title: 13455545-13455534 - H3K4me2_Col_I_IP vs H3K4me2_Col_I_INPUT

hyb_protocol: H3K4me2_Col_I_INPUT Cy5 / H3K4me2_Col_I_IP Cy3 : 80pmol.

extract_protocol: Col_seedlings_I:50ug.  antibody: H3K4me2 (upstate_07-030);


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 41

status: Public on May 17 2011

type: genomic

city: San Francisco

first: Brian

middle: M

last: Green

state: CA

address: 600 16th Street, S376 Genentech Hall

department: Department of Biochemistry

country: USA

institute: University of California, San Francisco

description: Supp Table 2

hyb_protocol: Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 16 to 24 hours

scan_protocol: Arrays were scanned with an Axon 3000B scanner using GenePix4.0.

data_processing:
Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.
Value is the log2 of the normalized ratio of Cy5 to Cy3 – note that to convert to usable replication profiles, raise two to the indicated value.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: red sector arising after re-replication at ChrIV567

label_protocol: amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.

extract_protocol: see BM Green et al. 2006

tag: strain

tag: sector induction

value: re-replication at ChrIV567

tag: sample type

source_name: negative control MC2A strain in G2/M

value: negative control MC2A strain in G2/M


title: 12051302Col - H3K27me3_Col_I_IP vs H3K27me3_Col_I_INPUT

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

description:
arabidopsis thaliana (col-0)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K27me3_Col_I_INPUT Cy5 / H3K27me3_Col_I_IP Cy3 : 80pmol.

scan_protocol: NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%

data_processing: For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf  is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA  .

growth_protocol: seedling - 15 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

treatment_protocol: no treatment

tag: age

value: 15 day

tag: tissue

value: seedling

value: input DNA

extract_protocol: Col_I:50ug.  antibody: H3K27me3 (Upstate 07-449);

tag: antibody

tag: antibody manufacturer

value: Upstate

tag: antibody catalog #


title: 14980502Cvi - H3K27me3_Cvi_II_IP vs H3K27me3_Cvi_II_INPUT

description:
arabidopsis thaliana (cape verde islands)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K27me3_Cvi_II_INPUT Cy5 / H3K27me3_Cvi_II_IP Cy3 : 80pmol.

value: cape verde islands

extract_protocol: Cvi_WT_II:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: 14980502Col - H3K27me3_Col_I_INPUT vs H3K27me3_Col_I_IP

hyb_protocol: H3K27me3_Col_I_IP Cy5 / H3K27me3_Col_I_INPUT Cy3 : 80pmol.


title: 134555902-13455534 - H3K4me2_Col_II_IP vs H3K4me2_Col_II_INPUT

description:
arabidopsis thaliana (col-0)  - age: 10day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K4me2_Col_II_INPUT Cy5 / H3K4me2_Col_II_IP Cy3 : 80pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100%

data_processing: Data were normalized as ChIP-chip data in Turck e al.(2007). This method is based on the properties of dye-swaps to remove technical biases. To be specific, let Yij be the signal of the sample labeled with the dye j on the array i. Given that the second array is a technical replicate of the first one, the distribution of Y21 (respectively Y22) should be close to that of Y12 (respectively Y11). In practice, the relationship between Y21 and Y12 is linear but it is not the identity function. The parameters of the two linear models are estimated by Y21=a+bY12+N(0,sigma2) and Y22=c+dY11+N(0,sigma2),and these estimates are used to define the normalized IP and INPUT values of the second array relative to the first one: Y21=(Y21-a)/b and Y22=(Y22-c)/d.For each sample and for each tile, the values of the two arrays of the dye-swap are then averaged.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, DNA  .

growth_protocol: seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

value: 10 day

extract_protocol: Col_seedlings_II:50ug.  antibody: H3K4me2 (upstate_07-030);

value: upstate


title: 1345533-13455540 - H3K4me2_Col_IV_INPUT vs H3K4me2_Col_IV_IP

hyb_protocol: H3K4me2_Col_IV_IP Cy5 / H3K4me2_Col_IV_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 39

description: Supp Table 2

value: red sector arising after re-replication at ChrIV567


title: 13455894-13455544 - H3K4me2_ColxC24_II_INPUT vs H3K4me2_ColxC24_II_IP

description:
arabidopsis thaliana (c24)  - age: 10day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K4me2_ColxC24_II_IP Cy5 / H3K4me2_ColxC24_II_INPUT Cy3 : 80pmol.

extract_protocol: ColxC24_II:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 13455543-13455544 - H3K4me2_Col_I_INPUT vs H3K4me2_Col_I_IP

hyb_protocol: H3K4me2_Col_I_IP Cy5 / H3K4me2_Col_I_INPUT Cy3 : 80pmol.


title: 13460809-13455531 - H3K4me2_Col_IV_IP vs H3K4me2_Col_IV_INPUT

hyb_protocol: H3K4me2_Col_IV_INPUT Cy5 / H3K4me2_Col_IV_IP Cy3 : 80pmol.


title: 13455893-13455534 - H3K4me2_ColxC24_I_IP vs H3K4me2_ColxC24_I_INPUT

hyb_protocol: H3K4me2_ColxC24_I_INPUT Cy5 / H3K4me2_ColxC24_I_IP Cy3 : 80pmol.

extract_protocol: ColxC24_I:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 134555902-13455544 - H3K4me2_ColxC24_I_INPUT vs H3K4me2_ColxC24_I_IP

hyb_protocol: H3K4me2_ColxC24_I_IP Cy5 / H3K4me2_ColxC24_I_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 38

description: Supp Table 2


title: single hyphal tip, biological rep1

type: RNA

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

description:
Gene expression data from a single hyphal tip collected from periphery material of a single colony
101301-1

hyb_protocol: The labeled cDNA was hybridized to Affymetrix GeneChip A. niger Genome Arrays. The GeneChip Hybridization, Wash and Stain Kit (Affymetrix, CA) was used for the hybridizations according to the protocol of the manufacturer with the modification that the hybridization cocktail was prepared according to the Encore Biotin Module and that the hybridization time was extended to 40 h.

scan_protocol: GeneChips were scanned using the Agilent GCS3000 HR GeneChip Scanner and Affymetrix GeneChip Command Console Software (AGCC v1.1)

data_processing: The data were analyzed with the R statistical programming language (R-2.11.1) and the bioconductor affy package. Present/absent call were generated with the MAS5 algorithm and summarized probesets values using the RMA algorithm

label: biotin

molecule: total RNA

organism: Aspergillus niger

source_name: exploring hyphae

label_protocol: Five µg of amplified cDNA was fragmented via combined chemical and enzymatic fragmentation using the protocol of the Encore Biotin Module (Nugen, CA). The fragments were biotin-labeled to the 3-hydroxyl end using the same Module following the instructions of the manufacturer.

growth_protocol: A. niger Strain AR9#2 was cultured as a sandwiched colony at 30 °C in the light. To this end, the fungus was grown between a perforated polycarbonate (PC) membrane (diameter 76 mm, pore size 0.1 µm; Osmonics, GE Water Technologies, MN) and a Lumox membrane (diameter 76 mm; Greiner Bio-One, Germany) (10). The PC membrane was placed on top of solidified (1.5% agar) minimal medium (MM) (15) containing 25 mM maltose as a carbon source. Freshly harvested spores (1.5 µl of a solution of 0.8% NaCl and 0.005% Tween-80 containing 108 spores ml-1) were placed in the center of the PC membrane. The droplet was allowed to dry, after which the Lumox membrane was placed on top of the PC membrane with its hydrophobic side facing the inoculum.

extract_protocol: Hyphal material that was collected in 50 µl RNAlater was transferred to a 2 ml Eppendorf tube by a quick centrifugation step. After snap-freezing in liquid nitrogen, 2 pre-cooled metal bullets (4.76 mm in diameter) were added and samples were ground in a Micro-Dismembrator U (B. Braun Biotech Int.) in a chilled container at 1500 rpm for 60 s. The frozen material was taken up in 250 µl Trizol Reagent (Invitrogen, CA) by vortexing. After removing the metal bullets, 200 µl chloroform was added. After mixing well, samples were centrifuged at 10.000 g for 10 min. The water phase (approximately 200 µl) was mixed with 700 µl RLT from the RNeasy MinElute Cleanup Kit (Qiagen, Germany) to which 143 mM ß-mercaptoethanol was added. RNA was purified following instructions of the manufacturer and was eluted with 12 µl RNAse free water. RNA samples were amplified using the WT-Ovation One-Direct RNA Amplification System (Nugen, CA). The quality and quantity of the cDNA samples were checked using a Bioanalyzer (Agilent Technologies, CA) and a Nanodrop (Nanodrop Technologies, DE), respectively.

treatment_protocol: After removing the Lumox membrane from the sandwiched colony, the mycelium and the underlying PC membrane were cut with a scalpel and part of the periphery of the colony was placed upside down onto a nucleotide and RNAse free glass slide. The PC membrane that was now facing the air was removed and the mycelium was fixed with 70% ethanol and air-dried. The hyphal tips were isolated by laser pressure catapulting (LPC) using the PALM CombiSystem (Carl Zeiss MicroImaging, Germany). This system was equipped with an Axiovert 200M Zeiss inverted microscope (Carl Zeiss, Germany) and a 3CCD color camera (HV-D30, Hitachi Kokusai Electric, Japan). The PALM CombiSystem was operated with PALM RoboSoftware V4.0 (Carl Zeiss MicroImaging, Germany). The autoLPC option was routinely used in combination with a 40x objective. Hyphal material was catapulted into lids of 0.5 ml Eppendorf tubes that contained 50 µl RNAlater (Qiagen, Germany).

tag: biological rep

value: hyphal tip


title: single hyphal tip, biological rep2

description:
Gene expression data from a single hyphal tip collected from periphery material of a single colony
101301-2


title: single hyphal tip, biological rep5

description:
Gene expression data from a single hyphal tip collected from periphery material of a single colony
101301-5


title: 13460815-13455531 - H3K4me2_Col_III_IP vs H3K4me2_Col_III_INPUT

hyb_protocol: H3K4me2_Col_III_INPUT Cy5 / H3K4me2_Col_III_IP Cy3 : 80pmol.


title: single hyphal tip, biological rep3

description:
Gene expression data from a single hyphal tip collected from periphery material of a single colony
101301-3


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 36

description: Supp Table 2


title: 1345533-13455531 - H3K4me2_ColxC24_III_IP vs H3K4me2_ColxC24_III_INPUT

hyb_protocol: H3K4me2_ColxC24_III_INPUT Cy5 / H3K4me2_ColxC24_III_IP Cy3 : 80pmol.

extract_protocol: ColxC24_III:50ug.  antibody: H3K4me2 (upstate_07-030);


title: single hyphal tip, biological rep4

description:
Gene expression data from a single hyphal tip collected from periphery material of a single colony
101301-4


title: 13455900-13455534 - H3K4me2_ColxC24_II_IP vs H3K4me2_ColxC24_II_INPUT

hyb_protocol: H3K4me2_ColxC24_II_INPUT Cy5 / H3K4me2_ColxC24_II_IP Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 37

description: Supp Table 2


title: 14984002Cvi - H3K27me3_Cvi_II_INPUT vs H3K27me3_Cvi_II_IP

hyb_protocol: H3K27me3_Cvi_II_IP Cy5 / H3K27me3_Cvi_II_INPUT Cy3 : 80pmol.


title: 12051302Cvi - H3K27me3_Cvi_I_INPUT vs H3K27me3_Cvi_I_IP

hyb_protocol: H3K27me3_Cvi_I_IP Cy5 / H3K27me3_Cvi_I_INPUT Cy3 : 80pmol.

extract_protocol: Cvi_WT_I:50ug.  antibody: H3K27me3 (Upstate 07-449);


title: 1345518-13455540 - H3K4me2_Col_III_INPUT vs H3K4me2_Col_III_IP

hyb_protocol: H3K4me2_Col_III_IP Cy5 / H3K4me2_Col_III_INPUT Cy3 : 80pmol.


title: 1345532-13455531 - H3K4me2_ColxC24_IV_IP vs H3K4me2_ColxC24_IV_INPUT

hyb_protocol: H3K4me2_ColxC24_IV_INPUT Cy5 / H3K4me2_ColxC24_IV_IP Cy3 : 80pmol.

extract_protocol: ColxC24_IV:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 13460809-13455540 - H3K4me2_ColxC24_III_INPUT vs H3K4me2_ColxC24_III_IP

hyb_protocol: H3K4me2_ColxC24_III_IP Cy5 / H3K4me2_ColxC24_III_INPUT Cy3 : 80pmol.


title: 13455900-13455544 - H3K4me2_C24_II_INPUT vs H3K4me2_C24_II_IP

hyb_protocol: H3K4me2_C24_II_IP Cy5 / H3K4me2_C24_II_INPUT Cy3 : 80pmol.

extract_protocol: C24_II:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 13455545-13455544 - H3K4me2_C24_I_INPUT vs H3K4me2_C24_I_IP

hyb_protocol: H3K4me2_C24_I_IP Cy5 / H3K4me2_C24_I_INPUT Cy3 : 80pmol.

extract_protocol: C24_I:50ug.  antibody: H3K4me2 (upstate_07-030);


title: 13460814-13455540 - H3K4me2_ColxC24_IV_INPUT vs H3K4me2_ColxC24_IV_IP

hyb_protocol: H3K4me2_ColxC24_IV_IP Cy5 / H3K4me2_ColxC24_IV_INPUT Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 34

description: Supp Table 2

hyb_protocol: Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 16 to 24 hours


title: 6300802ColCvi - H3K27me3_ColxCvi_II_INPUT vs H3K27me3_ColxCvi_II_IP

description:
arabidopsis thaliana (colxcvi hybrids)  - age: 15day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between

hyb_protocol: H3K27me3_ColxCvi_II_IP Cy5 / H3K27me3_ColxCvi_II_INPUT Cy3 : 80pmol.

extract_protocol: ColxCvi_II:20ug.  antibody: H3K27me3 (Upstate 07-449);

value: colxcvi hybrids


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 35

description: Supp Table 2


title: 14981802ColCvi - H3K27me3_ColxCvi_I_IP vs H3K27me3_ColxCvi_I_INPUT

hyb_protocol: H3K27me3_ColxCvi_I_INPUT Cy5 / H3K27me3_ColxCvi_I_IP Cy3 : 80pmol.

extract_protocol: ColxCvi_I:20ug.  antibody: H3K27me3 (Upstate 07-449);


title: 6300802Cvi - H3K27me3_Cvi_I_IP vs H3K27me3_Cvi_I_INPUT

hyb_protocol: H3K27me3_Cvi_I_INPUT Cy5 / H3K27me3_Cvi_I_IP Cy3 : 80pmol.


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 33

description: Supp Table 2


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 32

description: Supp Table 2


title: 13455894-13455534 - H3K4me2_C24_II_IP vs H3K4me2_C24_II_INPUT

hyb_protocol: H3K4me2_C24_II_INPUT Cy5 / H3K4me2_C24_II_IP Cy3 : 80pmol.


title: gp130F/F mutant liver treated LPS , replicate 1

city: Clayton

first: Jodee

middle: Ann

last: Gould

state: Victoria

address: 27-31 Wright Street

country: Australia

institute: Monash Institute of Medical Research

hyb_protocol: 5ugs of labelled extract, both reference and sample was combined in a total volume of 11ul to which 8ul of 20XSSC, 20ul Deionised Formamide and 1ul 20% SDS was added.  Microarray slides were immersed in 50 ml of hot Milli-Q water (80-95C) and agitated gently for 5 mins prior to hybridisation.  Prior to loading sample onto array, the mixture was heated to 70oC for 1 min. Arrays were hybridised overnight at 42oC in a humidified chamber.  The array slide was then immersed in a solution of 0.5 X SSC and 0.01% SDS until the coverslip detached from the slide.  Afte discarding the coverslip, the slide was washed in 0.5 X SSC and 0.1% SDS for 5 mins, and then 0.5 X SSC for 5 mins and then 0.2 X SSC for 3 mins.  The slide was then dried in a centrifuge at 750 rpm for 5 mins and stored in the dark prior to scanning.

scan_protocol: The microarray slides were scanned using an Agilent G2505B DNA microarray scanner.  Images were analysed with DigitalGENOME (Molecularware).

data_processing: Genespring GX 7.3 (Agilent) software was used for all data processing. LOWESS normalised.  Data Transformation: Set measurements less than 0.01 to 0.01 .  All 6 wildtype samples have been normalised to the median of the 3 control wildtype samples.  All 6 gp130F/F  samples have been normalised to the median of the 3 control gp130F/F samples.

label: Alexa Fluor 555 (green)

organism: Mus musculus

source_name: gp130F/F mutant Liver

label_protocol: Extracts were labelled using the Amino Allyl MessageAmp II a RNA amplification kit (Ambion) according to the manufacturers instructions.  An IVT incubation time of 5 hours was used as well as Invitrogens Alexa Fluor Dye Decapacks.

growth_protocol: Mice were kept under regular 12hr light/dark cycles, and fed ad libitum.

extract_protocol: Total RNA was extracted using Trizol Reagent according to the manufacturers instructions and then purified and DNAse treated using the Qiagen Rneasy mini columns according to the manufacturers instructions

tag: genotype

value: gp130Y757F knock-in mutation

value: Liver

value: 12 weeks

tag: gender

value: Female

tag: treatment

value: LPS

tag: treatment protocol

value: Mice were injected with 4mg/kg of purified LPS intraperitoneal and  humanely culled 6hr later and liver tissue collected and snap frozen in liquid nitrogen.

label: Alexa Fluor 647 (red)

source_name: Pooled whole mouse embryos e17.5

tag: developmental stage

value: embryo

value: wild type

value: 17.5 days post coitus

value: Reference

value: Mice were mated, and the day of vaginal plug detection deemed 0.5 days post coitus (dpc).  Mice were humanely culled on the appropriate day of pregnancy (d17.5)and the embryos collected


title: Epicardial_adipose_tissue_CABG 6

city: Quebec

first: Sandra

last: Guauque-Olarte

address: 2725, chemin Sainte-Foy

country: Canada

institute: CRIUCPQ

description:
patient undergoing coronary artery bypass grafting
EAT6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with LUMI package in R

organism: Homo sapiens

source_name: Heart surface

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep RNA Amplification Kit.

extract_protocol: RNA was isolated from 100 mg of tissue using the RNeasy Lipid Tissue Mini Kit (QIAGEN) according to manufacturer’s instructions. Before proceeding with microarrays experiments, the integrity of the RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies).

tag: bmi


title: 12051402ColCvi - H3K27me3_ColxCvi_I_INPUT vs H3K27me3_ColxCvi_I_IP

hyb_protocol: H3K27me3_ColxCvi_I_IP Cy5 / H3K27me3_ColxCvi_I_INPUT Cy3 : 80pmol.

value: 15 day

value: seedling

value: Upstate

value: input DNA


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 30

description: Supp Table 2

value: negative control MC2A strain in G2/M

value: re-replication at ChrIV567

value: red sector arising after re-replication at ChrIV567


title: 13460814-13455531 - H3K4me2_C24_IV_IP vs H3K4me2_C24_IV_INPUT

hyb_protocol: H3K4me2_C24_IV_INPUT Cy5 / H3K4me2_C24_IV_IP Cy3 : 80pmol.

value: 10 day

extract_protocol: C24_IV:50ug.  antibody: H3K4me2 (upstate_07-030);

value: upstate


title: gp130F/F mutant liver treated LPS , replicate 3

value: gp130Y757F knock-in mutation

value: Liver

value: 12 weeks

value: Female


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 29

description: Supp Table 2

extract_protocol: see BM Green et al. 2006


title: 13460815-13455540 - H3K4me2_C24_III_INPUT vs H3K4me2_C24_III_IP

hyb_protocol: H3K4me2_C24_III_IP Cy5 / H3K4me2_C24_III_INPUT Cy3 : 80pmol.

extract_protocol: C24_III:50ug.  antibody: H3K4me2 (upstate_07-030);


title: gp130F/F mutant liver treated LPS , replicate 2

value: LPS

value: Mice were injected with 4mg/kg of purified LPS intraperitoneal and  humanely culled 6hr later and liver tissue collected and snap frozen in liquid nitrogen.

value: embryo

value: wild type


title: gp130F/F mutant liver control, replicate 1

value: control

value: Control mice were humanely culled and liver tissue collected and snap frozen in liquid nitrogen

value: 17.5 days post coitus

value: Reference

value: Mice were mated, and the day of vaginal plug detection deemed 0.5 days post coitus (dpc).  Mice were humanely culled on the appropriate day of pregnancy (d17.5)and the embryos collected


title: 1345532-13455540 - H3K4me2_C24_IV_INPUT vs H3K4me2_C24_IV_IP

hyb_protocol: H3K4me2_C24_IV_IP Cy5 / H3K4me2_C24_IV_INPUT Cy3 : 80pmol.

value: seedling

value: input DNA


title: gp130F/F mutant liver control, replicate 3


title: 1345518-13455531 - H3K4me2_C24_III_IP vs H3K4me2_C24_III_INPUT

hyb_protocol: H3K4me2_C24_III_INPUT Cy5 / H3K4me2_C24_III_IP Cy3 : 80pmol.

value: 10 day


title: Subcutaneous_adipose_tissue_CABG 6

description:
patient undergoing coronary artery bypass grafting
SAT6

source_name: Chest


title: Mediastinal_adipose_tissue_CABG 6

description:
patient undergoing coronary artery bypass grafting
MAT6

source_name: Mediastino


title: 13455543-13455534 - H3K4me2_C24_I_IP vs H3K4me2_C24_I_INPUT

hyb_protocol: H3K4me2_C24_I_INPUT Cy5 / H3K4me2_C24_I_IP Cy3 : 80pmol.

value: upstate


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 31

description: Supp Table 2

value: negative control MC2A strain in G2/M

value: re-replication at ChrIV567

value: red sector arising after re-replication at ChrIV567


title: gp130F/F mutant liver control, replicate 2

value: gp130Y757F knock-in mutation

value: Liver

value: 12 weeks

value: Female


title: wild type liver treated LPS, replicate 3

source_name: wildtype Liver

value: Wild type

value: LPS

value: Mice were injected with 4mg/kg of purified LPS intraperitoneal and  humanely culled 6hr later and liver tissue collected and snap frozen in liquid nitrogen.

value: embryo

value: wild type


title: wild type liver treated LPS, replicate 1

value: 17.5 days post coitus

value: Reference

value: Mice were mated, and the day of vaginal plug detection deemed 0.5 days post coitus (dpc).  Mice were humanely culled on the appropriate day of pregnancy (d17.5)and the embryos collected


title: Epicardial_adipose_tissue_CABG 5

description:
patient undergoing coronary artery bypass grafting
EAT5


title: Mediastinal_adipose_tissue_CABG 5

description:
patient undergoing coronary artery bypass grafting
MAT5


title: 14984002ColCvi - H3K27me3_ColxCvi_II_IP vs H3K27me3_ColxCvi_II_INPUT

hyb_protocol: H3K27me3_ColxCvi_II_INPUT Cy5 / H3K27me3_ColxCvi_II_IP Cy3 : 80pmol.

value: colxcvi hybrids

value: 15 day

value: seedling

value: input DNA

value: Upstate


title: Subcutaneous_adipose_tissue_CABG 5

description:
patient undergoing coronary artery bypass grafting
SAT5


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 26

description: Supp Table 2

value: negative control MC2A strain in G2/M

value: re-replication at ChrIV567

value: red sector arising after re-replication at ChrIV567


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 27

description: Supp Table 2


title: wild type liver treated LPS, replicate 2

value: Liver

value: 12 weeks

value: Female


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 24

description: Supp Table 2


title: wild type liver control, replicate 3

value: Wild type

value: control

value: Control mice were humanely culled and liver tissue collected and snap frozen in liquid nitrogen


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 21

description: Supp Table 2


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 22

description: Supp Table 2


title: Epicardial_adipose_tissue_CABG 4

description:
patient undergoing coronary artery bypass grafting
EAT4


title: Mediastinal_adipose_tissue_CABG 4

description:
patient undergoing coronary artery bypass grafting
MAT4


title: Epicardial_adipose_tissue_CABG 3

description:
patient undergoing coronary artery bypass grafting
EAT3


title: 947

city: Göteborg

first: Kristina

last: Levan

address: Blå Stråket 2

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

hyb_protocol: The probes were purified using ChipShot™ labelling cleanup system (Promega). The hybridizations were carried out using Pronto! Micro Array reagent systems (Corning Inc.). For each sample, labelled tumour cDNA and reference cDNA were co-precipitated and hybridised to the oligoarray slide. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Genepix 6.0.0.45 (Axon Instruments).

data_processing: Data processing Intensities were calculated by median spot - median background. Flagged spots and spots for which background adjusted intensities were <0 or >65 000 were excluded as well as spots with intensities below 20 in both channels. Intensities below 20 in one channel were set to 20 to compensate for extreme quotients. pin-based Lowess normalization were performed with 12 blocks in each group

source_name: fresh frozen tumour from endometrial cancer patients

label_protocol: Probes labelled with Cy3 were synthesized from 5 µg of the total tumour RNA and reference labelled with Cy5 were synthesized from 5 µg of commercial reference RNA by reverse transcription.

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

tag: status

value: Alive

tag: surgical stage

value: Ib

tag: differentation grade

value: well

tag: age at diagnosis

value: fresh frozen tumour

source_name: Universal Human Reference RNA purchased from Stratagene

value: reference


title: 1139

value: Dead


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 20

description: Supp Table 2

tag: strain

tag: sector induction

tag: sample type


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 25

description: Supp Table 2


title: 760

value: Ia

value: moderate

tag: tissue


title: wild type liver control, replicate 1

tag: age

value: embryo

value: wild type

value: 17.5 days post coitus

value: Reference

value: Mice were mated, and the day of vaginal plug detection deemed 0.5 days post coitus (dpc).  Mice were humanely culled on the appropriate day of pregnancy (d17.5)and the embryos collected


title: 867


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 28

description: Supp Table 2

value: negative control MC2A strain in G2/M

value: re-replication at ChrIV567

value: red sector arising after re-replication at ChrIV567


title: Subcutaneous_adipose_tissue_CABG 4

description:
patient undergoing coronary artery bypass grafting
SAT4


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 23

description: Supp Table 2


title: 1019

value: IIa


title: wild type liver control, replicate 2

value: Wild type

value: Liver

value: 12 weeks

value: Female

value: control

value: Control mice were humanely culled and liver tissue collected and snap frozen in liquid nitrogen


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 19

description: Supp Table 2


title: Subcutaneous_adipose_tissue_CABG 3

description:
patient undergoing coronary artery bypass grafting
SAT3


title: 999

value: Alive

value: Ia

value: well

value: fresh frozen tumour

value: reference


title: 694

value: Ib

value: moderate


title: Mediastinal_adipose_tissue_CABG 3

description:
patient undergoing coronary artery bypass grafting
MAT3


title: WT HSCs, Biological rep2

city: Worcester

first: shaoguang

last: Li

state: MA

address: 364 Plantation street

institute: Worcester

description: Gene expression data from WT HSCs

hyb_protocol: Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: the arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.

data_processing:
DNA microarray analysis was carried out to compare gene expression between WT HSCs and Alox15-/- HSCs.
Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm.  These values were read into R/maanova and quantile-normalized.  For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003).  Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003).  Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002).  Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

source_name: WT HSCs

label_protocol: The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.

growth_protocol: We  compare the gene profile of HSCs between WT and Alox15-/- mice.  Bone marrow cells were isolated and subsequently sorted by FACS for HSCs (Lin-c-Kit+Sca-1+) .

extract_protocol: Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.

tag: cell type

value: HSCs

tag: genotype/variation

value: WT

value: 8 weeks


title: Epicardial_adipose_tissue_CABG 2

description:
patient undergoing coronary artery bypass grafting
EAT2


title: WT HSCs, Biological rep1

description: Gene expression data from WT HSCs


title: Mediastinal_adipose_tissue_CABG 2

description:
patient undergoing coronary artery bypass grafting
MAT2


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 18

description: Supp Table 2

value: negative control MC2A strain in G2/M

value: re-replication at ChrIV567

value: red sector arising after re-replication at ChrIV567


title: 684


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 17

description: Supp Table 2


title: Epicardial_adipose_tissue_CABG 1

description:
patient undergoing coronary artery bypass grafting
EAT1


title: 649

value: Dead

value: IVb

value: poor


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 16

description: Supp Figure 3C

source_name: red sector arising after re-replication at ChrIV1089

value: re-replication at ChrIV1089


title: genomic_changes_due_to_re-replication_at_ChrIV1089 sample 15

description: Supp Figure 3C

value: red sector arising after re-replication at ChrIV1089


title: Subcutaneous_adipose_tissue_CABG 1

description:
patient undergoing coronary artery bypass grafting
SAT1


title: 515


title: yeast diclofenac rep2

last: Vos

address: de Boelelaan 1083

department: Chemistry and Pharmaceutical Sciences

institute: Vrije Universiteit

hyb_protocol: Standard Affymetrix protocol, performed by microarray department (http://www.micro-array.nl/).

data_processing: The data were analyzed with MAS 5.0 using default analysis settings.

source_name: yeast cells, 100 µM diclofenac, 75h

growth_protocol: An overnight culture of W303-1A was diluted to OD600=0.1 in YNB and divided over 10 tubes. Cultures were grown at 30C and diluted every 24h to OD=0.1. 75 hours after first dilution, RNA was extracted.

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: Cultures were grown in the presence of either 100 µM diclofenac or 0.1% DMSO (controls).

value: diclofenac


title: 221

value: Alive

value: IIa


title: 528

value: fresh frozen tumour

value: reference


title: negative_control_M_ARS317+_1089 sample 14

description: Supp Figure 3A

hyb_protocol: Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 16 to 24 hours

source_name: negative control M ARS317+ 1089 strain in G2/M induced in galactose for 3 h

source_name: negative control strain in G2/M

value: negative control strain in G2/M


title: yeast diclofenac rep3

scan_protocol: Standard Affymetrix protocol, performed by microarray department (http://www.micro-array.nl/).


title: yeast diclofenac rep4

label: Standard Affymetrix protocol, performed by microarray department (http://www.micro-array.nl/).


title: KLF5 Adeno Treated

city: Tokyo

first: Katsuhito

last: Fujiu

address: 7-3-1 Hongo, Bunkyo

department: Cardiovascular Medicine

country: Japan

institute: University of Tokyo

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software ver. 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: KLF5 overexpressed mIMCD-3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mIMCD-3 cell were cultured as manufactured recommended.

extract_protocol: total RNA was performed by Rneasy according to the manufacturer's instructions.

treatment_protocol: mIMCD-3 cell were infected by control adenovirus or KLF5 adenovirus

tag: cell line

value: renal collecting duct epithelial cells


title: Alox15-/-  HSCs, Biological rep1

description: Gene expression data from Alox15-/- HSCs

source_name: Alox15-/- HSCs

value: HSCs


title: 193


title: yeast diclofenac rep5

label_protocol: Standard Affymetrix protocol, performed by microarray department (http://www.micro-array.nl/).


title: Control Adeno Treated

source_name: control mIMCD-3


title: yeast diclofenac rep1


title: negative_control_MC2A_ars317-_1089 sample 12

description: Supp Figure 3A

source_name: negative control MC2A ars317- 1089 strain in G2/M induced in galactose for 3 h

source_name: negative control MC2A strain in G2/M


title: Alox15-/- HSCs, Biological rep2

value: 8 weeks


title: 180

value: IIb

value: moderate


title: 168

value: IIIb


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 11

description: Old Figure 3

value: negative control MC2A strain in G2/M

source_name: red sector arising after re-replication at ChrIV567

value: re-replication at ChrIV567


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 10

description: Figure 1C

value: red sector arising after re-replication at ChrIV567

source_name: negative control M strain in G2/M

value: negative control M strain in G2/M


title: Subcutaneous_adipose_tissue_CABG 2

description:
patient undergoing coronary artery bypass grafting
SAT2

source_name: Chest


title: LPS 92B

city: Vancouver

first: Christopher

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

institute: University of British Columbia

description: PBMCs treated with LPS, donor 92

data_processing: The data were normalised using quantile normalisation with the limma package in R

source_name: PBMCs, donor 92

label_protocol: Standard Illumina labelling protocol.

extract_protocol: RNA samples obtained 4 hours post treatment of PBMCs, RNA was isolated from cell lysates using Qiagen RNA Isolation Kit (RNeasy®Mini Kit (Qiagen, Valencia, CA), treated with RNase free DNase (Qiagen, Valencia, CA) and eluted in RNase-free water (Ambion, Austin, TX) as per the manufacturer’s instruction.

treatment_protocol: Venous blood was collected from healthy volunteers into heparin-containing Vacutainer tubes. Peripheral blood mononuclear cells (PBMC) and monocyte derived macrophages (MDM) were isolated and cultured in RPMI 1640 medium supplemented with 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS), 2mM L-glutamine, 25mM HEPES and 1mM sodium pyruvate before treatment with LPS or LL37

value: peripheral blood mononuclear cells

value: PBMCs treated with LPS

tag: individual

value: donor 92


title: yeast control rep2

source_name: yeast cells, control, 75h

tag: treatment

value: control


title: yeast control rep3


title: yeast control rep1


title: yeast control rep4


title: 104

source_name: fresh frozen tumour from endometrial cancer patients

value: Dead

value: Ia

value: fresh frozen tumour


title: LPS/LPS  92D

description: PBMCs treated with LPS twice, the second treatment 24 hr after the first,donor 92


title: 146

value: Alive

source_name: Universal Human Reference RNA purchased from Stratagene

value: reference


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 8

description: Figure 1C


title: LPS/LPS  86D

description: PBMCs treated with LPS twice, the second treatment 24 hr after the first,donor 86

source_name: PBMCs, donor 86

value: donor 86


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 7

description: Figure 1C


title: 80

value: Ib

value: poor


title: 61

value: moderate


title: Untreated 92A

description: untreated PBMCs, donor 92

value: untreated PBMCs


title: re-replication_MC2A_ARS317+_1089 sample 13

description: Supp Figure 3A

source_name: re-replicating MC2A ARS317+ 1089 strain in G2/M induced in galactose for 3 h

value: negative control MC2A strain in G2/M


title: LPS 86B

description: PBMCs treated with LPS, donor 86


title: LPS/LPS  46D

description: PBMCs treated with LPS twice, the second treatment 24 hr after the first,donor 46

source_name: PBMCs, donor 46

value: donor 46


title: Untreated 46A

description: untreated PBMCs, donor 46


title: negative_control_M_ARS317+_567 sample 3

description: Figure 1A

source_name: negative control M ARS317+ 567 strain in G2/M induced in galactose for 3 h

source_name: negative control MC2A strain in G1

value: negative control MC2A strain in G1


title: LPS 46B

description: PBMCs treated with LPS, donor 46

value: peripheral blood mononuclear cells


title: Untreated 21A

description: untreated PBMCs, donor 21

source_name: PBMCs, donor 21

value: donor 21


title: HSC, Biological rep2

description:
Vector_2..70.
Gene expression data from HSCs

data_processing:
DNA microarray analysis was carried out to compare gene expression between BCR-ABL-expressing WT LSCs and BCR-ABL-expressing Alox5-/- LSCs  and non-BCR-ABL-expressing Lin-c-Kit+Sca-1+ cells.
Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm.  These values were read into R/maanova and quantile-normalized.  For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003).  Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003).  Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002).  Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

source_name: HSCs (i.e., non-BCR-ABL-expressing Lin-c-Kit+Sca-1+ cells)

growth_protocol: We used the bone marrow transplantation mouse model of CML as an assay system, in which bone marrow cells from donor mice pre-treated with 5-fluorouracil (5-FU) and transduced with BCR-ABL result in development of CML in recipient mice. We transduced bone marrow cells from C57BL/6 (B6) mice or Alox5-/- mice with retrovirus containing BCR-ABL/GFP or GFP alone under conditions for induction of CML, followed by transplantation of the transduced cells into B6 recipient mice. 14 days after BMT, bone marrow cells were isolated and subsequently sorted by FACS for LSCs (GFP+Lin-c-Kit+Sca-1+) .

value: HSCs

value: WT

value: 8 weeks


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 5

description: Figure 1C

value: re-replication at ChrIV567

value: red sector arising after re-replication at ChrIV567


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 4

description: Figure 1C


title: HSC, Biological rep1

description:
Vector_1..66.
Gene expression data from HSCs


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 6

description: Figure 1C

value: negative control M strain in G2/M


title: LPS/LPS  21D

description: PBMCs treated with LPS twice, the second treatment 24 hr after the first,donor 21


title: LSC, Biological rep2

description:
B6_P210_1..71.
Gene expression data from LSCs

source_name: LSCs

value: LSCs


title: yeast control rep5

value: control


title: re-replication_MC2A_ARS317+_567 sample 2

description: Figure 1A

source_name: re-replicating MC2A ARS317+ 567 strain in G2/M induced in galactose for 3 h


title: PHB Utilization 2

city: Cambridge

middle: John

last: Brigham

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

description: Gene expression interogated with 15 perfect match and 15 mismatch probes = 183480 probes. The 37784 remaining probe positions were used for tiling array.

hyb_protocol: Samples were hybridized to the arrays at 45C for 16h Arrays were washed using Affymtrix Genechip Fluidics Station 450 and Affymetrix washing kit (900720)

scan_protocol: Arrays were scaned using Affymtrix Genechip scanner 7G

data_processing: Expression data was examined using ArrayStar software by DNAStar, with RMA normailzation, and Student's t test and ANOVA statistical method

organism: Cupriavidus necator

source_name: R. eutropha H16

label_protocol: RNA samples were quanitified using the Agilent Bioanalyzer 2100. 100ng of total RNA was labelled using the Ambion MessageAmpII-Bacteria prokaryotic RNA Kit (Ambion-AM1790)

growth_protocol: Cells were grown initially in tryptic soy broth at 30C overnight, then transferred to PHB production medium with 0.1% ammonium chloride and 2.0% fructose to an initial OD600 = 0.1, and grown at 30C for 24h. Cells were subcultured into PHB production medium with 0.05% ammonium chloride, with the same carbon sources, to an initial OD600 = 0.05 and grown for 12h at 30C. Cells were subcultured again to an initial OD = 0.05 and grown for 48 h to allow for polyhydroxybutyrate accumulation. Cells were washed and subcultured into minimal medium with no exogenous carbon source and 1.0% ammonium chloride and grown at 30C for 6 h. Cells were harvested during PHB utilization as determined by crotonic acid quantitation assays.

extract_protocol: Total cellular RNA was extracted using the QIAgen RNEasy Mini RNA isolation kit, following the manufacturer's instructions.

treatment_protocol: Cells were treated with QIAgen RNA Protect reagent before freezing in a dry ice/ethanol slurry, then frozen at -80C.

tag: phase in phb production cycle

value: Mid PHB utilization phase


title: LSC without Alox5, Biological rep2

description:
Mut_A_2..68.
Gene expression data from LSCs without Alox5 gene

source_name: LSCs without Alox5 gene


title: LPS 21B

description: PBMCs treated with LPS, donor 21

value: PBMCs treated with LPS


title: PHB Utilization 1


title: PHB Utilization 3


title: LCL 4 (HuEx)

city: Durham

first: Luftig

last: Laboratory

state: NC

address: 220 CARL Bldg Duke U Med Center

department: MGM

institute: Duke University

description: See Exon Array Labeling kit (Affymetrix #900671)

hyb_protocol: Hybridization targets were prepared  from totalRNA and hybridized to GeneChip HuEx 1.0 ST and U133 2.0 Plus arrays according to standard Affymetrix (Santa Clara,CA) protocols

scan_protocol: GeneChip Scanner 3000 7G with GeneChip Fluidics Station 450

data_processing:
Raw .CEL data was normailized and consolidated into a probeset level expression file via Affymetrix Power Tools RMA (rma sketch) normalization of the 8 .CEL files.  Power tools settings were as follows for the HuEX analysis: rma-sketch, dabg, HuEx-1_0-st-v2.r2.pgf, HuEx-1_0-st-v2.r2.clf, HuEx-1_0-st-v2.r2.clf, background probes file HuEx-1_0-st-v2.r2.antigenomic.bgp, filter - HuEx_PSID_filer.txt (only exons overlapping known transcripts): FOR U133 ANALYIS: rma-sketch, dabg, HG-U133_Plus_2.cdf, U133_UCSC_PSID_filter.txt (only probesets that overlap known UCSC transcripts)
HuEx-1_0-st-v2.r2.pgf, HuEx-1_0-st-v2.r2.clf for Exon Array and HG-U133_Plus_2.cdf for U133

source_name: Monoclonal LCL derived by limited EBV dilution on PBMCs

label_protocol: cDNA preparation, labeling, fragmentation performed with Gene Chip cDNA synthesis/amplification kit (Affymetrix # 900673) and Exon Array Labeling kit (Affymetrix #900671) for HuEx samples and by 1-cycle IVT GeneChip labeling (Affymetrix#900449) and Affy Hyb, Wash, Stain kit (#900720) for labeling of cRNA for U133

growth_protocol: Infected cells (PBMCs) were maintained in RPMI 1640 + 15% FCS + cyclosporin A + Pen/Strep

extract_protocol: CD19+ B cells were purified from PBMC using the BD iMag Negative Isolation Kit (BD #558007).  Total RNA from CD19+ B cells or monocloncal LCLs was isolated via miRvana organic extraction (Ambion Inc) according to manufacturer's protocol

treatment_protocol: Infected cells were incubated with EBV for 1h at 37 C.  CFSE treatment was performed as described (Quah et al, Nature Protocols 2007).

tag: infection

value: Epstein-Barr virus infected, immortalized

value: Lymphoblastoid Cell Line, EBV-infected, monoclonal

tag: day post infection of extraction


title: LSC, Biological rep1

description:
B6_P210.69.
Gene expression data from LSCs


title: LCL 2 (HuEx)


title: negative_control_MC2A_ars317-_567 sample 1

source_name: negative control MC2A ars317- 567 strain in G2/M induced in galactose for 3 h

source_name: negative control strain in G2/M

value: negative control strain in G2/M


title: B Cell 2 (HuEx)

source_name: Purified B Cells from PBMCs

value: uninfected

value: Purified B Cells, from negative selection of PBMCs


title: Pf-5_FeCl3 deprived_replicate 5

status: Public on May 16 2011

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

description: Technical replicate 2 of biological replicate 3

hyb_protocol: Microarray slides were immersed in pre-hybridization buffer (1 % BSA, 5X SSC, 0.1 % SDS, 0.45 mm-filtered) before hybridization. Slides were washed with sterile water (4x) and isopropanol (3x), spin-dried and covered with lifterslip. cDNA probes were dried using Speedvac and then resuspended in hybridization buffer (50 % formamide, 5X SSC, 0.1 % SDS, 0.45 mm-filtered). Probes were heated at 95 degrees Celcius (15 min) before applying to the slides. Hybridization was performed overnight at 42 degrees Celcius. After hybridization, slides were washed with the following steps: 2x wash buffer 1 (1X SSC, 0.2% SDS) at 42 degrees Celcius, 1x wash buffer 2 (0.1X SSC, 0.1% SDS) and 3x wash buffer 3 (0.1X SSC, 0.1% SDS).

scan_protocol: Images were scanned with Axon 4000B scanner and GenPix 4.0 software

data_processing: The microarray data was analyzed with Spotfinder (TIGR) and normalized using the LOWESS algorithm in the TIGR-MIDAS package with block mode and smoothing parameter value of 0.33

label: Alexa fluor 647

organism: Pseudomonas fluorescens

source_name: Pseudomonas fluorescens Pf-5, non-iron treated

label_protocol: Reverse transcription of RNA samples was performed using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) with random hexamer primers. Approximately 7 µg of total RNA was used for cDNA synthesis in each reaction. cDNA samples were labeled with either Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen) according to manufacturer's instruction. Spike-in controls were made from RNA transcribed from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) with the MegaScript Kit (Ambion). Spike-in control were prepared as follow. For Alexa Fluor 555 pool,  0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.06 ng ltp6 RNA, 0.25 ng crp1 RNA, 0.95 ng nac RNA, 0.08 ng xcp2 RNA, 0.17 ng prk RNA and 0.21 ng tim RNA. For Alexa Fluor 647 pool, 0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.02 ng ltp6 RNA, 0.08 ng crp1 RNA, 0.31 ng nac RNA, 0.25 ng xcp2 RNA, 0.50 ng prk RNA and 0.63 ng tim RNA.

growth_protocol: Pseudomonas fluorescens Pf-5 was grown in M9 minimal media supplemented with 100 µM calcium chloride, 2 mM magnesium sulphate and 0.4 % glucose. The cultures were grown aerobically with shaking at room temperature until early to mid exponential phase; about OD600= 0.7 for iron-limited cultures and about OD600= 1 for iron-replete cultures.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) and and treated with RNAse-free DNAse (Ambion) as per manufacturer's instruction

treatment_protocol: The iron-replete cultures were supplemented with 100 µM iron(III) chloride whereas the iron-limited cultures were not treated with any iron supplementation

tag: agent

label: Alexa fluor 555

source_name: Pseudomonas fluorescens Pf-5, iron(III) chloride treated

value: iron(III) chloride


title: Pf-5_FeCl3 deprived_replicate 6

description: Technical replicate 3 of biological replicate 3


title: Pf-5_FeCl3 deprived_replicate 4

description: Technical replicate 1 of biological replicate 3


title: B Cell 4 (HuEx)


title: B Cell 3 (HuEx)


title: Pf-5_FeCl3 deprived_replicate 3

description: Technical replicate 2 of biological replicate 2


title: Pf-5_FeCl2 deprived_replicate 2

description: Biological replicate 2

treatment_protocol: The iron-replete cultures were supplemented with 100 µM iron(II) chloride whereas the iron-limited cultures were not treated with any iron supplementation

source_name: Pseudomonas fluorescens Pf-5, iron(II) chloride treated

value: iron(II) chloride


title: Pf-5_FeCl3 deprived_replicate 1

description: Biological replicate 1


title: LCL 3 (HuEx)


title: Pf-5_FeCl2 deprived_replicate 1

description: Biological replicate 1


title: Pf-5_FeCl2 deprived_replicate 4


title: TMK-1 cells stably expressing miR-NRDc clone #1

city: Kyoto

first: Hideyuki

last: Komekado

address: 54 Kawara-cho, Shogoin, Sakyo-ku,

department: Gastroenterology and Hepatology

institute: Graduate School of Medicine, Kyoto University

description: Reduced expressin of NRDc by RNAi

hyb_protocol: Sense-strand DNA was hybridized on Affymetrix GeneChip Human Gene 1.0 ST Array.

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

data_processing: Microarray data were analyzed with Affymetrix GeneChip Command Console Software (Affymetrix) and GeneSpring GX Version 10.0.2 (Agilent Technologies) and normalized by RMA16 algorithm.

source_name: TMK-1 gastric cancer cell line

label_protocol: Biotinylated sense-strand DNA was generated from 100 ng of total RNA with WT Sense Target Labeling and Control Reagent (Affymetrix).

growth_protocol: TMK-1 gastric cancer cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum and 5 mg/ml blastcidin.

extract_protocol: Total RNA was extracted using RNeasy mini kit (QIAGEN) and digested with DNase.

treatment_protocol: TMK-1 clones stablly expressing control vector (miR-NC, non-targeting sequence) or miR against NRDc (target sequence: 5’-CTGATGCAAACAGAAAGGAAA-3’) were established by selection with blastcidin.

value: gastric adenocarcinoma

value: TMK-1 cells stably expressing miR-NRDc


title: TMK-1 cells stably expressing miR-negative control clone #4

description: control RNAi by non-targeting sequence


title: Pf-5_FeCl3 deprived_replicate 2

description: Technical replicate 1 of biological replicate 2


title: Mediastinal_adipose_tissue_CABG 1

description:
patient undergoing coronary artery bypass grafting
MAT1

hyb_protocol: Standard Illumina hybridization protocol

source_name: Mediastino

tag: bmi


title: Pf-5_FeCl2 deprived_replicate 3


title: LCL 1 (HuEx)


title: B Cell 1 (HuEx)


title: Pf-5_FeCl2 deprived_replicate 5


title: OVCAR8

first: Ken

last: Yamaguchi

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Data were RMA normalized using RMAExpress.

source_name: ovarian cancer cells

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

extract_protocol: Qiagen RNeasy.

value: ovarian cancer cells

tag: gender

value: female

tag: histology

value: non-OCCC


title: BG1


title: PEO1


title: MCAS

value: MCAS


title: LSC without Alox5, Biological rep1

description:
Mut_A_1..64.
Gene expression data from LSCs without Alox5 gene

tag: strain

value: LSCs

value: 8 weeks


title: TYK-nu

value: TYK-nu


title: OMC-3


title: A2780


title: JHOM-2B


title: JHOM-1


title: genomic_changes_due_to_re-replication_at_ChrIV567 sample 9

description: Figure 1C

data_processing:
Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.
Value is the log2 of the normalized ratio of Cy5 to Cy3 – note that to convert to usable replication profiles, raise two to the indicated value.

source_name: red sector arising after re-replication at ChrIV567

tag: sector induction

value: re-replication at ChrIV567

source_name: negative control M strain in G2/M

value: negative control M strain in G2/M


title: RMG-5

value: OCCC


title: TOV-112D


title: JHOC-7


title: KOC-5C


title: JHOC-9


title: TOV-21G


title: TAYA

value: TAYA


title: OVCA433


title: RMG-2


title: JHOC-8


title: Untreated 86A

description: PBMCs, donor 86

source_name: PBMCs, donor 86

value: peripheral blood mononuclear cells

value: untreated PBMCs

value: donor 86


title: RMG-1


title: OVK-18


title: OVCAR3


title: KOC-7C


title: IGROV1


title: OVTOKO

value: OVTOKO


title: OVCA432


title: OV90


title: OVARY1847

description: 1317_2745_13746_OVARY1847_HG-U133A+2.CEL


title: OVCA429


title: OVISE

value: OVISE


title: JHOC-5


title: JHOS-3


title: OVCA420


title: JHOS-4


title: HEY

value: HEY


title: JHOS-2

value: ovarian cancer cells


title: SKOV3

value: female


title: CAOV3

value: non-OCCC


title: control iPSC #3 replicate 3

first: Mathias

last: Pawlak

address: 9 Cambridge Center

institute: Whitehead Institute

description: replicate 3

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of  825ng cy3- and 825ng cy5-dye labeled cRNA, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 17 hours at 60°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetronitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

scan_protocol: Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.

data_processing: Microarrays were normalized across channels by loess (locally weighted scatterplot smoothing) and between arrays by quantile normalization of average intensities (Aquantile), as implemented by the limma package in Bioconductor.

source_name: control iPSC #3

label_protocol: Cy3/Cy5-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 2µg total RNA.

growth_protocol: iPS cell lines were grown under typical mouse ESC conditions on irradiated mouse embryonic fibroblasts (MEFs). The cells were passaged once or twice on gelatin before RNA isolation without replenishing feeders to lower potential background.

extract_protocol: Total RNA was extracted with the Rneasy Kit from Qiagen according to the instructions of the manufacturer

value: control iPSC

tag: data processing

value: Included in the subsequent statistical analysis included in the publication

source_name: B2 Dnmt3ab iPSC (some signs of differentiation)

value: Dnmt3ab deficient iPSC

value: Not included in the subsequent statistical analysis included in the publication


title: control iPSC #3 replicate 2

description: replicate 2

source_name: A6 Dnmt3ab iPSC (some signs of differentiation)


title: Male_Testis_4

first: Dean

last: Baker

address: Department of Genetics, Downing Street

country: United Kingdom

institute: University of Cambridge

description: Anopheles male testis

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Plasmodium/Anopheles Genome Array. 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 [R] Bioconductor using the GC-RMA normalization and MAS probe detection libraries.

organism: Anopheles gambiae

source_name: Anopheles male testis

label_protocol: Biotinylated cRNA was prepared according to the standard two-cycle Affymetrix protocol from 50ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: 5 day old male and female mosquitoes.  Samples for males and females where blooded after the bloodmeal over at three time points over 72hrs (24hrs, 48hr, 72hrs)

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen)

treatment_protocol: Mosquitoes were anaesthetised briefly by chilling on ice, then immediately dissected.

tag: stage

value: adult

tag: tissue

value: testis

value: male


title: control iPSC #4 replicate 2

description: replicate 2

source_name: control iPSC #4


title: Male_Testis_2

description: Anopheles male testis


title: Male_Salivary_3

description: Anopheles male salivary gland

source_name: Anopheles male salivary gland

value: salivary gland


title: Male_Salivary_1

description: Anopheles male salivary gland


title: Female_Ovary_4

description: Anopheles female ovary

source_name: Anopheles female ovary

value: ovary


title: Male_Salivary_2

description: Anopheles male salivary gland


title: Female_Salivary_3

description: Anopheles female salivary gland

source_name: Anopheles female salivary gland


title: Female_Ovary_3

description: Anopheles female ovary


title: Male_Testis_3

description: Anopheles male testis


title: control iPSC #6 replicate 2

description: replicate 2

source_name: control iPSC #6


title: control iPSC #5 replicate 3

description: replicate 3

source_name: control iPSC #5


title: Male_Testis_1

description: Anopheles male testis


title: control iPSC #4 replicate 3

description: replicate 3


title: Female_Salivary_2

description: Anopheles female salivary gland


title: control iPSC #6 replicate 3

description: replicate 3


title: Female_Salivary_4

description: Anopheles female salivary gland


title: Male_Salivary_4

description: Anopheles male salivary gland


title: control iPSC #5 replicate 2

description: replicate 2


title: Female_Salivary_1

description: Anopheles female salivary gland


title: Female_Ovary_2

description: Anopheles female ovary


title: Pf-5_FeCl2 deprived_replicate 6

description: Biological replicate 4

source_name: Pseudomonas fluorescens Pf-5, non-iron treated

value: control

source_name: Pseudomonas fluorescens Pf-5, iron(II) chloride treated

value: iron(II) chloride


title: Male_Midgut_4

description: Anopheles male midgut

source_name: Anopheles male midgut

value: midgut


title: Male_Midgut_1

description: Anopheles male midgut


title: continuous light T = 68 hours

first: Vikram

last: Vijayan

address: 52 Oxford Street, Room 440

institute: Harvard University

hyb_protocol: Each array was hybridized with ~750 ng Cy3 and ~750 ng Cy5 labeled cDNA and rotated (5 rotations min−1) at 60 °C for 17 hours in SureHyb chambers (Agilent). Arrays were subsequently washed in 6.7× SSPE and 0.005% N-lauryl sarcosine buffer for at least 1 min, 0.67× SSPE and 0.005% N-lauryl sarcosine buffer for 1 minute, and then Agilent drying and ozone protection wash for 30 seconds at room temperature (1× SSPE = 0.15 M NaCl, 10 μM sodium phosphate, 1 mM EDTA, pH 7.4).

scan_protocol: The arrays were immediately scanned using an Axon 4000B scanner at 5-μm resolution.

data_processing: The median intensity of the Cy3 and Cy5 florescence at each spot was extracted using the GenePix software (Molecular Devices).

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: continuous light T = 68 hours

label_protocol: cDNA was prepared for each individual timepoint (foreground channel) as well as for a pool of all timepoints (background channel). The background channel consisted of a pool of samples collected at four hour intervals from times 24 through 84 hours after release into continuous light. The foreground channel consisted of individual timepoints 60, 68, 72, and 80 hours after release into continuous light. Spike-in RNA was introduced at different concentrations and ratios to the foreground and background channels before reverse transcription to ensure proper ratio detection over a wide dynamic range. Five μg total RNA (plus spike-ins) was reverse-transcribed with random 15-mer primers (Operon) and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma) using SuperScript III reverse-transcriptase system without amplification. RNA was hydrolyzed and cDNA was purified using Microcon 30 spin column (Millipore).   First-strand cDNA was labeled with N-hydroxysuccinimide-ester cyanine 3 (Cy3, foreground) or cyanine 5 (Cy5, background) (GE Biosciences) in 0.1 M sodium bicarbonate pH 9.0 for 6 hours. Labeled cDNA was purified (Microcon 30) in preparation for hybridization.

growth_protocol: A continuous culture apparatus kept cells in constant light and growth conditions and provided real-time bioluminescence readings. S. elongatus (stain AMC 408): psbAI::luxCDE fusion in NS1 (spectinomycin and streptomycin) and purF::luxAB fusion in NSII (chloramphenicol) was grown in a 6-L cylindrical spinner flask at a volume of 4.5 L. Cells were grown in BG-11 medium with the following modifications: 0.0010 g/L FeNH4 citrate was used instead of 0.0012 g/L FeNH4 citrate and citric acid was supplemented at 0.00066 g/L. Cells were initially inoculated in the presence of antibiotics (5 μg/mL spectinomycin and 5 μg/mL chloramphenicol), and subsequently diluted with modified BG-11 lacking antibiotics. Cells were exposed to surface flux of approximately 25 μmol photons m−2 s−1 cool white florescent light, bubbled with 500 mL/min 1% CO2 in air, maintained at 30 °C, and stirred at 1 rotation per second. Constant optical density (OD750 0.15) and volume are achieved via a two state controller. OD does not fluctuate greater than 8% during an experiment. Cells are exposed to two twelve hour light–dark cycles for entrainment before release into continuous light.

extract_protocol: RNA was extracted from frozen cells in two steps. First, cells were lysed in 65° C phenol/SDS (sodium dodecyl sulfate) by vortexing and the total RNA was purified by phenol/chloroform extraction. Second, total RNA was subjected to DNase I (Promega) treatment followed by a second phenol/chloroform extraction. Total RNA was analyzed on agarose gel and Agilent Bioanalyzer for integrity.

tag: continuous light time

value: 68 hrs

source_name: average of T = 24 through 80 in 4 hour intervals


title: continuous light T = 60 hours

source_name: continuous light T = 60 hours

value: 60 hrs

value: average of T = 24 through 80 in 4 hour intervals


title: continuous light T = 72 hours

source_name: continuous light T = 72 hours

value: 72 hrs


title: Male_Midgut_2

description: Anopheles male midgut


title: Female_Midgut_3

description: Anopheles female midgut

source_name: Anopheles female midgut

value: female


title: control iPSC #5 replicate 1

description: replicate 1

value: control iPSC

source_name: #8 Dnmt3ab iPSC (some signs of differentiation)


title: Male_Midgut_3

description: Anopheles male midgut


title: control iPSC #3 replicate 1

description: replicate 1

source_name: control iPSC #3

value: Included in the subsequent statistical analysis included in the publication


title: A6 Dnmt3ab iPSC replicate 2

description: replicate 2

source_name: V6.5 ESC

value: V6.5 ESC

source_name: A6 Dnmt3ab iPSC

value: Dnmt3ab deficient iPSC


title: Female_Midgut_2

description: Anopheles female midgut

value: adult


title: Female_Ovary_1

description: Anopheles female ovary


title: Male_Malpighian_3

description: Anopheles male malpighian

source_name: Anopheles male malpighian

value: malpighian


title: Female_Midgut_4

description: Anopheles female midgut


title: Male_Malpighian_4

description: Anopheles male malpighian

value: male


title: Female_Midgut_1

description: Anopheles female midgut


title: continuous light T = 80 hours

source_name: continuous light T = 80 hours

value: 80 hrs


title: control iPSC #6 replicate 1

description: replicate 1

value: Not included in the subsequent statistical analysis included in the publication


title: control iPSC #4 replicate 1

description: replicate 1

source_name: control iPSC #4


title: #8 Dnmt3ab iPSC replicate 2

description: replicate 2

source_name: #8 Dnmt3ab iPSC


title: B2 Dnmt3ab iPSC replicate 2

description: replicate 2

source_name: B2 Dnmt3ab iPSC


title: A6 Dnmt3ab iPSC replicate 1

description: replicate 1

source_name: MEF

value: MEF


title: Female_Malpighian_3

description: Anopheles female malpighian

source_name: Anopheles female malpighian


title: Female_Malpighian_2

description: Anopheles female malpighian


title: Male_Head_3

description: Anopheles male head

source_name: Anopheles male head

value: head


title: Bj_paraquat prolonged exposure vs. no treatment_Rep1

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

institute: University of Texas at Arlington

description: Transcriptional profiling of paraquat treated cells compared to non-treated cells.

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined and averaged. Significant genes were selected based on a 1.5-cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: No Treatment Replication 1

label_protocol: 30 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Five micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

tag: 'strain

value: USDA 110', 'Treatment type:None', 'Media:Arabinose-gluconate'

source_name: Paraquat prolonged exposure treatment_Replication 1

value: USDA 110', 'Treatment type:paraquat', 'Treatment concentration:0.1 mM', 'Treatment time:entire growth period', 'Media:Arabinose-gluconate'


title: Female_Head_1

description: Anopheles female head

source_name: Anopheles female head


title: #8 Dnmt3ab iPSC replicate 1

description: replicate 1

tag: cell line


title: Bj_paraquat fulminant shock vs. no treatment_Rep1_dyeswap

source_name: Paraquat fulminant shock treatment_Replication 1

value: USDA 110', 'Treatment type:paraquat', 'Treatment concentration:5 mM', 'Treatment time:10 minutes', 'Medium:Arabinose-gluconate'

value: USDA 110', 'Treatment type:None', 'Medium:Arabinose-gluconate'


title: Bj_paraquat prolonged exposure vs. no treatment_Rep1_dyeswap

source_name: Paraquat prolonged exposure treatment Replication 1

value: USDA 110', 'Treatment type:paraquat', 'Treament concentration:0.1 mM', 'Treatment time:entire growth period', 'Media:Arabinose-gluconate'


title: Bj_paraquat prolonged exposure vs. no treatment_Rep2

source_name: No Treatment Replication 2

source_name: Paraquat prolonged exposure treatment Replication 2


title: Bj_paraquat fulminant shock vs. no treatment_Rep3_dyeswap

source_name: Paraquat fulminant shock treatment_Replication 3

value: USDA 110', 'Treatment type:paraquat', 'Treatment concentration:5 mM', 'Treatment time; 10 minutes', 'Media:Arabinose-gluconate'

source_name: No Treatment Replication 3


title: Male_Head_4

description: Anopheles male head


title: Male_Malpighian_1

description: Anopheles male malpighian

source_name: Anopheles male malpighian


title: Bj_paraquat fulminant shock vs. no treatment_Rep3

source_name: Paraquat fulminant shock treatment Replication 3

value: USDA 110', 'Treatment type:paraquat', 'Treatment concentration:5 mM', 'Treatment time:10 minutes', 'Media:Arabinose-gluconate'


title: Female_Head_3

description: Anopheles female head

value: female


title: Female_Malpighian_1

description: Anopheles female malpighian


title: Male_Head_2

description: Anopheles male head


title: B2 Dnmt3ab iPSC replicate 1

description: replicate 1

value: Included in the subsequent statistical analysis included in the publication


title: Female_Head_4

description: Anopheles female head


title: Male_Carcass_2

description: Anopheles male carcass

source_name: Anopheles male carcass

value: carcass


title: Bj_paraquat prolonged exposure vs. no treatment_Rep3_dyeswap

source_name: Paraquat prolonged exposure treatment Replication 3


title: Male_Carcass_1

description: Anopheles male carcass

value: adult


title: Male_Head_1

description: Anopheles male head


title: Female_Malpighian_4

description: Anopheles female malpighian

value: malpighian


title: Male_Carcass_3

description: Anopheles male carcass

value: male


title: Female_Head_2

description: Anopheles female head


title: Bj_paraquat prolonged exposure vs. no treatment_Rep3


title: Male_Carcass_4

description: Anopheles male carcass


title: Bj_paraquat fulminant shock vs. no treatment_Rep1


title: Female_Carcass_4

description: Anopheles female carcass

source_name: Anopheles female carcass


title: Female_Carcass_2

description: Anopheles female carcass


title: Female_Carcass_3

description: Anopheles female carcass


title: medulloblastoma, M2_cMYC_silenced, rep3

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: Gene expression data.

hyb_protocol: Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.

data_processing: Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).

source_name: medulloblastoma, M2, cMYC silenced

label_protocol: This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).

growth_protocol: DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.

extract_protocol: Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).

treatment_protocol: DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.

value: DAOY M2.1

tag: cell type

value: medulloblastoma

tag: genetic modification

value: siRNA cMYC silenced


title: medulloblastoma, M2_cMYC_silenced, rep2

description: Gene expression data.


title: medulloblastoma, M2_scrambled, rep3

description: Gene expression data.

source_name: medulloblastoma, M2, scrambled

value: siRNA scrambled


title: medulloblastoma, M14, rep3

description: Gene expression data.

source_name: medulloblastoma, M14

value: DAOY M14

value: pMYCEGFP vector-transfected


title: medulloblastoma, M2_scrambled, rep1

description: Gene expression data.


title: medulloblastoma, M2_scrambled, rep2

description: Gene expression data.


title: medulloblastoma, M2_cMYC_silenced, rep1

description: Gene expression data.


title: medulloblastoma, M14, rep1

description: Gene expression data.


title: Male_Body_4

description: Anopheles male body

source_name: Anopheles male body

value: body


title: WT-3

city: Minneapolis

first: Rita

last: Perlingeiro

state: MN

address: 312 Church ST SE; NHH 4-124

institute: University of Minnesota

description: replicate 3

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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. Quality control was performed with Agilent Bioanalyser.

value: Differentiated day 3 EBs


title: Bj_paraquat prolonged exposure vs. no treatment_Rep2_dyeswap

value: USDA 110', 'Treatment type:paraquat', 'Treatment concentration:0.1 mM', 'Treatment time:entire growth period', 'Media:Arabinose-gluconate'

value: USDA 110', 'Treatment type:none', 'Media:Arabinose-gluconate'


title: medulloblastoma, M14, rep2

description: Gene expression data.


title: Female_Carcass_1

description: Anopheles female carcass


title: Male_Body_3

description: Anopheles male body


title: KO-3

description: replicate 3


title: Male_Body_1

description: Anopheles male body


title: Male_Malpighian_2

description: Anopheles male malpighian


title: Male_Body_2

description: Anopheles male body


title: medulloblastoma, V11, rep2

description: Gene expression data.

source_name: medulloblastoma, V11

value: DAOY V11

value: pEGFP vector-transfected


title: medulloblastoma, M2, rep3

description: Gene expression data.

source_name: medulloblastoma, M2


title: WT-1

description: replicate 1


title: medulloblastoma, V11, rep3

description: Gene expression data.


title: Female_Body_3

description: Anopheles female body

source_name: Anopheles female body

value: female


title: KO-2

description: replicate 2


title: Bj_paraquat fulminant shock vs. no treatment_Rep2

value: USDA 110', 'Treatment type:none', 'Medium:Arabinose-Gluconate'

source_name: Paraquat fulminant shock treatment Replication 2

value: USDA 110', 'Treatment type:paraquat', 'Treatment concentration:5mM', 'Treatment time:10 minutes', 'Medium:Arabinose-Gluconate'


title: Female_Body_2

description: Anopheles female body

value: adult


title: WT-2

description: replicate 2


title: KO-1

description: replicate 1


title: Female_Body_4

description: Anopheles female body


title: Female_Body_1

description: Anopheles female body


title: medulloblastoma, M2, rep2

description: Gene expression data.


title: optic nerve_P4_rep2

city: Montreal

first: Hana

middle: C.

last: Friedman

address: 687 Pine Ave. West

institute: McGill University

description: The microarray experiments were performed at the McGill University and Génome Québec Innovation Centre, Montréal, Canada

hyb_protocol: According to the Affymetrix protocol: the hybridization mixture was prepared by mixing 15 µg of the biotinylated probe cRNA with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Invitrogen Life Technologies) in a final volume of 300 µL of 1X MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99°C, incubated for 5 minutes at 45°C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized with 200 µL of 1X hybridization buffer for 10–20 minutes at 45°C. The prehybridization solution was removed and 200 µL ofthe hybridization mix was added to the array. The array and probe fragments were incubated at 45°C overnight (16–20 hours) in a rotating oven (Affymetrix).

scan_protocol: According to the Affymetrix protocol: after hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (6x SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50oC) were per- formed (all reagents from Sigma). Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix).

data_processing: Robust multichip analysis method (RMA)

source_name: optic nerves, 55 P4 mouse pups

label_protocol: The Affymetrix One-cycle Target Labeling protocol was used. The RNA samples were first converted to double stranded cDNA. 10 micrograms of total RNA were mixed with 100 pM of T7-(T)24 primer (Genset, 5’ GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(dT)24-3’) in a 10 µl volume. The primer-RNA mixture was denatured for 10 minutes at 70°C and then chilled on ice. First-strand cDNA synthesis was performed using 2 µL Superscript II reverse transcriptase (Invitrogen Life Technologies) in a 20-µL reaction volume containing 10 µM dithiothreitol, 500 µM each dNTP, and 1X first-strand buffer(all from Invitrogen Life Technologies) for 60 minutes at 42°C. Second-strand synthesis was performed by adding to the first strand reaction mix: 40 units DNA polymerase I,(Invitrogen Life Technologies) 10 units Escherichia coli DNA ligase, (Invitrogen Life Technologies) and 2 units RNase H (MBI Fermentas) in a final reaction volume of 150 µL containing 1X second-strand buffer (Invitrogen Life Technologies). The reaction mixture was incubated at 16°C for 2 hours. Ten units of T4 DNA polymerase(MBI Fermentas)was added and incubated at 16°C for 5 minutes followed by the addition of 10 µL of 0.5 M EDTA (Sigma). After second-strand synthesis, the cDNA was purified by phenol chloroform extraction with Phase-Lock tubes (Eppendorf). The purified cDNA was used to generate the biotinylated cRNA probe with the Bioarray High Yield RNA transcript labeling kit (Enzo diagnostics)as indicated by the supplier. The labeled cRNA was then purified using the RNeasy total RNA clean up protocol(Qiagen).

extract_protocol: Optic nerves were dissected into RNAlater (Ambion) and placed at 4∞C overnight before being stored at –80. Each pool of optic nerves was homogenized in Trizol (Life Technologies) using a glass/glass homogenizer.  Following chloroform extraction, the lysate was purified using an RNAeasy column (Qiagen).  RNA quality was assessed using an Agilent Bioanalyzer.

tag: age

value: optic nerve


title: medulloblastoma, V11, rep1

description: Gene expression data.


title: optic nerve_P4_rep1

source_name: optic nerve, 75 at P4


title: medulloblastoma, M2, rep1

description: Gene expression data.

value: DAOY M2.1


title: ACPS_4

description: Anopheles male Acps

source_name: Anopheles male Acps

value: acps

value: male


title: WT, biological rep2

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
GPL13185_mjay.pgf
GPL13185_mjay.clf

source_name: wild-type brain

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Target Labeling Kit (Affymetrix)

growth_protocol: Brains dissected from Rbfox1-KO mice or WT mice, 1 month of age

extract_protocol: Mice were genotyped and whole brains were dissected from 3 mutant and 3 wild-type animals. Total RNA was extracted using Trizol and samples were treated with RiboMinus™ Transcriptome Isolation Kit (Invitrogen). cDNA synthesis and amplification was performed using the GeneChip® Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix).

value: 1 mo

value: brain

tag: genotype

value: wild-type

value: Male

tag: genetic background

value: mixed 129S2/Sv and C57BL/6J


title: WT, biological rep1


title: optic nerve_P10_rep3

source_name: optic nerves, 50 P10 mouse pups


title: SACOL2645_mutant_rep1

city: Bethesda

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

description: We did four hybridizations for this experiment, including a biological replicate and a dye-swap experiment for each replicate to account for dye-bias.The data from the replicates were combined (using the median value) and a one-sample t-test was performed. The volcano plot was used with a fold change cut-off of >= 2 and a p-value of <0.05, to filter the genes that were differentially expressed.

hyb_protocol: Labeled cDNA was purified using MinElute PCR purification kit and hybridized with S. aureus COL genome microarrays version 6.0, provided by Pathogen Functional Genomics Resource Center (PFGRC), as per the TIGR protocol (Standard operating procedure no. M008: http://pfgrc.jcvi.org/index.php/microarray/protocols.html). Briefly, the slides were treated with a preheated pre-hybridization buffer (5 X SSC [Ambion], 0.1 % SDS and 1 % BSA [Sigma, St. Louis, MO]) at 42oC for 1 hr. Slides were then washed with distilled water followed by washing with isopropanol and dried by centrifuging. The dried Cy3 and Cy5 labeled cDNA was resuspended using hybridization buffer (50 % formamide, 5 X SSC, 0.1 % SDS and 300 µg sheared salmon sperm DNA [Ambion]) and denatured at 95oC. The sample was then applied to the pre-hybridized slides under the LifterSlip (Fisher, Pittsburg, PA). The slides were incubated at 42oC overnight. The hybridized slides were serially washed with low, medium and high stringency wash buffers and dried by centrifuging.

scan_protocol: Scanning was done using Axon 4200A scanner (Molecular Devices, Sunnyvale, CA). The microarray scans were saved as TIFF image files.

data_processing: GenePix Pro 6 (Molecular Devices) was used to extract the spot intensity values and generate GPR files from the microarray image files. Further data analysis was done using the Acuity 4.0 software (Molecular Devices). Spots flagged as empty or bad were excluded and the raw data from each slide was normalized using LOWESS method, with background correction.

organism: Staphylococcus aureus

label_protocol: RNA labeling and hybridization were done as per TIGR protocol (Standard operating procedure no. M007: http://pfgrc.jcvi.org/index.php/microarray/protocols.html). Briefly, random hexamers (Invitrogen) as primers were annealed to 2.5 µg of the total RNA (70oC for 10 min, followed by snap-freezing in ice for 1 min), along with RNaseOUT recombinant ribonuclease inhibitor (Invitrogen). The primers were then extended using SuperScript II reverse transcriptase (Invitrogen) with 0.1 M DTT and 12.5 M of aa-dNTP/aa-dUTP mix (Ambion, Austin, TX) at 42oC overnight.  Residual RNA was removed by alkaline treatment with 1 M NaOH followed by neutralization with 1 M Tris (pH 7.4). The resulting cDNA was purified using Qiagen MinElute PCR purification kit (Qiagen) and labeled with Cy3 and Cy5 mono-Reactive dyes (Amersham Biosciences, Pittsburg, PA) as per manufacturer’s instruction.

extract_protocol: Overnight culture was grown in 100ml TSB containing erythromycin 10 ug/ml. Next day 1 ml of that overnight culture was inoculated in to 100 ml TSB without antibiotics and grown for 3 hours. After 3 hours that culture was used to inoculate another flask of 100 ml TSB without antibiotics to an OD of 0.05 at 600 nm. After 3 hours of incubation, 3 ml of this culture is mixed with 6 ml of Bacterial RNA Protect solution (Qiagen, Valencia, CA). The cells were harvested by centrifuging the mixture for 10 min at 7300 rpm in a table top centrifuge. The pellets were then resuspended in 1 ml of Trizol (Invitrogen, Grand Island, NY). Resuspended cells were broken using the FastPrep sytem (Qbiogene, Irvine, CA) at a speed of 6.0 for 40 seconds and RNA from the lysate was extracted as per the manufacturer’s instructions. RNeasy mini kit (Qiagen) was used to purify the extracted RNA. An on-column DNase (Qiagen) treatment was done. The quality and the concentration of the RNA were then analyzed using the RNA 6000 Nano LabChip system (Agilent Technologies, Santa Clara, CA).

value: SACOL2645 mutant

value: wildtype


title: SACOL2645_mutant_rep1_dyeswap


title: SACOL2645_mutant_rep2


title: SACOL2645_mutant_rep2_dyeswap


title: Rbfox1 KO, biological rep2

source_name: Rbfox1 -/- brain

value: Rbfox1 KO


title: WT, biological rep3


title: 132h_Con_3

status: Public on May 15 2011

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

hyb_protocol: Appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES and 3 × SSC, resulting in a final volume of 70μl. The hybridization mixtures were boiled for 2 min at 99°C and allowed to cool at room temperature for 5 min. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63°C. Microarrays were washed twice in 0.6 × SSC, 0.01% SDS and were kept in 0.06 × SSC until analysis.

scan_protocol: Slides were dried via centrifugation and scanned using an Axon 4000B scanner. The experimental setup followed a reference design, i.e. all samples were hybridized against the same pool made up of equal amounts of aRNA from all samples.

data_processing: TIGR Spotfinder 2.2.3 was used to extract spot intensities and subtract background (Saeed et al. 2003). The data were normalized using TIGR MIDAS 2.21 printtip-specific LOWESS followed by in-slide replicates analyses (Saeed et al. 2003).

label: cy3 (IA)

organism: Orbicella faveolata

source_name: reference

label_protocol: Total RNA of approximately 1,000 coral embryos was isolated using Qiazol lysis reagent (Qiagen) according to manufacturer's instructions. RNA quantity and integrity was assessed using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. For each sample, 1ug of total RNA was amplified using the MessageAmp II aRNA kit (Ambion). Subsequent cDNA synthesis and dye-labeling was performed using 3 ug aRNA per sample were primed with 3.5 nmol random pentadecamer for 10min at 70°C. Reverse transcription (RT) lasted for 2 hours at 42°C using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP. Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 uL 0.5M EDTA and 10 uL 1M NaOH for 15min at 65°C. After hydrolysis, RT reactions were cleaned using the MinElute Cleanup kit (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark. Dye-coupled cDNAs were cleaned using the MinElute Cleanup kit (Qiagen). Appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES and 3 × SSC, resulting in a final volume of 70ul.

extract_protocol: Total RNA Qiazol extraction, aRNA amplification, cDNA Superscript III

tag: larvae

value: pooled reference

label: cy3 (IB)

value: sample


title: 132h_UV_2


title: 132h_UV_3


title: 84h_UV_1


title: ACPS_2

description: Anopheles male Acps


title: 132h_Con_2


title: Rbfox1 KO, biological rep3


title: 84h_UV_2


title: optic nerve_P10_rep2

description: The microarray experiments were performed at the McGill University and Génome Québec Innovation Centre, Montréal, Canada.


title: 132h_Con_1


title: 84h_UV_3


title: medulloblastoma, wt, rep3

description: Gene expression data.

source_name: medulloblastoma, wt

value: DAOY

value: medulloblastoma

value: none (wildtype)


title: 84h_Con_2


title: 132h_UV_1


title: 84h_Con_3


title: 60h_UV_2


title: medulloblastoma, wt, rep2

description: Gene expression data.


title: optic nerve_P10_rep1

source_name: optic nerves, 70 P10 mouse pups

extract_protocol: Optic nerves were dissected into RNAlater (Ambion) and placed at 4C overnight before being stored at –80. Each pool of optic nerves was homogenized in Trizol (Life Technologies) using a glass/glass homogenizer.  Following chloroform extraction, the lysate was purified using an RNAeasy column (Qiagen).  RNA quality was assessed using an Agilent Bioanalyzer.

value: optic nerve


title: ACPS_1

description: Anopheles male Acps

value: adult


title: 84h_Con_1


title: medulloblastoma, wt, rep1

description: Gene expression data.


title: 60h_UV_3


title: 60h_Con_3


title: 60h_UV_1


title: Bj_paraquat fulminant shock vs. no treatment_Rep2_dyeswap

source_name: Paraquat fulminant shock treatment_Replication 2

value: USDA 110', 'Treatment type:paraquat', 'Treatment concentration:5 mM', 'Treatment time:10 minutes' 'Media:Arabinose-Gluconate'

source_name: No Treatment_Replication 2

value: USDA 110' 'Treatment type:None' 'Media:Arabinose-Gluconate'


title: 36h_Con_3


title: 60h_Con_2


title: 36h_Con_2


title: 36h_Con_1


title: 12h_UV_3


title: 12h_Con_3

value: reference


title: 36h_UV_3


title: Rbfox1 KO, biological rep1

value: 1 mo

value: brain


title: 12h_UV_1


title: 36h_UV_2


title: 12h_Con_2


title: 12h_Con_1


title: 36h_UV_1


title: 12h_UV_2