title: epiRIL488_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=511503_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=511527_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: epiRIL488_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: epiRIL480_Col_BC1-S7_IP vs WT_Col_INPUT

status: Public on Sep 03 2012

type: genomic

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=359196_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388777_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

molecule: genomic DNA

organism: Arabidopsis thaliana

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.

treatment_protocol: no treatment

tag: ecotype

tag: age

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

tag: developmental stage

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: epiRIL480_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: epiRIL473_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=359196_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388777_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.

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

extract_protocol: epiRIL473_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: epiRIL466_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=450036_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449931_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: epiRIL466_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: epiRIL458_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=450036_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449931_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: epiRIL458_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: epiRIL471_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465372-3_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465397-3_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: epiRIL471_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: epiRIL467_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448459_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448304_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: epiRIL467_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: epiRIL438_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429782_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429761_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: epiRIL438_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: epiRIL454_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388458_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388466_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: epiRIL454_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: epiRIL437_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465394_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465397_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: epiRIL437_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: epiRIL439_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448301_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448300_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: epiRIL439_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: epiRIL410_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429945_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429943_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: epiRIL410_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: epiRIL366_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448374_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448353_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: epiRIL366_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: epiRIL368_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465404-2_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465404-2_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: epiRIL368_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: epiRIL434_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429894_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429893_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: epiRIL434_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: epiRIL425_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465372-2_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465397-2_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: epiRIL425_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: epiRIL393_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429805_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429775_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: WT_Col_INPUT: DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL393_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: epiRIL394_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429945_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429943_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: epiRIL394_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: epiRIL363_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465372-3_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465397-3_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: epiRIL363_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: epiRIL432_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448374_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448353_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: epiRIL432_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: epiRIL371_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388458_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388466_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: epiRIL371_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: epiRIL375_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429795_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429786_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: epiRIL375_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: epiRIL391_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388464_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388463_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: epiRIL391_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: epiRIL362_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=465406-2_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=465394-2_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: epiRIL362_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: epiRIL361_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388447_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=383565_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: epiRIL361_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: epiRIL408_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429805_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429775_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: epiRIL408_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: epiRIL477_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448374_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448353_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: epiRIL477_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: epiRIL356_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449881_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449879_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: epiRIL356_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: epiRIL350_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449878_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449803_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: epiRIL350_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: epiRIL400_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=430329_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=430117_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: epiRIL400_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_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=389996_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=389573_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: epiRIL344_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: epiRIL326_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=430329_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=430117_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: epiRIL326_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: epiRIL340_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449928_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449887_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: WT_Col_INPUT: DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor.

extract_protocol: epiRIL340_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: epiRIL305_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448448_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448447_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: epiRIL305_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: epiRIL323_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388447_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=383565_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: epiRIL323_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: epiRIL333_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388629_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388615_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: epiRIL333_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: epiRIL276_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449611_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449193_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: epiRIL276_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: epiRIL297_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448352_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448316_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: epiRIL297_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: epiRIL275_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388487_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388484_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: epiRIL275_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: epiRIL252_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429872_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448090_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: epiRIL252_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: epiRIL238_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388451_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388657_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: epiRIL238_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: epiRIL229_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429894_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429893_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: epiRIL229_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: epiRIL262_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=511503_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=511527_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: epiRIL262_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: epiRIL260_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388487_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388484_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: epiRIL260_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: epiRIL258_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448352_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448316_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: epiRIL258_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: epiRIL232_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=389197_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=389295_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: epiRIL232_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: epiRIL277_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=430073_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=430069_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: epiRIL277_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: epiRIL195_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=388454_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=388453_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: epiRIL195_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: epiRIL225_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429888_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429771_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: epiRIL225_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: epiRIL183_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448459_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448304_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: epiRIL183_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: epiRIL257_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=430329_635_A01.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=430117_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: epiRIL257_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: epiRIL215_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=448079_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=448069_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: epiRIL215_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: epiRIL222_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=389996_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=389573_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: epiRIL222_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: epiRIL193_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=449881_635_A02.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=449879_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: epiRIL193_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: epiRIL216_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=358095_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=358094_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: epiRIL216_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: epiRIL208_Col_BC1-S7_IP vs WT_Col_INPUT

description:
Methylome analysis in dye-swap. 1st hybridization raw data:  IP=429953_635_A03.pair - INPUT=INPUTwt_532_3rep.pair ; swap raw data: IP=429952_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: epiRIL208_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.