title: UTX knockout (KO) cell line 2

first: Chaochen

last: Wang

address: 9000 Rockville Pike

department: LGP

institute: NIDDK

description: Gene expression data from KO2 ES cells

hyb_protocol: standard Affymetrix hyb protocol

scan_protocol: standard Affymetrix scan protocol

data_processing: The data were normalized by the  methods Microarray Suite version 5.0 (MAS 5.0)

source_name: embryonic stem cells

label_protocol: standard Affymetrix label protocol

growth_protocol: Mouse ES cells were maintained on irradiated embryonic fibroblast feeder cells and cultured in ES medium (DMEM supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 0.1 mM  nonessential amino acids, 50 u/ml Penicillin/Streptomycin, 15% ES cell-qualified FBS, and 1000 u/ml LIF (Millipore)). Cells were passaged twice on 0.1% gelatin-coated dishes to remove feeder cells and then cultured in ES medium on gelatin-coated dishes.

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNeasy mini kit purification was performed according to the manufacturer's instructions.

tag: cell

value: ES cells

value: UTX knockout


title: UTX conditional knockout (cKO) cell line 2

status: Public on Sep 04 2012

type: RNA

city: Bethesda

state: MD

country: USA

description: Gene expression data from cKO2 ES cells

label: biotin

molecule: total RNA

organism: Mus musculus

tag: genotype/variation

value: UTX conditional knockout


title: UTX knockout (KO) cell line 1

description: Gene expression data from KO1 ES cells


title: Hu_hipp_6

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing:
R (expresso), quantile normalization:
bgcorrect.method=mas
normalize.method=quantiles
pmcorrect.method=mas

organism: Homo sapiens

label_protocol: Affymetrix

extract_protocol: Qiagen Rneasy kit

tag: brain region

value: hipp

tag: sample identifier


title: NC1, biological replicate 6

city: Iowa City

first: Shyam

last: Ramachandran

address: 240G EMRB

department: Pediatrics

institute: Univ of Iowa

hyb_protocol: The resultant biotinylated cRNA is fragmented and then hybridized to The GeneChip® Porcine Genome Array. The GeneChip® Porcine Genome Array provides comprehensive coverage of the Sus scrofa transcriptome. The array contains 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes.

scan_protocol: The arrays are washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner using the manufacturer’s recommended protocols, and the data collected using the GeneChip Operating Software (GCOS), v.1.4.

data_processing: Data processing and analysis was performed using the Partek Genomics Suite v.6.3 (RMA normalization).

label_protocol: Total RNA (5 μg) is processed using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix) according to the manufacturer’s recommended protocols.

growth_protocol: Calu-3 cells were grown in complete mendia

extract_protocol: TriZOL and manufacturer's recommended protocol was followed to extract RNA from primary cultures

treatment_protocol: Cells were transfected with oligonucleotides using lipofectamine RNAiMAX.

tag: cell line

tag: cell type

value: airway epithelia cells


title: miR-138 mimic, biological replicate 1

description: miR-138 mimic-1

source_name: Calu-3_miR-138 mimic

tag: treated with

value: miR-138 mimic


title: NC1, biological replicate 5


title: UTX conditional knockout (cKO) cell line 1

description: Gene expression data from cKO1 ES cells


title: 2_TNwt_a

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: group 2

hyb_protocol: hybridization was performed according to standard Affymetrix procedure

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: probesets were summarized and probeset-level values normalized with rma(target=core) function from R/Bioconductor package oligo (version 1.14.0)

source_name: Terminal neurons (TN)

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

growth_protocol: Wildtype, RESTko or RESTwt embryonic stem cells were differentiated into neuronal progenitors and/or terminal neurons as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)).

extract_protocol: Total RNA was prepared using TRIzol (Invitrogen) and Rneasy kit from Qiagen (for RNA cleanup)

tag: strain

value: mixed 129Sv-C57Bl/6

value: Terminal neurons (TN)

value: wildtype

tag: biological replicate

value: a


title: Hu_caud_6

value: caud


title: 2_NPwt_b

description: group 2

source_name: Neuronal progenitors (NP)

value: Neuronal progenitors (NP)

value: b


title: SIN3A siRNA, biological replicate 3

source_name: Calu-3_SIN3A siRNA

value: SIN3A siRNA


title: Hu_hipp_5


title: 2_TNwt_b

description: group 2


title: 2_NPwt_a

description: group 2


title: Hu_hipp_4


title: SIN3A siRNA, biological replicate 2


title: 2_ESwt_b

description: group 2

source_name: Embryonic Stem Cells (ESCs) wildtype

value: Embryonic Stem Cells (ESCs)


title: miR-138 mimic, biological replicate 3

description: miR-138 mimic-3


title: young non-growng oocyte-2

city: Setagaya

first: Maki

last: Kusumi

state: Tokyo

department: Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

description: Young non-growing oocyte-2 were derived from 6-8-week-old C57BL/6 mice. The oocytes were selected as the diameter of smaller than 60 um.

hyb_protocol: according to manufacturer protocol

scan_protocol: Microarray slides were scanned at 5-um resolution using an Agilent microarray scanner G2565BA (Agilent technology).

data_processing: Exactly 100ng of total RNA were used for each samples. The resulting images were quantified using Agilent Feature Extraction Software V 9.5. The signal =< 10 and negative were normalized to 0.

label: cyanine 3

source_name: young non-growing oocyte-2

label_protocol: according to manufacturer protocol

extract_protocol: Total RNAs were isolated using mirVana miRNA Isolation Kit (Applied Biosystems).

tag: age

value: 6-8 weeks old

tag: tissue

value: oocytes

tag: developmental stage

value: promordial follicle (20-50um diameter)


title: young non-growing oocyte-1

description: Young non-growing oocyte-1 were derived from 6-8-week-old C57BL/6 mice. The oocytes were selected as the diameter of smaller than 60 um.

source_name: young non-growng oocyte-1


title: aged growing oocyte-2

description: Aged growing oocyte-2 were derived from 42-44-week-old C57BL/6 mice. The oocytes were selected as the diameter of more than 60 um.

source_name: aged growing oocyte-2

value: 41-43 weeks old

value: growing (60-80um diameter)


title: aged growing oocyte-1

description: Aged growing oocyte-1 were derived from 42-44-week-old C57BL/6 mice. The oocytes were selected as the diameter of more than 60 um.

source_name: aged growing oocyte-1


title: Hu_FP_2

value: FP


title: NC1, biological replicate 3

value: airway epithelia cells


title: Hu_FP_3


title: Hu_caud_5


title: SIN3A siRNA, biological replicate 1


title: 2_ESwt_a

description: group 2


title: leukemia rep3

city: La Jolla

first: Dong-Er

last: Zhang

state: CA

address: 3855 Health Sciences Drive, Mail Stop 0815

department: Cancer Center

institute: University of California San Diego

description: Gene expression data from Lin-/Sca1-/cKit+ cells of AE9a leukemia mice.

hyb_protocol: Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps (see the attached EXP files).

data_processing: The data were analyzed using the RMA algorithm. Affymetrix default analysis settings and global scaling were used as normalization method.

source_name: MF1 AE9a leukemia mouse #3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen RNeasy Mini column extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: AE9a leukemia mice were generated by transplantation of AE9a transduced hematopoietic progenitor cells into lethally-irradiated adult MF1 mice.

value: spleen

tag: genotype

value: wild-type mouse transplanted with AE9a transduced hematopoietic progenitor cells

value: 12-16 weeks old

value: Lin-/Sca1-/cKit+ cells


title: young growing oocyte-2

description: Young growing oocyte-2 were derived from 6-8-week-old C57BL/6 mice. The oocytes were selected as the diameter of more than 60 um.

data_processing: The resulting images were quantified using Agilent Feature Extraction Software V 9.5. Exactly 100ng of total RNA were used for each samples. The signal =< 10 and negative were normalized to 0.

source_name: young growing oocyte-2


title: leukemia rep2

scan_protocol: Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps (see the attached EXP files).

source_name: MF1 AE9a leukemia mouse #2


title: young growing oocyte-1

description: Young growing oocyte-1 were derived from 6-8-week-old C57BL/6 mice. The oocytes were selected as the diameter of more than 60 um.

source_name: young growing oocyte-1


title: NC1, biological replicate 2


title: Hu_caud_4


title: Pt_caud_2

organism: Pan troglodytes


title: Hu_FP_4


title: 2_TN_RESThet_c

growth_protocol: REST wildtype, REST heterozygous knock-out and REST knock-out embryonic stem cells were differentiated into terminal neurons as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)).

value: Black Agouti 129

value: Terminal neurons (TN)

value: RESThet

value: c


title: wild-type rep3

description: Gene expression data from Lin-/Sca1-/cKit+ cells of wild-type mice.

source_name: MF1 wild-type mice

value: bone marrow

value: wild-type


title: NC1, biological replicate 1


title: leukemia rep1

source_name: MF1 AE9a leukemia mouse #1


title: Hu_hipp_3

value: hipp


title: Hu_caud_3

value: caud


title: wild-type rep2


title: wild-type rep1


title: MCF7_MIR9_2X_3

city: Galway

first: Charles

last: Spillane

state: Galway

address: University Road

department: Botany and Plant Science

country: Ireland

institute: National University of Ireland, Galway

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All data was variance stabiliziation transformed and between chip robust spline normalized using the lumi package in Bioconductor

label_protocol: Standard Illumina labeling protocol

growth_protocol: MCF-7 cells were grown in DMEM, supplemented with 10% fetal bovine serum and 1% pen/strep

extract_protocol: RNA was extracted with Trizol reagent, DNase treatment was done with Turbo DNA-free kit in accordance with the prescribed protocol provided with the kit. Sampes were cleaned using isopropanol precipitation method. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with 12.5nM (1X) and 25nM (2X) of pre-9 (mir-9 mimic) or pre-ctr (scrambled control mimic) in 3 biological relicates. 48 hours post-transfection RNA was extracted.

value: epithelial breast cancer cell line

tag: treatment

value: MIR9 2X


title: Hu_hipp_2


title: miR-138 mimic, biological replicate 2

description: miR-138 mimic-2

value: miR-138 mimic


title: 2_TN_RESThet_b

value: b


title: 2_TN_RESTko_c

value: RESTko


title: MCF7_MIR9_2X_2

description: replicate 2


title: MCF7_MIR9_2X_1

description: replicate 1


title: MCF7_MIR9_1X_3

description: replicate 3

value: MIR9 1X


title: Hu_caud_1


title: MCF7_MIR9_1X_2

description: replicate 2


title: 2_TN_RESTko_b


title: Hu_hipp_1


title: 2_TN_RESThet_a

value: a


title: Hu_FP_1

value: FP


title: Mm_FP_4

organism: Macaca mulatta


title: 2_TN_RESTko_a


title: 1_ES_RESTwt_c

source_name: Embryonic Stem Cells (ES)

value: Embryonic Stem Cells (ES)

value: RESTwt


title: MCF7_CTR_2X_3

description: replicate 3

value: CTR 2X


title: Hu_caud_2


title: 1_ES_RESTwt_b

value: Black Agouti 129


title: LMN-1 vs GFP DamID- set-25(n5021) met-2(n4256)-replica#3

type: genomic

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

description: enrichment of chromatin at the nucelar lamina

hyb_protocol: Hybridization was performed according to standard Nimblegen procedure  (http://www.nimblegen.com/products/lit/06584098001_NG_Epigenetics_UGuide_v1p0.pdf)

scan_protocol: Scanning was performed with NImbleScan (NimbleGen MS 200 microarray scanner)

data_processing: The arrays were loess normalized using the package Ringo

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: LMN-1-DamID from set-25(n5021) met-2(n4256) C. elegans embryos

label_protocol: According to Nimblegen guidelines (http://www.nimblegen.com/products/lit/06584098001_NG_Epigenetics_UGuide_v1p0.pdf)

growth_protocol: 35000 L1 larvae were grown synchronously to adults in 50mL S-medium containing dam- GM119 E. coli strain as food source. Embryonic progeny was  harvested from adult worms using hypochlorite treatment

extract_protocol: Wild-type and set-25 met-2 strains carrying identical single-copy LMN-1-Dam or GFP-Dam constructs were grown in parallel and in three independent biological replicates. For each of the twelve cultures, 35000 L1 larvae were grown synchronously to adults in 50mL S-medium containing dam- GM119 E. coli strain as food source under  ontinuous agitation (180rpm) at 20º C for 66h. Embryonic progeny was harvested from adult worms using hypochlorite treatment and genomic DNA (gDNA) was  purified from 30mg of embryos. Methylated fragments were amplified from 5μg of gDNA by sequential DpnI / DpnII digest, adaptor ligation and PCR using adaptor-specific primers as described (Greil et al., 2006). 1μg of PCR product of LMN-1-Dam and GFP-Dam samples were fluorescently labeled and competitively hybridized on NimbleGen  C. elegans whole genome-tiling arrays (NimbleGen_Celegans_2.1M array).

tag: transgene

value: LMN-1 DamID

tag: genetic background

value: whole embryo

tag: gender

value: hermaphrodite

value: early embryo

tag: growth temperature

source_name: GFP-DamID from set-25(n5021) met-2(n4256) C. elegans embryos

value: GFP-DamID


title: NC1, biological replicate 4

value: airway epithelia cells


title: 1_ES_RESTko_c

tag: genotype/variation

value: c


title: 1_ES_RESTko_a


title: LMN-1 vs GFP DamID-wildtype-replica#2

source_name: LMN-1-DamID from wild-type C. elegans embryos

value: wildtype

source_name: GFP-DamID from wild-type C. elegans embryos


title: MCF7_CTR_1X_3

description: replicate 3

value: epithelial breast cancer cell line

value: CTR 1X


title: MCF7_CTR_2X_1

description: replicate 1


title: Mm_FP_3

tag: brain region


title: LMN-1 vs GFP DamID-wildtype-replica#1


title: 1_ES_RESTko_b

value: RESTko

value: b


title: MCF7_CTR_1X_2

description: replicate 2


title: MCF7_CTR_2X_2

description: replicate 2


title: Mm_caud_4

value: caud

tag: sample identifier


title: LMN-1 vs GFP DamID-wildtype-replica#3


title: LMN-1 vs GFP DamID- set-25(n5021) met-2(n4256)-replica#2


title: Mm_hipp_4

value: hipp


title: Mm_hipp_3


title: 1_NP_RESTwt_c

description: group 1

source_name: Neuronal progenitors (NP)

value: Neuronal progenitors (NP)

value: RESTwt


title: MCF7_CTR_1X_1

description: replicate 1


title: Mm_FP_2

value: FP


title: Mm_hipp_2


title: 1_NP_RESTwt_b

description: group 1

value: Black Agouti 129


title: 1_ES_RESTwt_a

value: Embryonic Stem Cells (ES)

value: a


title: Mm_caud_3


title: Mm_caud_1


title: 1_NP_RESTko_b

description: group 1


title: 1_NP_RESTko_c

description: group 1


title: single (control) plants rep2

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

hyb_protocol: The (#900720) GeneChip Hybridization, Wash and Stain Kit was used for hybridization, washing, staining and scanning of the chips.

scan_protocol: The software program Affymetrix 'GeneChip Command Console (v3.1)' was used to operate the staning, washing and scanning of the GeneChips and visual inspection of the array images. Chips were scanned using the Affymetrix 3000G scanner.

data_processing: Data were processed using the Bioconductor packages in R (version 2.15.0) and using the RMA normalization algorithm.

organism: Arabidopsis thaliana

source_name: Arabidopsis petioles_single grown

label_protocol: The Affymetrix 3'IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labelling reactions.

growth_protocol: Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (180 µmol / m2 / s, 20°C, 70% RH), 15 h dark) where they were transferred to individual pots after 10 d and grown until canopies reached a leaf area index = 0.9 (approx. 23 days after sowing).

extract_protocol: Total RNA was isolated from homogenized material using the RNeasy plant mini kit (Qiagen) with on-column DNA digestion following the company’s instructions.

treatment_protocol: Plants were grown single in pots that were either kept separate (single plants; control) or places in a 2066 plants / m2 dense canopy directly after transfer to these pots. 2 young petioles per plant were harvested in liquid N2 and petioles from 4 plants were pooled per biological replicate.

value: petiole


title: 5798

status: Public on Sep 03 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Patients with X-linked intellectual disability (XLID)

hyb_protocol: Dye incorporations of post-labeling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies). Fluorescent-labeled reference and disease DNAs were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and were hybridized to Human custom Ag-VIBxp1122v2-4X44 CGH Microarray (Agilent Technologies). Slides were hybridized using a Hybridization gasket slide (Agilent Technologies), placed in rotisserie (20 RPM rotation speed) in the hybridization oven at 65° C for 24 hrs (Agilent Technologies). After hybridization the slides were washed with Agilent washing solutions (including Stabilization and Drying solutions), according to Agilent Oligonucleotide array-based CGH for genomic DNA analysis protocol (version 6.0).

scan_protocol: After washing, the slides were scanned at 5 µm resolution by using a DNA microarray scanner (Agilent Technologies). Scan settings: Scan region was set to Scan Area (61 × 21.6 mm), Green PMT was set to 100%, Red PMT was set to 100%. Images were processed with the Feature Extraction Software version 9.5.3.1 (Agilent Technologies).

data_processing: Prior to normalization, data from control and empty spots was removed. Due to the large number of probes on the X chromosome that are duplicated, the Loess based normalization as Prior to normalization, data from control and empty spots was removed. Due to the large number of probes on the X chromosome that are duplicated, the Loess based normalization as performed within the Agilent Feature extraction software (version 9.5.3.1) fails. Therefore, we fit the Loess regression line through a subset of the data, i.e., those probes that are not located in the region that is expected to be duplicated/deleted. We base ourselves on the uncorrected intensities obtained with the Agilent Feature extraction software (version 9.5.3.1) and we base our Loess fit on the subset of clones that map outside of the region 52.8 and 54.0Mb on the X chromosome. We omit data from unmapped clones and from spots that were not above background in both channels. The presented values are log-(Cy5/Cy3)-ratios. In case of multiple probes for the same Agilent ID, log-ratios were averaged.

source_name: FTD-XY

label_protocol: 500 ng genomic DNA was digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy5-dUTP using the Agilent Genomic DNA Labeling kit PLUS (Agilent Technologies). Briefly, 50 ul reaction mix was incubated with Exo-Klenow Fragment at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.

extract_protocol: Genomic DNA from patients as well as from healthy controls was isolated from peripheral blood using the Wizard Genomic DNA purification Kit (Promega, Madison, WI) and using manufacturer’s protocol.

value: male

value: white blood cells

label_protocol: 500 ng genomic DNA was digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP using the Agilent Genomic DNA Labeling kit PLUS(Agilent Technologies). Briefly, 50 ul reaction mix was incubated with Exo-Klenow Fragment at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.


title: Mm_hipp_1


title: LMN-1 vs GFP DamID- set-25(n5021) met-2(n4256)-replica#1

value: LMN-1 DamID

value: whole embryo

value: hermaphrodite

value: early embryo

value: GFP-DamID


title: single (control) plants rep3


title: single (control) plants rep1


title: 5797


title: Mm_FP_1


title: 5484


title: MCF7_MIR9_1X_1

description: replicate 1

value: epithelial breast cancer cell line

value: MIR9 1X


title: 1_NP_RESTko_a

description: group 1

value: RESTko


title: 5482


title: 5795


title: 5796

source_name: AZ-XY


title: 5485


title: canopy plants rep1

source_name: Arabidopsis petioles_dense canopy


title: canopy plants rep2


title: canopy plants rep3


title: 5483


title: 1_NP_RESTwt_a

description: group 1

value: Neuronal progenitors (NP)


title: epiRIL579_Col_BC1-S7_IP vs WT_Col_INPUT

city: PARIS

first: Vincent

last: Colot

address: 46 rue d'Ulm

country: France

institute: IBENS - CNRS UMR8197 - INSERM U1024

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465404-3_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465394-3_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

hyb_protocol: Co-hybridization was performed using the NimbleGen 3x720K array design and following manufacturer's instructions

scan_protocol: Data acquisition was performed according to Roche Nimblegen instructions.

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-wt input signal as a common input for all samples. For each sample one extra dye-swap experiment was available except for the parents (3 and 2 dye-swapped replicates for Col-wt and Col-ddm1 respectively). The dye-swapped replicates were in all cases averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

label: Cy3, Cy5

label_protocol: INPUT DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit according to manufacturer's instructions. Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer's instructions.

growth_protocol: Replicates 1 and 2 : 12 days-old seedlings grown in liquid media, 16 hours photoperiod. Replicate 3 : Aerial parts of 21 day-old plants grown in soil, 16 hours photoperiod.

extract_protocol: WT_Col_INPUT: DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor.

treatment_protocol: no treatment

tag: ecotype

value: 12 days for replicates 1 and 2, 21 days for replicate 3

value: Seedlings for replicates 1 and 2, aerial part for replicate 3

tag: antibody

value: none (input)

label: Cy5, Cy3

label_protocol: IP DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit according to manufacturer's instructions. Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer's instructions.

extract_protocol: epiRIL579_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

value: 21 days

value: aerial parts

tag: vendor

value: Diagenode

tag: catalog#


title: Mm_caud_2

value: caud


title: WT_Col_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=IPwt_635_3rep.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=IPwt_532_3rep.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. The 3 dye-swapped replicates were averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

extract_protocol: WT_Col_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL567_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465404-3_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448851-3_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

growth_protocol: Aerial parts of 21 day-old plants grown in soil, 16 hours photoperiod.

extract_protocol: epiRIL567_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: ddm1_Col_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=IPddm1_635_2rep.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=IPddm1_532_2rep.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-wt input signal as a common input for all samples. The 2 IP replicates dye-swapped were averaged. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

label_protocol: INPUT DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit according to manufacturer's instructions. Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions.

growth_protocol: Replicate 1 : 12 days-old seedlings grown in liquid media, 16 hours photoperiod. Replicate 2 : Aerial parts of 21 day-old plants grown in soil, 16 hours photoperiod.

extract_protocol: ddm1_Col_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

value: 12 days for replicate 1, 21 days for replicate 2

value: Seedlings for replicate 1, aerial part for replicate 2


title: epiRIL556_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465399-2_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465399-2_532_A02.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL556_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL570_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448079_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448069_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL570_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL497_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429932_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429889_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL497_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL539_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429785_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429785_532_A02.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL539_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL572_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448301_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448300_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL572_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL573_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=450036_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449931_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL573_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL344_BC1-S6_IP vs epiRIL344_BC1-S6_INPUT

description: Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465552_635_A03.pair - INPUT=465552_532_A03.pair ; swap raw data: IP=465397_532_A01.pair - INPUT=465397_635_A01.pair

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-epiRIL344_BC1-S6 input signal as a common input for all samples. For each sample one extra dye-swap experiment was available except for the parents (3 and 2 dye-swapped replicates for Col-epiRIL344_BC1-S6 and Col-ddm1 respectively). The dye-swapped replicates were in all cases averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

growth_protocol: leaves of 21 day-old plants grown in soil, 16 hours photoperiod.

extract_protocol: epiRIL344_BC1-S6_INPUT: DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor.

value: leaves

extract_protocol: epiRIL344_BC1-S6_IP. DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL559_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465372-3_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465397-3_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL559_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL561_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448470_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449787_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL561_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL506_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449878_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449803_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL506_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL344_BC1-S3_IP vs epiRIL344_BC1-S3_INPUT

description: Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465398_635_A03.pair - INPUT=465398_532_A03.pair ; swap raw data: IP=465399_532_A03.pair - INPUT=465399_635_A03.pair

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-epiRIL344_BC1-S3 input signal as a common input for all samples. For each sample one extra dye-swap experiment was available except for the parents (3 and 2 dye-swapped replicates for Col-epiRIL344_BC1-S3 and Col-ddm1 respectively). The dye-swapped replicates were in all cases averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

extract_protocol: epiRIL344_BC1-S3_INPUT: DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL344_BC1-S3_IP. DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL494_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=511503-2_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=511527-2_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: WT_Col_INPUT: DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL494_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL558_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448448_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448447_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL558_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL344_BC1-S4_IP vs epiRIL344_BC1-S4_INPUT

description: Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465552_635_A01.pair - INPUT=465552_532_A01.pair ; swap raw data: IP=465402_532_A01.pair - INPUT=465402_635_A01.pair

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-epiRIL344_BC1-S4 input signal as a common input for all samples. For each sample one extra dye-swap experiment was available except for the parents (3 and 2 dye-swapped replicates for Col-epiRIL344_BC1-S4 and Col-ddm1 respectively). The dye-swapped replicates were in all cases averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

extract_protocol: epiRIL344_BC1-S4_INPUT: DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL344_BC1-S4_IP. DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL495_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429932_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429889_532_A02.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL495_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL344_BC1-S2_IP vs epiRIL344_BC1-S2_INPUT

description: Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465398_635_A02.pair - INPUT=465398_532_A02.pair ; swap raw data: IP=465399_532_A02.pair - INPUT=465399_635_A02.pair

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-epiRIL344_BC1-S2 input signal as a common input for all samples. For each sample one extra dye-swap experiment was available except for the parents (3 and 2 dye-swapped replicates for Col-epiRIL344_BC1-S2 and Col-ddm1 respectively). The dye-swapped replicates were in all cases averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

extract_protocol: epiRIL344_BC1-S2_INPUT: DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL344_BC1-S2_IP. DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL538_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449928_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449887_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL538_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL503_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429887_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429884_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL503_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL492_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449928_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449887_532_A02.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL492_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL500_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388458_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388466_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL500_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL523_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388629_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388615_532_A02.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL523_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL493_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429945_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429943_532_A03.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL493_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL344_BC1-S5_IP vs epiRIL344_BC1-S5_INPUT

description: Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465552_635_A02.pair - INPUT=465552_532_A02.pair ; swap raw data: IP=465402_532_A02.pair - INPUT=465402_635_A02.pair

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-epiRIL344_BC1-S5 input signal as a common input for all samples. For each sample one extra dye-swap experiment was available except for the parents (3 and 2 dye-swapped replicates for Col-epiRIL344_BC1-S5 and Col-ddm1 respectively). The dye-swapped replicates were in all cases averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

extract_protocol: epiRIL344_BC1-S5_INPUT: DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL344_BC1-S5_IP. DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL508_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465404-3_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448851-3_532_A01.pair - INPUT=INPUTwt_635_3rep.pair
Raw files INPUTwt_532_3rep.pair, INPUTwt_635_3rep.pair are linked as supplementary files on the Series record.

extract_protocol: epiRIL508_Col_BC1-S7_IP. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: epiRIL344_BC1-S1_IP vs epiRIL344_BC1-S1_INPUT

description: Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465398_635_A01.pair - INPUT=465398_532_A01.pair ; swap raw data: IP=465399_532_A01.pair - INPUT=465399_635_A01.pair

data_processing: The rescaling of the MeDIP data was done using R computing software (version 2.10.1) as described in [1]. Signals were re-expressed as log2 ratios of IP and INPUT signal. We used the averaged Col-epiRIL344_BC1-S1 input signal as a common input for all samples. For each sample one extra dye-swap experiment was available except for the parents (3 and 2 dye-swapped replicates for Col-epiRIL344_BC1-S1 and Col-ddm1 respectively). The dye-swapped replicates were in all cases averaged to account for possible dye bias. We standardized the overall signal distribution by expressing it in terms of the standard deviation of the intron probe signal distribution (probes that match with intron sequences). This has the effect of placing the mean of the intron probe signal at zero and rescaling the values as standard deviation values. We applied a HMM model to the data to call methylated, intermediate methylated and unmethylated probes, as described in [1]. We used the signal distribution of the probes that match with intron sequences to obtain the emission probability of the unmethylated hidden state (intron sequences are in general unmethylated). The signal distribution of the introns was approximated with a mixture of 30 Gaussian distributions (estimation was carried with the EM algorithm [2], which was implemented in R). The emission probability of the methylated hidden state was a Gaussian with mean fixed at the 99th quantile of the emission probability of the unmethylated state (i.e. the signal distribution for introns) and the variance of the distribution was estimated (Baum-Welch algorithm [3,4]). The emission probability for the intermediate methylated probes was a Gaussian with mean fixed between the mean of the emission probability of the unmethylated hidden state (i.e. the intron distribution) and the mean of the emission probability of the methylated hidden state, and variance equal to the variance of the emission probability of the methylated hidden state. [1] Cortijo S, Wardenaar R, Colome-Tatche M, Johannes F and Colot V (2012) Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. In: McKeown P and Spillane C (Eds) Plant Epigenome: Understanding and Analysis, Humana Press/Springer: New York. [2] McLachlan and Peel (2000), Finite Mixture Models, John Wiley and Sons, ISBN: 0471006262, 9780471006268, New York. [3] Baum LE, T. Petrie, G. Soules, and N. Weiss (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains, Ann. Math. Stat., 41, 164–171. [4] Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-286

extract_protocol: epiRIL344_BC1-S1_INPUT: DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL344_BC1-S1_IP. DNA was extracted from leaves of 5 plants individually using the Qiagen MaxiPrep kit (Qiagen) then pooled and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.