title: OS_RS_CON4 [OS-RSCON4]

description:
processed data file: OS-RSCON.fwd.merged.bw
processed data file: OS-RSCON.rev.merged.bw

organism: Oryza sativa Japonica Group

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

value: Oryza sativa japonica cv Nipponbare

value: Ribosome footprints


title: OS_RS_SUB4 [OS-RSSUB4]

status: Public on Sep 19 2019

type: SRA

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

country: USA

institute: Emory University

description:
processed data file: OS-RSSUB.fwd.merged.bw
processed data file: OS-RSSUB.rev.merged.bw

library_source: transcriptomic

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

molecule: total RNA

source_name: 7 days-old seedling 1 cm roots 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

tag: cultivar

tag: line

tag: tissue

value: 7 days-old seedling 1 cm roots tips

tag: experiment type

tag: molecule subtype

value: Riboseq RNA


title: TOTSUBSPSHOOTC [C04_TOTAL]

organism: Solanum pennellii

source_name: 7 days-old seedling shoot apical meristem

extract_protocol:
For cellular mRNA, 35S:His6:FLAG-GFP-AtRPL18-1 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: Solanum pennellii LA0716

value: Random primed libraries

value: polyA RNA


title: TRASUBSPSHOOTC [C04_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: 7 days-old seedling shoot apical meristem

value: TRAP RNA


title: ATAC_Barley_7days_leaf_rep2

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

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

organism: Hordeum vulgare

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: Morex

value: leaf

tag: age


title: OS_RS_SUB3 [OS-RSSUB3]


title: TOTCONSPSHOOTD [D03_TOTAL]


title: ATAC_Barley_7days_leaf_rep1


title: RS-MT-SUB1 [MT-RSSUBHAIRYROOTMT1]

description: processed data file: MT-RS-SUB.merged.bw

organism: Medicago truncatula

source_name: 4 week-old composite plant 1 cm root tips

treatment_protocol:
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 the 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
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: Medicago truncatula Jemalong A17

value: 35S:His6:FLAG-GFP-MtRPL18-3 injection transformed root tips


title: ChIP_Barley_7days_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: TRACONSPSHOOTC [C03_TRAP]


title: OS_RS_SUB1 [OS-RSSUB1]


title: TRASUBSPSHOOTB [B04_TRAP]


title: ChIP_Setaria_7days_leaf_H3

organism: Setaria viridis


title: OS_RS_CON1 [OS-RSCON1]


title: ChIP_Barley_7days_leaf_H2A.Z


title: ChIP_ClsN_input_Sac_sta_rep1

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Kyoto University

library_source: genomic

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.

molecule: genomic DNA

organism: Sulfolobus acidocaldarius

source_name: Microorganism

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

tag: strain

value: DSM 639

tag: genotype

value: Wild type

tag: growth phase

value: Stationary-phase cells

tag: chip antibody


title: ChIP_ClsN_input_Sac_ActD30_rep1

tag: treatment

value: Log-phase cells treated with actinomycin D for 30 min


title: TOTSUBSPSHOOTB [B04_TOTAL]


title: OS_RS_CON3 [OS-RSCON3]

value: Oryza sativa japonica cv Nipponbare


title: ChIP_Barley_7days_leaf_H3K4me1


title: ChIP_Barley_7days_leaf_H3K4me3


title: RNA_Sac_log_rep1

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: Log-phase cells


title: TRACONSPSHOOTB [B03_TRAP]


title: ChIP_ClsN_input_Sac_ActD15_rep1

value: Log-phase cells treated with actinomycin D for 15 min


title: ChIP_ClsN_input_Sac_log_rep2


title: TOTCONSPSHOOTB [B03_TOTAL]


title: OS_TRA_SUB4 [OS-TRASUB4]

description: processed data file: OS-TRASUB.filt.merged.bw

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

value: 7 days-old seedling 1 cm roots tips


title: OS_TRA_CON4 [OS-TRACON4]

description: processed data file: OS-TRACON.filt.merged.bw


title: ChIP_ClsN_input_Sac_log_rep1


title: ChIP_ClsN_IP_Sac_sta_rep2

value: ClsN (custom)


title: ChIP_ClsN_input_Sac_sta_rep2


title: ChIP_Barley_7days_leaf_H3K36me3


title: ChIP_Barley_7days_leaf_H3K27me3


title: OS_TRA_CON3 [OS-TRACON3]

value: Random primed libraries


title: Mt_TRAP_S3_R [MT-TRASUB3]

description: processed data file: MT-TRA-SUB.merged.bw

value: 4 week-old composite plant 1 cm root tips


title: OS_TRA_SUB3 [OS-TRASUB3]


title: Mt_TRAP_S2_R [MT-TRASUB2]


title: ChIP_Barley_7days_leaf_H3


title: OS_TRA_SUB2 [OS-TRASUB2]


title: ChIP_ClsN_IP_Sac_ActD30_rep1


title: ChIP_ClsN_IP_Sac_sta_rep1


title: OS_TRA_CON2 [OS-TRACON2]


title: RNA_Barley_7days_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


title: Mt_TRAP_S1_R [MT-TRASUB1]


title: Mt_TRAP_C4_R [MT-TRACON4]

description: processed data file: MT-TRA-CON.merged.bw


title: ChIP_ClsN_IP_Sac_ActD15_rep1


title: OS_TRA_SUB1 [OS-TRASUB1]


title: RNA_Barley_7days_leaf_rep1


title: ChIP_Barley_7days_leaf_H3K56ac


title: OS_TRA_CON1 [OS-TRACON1]


title: Mt_TRAP_C3_R [MT-TRACON3]


title: ChIP_ClsN_IP_Sac_log_rep1


title: Mt_TRAP_S4_R [MT-TRASUB4]


title: Mt_TRAP_C2_R [MT-TRACON2]


title: ATAC_duckweed_3days_after_tranferring_Input

organism: Spirodela polyrhiza

value: whole seedlings

value: 3days after transferring to new base


title: ChIP_ClsN_IP_Sac_log_rep2


title: ATAC_duckweed_3days_after_tranferring_rep2


title: OS_TOT_CON4 [OS-TOTCON4]

description: processed data file: OS-TOTCON.filt.merged.bw

extract_protocol:
For cellular mRNA, 35S:His6:FLAG:OsRPL18-2 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
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)
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

value: polyA RNA


title: Mt_TRAP_C1_R [MT-TRACON1]

value: TRAP RNA


title: Mt_TOT_S4_R1 [MT-TOTSUB4]

description: processed data file: MT-TOT-SUB.merged.bw

extract_protocol:
For cellular mRNA, p35S:His6-FLAG-GFP-MtRPL18-3 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009. Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2015
RNA-seq libraries  were prepared from poly(A)+ selected mRNA and  described by Townsley et al. (2014) for random primer primed libraries.
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Bajic et al 2018), with slight modifications. For rice, minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3)using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for nRNA (pre-rRNA and rRNA digested), polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least four biological replicates for each condition and species
Ribo-seq libraries were generated as described by (Juntawong et al 2015) but with ribosome isolation by TRAP as described by (Bazin et al 2017) starting with pulverized frozen root tip tissue (~1000 1 cm root tip) thawed in 5 mL of Polysome Extraction Buffer and using ɑ-FLAG conjugated IgG Dynabeads for binding instead of anti-FLAG M2 magnetic beads. Manipulations were as previously described by (Bazin et al 2017) through to the generation of ribosome footprint fragments (RFs) and on-magnetic bead digestion of 1 mL of resuspended beads with 2000 units of RNase I (Ambion; ca. 15 U/μg RNA) by incubation for 180 min at 23-25 °C. RFs of  26-34 nt were gel purified, dephosphorylated using T4 polynucleotide kinase, ligated 500 ng preadenylylated miRNA cloning linker (IDT, miRNA cloning linker #1). The ligated-RFs were excised, recovered and resuspended in 10.0 μl of 10 mM Tris (pH 8). After this step, rRNA removal of RFs was done by use of Ribo-Zero rRNA Removal Kit (Plant; Illumina) probe solution

value: Medicago truncatula Jemalong A17

value: 35S:NTF injection transformed root tips


title: ChIP_duckweed_3days_after_tranferring_Input


title: HiC_Sac_sta_rep1

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

value: DSM 639


title: ATAC_duckweed_3days_after_tranferring_rep1


title: OS_TOT_SUB3 [OS-TOTSUB3]

description: processed data file: OS-TOTSUB.filt.merged.bw


title: HiC_Sac_ActD30_rep2

value: Wild type


title: Mt_TOT_S3_R1 [MT-TOTSUB3]


title: OS_TOT_CON3 [OS-TOTCON3]


title: ChIP_duckweed_3days_after_tranferring_H2A.Z


title: Mt_TOT_S2_R1 [MT-TOTSUB2]


title: OS_TOT_SUB2 [OS-TOTSUB2]


title: ChIP_duckweed_3days_after_tranferring_H3K4me1


title: HiC_Sac_sta_rep2

value: Stationary-phase cells


title: OS_TOT_CON2 [OS-TOTCON2]


title: OS_TOT_SUB4 [OS-TOTSUB4]


title: Mt_TOT_S1_R1 [MT-TOTSUB1]


title: HiC_Sac_ActD15_rep2


title: Mt_TOT_C4_R1 [MT-TOTCON4]

description: processed data file: MT-TOT-CON.merged.bw


title: ChIP_duckweed_3days_after_tranferring_H3K56ac


title: ChIP_duckweed_3days_after_tranferring_H3K4me3


title: HiC_Sac_ActD30_rep1

value: Log-phase cells treated with actinomycin D for 30 min


title: Mt_TOT_C3_R1 [MT-TOTCON3]


title: HiC_Sac_ActD15_rep1


title: OS_TOT_SUB1 [OS-TOTSUB1]

value: Oryza sativa japonica cv Nipponbare


title: HiC_Sac_log_rep3

value: Log-phase cells


title: OS_TOT_CON1 [OS-TOTCON1]


title: OS_INRNA_SUB4 [OS-INRNASUB4]

description: processed data file: OS-INRNASUB.filt.merged.bw

extract_protocol:
Nuclei were purified from frozen and pulverized tissue as previously described for A. thaliana (Wang and Deal, 2015) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
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)
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: nuclear RNA


title: ChIP_duckweed_3days_after_tranferring_H3K27me3


title: HiC_Sac_log_rep2


title: ChIP_duckweed_3days_after_tranferring_H3


title: OS_INRNA_CON4 [OS-INRNACON4]

description: processed data file: OS-INRNACON.filt.merged.bw

value: 7 days-old seedling 1 cm roots tips


title: HiC_Sac_log_rep1


title: Mt_INT_S4 [MT-INRNASUBMT4]

description: processed data file: MT-INRNA-SUB.merged.bw

treatment_protocol:
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 the 35S:NTF;AtACT2p:mBirA 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
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


title: Mt_TOT_C1_R1 [MT-TOTCON1]


title: RNA_duckweed_3days_after_tranferring_rep2


title: SL-gDNA [SL-gDNA]

organism: Solanum lycopersicum

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

treatment_protocol:
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: Solanum lycopersicum cv. M82

value: Tagmented libraries


title: Mt_INT_S3 [MT-INRNASUBMT3]

value: 4 week-old composite plant 1 cm root tips

value: Random primed libraries


title: OS_INRNA_SUB3 [OS-INRNASUB3]


title: ATACSUBSLROOT2 [ATAC-E14]

description: processed data file: ATAC_SL_R_SUB.bw

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


title: RNA_duckweed_3days_after_tranferring_rep1

value: whole seedlings

value: 3days after transferring to new base


title: OS_INRNA_CON3 [OS-INRNACON3]


title: OS_INRNA_SUB2 [OS-INRNASUB2]


title: ATAC_Phaseolus_10days_leaf_Input

organism: Phaseolus vulgaris

value: leaf


title: Mt_INT_S2 [MT-INRNASUBMT2]

value: Medicago truncatula Jemalong A17


title: ATAC_Phaseolus_10days_leaf_rep2


title: OS_INRNA_CON2 [OS-INRNACON2]


title: ChIP_duckweed_3days_after_tranferring_H3K36me3


title: ATACSUBSLROOT1 [ATAC-E13]

description: processed data file: ATAC_SL_R_SUB.bw


title: OS_INRNA_SUB1 [OS-INRNASUB1]


title: ATACCONSLSHOOT1 [ATAC-E05]

description: processed data file: ATAC_SL_SH_CON.bw

value: 7 days-old seedling shoot apical meristem


title: Mt_INT_C4 [MT-INRNACONMT4]

description: processed data file: MT-INRNA-CON.merged.bw

value: 35S:NTF injection transformed root tips


title: ATACCONHAIRYROOT2B [ATAC-C21]

description: processed data file: ATAC_SL_H_CON.bw

source_name: hairy root culture 1cm root tips

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

value: hairy root culture 1cm root tips


title: Mt_INT_C3 [MT-INRNACONMT3]


title: ATACCONSLROOT2 [ATAC-C13]

description: processed data file: ATAC_SL_R_CON.bw


title: Mt_INT_C2 [MT-INRNACONMT2]


title: ChIP_Phaseolus_10days_leaf_Input


title: ChIP_Phaseolus_10days_leaf_H2A.Z


title: OS_ATAC_SUB4 [OS-ATACSUB4]

description: processed data file: ATAC_OS_SUB.bw


title: ATACCONSLROOT1 [ATAC-C103]

description: processed data file: ATAC_SL_R_CON.bw


title: OS_INRNA_CON1 [OS-INRNACON1]


title: Mt_INT_C1 [MT-INRNASUBMT1]


title: OS_ATAC_SUB3 [OS-ATACSUB3]

description: processed data file: ATAC_OS_SUB.bw


title: ATACSUBSPSHOOT2 [ATAC-C08]

description: processed data file: ATAC_SP_SH_SUB.bw

value: Solanum pennellii LA0716


title: ChIP_Phaseolus_10days_leaf_H3K4me1


title: Mt_INT_S1 [MT-INRNACONMT1]


title: Mt_TOT_C2_R1 [MT-TOTCON2]

value: polyA RNA


title: OS_ATAC_SUB2 [OS-ATACSUB2]

description: processed data file: ATAC_OS_SUB.bw

value: Oryza sativa japonica cv Nipponbare


title: ChIP_Phaseolus_10days_leaf_H3K4me3


title: OS_ATAC_CON4 [OS-ATACCON4]

description: processed data file: ATAC_OS_CON.bw


title: ATACCONSLSHOOT2 [ATAC-C05]

description: processed data file: ATAC_SL_SH_CON.bw


title: Mt_ATAC_S3 [MT-ATACSUB3]

description: processed data file: ATAC_MT_SUB.bw


title: ChIP_Phaseolus_10days_leaf_H3K56ac


title: Mt_ATAC_S2 [MT-ATACSUB2]

description: processed data file: ATAC_MT_SUB.bw


title: ChIP_Phaseolus_10days_leaf_H3K36me3


title: OS_ATAC_CON3 [OS-ATACCON3]

description: processed data file: ATAC_OS_CON.bw


title: ATAC_Phaseolus_10days_leaf_rep1


title: ATACCONHAIRYROOT2 [ATAC-B23]

description: processed data file: ATAC_SL_H_CON.bw


title: Mt_ATAC_S1 [MT-ATACSUB1]

description: processed data file: ATAC_MT_SUB.bw


title: OS_ATAC_CON1 [OS-ATACCON1]

description: processed data file: ATAC_OS_CON.bw


title: ChIP_Phaseolus_10days_leaf_H3K27me3


title: ChIP_Phaseolus_10days_leaf_H3


title: 27: Metastases3

city: Leiden

first: Lanpeng

last: Chen

state: South Holland

address: Einsteinweg 55, GW3.19

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: Metastases at zebrafish caudal hematopoietic tissue

data_processing:
All RNAseq libraries (150–750 bp inserts) were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single-end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample.
Illumina reads were aligned against the human (GRCh38.p3) and zebrafish (GRCz10.80) reference genome sequences using TopHat (version 2.0.5). Secondary alignments of reads were excluded by filtering the files using SAMtools (version 0.1.18)
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9).
To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor, library size estimates determined using the R/Bioconductor (release 2.11) package DESeq were employed
Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools.
Supplementary_files_format_and_content: tab-delimited text files include gene name, ID, reads and normalized comparision between each groups

organism:
Danio rerio
Homo sapiens

source_name: PC-3M-Pro4-injected fish

growth_protocol: PC-3M-Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200-400 PC-3M-Pro4 cells were injected into the duct of cuvier (DoC) of the zebrafish embryos using a Pneumatic Picopump and a manipulator (WPI). After transplantation, 120 well-engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.

extract_protocol:
Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area (80 fish per group randomly chosen from >100 engrafted fish) at 6dpi (8dpf) with a micro dissection scissor (WPI). The samples were immediately washed with cold PBS and stored in TRIzol (Sigma) at -80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at  -80 ˚C. RNA isolation was further performed using RNeasy mini kit (qiagen)
then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina, San Diego CA, USA).

tag: FISH strain

value: 8 days post fertilization


title: ATACSUBCONSLSHOOT2 [ATAC-B06]

description: processed data file: ATAC_SL_SH_SUB.bw


title: ATACSUBHAIRYROOT1 [ATAC-A22]

description: processed data file: ATAC_SL_H_SUB.bw


title: Mt_ATAC_C2 [MT-ATACCON2]

description: processed data file: ATAC_MT_CON.bw


title: RNA_Phaseolus_10days_leaf_rep2


title: MT-gDNA [MT-gDNA]


title: 26: Metastases2

value: Metastases at zebrafish caudal hematopoietic tissue


title: ATACCONHAIRYROOT1 [ATAC-A21]

description: processed data file: ATAC_SL_H_CON.bw


title: Mt_ATAC_C1 [MT-ATACCON1]

description: processed data file: ATAC_MT_CON.bw


title: 25: Metastases1


title: RNA_Phaseolus_10days_leaf_rep1


title: ATACSUBHAIRYROOT2 [ATAC-B22]

description: processed data file: ATAC_SL_H_SUB.bw


title: Mt_ATAC_C3 [MT-ATACCON3]

description: processed data file: ATAC_MT_CON.bw


title: gWT/gMUT library Rep2 RNA

status: Public on Sep 18 2019

city: St. Louis

first: Dana

middle: M

last: King

state: Missouri

address: 4523 CLAYTON AVE, CB 8510

department: Department of Genetics

institute: Washington University

description: Demultiplexing barcode sequence of 'GCTCGAT' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library

data_processing:
All raw reads (SRA accession number SRR7515851) were process regardless of quality scores. Briefly, reads with the expected in-line multiplexing barcode sequence for each replicate followed by the restriction site used for library construction were identified. Demultiplexed reads were then used to determine the number of unique occurances of 9 bp sequences in the barcoded region of the reporter construct. Barcodes that exactly matched designed sequences were then written to file along with the barcode's raw read count, all other counts were discarded.
Supplementary_files_format_and_content: Processed count text files include read counts in first column, barcode sequence in second column, and the putative regulatory element/sequence identifier in the last column.

organism: Mus musculus

source_name: RW.4 mESCs

growth_protocol: RW4 mouse ESCs (ATCC SCRC-1018) were cultured on on 2% gelatin coated plates in standard media (DMEM, 10% fetal bovine serum, 10% newborn calf serum, nucleoside supplement, 1000 U/ml leukemia inhibitory factor (LIF), and 0.1 uM B-mercaptoethanol)

extract_protocol:
Total RNA was extracted from approximately 9 million cells using the PureLink RNA mini kit (Life Technologies) according to the manufactor's instructions, removing any residual DNA from the RNA pool using TURBO DNA-free kit (Life Technologies).
First strand cDNA was prepared from total RNA using SuperScript RT III (Life Technologies) with oligo dT primers. Target library reporter sequences were amplified from cDNA and DNA pools using primers CF150, 'TACACCGTGGTGGAGCAGTA', and CF151b, 'AGCGTACTCGAGTTGTTAACTTGTTTATTGCAGCTT', followed by digestion with XbaI and XhoI (NEB). Digested amplicons were then ligated to custom Illumina adapters,each including an in-line barcode sequence to identify each sample. Ligated products were then further amplified using primers CF52, 'AATGATACGGCGACCACCGAG', and CF53, 'CAAGCAGAAGACGGCATACGA'.

treatment_protocol: Approximately 1 million RW.4 cells were seeded in 6-well plates and transfected with 3 ug of MPRA library plasmid (SYN or gWT/gMUT ) and 0.3 ug of CF128, a GFP control plasmid.

tag: strain background

tag: cell line

tag: cell type

value: Embryonic stem cell

tag: passage number


title: gWT/gMUT library Rep1 RNA

description: Demultiplexing barcode sequence of 'GGAGGTG' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library


title: SYN library Rep3 RNA

description: Demultiplexing barcode sequence of 'CTGTCAT' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library


title: SYN library Rep2 RNA

description: Demultiplexing barcode sequence of 'TCTAAGC' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library


title: E13379

city: Austin

first: Grace

last: Chappell

state: TX

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

institute: ToxStrategies, Inc.

description:
RNA extracted from FFPE tissue.
processed data file: SP0071_gene_counts_GEO.csv

data_processing:
No adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters.
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing.
Fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: SP0071_gene_counts_GEO.csv: Comma-separated text file includes raw count values for each gene_probe.

source_name: FFPE duodenum

growth_protocol: Male B6C3F1 mice were bred, reared, and administered test compounds at Charles River Laboratories.

extract_protocol:
Formalin-fixed, paraffin-embedded duodenum tissue was scraped from sections mounted to glass slides directly into lysis buffer.
The TempO-Seq (BioSpyder Industries) targeted expression assay protocol was followed for library construction: RNA for approximately 3000 genes was amplified using targeted oligomers.

treatment_protocol: B6C3F1 mice exposed to either Cr(VI) (180ppm in drinking water), captan (≤12000ppm in diet), or folpet (≤16000ppm in diet) for 28 days.

tag: strain/background

tag: genotype/variation

value: wildtype

tag: gender

value: male

value: duodenum

value: Folpet 16000ppm


title: E13380

tag: tissue


title: gWT/gMUT library Rep3 RNA

description: Demultiplexing barcode sequence of 'TAGAGTA' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library


title: Hela_ΔE_IL8_IL1_rep1

type: RNA

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

hyb_protocol: cRNA synthesis, cRNA fragmentation, hybridization and washing was carried out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol’ V5.7 (Agilent Technologies).

scan_protocol: Slides were scanned on an Agilent Microarray Scanner G2565 CA with a pixel resolution of 5 µm and a bit depth of 20.

data_processing: Data extraction was performed with the ‘Feature Extraction Software’ V10.7.3.1 by using the default extraction protocol file ‘GE1_107_Sep09.xml’. Extracted data were imported into Genespring GX software (Agilent Technologies Inc., Santa Clara, CA) V12.0. Data were log2 transformed and quantile normalized in Genespring GX.

organism: Homo sapiens

source_name: HeLa Δp65eIL8

label_protocol: cRNA synthesis was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies).

growth_protocol: Cells were cultured in DMEM, 10% FCS, to subconfluency.

extract_protocol: Total RNA utilized for microarray experiments was prepared with NucleoSpin RNA Kit (#740955.50, Macherey-Nagel, Düren, Germany) according to the manufacturer’s recommendations.

treatment_protocol: Human HeLa cells and three p65 enhancer-deletion lines (Δp65eIL8, Δp65eCXCL2 and Δp65eIL8+eCXCL2) were left untreated or treated with Interleukin-1-alpha (10ng/µl) for 1 hour. IL-1α was added directly to the cell culture medium.


title: HeLa_IL1_rep1

source_name: HeLa empty vector


title: Hela_ΔE_IL8+CXCL2_rep1

source_name: HeLa Δp65eIL8+eCXCL2


title: Hela_ΔE_IL8+CXCL2_rep2


title: Hela_ΔE_IL8_rep2


title: Hela_ΔE_IL8_IL1_rep2


title: HeLa_IL1_rep3


title: Hela_ΔE_CXCL2_IL1_rep2

source_name: HeLa Δp65eCXCL2


title: Hela_ΔE_CXCL2_rep1


title: HeLa_vector_IL-1_rep1


title: Hela_ΔE_CXCL2_IL1_rep1


title: Hela_ΔE_IL8_rep1


title: Hela_ΔE_CXCL2_rep2


title: HeLa_IL1_rep4


title: Hela_ΔE_IL8+CXCL2_IL1_rep2


title: Hela_ΔE_IL8+CXCL2_IL1_rep1


title: SYN library Rep1 RNA

description: Demultiplexing barcode sequence of 'AACCTCA' upstream of restriction site sequence 'CTAGAC' and then a 9bp designed library barcode.


title: HeLa_vector_IL-1_rep4


title: HeLa_vector_IL-1_rep3


title: E13377


title: E13378


title: HeLa_vector_IL-1_rep2


title: E13375


title: HeLa_IL1_rep2


title: 99-27918

city: Vancouver

first: Christian

last: Steidl

state: British Columbia

address: 675 10th Avenue West

department: Lymphoid Cancer Research

country: Canada

institute: BC Cancer

hyb_protocol: Nucleic acids were diluted to a final concentration of 100ng/ul and array hybridization was performed at Sick Kids Hospital using the HumanHT-12 v4.0 Expression BeadChip.

scan_protocol: standard Illumina

data_processing: The limma and beadarray R packages were used to analyse probe-level expression data. A normal-exponential convolution model was applied for background correction and normalization of the data, followed by log2-transformation and quality assessment. Probes below the detection score (i.e. considered to be not expressed) in at least three arrays were removed (27,446 probes remained). One case of the sequencing cohort was identified as an outlier by both, multidimensional scaling and principal component analysis (PCA), and was therefore removed. Following exclusion of case PA012, 68 cases were available for integrative analyses. Annotation of probes with quality and gene symbol information was performed using the IlluminaHumanv4.db probe annotation database (Illumina). Probes annotated as having “bad” quality or had no gene match were removed. A total of 24,501 probes representing 17,027 genes remained, with 4,659 of those being represented by more than one probe (i.e. ambiguous transcript).

label: biotin

source_name: tumor

label_protocol: standard Illumina

extract_protocol: RNA was extracted using either the RNeasy mini kit or AllPrep FFPE kit and measured using a Nanodrop spectrophotometer

tag: patient diagnosis

value: primary mediastinal B-cell lymphoma

value: tumor


title: E13373


title: 01-27374


title: E13372


title: E13367

value: Folpet 6000ppm


title: E13368


title: E13364


title: E13363


title: E13361


title: E13362


title: E13330

value: CrVI 180ppm


title: 04-26715


title: E13370


title: 91-32362


title: E13337


title: 90-34978


title: E13336


title: 99-17798


title: E13328


title: 81-15319


title: HiC_Sac_noXL_rep1

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

value: DSM 639

value: Wild type

value: Log-phase cells


title: 99-22935


title: 95-10543


title: 84-30108


title: 04-28559


title: 95-23228


title: 97-17301


title: E13334


title: E13355

value: Captan 12000ppm


title: E13329


title: E13354


title: 90-35480


title: 93-63169


title: E13353


title: 97-15821


title: 90-30515


title: 02-27185


title: 89-32591


title: E13349


title: E13358


title: E13332


title: E13356


title: 96-30619


title: 95-10719


title: 98-24444


title: E13339

value: Captan 6000ppm


title: 96-20971


title: E13340


title: E13346


title: 91-35233


title: E13345


title: E13344


title: E13352


title: 96-29260


title: 02-20235


title: 97-10764


title: 01-13113


title: E13319

value: control


title: 81-14221


title: E13341


title: E13338


title: E13325


title: E13324


title: 01-17164


title: 02-22828


title: 80-15607


title: 07-41887


title: IS rep1

city: Utrecht

first: Caroline

last: Cheng

state: Nederland

address: Heidelberglaan 100

department: Nephrology and Hypertension

institute: Universitair Medisch Centrum Utrecht

data_processing:
STAR version 2.4.2a was used to align sequenced reads.
Picard AddOrReplaceReadGroups (v1.98) was used to add read groups to the BAM files, which were sorted with Sambamba v0.4.5.
Transcript abundances were quantified with HTSeq-count, version 0.6.1p1, using the union mode.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files contains the raw counts per transcript for each sample.

molecule: polyA RNA

source_name: anonymous newborn

extract_protocol:
Total RNA isolation was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. Polyadenylated mRNA was further selected using Poly(A) Beads (NEXTflexTM).
Libraries were generated using the NEXTflexTM Rapid RNA-seq Kit (Bio Scientific).

value: fresh umbilical cords

tag: condition

value: cultured in the stimulation medium containing indoxyl sulfate

tag: stimulation duration


title: 03-25641


title: 01-13563


title: 00-20098


title: IS rep2


title: Hum_serum_small

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

description: Blood samples discarded by Pathology lab were from anonymized donors undergoing maternity care at Montefiore Medical Center. For each lot, at least 10 donors were pooled

data_processing:
Base-calling and de-multiplexing in each Proton run was executed by Torrent Suite software by filtering subthreshold reads and trimming adapter sequences
UBAM or BAM files generated by Proton were used for the further analysis.
Total transcriptome reads were aligned to mm10 mouse genome reference with Proton instrument RNASeqAnalysis Plugin tool v5.2.0.5.  Absolute normalized reads table generated by above tools was used for the further data analyses
Human serum exosome or mouse liver small RNA sequencing data were aligned to mirBase21 reference (human or mouse respectively) using Proton SmallRNA v5.6.0.0 plugin tool
Genome_build: mmu10, miBase21 human (RNA) and mouse (RNA)
Supplementary_files_format_and_content: Tab-delimited text files were generated by Torrent Proton RNASeqAnalysis or SmallRNA plugin tools and include reads per mln values, absolute reads, FPKM values for isoforms

source_name: exosomes

extract_protocol:
Total liver RNA and exosome RNA were isolated with Norgen total RNA purification kit according to kit's protocols for each type of samples (Norgen Biotek Corp., Canada), small RNAs were enriched using Ion Total RNA-Seq Kit v2 (Life Technologies).
2 µg total RNA from the pool of 3 sampes per each condition was depleted for ribosomal RNA with RiboMinus Eukaryote System v2 (cat # A15026, Ambion, ThermoFisher Scientific), transcriptome RNA and small RNA  libraries were prepared with Ion Total RNA-Seq Kit v2 according to the kit manual

value: Blood serum


title: IS rep3


title: 01-29960


title: E13326

value: wildtype


title: Ctrl rep3

value: cultured in the control medium containing potassium chloride


title: 06-11792


title: 01-19113


title: 06-12841


title: E13323

value: male

value: duodenum


title: 01-16172

value: primary mediastinal B-cell lymphoma


title: Ctrl rep2


title: differentiated type (myofibroblast) 4

city: Omaha

first: Tu

last: Yaping

state: NE

address: 2500 California Plaza

department: Pharmacology

institute: Creighton University School of Medicine

description: fibroblast cells treated with 1 ng/mL TGF-β1 for 48 h

data_processing:
trim adapter using cutadapt.
map trimmed reads on miRNA precursors using SHiMPS aligner
counts reads associated to mature miRNAs
Genome_build: miRBase 21
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: human primary lung fibroblast cells (HFL)

growth_protocol: Cells were cultured in DMEM/F12 medium with 10% fetal bovine serum

extract_protocol:
Total RNA was isolated from samples using mirVana miRNA isolation kit (Invitrogen). NEXTflexTM Small RNA-Seq Kit v3 (Bioo Scientic #5132-05) was used with 1 ug of total RNA for the construction of small RNA sequencing libraries.
small RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 1 ng/mL TGF-β1 or saline for 48 h.

tag: mophology

value: myofibroblast-like

tag: passage


title: differentiated type (myofibroblast) 3


title: Ctrl rep1


title: 01-13248

value: tumor


title: differentiated type (myofibroblast) 2