according to the company’s standard operating procedures.  The purity and quantity of total RNA samples were determined by absorbance readings at 260 and 280 nm using a NanoDrop ND-1000 UV spectrophotometer.  The integrity of total RNA was qualified by Agilent Bioanalyzer 2100 capillary electrophoresis. Total RNA (100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using a Message Amp™ II-based protocol (Ambion Inc., Austin, TX) and one round of amplification.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNAse I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. The purity and quantity of total RNA samples were determined by absorbance readings at 260 and 280 nm using a NanoDrop ND-1000 UV spectrophotometer.  The integrity of total RNA was qualified by Agilent Bioanalyzer 2100 capillary electrophoresis.

value: Retrovirus immortalized conjunctival epithelial cell line


title: Sample16613-EAC-G3


title: Reference Design timecourse c_t8.1


title: Immortalized conjunctival epithelial cells Vehicle Treated Biological Replicate 3

description: Biological Replicate 3


title: Immortalized corneal epithelial cells DHT Treated Biological Replicate 2

description: Biological Replicate 2

source_name: Cornea

value: Retrovirus immortalized corneal epithelial cell line


title: Immortalized conjunctival epithelial cells Vehicle Treated Biological Replicate 2

description: Biological Replicate 2


title: Immortalized conjunctival epithelial cells DHT Treated Biological Replicate 3

description: Biological Replicate 3


title: Immortalized corneal epithelial cells DHT Treated Biological Replicate 3

description: Biological Replicate 3


title: Sample10623-EAC-G3


title: Reference Design timecourse c_t7.1


title: Immortalized conjunctival epithelial cells DHT Treated Biological Replicate 2

description: Biological Replicate 2


title: Immortalized corneal epithelial cells Vehicle Treated Biological Replicate 3

description: Biological Replicate 3


title: Immortalized corneal epithelial cells DHT Treated Biological Replicate 1

description: Biological Replicate 1


title: Reference Design timecourse c_t5.1


title: Immortalized conjunctival epithelial cells Vehicle Treated Biological Replicate 1

description: Biological Replicate 1


title: Reference Design timecourse c_t6.1


title: Reference Design timecourse c_t11.2


title: akm_1004

value: Boxer


title: Reference Design timecourse c_t4.1


title: Sample17205-EAC-G1


title: RNA PolII in the paternal allele along distal chr7

description: chip_id:  = 8523602

source_name: RNA Polymerse II ChIP DNA from  PatDup.dist7 MEFs

extract_protocol: MEFs were grown in 25 ml of culture medium (Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 10–4 M β-mercaptoethanol, nonessential amino acids, L-glutamine, and antibiotics at standard concentrations). Confluent 15-cm plates provided about 15 to 35 million cells. Formaldehyde (1% final concentration) was added directly into the medium, and the dishes were incubated at room temperature for exactly 2 min (for native ChIP [N-ChIP] assay) or 10 min (for cross-linking and ChIP [X-ChIP]) on an orbiting platform. Cross-linking was stopped with a 0.125 M final concentration of glycine solution. Cells were washed twice with 20 ml of ice-cold phosphate-buffered saline and scraped off the plate with a rubber policeman; cells were then pelleted by centrifugation for 3 min at 250 x g and resuspended in 750 µl of ChIP lysis buffer (1% sodium dodecyl sulfate, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) containing protease inhibitors (Complete protease inhibitor cocktail tablets, catalog number 1697498; Roche Applied Science). Sonication was carried out on ice in 1.7-ml Eppendorff tubes using a Branson Sonifer with a micro tip three or four times (N-ChIP or X-ChIP, respectively) for 10 s at 40% output. The sheared chromatin was centrifuged at 13,000 rpm for 15 min at 4°C. The supernatant was transferred to a fresh tube. An aliquot of the chromatin preparation was reverse cross-linked, proteinase K digested, phenol-chloroform extracted, precipitated, and resuspended in Tris-EDTA buffer. DNA concentration was determined using a UV spectrophotometer. One microgram of DNA was resolved on a 1.5% agarose gel to check sonication efficiency. Fragment sizes ranged from 0.2 to 1.5 kb, with a peak at 0.8 kb. Chromatin preparations were diluted to 0.4 µg/µl with ChIP lysis buffer containing protease inhibitors and were snap-frozen in liquid nitrogen in small aliquots and stored at –80 °C. 10 µl (4 µg) of chromatin and 4 µg of specific antibody was used for each immunoprecipitation. The immunoprecipitated chromatin was eluted from 40 µl of protein A/G agarose beads and reverse cross-linked, and DNA was isolated with a QIAquick kit, (Qiagen, Germany) and eluted in 100 µl of Elution Buffer.  RNA was isolated from MatDup.dist7 and PatDup.dist7 MEFs using RNA-Bee according to manufacturer’s instructions (Tel-Test). The pellet was dissolved in DEPC water containing RNasin (Promega) and 10 mM DTT. Contaminating DNA was removed with the DNA-free Kit (Ambion). ds cDNA was prepared from 10 g of  MatDup.dist7 and PatDup.dist7 MEF total RNA according to NimbleGen Arrays User’s Guide (http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf) using SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen). The ds cDNA was purified using QIAquick PCR Purification Kit (Qiagen) for hybridization.  For MIRA The methylated fraction of sonicated genomic DNA was captured using recombinant MBD3L1 and MBD2b proteins.

value: Pol II

source_name: Input DNA from Patdup.dist7 MEFs


title: CCA1OX 3160min rep1

city: Davis

first: Julin

middle: N

last: Maloof

address: One Shields Ave

department: Plant Biology

institute: University of California, Davis

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159321
K Nozue 07.12.05 22 ATH1.CEL
Sample name: A22

hyb_protocol: Hybridization was performed according to the EukGE-WS2v4_450 protocol

scan_protocol: Scanning was performed on a GCS3000 scanner

data_processing: Data was normalized using the rma function of the affy package in R/Bioconductor

source_name: CCA1OX seedlings, dark, 3160 minutes after dawn day 4

label_protocol: Biotinolyated cRNA was obtained using the protocol described by Schmid, M. et al. Nat. Genet. 37, 501-506 (2005)

growth_protocol: Plants were grown on 1X MSMO media supplemented with 3% sucrose

extract_protocol: total RNA was extracted using Qiagen RNeasy Plant Mini kit and manufactuer's instructions

tag: days after germination

tag: minutes after dawn day 4

tag: light

value: dark

tag: growth

value: growing


title: Immortalized corneal epithelial cells Vehicle Treated Biological Replicate 2

description: Biological Replicate 2


title: Primary corneal epithelial cells DHT Treated Biological Replicate 3

description: Biological Replicate 3

value: Primary corneal epithelial cells


title: CCA1OX 4120min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159326
K Nozue 07.12.05 24 ATH1.CEL
Sample name: A24

source_name: CCA1OX seedlings, dark, 4120 minutes after dawn day 4

tag: genotype


title: Immortalized corneal epithelial cells Vehicle Treated Biological Replicate 1

description: Biological Replicate 1

tag: cell line


title: CCA1OX 1720min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159302
K Nozue 07.12.05 18 ATH1.CEL
Sample name: A18

source_name: CCA1OX seedlings, dark, 1720 minutes after dawn day 4


title: E47

city: New York

first: FANG

last: FANG

address: 1275 York Avenue

department: The Human Oncology and Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression data for breast cancer primary tumor

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using  Affymetrix GeneArray scanner 7G.

data_processing: data was normalized and analyzed using partek software and R packages. Specifically log2 transformation was used for data normalization.

source_name: breast cancer

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: The RNA  was extracted using Agencourt RNAdvance Tissue Kit according to the manufacturer's instructions.

tag: tissue

value: frozen tissue for primary tumor

tag: b-cimp phenotype

value: CIMP positive


title: E53


title: Reference Design timecourse c_t3.1


title: CCA1OX 2680min rep1_A20

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159304
K Nozue 07.12.05 20 ATH1.CEL
Sample name: A20

source_name: CCA1OX seedlings, dark, 2680 minutes after dawn day 4


title: E46


title: Primary corneal epithelial cells DHT Treated Biological Replicate 1

description: Biological Replicate 1


title: Reference Design timecourse c_t1.1


title: Primary corneal epithelial cells DHT Treated Biological Replicate 2

description: Biological Replicate 2


title: Reference Design timecourse c_t2.1


title: E51


title: RNA PolII in the maternal allele along distal chr7

description: chip_id:  = 8537702

source_name: RNA Polymerse II ChIP DNA from  MatDup.dist7 MEFs

tag: parental duplication of  distal chr7

tag: epigenetic feature

value: MEF

source_name: Input DNA from Matdup.dist7 MEFs

value: none, input DNA


title: DNA methylation in the paternal allele along distal chr7

description: chip_id:  = 12602902

source_name: methylated-CpG island recovery assay (MIRA) DNA from  PatDup.dist7 MEFs

value: DNA methylation

tag: cell type


title: CCA1OX 1240min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159301
K Nozue 06.24.05 16 ATH1.CEL
Sample name: A16

source_name: CCA1OX seedlings, dark, 1240 minutes after dawn day 4


title: Primary corneal epithelial cells Vehicle Treated Biological Replicate 3

description: Biological Replicate 3


title: Primary corneal epithelial cells Vehicle Treated Biological Replicate 2

description: Biological Replicate 2


title: E45


title: Primary corneal epithelial cells Vehicle Treated Biological Replicate 1

description: Biological Replicate 1


title: Immortalized meibomian epithelial cells  DHT Treated  Biological Replicate 3

description: Biological Replicate 3

source_name: Meibomian gland

value: Retrovirus immortalized meibomian epithelial cell line generated in our laboratory


title: E20


title: E42


title: E38


title: Immortalized meibomian epithelial cells  DHT Treated  Biological Replicate 2

description: Biological Replicate 2


title: Immortalized meibomian epithelial cells  Vehicle Treated Biological Replicate 3

description: Biological Replicate 3


title: Immortalized meibomian epithelial cells  DHT Treated  Biological Replicate 1

description: Biological Replicate 1


title: H3K27me3 in the paternal allele along distal chr7

description: chip_id:  = 9690402

source_name: H3K27me3  ChIP DNA from  PatDup.dist7 MEFs


title: DNA methylation in the maternal allele along distal chr7

description: chip_id:  = 12596402

source_name: methylated-CpG island recovery assay (MIRA) DNA from  MatDup.dist7 MEFs


title: H3K79me3 in the paternal allele along distal chr7

description: chip_id:  = 9687502

source_name: H3K79me3  ChIP DNA from  PatDup.dist7 MEFs


title: Col 4120min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159299
K Nozue 07.12.05 12 ATH1.CEL
Sample name: A12

source_name: Col seedlings, dark, 4120 minutes after dawn day 4

value: Col

value: not growing


title: Immortalized meibomian epithelial cells  Vehicle Treated Biological Replicate 2

description: Biological Replicate 2


title: H3K9me3-17-625 in the paternal allele along distal chr7

description: chip_id:  = 20507202

source_name: H3K9me3 ChIP DNA from  PatDup.dist7 MEFs


title: E7


title: E54

value: CIMP negative


title: H3K27me3 in the maternal allele along distal chr7

description: chip_id:  = 9690202

source_name: H3K27me3  ChIP DNA from  MatDup.dist7 MEFs


title: S29

description: Gene methylation data data for breast cancer primary tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: data was normalized and analyzed using partek software and R packages. Specifically centered logit transformation was used for data normalization.

label: C-Bio and A-DNP

label_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

extract_protocol: The genomic DNA was extracted from snap-frozen sections from the breast cancer patients by using a DNeasy Tissue kit (Qiagen)

tag: tissue type

tag: cimp status

value: CIMP-


title: H3K79me3 in the maternal allele along distal chr7

description: chip_id:  = 9706702

source_name: H3K79me3 ChIP DNA from  MatDup.dist7 MEFs


title: Immortalized meibomian epithelial cells  Vehicle Treated Biological Replicate 1

description: Biological Replicate 1


title: Col 3160min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159298
K Nozue 07.12.05 10 ATH1.CEL
Sample name: A10

source_name: Col seedlings, dark, 3160 minutes after dawn day 4


title: H3K9me3-17-625 in the maternal allele along distal chr7

description: chip_id:  = 20507102

source_name: H3K9me3 ChIP DNA from  MatDup.dist7 MEFs


title: E44


title: E36


title: E11


title: H3K79me2 in the paternal allele along distal chr7

description: chip_id:  = 10285602

source_name: H3K79me2 ChIP DNA from  PatDup.dist7 MEFs

source_name: Input DNA from Patdup.dist7 MEFs


title: Col 2680min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159291
K Nozue 07.12.05 08 ATH1.CEL
Sample name: A8

source_name: Col seedlings, dark, 2680 minutes after dawn day 4


title: E33

source_name: breast cancer


title: S53

value: CIMP+


title: E52


title: H3K4me3 in the paternal allele along distal chr7

description: chip_id:  = 8524302

source_name: H3K4me3 ChIP DNA from  PatDup.dist7 MEFs


title: CCA1OX 280min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159300
K Nozue 06.24.05 14 ATH1.CEL
Sample name: A14

source_name: CCA1OX seedlings, dark, 280 minutes after dawn day 4


title: H3K79me2 in the maternal allele along distal chr7

description: chip_id:  = 9690302

source_name: H3K79me2 ChIP DNA from  MatDup.dist7 MEFs

source_name: Input DNA from Matdup.dist7 MEFs


title: Col 1720min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM159273
K Nozue 07.12.05 06 ATH1.CEL
Sample name: A6

source_name: Col seedlings, dark, 1720 minutes after dawn day 4


title: H3K4me2 in the maternal allele along distal chr7

description: chip_id:  = 8523102

source_name: H3K4me2 ChIP DNA from  MatDup.dist7 MEFs


title: S52


title: E31


title: S51


title: H3K4me2 in the paternal allele along distal chr7

description: chip_id:  = 8523702

source_name: H3K4me2 ChIP DNA from  PatDup.dist7 MEFs


title: H3K4me3 in the maternal allele along distal chr7

description: chip_id:  = 8523902

source_name: H3K4me3 ChIP DNA from  MatDup.dist7 MEFs


title: S54


title: Col 1240min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM158681
K Nozue 06.24.05 04 ATH1.CEL
Sample name: A4

source_name: Col seedlings, dark, 1240 minutes after dawn day 4


title: S48


title: E2


title: S50


title: E21


title: Col 280min rep1

description:
Gene expression data from Arabidopsis seedlings grown under alternating light / dark samples.
Re-analysis of GSM158680
K Nozue 06.24.05 02 ATH1.CEL
Sample name: A2

source_name: Col seedlings, dark, 280 minutes after dawn day 4


title: S47


title: E19


title: S49


title: MCF-7 cells-40mM g-T3, biological rep 4

city: Washington

first: Habtom

last: Ressom

state: DC

address: 4000 Reservoir Rd.

institute: Georgetown University

description: Gene expression data from MCF-7 cells treated with gamma tocotrienol

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix U133A2 GeneChip Array following manufacturer's instructions.

scan_protocol: GeneChip Scanner 3000

data_processing: RMA for background adjustment, quantile method for normalization, and a robust multi-array average for summarization

source_name: treated MCF-7 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were grown in 100 mm dishes in DMEM with 5% FBS at 37oC with 5%CO2

extract_protocol: RNA was isolated using trizol following manufacturer's instructions

treatment_protocol: Cells were treated in complete medium with DMSO (control) or 40 uM gamma tocotrienol for 24h

tag: agent

value: gamma tocotrienol


title: S44


title: H4k91ac in the maternal allele along distal chr7

description: chip_id:  = 9687602

source_name: H4K91ac ChIP DNA from  MatDup.dist7 MEFs


title: LGMP460

first: Andrei

middle: V.

last: Krivtsov

address: 1 Blackfan circle

department: Hem Onc

institute: Children's Hospital

description: Purified Lineage- Sca1- CD117+ CD16/32high CD34-/low from mouse sucumbed to AML

hyb_protocol: 3.75 micrograms of biotinylated material was hybridized according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

source_name: Lin(CD3e; CD4, CD8a, CD19, CD45R, CD127; Gr1, TER119)- Sca1- CD117+ CD34+/low CD16/32high

label_protocol: 10 to 50 nanograms of total RNA was amplified and processed to produce biotinylated cDNA targets using two round of in vitro RNA synthesis

extract_protocol: Trizol extraction following manufacturer's protocol.

tag: genetic background

value: leukemia stem cels originated form HSC


title: CTCF in the paternal allele along distal chr7

description: chip_id:  = 12592402

source_name: transcription factor CTCF ChIP DNA from PatDup.dist7 MEFs

value: CTCF binding


title: LGMP459


title: HCT116-DKO

description: HCT116 DNMT1 DNMT3b double knockout

hyb_protocol: Standard Affymetrix Protocol, as described in GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx)

data_processing: Processed with Affymetrix ExpressionConsole v1.1.1 using RMA

growth_protocol: cells were cultured in McCoy’s 5A medium with 10% FBS.

extract_protocol: Qiagen RNAeasy purification kit

treatment_protocol: no treatment

value: colon cancer cell

value: HCT116 DNMT1-/- DNMT3b -/-


title: MCF-7 cells-40mM g-T3, biological rep 3


title: S43


title: ds cDNA in the paternal allele along distal chr7

description: chip_id:  = 325166

source_name: double stranded cDNA from PatDup.dist7 MEFs

value: Gene Expression

source_name: Input DNA from Patdup.dist7 MEFs


title: S7

source_name: breast cancer

value: frozen tissue for primary tumor


title: H3K9ac in the paternal allele along distal chr7

description: chip_id:  = 9690102

source_name: H3K9ac ChIP DNA from  PatDup.dist7 MEFs


title: H3K9ac in the maternal allele along distal chr7

description: chip_id:  = 9689002

source_name: H3K9ac ChIP DNA from  MatDup.dist7 MEFs


title: LGMP458


title: S46


title: MCF-7 cells-40mM g-T3, biological rep 2


title: S42


title: LGMP625

value: leukemia stem cels originated form GMP


title: S41


title: LGMP623


title: S4


title: MCF-7 cells-control, biological rep 4

description: Gene expression data from MCF-7 cells treated with vehicle control (DMSO)

source_name: control MCF-7 cells

value: control


title: H4k91ac in the paternal allele along distal chr7

description: chip_id:  = 9687702

source_name: H4K91ac ChIP DNA from  PatDup.dist7 MEFs

value: MEF

value: none, input DNA


title: E23


title: E29


title: LGMP457


title: HCT116

description: HCT116 WT

scan_protocol: Standard Affymetrix Protocol, as described in GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx)


title: ds cDNA in the maternal allele along distal chr7

description: chip_id:  = 325233

source_name: double stranded cDNA from MatDup.dist7 MEFs

source_name: Input DNA from Matdup.dist7 MEFs


title: SO16-2

city: Gothenburg

first: Kuk-Ki

last: Hong

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae grown on galactose medium

label_protocol: Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated from ground frozen mycelium using the Qiagen RNeasy Mini Kit.

tag: mutant

tag: strain

value: S. cerevisiae CEN.PK113-7D

tag: medium

value: Minimal galactose-based medium

tag: growth conditions

value: Controlled fermenter kept at pH 5.0

tag: sampling time

value: mid exponential phase

tag: replicate no


title: LGMP644


title: MCF-7 cells-control, biological rep 3


title: MCF-7 cells-control, biological rep 2


title: CTCF in the maternal allele along distal chr7

description: chip_id:  = 12604202

source_name: transcription factor CTCF ChIP DNA from MatDup.dist7 MEFs


title: S34

value: CIMP-


title: MCF-7 cells-control, biological rep 1


title: SO16-1


title: S38

value: CIMP+


title: LGMP477


title: GMP sample 3

description: purified Lineage-  Sca1- CD117+ CD34+ CD16/32+ cells form 8 week old female mice

value: GMP


title: S33


title: S32


title: PGM2-2


title: GMP sample 2


title: PGM2-1


title: 016 BJ Cyclin E c-Myc

city: Jerusalem

first: Batsheva

last: kerem

address: Edmond Safra Campus

department: Department of Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Gene expression data from iPS cell line 41 derived from patient B

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

source_name: BJ-hTERT cells coexpressing human cyclin E and c-Myc

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: BJ hTERT cells grown in DMEM supplemented with 10% FBS, 100,000 U/L penicillin, 100 µg/L streptomycin

extract_protocol: RNA  was isolated using Qiagen Rneasy mini kit

treatment_protocol: Total RNA was isolated from cells infected with empty vector or cyclin E, c-Myc or both 2-4 week following c-Myc expression

tag: gender

value: Male

value: fibroblast

tag: iPS cell line


title: E62C-2


title: E62C-1


title: 03 BJ c-Myc

description: Gene expression data from iPS cell line 36 derived from patient B

source_name: BJ-hTERT cells expressing human c-Myc

tag: tissue


title: GMP sample 1


title: S31


title: 015 BJ c-Myc

description: Gene expression data from fibroblast - B


title: S30


title: 04 BJ Cyclin E c-Myc


title: MEP sample 3

description: purified Lineage-  Sca1- CD117+ CD34- CD16/32-/low cells form 8 week old female mice

value: MEP


title: S3


title: E62B-2


title: 02 BJ cyclin E

description: Gene expression data from iPS cell line 11 derived from patient A

source_name: BJ-hTERT cells expressing human cyclin E


title: Huh7 un-treated for 24hr, biological rep3

description: Gene expression data from hepatomacellular carcinoma Huh7 cell untreated drug

hyb_protocol: One μg of total RNA, labeled according to the GeneChip® Whole Transcript Sense Target Labeling Assay manual of the manufacturer (Affymetrix) was hybridized to Human Exon 1.0 ST Arrays (Affymetrix) for 16 hours at 45°C. The hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G and Gene-Chip Operating Software v. 1.3 to produce. We get the probe cells and compute an intensity for each cell by GeneChip® Operating Software (Affymetrix, Santa Clara, CA) on a PC-compatible workstation.

data_processing:
The values of the hybridized probesets were normalized and analyzed for gene expression using dChip2006 software (http://biosun1.harvard.edu/~cli/dchip2006. exe).  The GeneChip® Human Exon 1.0 ST microarray system has only perfect match probes, but no mismatch (MM) probes available to perform data normalization. Instead of the MM probes, we inferred and removed the existing systematic biases based on the observed intensities of the background probes (BGP) that were pre-designed by Affymetrix. To find the differentially expressed genes, We calculate the mean intensity for each set of 3 replicates. The following, we consider the task of finding differentially expressed genes between the control and amiloride-treatment samples using the p-value and log2 ratio. Single probe set mappings were performed over NCBI RefSeqs and the exon-intron genomic coordinates of each known human transcript were downloaded from UCSC Table Browser version hg18. We applied three criteria to filter the putative AS events from the exon chip. First, Pearson’s correlation coefficient was used to compare the gene expression profiles between control and amiloride samples. Second and third, we used the normalized values of array intensities of exon expression for calculating the splicing index, as previously described (Methods 37: 345-359, 2005), and also for obtaining the log2 ratio. The 3 criteria are combined to filter the putative AS events.
probe group file: HuEx-1_0-st-v2.r2.pgf

label_protocol: All procedures and hybridizations were performed according to the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual. In brief, 1 μg of total RNA was processed using a pre-commercial version of the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay. Pre-commercial versions of the GeneChip WT cDNA Synthesis Kit, WT cDNA Amplification Kit, and WT Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA), containing identical formulations to the commercial kits, were used for target preparation. Eight µg of cRNA were added into the second cycle cDNA reaction.

growth_protocol: The human hepatoma cell line, Huh-7, originally purchased from Food Industry Research and Development Institute (Hsinchu, Taiwan), was grown in DMEM supplemented with 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin (Invitrogen Inc, USA) at 37℃ in a humidified 5% CO2 incubator. All chemical reagents including amiloride, amiloride derivatives, okadaic acid, AKT pathway inhibitors and cell culture grade anhydride DMSO were obtained from Sigma Chemical Co., USA. Stock solution of amiloride (250 mM) was prepared in DMSO. For dose response experiments, we treated cells (1x106/ml plated on a 100-mm dish overnight) with various concentrations of drugs in the growth medium for 24 hours. For kinetic studies, we added 0.5 mM amiloride to the medium and harvested the cells at various time points.

extract_protocol: RNeasy Mini kit (Qiagen Inc., USA) to isolate total RNA according to the manufacturer’s instructions and verified the RNA quality by using RNA 6000 NanoAssay on an 2100 Bioanalyzer (Agilent).

tag: cell line

value: Hepatocellular Carcinoma Huh-7 cell line

value: untreated


title: Huh7 un-treated for 24hr, biological rep2

treatment_protocol: Stock solution of amiloride (250 mM) was prepared in DMSO. For dose response experiments, we treated cells (1x106/ml plated on a 100-mm dish overnight) with various concentrations of drugs in the growth medium for 24 hours. For kinetic studies, we added 0.5 mM amiloride to the medium and harvested the cells at various time points.


title: CMP sample 3

description: purified Lineage-  Sca1- CD117+ CD34+/low CD16/32-low cells form 8 week old female mice

value: CMP


title: Huh7 un-treated for 24hr, biological rep1


title: S27

description: Gene methylation data data for breast cancer primary tumor

value: frozen tissue for primary tumor


title: MEP sample 2


title: MEP sample 1


title: MCF-7 cells-40mM g-T3, biological rep 1

source_name: treated MCF-7 cells

value: gamma tocotrienol


title: Huh7 treated 0.5mM amiloride for 24hr, biological rep3

description: Gene expression data from hepatocellular carcinoma Huh7 cell treatment 0.5mM amiloride for 24hr

value: amiloride


title: REF-1

value: ref


title: S23


title: REF-2

value: S. cerevisiae CEN.PK113-7D


title: S36


title: 014 BJ cyclin E

description: Gene expression data from iPS cell line 26 derived from patient A


title: S28


title: S24


title: E62A-1

value: Minimal galactose-based medium


title: E62B-1

value: Controlled fermenter kept at pH 5.0


title: CMP sample 2


title: CMP sample 1


title: E62A-2

value: mid exponential phase


title: KLS sample 3

description: purified Lineage-  CD117+ Sca1+ cells form 8 week old female mice

value: KLS


title: cDNA form HBEC biological triplicate#2

description: Expression profile of human bronchial epithelia cells immortalized with hTERT and CDK4

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: RNA from human bronchial epithelia cells immortalized with hTERT and CDK4

label_protocol: Standard Affymetrix Protocol, as described in GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 (available at http://www.affymetrix.com/support/technical/product_updates/wt_1_1_assay.affx)

growth_protocol: cells were cultured in K-SFM media (Invitrogen, Carlsbad, CA).

value: human bronchial epithelia cells

value: HBEC


title: cDNA form HBEC biological triplicate#1


title: TW01TetER_cl19, doxycycline 24 h, rep1

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

institute: National Health Research Institutes, Taiwan

description: Cell densitiy was maintained at 150,000 / ml before induction.

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST Arrays (Affymetrix) and scanned at the NHRI Microarray Core Facility (Miaoli County, Taiwan).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.1) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

source_name: TW01TetER_cl19 (high Rta expression)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were grown to log-phase in DMEM supplemented with 10% tetracycline-free fetal bovine serum before induction.

extract_protocol: Total RNA was extracted using a RNeasy Mini kit (Qiagene), according to the manufacturer’s instructions. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with doxycycline (50 nanogram/ml) for 24 h.

value: nasopharyngeal carcinoma

tag: immortalization method

value: EBV negative


title: KLS sample 2


title: Huh7 treated 0.5mM amiloride for 24hr, biological rep1


title: S26

value: CIMP-


title: BJ vector

description: Gene expression data from iPS cell line 20 derived from patient A

source_name: BJ-hTERT cells expressing empty vector

value: Male

value: fibroblast


title: TW01TetER_cl7, doxycycline 24 h, rep1

source_name: TW01TetER_cl7 (low Rta expression)


title: KLS sample 1


title: Control, doxcycline 24 h, rep 1


title: cDNA form HBEC biological triplicate#3


title: S22

source_name: breast cancer

value: CIMP+


title: S21

value: frozen tissue for primary tumor


title: S2


title: seedlings_mutant and wild type_rep6

city: Oslo

first: Reidunn

middle: B.

last: Aalen

address: P.O.Box 1066 Blindern

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Two color microarray. Biological replicas are dyeswaped between slides. Log2 ratios in matrix table are multiplied with -1 to adjust for dyeswapping

hyb_protocol: Hybridizations were performed in a Slide Booster Hybridization Station (Advalytix, Brunnthal, Germany), and the slides were washed according to the manufacturers’ descriptions (Genisphere and Advalytix).

scan_protocol: The slides were scanned at 10 mm resolution on a G2505B Agilent DNA microarray scanner (Agilent Technologies,Palo Alto, CA, USA). The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).

data_processing: The data sets were normalized using variance stabilization and normalization (vsn)  and differentially expressed genes identified using the limma software package.

source_name: Seedlings from wt (Colombia ecotype) (biological replica 6)

label_protocol: Total RNA (15 mg) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction.  Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.

growth_protocol: Seeds were sown out on soil and grown under the following conditions; 22oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 μmol/m2/sek in light intensity

extract_protocol: Total RNA was extracted using RNeasy midi kit (Qiagen).

tag: genotype/variation

value: wt

tag: ecotype

value: Colombia

tag: biological replica

source_name: Seedlings from mutant ashh2-1/sdg8-1 (biological replica 6)

value: mutant ashh2-1/sdg8-1


title: 293TetER doxycycline 48 h, rep2

description: Cell densitiy was maintained at 200,000 / ml before induction.

source_name: 293 EBV Rta inducible line, doxycycline 48 h

treatment_protocol: Cells were treated with doxycycline (50 nanogram/ml) for 48 h.

value: embryonic kidney cell

value: transformed with sheared Ad5 DNA


title: S20

tag: tissue type

tag: cimp status


title: 293TetER doxycycline 48 h, rep1


title: seedlings_mutant and wild type_rep4

source_name: Seedlings from wt (Colombia ecotype) (biological replica 4)

source_name: Seedlings from mutant ashh2-1/sdg8-1 (biological replica 4)


title: S19


title: seedlings_mutant and wild type_rep5

description: Two color microarray. Biological replicas are dyeswaped between slides.

source_name: Seedlings from mutant ashh2-1/sdg8-1 (biological replica 5)

source_name: Seedlings from wt (Colombia ecotype) (biological replica 5)


title: Immobilized, Day 17, rep 2

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: RNA from the immobilized beads were extracted essentially as described by Kruckeberg et al.,2009

hyb_protocol: per standard protocol, fragmented cRNA was hybridized 16 hrs at 45C with 60 rpm rotation to Yeast Genome 2.0 GeneChips, followed by washing and staining in a GCOS Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCOS Scanner 7G.

data_processing: CEL files were RMA normalized and analyzed using GeneSpring GX 7.3

source_name: Yeast immobilized in alginate beads, harvest at day 17

label_protocol: biotinylated cRNA was prepared according to the standard one-cycle Affymetrix protocol (Expression Analysis Technical Manual, 2004)

growth_protocol: Haploid S288C Mat-alpha yeast was gel encapsulated in calcium alginate as described by Kruckeberg et al., 2009. 3mm diameter alginate beads containing immobilized yeast were packed to a volume of 100 mL in a custom-built immobilized cell reactor of 300 mL capacity. The reactor was fed continuously at a rate of 6 L h-1 with synthetic defined media described by Verduyn et al., 1992 containing 100 gL-1 glucose. pH and temperature were maintained at 5.5 and 32.5°C, respectively. Glucose content of feed was regularly monitored over the course of 17-day experiments; whenever glucose content fell below 1%, spent media was replaced with fresh synthetic media containing 100 gL-1 glucose.

extract_protocol: two extraction methods were used depending on whether yeast was immobilized in alginate beads; these are detailed in the growth protocol above

tag: growth condition

value: IMMOBILIZED


title: seedlings_mutant and wild type_rep3

source_name: Seedlings from mutant ashh2-1/sdg8-1 (biological replica 3)

source_name: Seedlings from wt (Colombia ecotype) (biological replica 3)


title: S18


title: Immobilized, Day 10, rep 1

source_name: Yeast immobilized in alginate beads, harvest at day 10


title: seedlings_mutant and wild type_rep2

source_name: Seedlings from wt (Colombia ecotype) (biological replica 2)

source_name: Seedlings from mutant ashh2-1/sdg8-1 (biological replica 2)


title: Immobilized, Day 17, rep 3


title: Control, 293TetLuc, doxcycline 48 h, rep2

source_name: 293 luciferase inducible line, doxycycline 48 h


title: Immobilized, Day 5, rep 3

source_name: Yeast immobilized in alginate beads, harvest at day 5


title: Immobilized, Day 5, rep 4

description: RNA from the immobilized beads were extracted essentially as described by Kruckebeg et al.,2009


title: Control, 293TetLuc, doxcycline 48 h, rep1


title: S17


title: Huh7 treated 0.5mM amiloride for 24hr, biological rep2

value: Hepatocellular Carcinoma Huh-7 cell line

tag: agent

value: amiloride


title: Immobilized, Day 10, rep 3


title: Immobilized, Day 17, rep 1


title: Immobilized, Day 5, rep 2


title: S16


title: S14


title: S11


title: Immobilized, Day 5, rep 1


title: seedlings_mutant and wild type_rep1

source_name: Seedlings from mutant ashh2-1/sdg8-1 (biological replica 1)

source_name: Seedlings from wt (Colombia ecotype) (biological replica 1)


title: Immobilized, Day 3, rep 3

source_name: Yeast immobilized in alginate beads, harvest at day 3


title: cDNA from HBEC after transcfection with noncoding siRNA

description: Expressional changes associated with noncoding siRNA transfection in HBEC

data_processing: Transcript level expression was summarized by RMA method implemented in Partek Genomic Suite

source_name: RNA from human bronchial epithelia cells immortalized with hTERT and CDK4

treatment_protocol: cells were transfected with siRNA using Lipofectamine 2000 for 96 hours

tag: cell type

value: human bronchial epithelia cells

tag: transcfection

value: non coding siRNA


title: cDNA from HBEC after transcfection with SETD2 siRNA

description: Expressional changes associated with SETD2 siRNA transfection in HBEC

value: HBEC

value: SETD2 siRNA


title: Immobilized, Day 3, rep 4


title: Immobilized, Day 1, rep 4

source_name: Yeast immobilized in alginate beads, harvest at day 1


title: Immobilized, Day 1, rep 3


title: Immobilized, Day 3, rep 1


title: Immobilized, Day 3, rep 2


title: Immobilized, Day 1, rep 1


title: Immobilized, Day 1, rep 2


title: HCT116 H3K36me3

description: ChIp-ChIp HCT116 H3K36me3

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Cy5/Cy3 log2 ratio scaled by NimbleScan software v2.5 with Tukey Biweight mean

source_name: H3K36me3 ChIp DNA from HCT116

label_protocol: According to standard NimbleGen Protocol

extract_protocol: For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For UMC, sonicated DNA was treated according to the manufacturer’s instructions for the UMC kit (Active Motif), purified and amplified by using LM-PCR. For ChIP-chip experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by 0.125 M glycine. 8 µg of sonicated chromatin was incubated with appropriate antibodies overnight and captured with A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR.

value: colon cancer cell

tag: enrichment procedure

value: ChIp H3K36me3

tag: antibody vendor/catalog number

tag: antibody lot#

source_name: Input DNA from HCT116

value: none, Input


title: Day 0, preimmobilized, rep 1

source_name: Yeast harvested at time 0 (immedeately after immobilization).


title: HBEC UMC

description: HBEC UMC

source_name: unmethylated DNA fraction enriched by UMC. DNA was isolated from HBEC

value: human bronchial epitelia cells

value: HBEC immortalized with hTERT and CDK4

value: Unmethyl Collector kit

value: Active Motif #55004

source_name: Input DNA from HBEC


title: HBEC H3K36me3

description: ChIp-ChIp HBEC H3K36me3

source_name: H3K36me3 ChIp DNA from HBEC


title: Day 0, preimmobilized, rep 2


title: HBEC MIRA

description: HBEC MIRA

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from HBEC

value: MIRA

value: In Lab purified His-MBD3L1 & GST-MBD2b


title: Immobilized, Day 10, rep 2

source_name: Yeast immobilized in alginate beads, harvest at day 10


title: HBEC H4K20me3

description: ChIp-ChIp HBEC H4K20me3

source_name: H4K20me3 ChIp DNA from HBEC

value: ChIp H4K20me3


title: Chemostat growth, rep 2

description: RNA from the planktonic cells was extracted as described by Ferea et al., 1999

source_name: Yeast grown to steady state, by chemostat mode of cultivation for 72h, in a custom-made glass bioreactors

growth_protocol: Haploid S288C Mat-alpha yeast was cultured at 32.5°C, pH 5.5in synthetic defined media described by Verduyn et al., 1992. Cells were propagated in 200 mL working volume bioreactors continuously fed at a dilution rate, D=0.15 h-1 with media containing 1 gL-1 glucose as the limiting growth substrate. Cultures were made anaerobic through the use of sterile, humidified N2(g). Cells were harvested at steady state 72 hrs after inoculation (10 generations) by rapidly filtering ~50mL of culture, then freezing the filtrate in liquid N2.

value: CHEMOSTAT


title: HCT116 H3K9me3

description: ChIp-ChIp  HCT116 H3K9me3

source_name: H3K9me3 ChIp DNA from HCT116

value: ChIp H3K9me3

value: Millipore #07-442


title: Chemostat growth, rep 1

source_name: Yeast grown to steady state by chemostat mode of cultivation for 72h, in a custom-made glass bioreactors


title: HBEC siRNA SETD2 MIRA

description: HBEC siRNA SETD2 MIRA

source_name: methylated DNA fraction enriched by MIRA, DNA was isolated from HBEC after transcfection with noncoding siRNA

source_name: Input DNA from HBEC after transcfection with SETD2 siRNA


title: Batch growth, stationary phase, rep 1

source_name: Yeast grown for 72 hrs (stationary phase) by batch mode of cultivation, in a custom-made glass bioreactors

growth_protocol: Haploid S288C Mat-alpha yeast was cultured at 32.5°C, pH 5.5 in synthetic defined media described by Verduyn et al., 1992. Batch cultures were initiated with 10 gL-1 glucose. Cells were propagated in 200 mL working volume custom-made glass bioreactors, where stirring was accomplished by sparged gas. Cultures were made anaerobic through the use of sterile, humidified N2(g). Stationary phase batch-cultured cells were harvested 72 hrs post inoculation following onset of diauxy by rapidly filtering ~50mL of culture, then freezing filtrate in liquid N2.

value: STATIONARY PHASE


description:
chip_id: = 18768802
DNA methylation in the maternal allele along distal chr15

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: methylated-CpG island recovery assay (MIRA) DNA from  PatDup.dist7 MEFs

extract_protocol: MEFs were grown in 25 ml of culture medium (Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 10–4 M β-mercaptoethanol, nonessential amino acids, L-glutamine, and antibiotics at standard concentrations). Confluent 15-cm plates provided about 15 to 35 million cells. Formaldehyde (1% final concentration) was added directly into the medium, and the dishes were incubated at room temperature for exactly 2 min (for native ChIP [N-ChIP] assay) or 10 min (for cross-linking and ChIP [X-ChIP]) on an orbiting platform. Cross-linking was stopped with a 0.125 M final concentration of glycine solution. Cells were washed twice with 20 ml of ice-cold phosphate-buffered saline and scraped off the plate with a rubber policeman; cells were then pelleted by centrifugation for 3 min at 250 x g and resuspended in 750 µl of ChIP lysis buffer (1% sodium dodecyl sulfate, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) containing protease inhibitors (Complete protease inhibitor cocktail tablets, catalog number 1697498; Roche Applied Science). Sonication was carried out on ice in 1.7-ml Eppendorff tubes using a Branson Sonifer with a micro tip three or four times (N-ChIP or X-ChIP, respectively) for 10 s at 40% output. The sheared chromatin was centrifuged at 13,000 rpm for 15 min at 4°C. The supernatant was transferred to a fresh tube. An aliquot of the chromatin preparation was reverse cross-linked, proteinase K digested, phenol-chloroform extracted, precipitated, and resuspended in Tris-EDTA buffer. DNA concentration was determined using a UV spectrophotometer. One microgram of DNA was resolved on a 1.5% agarose gel to check sonication efficiency. Fragment sizes ranged from 0.2 to 1.5 kb, with a peak at 0.8 kb. Chromatin preparations were diluted to 0.4 µg/µl with ChIP lysis buffer containing protease inhibitors and were snap-frozen in liquid nitrogen in small aliquots and stored at –80 °C. 10 µl (4 µg) of chromatin and 4 µg of specific antibody was used for each immunoprecipitation. The immunoprecipitated chromatin was eluted from 40 µl of protein A/G agarose beads and reverse cross-linked, and DNA was isolated with a QIAquick kit, (Qiagen, Germany) and eluted in 100 µl of Elution Buffer.

tag: parental duplication of  distal chr7

tag: epigenetic feature

value: DNA methylation

value: MEF

source_name: Input DNA from PatDup.dist7 MEFs

tag: parental duplication of  distal chr15

value: none, input DNA


title: Batch growth, stationary phase, rep 2

source_name: Yeast grown for 72 hrs (stationary phase)by batch mode of cultivation, in a custom-made glass bioreactors


description:
chip_id: = 18769202
DNA methylation in the paternal allele along distal chr15

source_name: methylated-CpG island recovery assay (MIRA) DNA from  MatDup.dist7 MEFs

source_name: Input DNA from MatDup.dist7 MEFs


description:
chip_id: = 18769802
H3K9me3 in the maternal allele along distal chr15

source_name: H3K9me3 ChIP DNA from  PatDup.dist7 MEFs


description:
chip_id: = 18771002
H3K4me3 in the maternal allele along distal chr15

source_name: H3K4me3 ChIP DNA from  PatDup.dist7 MEFs


title: HBEC siRNA SETD2 H3K36me3

description: ChIp-ChIp HBEC siRNA SETD2 H3K36me3

source_name: H3K36me3 ChIp DNA from HBEC after transcfection with noncoding siRNA

tag: cell line

value: HBEC


title: Labellum_4dayspollination_Rep5fwd

city: Lisboa

first: Filipa

middle: Isabel de Almeida

last: Monteiro

address: Ed. ICAT, Faculty of Sciences, Rua Ernesto Vasconcelos, Campo Grande

department: BioFIG

country: Portugal

institute: Plant Systems Biology Lab

description: Technical replicate 2 of 2. Repetition of labelling and hybridization from biological replicate 5, comparison of nonpollinated labella vs. pollinated, 4 days after pollination. Both files coming from Versarray and edited for GEPAS are provided.

hyb_protocol: The hybridization mix consisted of 40μL labelled cDNA, 1.7 μL of poly-A DNA (10 mg mL-1) (Sigma), 1.6 μL salmon sperm DNA (5 mg mL-1) (Invitrogen), 1.6 μL of 50X Denhardt´s solution (1% Ficoll (type 400), 1% PVP-40, 1% BSA), 8.45 μL of 20X SSC and 1.69 μL of 10% SDS(w/v). Mixture was denatured at 97ºC for 2 min, cooled to 60ºC and then 1μl of 10X DIG blocking (Roche Diagnostic GmbH, Mannheim, Germany) buffer was added. Hybridization was carried out at 60º C for 17 hours in chambers ArrayIt (Telechem International).

scan_protocol: Slides were scanned using VersArray ChipReader® vs 3.1. build 1.68 (Bio-Rad, USA) and spot and background intensities quantified using VersArray AnalyserTM software vs 4.5.1.46 (Bio-Rad, USA).

data_processing: Data files were imported into GEPAS (http://gepas.bioinfo.cipf.es) and log2-transformed prior to normalization (DNMAD).Print-tip Lowess was used for within-slide normalization considering background subtraction. Impute missing values (median). Patterns with less than 70% removed. VersArray.txt files correspond to raw data files retrieved by VersArray Analyser software (Bio-Rad). GEPAS.txt files correspond to raw data files (with flags indicated) ready to go for GEPAS software for normalization.

organism: Ophrys fusca

source_name: 4days after pollination

label_protocol: 2 µg of each aRNA was used were reverse transcribed and labelled with either Cy3 or Cy5 dye molecules, according the RPN 5660 CyScribeTM cDNA Post Labeling Kit and CyScribeTM GFXTM purification kit (Amersham, GE Healthcare).

growth_protocol: Ophrys fusca plants were sampled from a Portuguese natural occurring population. Hundred plants were selected in the field, accordingly their stage of development with fully opened flowers, with pollinia and with roughly the same stage of development. Five biological replicates was achieved from each condition assessed, each biological replicate represented by 5 labella.Plants were covered with a white and inert net, built specially for preventing pollinator’s visits either in pollinated or unpollinated flowers. Cross- pollination was performed manually with a sterile plastic stick.

extract_protocol: Total RNA from Ophrys fusca labella was isolated following the Hot Borate method (Wan and Wilkins, 1994) with minor modifications. About 1 μg of total RNA extracted from each biological replicate was used for aRNA amplification, by using the MessageAmpTM II aRNA Amplification Kit (Ambion, Applied Biosystems).

treatment_protocol: RNA was extracted from labella from unpollinated and pollinated plants, at both 2 days and 4 days after pollination

tag: condition

value: unpollinated _4DAP

tag: tissue

value: labellum

value: pollinated _4DAP


description:
chip_id: = 18771302
H3K9ac in the paternal allele along distal chr15

source_name: H3K9ac ChIP DNA from  MatDup.dist7 MEFs


title: HBEC siNonCoding H3K36me3

description: ChIp-ChIp HBEC siNonCoding H3K36me3

value: human bronchial epitelia cells

tag: genotype/variation

value: HBEC immortalized with hTERT and CDK4

value: ChIp H3K36me3

source_name: Input DNA from HBEC after transcfection with noncoding siRNA

value: none, Input


title: Batch growth, log phase, rep 2

source_name: Yeast grown 12 hrs (log phase)by batch mode of cultivation, in a custom - made glass bioreactors

growth_protocol: Haploid S288C Mat-alpha yeast was cultured at 32.5°C, pH 5.5 in synthetic defined media as described by Verduyn et al., 1992. Batch cultures were initiated with 10 gL-1 glucose. Cells were propagated in 200 mL working volume custom-made glass bioreactors, where stirring was accomplished by sparged gas. Cultures were made anaerobic through the use of sterile, humidified N2(g). Mid-log phase batch-cultured cells were harvested 12 hrs post inoculation by rapidly filtering ~50mL of culture, then freezing the filtrate in liquid N2.

value: LOG-PHASE


title: At-hh pRNAi 12K-02

hyb_protocol: cRNA probes were hybridized to a microarray in Hybridization buffer (5x SSC, 0.1% SDS, 10% formamide) at 42˚C for 16-20 h.

scan_protocol: Microarray slides were scanned using a GenePix 4000B Scanner (Molecular Devices).

data_processing: Obtained images were analyzed using an Array-Pro Analyzer Ver. 4.5 (Media Cybernetics, Inc.). The quantitative data were subjected to Loess normalization.

source_name: At-hh pRNAi embryos

label_protocol: cRNA labeled with Cy3 was prepared from 2 µg of total RNA using RNA Transcript SureLABEL Core Kit (Takara).

extract_protocol: Total RNA was extracted from approximately 250 embryos of the same stage using MagExtractor (Toyobo). RNA integrity was examined with an Agilent Bioanalyzer 2100.

value: whole embryo

tag: developmental stage

value: late stage 5

tag: treatment

value: At-hh pRNAi

source_name: Normal embryos

label_protocol: cRNA labeled with Cy5 was prepared from 2 µg of total RNA using RNA Transcript SureLABEL Core Kit (Takara).


title: HBEC H3K27me3

description: ChIp-ChIp HBEC H3K27me3

source_name: H3K27me3 ChIp DNA from HBEC

value: ChIp H3K27me3

value: Millipore #07-449

source_name: Input DNA from HBEC


title: Labellum_4dayspollination_Rep1fwd

description: Technical replicate 1 of 2. Repetition of labelling and hybridization from biological replicate 1, comparison of nonpollinated labella vs. pollinated, 4 days after pollination. Both files coming from Versarray and edited for GEPAS are provided.


description:
chip_id: = 18770002
H3K4me3 in the paternal allele along distal chr15

source_name: H3K4me3 ChIP DNA from  MatDup.dist7 MEFs


title: HBEC siNonCoding MIRA

description: HBEC siNonCoding MIRA

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from HBEC after transcfection with noncoding siRNA

value: MIRA

value: In Lab purified His-MBD3L1 & GST-MBD2b


description:
chip_id: = 18769402
H3K9me3 in the paternal allele along distal chr15

source_name: H3K9me3 ChIP DNA from  MatDup.dist7 MEFs

value: MEF

value: none, input DNA


title: Batch growth, log phase, rep 1

source_name: Yeast grown 12 hrs (log phase) by batch mode of cultivation, in a custom - made glass bioreactors


title: HCT116-DKO H3K36me3

description: ChIp-ChIp HCT116-DKO H3K36me3

source_name: H3K36me3 ChIp DNA from HCT116-DKO

value: colon cancer cell

value: HCT116 DNMT1-/- DNMT3b -/-

source_name: Input DNA from HCT116-DKO


title: HCT116-DKO MIRA

description: HCT116-DKO MIRA

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from HCT116-DKO


title: CSF2_Cy3_A4

city: Gainesville

first: Peter

middle: J

last: Hansen

state: FL

address: 1812 Shealy Drive

department: Animal Sciences

institute: University of Florida

description: CFS2 treated embryos group 4

hyb_protocol: Hybridizations were set up using 2 µg of each sample (Cy3 and Cy5 components) for a total of 4 µg per array.  Volumes were brought to 44 µl with Diethylpyrocarbonate (DEPC)-water and then 11 µl of Agilent 10x GE Blocking Agent was added.  The mixtures were incubated at 98oC for 3 minutes and then cooled to room temperature for 5 minutes before adding 55 µl of Agilent 2x Hi-RPM Hybridization buffer.  Tubes were flash-spinned on a microfuge and lightly vortexed before loading 100 µl of the hybridization mixture onto each array. Hybridization was carried out for 17 h at 65°C and 10 rpm in a SureHyb gasket slide (Agilent). Washing and scanning procedures were carried out using standard Agilent guidelines for gene expression microarray processing.

scan_protocol: At the end of hybridization, microarray slides were sequentially washed using standard Agilent guidelines for gene expression microarray processing.  Microarray slides were scanned immediately using an Agilent G2505B scanner.

data_processing: Images were extracted and pre-processed using the Agilent Feature Extraction Software v 9.5 with default analysis parameters for the initial extraction, signal quantiﬁcations, and scaling of the generated data. The software produces background adjustment and normalizations for the dye of individual genes. The intensity of each spot was summarized as the median pixel intensity. All the generated values were then transformed to log2. The Lowess method was used for intensity normalization within each array. JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used for data global normalization and identification of differentially expressed genes. The PROC ANOVA procedure was used for simultaneous comparisons and the quantile method for intensity normalization.  The model included replicate and treatment. Replicate (array) was considered random and treatment was considered fixed. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995).  Only genes with median pixel intensity of at least 2.8 were considered to be expressed.  Genes with a 1.5-fold difference and false discovery rate ≤ 0.01 were considered differentially expressed.

organism: Bos taurus

source_name: embryos that were treated with CFS2 at Day 5 of development for 24h

label_protocol: samples of RNA (1.5-3.0 pg/µl) were concentrated to 5 µl using Savant SpeedVac (Therno Scientific) at low heat and amplified into ss-cDNA using the NuGEN WT-Ovation Pico RNA amplification System (NuGen Technologies, Inc, San Carlos, CA, USA) following manufacturer's instructions. Amplified ss-cDNA was purified using Zymo Spin IIC columns (Zymo Research, Orange, California, USA) and stored at -20 oC overnight. Product yield and purity were determined by the Nanodrop 1000 spectrophotometer assuming that 1 absorbance unit at 260 nm of ss-cDNA is equal to 33 µg/ml.  All 260/230 values were greater than 2.    Aliquots containing 2 µg of ss-cDNA were labeled with the Agilent Genomic DNA Enzymatic Labeling kit to incorporate cyanine 3- or 5-labeled CTP.  For half the replicates, ss-cDNA from control embryos was labeled with Cy3 and ss-cDNA from CSF2-treated embryos was labeled with Cy5. For the other replicates, control embryos were labeled with Cy 5 and CSF2-treated embryos with Cy3.

growth_protocol: Cumulus oocyte complexes (COCs) from ovaries from a mixture of beef and dairy cattle were collected in Tissue Culture Medium-199 (TCM-199) with Hank’s salts without phenol red (Hyclone, Logan UT) supplemented with 2% (v/v) bovine steer serum containing 2 U/ml heparin, 100 U/ml penicillin-G, 0.1 mg/ml streptomycin, and 1 mM glutamine.  Oocytes were allowed to mature for 20-22 h in groups of 10 in 50 µl microdrops of TCM-199  with Earle’s salts supplemented with 10% (v/v) bovine steer serum, 2 µg/ml estradiol ,17- 20 µg/ml bovine follicle stimulating hormone (Folltropin-V; Belleville, ON, Canada), 22 µg/ml sodium pyruvate, 50 µg/ml gentamicin sulfate, and 1 mM glutamine.  Embryos were cultured at 38.5oC in a humidified atmosphere of 5% CO2 or 5% CO2, 5% O2, and 90% N2 (v/v).  Cleavage rate was assessed at Day 3 after insemination.

extract_protocol: Total RNA was extracted from embryos with the RNeasy Plus Micro kit (Qiagen-Inc, CA, USA) following manufacturer’s instructions. Concentration of the input RNA was determined by Nanodrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and RNA integrity was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano LabChip kit (Agilent Technologies, Santa Clara CA, USA).  Only samples that showed RNA integrity > 7 were used for the microarray hybridization and quantitative PCR analysis. Extracted RNA was stored at -80oC until microarray analysis.

treatment_protocol: At day 5 after insemination, 5 µl of KSOM-BE2 or 5 µl of KSOM-BE2 containing 100 ng/ml CSF2 were added to each drop to achieve a final CSF2 concentration of 0 or 10 ng/ml. On Day 6, 24 hours after treatment, morulae and early blastocysts were selected and washed three times in 50 µl microdrops of 10 mM PO4 buffer, pH 7.4 containing 0.9% (w/v) NaCl and 1 mg/ml polyvinylpyrrolidone (PBS-PVP) by transferring the embryos from microdrop to microdrop. Embryos were frozen at -80°C in PBS-PVP in groups of 50. A total of 4 groups of embryos from each treatment were prepared in a total of 6 replicates of in vitro production.

tag: embryo

value: in vitro produced embryo - Day 6 of development


title: Labellum_4dayspollination_Rep4

description: Biological replicate 4 of 5. Comparison of nonpollinated labella vs. pollinated, 4 days after pollination. Both files coming from Versarray and edited for GEPAS are provided

value: unpollinated _4DAP

value: labellum

value: pollinated _4DAP


title: HBEC H3K9me3

description: ChIp-ChIp HBEC H3K9me3

source_name: H3K9me3 ChIp DNA from HBEC

value: human bronchial epitelia cells

value: HBEC

value: HBEC immortalized with hTERT and CDK4

value: ChIp H3K9me3

value: Millipore #07-442

value: none, Input


title: CSF2_Cy5_A3

description: CFS2 treated embryos group 3


title: HCT116-DKO H3K9me3

description: ChIp-ChIp HCT116-DKO H3K9me3

source_name: H3K9me3 ChIp DNA from HCT116-DKO


description:
chip_id: = 18772002
H3K9ac in the maternal allele along distal chr15

source_name: H3K9ac ChIP DNA from  PatDup.dist7 MEFs

source_name: Input DNA from PatDup.dist7 MEFs


title: Labellum_4dayspollination_Rep3

description: Biological replicate 3 of 5. Comparison of nonpollinated labella vs. pollinated, 4 days after pollination. Both files coming from Versarray and edited for GEPAS are provided

source_name: 4days after pollination


description:
chip_id: = 332240
CTCFin the maternal allele along distal chr15

source_name: transcription factor CTCF ChIP DNA from PatDup.dist7 MEFs

value: CTCF binding


description:
chip_id: = 332017
CTCFin the paternal allele along distal chr15

source_name: transcription factor CTCF ChIP DNA from MatDup.dist7 MEFs

source_name: Input DNA from MatDup.dist7 MEFs


title: Labellum_4dayspollination_Rep2

description: Biological replicate 2 of 5. Comparison of nonpollinated labella vs. pollinated, 4 days after pollination. Both files coming from Versarray and edited for GEPAS are provided


title: Labellum_4dayspollination_Rep1

description: Biological replicate 1 of 5. Comparison of nonpollinated labella vs. pollinated, 4 days after pollination. Both files coming from Versarray and edited for GEPAS are provided


title: Labellum_2dayspollination_Rep3fwd

description: Technical replicate 2 of 2. Repetition of labelling and hybridization from biological replicate 3, comparison of nonpollinated labella vs. pollinated, 2 days after pollination. Both files coming from Versarray and edited for GEPAS are provided.

source_name: 2days after pollination

value: unpollinated _2DAP

value: pollinated _2DAP


title: Labellum_2dayspollination_Rep1fwd

description: Technical replicate 1 of 2. Repetition of labelling and hybridization from biological replicate 1, comparison of nonpollinated labella vs. pollinated, 2 days after pollination. Both files coming from Versarray and edited for GEPAS are provided.


title: Control_Cy3_A3

description: Control embryos group 3

source_name: embryos that were not treated with CFS2 at Day 5 of development


title: HCT116 MIRA

description: HCT116 MIRA

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from HCT116

value: MIRA

value: In Lab purified His-MBD3L1 & GST-MBD2b

source_name: Input DNA from HCT116


title: HBEC H3K4me3

description: ChIp-ChIp HBEC H3K4me3

source_name: H3K4me3 ChIp DNA from HBEC

value: ChIp H3K4me3

value: Millipore #17-614

source_name: Input DNA from HBEC


title: Control_Cy5_A2

description: Control embryos group 2

value: in vitro produced embryo - Day 6 of development


title: ExVivoAmygdala_6hr_KO LPS_rep1-4

city: Budapest

first: Cecilia

last: Katalin

address: Szigony 43

department: Pharmacology

country: Hungary

institute: IEM HAS

description:
Normalization from 4 replicates:
GF4 _013
GF4 _014
GF4 _015
GF4 _016

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (platform szám ) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner (Extended Dynamic Range)  (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded from further analysis.

source_name: Amygdala, 6hr, LPS treatment, P2X7R KO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) and One-color microarray-based gene expression analysis (Quick Amp Labeling) 5.7 Version according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA were isolated from amygdala using the RNeasy® Lipid Tissue Mini Kit (Qiagen), according to the manufacturer’s instructions. Total RNA profile was analyzed using Agilent RNA 6000 Nano LabChip® kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Animals were randomly assigned to experimental groups and there were 4 mice in each group. All animals were given an intraperitoneal (i.p.) injection of sterile saline (0.9% NaCl) or lipopolysaccharide (LPS, 7.5 µg/mouse). Animals were killed by decapitation 6h after lipopolysaccharide injection. The amygdalae were collected, snap-frozen on liquid nitrogen and stored at -80ºC until further investigation.

value: whole amygdala

tag: strain

tag: gender

value: male

tag: age

value: 10 weeks


title: CSF2_Cy5_A1

description: CFS2 treated embryos group 1


title: rodZ (fresh)

city: Shinjuku

first: Jiro

last: Mitobe

address: 1-23-1 Toyama

department: Bacteriology

institute: National Institute of Infectious Diseases

description: Deletion mutant of rodZ gene in S. sonnei. The culture without rifampicin treatment.

hyb_protocol: Hybridization was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

organism: Shigella sonnei

source_name: delta-rodZ mutant (fresh)

label_protocol: Conversion of RNA to cDNA and labeling with Cy3 was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown in LB medium (37°C, 180 rpm) to OD 600 = 0.8. 400 ml fermentors per strain (wild-type and the deletion mutant of rodZ gene).

extract_protocol: Cells were immediately mixed with 15 ml of 5% acid-phenol in ethanol (Bhagwat et al, Microbiol Methods 55(2): 399), then chilled on ice, centrifuged, and the pelletted before storing at –80°C. Total RNA was extracted using the RNeasy Midi kit (Qiagen), and DNA was removed by digestion with RNase-Free DNase I. RNA quality and concentration was checked with an Agilent bioanalyzer at the University of Florida Gene Expression core before submitting the RNA to Roche Nimblegen in Iceland for analysis.

treatment_protocol: Half of the samples (200 ml) were taken at OD = 0.8, then proceed to extract protocol. The remaining halves were continued the incubation in the presence of rifampicin (100 microgram per ml) for 4 minutes at 37°C. Then proceed to extract protocol.

tag: srain

tag: genome/variation

value: deletion mutant of rodZ gene


title: ExVivoAmygdala_6hr_KO_rep1-4

description:
Normalization from 4 replicates:
GF3 _009
GF3 _010
GF3 _011
GF3 _012

source_name: Amygdala, 6hr, saline control, P2X7R KO


title: rodZ (rifampicin 4 min)

description: Deletion mutant of rodZ gene in S. sonnei. Rifampicin treatment for 4 minutes.

source_name: delta-rodZ mutant (rifampicin 4 min)


title: CSF2_Cy3_A2

description: CFS2 treated embryos group 2

source_name: embryos that were treated with CFS2 at Day 5 of development for 24h


title: ExVivoAmygdala_6hr_WT LPS_rep1-4

description:
Normalization from 4 replicates:
GF2 _005
GF2 _006
GF2 _007
GF2 _008

source_name: Amygdala, 6hr, LPS treatment, WT


title: ExVivoAmygdala_6hr_WT_rep1-4

description:
Normalization from 4 replicates:
GF1 _001
GF1 _002
GF1 _003
GF1 _004

source_name: Amygdala, 6hr, saline control, WT


title: wild-type (rifampicin 4 min)

description: Wild-type S. sonnei culture. Rifampicin treatment for 4 minutes.

source_name: wild-type (rifampicin 4 min)

value: wild-type


title: Control_Cy3_A1

description: Control embryos group 1


title: Labellum_2dayspollination_Rep5

description: Biological replicate 5 of 5. Comparison of nonpollinated labella vs. pollinated, 2 days after pollination. Both files coming from Versarray and edited for GEPAS are provided

value: labellum


title: Labellum_2dayspollination_Rep3

description: Biological replicate 3 of 5. Comparison of nonpollinated labella vs. pollinated, 2 days after pollination. Both files coming from Versarray and edited for GEPAS are provided


title: Labellum_2dayspollination_Rep4

description: Biological replicate 4 of 5. Comparison of nonpollinated labella vs. pollinated, 2 days after pollination. Both files coming from Versarray and edited for GEPAS are provided


title: wild-type (fresh)

description: Wild-type S. sonnei culture without rifampicin treatment.

source_name: wild-type (fresh)


title: Labellum_2dayspollination_Rep2

description: Biological replicate 2 of 5. Comparison of nonpollinated labella vs. pollinated, 2 days after pollination. Both files coming from Versarray and edited for GEPAS are provided


title: Control_Cy5_A4

description: Control embryos group 4


title: Labellum_2dayspollination_Rep1

description: Biological replicate 1 of 5. Comparison of nonpollinated labella vs. pollinated, 2 days after pollination. Both files coming from Versarray and edited for GEPAS are provided