title: B6.CAST_E7.5_ExE_PBAT_2

description:
Bisulphite_100CpGwindows_E7.5Epi_ExE_DNAme.txt
Bisulphite_100CpGwindows_E7.5Epi_ExE_allelicDNAme.txt

data_processing:
DNA methylation was quantitated for each replicate using the bisulphite-seq quantitation pipeline in SeqMonk over 100CpG running windows.  Values are given for windows with a minimum of 10 informative CpGs.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Extra-embryonic ectoderm

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 7.5 (E7.5). The epiblast (Epi) and extra-embryonic ectoderm (ExE) for each embryo were manually separated.  Individual E7.5 epiblast and ExE samples were washed in PBS, and then flash frozen in 10µL of RLT+ buffer (Qiagen). Samples were digested at 37°C for 1 hour.   DNA samples were then bisulfite converted using the EZ DNA Methylation Direct kit (Zymo Research).
The resulting DNA was purified using columns from EZ DNA Methylation Direct kit (Zymo Research). The bisulfite conversion reaction was repeated due to poor initial conversion.  First strand synthesis was then performed using Klenow Exo- (New England Biolabs) with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This was followed by exonuclease I (New England Biolabs) treatment and binding to Dynabeads M-280 Streptavidin beads (ThermoFisher Scientific). Samples were then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase (New England Biolabs). Quantification was done using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification kit (KAPA).  Samples were multiplexed using 150bp paired-end sequencing on Illumina NextSeq500.

value: Extra-embryonic ectoderm

tag: genotype

value: Wildtype

tag: hybrid strain

value: C57BL6/Babr x CAST/Ei


title: CAST.B6_E7.5_Epi_PBAT_2

status: Public on Sep 19 2019

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Epiblast

tag: tissue

value: Epiblast

tag: age

value: CAST/Ei x C57BL6/Babr


title: CAST.B6_E7.5_ExE_PBAT_2


title: B6.CAST_E7.5_ExE_PBAT_1


title: CAST.B6_E7.5_Epi_PBAT_1


title: OCT4_ChIP_96h_Dox_Rep1

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

country: USA

institute: HSCRB

description:
RPKM_Table_ChIP_ATAC.xlsx
SampleMapping_ChIP_ATAC.xlsx

data_processing:
Sequencing read were aligned to the mouse genome (mm10) using bowtie with default parameters
Peaks for OCT4 ChIPs were called using MACS2 and IDR framework.
IDR called OCT4 peaks from different conditions were further processed using in-house pipeline. Peaks from different conditions were merged together if they were found to be overlapping. New peak summit for these merged peak was calcualted based on their relative contributions (heights) as a measure of distance. After calculating and assigning new peak summit to the merged peaks, peaks boundries were also redefined by extending them by 300 bps in both directions from the newly assigned peak summit.
These peaks were then used for downstream analysis. We calculated RPKM for these 600bp peaks. A meta table was created for these 600bp peaks with RPKM values for TFs, histone marks as well as ATAC signal.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with coordinates and RPKM.

growth_protocol: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP were maintained on CF1 mouse embryonic fibroblasts (MEFs) in KO-DMEM containing 15% fetal bovine serum (FBS), 1% penicillin/streptomycin, 1X glutaMAX supplement (Gibco), 1% nonessential amino acid, and 5 × 10^5 U LIF. To perform the ChIP assay, iPSCs were first changed into serum-free N2B27 medium supplemented with LIF and 2i (3 μM CHIR99021 and 1 μM PD0325901) for a minimum of 24 hours. Differentiation was induced by rinsing iPSCs thoroughly with 1X PBS and changing to N2B27 media without LIF 2i. To test colony-forming potential, differentiated cells were trypsinized to single cells and seeded at very low density (~1,300 cells/cm2) on CF1 MEFs in KO-DMEM containing 15% serum and LIF (no dox condition) or supplemented with 2 μg/ml dox (+dox condition).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells were crosslinked in 1% formaldehyde for 10 minutes at 37°C with constant stirring, followed by quenching with 125 mM glycine for 5 min at room temperature. Cells were rinsed with 1X PBS and lysed, and chromatin was sheared using a Branson sonicator until the majority of DNA was in the range of 200-1,000 base pairs. Chromatin was incubated with antibody at 4°C overnight with constant stirring. Co-immunoprecipitation of antibody-protein complexes was performed using Protein A or Protein G Dynabeads for 1h at 4°C. ChIPs were completed using previously reported methods with the following antibodies: OCT4 (Santa Cruz, sc-8628x), H3K4me2 (Millipore, 07-030),H3K27ac () .Immunoprecipitated DNA was end repaired using the End-IT DNA End-Repair Kit (Epicentre), extended using Klenow fragment (3’-5’ exo) (NEB), and ligated to sequencing adapter oligos (Illumina). Each library was PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 base pairs selected for sequencing. Libraries were sequenced on the Illumina Hiseq 2000.

treatment_protocol: Dox-treatment was performed as explained above

tag: chip antibody

value: OCT4 (Santa Cruz, sc-8628x)

tag: cell type

tag: time

tag: treatment

value: Dox


title: Chip B73 leaf H3 rep1

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: processed_data_file: mapped_chip_B73_leaf_H3_rep1.bed.gz

data_processing:
MethylC-seq: analysis was performed by Methylpy 1.3
RNA-seq: analysis was performed by hisat2 v2.0.5 and StringTie v1.3.3b
ChIP-seq: analysis was performed by bowtie1.1.1
DAP-seq:  analysis was performed by bowtie2.2.8 and GEM v2.5
ATAC-seq: analysis was performed by bowtie1.1.1
HiC-seq: analysis was performed by HiC-pro v2.8.0 and Juicertools v0.7.0
Genome_build: Zea mays assembly AGP.v4 reference genome
Supplementary_files_format_and_content: methylome tab delimited text file, see "allc_column_header_descriptions.txt for column headers
Supplementary_files_format_and_content: RNA tab delimited text file, see "RNA_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ChIP bed file, see "ChIP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: DAP bed file, see "DAP_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: ATAC tbed file, see "ATAC_column_header_descriptions.txt" for column headers
Supplementary_files_format_and_content: HiC tab delimited text file, see "HiC_column_header_descriptions.txt" for column headers

organism: Zea mays

source_name: B73 leaf

growth_protocol:
There are two separate growth protocols—one for the second leaf and one for the ear primordia.  For both samples, plants were grown from seed collected from field-grown ears grown during the summer of 2017 in Athens, Georgia.
Second leaf protocol: kernels were sown in Sungro Horticulture professional growing mix (Sungro Horticulture Canada Ltd., 52130 RR 65, P.O. Box 189, Seba Beach, AB T0E 2B0 Canada) approximately 0.5 inches below the soil surface.  Soil was saturated with tap water and placed under a 50/50 mixture of 4100K (Sylvania Supersaver Cool White Delux F34CWX/SS, 34W) and 3000K (GE Ecolux w/ starcoat, F40CX30ECO, 40W) light.  The photoperiod was 16 hours of light, eight hours of dark.  The temperature was approximately 25°C during light hours. The relative humidity was approximately 54%.  Seedlings were grown for approximately six days and harvested from four to six hours after photoperiod dawn.  Seedlings were harvested when the V1 leaf had emerged two to three centimeters above the apical tip of the coleoptile. The seedlings were cut approximately three millimeters above the coleoptile-mesocotyl boundary, excluding the shoot apical meristem, and the V2 leaf was removed from within the sheath of the V1 leaf.  Only the inner V2 leaves were used for experiments.
Ear primordia protocol: Plants were grown in greenhouse or field conditions.  Plants were harvested approximately one month after sowing and ear primordia were dissected from shoots. Ear primordia were harvested from any node of the shoot if they were within the desired size range: between 3 to 8 millimeters from the base to the apical tip of the ear.

extract_protocol:
MethylC-seq: prepared as previously described in (Urich et al. 2015).
RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol.
ChIP-seq: ChiP-seq was performed following the methods of (Zhang et al. 2007).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.
DAP-seq: DAP-seq experiments involving maize ARF samples were processed according to (Galli et al. 2018). All other TFs were processed according to (Bartlett et al. 2017) with the exception that 1ug of pIX-HALO-TF plasmid DNA was used for protein expression and 1ug of adapter ligated library prepared from B73 ear genomic DNA was used for DNA binding.
ATAC-seq libraries were prepared following the ATAC-seq protocol  as previously described in (Lu et al. 2016).
Hi-C libraries were prepared following the HiChIP protocol described in (Mumbach et al. 2016) with modifications described in the text.

tag: line

value: 7-day-old 2nd leaf


title: Chip B73 leaf H3 rep2

description: processed_data_file: mapped_chip_B73_leaf_H3_rep2.bed.gz


title: Corsica19508

type: genomic

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2.0 with GT module 2.0.4 (Illumina).

label: Cy3, Cy5

organism: Homo sapiens

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: blood

tag: geographical region

value: Corsica


title: TP- stimulated macrophages_24h_rap2

type: RNA

city: nanjing

first: Wenlong

last: Hu

address: Jiangwangmiao Street

department: Institute of Dermatology

country: China

institute: Chinese Academy of Medical Science & Peking Union Medical College

description: Macrophage culture supernatants with T. pallidum inoculation at a multiplicity of infection (MOI) of 30 (12 h), washed in PBS twice and further grown in fresh medium for 24 h to collect exosomes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

source_name: TP- stimulated, macrophages, 24h, replicate2

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

growth_protocol: THP-1 cell were cultured in RPMI 1640 containing 10% FBS and 1% penicillin/streptomycin. Macrophages were derived by stimulating THP-1 cells with 100 ng/ml PMA and cultured in RPMI-1640 containing 10% FBS

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: A total of 2×106 macrophages grown in RPMI-1640 containing 10% exosome-free FBS. Exosomes were acquired from macrophage culture supernatants with or without T. pallidum inoculation at a multiplicity of infection (MOI) of 30 (12 h). Briefly, macrophages were washed in PBS twice and further grown in fresh medium for 12 h, 24 h and 48 h to collect exosomes

tag: cell line

tag: agent

value: Treponema pallidum

tag: time point


title: TP- stimulated macrophages_48h_rap1

description: Macrophage culture supernatants with T. pallidum inoculation at a multiplicity of infection (MOI) of 30 (12 h), washed in PBS twice and further grown in fresh medium for 48 h to collect exosomes

source_name: TP- stimulated, macrophages, 48h, replicate1


title: B6.CAST_E7.5_Epi_PBAT_2


title: CorsicaS03308


title: CTL1: Healthy control

city: Tsukuba

first: Munkhzul

last: Ganbold

state: Ibaraki Prefecture

address: 1 Chome-1-1 Tennodai

country: Japan

institute: AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL)

description: Gene expression data from untreated healthy mouse liver

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome Array (MS-430 PM). GeneChip was washed and stained in the Gene Atlas Fluidics Station

scan_protocol: GeneChip was scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).

label: biotin

source_name: Healthy control, technical rep-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: Six-week-old male C57BL/6J mice (Charles River Laboratories JAPAN Inc., Kanagawa, Japan) were maintained at room temperature in a 12h light/dark cycle. After one week of acclimatization with standard chow diet and tap water ad libitum, all animals were randomly assigned (Day 0) into three experimental groups (n = 8 / group): Control (CTL), NASH, and NASH treated with isorhamnetin (NASH+ISO). All animal procedures were approved by the Animal Study Committee of University of Tsukuba (No.17-312) and were handled according to the Guiding Principles for the Care and Use of Animals in the Field of Physiological Sciences approved by The Physiological Society of Japan.

extract_protocol: Total RNA was extracted from liver tissue stocked at -80°C using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The total RNA was resuspended in Tris-EDTA and stocked at -80°C until use.

treatment_protocol: CTL group mice were fed with laboratory chow diet and received vehicles. NASH and NASH+ISO groups were subjected to high fat diet (60% cal from fat, D12492, Research Diets Inc., New Brunswick, NJ, USA) from Day 0-24. Rodents received intraperitoneal injections of CCl4 at 0.1ml/kg of body weight 4 times (Day 14, 17, 21, and 24), and T0901317 at 2.5ml/kg of body weight 5 times (Day 20-24) to induce NASH. Corn oil and dimethyl sulfoxide (DMSO) were used as vehicle for CCl4 and T0901317 injections respectively. NASH+ISO group was treated with daily oral administration of isorhamnetin at 50 mg/kg of body weight (vehicle for CTL and NASH group) for last two weeks (Day 11-24).

value: Liver


title: TP- stimulated macrophages_24h_rap1

source_name: TP- stimulated, macrophages, 24h, replicate1


title: TP- stimulated macrophages_48h_rap2

source_name: TP- stimulated, macrophages, 48h, replicate2


title: OCT4_ChIP_96h_NoDox_Rep1

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP

value: NoDox


title: Chip B73 leaf H3K9ac rep2

description: processed_data_file: mapped_chip_B73_leaf_H3K9ac_rep2.bed.gz


title: Corsica29708


title: Corsica14708


title: B6.CAST_E7.5_Epi_PBAT_1


title: CorsicaS29908


title: Chip B73 leaf H3K9ac rep1

description: processed_data_file: mapped_chip_B73_leaf_H3K9ac_rep1.bed.gz


title: K27ac_ChIP_0h_Rep1

value: K27ac (Diagenode, C15410196)


title: CAST.B6_E7.5_ExE_PBAT_1


title: OCT4_ChIP_96h_NoDox_Rep2


title: corsica1308


title: TP- stimulated macrophages_12h_rap2

description: Macrophage culture supernatants with T. pallidum inoculation at a multiplicity of infection (MOI) of 30 (12 h), washed in PBS twice and further grown in fresh medium for 12 h to collect exosomes

source_name: TP- stimulated, macrophages, 12h, replicate2


title: Chip B73 leaf H3K56ac rep2

description: processed_data_file: mapped_chip_B73_leaf_H3K56ac_rep2.bed.gz


title: OCT4_ChIP_96h_Rep1


title: Chip B73 leaf H3K56ac rep1

description: processed_data_file: mapped_chip_B73_leaf_H3K56ac_rep1.bed.gz


title: DKO.CAST_E6.5_ExE_Input_2

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>

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


title: TP- stimulated macrophages_12h_rap1

source_name: TP- stimulated, macrophages, 12h, replicate1


title: OCT4_ChIP_48h_Dox_Rep2


title: Chip B73 leaf H3K4me3 rep2

description: processed_data_file: mapped_chip_B73_leaf_H3K4me3_rep2.bed.gz


title: DKO.CAST_E6.5_Epi_Input_3


title: Chip B73 leaf H3K4me3 rep1

description: processed_data_file: mapped_chip_B73_leaf_H3K4me3_rep1.bed.gz


title: RNAseq3_CAD_DKO_pUC19DNA_2days_postserum_2

first: Jennifer

middle: M

last: Cherone

state: Ma

address: 400 Main Street, 68-259

department: Biology

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing:
For the RNA-seq, reads were aligned to the mm9 genome using STAR (Dobin et al., 2013), expression levels were quantified, and differentially expressed genes were assessed using DESeq2 (Love et al., 2014).
Adapter sequences were trimmed from reads using cutadapt, and then reads with identical 4 bp barcodes on the 5' and 3' ends (8 bp total with a constrained distance in between) were collapsed to single reads, yielding 4-7 M unique reads remaining per replicate. Barcode sequences were trimmed from each end using cutadapt, and reads were mapped to the miRBase genome annotations using bwa with the following options: -n 1 -o 0 -e 0 -k 1, resulting in 50-66% of reads mapped per replicate. The miRNAs were filtered, requiring a minimum of 5 counts in at least one of the samples. Differential expression was assessed using DESeq (Anders and Huber, 2010). Size factors used for normalization were calculated from two spike-in miRNAs from different species: dme-miR-14-5p (Drosophila) and xtr-miR-427 (Xenopus).
Genome_build: mm9, miRbase_v21
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene within each sample.

source_name: neuroblastoma cells

growth_protocol: All CAD cells (WT and knockout lines) were grown in DMEM/F12 (Gibco) supplemented with 10% fetal bovine serum (FBS) and differentiated in DMEM/F12 with no FBS added.

extract_protocol:
For RNA-seq, total RNA was collected with a Qiagen RNeasy Mini kit. For the small RNA-seq, total RNA was harvested from CAD cells in serum or 4 days after serum withdrawal using the miRVana kit (Thermo Fisher).
For the WT and mir-138 DKO CAD cells in serum or 24-96 h without serum, strand-specific, polyA-selected libraries were constructed using the dUTP incorporation method and sequenced on an Illumina NextSeq sequencer with paired-end 75-bp reads. Samples were prepared and sequenced in duplicate or triplicate (WT 0 and 96 h without serum), yielding approximately 30-45 million read pairs per replicate. For the mir-138 DKO CAD cells transfected with either a miR-138 mimic, miR-137 mimic, or pUC19 DNA, strand-specific, polyA-selected libraries were constructed in duplicate with the Illumina’s TruSeq Stranded mRNA Library Prep Kit for Neoprep and sequenced on an Illumina NextSeq sequencer with 50 bp single-end reads, yielding 18-36 M reads per replicate. For small RNA-seq, 1000 ng of total RNA was used with the Bioo Scientific NEXTflex Small RNA Sequencing Kit v2 and libraries were sequenced on an Illumina HighSeq Sequencer in triplicate, yielding 9-18 M reads per replicate.
RNA-seq (Samples 7-34) and small RNA-seq (Samples 1-6)

treatment_protocol: (Samples 1-20): For sequencing WT and miR-138 DKO cell lines before and after serum withdrawal, cells were plated in a 6-well plate. For wells intended to differentiate, the media was replaced with serum-free media after 24 h. (Samples 21-34): mir-138 DKO cells were plated at 0.6e5 cells/well in a poly-l-lysine coated 12-well dish. miR-138 or miR-137 mirVana miRNA mimics were transfected at a concentration of 3 nM with the Lipofectamine RNAiMAX reagent. Media was changed to serum-free media 48 h later. Total RNA was collected at 0 and 2 days after serum withdrawal using the Qiagen RNeasy kit.

value: CAD cells

value: mir-138 DKO

tag: days post serum withdrawal

value: 2 days


title: Control macrophages exosomes_rap2

description: miRNA expression of exosomes from macrophages, untreated

source_name: Control, macrophages exosomes, replicate2

value: PBS


title: Chip B73 leaf H3K4me1 rep2

description: processed_data_file: mapped_chip_B73_leaf_H3K4me1_rep2.bed.gz


title: ATAC_Soybean_10days_leaf_rep2

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: Glycine max

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: William 82

value: leaf


title: OCT4_ChIP_48h_Dox_Rep1

value: OCT4 (Santa Cruz, sc-8628x)


title: OCT4_ChIP_48h_NoDox_Rep2


title: B6.CAST_E6.5_Epi_Input_3

value: Epiblast

value: Wildtype

value: C57BL6/Babr x CAST/Ei


title: ATAC_Soybean_10days_leaf_Input


title: RNAseq3_CAD_DKO_pUC19DNA_2days_postserum_1


title: Control macrophages exosomes_rap3

source_name: Control, macrophages exosomes, replicate3


title: Control macrophages exosomes_rap1

source_name: Control, macrophages exosomes, replicate1


title: Corsica03708

value: blood

value: Corsica


title: Chip B73 leaf H3K4me1 rep1

description: processed_data_file: mapped_chip_B73_leaf_H3K4me1_rep1.bed.gz

value: 7-day-old 2nd leaf


title: OCT4_ChIP_48h_Rep2

description:
RPKM_Table_ChIP_ATAC.xlsx
SampleMapping_ChIP_ATAC.xlsx

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP


title: ChIP_Soybean_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: OCT4_ChIP_48h_NoDox_Rep1

value: NoDox


title: OCT4_ChIP_0h_Dox_Rep2

value: Dox


title: RNAseq3_CAD_DKO_137mimic_2days_postserum_2


title: Chip B73 leaf H3K36me3 rep1

description: processed_data_file: mapped_chip_B73_leaf_H3K36me3_rep1.bed.gz


title: RNAseq3_CAD_DKO_137mimic_2days_postserum_1


title: ATAC_Soybean_10days_leaf_rep1


title: Chip B73 leaf H3K36me3 rep2

description: processed_data_file: mapped_chip_B73_leaf_H3K36me3_rep2.bed.gz


title: OCT4_ChIP_48h_Rep1


title: ChIP_Soybean_10days_leaf_H2A.Z


title: corsica11908

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).


title: RNAseq3_CAD_DKO_138mimic_2days_postserum_2


title: ItalyPiedmont136

value: Italy, Piedmont


title: Chip B73 leaf H3K27me3 rep2

description: processed_data_file: mapped_chip_B73_leaf_H3K27me3_rep2.bed.gz


title: OCT4_ChIP_0h_Dox_Rep1


title: ItalyPiedmont119


title: ChIP_Soybean_10days_leaf_H3K4me1


title: OCT4_ChIP_0h_NoDox_Rep2


title: Chip B73 leaf H3K27me3 rep1

description: processed_data_file: mapped_chip_B73_leaf_H3K27me3_rep1.bed.gz


title: ChIP_Soybean_10days_leaf_H3K4me3


title: ChIP_Soybean_10days_leaf_H3K56ac


title: RNAseq3_CAD_DKO_pUC19DNA_serum_2

value: CAD cells

value: 0 days


title: Chip B73 leaf H3K27ac rep2

description: processed_data_file: mapped_chip_B73_leaf_H3K27ac_rep2.bed.gz


title: OCT4_ChIP_0h_NoDox_Rep1


title: OCT4_ChIP_0h_Rep2


title: Chip B73 leaf H3K27ac rep1

description: processed_data_file: mapped_chip_B73_leaf_H3K27ac_rep1.bed.gz


title: RNAseq3_CAD_DKO_pUC19DNA_serum_1

value: mir-138 DKO


title: RNAseq3_CAD_DKO_137mimic_serum_2


title: RNAseq3_CAD_DKO_137mimic_serum_1


title: Chip B73 leaf H2AZ rep2

description: processed_data_file: mapped_chip_B73_leaf_H2AZ_rep2.bed.gz


title: ChIP_Soybean_10days_leaf_H3K36me3


title: ChIP_Soybean_10days_leaf_H3K27me3


title: Corsica24508


title: OCT4_ChIP_0h_Rep1


title: ATAC_96h_Dox_Rep3

data_processing:
Sequencing read were aligned to the mouse genome (mm10) using bowtie with default parameters
For each OCT4 consensus peak, the Bioconducter package QuasR  was used to count the number of ATAC-seq reads within a centered 600bp window. Read counts were normalized by library size to get RPKM.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with coordinates and RPKM.

extract_protocol:
Nuclei were isolated from 50,000 cells and incubated with Tn5 transposase (Illumina) for 30 min at 37°C.
DNA was purified and PCR-amplified using customized Nextera PCR primers. A size range of 200-1000 base pairs was selected for sequencing on the Illumina Hiseq 2000.


title: RNAseq3_CAD_DKO_138mimic_serum_2


title: Chip B73 leaf H2AZ rep1

description: processed_data_file: mapped_chip_B73_leaf_H2AZ_rep1.bed.gz


title: ChIP_Soybean_10days_leaf_H3


title: RNAseq3_CAD_DKO_138mimic_2days_postserum_1

value: 2 days


title: ATAC_96h_Dox_Rep1


title: ATAC_96h_Dox_Rep2


title: RNA_Soybean_10days_leaf_rep2

source_name: mRNA

extract_protocol: RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol

value: William 82


title: RNA B73 ear rep3

source_name: B73 ear


title: RNAseq3_CAD_DKO_138mimic_serum_1


title: RNAseq3_CAD_DKO_2_serum_2


title: RNA B73 ear rep2


title: RNA_Soybean_10days_leaf_rep1

value: leaf


title: ATAC_96h_NoDox_Rep1


title: ATAC_96h_Rep2


title: RNA B73 ear rep1


title: RNA B73 leaf rep1


title: ATAC_96h_Rep1


title: RNAseq2_CAD_WT_2_d4_2

value: 4 days


title: RNA B73 leaf rep2


title: RSSUBHAIRYROOTT4F4 [RS-SUB-4]

city: Atlanta

first: Roger

middle: B

last: Deal

address: 1510 Clifton Rd NE

institute: Emory University

description: processed data file: RS-SUB-SL-H.merged.bw

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

organism: Solanum lycopersicum

source_name: hairy root culture 1cm root tips

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)
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 . Library construction continued as described by Bazin et al 2017, and the resultant 130 nt RF cDNAs were circularized and contaminating rRNA was subtracted by a second hybridization with custom-designed biotinylated oligos corresponding to pre-rRNA and rRNA as described (14). rRNA-subtracted circularized fragments were used for 12 cycles of 10s at 98°C, 10s at 60°C, and 5s at 72 °C PCR amplification including library and indexing primers
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:
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

tag: cultivar

value: Solanum lycopersicum cv. M82

value: hairy root culture 1cm root tips

tag: experiment type

value: Ribosome footprints

tag: molecule subtype

value: Riboseq RNA


title: RSSUBHAIRYROOTT4F3 [RS-SUB-3]

description: processed data file: RS-CON-SL-H.merged.bw


title: ATAC_48h_Dox_Rep2


title: RNAseq2_CAD_WT_2_d4_1

tag: genotype


title: ATAC_48h_Dox_Rep1


title: RNAseq2_CAD_WT_2_serum_3

value: wild type


title: RSSUBHAIRYROOTT2F1 [RS-SUB-1]

tag: tissue


title: RNAseq2_CAD_WT_2_serum_2


title: RSCONHAIRYROOTT4F4 [RS-CON-4]


title: NP23-NHD13 BM AML 4

city: Bethesda

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

institute: CCR-NCI-NIH

data_processing:
Unaligned raw reads were trimmed for bases for low Phred score and trimmmed from 3-prime(right end) end using Partek Flow tool.
Trimmed reads were used to generate aligned reads using STAR-2.5.3a aligner available on Partek Flow tool followed by post alignment QA/QC.
Partek E/M was used to quantify reads with annotation model : mm10_refseq_16_05_02_v2 on Partek Flow tool to generate Gene counts.
Gene counts were normalized using FPKM method on Partek Flow tool.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with matrix table of normalized count with FPKM values for each sample on column and features on rows.

source_name: Bone marrow (BM)

extract_protocol:
Total RNA was extracted from cryopreserved cells using Trizol and the manufacturer's recommended protocol.
Libraries were contructed at ACGT Inc using a TruSeq mRNA kit using 1 ug of total RNA as starting material.

tag: strain

tag: genotype/variation

tag: disease state

value: AML


title: NP23-NHD13 BM AML 2


title: ATAC_48h_NoDox_Rep2

tag: cell type

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP

tag: time


title: RSCONHAIRYROOTT4F3 [RS-CON-3]

tag: line


title: RNAseq3_CAD_DKO_2_serum_1


title: RNAseq2_CAD_WT_2_d4_3


title: RSCONHAIRYROOTT2AF1 [RS-CON-1]


title: NP23-NHD13 BM AML 1


title: ATAC_48h_NoDox_Rep1

tag: treatment

value: NoDox


title: ATAC_48h_Rep2


title: RSSUBHAIRYROOTT2F2 [RS-SUB-2]


title: ATAC_48h_Rep1


title: NHD13 BM AML 3


title: RNAseq1_CAD_DKO_d1_1

value: 1 day


title: ATAC_0h_Dox_Rep2

value: Dox


title: TOTSUBSLSHOOTD [D02 TOTAL repeat]

source_name: 7 days-old seedling shoot apical meristem

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

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

value: Random primed libraries

value: polyA RNA


title: RNAseq1_CAD_DKO_serum_2

value: CAD cells

value: mir-138 DKO

value: 0 days


title: NHD13 BM AML 2


title: NP23-NHD13 BM AML 3


title: NHD13 BM AML 1


title: ATAC_0h_Dox_Rep1


title: RNAseq2_CAD_WT_2_serum_1


title: INRNACONHAIRYROOTI6D [IN_D19]

extract_protocol:
Nuclei were purified from frozen and pulverized tissue as described previously for Arabidopsis thaliana (Wang and Deal, 2015) with only minor modifications including 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 (Celltrics) 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 (this suspension is considered input of the purification), Twenty-five microliters of M-280 streptavidin-coated Dynabeads (~1.5 x 107 beads; Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated to allow capture of the nuclei 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 7 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 7 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube. For RNA extraction, the bead-bound nuclei mixture was placed on a 2 mL tube magnet for 4 min at 4° C to capture the nuclei, which were resuspended in 20 µl NPB before proceeding to the extraction
For nuclear RNA libraries, rRNA was degraded with probes that were hybridized with up to 1 µg RNA in a 6 μl reaction containing 0.1 μM of each probe and 1 μl of 5x hybridization buffer (0.5 M Tris-HCl [pH 7.0], 1 M NaCl). The probe concentration was scaled down proportionally for lower amounts of RNA. For denaturation and hybridization, the sample was heated to 95 °C for 2 min, cooled to 45 °C at 0.1 °C/s and incubated at 45 °C for 5 min. For RNase treatment, the hybridization reaction at 45 °C was  increased to 10 μl by adding 5 U of thermostable RNase H Hybridase (Epicentre) and 1 μl of Hybridase buffer (500 mM Tris-HCl [pH 7.4], 1 M NaCl, 200 mM MgCl2), and incubated at 45 °C for 30 min. To remove the DNA probes and degraded RNA from the samples, the sample was re-treated with Turbo DNase I (ThermoFisher Scientific) and cleaned up with Agencourt RNAClean XP beads (Beckman Coulter). RNA-seq libraries of pre/rRNA degraded nuclear were prepared as described by Townsley et al. (2014)
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:
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: nuclear RNA


title: ATAC_0h_NoDox_Rep2


title: NP23 BM AML 2


title: RNAseq1_CAD_WT_d1_2


title: INRNACONSLROOTE1 [IN_E13]

source_name: 7 days-old seedling 1 cm roots tips

value: 7 days-old seedling 1 cm roots tips


title: RNAseq1_CAD_DKO_d1_2


title: ATAC_0h_NoDox_Rep1


title: RNAseq1_CAD_WT_d1_1


title: ATAC_0h_Rep2


title: NP23 BM AML 1


title: INRNASUBSLROOTD [IN_D14]

value: Solanum lycopersicum cv. M82


title: RNAseq1_CAD_WT_serum_2


title: INRNACONSLSHOOTD [IN_D05]

value: 7 days-old seedling shoot apical meristem


title: WT lineage negative BM 1

description: WT Lin-BM_5559

value: WT

value: Normal BM


title: INRNASUBSLSHOOTD [IN_D06]


title: BirA/FLBIO-Klf9 Pulldown 4

city: Palo Alto

first: Joseph

middle: Riley

last: Knoedler

state: CA

address: 1201 Welch Road

department: Psychiatry and Behavioral Sciences

institute: Stanford Univesity

data_processing:
Basecalls were performed 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 38 -n 1 -m 1 -p7
Peaks from BirA and BirA/FLBIO-Klf9 samples were first called using MACS and refined using Peaksplitter with Peaksplitter cutoff of 20 mapped reads and 40 percent valley.
Peaks were independently called using PePr.
The intersectBed option from Bedtools was used to identify peaks identified by both Peaksplitter and PePr
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited text file indicates genomic location. Wig file indicates total mapped sequencing read density across mouse genome for BirA and BirA/FLBIO-Klf9 samples.

growth_protocol: Stably transfected HT22 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Selection was  maintained with zeocin (HT22[BirA]) or zeocin+puromycin (HT22[BirA/FLBIO-Klf9])

extract_protocol:
Cells were crosslinked with 1% paraformaldehyde and 25 mM dithiobis(succinimydl propionate) and lysed with sodium dodecyl sulfate (SDS) buffer. Chromatin was sheared with a Covaris sonicator to 200-1000 bp fragments and protein-DNA complexes were isolated with
Libraries were constructed using standard Illumina protocols.

tag: stably transfected construct


title: RNAseq1_CAD_DKO_serum_1


title: DKO.CAST_E6.5_ExE_Input_PBAT_3

description: Bisulfite_100_CpG_windows_Epi_ExE_DNAme.txt

data_processing:
Raw reads were trimmed with Trim Galore (v0.4.4) to remove poor quality basecalls, adapter contamination and trim of 9 bp from the 5' end of both read 1 and read 2 (options: --clip_r1 9 --clip_r2 9 --paired). Trimmed reads were then aligned to N-masked versions of the GRCm38 genome (Black6/Castaneus hybrids) using Bismark (v0.20.0, options: --pbat). Following alignments, reads were deduplicated and subjected to allele-specific sorting with SNPsplit (v0.3.4; https://github.com/FelixKrueger/SNPsplit). The DKO data required some additional treatment, please see the Materials and Methods section of the manuscript.
DNA methylation was quantitated for each replicate using the bisulphite-seq quantitation pipeline in SeqMonk over 100 CpG running windows.  Values are given for windows with a minimum of 10 informative CpGs.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Extra-embryonic ectoderm

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.   Prior to the immunoprecipitation, one 10% input  was taken from each chromatin sample for bisulphite sequencing. 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.  DNA samples were then bisulfite converted using the EZ DNA Methylation Direct kit (Zymo Research).
The resulting DNA was purified using columns from EZ DNA Methylation Direct kit (Zymo Research). First strand synthesis was then performed using Klenow Exo- (New England Biolabs) with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This was followed by exonuclease I (New England Biolabs) treatment and binding to Dynabeads M-280 Streptavidin beads (ThermoFisher Scientific). Samples were then subjected to second strand synthesis similar to the first strand synthesis, followed by 12 PCR amplification cycles using Phusion High-Fidelity DNA polymerase (New England Biolabs). Quantification was done using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification kit (KAPA).  Samples were multiplexed using 75bp paired-end sequencing on Illumina NextSeq500.

value: Extra-embryonic ectoderm

tag: age

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

tag: hybrid strain

value: C57BL6/Babr/129 x CAST/Ei


title: NP23 BM AML 3

value: AML


title: iPSC_2 (RNA-Seq)

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
Reads were aligned to mouse reference genome mm10;GRCm38.p5 using STAR (v2.5.0a) supplied with corresponding gencode vM16 annotation with default parameters followed by conversion to BAM format sorted by coordinate. A minimun of 79% of reads were uniquely mapped.
Mapped reads were assigned to genomic features using the featureCounts function from the “Rsubread” (v1.5.2) package in R (v3.5.2).
Differential gene expression analysis was performed using the DESEQ2 package (v1.21.22) in R.
Genome_build: mm10; GRCm38.p5
Supplementary_files_format_and_content: File of matrix containing all samples with read counts normalized by library size

source_name: induced pluripotent stem cells

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:
Briefly, samples were collected in TRIzol (Invitrogen, 15596026) and stored in -80°C until cells from all timepoints were collected. Next, all samples were processed together to extract RNA following manufacturer’s protocol.
Libraries were prepared as described before (Song et al., 2018a). Libraries were pooled in equimolar amounts for single-end sequencing on an Illumina HiSeq 4000 instrument (Illumina).

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.

value: Col1a1-tetO-OKSM, Rosa26-M2rtTA

value: induced pluripotent stem cells

value: iPSCs


title: INRNASUBHAIRYROOTI4C [IN_C24]

value: hairy root culture 1cm root tips

value: Random primed libraries


title: INRNACONHAIRYROOTI4C [IN_C23]


title: BirA/FLBIO-Klf9 Pulldown 3


title: DKO.CAST_E6.5_ExE_Input_PBAT_2


title: iPSC_1 (RNA-Seq)


title: BirA/FLBIO-Klf9 Pulldown 2


title: OCT4_ChIP_96h_Rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells were crosslinked in 1% formaldehyde for 10 minutes at 37°C with constant stirring, followed by quenching with 125 mM glycine for 5 min at room temperature. Cells were rinsed with 1X PBS and lysed, and chromatin was sheared using a Branson sonicator until the majority of DNA was in the range of 200-1,000 base pairs. Chromatin was incubated with antibody at 4°C overnight with constant stirring. Co-immunoprecipitation of antibody-protein complexes was performed using Protein A or Protein G Dynabeads for 1h at 4°C. ChIPs were completed using previously reported methods with the following antibodies: OCT4 (Santa Cruz, sc-8628x), H3K4me2 (Millipore, 07-030),H3K27ac () .Immunoprecipitated DNA was end repaired using the End-IT DNA End-Repair Kit (Epicentre), extended using Klenow fragment (3’-5’ exo) (NEB), and ligated to sequencing adapter oligos (Illumina). Each library was PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 base pairs selected for sequencing. Libraries were sequenced on the Illumina Hiseq 2000.

tag: chip antibody

value: OCT4 (Santa Cruz, sc-8628x)

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP


title: CAST.B6_E6.5_Epi_Input_3

source_name: Epiblast

value: Epiblast

value: Wildtype

value: CAST/Ei x C57BL6/Babr


title: INRNACONSLROOTD [IN_D13]

value: Solanum lycopersicum cv. M82

value: 7 days-old seedling 1 cm roots tips

value: nuclear RNA


title: DKO.CAST_E6.5_ExE_Input_PBAT_1

value: Extra-embryonic ectoderm


title: D3_Tox4_siRNA_noDOX_2 (RNA-Seq)

source_name: MEF reprogramming intermediate

value: MEF reprogramming intermediate

tag: protocol

tag: agent

value: noDOX


title: INRNASUBSLSHOOTE1 [IN_E06]

tag: cultivar

value: 7 days-old seedling shoot apical meristem

tag: experiment type


title: WT lineage negative BM 2

description: WT Lin-BM_176

value: WT

value: Normal BM


title: RNAseq1_CAD_WT_serum_1

value: CAD cells

tag: genotype

value: wild type

tag: days post serum withdrawal

value: 0 days


title: INRNASUBHAIRYROOTI2C [IN_C22]

tag: tissue

value: hairy root culture 1cm root tips

value: Random primed libraries

tag: molecule subtype


title: D3_Tox4_siRNA_noDOX_1 (RNA-Seq)

tag: strain

value: Col1a1-tetO-OKSM, Rosa26-M2rtTA


title: BirA/FLBIO-Klf9 Input Sample


title: ATAC_0h_Rep1

tag: cell type

value: Doxycycline (dox)-inducible secondary iPSCs containing GFP targeted to the endogenous Nanog locus and constitutive nuclear RFP


title: DKO.CAST_E6.5_Epi_Input_PBAT_1

value: Epiblast

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

value: C57BL6/Babr/129 x CAST/Ei


title: INRNASUBSLROOTC1 [IN_C13]

value: Solanum lycopersicum cv. M82

value: 7 days-old seedling 1 cm roots tips

value: nuclear RNA


title: DKO.CAST_E6.5_Epi_Input_PBAT_3


title: D3_Tox4_siRNA_DOX_2 (RNA-Seq)

value: MEF reprogramming intermediate

value: DOX

tag: time


title: CAST.B6_E6.5_ExE_Input_PBAT_2

value: Extra-embryonic ectoderm

value: Wildtype

value: CAST/Ei x C57BL6/Babr


title: INRNACONHAIRYROOTI2C [IN_C21]

tag: line


title: D3_Tox4_siRNA_DOX_1 (RNA-Seq)


title: INRNASUBSLSHOOTC [IN_C06]

value: 7 days-old seedling shoot apical meristem


title: BirA Pulldown 4


title: BirA Pulldown 3


title: CAST.B6_E6.5_ExE_Input_PBAT_1


title: BirA/FLBIO-Klf9 Pulldown 1


title: CAST.B6_E6.5_Epi_Input_PBAT_3


title: BirA Pulldown 2


title: INRNASUBHAIRYROOTI3B [IN_B24]


title: D3_Control_siRNA_noDOX_2 (RNA-Seq)

value: noDOX


title: BirA Pulldown 1


title: D3_Control_siRNA_noDOX_1 (RNA-Seq)


title: CAST.B6_E6.5_Epi_Input_PBAT_2


title: INRNACONSLSHOOTC [IN_C05]


title: INRNACONHAIRYROOTI3B [IN_B23]

value: hairy root culture 1cm root tips


title: CAST.B6_E6.5_Epi_Input_PBAT_1


title: INRNASUBHAIRYROOTI2B [IN_B22]

value: Random primed libraries


title: D3_Control_siRNA_DOX_2 (RNA-Seq)

value: Col1a1-tetO-OKSM, Rosa26-M2rtTA


title: BirA Input Sample


title: D3_Control_siRNA_DOX_1 (RNA-Seq)


title: D0_MEF_2 (RNA-Seq)

source_name: MEF

value: MEF


title: B6.CAST_E6.5_ExE_Input_PBAT_1

value: C57BL6/Babr x CAST/Ei


title: B6.CAST_E6.5_ExE_Input_PBAT_2


title: D0_MEF_1 (RNA-Seq)


title: TR/TO-Klf9 dox-treated 1

description: TR/TO-Klf9 dox-treated 1

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).

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: HT22 cells stably transfected with pCDNA6:TR and pCDNA4:TO-Klf9


title: TR/TO-Klf9 vehicle-treated 3

description: TR/TO-Klf9 vehicle-treated 3


title: TR/TO-Klf9 dox-treated 2

description: TR/TO-Klf9 dox-treated 2


title: INRNACONHAIRYROOTI2B [IN_B21]


title: iPSC_2 (ATAC-Seq)

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

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

value: induced pluripotent stem cells

value: iPSCs


title: B6.CAST_E6.5_Epi_Input_PBAT_4

value: Epiblast


title: B6.CAST_E6.5_Epi_Input_PBAT_3


title: TR/TO-Klf9 vehicle-treated 2

description: TR/TO-Klf9 vehicle-treated 2


title: TR/TO-Klf9 vehicle-treated 1

description: TR/TO-Klf9 vehicle-treated 1


title: INRNASUBSLSHOOTB [IN_B06]

value: Solanum lycopersicum cv. M82

value: nuclear RNA


title: iPSC_1 (ATAC-Seq)


title: INRNACONSLROOTB [IN_B13]

value: 7 days-old seedling 1 cm roots tips


title: B6.CAST_E6.5_ExE_Input_2

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: Extra-embryonic ectoderm


title: Parent line dox-treated 3

description: Parent line dox-treated 3

source_name: HT22 parent cell line

value: pSV40-immortalized mouse hippocampal cell line


title: D3_Tox4_siRNA_DOX_2 (ATAC-Seq)

value: MEF reprogramming intermediate

value: DOX


title: INRNASUBHAIRYROOTI2A [IN_A22]


title: INRNACONSLSHOOTB [IN_B05]

value: 7 days-old seedling shoot apical meristem


title: INRNASUBSLROOTB [IN_B14]


title: B6.CAST_E6.5_ExE_Input_1

value: Wildtype


title: D3_Control_siRNA_DOX_2 (ATAC-Seq)


title: Parent line dox-treated 2

description: Parent line dox-treated 2


title: INRNACONHAIRYROOTI2A [IN_A21]

value: hairy root culture 1cm root tips

value: Random primed libraries


title: Parent line vehicle-treated 3

description: Parent line vehicle-treated 3


title: INRNASUBSLROOTE2 [IN_E14_redo]


title: INRNACONSLROOTC [IN_C103_redo]


title: D0_MEF_2 (ATAC-Seq)

value: Col1a1-tetO-OKSM, Rosa26-M2rtTA

value: MEF


title: D0_MEF_1 (ATAC-Seq)


title: RNA B73 ear rep4

extract_protocol:
MethylC-seq: prepared as previously described in (Urich et al. 2015).
RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol.
ChIP-seq: ChiP-seq was performed following the methods of (Zhang et al. 2007).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.
DAP-seq: DAP-seq experiments involving maize ARF samples were processed according to (Galli et al. 2018). All other TFs were processed according to (Bartlett et al. 2017) with the exception that 1ug of pIX-HALO-TF plasmid DNA was used for protein expression and 1ug of adapter ligated library prepared from B73 ear genomic DNA was used for DNA binding.
ATAC-seq libraries were prepared following the ATAC-seq protocol  as previously described in (Lu et al. 2016).
Hi-C libraries were prepared following the HiChIP protocol described in (Mumbach et al. 2016) with modifications described in the text.

value: 7-day-old 2nd leaf


title: RNA_Sis_65deg_rep2

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

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.

value: DpyrEF DlacS

tag: developmental stage

value: After cold shock treatment


title: B6.CAST_E6.5_Epi_Input_PBAT_1

value: Epiblast

tag: age

value: C57BL6/Babr x CAST/Ei


title: Parent line vehicle-treated 1

description: Parent line vehicle-treated 1


title: RNA_Sis_78deg_rep2

value: Before cold shock treatment


title: D3_Tox4_siRNA_DOX_1 (ATAC-Seq)


title: B6.CAST_E6.5_Epi_Input_2

tag: hybrid strain


title: Parent line dox-treated 1

description: Parent line dox-treated 1


title: RNA_Sis_65deg_rep1


title: RNA_Sis_78deg_rep1


title: TRACONSLROOTE [E09_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: Solanum lycopersicum cv. M82

value: 7 days-old seedling 1 cm roots tips

value: TRAP RNA