title: TOTCONSLROOTE [E09_TOTAL]

extract_protocol:
For cellular mRNA, 35S:His6:FLAG-GFP-AtRPL18-5 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009. Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

value: polyA RNA


title: TRASUBSLSHOOTE [E02_TRAP]

status: Public on Sep 19 2019

type: SRA

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

country: USA

institute: Emory University

library_source: transcriptomic

data_processing:
Genome_build: Genome_build:  RICE: IRGSP-1.0-30 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html), MEDICAGO: Mt4.0 (http://www.medicagogenome.org/downloads), SOLANUM LYCOPERSICUM: ITAG3.10 (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/), SOLANUM PENNELLII: Spenn-ENA-HG975439-HG975452 (https://www.ebi.ac.uk/ena/data/view/HG975439-HG975452)
Rice and Medicago RNA-seq raw reads were aligned to the IGRSP-1.0-30 and Mt4.0 genome, respectively, with the splice junction aware short read alignment suite Bowtie2/Tophat2, allowing unique alignments with 2 or less mismatches
Rice and Medicago nRNA, polyadenylated total RNA, and polyadenylated TRAP RNA filtering was done by first aligning the reads to mitochondrial and chloroplast genomes before mapping to the nuclear genome
Rice and Medicago read count data for RNA-seq was generated for features of exons-by-genes using the summarize Overlaps function of the GenomicRanges package.
Solanum RNA-seq mapping was performed in the CyVerse Discovery Environment
Solanum nRNA-seq reads were filtered, using STAR v2.4.0.1, by first aligning to organelle sequences (S. lycoperscium AFYB01.1 mitochondrial sequence, S. lycopersicum NC_007898.3 chloroplast sequence, and S. pennellii HG74452 chloroplast sequence) and then to either S. lycopersicum ITAG3.10 or S. pennellii exonic sequences
Solanum read count data for RNA-seq was generated the est_count feature of eXpress v1.5.1
ATAC-seq raw reads were aligned to each species' corresponding genome using Bowtie2 with default parameters
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<2.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1"
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option
For accurate visualization, all filtered ATAC-seq bam files for a given tissue were scaled to the same number of reads and combined per condition to create a single merged bam file for a condition in a tissue type. The merged bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option
Filtered ATAC-seq bam files from genomic DNA samples were scaled to the total number of reads present in the merged bam files for a given tissue type. The scaled bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option
Supplementary_files_format_and_content: Reads per kilobase per million reads (RPKM) values for nRNA, polyA RNA or TRAP RNA datasets were calculated from count data after quantile normalization
Supplementary_files_format_and_content: .bed files contain Transposase Hypersensitive Site (THS) coordinates for individual samples or for each tissue type they are organized as (All) all the replicated THSs identified in that sample set in either control or submergence samples, (Up) THSs upregulated in submergence samples, and (Down) THSs downregulated in submergence samples
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples, or combined samples for a specific condition of a given tissue, at a resolution of 1 bp bin sized windows

molecule: total RNA

organism: Solanum lycopersicum

source_name: 7 days-old seedling shoot apical meristem

growth_protocol: For rice, seeds were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min, rinsed ten times with sterile distilled water and grown on plates (100 cm2) containing 0.5x Murashige and Skoog medium (MS), 1% (w/v) agar 1% (w/v) sucrose for 7 days (16h day / 8h night; at 28°C/25°C day/night; 110 μEm-2s-1). For tomato, seeds were surface sterilized in 50% (v/v) bleach solution for 5 min (S. pennellii) or 20 min (S. lycopersicum) and then rinsed three times with sterile distilled water. Growth was on vertical plates (10 cm x 10 cm) containing full-strength MS without vitamins, with 1% (w/v) agar (w/v) and 1% (w/v) sucrose.  Hairy root cultures of Agrobacterium rhizogenes transformed S. lycopersicum were initiated and cultivated as described (Ron et al. 2014). Cultures were subcloned using a 2-cm hairy root segment, grown on horizontal plates (10 cm x 10 cm) containing full-strength MS with vitamins, with 1% (w/v) agar (w/v) and 3% (w/v) sucrose, 200 mg/L kanamycin and 200 mg/L cefotaxime. All tomato root cultures or germinating seeds were grown for 7 days in a growth chamber (at 25°C, 16h day/8h night; 60-65 μEm-2s-1). M. truncatula seeds were surface-sterilized by incubating in concentrated sulfuric acid for 8 minutes with gentle stirring, washing 3 times with 4°C sterile, distilled water, then 4-8 minutes in 3% (w/v) hypochlorite (diluted bleach), washing 4 times with sterile, distilled water, and finally placing the seeds onto moist filter paper. Seeds were germinated without vernalization on moist filter papers in inverted Petri dishes wrapped with surgical tape wrapping. These were kept in the growth room in the dark at 20°C for 2 days. Hairy root composite M. truncatula plants were initiated by injecting with A. rhizogenes K599. To do so, the day before injection, a volume of fresh overnight culture of A. rhizogenes K599 carrying either 35S:NTF;AtACT2p:mBirA or 35S:His6-FLAG-GFP-MtRPL18-3 plasmid was used to inoculate  5 ml of Yeast Extract Beef media (5 g/L tryptone, 1 g/L yeast extract, 5 g/L nutrient broth, 5 g/L sucrose, 0.49 g/L MgSO4x7H2O, 15 g/L agar, pH=7.2) additionally containing 100 mg/L Spectinomycin and grown overnight at 28°C at 200 rpm. When the OD600 was equal to 1.0, cultures were centrifuged at 5000 rpm for 5 min. The supernatant was poured off and the pellet was resuspended in Injection Media (IM) (1X PBS, 100 uM acetosyringone, 1/10000 (v/v) Silwet). Seedlings germinating for 2.5-days were injected by placing them in 5 mL of IM-resuspended A. rhizogenes poured out on a Petri dish and stabbing the root a few times with an 18G1 needle. Additionally, 1-2 mm of the primary root tip was cut off. Injected seedlings were moved to slanted Fahräeus Media (FM) plates (0.5 mM MgSO4, 0.7 mM KH2PO4, 0.8 mM Na2HPO4, 50 nM FeEDTA, 0.5 mM NH4NO3, 1mM CaCl2, 0.1 mg of MnSO4, CuSO4, Zn SO4, H3BO3, and Na2MoO4, 8 g/L Phytoblend agar, pH 6.5) with no selection and were grown horizontally for 3 days, and then were moved to FM plates with 5 mg/L phosphinothricin and were grown vertically for 3 wk before transfer to 1X MS media without vitamins (1% w/v agar, 1% w/v sucrose). Plants were grown vertically for 1 wk before being used for the submergence experiment. The day before the experiment was performed, root tips from one plate were collected and visualized on a fluorescence stereomicroscope to check for GFP expression. Transformation efficiency was calculated as the percentage of root tips with ubiquitous GFP expression

extract_protocol:
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (Townsley et al 2014)
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

treatment_protocol:
Transgenic Solanum seeds from transgenic lines were surface sterilized in 50% (v/v) bleach solution for 5 min (S. pennellii) or 20 min (S. lycopersicum) and then rinsed three times with sterile distilled water. Seedlings were grown on plates (10 cm x 10 cm) containing full-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 7 days in a growth chamber (16 h day / 8 h night;  at 22°C/22°C day/night; 60-65 μEm-2s-1). For submergence treatment ("SUB"), plates were opened and placed horizontally under 5 cm of autoclaved distilled water at ZT 4h. Root tips (apical 1 cm) and shoot apical meristems were harvested at ZT 6h (2h before relative noon). Control plates ("CON") were not opened, but positioned similarly horizontally and also harvested at ZT 6h.
Four independent biological replicates were grown for each species. For whole plant submergence, plates were placed horizontally, opened and the seedlings covered with 5 cm of autoclaved distilled water at ZT 4h. Root tips (apical 1 cm; all four species) and the shoot apical meristem region (Solanum species) were harvested at ZT 6h (2h before relative noon). Control plates were not opened, but positioned horizontally for the duration of the treatment and harvested at ZT 6h. Oxygen partial pressure was measured with the NeoFox Sport O2 sensor and probe (Ocean Optics). The dissolved oxygen content in the water covering the plants remained above 18% (v/v) for the 2 h duration of the stress treatment

tag: cultivar

value: Solanum lycopersicum cv. M82

tag: line

tag: tissue

tag: experiment type

value: Random primed libraries

tag: molecule subtype

value: TRAP RNA


title: TOTSUBSLROOTE [E10_TOTAL]

source_name: 7 days-old seedling 1 cm roots tips

value: 7 days-old seedling 1 cm roots tips


title: D3_Control_siRNA_DOX_1 (ATAC-Seq)

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

library_source: genomic

data_processing:
Single-end ATAC-seq raw data were analysed using the ATAC-seq pipeline from the Kundaje lab (v1.1.5) with default parameters as described before (Lee et al., 2016). Reads were aligned to the ENCODE mouse reference genome GRCm38/mm10 (ENCSR425FOI).
Differential chromatin accessibility analysis was performed using the DiffBind (v2.10.0) and DESEQ2  (v1.21.22) package.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage, normalizing using RPKM with binsize 1

molecule: genomic DNA

organism: Mus musculus

source_name: MEF reprogramming intermediate

growth_protocol: MEFs were cultured in MEF medium (DMEM (Gibco, 41966-052) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10270-106), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140-122), 1% (v/v) GlutaMAX (Gibco, 35050-061), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140-050), and 0.8% (v/v) beta-mercaptoethanol (Sigma, M7522).

extract_protocol:
50,000 viable cells were pelleted at 500 RCF at 4°C for 5 min in a fixed angle centrifuge
ATAC-seq was performed using the Omni-ATAC protocol as described before (Corces et al., 2017; Song et al., 2018a). Libraries were pooled in equimolar amounts for single-end sequencing on an Illumina HiSeq 4000 instrument

treatment_protocol: 15,000 MEFs were plated at passage 1-2  in each well of a 12-well plate precoated with gelatin (from porcine skin, 0.1% g/v final, Sigma, G2500) in mouse ESC medium (S/L condition). Reprogramming was induced by addition of doxycycline (dox, final 2 µg/ml) for the next 12 to 15 days. Medium was replaced every two days.

tag: strain

value: Col1a1-tetO-OKSM, Rosa26-M2rtTA

tag: cell type

value: MEF reprogramming intermediate

tag: protocol

tag: agent

value: DOX

tag: time


title: TOTSUBSLSHOOTE [E02_TOTAL]

value: 7 days-old seedling shoot apical meristem


title: TRASUBSLROOTE [E10_TRAP]


title: RNA_Sis_pSSRgD_ClsN_post_rep1

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Kyoto University

data_processing:
Hi-C reads were mapped to the genome of S. acidocaldarius DSM639 (GenBank ID: CP000077.1) or S. islandicus REY15A (GenBank ID: CP002425.1) using HiC-Pro version 2.9.0 (Servant et al., 2015) with default parameters. The genomic coordinates of each Sulfolobus species were re-defined so that they started from the first base of the HindIII site in the original definition. For the overexpression experiment of ClsN, reads were also mapped to the sequence of pSSRgD-ClsN. Valid read were used to generate raw Hi-C matrices. The genome was binned at 15-kb for S. acidocaldarius and 30-kb for S. islandicus. The intra-bin ligations were discarded by setting the values on the corresponding diagonal to zero. The data were iteratively corrected with MAX_ITER = 500 and EPS = 0.1.
ChIP DNA and input DNA were mapped to the genome of S. acidocaldarius DSM639 or S. islandicus REY15A using Bowtie 2 version 2.3.2 with default parameters (Langmead and Salzberg, 2012). Multi-mapping reads were retained for downstream analyses. For a plasmid-containing strain of S. islandicus, reads were separately mapped to the genome or the corresponding plasmid. Read coverage on the chromosome was normalized with the number of reads mapped to the chromosome. To normalize read coverage on the plasmid, numbers of reads mapped to the chromosome and the plasmid were summed and used for read number normalization.
To calculate Transcripts Per Million (TPM), RNA-seq reads from each biological replicate were mapped to protein-coding genes in a strand-specific manner using Salmon version 0.8.2 (Patro et al., 2017).
For marker frequency analysis, reads were mapped to the S. isladicus REY15A genome as described previously (Samson et al., 2013). Read counts were grouped in 1-kb bins.
Genome_build: CP000077.1, CP002425.1
Supplementary_files_format_and_content: Hi-C: tab-delimited tables. The first and second columns show genomic bins. In plasmid-containing strains, bin 86 refers to a corresponding plasmid. The third column shows normalized interaction scores between bins in the first and second columns. ChIP-seq: tab-delimited tables. The first column shows the name of a chromosome or a plasmid. The second column shows coordinates on the chromosome or the plasmid. The third column shows normalized read coverages. RNA-seq: tab-delimited tables showing Transcripts Per Million (TPM) values for each protein-coding genes. Marker frequency analysis: tab-delimited tables showing read counts for each 1-kb bin.

organism: Saccharolobus islandicus

source_name: Microorganism

extract_protocol:
RNA was extracted from cells using the method described previously (Samson et al., 2008). After treatment with DNase, the RNA was ethanol-precipitated and dissolved in DEPC-treated water.
Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Sequencing was performed on the Illumina NextSeq 500 platform.

tag: genotype

value: DargD pSSRgD-ClsN

tag: developmental stage

value: 4-hour arabinose induction


title: B6.CAST_E6.5_Epi_H3K4me3_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
ChIP_Epi_ExE_RPKM.txt
B6.CAST_Epi_H3K4me3.txt
Allelic_H3K4me3_dedupH3K4me3peaks_Epi_Readcount.txt

data_processing:
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. Mapping of ChIP-Seq data was performed using Bowtie 2 v2.3.2 against N-masked genomes of the mouse GRCm38 assembly (Black6/CAST). The resulting hits were filtered to remove mappings with a MAPQ scores of < 20. Following alignment, reads were split allele-specifically using SNPsplit (v0.3.4, https://github.com/FelixKrueger/SNPsplit).
Peak calling for each histone mark in epiblast and ExE for B6/CAST and CAST/B6 reciprocal hybrids was done using chromstaR, using a bins size of 1kb and step size of 500bp
ChIP-seq relicates were quantitated as RPKM per 1kb running window
Allelic histone enrichment was calculated for each allelically mapped replicate over peaks (merging and deduplicating peaks from reciprocal hybrids for a given mark in a given tissue) as raw read counts
Genome_build: GRCm38
Supplementary_files_format_and_content: [ChIP RPKM report] Annotated SeqMonk report for 1kb running windows annotated to the nearest gene within 10kb. The report is tab-delimited probe coordinates and their log2(RPKM) values as follows: col 1: <ID>, col2: <Chromosome>, col 3: <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.
Supplementary_files_format_and_content: [Allelic peak report] Annotated SeqMonk report for peaks for the relevant mark and tissue, annotated to the nearest gene within 10kb. The report is tab-delimited probe coordinates and their log2(RPKM) values as follows: col 1: <ID>, col2: <Chromosome>, col 3: <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.
Supplementary_files_format_and_content: [Peak calling file] The peak calling files are tab delimited, and contain the following relevant information in columns 1-4: <chromosome>,<start>, <end>, <histone mark>

source_name: Epiblast

extract_protocol:
Reciprocal natural timed matings were set up between C57BL6/Babr and CAST animals (denoted as B6/CAST and CAST/B6), and embryos were collected on embryonic day 6.5 (E6.5).  Natural timed matings were set up between Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 +ve B6/129 females (resulting in ablation of DNA methylation in the oocyte) and CAST males (denoted as DKO.CAST). The epiblast (Epi) and extra-embryonic ectoderm (ExE) for each embryo were manually separated.  E6.5 epiblast (N=4) and ExE (N=8) samples were pooled (an estimated ~2500 cells), washed in PBS, and then flash frozen in 10µL of nuclear lysis buffer (Sigma).  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease (New England Biolabs) in prepared digestion buffer, as previously described (Brind'Amour et al. 2015 Nat Comm).  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with 100mM EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Prior to the immunoprecipitation with antibody-bound beads, each chromatin sample was divided into 5 aliquots: one for each antibody, one 10% input and one 10% input for bisulphite sequencing.  For each immunoprecipitation, 250ng of anti-H3K4me3 (Diagenode K02921004), 125ng of anti-H3K27me3 (Millipore 07-449) and 250ng of anti-H3K36me3 (C15410192) was used.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using solid phase reversible immobilization (SPRI) purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads (Fisher Scientific) at a 1.8:1 ratio.
Library preparation was completed using the MicroPlex Library Preparation kit v2 (Diagenode) using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations, and all libraries were amplified using 15 amplification cycles.  Libraries were purified with SPRI beads at a 1:1 ratio, and size and quality were assessed using a 2100 Bioanalyzer Instrument (Agilent) and Kapa library qPCR quantitation (Illumina).  Samples were multiplexed using 75bp paired-end sequencing on Illumina NextSeq500.

value: Epiblast

tag: age

value: Wildtype

tag: hybrid strain

value: C57BL6/Babr x CAST/Ei

tag: chip antibody

value: anti-H3K4me3 (Diagenode K02921004)


title: AT-4: Atheroesclerotic_pool4

type: RNA

city: Barcelona

first: Elena

last: Palà

address: Pg Vall d’Hebron 119-129

country: Spain

institute: Institut de Recerca Hospital Vall d’Hebron

description: Gene expression data from blood samples 4.5 hours after ischemic stroke

hyb_protocol: cDNA was hybridized in GeneChip Human Exon 1.0 ST arrays Affymetrix microarrays for 16 hours with rotation

scan_protocol: Microarrays were scanned in Affymetrix Genechip Scanner 3000

data_processing: The images were processed with the Affymetrix GeneChip Command Console software (Affymetrix) for CEL file generation. To check the array quality, Affymetrix Expression Console was used. Samples that demonstrated good quality results (pm mean, bgrd mean, pos vs neg auc, ...) were subjected to subsequent analysis. Raw expression values obtained directly from .CEL files were preprocessed using the RMA method.  Statistical language R and Bioconductor associated packages were used to process data.

label: biotin

organism: Homo sapiens

source_name: Blood buffy coat, LAA

label_protocol: Samples were amplified with Ovation Pico WTA kit (Nugen) and fragmented and labeled with Encore Biotin Module (Nugen).

growth_protocol: Blood buffy coat samples were frozen at -80°C until RNA isolation.

extract_protocol: Total RNA was isolated with the RiboPure-Blood kit (Ambion) and depleted with the GLOBINclear kit (Ambion)

treatment_protocol: Blood samples were collected into EDTA tubes within 4.5 hours from stroke onset. Buffy coat was collected after centrifugation at 1500 g, 4°C for 15 minutes and mixed with RNAlater solution (Ambion).

tag: diagnosis

value: ischemic stroke

value: blood

tag: # pooled samples

tag: average age


title: Parent line vehicle-treated 2

city: Palo Alto

first: Joseph

middle: Riley

last: Knoedler

state: CA

address: 1201 Welch Road

department: Psychiatry and Behavioral Sciences

institute: Stanford Univesity

description: Parent line vehicle-treated 2

data_processing:
Bases were called using CASAVA.
Reads were filtered using FastQC, redundant reads were removed using custom scripts, and reads were aligned to the mm8 genome using Bowtie (parameters -t -q -5 2 -3 2 -l 34 -n 1 -m 1 -p7
Transcript abundant was quantified using DESeq.
Genome_build: mm8
Supplementary_files_format_and_content: Excel spreadsheet contains raw mapped read counts of all protein-coding transcripts for each sample. Counts are not normalized to library size (this is part of further DESeq analysis).

source_name: HT22 parent cell line

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Stably transfected cells (HT22[TR/TO-Klf9] were maintained in media with zeocin and blasticidin.

extract_protocol:
Total RNA was extracted using TRIzol according to manufacturer’s instructions. RNA pellets were resuspended in nuclease-free water.
Oligo-dT-primed RNA libraries were prepared using standard Illumina protocols

treatment_protocol: Cells were seeded in 6-well plates at a density of ~250,000 cells/well. 24 hours after plating cells were treated with either 0.5 μg/ml doxycycline or vehicle (DMSO) for 8 hours.

tag: cell line

value: pSV40-immortalized mouse hippocampal cell line


title: B6.CAST_E6.5_Epi_Input_1

tag: tissue


title: AT-2: Atheroesclerotic_pool2


title: AT-3: Atheroesclerotic_pool3


title: AT-1: Atheroesclerotic_pool1


title: B6.CAST_E6.5_Epi_H3K4me3_1


title: TOTCONSLSHOOTE [E01_TOTAL]

tag: cultivar

value: Solanum lycopersicum cv. M82

tag: line

tag: experiment type

value: polyA RNA


title: RNA_Sis_pSSRgD_post_rep1

tag: strain

value: DargD pSSRgD


title: B6.CAST_E6.5_Epi_H3K36me3_2

description:
ChIP_Epi_ExE_RPKM.txt
B6.CAST_Epi_H3K36me3.txt
Allelic_H3K36me3_dedupH3K36me3peaks_Epi_Readcount.txt


title: CE-7: Cardioembolic_pool7

source_name: Blood buffy coat, CE


title: RNA_Sis_pSSRgD_pre_rep1

value: Before arabinose induction


title: TRASUBHAIRYROOTT3D [D18_TRAP]

source_name: hairy root culture 1cm root tips

treatment_protocol:
Hairy root lines were generated as described (Ron et al. 2014) and grown on horizontal plates (10 cm x 10 cm) containing full-strength MS with vitamins, with agar (1% w/v) and 3% w/v sucrose, 200 mg/L kanamycin and 200 mg/L cefotaxime. Subcloned roots were grown horizontally for 7 days in a growth chamber (16 h day / 8 h night;  at 22°C/22°C day/night; 60-65 μEm-2s-1) prior to the harvest. For submergence treatment ("SUB"), plates were opened and placed horizontally under 5 cm of autoclaved distilled water at ZT 4h. Root tips (apical 1 cm) were harvested at ZT 6h (2h before relative noon). Control plates ("CON") were not opened, but positioned similarly horizontally and also harvested at ZT 6h.
Four independent biological replicates were grown for each species. For whole plant submergence, plates were placed horizontally, opened and the seedlings covered with 5 cm of autoclaved distilled water at ZT 4h. Root tips (apical 1 cm; all four species) and the shoot apical meristem region (Solanum species) were harvested at ZT 6h (2h before relative noon). Control plates were not opened, but positioned horizontally for the duration of the treatment and harvested at ZT 6h. Oxygen partial pressure was measured with the NeoFox Sport O2 sensor and probe (Ocean Optics). The dissolved oxygen content in the water covering the plants remained above 18% (v/v) for the 2 h duration of the stress treatment

value: hairy root culture 1cm root tips

value: Random primed libraries

tag: molecule subtype

value: TRAP RNA


title: TRACONSLSHOOTE [E01_TRAP]

value: 7 days-old seedling shoot apical meristem


title: TOTSUBHAIRYROOTT3D [D18_TOTAL]

extract_protocol:
For cellular mRNA, 35S:His6:FLAG-GFP-AtRPL18-HR3 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009. Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution


title: B6.CAST_E6.5_Epi_H3K27me3_2

description:
ChIP_Epi_ExE_RPKM.txt
B6.CAST_Epi_H3K27me3.txt
Allelic_H3K27me3_dedupH3K27me3peaks_Epi_Readcount.txt

value: anti-H3K27me3 (Millipore 07-449)


title: B6.CAST_E6.5_Epi_H3K36me3_1


title: ChIP_ClsN_input_Sis_78deg_rep2

extract_protocol:
Crosslinked cells were lysed by sonication, and the extract was clarified by centrifugation. Protein-DNA complexes were purified from the extract with antisera. After reversal of crosslinks, ChIP DNA and input DNA were extracted with phenol:chloroform:isoamyl alcohol and then precipitated in ethanol.
Libraries were constructed using Illumina TruSeq ChIP Library Preparation Kits and were sequenced on the Illumina NextSeq 500 platform.

value: DpyrEF DlacS

value: Before cold shock treatment


title: ChIP_ClsN_input_Sis_65deg_rep2

value: After cold shock treatment


title: RNA_Sis_pSSRgD_ClsN_pre_rep1

value: DargD pSSRgD-ClsN


title: CE-6: Cardioembolic_pool6


title: CE-5: Cardioembolic_pool5


title: TRASUBSLROOTD [D10_TRAP]

value: 7 days-old seedling 1 cm roots tips


title: CE-4: Cardioembolic_pool4

value: ischemic stroke


title: CE-3: Cardioembolic_pool3

value: blood


title: ChIP_ClsN_input_Sis_78deg_rep1


title: TOTSUBSLROOTD [D10_TOTAL]


title: DKO.CAST_E6.5_ExE_Input_3

source_name: Extra-embryonic ectoderm

value: Extra-embryonic ectoderm

value: Dnmt3a -/+, Dnmt3b -/+ (maternal inheritance)

value: C57BL6/Babr/129 x CAST/Ei


title: B6.CAST_E6.5_Epi_H3K27me3_1

value: Epiblast

value: Wildtype

value: C57BL6/Babr x CAST/Ei


title: DKO.CAST_E6.5_ExE_H3K4me3_3

description:
ChIP_Epi_ExE_RPKM.txt
Allelic_H3K4me3_dedupH3K4me3peaks_ExE_Readcount.txt

value: anti-H3K4me3 (Diagenode K02921004)


title: TRACONSLROOTD [D09_TRAP]

value: Solanum lycopersicum cv. M82

value: Random primed libraries

value: TRAP RNA


title: FGF2 - pPPR explants Input

city: London

first: Andrea

last: Streit

address: Centre for Craniofacial & Regenerative Biology, King's College London

institute: Kings College London

data_processing:
Basecalls performed using Sanger/Illumina 1.9
Trimming was carried out at the 3' end when sequence quality was poor (Phred score<10) Trimmed reads were then aligned to the chick genome Galgal4.71 using Novoalign (Novocraft 2.08.01)
Peak calling was carried out using Homer (FC>1.5 relative to input; FDR 0.01) and MACS (p-value 1e-5; FDR 0.05)
Putative enhancers were identified in the following way: regions of up to 3 kb flanked by H3K27ac and devoid of H3K27me3 peaks were identified and assigned to the nearest gene using gene annotations from Ensembl (Galgal4.71) and refGene (Nov. 2011 ICGSC Gallus_gallus-4.0/galGal4).
Common and unique putative enhancers for +FGF2-treated and control samples were identified using the R package ChIPpeakAnno
Genome_build: gg4

organism: Gallus gallus

source_name: FGF2 - pPPR explants cultured for 6hrs +FGF4

growth_protocol: Fertilized chicken eggs incubated in a humidified incubator at 38°C until reached HH6 (0 somites), embryos were collected in Tyrode’s saline and progenitors (pPPR) were dissected using fine needles, and cultured in DMEM for 6hrs

extract_protocol:
Explants were dissociated in 0.5ml of Nuclei Extraction Buffer, homogenized and cross-linked using 1% formaldehyde for 9 min at room temprature, 0.125M glycine final concentration was used to stop fixation. Total of 100 tissues were pulled together and sonicated.
Chromatin was amplified with a step of linear amplification (15 cycles) following the protocol described in (Adli and Bernstein, 2011). Libraries were prepared according to nano-ChIP-seq (Adli and Bernstein, 2011) with the exception that only 12 cycles were used in the PCR amplification, following Illumina's instructions.

treatment_protocol: Expants were supplemented with FGF2 (0.25ng/ul; R&D)

tag: developemntal stage

value: HH6 + 6hrs culture

tag: culture condition

value: DMEM supplemented with FGF2 (0.25ng/ l; R&D)


title: FGF2 - pPPR explants H3K27me3_ChIP-seq

department: Centre for Craniofacial & Regenerative Biology

source_name: FGF2 - pPPR explants cultured for 6hrs +FGF3

value: anti-H3K27me3 - Cell signaling - C36B11 (2.5ug Rabbit)


title: ChIP_ClsN_input_Sis_pSSRgD_ClsN_post_rep1

tag: genotype

value: DargD pSSRgD-ClsN

value: 4-hour arabinose induction


title: CE-2: Cardioembolic_pool2

value: ischemic stroke


title: CE-1: Cardioembolic_pool1

value: blood


title: DKO.CAST_E6.5_ExE_H3K4me3_2

value: Extra-embryonic ectoderm


title: FGF2 - pPPR explants H3K27ac_ChIP-seq

source_name: FGF2 - pPPR explants cultured for 6hrs +FGF2

value: anti-H3K27ac - Abcam - ab4729 (1 ug/ul Rabbit)


title: DKO.CAST_E6.5_ExE_H3K36me3_3

description:
ChIP_Epi_ExE_RPKM.txt
Allelic_H3K36me3_dedupH3K36me3peaks_ExE_Readcount.txt

value: Dnmt3a -/+, Dnmt3b -/+ (maternal inheritance)

value: C57BL6/Babr/129 x CAST/Ei


title: TOTCONHAIRYROOTT3D [D17_TOTAL]

value: hairy root culture 1cm root tips

value: polyA RNA


title: TOTCONSLROOTD [D09_TOTAL]

extract_protocol:
For cellular mRNA, p35S:HF-FLAG-OsRPL8 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009). Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

value: 7 days-old seedling 1 cm roots tips


title: Cnt - pPPR explants Input

source_name: Cnt - pPPR explants cultured for 6hrs

value: DMEM


title: TRASUBSLSHOOTD [D02_TRAP]

value: Solanum lycopersicum cv. M82

value: 7 days-old seedling shoot apical meristem

value: Random primed libraries


title: DKO.CAST_E6.5_ExE_H3K36me3_2


title: DKO.CAST_E6.5_ExE_H3K27me3_3

description:
ChIP_Epi_ExE_RPKM.txt
Allelic_H3K27me3_dedupH3K27me3peaks_ExE_Readcount.txt

value: anti-H3K27me3 (Millipore 07-449)


title: ChIP_ClsN_input_Sis_pSSRgD_post_rep1

value: DargD pSSRgD

tag: developmental stage


title: ChIP_ClsN_input_Sis_pSSRgD_pre_rep1

value: Before arabinose induction


title: Cnt - pPPR explants H3K27ac_ChIP-seq

value: HH6 + 6hrs culture


title: ChIP_ClsN_IP_Sis_65deg_rep2

value: DpyrEF DlacS

value: After cold shock treatment

value: ClsN (custom)


title: DKO.CAST_E6.5_ExE_H3K27me3_2

value: Extra-embryonic ectoderm

tag: age


title: ChIP_ClsN_IP_Sis_65deg_rep1


title: TRACONSLSHOOTD [D01_TRAP]

value: TRAP RNA


title: TRASUBHAIRYROOTT4C [C20_TOTAL]

extract_protocol:
For cellular mRNA, 35S:His6:FLAG-GFP-AtRPL18-HR4 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009. Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution


title: TOTSUBHAIRYROOTT4C [C20_TRAP]


title: TOTCONSLSHOOTD [D01_TOTAL]


title: ChIP_ClsN_IP_Sis_78deg_rep2

value: Before cold shock treatment


title: ChIP_ClsN_input_Sis_65deg_rep1


title: DKO.CAST_E6.5_Epi_Input_2

value: Epiblast

value: Dnmt3a -/+, Dnmt3b -/+ (maternal inheritance)

tag: hybrid strain

value: C57BL6/Babr/129 x CAST/Ei


title: DKO.CAST_E6.5_Epi_Input_1

tag: chip antibody


title: TOTCONHAIRYROOTT4C [C19_TRAP]

value: hairy root culture 1cm root tips

value: polyA RNA


title: Cnt - pPPR explants H3K27me3_ChIP-seq

value: DMEM

value: anti-H3K27me3 - Cell signaling - C36B11 (2.5ug Rabbit)


title: ChIP_ClsN_input_Sis_pSSRgD_ClsN_pre_rep1

value: DargD pSSRgD-ClsN


title: ChIP_ClsN_IP_Sis_78deg_rep1


title: DKO.CAST_E6.5_Epi_H3K4me3_2

description:
ChIP_Epi_ExE_RPKM.txt
Allelic_H3K4me3_dedupH3K4me3peaks_Epi_Readcount.txt

value: anti-H3K4me3 (Diagenode K02921004)


title: TRACONHAIRYROOTT4C [C19_TOTAL]

value: Solanum lycopersicum cv. M82

value: Random primed libraries


title: ChIP_ClsN_IP_Sis_pSSRgD_ClsN_post_rep1

value: 4-hour arabinose induction


title: TOTSUBHAIRYROOTT6C [C18_TRAP]

extract_protocol:
For cellular mRNA, 35S:His6:FLAG-GFP-AtRPL18-HR6 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009. Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution


title: DKO.CAST_E6.5_Epi_H3K36me3_3

description:
ChIP_Epi_ExE_RPKM.txt
Allelic_H3K36me3_dedupH3K36me3peaks_Epi_Readcount.txt


title: ChIP_ClsN_IP_Sis_pSSRgD_ClsN_pre_rep1

value: Before arabinose induction


title: TRASUBHAIRYROOTT6C [C18_TOTAL]


title: TOTCONHAIRYROOTT6C [C17_TRAP]


title: ChIP_ClsN_IP_Sis_pSSRgD_post_rep1

value: DargD pSSRgD

value: ClsN (custom)


title: DKO.CAST_E6.5_Epi_H3K36me3_2


title: ChIP_ClsN_IP_Sis_pSSRgD_pre_rep1


title: TRACONHAIRYROOTT6C [C17_TOTAL]

value: TRAP RNA


title: DKO.CAST_E6.5_Epi_H3K27me3_1

description:
ChIP_Epi_ExE_RPKM.txt
Allelic_H3K27me3_dedupH3K27me3peaks_Epi_Readcount.txt

value: anti-H3K27me3 (Millipore 07-449)


title: DKO.CAST_E6.5_Epi_H3K27me3_2

value: Epiblast


title: TRASUBSLROOTC [C10_TRAP]

value: 7 days-old seedling 1 cm roots tips


title: TOTSUBSLROOTC [C10_TOTAL]


title: DKO.CAST_E6.5_Epi_H3K4me3_1

value: Dnmt3a -/+, Dnmt3b -/+ (maternal inheritance)

value: C57BL6/Babr/129 x CAST/Ei


title: HiC_Sis_65deg_rep2

extract_protocol:
Cells were crosslinked, permeabilized, and treated with HindIII to digest cellular DNA. The DNA was end-labeled with biotin and subjected to priximity ligation. After reversal of crosslinks, the DNA was extracted with phenol:chloroform:isoamyl alcohol, precipitated in isopropanol, and sonicated.
Libraries were constructed using NEBNext Ultra DNA Library Prep Kit for Illumina. Biotin-labeled DNA was purified with streptavidin before PCR. Sequencing was performed on the Illumina NextSeq 500 platform.

value: DpyrEF DlacS

value: After cold shock treatment


title: HiC_Sis_65deg_rep1


title: HiC_Sis_78deg_rep2

value: Before cold shock treatment


title: TRACONSLROOTC [C09_TRAP]


title: CAST.B6_E6.5_ExE_Input_2

value: Extra-embryonic ectoderm

value: Wildtype

value: CAST/Ei x C57BL6/Babr


title: HiC_Sis_78deg_rep1


title: TOTCONSLROOTC [C09_TOTAL]

value: Solanum lycopersicum cv. M82

value: Random primed libraries

value: polyA RNA


title: CAST.B6_E6.5_ExE_Input_1


title: 173446

type: genomic

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridized with the hybridization kit according to the Agilent protocol.

scan_protocol: We used a SureScan provided by Agilent and controled by SureScan Software.

data_processing: The data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method - CGH v2 proposed by Agilent.

source_name: chromophobe rcc

label_protocol: DNA was labeled with the sureTag labeling kit according to the Agilent protocol.

extract_protocol: DNA was extracted from fresh, frozen or formol fixed-paraffin embedded fragments using Qiamp DNA mini kit.

value: Chromophobe renal cell carcinoma

source_name: Male DNA control provided in SureTag Labeling kit

extract_protocol: DNA was provided in SureTag Labeling kit.

tag: sample type

value: Commercial DNA from cell lines


title: 181984


title: CAST.B6_E6.5_ExE_H3K4me3_2

description:
ChIP_Epi_ExE_RPKM.txt
CAST.B6_ExE_H3K4me3.txt
Allelic_H3K4me3_dedupH3K4me3peaks_ExE_Readcount.txt

value: anti-H3K4me3 (Diagenode K02921004)


title: HiC_Sis_pSSRgD_ClsN_post_rep1

value: DargD pSSRgD-ClsN

value: 4-hour arabinose induction


title: CAST.B6_E6.5_ExE_H3K4me3_1


title: HiC_Sis_pSSRgD_ClsN_pre_rep1

value: Before arabinose induction


title: 184573

source_name: Female DNA control provided in SureTag Labeling kit


title: CAST.B6_E6.5_ExE_H3K36me3_2

description:
ChIP_Epi_ExE_RPKM.txt
CAST.B6_ExE_H3K36me3.txt
Allelic_H3K36me3_dedupH3K36me3peaks_ExE_Readcount.txt


title: 171859


title: 192078


title: TOTSUBSLSHOOTC [C02_TOTAL]

source_name: 7 days-old seedling shoot apical meristem


title: 180624


title: 173365


title: 164423


title: TRASUBSLSHOOTC [C02_TRAP]

value: 7 days-old seedling shoot apical meristem

value: TRAP RNA


title: HiC_Sis_pSSRgD_post_rep1

value: DargD pSSRgD


title: CAST.B6_E6.5_ExE_H3K36me3_1


title: TRACONSLSHOOTC [C01_TRAP]


title: HiC_Sis_pSSRgD_pre_rep1


title: TOTCONSLSHOOTC [C01_TOTAL]


title: MFA_Sis_oriC1_sta_rep1

extract_protocol:
DNA was purified from exponentially growing cells as described previously (Samson et al., 2013)
Libraries were constructed using NEBNext Ultra DNA Library Prep Kit for Illumina. Sequencing was performed on the Illumina NextSeq 500 platform.

value: DpyrEF DlacS DoriC1

tag: growth phase

value: Stationary-phase cells


title: CAST.B6_E6.5_ExE_H3K27me3_2

description:
ChIP_Epi_ExE_RPKM.txt
CAST.B6_ExE_H3K27me3.txt
Allelic_H3K27me3_dedupH3K27me3peaks_ExE_Readcount.txt

value: Extra-embryonic ectoderm

value: anti-H3K27me3 (Millipore 07-449)


title: CAST.B6_E6.5_ExE_H3K27me3_1

value: Wildtype

value: CAST/Ei x C57BL6/Babr


title: 162566


title: 160318


title: TRASUBHAIRYROOTT2B [B20_TRAP]

value: Solanum lycopersicum cv. M82

value: hairy root culture 1cm root tips

value: Random primed libraries


title: 152493

value: Chromophobe renal cell carcinoma

value: Commercial DNA from cell lines


title: 163302


title: 173140


title: CAST.B6_E6.5_Epi_Input_2

value: Epiblast


title: TOTSUBHAIRYROOTT2B [B20_TOTAL]

extract_protocol:
For cellular mRNA, 35S:His6:FLAG-GFP-AtRPL18-HR2 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009. Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

value: polyA RNA


title: RNA_Sis_log_rep1

value: DpyrEF DlacS

value: Log-phase cells


title: RNA_Sis_log_rep2


title: OS_gDNA [OS-gDNA]

organism: Oryza sativa Japonica Group

source_name: 7 days-old seedling 1 cm roots tips

extract_protocol:
Genomic DNA was isolated using the Dneasy Plant MiniKit (Qiagen)
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using isolated DNA as previously described (Maher et al 2017, Bajic et al 2018)
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

treatment_protocol:
Seeds were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min, rinsed ten times with sterile distilled water and grown on plates (100 cm2) containing 0.5x Murashige and Skoog medium (MS), 1% (w/v) agar 1% (w/v) sucrose for 7 days (16h day / 8h night; at 28°C/25°C day/night; 110 μEm-2s-1). For tomato, seeds were surface sterilized in 50% (v/v) bleach solution for 5 min (S. pennellii) or 20 min (S. lycopersicum) and then rinsed three times with sterile distilled water. Growth was on vertical plates (10 cm x 10 cm) containing full-strength MS without vitamins, with 1% (w/v) agar (w/v) and 1% (w/v) sucrose
Four independent biological replicates were grown for each species. For whole plant submergence, plates were placed horizontally, opened and the seedlings covered with 5 cm of autoclaved distilled water at ZT 4h. Root tips (apical 1 cm; all four species) and the shoot apical meristem region (Solanum species) were harvested at ZT 6h (2h before relative noon). Control plates were not opened, but positioned horizontally for the duration of the treatment and harvested at ZT 6h. Oxygen partial pressure was measured with the NeoFox Sport O2 sensor and probe (Ocean Optics). The dissolved oxygen content in the water covering the plants remained above 18% (v/v) for the 2 h duration of the stress treatment

value: Oryza sativa japonica cv Nipponbare

value: 7 days-old seedling 1 cm roots tips

value: Tagmented libraries


title: TRACONHAIRYROOTT2B [B19_TRAP]

extract_protocol:
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (Townsley et al 2014)
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

value: TRAP RNA


title: OS_ATAC_CON2 [OS-ATACCON2]

description: processed data file: ATAC_OS_CON.bw

extract_protocol:
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018)
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution


title: TOTCONHAIRYROOTT2B [B19_TOTAL]


title: 150098


title: TRASUBHAIRYROOTT6B [B18_TRAP]


title: CAST.B6_E6.5_Epi_H3K4me3_2

description:
ChIP_Epi_ExE_RPKM.txt
CAST.B6_Epi_H3K4me3.txt
Allelic_H3K4me3_dedupH3K4me3peaks_Epi_Readcount.txt

extract_protocol:
Reciprocal natural timed matings were set up between C57BL6/Babr and CAST animals (denoted as B6/CAST and CAST/B6), and embryos were collected on embryonic day 6.5 (E6.5).  Natural timed matings were set up between Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 +ve B6/129 females (resulting in ablation of DNA methylation in the oocyte) and CAST males (denoted as DKO.CAST). The epiblast (Epi) and extra-embryonic ectoderm (ExE) for each embryo were manually separated.  E6.5 epiblast (N=4) and ExE (N=8) samples were pooled (an estimated ~2500 cells), washed in PBS, and then flash frozen in 10µL of nuclear lysis buffer (Sigma).  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease (New England Biolabs) in prepared digestion buffer, as previously described (Brind'Amour et al. 2015 Nat Comm).  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with 100mM EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Prior to the immunoprecipitation with antibody-bound beads, each chromatin sample was divided into 5 aliquots: one for each antibody, one 10% input and one 10% input for bisulphite sequencing.  For each immunoprecipitation, 250ng of anti-H3K4me3 (Diagenode K02921004), 125ng of anti-H3K27me3 (Millipore 07-449) and 250ng of anti-H3K36me3 (C15410192) was used.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using solid phase reversible immobilization (SPRI) purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads (Fisher Scientific) at a 1.8:1 ratio.
Library preparation was completed using the MicroPlex Library Preparation kit v2 (Diagenode) using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations, and all libraries were amplified using 15 amplification cycles.  Libraries were purified with SPRI beads at a 1:1 ratio, and size and quality were assessed using a 2100 Bioanalyzer Instrument (Agilent) and Kapa library qPCR quantitation (Illumina).  Samples were multiplexed using 75bp paired-end sequencing on Illumina NextSeq500.

value: anti-H3K4me3 (Diagenode K02921004)


title: CAST.B6_E6.5_Epi_H3K4me3_3


title: 142020


title: MFA_Sis_oriC1_log_rep1

value: DpyrEF DlacS DoriC1


title: HiC_Sis_noXL_rep1

extract_protocol:
DNA purified from non-crosslinked cells was digested with HindIII, end-labeled with biotin, and subjected to priximity ligation. The DNA was extracted with phenol:chloroform:isoamyl alcohol, precipitated in ethanol, and sonicated.
Libraries were constructed using NEBNext Ultra DNA Library Prep Kit for Illumina. Biotin-labeled DNA was purified with streptavidin before PCR. Sequencing was performed on the Illumina NextSeq 500 platform.


title: ChIP_ClsN_input_Sis_log_rep2

extract_protocol:
Crosslinked cells were lysed by sonication, and the extract was clarified by centrifugation. Protein-DNA complexes were purified from the extract with antisera. After reversal of crosslinks, ChIP DNA and input DNA were extracted with phenol:chloroform:isoamyl alcohol and then precipitated in ethanol.
Libraries were constructed using Illumina TruSeq DNA Sample Preparation Kits and were sequenced on the Illumina GAIIx platform.


title: HiC_Sis_orc1_1_orc1_3_rep2

value: DpyrEF DlacS Dorc1-1 Dorc1-3


title: ChIP_ClsN_input_Sis_log_rep1


title: HiC_Sis_orc1_1_orc1_3_rep1


title: CAST.B6_E6.5_Epi_H3K36me3_2

description:
ChIP_Epi_ExE_RPKM.txt
CAST.B6_Epi_H3K36me3.txt
Allelic_H3K36me3_dedupH3K36me3peaks_Epi_Readcount.txt

value: Wildtype

value: CAST/Ei x C57BL6/Babr


title: CAST.B6_E6.5_Epi_Input_1


title: TRACONHAIRYROOTT6B [B17_TRAP]

value: Solanum lycopersicum cv. M82

value: hairy root culture 1cm root tips


title: HiC_Sis_orc1_1_rep2

value: DpyrEF DlacS Dorc1-1


title: ChIP_ClsN_IP_Sis_log_rep2

value: ClsN (custom)


title: CAST.B6_E6.5_Epi_H3K27me3_2

description:
ChIP_Epi_ExE_RPKM.txt
CAST.B6_Epi_H3K27me3.txt
Allelic_H3K27me3_dedupH3K27me3peaks_Epi_Readcount.txt

value: Epiblast

value: anti-H3K27me3 (Millipore 07-449)


title: OS_ATAC_SUB1 [OS-ATACSUB1]

description: processed data file: ATAC_OS_SUB.bw


title: TOTCONHAIRYROOTT6B [B17_TOTAL]

value: Random primed libraries

value: polyA RNA


title: HiC_Sis_orc1_1_rep1

value: Log-phase cells


title: ChIP_ClsN_IP_Sis_log_rep1

value: DpyrEF DlacS


title: CAST.B6_E6.5_Epi_H3K27me3_1


title: CAST.B6_E6.5_Epi_H3K36me3_1


title: ATAC_Brachypodium_7days_leaf_Input

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
RNA-seq: analysis was performed using Tophat v2.1.1 and cufflinks v2.2.1
ChIP-seq: analysis was performed using bowtie1.1.1
ATAC-seq:analysis was performed using bowtie1.1.1, macs2
Genome_build: Arabidopsis thaliana, Eutrema salsugineum, Phaseolus vulgaris,  Glycine max, Brachypodium distachyon, Oryza sativa, Setaria viridis, Populus trichocarpa, Sorghum bicolor genomes were from JGI (phytozome version 11) ; Zea mays from maizeGDB AGP_v4; Hordeum vulgare from ensemble (version 42) ; Asparagus officinalis from Asparagus genome project (http://asparagus.uga.edu/tripal/);  Spirodela polyrhiza from Michael et al..
Supplementary_files_format_and_content: *BED file, the identified regulatory regions, tab delimited text file, see ACR_column_header.txt for column headers
Supplementary_files_format_and_content: *BIGWIG , the genome coverage of each sample

organism: Brachypodium distachyon

source_name: DNA

growth_protocol: Arabidopsis thaliana (accession Col-0) were grown on 1/2MS plates under 25°C and continues light for 7 days. Leaves were collected for the experiments. Spirodela polyrhiza (accession 7498) were grown in liquid bases (Schenk and Hilldebrandt basak salt mixture) under 25°C and continuous light. Whole seedlings were collected 3 days after transferring to a new basis. Eutrema salsugineum (accession Shandong) and Asparagus officinalis (accession Gijnlim) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). All the young leaves were collected for the experiments. Phaseolus vulgaris (accession G19833) and Glycine max (accession William82) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). The 2nd and 3rd leaves were collected for the experiments. Brachypodium distachyon (accession Bd21), Oryza sativa (accession Nipponbare), Setaria viridis (accession A10), Sorghum bicolor, Zea mays (accession B73), and Hordeum vulgare (accession Morex) were grown in soil for ~6-7days under 25°C, 16 hours of light/8 hours of dark. The inner second leaves—which contains the third and fourth leaves sheathed inside—were used for experiments. Populus trichocarpa leaves were collected from the tree and flash-frozen with liquid N2 immediately for the following experiments.

extract_protocol: ATAC-seq libraries were prepared following the ATAC-seq protocol  as previously described in (Lu et al. 2016).

tag: accession

value: leaf


title: ATAC_Asparagus_10days_leaf_Input

organism: Asparagus officinalis

value: Gijnlim


title: TRASUBSLROOTB [B10_TRAP]

value: 7 days-old seedling 1 cm roots tips

value: TRAP RNA


title: TOTSUBHAIRYROOTT6B [B18_TOTAL]


title: ATAC_Asparagus_10days_leaf_rep2


title: TOTSUBSLROOTB [B10_TOTAL]

extract_protocol:
For cellular mRNA, 35S:His6:FLAG-GFP-AtRPL18-5 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009. Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution


title: ATAC_Brachypodium_7days_leaf_rep2


title: HiC_Sis_oriC1_rep1

source_name: Microorganism

value: DpyrEF DlacS DoriC1


title: ATAC_Asparagus_10days_leaf_rep1


title: 160181

value: Chromophobe renal cell carcinoma

value: Commercial DNA from cell lines


title: ATAC_Brachypodium_7days_leaf_rep1


title: TRACONSLROOTB [B09_TRAP]

value: Solanum lycopersicum cv. M82


title: ChIP_Asparagus_10days_leaf_Input

extract_protocol: ChIP-seq: ChiP-seq was performed following the methods of Zhang et al (2007) (https://www.ncbi.nlm.nih.gov/pubmed/17439305).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.


title: TOTCONSLROOTB [B09_TOTAL]


title: HiC_Sis_log_rep3


title: ChIP_Brachypodium_7days_leaf_Input


title: ChIP_Asparagus_10days_leaf_H2A.Z


title: ChIP_Asparagus_10days_leaf_H3K4me1


title: ChIP_Brachypodium_7days_leaf_H2A.Z


title: TOTSUBSLSHOOTB [B02_TOTAL]

value: 7 days-old seedling shoot apical meristem


title: ChIP_Asparagus_10days_leaf_H3K4me3


title: HiC_Sis_oriC1_rep2